US008372970B2

(12) United States Patent (10) Patent No.: US 8,372,970 B2 Vollrath et al. (45) Date of Patent: Feb. 12, 2013

(54) 8-ETHYL-6-(ARYL)PYRIDO2,3-D WO WO-2008-034008 3, 2008 PYRIMIDIN-7(8H)-ONES FOR THE WO WO-2008-051757 5, 2008 TREATMENT OF CNS DISORDERS WO WO-2008-055842 5, 2008 WO WO-2010-071846 6, 2010 (75) Inventors: Benedikt Vollrath, San Diego, CA (US); OTHER PUBLICATIONS David Campbell, San Diego, CA (US); Black et al., “Pathology of layer V pyramidal neurons in the Sergio G. Durón, San Diego, CA (US); prefrontal cortex of patients with schizophrenia.” Am J Psychiatry, Warren Wade, San Diego, CA (US) (2004) 161:742-744. Costa et al., “Learning deficits, but normal development and tumor (73) Assignee: Afraxis, Inc., La Jolla, CA (US) predisposition, in mice lacking exon 23a of Nfl.” Nature Genet. 27. 399-405 (2001). (*) Notice: Subject to any disclaimer, the term of this Dickstein et al., “Changes in the structural complexity of the aged patent is extended or adjusted under 35 brain.” Aging Cell (2007) 6:275-284. U.S.C. 154(b) by 0 days. Hajszan et al., “Short-term treatment with the antidepressant fluoxetine triggers pyramidal dendritic spine synapse formation in rat Appl. No.: 13/500,295 hippocampus.” Eur J Neurosci. (2005) 21:1299-1303. (21) Hayashi et al., “Altered cortical synaptic morphology and impaired PCT Fled: Oct. 8, 2010 memory consolidation in forebrain-specific dominant-negative PAK (22) transgenic mice.” Neuron (2004) 42(5):773-787. Hikida et al., “Dominant-negative DISC1 transgenic mice display (86) PCT NO.: PCT/US2O10/0521.06 Schizophrenia-associated phenotypes detected by measures translat S371 (c)(1), able to humans.” (2007), Proc Natl Acad Sci USA 104(36): 14501 14506. (2), (4) Date: Jun. 26, 2012 Knafo et al., Widespread changes in dendritic spines in a model of PCT Pub. No.: WO2O11AO44535 Alzheimer's disease, Cerebral Cortex 19(3):586-92 (2009). (87) Kreis et al., “The p21-activated kinase 3 implicated in mental retar PCT Pub. Date: Apr. 14, 2011 dation regulates spine morphogenesis through a Cdc42-dependent pathway,” J. Biol Chem (2007) 282(29) :21497-21506. (65) Prior Publication Data Neely et al., “Cortical regulation of dopamine depletion-induced dendritic spine loss in striatal medium spiny neurons. Neuroscience US 2012/O270866A1 Oct. 25, 2012 (2007) 149(2): 457-464. Penzes et al., “Rapid induction of dendritic spine morphogenesis by Related U.S. Application Data trans-synaptic ephrinB-EphB receptor activation of the Rho-GEF (60) Provisional application No. 61/250.262, filed on Oct. kalirin.” Neuron (2003)37:263-274. 9, 2009, provisional application No. 61/353,054, filed Science IP Search Report dated Oct. 27, 2011. Van Riezen et al. “Effects of psychotropic drugs on the behavior and on Jun. 9, 2010. neurochemistry of olfactory bulbectomized rats.” (1990), Pharmacol Ther, 47(1):21-34. (51) Int. C. Wong, “Modulation of dendritic spines in epilepsy: cellular mecha CO7D 413/4 (2006.01) nisms and functional implications.” Epilepsy and Behavior (2005) CO7D 47L/04 (2006.01) 7:569-577. CO7D 40/4 (2006.01) Young et al., “Progressive impairment in olfactory working memory C07D 239/00 (2006.01) in amouse model of Mild Cognitive Impairment.” (2009), Neurobiol (52) U.S. C...... 544/117: 544/122:544/279: 544/362 ogy of Aging, 30:1430-1443. Field of Classification Search ...... 544/117, Yu et al., “Enzyme-linked immunosorbent assay for the determina (58) tion of p21-activated kinase activity.” (2001) J. Biochem (Tokyo) 544/122, 279, 362 129(2): 243-251. See application file for complete search history. PCT/US2009/068855 Search Report dated Jun. 30, 2011. PCT/US2010/052106 Search Report dated Jun. 23, 2011. (56) References Cited Primary Examiner — Rebecca Anderson U.S. PATENT DOCUMENTS Assistant Examiner — Samantha Shterengarts 5,945,422 A 8/1999 Doherty et al. 2002/0107171 A1 8, 2002 Price et al. (74) Attorney, Agent, or Firm — Wilson, Sonsini, 2005/O182O78 A1 8, 2005 Barvian et al. Goodrich & Rosati FOREIGN PATENT DOCUMENTS (57) ABSTRACT WO WO-96-34867 11, 1996 WO WO-01-44258 6, 2001 Provided herein are PAK inhibitors and methods of utilizing WO WO O2-064594 8, 2002 PAK inhibitors for the treatment of CNS disorders such as WO WO-2005-034869 4/2005 neuropsychiatric disorders. WO WO-2006-082492 8, 2006 WO WO-2007-076092 7/2007 15 Claims, 3 Drawing Sheets U.S. Patent Feb. 12, 2013 Sheet 1 of 3 US 8,372,970 B2

Figure 1

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^ 8l ry: Y - x - - o a. r fix;xxis is striy Fussex:

& {{ is:

Ellipsoid flattened branched

(e) (f) (g) U.S. Patent Feb. 12, 2013 Sheet 2 of 3 US 8,372,970 B2

Figure 2

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Kolmogorov-Smirnov test; p < 0.0

.3 C.4 O.S OS O.7 O8 Spine head diameter U.S. Patent Feb. 12, 2013 Sheet 3 of 3 US 8,372,970 B2

Figure 3

Spine length US 8,372,970 B2 1. 2 8-ETHYL-6-(ARYL)PYRIDO2,3-D PYRIMIDIN-7(8H)-ONES FOR THE Formula I R7: TREATMENT OF CNS DISORDERS N1 N1 n CROSS-REFERENCE 5 (R) O 2 N N N O H This application is a U.S. National Phase application of Q PCT/US2010/052106, filed Oct. 8, 2010, which claims the benefit of U.S. Provisional Application No. 61/250.262, filed 10 wherein: Oct. 9, 2009, and U.S. Provisional Application No. 61/353, R7 is 054, filed Jun. 9, 2010, all of which are incorporated herein by reference in their entirety. (R), BACKGROUND OF THE INVENTION 15 R3 Central Nervous System (CNS) disorders are characterized by a variety of debilitating affective and cognitive impair ments. For example, a clinical sign of individuals with Alzhe 20 wherein ring T is an aryl, or a heteroaryl ring; imer's disease is progressive cognition deterioration. World R is a substituted or unsubstituted cycloalkyl, a substituted wide, approximately 24 million people have dementia, 60% or unsubstituted heteroaryl attached to ring T via a car of these cases are due to Alzheimer's. bonatom of R, or a substituted or unsubstituted hetero Other CNS disorders include, e.g., mood disorders, age cycloalkyl attached to ring T via a carbon atom of R: related cognitive decline, and neurological disorders (e.g., 25 Q is a substituted or unsubstituted alkyl, a substituted or epilepsy, Schizophrenia, Fragile X mental retardation syn unsubstituted heteroalkyl, a substituted or unsubstituted drome and Huntington's disease). The effects of CNS disor heterocycloalkyl, a substituted or unsubstituted ders are devastating to the quality of life of those afflicted as cycloalkyl, a Substituted or unsubstituted cycloalkyla well as that of their families. Moreover, CNS disorders lkyl, a substituted or unsubstituted heterocycloalkyla impose an enormous health care burden on Society. A number 30 lkyl, a substituted or unsubstituted aryl, a substituted or of CNS disorders, as well as other conditions that affect unsubstituted arylalkyl, a substituted or unsubstituted cognitive function, have been associated with alterations in heteroaryl, or a substituted or unsubstituted heteroary the morphology and/or density of dendritic spines, membra lalkyl: nous protrusions from dendritic shafts of neurons that serve as each R" is independently halogen, —CN, NO, -OH, highly specialized structures for the formation, maintenance, 35 –OCF, OCHF, OCFH, -CF, SR, and function of synapses. NR'S(=O).R. S(=O)N(R'), C(=O)R, OC(=O)R, COR', N(R'), C(=O)N (R), NRC(=O)R', NR'C(=O)CR', SUMMARY OF THE INVENTION - NR'C(=O)N(R'), a substituted or unsubstituted 40 alkyl, a substituted or unsubstituted alkoxy, a substituted Described herein are compounds, compositions and meth or unsubstituted heteroalkyl, a substituted or unsubsti ods for treating an individual suffering from a CNS disorder, tuted cycloalkyl, or a substituted or unsubstituted het Such as by way of example only schizophrenia, Fragile X erocycloalkyl; Syndrome (FXS), clinical depression, age-related cognitive R is Hor R: decline, Mild Cognitive Impairment, Huntington's disease, 45 R is a substituted or unsubstituted alkyl, a substituted or Parkinson's disease, neurofibromatosis, Alzheimer's disease, unsubstituted cycloalkyl, a substituted or unsubstituted epilepsy, autism spectrum disorders, mental retardation, heterocycloalkyl, a substituted or unsubstituted aryl, or a Down's syndrome or the like, by administering to an indi substituted or unsubstituted heteroaryl; vidual a pharmaceutical composition comprising a therapeu each R' is independently H, a substituted or unsubstituted tically effective amount of an inhibitor of a p21-activated 50 alkyl, a Substituted or unsubstituted cycloalkyl, a Substi kinase (PAK), e.g., an inhibitor of PAK1, PAK2, PAK3 or tuted or unsubstituted heterocycloalkyl, a substituted or PAK4, as described herein. PAK activation is shown to play a unsubstituted aryl, or a substituted or unsubstituted het key role in spine morphogenesis. In some instances, attenu eroaryl; or two R', together with the atoms to which ation of PAK activity reduces, prevents or reverses defects in they are attached form a heterocycle: spine morphogenesis. In some embodiments, inhibitors of 55 ring B is aryl or heteroaryl; one or more of Group I PAKs (PAK1, PAK2 and/or PAK3) each R is independently halogen, —CN, NO. —OH, and/or Group II PAKs (PAK4, PAK5 and/or PAK6) are SR, S(—O)R’, S(—O).R, NR'S(—O).R. administered to rescue defects in spine morphogenesis in S(=O)N(R'), C(=O)R, OC(=O)R’, individuals suffering from a condition in which dendritic COR, N(R0), C(=O)N(R0), NRC spine morphology, density, and/or function are aberrant, 60 (—O)R'', NRC(=O)CR'', NRC(=O)N including but not limited to abnormal spine density, spine (R') —OR', a substituted or unsubstituted alkyl, a size, spine shape, spine plasticity, spine motility or spine substituted or unsubstituted alkoxy, a substituted or plasticity leading to improvements in synaptic function, cog unsubstituted heteroalkyl, a substituted or unsubstituted nition and/or behavior. cycloalkyl, or a substituted or unsubstituted heterocy In one aspect is a compound having the structure of For 65 cloalkyl: mula I or pharmaceutically acceptable salt or N-oxide r is 0 to 8; and thereof: s is 0 to 4. US 8,372,970 B2 3 4 In one embodiment is a compound of Formula I wherein In another embodiment is a compound of Formula III hav ring T is an aryl ring. In another embodiment is a compound ing the structure of Formula V: of Formula I whereinring T is a heteroaryl ring. In yet another embodiment is a compound of Formula I, wherein ring T is selected from pyrrole, furan, thiophene, pyrazole, imidazole, Formula V isoxazole, oxazole, isothiazole, thiazole, 1,2,3-triazole, 1.3, R3 4-triazole, 1-Oxa-2,3-diazole, 1-Oxa-2,4-diazole, 1-Oxa-2,5- N diazole, 1-Oxa-3,4-diazole, 1-thia-2,3-diazole, 1-thia-2,4- H(R'); diazole, 1-thia-2,5-diazole, 1-thia-3,4-diazole, tetrazole, N1 N. 2 pyridine, pyridazine, pyrimidine, and pyrazine. In yet a fur 10 N ther embodiment is a compound of Formula I, wherein R is e-O. l 2 N N O a C-linked heterocycloalkyl. In another embodiment is a H compound of Formula I, wherein R is a substituted or unsub stituted C-linked heteroaryl. In another embodiment, R is a substituted or unsubstituted cycloalkyl. In a further embodi ment, cycloalkyl is selected from cyclopropyl, cyclobutyl, wherein s1 is 0 to 4. cyclopentyl, or cyclohexyl. In another embodiment is a compound of Formula III hav ing the structure of Formula Va: In yet another embodiment is a compound having the struc ture of Formula II: Formula Va.

Formula II R3 R3 25 N 2H(R'): (R), N N1 N. (R) ins 2 30 e-O. l N N O - O H

wherein s1 is 0 to 4. In a further embodiment is a compound having the struc 35 ture of Formula III: In another embodiment is a compound of Formula III hav ing the structure of Formula Vb:

Formula III Formula Vb 40 (R), (R), R R3.

N N N R3 N1 N1 N e-O. l 2 45 N N N O 2 H e-O. l N N N O H Q Q whereins 1 is 0 to 3. 50 In one embodiment is a compound of Formula I, II, III, IV. In yet a further embodiment is a compound of Formula III V. Va., or Vb wherein R is selected from pyrrole, furan, having the structure of Formula IV: thiophene, pyrazole, imidazole, isoxazole, oxazole, isothiaz ole, thiazole, 1,2,3-triazole, 1.3,4-triazole, 1-Oxa-2,3-diazole, 55 1-Oxa-2,4-diazole, 1-oxa-2,5-diazole, 1-Oxa-3,4-diazole, Formula IV 1-thia-2,3-diazole, 1-thia-2,4-diazole, 1-thia-2,5-diazole, R3 1-thia-3,4-diazole, tetrazole, pyridine, pyridazine, pyrimi N dine, and pyrazine. In a further embodiment is a compound of Formula I, II, III, 2 60 IV, V, Va, or Vb, wherein

65 (R)-(E) whereins 1 is 0 to 4. US 8,372,970 B2 5 6 is Vb wherein at least one of R is a substituted or unsubstituted piperazine, a Substituted or unsubstituted piperidine, a Sub stituted or unsubstituted pyrrolidine, or a substituted or N N1 N. unsubstituted morpholine. In one embodiment is a compound (R)- , (R) s of Formula I, II, III, IV, V, Va., or Vb, wherein at least one R 2 2n.2 is —OR". In another embodiment is a compound of Formula H I, II, III, IV, V, Va., or Vb, wherein R is independently halo O N gen, —CN, —OH, - OCF. —OCF, —OCF.H. —CF, e-?h s e-?h s —SR, a substituted or unsubstituted alkyl, or a substituted or N4 / N4 / 10 unsubstituted alkoxy. H H In one embodiment is a compound of Formula I, II, III, IV. N N V, Va., or Vb, whereins is zero. In a further embodiment is a compound of Formula I, II, III, e-f 2N/N. e-?hN-4N /N. IV, V, Va., or Vb, wherein Q is a substituted or unsubstituted H 15 alkyl, or a substituted or unsubstituted heteroalkyl. In another 1stryN 1stryO embodiment is a compound of Formula I, II, III, IV, V, Va., or (R) M s (R) / Vb, wherein Q is a substituted or unsubstituted cycloalkyl, or N 2 a substituted or unsubstituted heterocycloalkyl. In a further embodiment is a compound of Formula I, II, III, IV, V, Va., or Vb, wherein Q is a substituted or unsubstituted cycloalkyla (RS)- I - S N. (R) 1 's- lkyl, or a substituted or unsubstituted heterocycloalkylalkyl. In one embodiment is a compound of Formula I, II, III, IV. V. Va., or Vb, wherein Q is a substituted or unsubstituted aryl, or a substituted or unsubstituted heteroaryl. (R) 25 In one embodiment is a compound of Formula I, II, III, IV. V. Va, or Vb, wherein Q is a substituted or unsubstituted arylalkyl, or a substituted or unsubstituted heteroarylalkyl. Provided herein are pharmaceutical compositions com (R) prising a therapeutically effective amount of a compound of 30 Formula I, II, III, IV, V, Va, or Vb, or a pharmaceutically N N acceptable salt or N-oxide thereof, and a pharmaceutically 1 N-NH 1 s NH acceptable carrier, wherein the compound of Formula I-XV is (R)-H , (R)- N, as described herein. Na2 / 2N/ Provided herein, in some embodiments, are methods for H H 35 treating CNS disorders comprising administering to an indi N1S-N Sl-N vidual in need thereofatherapeutically effective amount of a e-1 N. (R) ! N. compound of Formula I-XV wherein compounds of Formula NeN/ NeN/ I-XV are as described herein. H N Also provided herein, in Some embodiments, are methods N S 40 for treating neuropsychiatric conditions comprising adminis 5 - || N-N 5 1st tering to an individual in need thereofatherapeutically effec (R) N, (R) / s tive amount of a compound of Formula I-XV wherein com NeN/ 21 pounds of Formula I-XV are as described herein. Also provided herein, in Some embodiments, are methods 5 1's-\ 5 -N1s 45 (R )r 7. (R )r s for treating neurodegenerative disorder comprising adminis 21 21N 21 tering to an individual in need thereofatherapeutically effec tive amount of a compound of Formula I-XV wherein com pounds of Formula I-XV are as described herein. (RS)-HN1 N1 N (R5)--O , or (R)-HO Also provided herein, in Some embodiments, are methods N4N4 N4 N4 50 for treating neurodevelopmental disorder comprising admin istering to an individual in need thereof a therapeutically effective amount of a compound of Formula I-XV wherein In another embodiment is a compound of Formula I, II, III, compounds of Formula I-XV are as described herein. IV. V. Va., or Vb, where R is halogen, —CN, OH, a substi Provided herein, in some embodiments, are methods of tuted or unsubstituted alkyl, -OR', NR'S(=O).R. 55 modulating a p21-activated kinase comprising contacting a —S(=O)N(R'), N(R'), C(=O)N(R'), p21-activated kinase with a compound of Formula I-XV. NRC(=O)R'', NRC(=O)CR', NRC(=O)N In some embodiments of any of the above methods, com (R'), or a substituted or unsubstituted heterocycloalkyl. pounds of any of Formula I-XV are inhibitors of p21-acti In one embodiment is a compound of Formula I, II, III, IV. vated kinase. In some embodiments, compounds of any of V. Va, or Vb, wherein at least one R is NR'S(=O).R. 60 Formula I-XV inhibit one or more of PAK1, PAK2, PAK3, —S(=O)N(R'), N(R'), C(=O)N(R'), PAK4, PAK5 or PAK6. In some embodiments of any of the NRC(=O)R'', NRC(=O)CR', NRC(=O)N above methods compounds of any of Formula I-XV inhibit (R'), or a substituted or unsubstituted heterocycloalkyl. one or more of PAK1, PAK2 or PAK3. In some embodiments In one embodiment is a compound of Formula I, II, III, IV. of any of the above methods, compounds of any of Formula V. Va, or Vb, wherein at least one R is N(R'), or a 65 I-XV inhibit PAK1 and PAK3. In some embodiments of any substituted or unsubstituted heterocycloalkyl. In a further of the above methods, compounds of any of Formula I-XV embodiment is a compound of Formula I, II, III, IV, V, Va., or inhibit PAK1 and PAK2. In some embodiments of any of the US 8,372,970 B2 7 8 above methods, compounds of any of Formula I-XV inhibit malize aberrant baseline synaptic transmission associated PAK1, PAK2 and PAK3. In some embodiments of any of the with a CNS disorder. In some embodiments of any of the above methods, compounds of any of Formula I-XV inhibit above methods, compounds of any of Formula I-XV normal PAK1 and PAK4. In some embodiments of any of the above ize or partially normalize aberrant synaptic plasticity associ methods, compounds of any of Formula I-XV inhibit PAK1, 5 ated with a CNS disorder. In some embodiments of any of the PAK2, PAK3 and PAK4. above methods, compounds of any of Formula I-XV normal In some embodiments of any of the above methods, com ize or partially normalize aberrant long term depression pounds of any of Formula I-XV inhibit PAK1. In some (LTD) associated with a CNS disorder. In some embodiments embodiments of any of the above methods, compounds of any of any of the above methods, compounds of any of Formula of Formula I-XV inhibit PAK2. In some embodiments of any 10 I-XV normalize or partially normalize aberrant long term of the above methods, compounds of any of Formula I-XV potentiation (LTP) associated with a CNS disorder. inhibit PAK3. In some embodiments of any of the above In some embodiments of any of the above methods, com methods, compounds of any of Formula I-XV inhibit PAK4. pounds of any of Formula I-XV normalize or partially nor In some embodiments of any of the above methods, a malize aberrant sensorimotor gating associated with a CNS therapeutically effective amount of compounds of any of 15 disorder Such as a neuropsychiatric disorder. In some embodi Formula I-XV causes substantially complete inhibition of ments of any of the above methods, compounds of any of one or more Group I p21-activated kinases. Formula I-XV reduce or reverse negative symptoms associ In some embodiments of any of the above methods, a ated with a CNS disorder. In some of such embodiments, the therapeutically effective amount of compounds of any of negative symptoms associated with a CNS disorder areaso Formula I-XV causes partial inhibition of one or more Group ciality, blunted affect, avolition, alogia, anhedonia or dyspho I p21-activated kinases. ric mood. In some embodiments of any of the above methods, In one embodiment the CNS disorder is a neurodegenera compounds of any of Formula I-XV reduce or reverse posi tive disorder, a neurodevelopmental disorder or a neuropsy tive symptoms associated with a CNS disorder. In some of chiatric disorder. Such embodiments, the positive symptoms associated with a In some embodiments of any of the above methods, the 25 CNS disorder are auditory, visual or tactile hallucinations. neuropsychiatric disorder is a psychotic disorder, a mood In some embodiments of any of the above methods, com disorder or cognitive impairment. pounds of any of Formula I-XV reduce or reverse cognitive In some embodiments of any of the above methods, the symptoms associated with a CNS disorder. In some of such CNS disorder is Schizophrenia, Psychotic disorder, schizoaf embodiments, the cognitive symptoms associated with a CNS fective disorder, schizophreniform, Alzheimer's disease, 30 disorder are impairment in executive function, comprehen Age-related cognitive decline, Mild cognitive impairment, Sion, inference, decision-making, planning, learning or cognitive decline associated with menopause, Parkinson’s memory. Disease, Huntington's Disease, Substance abuse and Sub In some embodiments of any of the above methods com stance dependence, Fragile X, Rett's syndrome, Angelman pounds of any of Formula I-XV halt or delay progression of Syndrome, Asperger's Syndrome, Autism, Autism Spectrum 35 cognitive impairment associated with a CNS disorder. In Disorders, Neurofibromatosis I, Neurofibromatosis II, Tuber Some of Such embodiments, the cognitive impairment is mild ous sclerosis, Clinical Depression, Bipolar Disorder, Mania, cognitive impairment. In some embodiments, the cognitive Epilepsy, Mental retardation, Down's syndrome, Niemann impairment is associated with Alzheimer's disease. Pick disease, Spongiform encephalitis, Lafora disease, Maple In some embodiments of any of the above methods, com syrup urine disease, maternal phenylketonuria, atypical phe 40 pounds of any of Formula I-XV reduce or reverse behavioral nylketonuria, Generalized Anxiety Disorder, Lowe Syn symptoms associated with a CNS disorder. In some of such drome, Turner Syndrome, Obsessive-compulsive disorder, embodiments, behavioral symptoms include, for example, Panic disorder, Phobias, Posttraumatic Stress Disorder, Anor repetitive behavior (stereotypy), hypersensitivity, hyperactiv exia Nervosa, and Bulimia Nervosa. ity, impaired social interaction, autism or the like. In some embodiments of any of the above methods, com 45 In some embodiments of any of the above methods, the pounds of any of Formula I-XV modulate dendritic spine method further comprises administration of a second thera morphology or synaptic function. In some embodiments of peutic agent that alleviates one or more symptoms associated any of the above methods, compounds of any of Formula with a CNS disorder. I-XV modulate dendritic spine density. In some embodiments In some embodiments, the second therapeutic agent is an of any of the above methods, compounds of any of Formula 50 antipsychotic agent, a cognition enhancer, a Group I mGluR I-XV modulate dendritic spine length. In some embodiments antagonist, a mGluR5 antagonist, a mGluR5 potentiator, a of any of the above methods, compounds of any of Formula nootropic agent, an alpha7 nicotinic receptor agonist, an I-XV modulate dendritic spine neck diameter. In some allosteric alpha7 nicotinic receptor potentiator, a nootropic embodiments of any of the above methods, compounds of any agent, a trophic agent, an antioxidant, a neuroprotectant, a of Formula I-XV modulate dendritic spine head volume. In 55 beta secretase inhibitor, a gamma secretase inhibitor or an Some embodiments of any of the above methods, compounds Abeta antibody. of any of Formula I-XV modulate dendritic spine head diam In some embodiments, administration of a therapeutically eter. In some embodiments of any of the above methods, effect amount of compounds of any of Formula I-XV to an compounds of any of Formula I-XV modulate the ratio of the individual in need thereof improves one or more of MAT number of mature spines to the number of immature spines. In 60 RICS cognition scores, Wisconsin Card Sort test scores, Some embodiments of any of the above methods, compounds Mini-Mental State Exam (MMSE) scores, Alzheimer Disease of any of Formula I-XV modulate the ratio of the spine head Assessment Scale-Cognitive (ADAS-cog) scale scores, diameter to spine length. In some embodiments of any of the ADAS-Behav scores, or Hopkins Verbal Learning Test above methods, compounds of any of Formula I-XV modu Revised scores for the individual. late synaptic function. 65 Provided herein are methods for reversing cortical hypo In some embodiments of any of the above methods, com frontality associated with a CNS disorder comprising admin pounds of any of Formula I-XV normalize or partially nor istering to an individual in need thereof a therapeutically US 8,372,970 B2 9 10 effective amount of a compound of any of Formula I-XV. Tuberous sclerosis, Clinical Depression, Bipolar Disorder, Provided herein are methods for reducing, stabilizing, or Mania, Epilepsy, Mental retardation, Down's syndrome, reversing neuronal withering and/or loss of synaptic function Niemann-Pick disease, Spongiform encephalitis, Lafora dis associated a CNS disorder comprising administering to an ease, Maple syrup urine disease, maternal phenylketonuria, individual in need thereof a therapeutically effective amount atypical phenylketonuria, Generalized Anxiety Disorder, of a compound of any of Formula I-XV. Provided herein are Turner Syndrome, Lowe Syndrome, Obsessive-compulsive methods for reducing, stabilizing or reversing atrophy or disorder, Panic disorder, Phobias, Posttraumatic Stress Dis degeneration of nervous tissue in the brain associated with a order. Anorexia Nervosa, and Bulimia Nervosa). CNS disorder comprising administering to an individual in A number of CNS disorders are characterized by abnormal need thereof a therapeutically effective amount of a com 10 dendritic spine morphology, spine size, spine plasticity and/ pound of any of Formula I-XV. or spine density as described in a number of studies referred Provided herein are methods of inhibiting the activity of one or more p21-activated kinases comprising contacting the to herein. PAK kinase activity has been implicated in spine one or more p21-activated kinases with a compound of any of morphogenesis, maturation, and maintenance. See, e.g., Formula I-XV. In some embodiments, the one or more p21 15 Kreis et al (2007), J Biol Chem, 282(29):21497-21506; activated kinase is contacted with a compound of any of Hayashi et al (2007), Proc Natl Acad Sci USA., 104(27): Formula I-XV in vitro. In some embodiments, the one or 11489-11494, Hayashi et al (2004), Neuron, 42(5):773-787: more p21-activated kinase is contacted with a compound of Penzes et al (2003), Neuron, 37:263-274. In some embodi any of Formula I-XV in vivo. ments, inhibition or partial inhibition of one or more PAKs Provided herein is the use of compounds of any of Formula normalizes aberrant dendritic spine morphology and/or syn I-XV in the manufacture of a medicament for the treatment of aptic function. CNS disorders that are treated by the methods a CNS disorder. described herein include, but are not limited to, Schizophre As used herein, compounds of any of Formula I-XV nia, Psychotic disorder, schizoaffective disorder, schizo includes compounds of Formula I, compounds of Formula II, phreniform, Alzheimer's disease, Age-related cognitive compounds of Formula III, compounds of Formula IV, or 25 decline, Mild cognitive impairment, cognitive decline asso compounds of Formula V. ciated with menopause, Parkinson's Disease, Huntington's Disease, Substance abuse and Substance dependence, Fragile BRIEF DESCRIPTION OF THE DRAWINGS X, Rett's syndrome, Angelman Syndrome, Asperger's Syn drome, Autism, Autism Spectrum Disorders, Neurofibroma The features of the present disclosure are set forth with 30 tosis I, Neurofibromatosis II, Tuberous sclerosis, Clinical particularity in the appended claims. A better understanding Depression, Bipolar Disorder, Mania, Epilepsy, Mental retar of the features and advantages of the present invention will be dation, Down’s syndrome, Niemann-Pick disease, Spongi obtained by reference to the following detailed description formencephalitis, Lafora disease, Maple syrup urine disease, that sets forth illustrative embodiments, in which the prin maternal phenylketonuria, atypical phenylketonuria, Gener ciples of the invention are utilized, and the accompanying 35 alized Anxiety Disorder. Obsessive-compulsive disorder, drawings of which: Panic disorder, Phobias, Posttraumatic Stress Disorder, Anor FIG. 1 describes illustrative shapes of dendritic spines. exia Nervosa, and Bulimia Nervosa. FIG. 2 describes modulation of dendritic spine head diam In some instances, CNS disorders are associated with eter by a small molecule PAK inhibitor. abnormal dendritic spine morphology, spine size, spine plas FIG.3 describes modulation of dendritic spine length by a 40 ticity, spine motility, spine density and/or abnormal synaptic small molecule PAK inhibitor. function. In some instances, activation of one or more of PAK1, PAK2, PAK3, PAK4, PAK5 and/or PAK6 kinases is DETAILED DESCRIPTION OF THE INVENTION implicated in defective spine morphogenesis, maturation, and maintenance. Described herein are methods for Suppressing Provided herein are methods for treatment of CNS condi 45 or reducing PAK activity (e.g., by administering a PAK tions by administration of inhibitors of certain p21 activated inhibitor for rescue of defects in spine morphology, size, kinases to individuals in need thereof. Such kinase inhibitors plasticity spine motility and/or density) associated with CNS are inhibitors of one or more of PAK1, PAK2, PAK3, PAK4, disorders as described herein. Accordingly, in some embodi PAK5 or PAK6 kinases. In certain embodiments, the indi ments, the methods described herein are used to treat an vidual has been diagnosed with or is suspected of Suffering 50 individual suffering from a CNS disorder wherein the disease from a CNS disorder such as a neuropsychiatric and/or neu is associated with abnormal dendritic spine density, spine rodegenerative and/or neurodevelopmental disease or condi size, spine plasticity, spine morphology, spine plasticity, or tion that is mediated by p21 activated kinases. In some spine motility. instances, provided herein are methods for treating conditions In some embodiments, any inhibitor of one or more p21 characterized by abnormal dendritic spine morphology and/ 55 activated kinases described herein reverses or partially or spine density and/or spine length and/or spine thickness reverses defects in dendritic spine morphology and/or den comprising inhibiting PAK activity by administration of a dritic spine density and/or synaptic function that are associ therapeutically effective amount of a PAK inhibitor to an ated with a CNS disorder. In some embodiments, modulation individual diagnosed with or Suspected of Suffering from a of dendritic spine morphology and/or dendritic spine density CNS disorder (e.g., Schizophrenia, Psychotic disorder, 60 and/or synaptic function alleviates or reverses cognitive schizoaffective disorder, schizophreniform, Alzheimer's dis impairment and/or negative behavioral symptoms (e.g., ease, Age-related cognitive decline, Mild cognitive impair social withdrawal, anhedonia or the like) associated with ment, cognitive decline associated with menopause, Parkin CNS disorders such as psychiatric conditions. In some son’s Disease, Huntington's Disease, Substance abuse and embodiments, modulation of dendritic spine morphology Substance dependence, Fragile X, Rett's syndrome, Angel 65 and/or dendritic spine density and/or synaptic function halts man Syndrome, Asperger's Syndrome, Autism, Autism Spec or delays progression of cognitive impairment and/or loss of trum Disorders, Neurofibromatosis I, Neurofibromatosis II, bodily functions associated with CNS disorders. US 8,372,970 B2 11 12 In some instances, cellular changes in brain cells contribute methods described herein are used to halt or delay progres to pathogenesis of a CNS disorder. In some instances, abnor sion of mild cognitive impairment (MCI) to early dementia, mal dendritic spine density in the brain contributes to the mid-stage dementia or late stage dementia in an individual pathogenesis of a CNS disorder. In some instances, abnormal Suffering from or Suspected of having mild cognitive impair dendritic spine morphology contributes to the pathogenesis 5 ment (MCI). In some instances, Alzheimer's disease is asso of a CNS disorder. In some instances, an abnormal pruning of ciated with abnormal dendritic spine morphology, spine size, dendritic spines or synapses during puberty contributes to the spine plasticity, spine motility, spine density and/or abnormal pathogenesis of a CNS disorder. In some instances, abnormal synaptic function. In some instances, soluble Abeta dimers synaptic function contributes to the pathogenesis of a CNS and/or oligomers increase PAK kinase activity at the synapse. disorder. In some instances, activation of one or more PAKS is 10 In some instances, Abeta plaques and/or insoluble Abeta associated with abnormal dendritic spine density and/or den aggregates increase PAK kinase activity at the synapse. In dritic morphology and/or synaptic function and contributes to Some instances, increased PAK kinase activity is associated the pathogenesis of a CNS disorder. In some instances, modu with defective spine morphogenesis, maturation, and main lation of PAK activity (e.g., attenuation, inhibition or partial tenance. In some instances, PAK inhibitors reverse defects in inhibition of PAK activity) reverses or reduces abnormalden 15 synaptic function and plasticity in a patient diagnosed with dritic spine morphology and/or dendritic spine density and/or Alzheimer's disease before Abeta plaques can be detected. In synaptic function. In certain embodiments, modulation of some embodiments, PAK inhibitors reverse defects in synap activity of one or more Group I PAKs (one or more of PAK1, tic morphology, synaptic transmission and/or synaptic plas PAK2 and/or PAK3) reverses or reduces abnormal dendritic ticity induced by soluble Abeta dimers and/or oligomers. In spine morphology and/or dendritic spine density and/or syn some embodiments, PAK inhibitors reverse defects in synap aptic function associated with CNS disorders. tic morphology, synaptic transmission and/or synaptic plas Abnormal dendritic spine morphology and/or density have ticity induced by Abeta oligomers and/or Abeta-containing been found in a number of CNS disorders as described below. plaques. Accordingly, in some embodiments, the methods described In some embodiments, the methods described herein are herein are used to treat an individual suffering from a CNS 25 used to treat an individual Suffering from epilepsy as disorder that is associated with abnormal dendritic spine den described in, for example, Example 20 herein. See, e.g., sity, spine size, spine plasticity, spine morphology, or spine Wong (2005), Epilepsy and Behavior. 7:569-577; Swannetal motility. In some embodiments, the methods described herein (2000), Hippocampus, 10:617-625; and Jiang et al (1998), J are used to treat an individual suffering from a CNS disorder, Neurosci, 18(20):8356-8368. Such as a psychotic disorder, as described in, by way of 30 In some embodiments, the methods described herein are example, Example 10 and Example 19 herein. Examples of used to treat an individual suffering from Parkinson's Disease psychotic disorders include, but are not limited to, schizo or Huntington's Disease. See, e.g., Neely et al (2007), Neu phrenia, schizoaffective disorder, schizophreniform disorder, roscience, 149(2):457-464; Spires etal (2004), Eur.I Neuro brief psychotic disorder, delusional disorder, shared psy sci, 19:2799-2807; Klapstein et al (2001), J Neurophysiol, chotic disorder (Folie a Deux). Substance induced psychosis, 35 86:2667-2677: Ferrante et al (1991), J Neurosci, 11:3877 and psychosis due to a general medical condition. See, e.g., 3887; and Graveland etal (1985), Science, 227:770-773. Blacket al. (2004), Am J Psychiatry, 161:742-744; Broadbelt In some embodiments, the methods described herein are et al. (2002), Schizophr Res, 58:75-81; Glantz et al. (2000), used to treat an individual Suffering from mental retardation, Arch Gen Psychiatry 57:65-73; and Kalus et al. (2000), Neu Fragile X syndrome, autism spectrum disorders or the like. roreport, 11:3621-3625. In some instances, aberrant spine 40 Examples for Autism spectrum Disorders include, but are not morphogenesis is associated with negative symptoms (e.g., limited to, Rett's syndrome, Angelman Syndrome, Asperg asociality, blunted affect, avolition, alogia, anhedonia or dys er's Syndrome, Fragile X syndrome or Tuberous sclerosis. phoric mood), and/or cognitive impairment symptomatic of In some embodiments, the methods described herein are Schizophrenia. In some instances, aberrant spine morphogen used to treat an individual Suffering from mental retardation. esis is associated with positive symptoms and behavioral 45 Mental retardation is a disorder characterized by significantly changes (e.g., social withdrawal, depersonalization, loss of impaired cognitive function and deficits in adaptive behav appetite, loss of hygiene, delusions, hallucinations, the sense iors. Mental retardation is often defined as an Intelligence of being controlled by outside forces or the like) symptomatic Quotient (IQ) score of less than 70. In some instances, mental of Schizophrenia. retardation is Down's syndrome, Fetal alcohol syndrome, In some embodiments, the methods described herein are 50 Klinefelter's syndrome, congenital hypothyroidism, Will used to treat an individual Suffering from a mood disorder. iams syndrome, Smith-Lemli-Opitz syndrome, Prader-Willi Examples of mood disorders include, but are not limited to, syndrome Phelan-McDermid syndrome, Mowat-Wilson syn clinical depression as described in, for example, Example 12 drome, ciliopathy or Lowe syndrome. herein, bipolar disorder, cyclothymia, and dysthymia. See, In some embodiments, the methods described herein are e.g., Hajszan et al (2005), Eur J Neurosci, 21:1299-1303: 55 used to treat an individual Suffering from neurofibromatosis. Law etal (2004) Am J Psychiatry, 161 (10): 1848-1855; Nor Neurofibromatosis (NF), also called von Recklinghaus dis rholm et al. (2001), Synapse, 42:151-163; and Rosoklija et al. ease, is an autosomal dominant genetically-inherited disorder (2000), Arch Gen Psychiatry, 57:349-356. in which the nerve tissue grows tumors (i.e., neurofibromas, In some embodiments, the methods described herein are ocular gliomas or the like). Patients with NF 1 exhibit a used to treat an individual Suffering from neurodegenerative 60 number of different disease symptoms including increased disorders (e.g., Parkinson's disease, Alzheimer's disease (as risk of forming nervous system tumors and cognitive deficits described in, for example, Example 12 herein) or the like). Such as defects in visual-spatial function, attention and motor See, e.g., Dickstein et al (2007), Aging Cell, 6:275-284; and coordination. Page et al. (2002), Neuroscience Letters, 317:37-41. In some NF is of Type 1 or Type 2. As used herein, NF includes Type embodiments, the methods described herein are used to treat 65 1 NF and Type 2 NF. In some instances, Type 1 NF is inherited an individual Suffering from or Suspected of having mild or results from spontaneous mutation of neurofibromin. In cognitive impairment (MCI). In some embodiments, the Some instances, NF Type 1 is associated with learning dis US 8,372,970 B2 13 14 abilities in individuals affected by the disease. In some illness. In some instances, a combination of genetic, familial instances the disease is associated with a partial absence and environmental factors play a role in manifestation of seizure disorder. In some instances NF Type 1 is associated disease symptoms. In some instances, mutations in genes with poor language, visual-spatial skills, learning disability resulting in a predisposition to a CNS disorders leads to (e.g., attention deficit hyperactivity disorder), headache, epi early-onset of the disease. lepsy or the like. Dendritic Spines Type 2 NF is inherited or results from spontaneous muta A dendritic spine is a Small membranous protrusion from a tion of merlin. In some instances, NF Type 2 causes Symp neuron's dendrite that serves as a specialized structure for the toms of hearing loss, tinnitus, headaches, epilepsy, cataracts formation, maintenance, and/or function of synapses. Den and/or retinal abnormalities, paralysis and/or learning dis 10 dritic spines vary in size and shape. In some instances, spines abilities. Patients with NF1 and NF2 are at increased risk of have a bulbous head (the spine head) of varying shape, and a forming nervous system tumors. In type 1 patients this thin neck that connects the head of the spine to the shaft of the includes dermal and plexiform neurofibromas, malignant dendrite. In some instances, spine numbers and shape are peripheral nerve sheath tumors (MPNST) and other malig regulated by physiological and pathological events. In some nant tumors, while type 2 patients may develop multiple 15 instances, a dendritic spine head is a site of synaptic contact. cranial and spinal tumors. In some instances, a dendritic spine shaft is a site of synaptic In some instances, developmental disability and/or behav contact. FIG. 1 shows examples of different shapes of den ioral problems associated with NF are associated with an dritic spines. Dendritic spines are “plastic.” In other words, abnormality in dendritic spine morphology and/or an abnor spines are dynamic and continually change in shape, Volume, mality in dendritic spine density and/or an abnormality in and number in a highly regulated process. In some instances, synaptic function. In some instances, an abnormality in den spines change in shape, Volume, length, thickness or number dritic spine morphology and/or dendritic spine density and/or in a few hours. In some instances, spines change in shape, synaptic function is associated with activation of p21-acti Volume, length, thickness or number occurs within a few vated kinase (PAK). In some instances, modulation of PAK minutes. In some instances, spines change in shape, Volume, activity (e.g., inhibition or partial inhibition of PAK) allevi 25 length, thickness or number occurs in response to synaptic ates, reverses or reduces abnormalities in dendritic spine mor transmission and/or induction of synaptic plasticity. By way phology and/or dendritic spine density and/or synaptic func of example, dendritic spines are headless (filopodia as shown, tion thereby reversing or partially reversing developmental for example, in FIG.1a), thin (for example, as shown in FIG. disability and/or behavioral problems associated with NF. In 1b), stubby (for example as shown in FIG. 1c), mushroom Some instances, modulation of PAK activity (e.g., inhibition 30 shaped (have door-knob heads with thick necks, for example or partial inhibition of PAK) alleviates, reverses or reduces as shown in FIG. 1d), ellipsoid (have prolate spheroid heads abnormalities in dendritic spine morphology and/or dendritic with thin necks, for example as shown in FIG. 1e), flattened spine density and/or synaptic function thereby reducing (flattened heads with thin neck, for example as shown in FIG. occurrence of seizures in individuals diagnosed with NF. In 1f) or branched (for example as shown in FIG. 1g). Some instances, modulation of PAK activity (e.g., inhibition 35 In some instances, mature spines have variably-shaped or partial inhibition of PAK) alleviates, reverses or reduces bulbous tips or heads, ~0.5-2 Lum in diameter, connected to a abnormalities in dendritic spine morphology and/or dendritic parent dendrite by thin stalks 0.1-1 um long. In some spine density and/or synaptic function thereby reducing or instances, an immature dendritic spine is filopodia-like, with reversing learning disabilities associated with NF. In some a length of 1.5-4 um and no detectable spine head. In some instances, modulation of PAK activity (e.g., inhibition or 40 instances, spine density ranges from 1 to 10 spines per partial inhibition of PAK) alleviates, reverses or reduces cog micrometer length of dendrite, and varies with maturational nitive deficits associated with NF. In some instances, modu stage of the spine and/or the neuronal cell. In some instances, lation of PAK activity (e.g., inhibition or partial inhibition of dendritic spine density ranges from 1 to 40 spines per 10 PAK) alleviates, reverses or reduces learning disability and/or micrometer in medium spiny neurons. epilepsy and/or any other symptoms associated with NF. In 45 In some instances, the shape of the dendritic spine head Some instances, modulation of PAK activity (e.g., inhibition determines sympatic function. Defects in dendritic spine mor or partial inhibition of PAK) alleviates, reverses or reduces phology and/or function have been described in neurological the incidence of tumor development associated with NF. diseases. As an example only, the density of dendritic spines In some embodiments, the methods described herein are has been shown to be reduced in pyramidal neurons from used to treat an individual suffering from Epilepsy, Niemann 50 patients with schizophrenia (Glanz, and Lewis, Arch Gen Psy Pick disease, Spongiform encephalitis, Lafora disease, Maple chiatry, 2000:57:65-73). In another example, neurons from syrup urine disease, maternal phenylketonuria, atypical phe patients with Fragile X mental retardation show a significant nylketonuria, age-related cognitive decline and cognitive increase in the overall density of dendritic spines, together decline associated with menopause. with an increase in the proportion of “immature', filopodia In some instances, development of a CNS disorder is asso 55 like spines and a corresponding reduction of "mature, mush ciated with a genetic component. Certain risk alleles and rooms-shaped spines (Irvin et al. Cerebral Cortex, 2000; genes that have been identified for CNS disorders. For 10:1038-1044). In many cases, the dendritic spine defects example, for Alzheimer's disease, risk alleles and genes found in Samples from human brains have been recapitulated include mutations in Amyloid Precursor Protein (APP), in rodent models of the disease and correlated to defective mutations in presenilin 1 and 2, the epsilon4 allele, the 91 bp 60 synapse function and/or plasticity. In some instances, den allele in the telomeric region of 12q, Apollipoprotein E-4 dritic spines with larger spine head diameterform more stable (APOE4) gene, SORL1 gene, reelin gene or the like. For synapses compared with dendritic spines with Smaller head example, in Some instances, development of schizophrenia is diameter. In some instances, a mushroom-shaped spine head associated with mutations in the DISC1 gene. In some is associated with normal or partially normal synaptic func instances, several risk alleles or genes are involved in etiology 65 tion. In some instances, a mushroom-shaped spine is a of a CNS disorder. In some instances, CNS disorders run in healthier spine (e.g., having normal or partially normal Syn families and there is a predisposition or vulnerability to the apses) compared to a spine with a reduced spine head size, US 8,372,970 B2 15 16 spine head volume and/or spine head diameter. In some herein is the use of a PAK inhibitor for manufacture of a instances, inhibition or partial inhibition of PAK activity medicament for treatment of one or more symptoms of a CNS results in an increase in spine head diameter and/or spine head disorder. Volume and/or reduction of spine length, thereby normalizing In some embodiments, the PAK inhibitor is a Group I PAK or partially normalizing synaptic function in individuals Suf inhibitor that inhibits, for example, one or more Group I PAK fering or suspected of suffering from a CNS disorder. polypeptides, for example, PAK1, PAK2, and/or PAK3. In p21-Activated Kinases (PAKs) some embodiments, the PAK inhibitor is a PAK1 inhibitor. In The PAKs constitute a family of serine-threonine kinases some embodiments, the PAK inhibitor is a PAK2 inhibitor. In that is composed of “conventional, or Group I PAKs, that some embodiments, the PAK inhibitor is a PAK3 inhibitor. In includes PAK1, PAK2, and PAK3, and “non-conventional', 10 some embodiments, the PAK inhibitor is a mixed PAK1/ or Group II PAKs, that includes PAK4, PAK5, and PAK6. PAK3 inhibitor. In some embodiments, the PAK inhibitor is a See, e.g., Zhao et al. (2005), Biochem J. 386:201-214. These mixed PAK1/PAK2 inhibitor. In some embodiments, the PAK kinases function downstream of the small GTPases Rac and/ inhibitor is a mixed PAK1/PAK4 inhibitor. In some embodi or Cdc42 to regulate multiple cellular functions, including 15 ments, the PAK inhibitor is a mixed PAK1/PAK2/PAK4 dendritic morphogenesis and maintenance (see, e.g., Ethellet inhibitor. In some embodiments, the PAK inhibitor is a mixed al(2005), Prog in Neurobiol, 75:161-205; Penzes etal (2003), PAK1/PAK2/PAK3/PAK4 inhibitor. In some embodiments, Neuron, 37:263-274), motility, morphogenesis, angiogen the PAK inhibitor inhibits all three Group I PAK isoforms esis, and apoptosis, (see, e.g., Bokochet al., 2003, Annu. Rev. (PAK1, 2 and PAK3) with equal or similar potency. In some Biochem., 72:743; and Hofmann et al., 2004, J. Cell Sci., embodiments, the PAK inhibitor is a Group II PAK inhibitor 117:4343;). GTP-bound Rac and/or Cdc42 bind to inactive that inhibits one or more Group II PAK polypeptides, for PAK, releasing steric constraints imposed by a PAK autoin example PAK4, PAK5, and/or PAK6. In some embodiments, hibitory domain and/or permitting PAK phosphorylation and/ the PAK inhibitor is a PAK4 inhibitor. In some embodiments, or activation. Numerous phosphorylation sites have been the PAK inhibitor is a PAK5 inhibitor. In some embodiments, identified that serve as markers for activated PAK. 25 the PAK inhibitor is a PAK6 inhibitor. In some instances, upstream effectors of PAK include, but In certain embodiments, a PAK inhibitor described herein are not limited to, TrkB receptors; NMDA receptors; adenos reduces or inhibits the activity of one or more of PAK1, ine receptors; estrogen receptors; integrins, EphB receptors; PAK2, PAK3, and/or PAK4 while not affecting the activity of CDK5, FMRP; Rho-family GTPases, including Cdc42, Rac PAK5 and PAK6. In some embodiments, a PAK inhibitor (including but not limited to Rac1 and Rac2), Chp, TC10, and 30 described herein reduces or inhibits the activity of one or Wrnch-1; guanine nucleotide exchange factors (“GEFs), more of PAK1, PAK2 and/or PAK3 while not affecting the such as but not limited to GEFT, C-p-2'-activated kinase activity of PAK4, PAK5 and/or PAK6. In some embodiments, interacting exchange factor (CPIX), Kalirin-7, and Tiam 1; G a PAK inhibitor described herein reduces or inhibits the activ protein-coupled receptor kinase-interacting protein 1 (GIT1). ity of one or more of PAK1, PAK2, PAK3, and/or one or more 35 of PAK4, PAK5 and/or PAK6. In some embodiments, a PAK and sphingosine. inhibitor described herein is a substantially complete inhibi In some instances, downstream effectors of PAK include, tor of one or more PAKs. As used herein, “substantially but are not limited to, substrates of PAK kinase, such as complete inhibition” means, for example, >95% inhibition of Myosin light chain kinase (MLCK), regulatory Myosin light one or more targeted PAKs. In other embodiments, “substan chain (R-MLC), Myosins I heavy chain, myosin II heavy 40 tially complete inhibition' means, for example, >90% inhi chain, Myosin VI, Caldesmon, Desmin, Op.18/stathmin, Mer bition of one or more targeted PAKs. In some other embodi lin, FilaminA, LIM kinase (LIMK), Ras, Raf, Mek, p47phox, ments, “substantially complete inhibition' means, for BAD, caspase 3, estrogen and/or progesterone receptors, example, >80% inhibition of one or more targeted PAKs. In RhoGEF, GEF-H1, NET1, Goz, phosphoglycerate mutase some embodiments, a PAK inhibitor described herein is a B. RhoGDI, prolactin, p41 Arc, cortactin and/or Aurora-A 45 partial inhibitor of one or more PAKs. As used herein, “partial (See, e.g., Bokochet al., 2003, Annu. Rev. Biochem., 72:743; inhibition” means, for example, between about 40% to about and Hofmann et al., 2004, J. Cell Sci., 117:4343). Other 60% inhibition of one or more targeted PAKs. In other substances that bind to PAK in cells include CIB. sphingolip embodiments, “partial inhibition” means, for example, ids; lysophosphatidic acid, G-protein B and/or Y subunits: between about 50% to about 70% inhibition of one or more PIX/COOL: GIT/PKL: Nef: Paxillin; NESH; SH3-contain 50 targeted PAKs. As used herein, where a PAK inhibitor sub ing proteins (e.g. Nck and/or Grb2); kinases (e.g. Akt, PDK1, stantially inhibits or partially inhibits the activity of a certain PI 3-kinase/p85, Cdk5, Cdc2, Src kinases, Abl, and/or protein PAK isoform while not affecting the activity of another iso kinase A (PKA)); and/or phosphatases (e.g. phosphatase form, it means, for example, less than about 10% inhibition of PP2A, POPX1, and/or POPX2). the non-affected isoform when the isoform is contacted with PAK Inhibitors 55 the same concentration of the PAK inhibitor as the other Described herein are PAK inhibitors that treat one or more substantially inhibited or partially inhibited isoforms. In symptoms associated with CNS disorders. Also described other instances, where a PAK inhibitor substantially inhibits herein are pharmaceutical compositions comprising a PAK or partially inhibits the activity of a certain PAK isoform inhibitor (e.g., a PAK inhibitor compound described herein) while not affecting the activity of another isoform, it means, for reversing or reducing one or more of cognitive impairment 60 for example, less than about 5% inhibition of the non-affected and/or dementia and/or negative symptoms and/or positive isoform when the isoform is contacted with the same concen symptoms associated with CNS disorders. Also described tration of the PAK inhibitor as the other substantially inhib herein are pharmaceutical compositions comprising a PAK ited or partially inhibited isoforms. In yet other instances, inhibitor (e.g., a PAK inhibitor compound described herein) where a PAK inhibitor substantially inhibits or partially for halting or delaying the progression of cognitive impair 65 inhibits the activity of a certain PAK isoform while not affect ment and/or dementia and/or negative symptoms and/or posi ing the activity of another isoform, it means, for example, less tive symptoms associated with CNS disorders. Described than about 1% inhibition of the non-affected isoform when US 8,372,970 B2 17 18 the isoform is contacted with the same concentration of the (R') —OR', a substituted or unsubstituted alkyl, a PAK inhibitor as the other substantially inhibited or partially substituted or unsubstituted alkoxy, a substituted or inhibited isoforms. unsubstituted heteroalkyl, a substituted or unsubstituted Provided herein, in certain embodiments, are compounds cycloalkyl, or a substituted or unsubstituted heterocy having the structure of Formula I orpharmaceutically accept cloalkyl: able salt or N-oxide thereof: r is 0 to 8; and s is 0 to 4. In one embodiment is a compound of Formula I wherein Formula I ring T is an aryl ring. In one embodiment, the aryl ring is a R7: 10 phenyl group. In another embodiment is a compound of For N1 N1 N mula I wherein ring T is a heteroaryl ring. In yet another (R) O 2 embodiment is a compound of Formula I, wherein ring T is N N N O selected from pyrrole, furan, thiophene, pyrazole, imidazole, H isoxazole, oxazole, isothiazole, thiazole, 1,2,3-triazole, 1.3, Q 15 4-triazole, 1-Oxa-2,3-diazole, 1-oxa-2,4-diazole, 1-Oxa-2,5- diazole, 1-Oxa-3,4-diazole, 1-thia-2,3-diazole, 1-thia-2,4- wherein: diazole, 1-thia-2,5-diazole, 1-thia-3,4-diazole, tetrazole, R" is pyridine, pyridazine, pyrimidine, and pyrazine. In another embodiment, ring T is thiazole. In a further embodiment is a compound of Formula I, (R), wherein R is a C-linked heterocycloalkyl. In one embodi ment, the C-linked heterocycloalkyl is oxetane, azetidine, tetrahydrofuran, pyrrolidine, tetrahydrothiophene, piperi R3 dine, tetrahydropyran, and morpholine. In a further embodi 25 ment, the C-linked heterocycloalkyl is substituted with at least one C-Calkyl or halogen. In another embodiment, the wherein ring T is an aryl, or a heteroaryl ring: C-Calkyl is methyl, ethyl, or n-propyl. In one embodiment R is a substituted or unsubstituted cycloalkyl, a substituted is a compound of Formula I, wherein R is a substituted or or unsubstituted heteroaryl attached to ring T via a car unsubstituted C-linked heteroaryl. In one embodiment, R is bonatom of R, or a substituted or unsubstituted hetero 30 selected from a C-linked pyrrole, furan, thiophene, pyrazole, cycloalkyl attached to ring T via a carbon atom of R: imidazole, isoxazole, oxazole, isothiazole, thiazole, 1,2,3- Q is a substituted or unsubstituted alkyl, a substituted or triazole, 1,3,4-triazole, 1-oxa-2,3-diazole, 1-oxa-2,4-diazole, unsubstituted heteroalkyl, a substituted or unsubstituted 1-Oxa-2,5-diazole, 1-Oxa-3,4-diazole, 1-thia-2,3-diazole, heterocycloalkyl, a substituted or unsubstituted 1-thia-2,4-diazole, 1-thia-2,5-diazole, 1-thia-3,4-diazole, tet cycloalkyl, a Substituted or unsubstituted cycloalkyla 35 razole, pyridine, pyridazine, pyrimidine, and pyrazine. In yet lkyl, a substituted or unsubstituted heterocycloalkyla another embodiment, R is a C-linked thiazole. In another lkyl, a substituted or unsubstituted aryl, a substituted or embodiment, R is a C-linked pyrazole. In a further embodi unsubstituted arylalkyl, a substituted or unsubstituted ment, Risa C-linkedoxadiazole. In another embodiment, R heteroaryl, or a substituted or unsubstituted heteroary is a substituted or unsubstituted cycloalkyl. In a further lalkyl: 40 embodiment, cycloalkyl is selected from cyclopropyl. each R" is independently halogen, —CN, NO, -OH, cyclobutyl, cyclopentyl, or cyclohexyl. In a further embodi –OCF, OCHF, OCFH, -CF, SR, ment, R is cyclopentyl. In another embodiment, R is cyclo NR'S(=O).R. S(=O)N(R'), C(=O)R, hexyl. OC(=O)R, COR', N(R'), C(=O)N In yet another embodiment, R is a C-linked heteroaryl (R0), NRC(=O)R', NRC(=O)CR, 45 Substituted with at least one group selected from halogen, - NR'C(=O)N(R'), a substituted or unsubstituted CN, NO, OH, SR, S(=O)R’, S(=O).R. alkyl, a substituted or unsubstituted alkoxy, a substituted NRS(=O),R, S(=O)N(R'), C(=O)R. OC or unsubstituted heteroalkyl, a substituted or unsubsti (—O)R, COR, N(R'), C(=O)N(R'), NRC tuted cycloalkyl, or a substituted or unsubstituted het (=O)R'9, NRC(=O)CR9, NRC(=O)N(R0), erocycloalkyl; 50 —OR', a substituted or unsubstituted alkyl, a substituted or R is Hor R: unsubstituted alkoxy, a substituted or unsubstituted het R is a substituted or unsubstituted alkyl, a substituted or eroalkyl, a substituted or unsubstituted cycloalkyl, or a sub unsubstituted cycloalkyl, a substituted or unsubstituted stituted or unsubstituted heterocycloalkyl. In one embodi heterocycloalkyl, a substituted or unsubstituted aryl, or a ment, the C-linked heteroaryl is substituted with C-Calkyl. substituted or unsubstituted heteroaryl; 55 In another embodiment, C-Calkyl is methyl, ethyl, n-pro each R' is independently H, a substituted or unsubstituted pyl, iso-propyl. n-butyl, iso-butyl, or tert-butyl. In a further alkyl, a Substituted or unsubstituted cycloalkyl, a Substi embodiment, the C-linked heteroaryl is substituted with tuted or unsubstituted heterocycloalkyl, a substituted or methyl. In another embodiment, ethyl. In a further embodi unsubstituted aryl, or a substituted or unsubstituted het ment, n-propyl or iso-propyl. eroaryl; or two R', together with the atoms to which 60 Also disclosed herein is a compound of Formula I wherein they are attached form a heterocycle; R" is independently halogen, —CN, NO, OH, OCF, ring B is aryl or heteroaryl; OCHF, OCFH, CF, SR, NR'S(=O).R. each R is independently halogen, —CN, NO. —OH, - S(=O)N(R'), C(=)R’, OC(=O)R, COR'', SR, S(—O)R, S(—O),R, NRS(—O).R. N(R'), C(=O)N(R'), NRC(=O)R'', S(=O)N(R'), C(=O)R, OC(=O)R’, 65 NR'C(=O)CR', and NR'C(=O)N(R'). In a fur COR, N(R0), C(=O)N(R0), NRC ther embodiment, R is a halogen. In yet another embodi (—O)R'', NRC(=O)CR'', NRC(=O)N ment, R is selected from F, Cl, Br, or I. In another embodi US 8,372,970 B2 19 20 ment, R is F. In yet another embodiment, R is a substituted In one embodiment is a compound of Formula I wherein or unsubstituted alkyl, a substituted or unsubstituted alkoxy, a substituted or unsubstituted heteroalkyl, a substituted or unsubstituted cycloalkyl, or a substituted or unsubstituted H heterocycloalkyl. In one embodiment, R is substituted or 5 unsubstituted alkyl selected from methyl, ethyl, n-propyl. R’-(O? iso-propyl. n-butyl, iso-butyl or tert-butyl. In another embodi (Dr. ment, R is OH. In a further embodiment, R is OCH. In yet another embodiment, R is OCF. 10 is selected from: In another embodiment, S is 1. In yet another embodiment, s is 0. In one embodiment, is a compound of Formula I wherein Q is a substituted or unsubstituted alkyl, a substituted or unsub- 15 stituted heteroalkyl, a substituted or unsubstituted heterocy- O cloalkyl, a substituted or unsubstituted cycloalkyl, a substi- W tuted or unsubstituted cycloalkylalkyl, a substituted or S S unsubstituted heterocycloalkylalkyl, a substituted or unsub- C C stituted aryl, a substituted or unsubstituted arylalkyl, a sub- 20 N stituted or unsubstituted heteroaryl, or a substituted or unsub H stituted heteroarylalkyl. In another embodiment, Q is a substituted or unsubstituted alkyl. In a further embodiment, Q N is an unsubstituted methyl, ethyl, n-propyl, iso-propyl. n-bu- 25 tyl, iso-butyl or tert-butyl. In a further embodiment, Q is O ethyl. S W S In yet another embodiment, is a compound of Formula I, wherein ring B is an aryl ring. In another embodiment, ring B is a substituted or unsubstituted phenyl. In a further embodi- 30 N ment, ring B is a substituted or unsubstituted naphthalene. In a further embodiment, is a compound of Formula I, wherein ring B is a heteroaryl ring selected from pyrrole, furan, thiophene, pyrazole, imidazole, isoxazole, oxazole, isothiaz- 35 s ole, thiazole, 1,2,3-triazole, 1.3,4-triazole, 1-Oxa-2,3-diazole, 1-Oxa-2,4-diazole, 1-oxa-2,5-diazole, 1-Oxa-3,4-diazole, 1-thia-2,3-diazole, 1-thia-2,4-diazole, 1-thia-2,5-diazole, 1-thia-3,4-diazole, tetrazole, pyridine, pyridazine, pyrimi dine, and pyrazine. 40 In yet a further embodiment, is a compound of Formula I, N wherein R is a C-C cycloalkyl ring; or a 3-6-membered H heterocycloalkyl ring comprising 1-3 Natoms, an O atom, a Satom; or any combination thereof, and wherein R is further 45 substituted by halogen, —CN, NO. —OH, SR, S(=O)R’, S(=O).R. NR'S(=O).R. S(=O)N N (R'), C(=O)R, OC(=O)R, COR', N(R'), C(=O)N(R0), NRC(=O)R9, NRC(=O) 50 OR', NR'C(=O)N(R'), OR', substituted or N unsubstituted alkyl, substituted or unsubstituted alkoxy, sub- \ stituted or unsubstituted heteroalkyl, substituted or unsubsti- y tuted cycloalkyl or substituted or unsubstituted heterocy cloalkyl. 55 In one embodiment, R is a C-Cacycloalkyl ring. In r another embodiment, the C-Cacycloalkyl ring is cyclopro pyl. In another embodiment, the C-Cacycloalkyl ring is --- cyclopentyl. In another embodiment, the C-C cycloalkyl is 60 H cyclohexyl. N s In another embodiment, R is OH or CN. In a further r embodiment, R is OCF, or CF. In yet another embodiment is a compound of Formula I 65 itsu F wherein r is 0. In another embodiment, r is 1. In a further embodiment, r is 2.

US 8,372,970 B2 23 24 -continued -continued Hy

N cC 10 In one embodiment, is a compound of Formula I, wherein R is halogen, —CN, OH, substituted or unsubstituted alkyl, OR', NR'S(=O).R. S(=O)N(R'), N(R'), C(=O)N(R'), NRC(=O)R 9, NR'C(=O)CR', NR'C(=O)N(R'), or substituted 15 or unsubstituted heterocycloalkyl. In one embodiment, R is selected from F, Cl, Br, or I. In another embodiment R is F. In another embodiment, is a compound of Formula I, wherein at least one R is NR'S(=O).R. —S(=O)N (R0), N(R0), C(=O)N(R0), NRC(=O)R 9, NR'C(=O)CR', NR'C(=O)N(R'), or substituted or unsubstituted heterocycloalkyl. In one embodiment, is a compound of Formula I, wherein at least one R is N(R'), or substituted or unsubstituted heterocycloalkyl. In yet 25 another embodiment, is a compound of Formula I wherein at least one of R is a substituted or unsubstituted piperazine, -N substituted or unsubstituted piperidine, substituted or unsub H stituted pyrrolidine or substituted or unsubstituted morpho line. In a further embodiment, is a compound of Formula I, 30 wherein at least one R is —OR''. In one embodiment is a y compound of Formula I, wherein at least one R is —OR' and R' is H. In another embodiment, R' is alkyl selected from methyl, ethyl, n-propyl, iso-propyl. n-butyl, iso-butyl, N and tert-butyl. 35 In one embodiment is a compound of Formula I wherein ring B is substituted with N(R'), wherein R' is each H independently selected from H and a substituted or unsubsti tuted heterocycloalkyl. In another embodiment is a com y pound of Formula I wherein ring B is substituted with 40 NHR' wherein R' is a substituted or unsubstituted pip erazine, substituted or unsubstituted piperidine, substituted HN or unsubstituted pyrrolidine or substituted or unsubstituted morpholine. In a further embodiment is a compound of For H mula I wherein ring B is substituted with N(CH)R' 45 wherein R' is a substituted or unsubstituted piperazine, sub y stituted or unsubstituted piperidine, substituted or unsubsti tuted pyrrolidine or substituted or unsubstituted morpholine. C s Also presented herein is a compound of Formula I wherein N ring B is substituted with —OR' wherein R' is a substituted 50 or unsubstituted heterocycloalkyl. In another embodiment is a compound of Formula I wherein ring B is substituted with —OR' wherein R' is a substituted or unsubstituted pipera zine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine or substituted or unsubstituted mor 55 pholine. In yet another embodiment is a compound of For mula I wherein ring B is substituted with at least one CF. In yet another embodiment, ring B is substituted with at least two R. In another embodiment, ring B is substituted with halogen and a substituted or unsubstituted heterocy 60 cloalkyl. In another embodiment, ring B is substituted with at least one F, Cl, Br, or I and a substituted or unsubstituted piperazine, Substituted or unsubstituted piperidine, Substi tuted or unsubstituted pyrrolidine, or substituted or unsubsti tuted morpholine. 65 In another aspect is a compound having the structure of N O Formula II or pharmaceutically acceptable salt or N-oxide thereof: US 8,372,970 B2 25 26 wherein s1 is 0 to 3 and ring T, ring B. R. R. R. Q and rare Formula II described previously. R3 In yet a further embodiment is a compound having the 5 structure of Formula IV:

N N N (R), 5 (R -O N l N2 N O H 10 Formula IV Q R3 N wherein: -- (R): ring T is an aryl, or a heteroaryl ring; N1 N1 N 2 R is a substituted or unsubstituted cycloalkyl, a substituted (RS) GE) us or unsubstituted heteroaryl attached to ring T via a car- * 2 bonatom of R, or a substituted or unsubstituted hetero cycloalkyl attached to ring T via a carbon atom of R: Q each R is independently halogen, —CN, NO. —OH, –OCF, OCFH, -CF, -SR, S(=O)R. - S(=O),R, NRS(=O),R, S(=O)N(R'), OR, C(=O)R, OC(=O)R, COR, N(R'), C(=O)N(R'), NR'C(=O)R', wherein s1 is 0 to 4 and ring B. R. R. R. Q and rare NRC(=O)CR', NRC(=O)N(R'), substi- as described previously. tuted or unsubstituted alkyl, substituted or unsubstituted In another embodiment is a compound having the structure heteroalkyl, substituted or unsubstituted cycloalkyl or of Formula V: substituted or unsubstituted heterocycloalkyl: R is Hor R: R is a substituted or unsubstituted alkyl, a substituted or 30 unsubstituted cycloalkyl, a substituted or unsubstituted heterocycloalkyl, a substituted or unsubstituted aryl, or a Formula V substituted or unsubstituted heteroaryl; each R' is independently H, substituted or unsubstituted N R3 alkyl, substituted or unsubstituted cycloalkyl, substi- 35 -- (R): tuted or unsubstituted heterocycloalkyl, substituted or sis unsubstituted aryl or substituted or unsubstituted het- N1 N1 N 21 eroaryl, or two R' together with the atoms to which they (R)5 2 are attached form a heterocycle; N N N O s is 0-4: 40 H ring- B is aryl or heteroaryl; Q each R is independently halogen, —CN, NO, -OH, SR, S(—O)R, S(—O),R, NRS(—O).R. S(=O)N(R'), C(=O)R, OC(=O)R’, COR, NOR"), C(=O)N(R'), NRC (NRC(O)OR, NRC(=O)N(R), OR, wherein s1 is 0 to 4 and ring B. R. R. R. Q and rare substituted or unsubstituted alkyl, substituted or unsub- described previously. stituted heteroalkyl, substituted or unsubstituted cycloalkyl or substituted or unsubstituted heterocy- In another embodiment is a compound having the structure cloalkyl; and 50 of Formula Va: r is 0-8. In a further embodiment is a compound having the struc ture of Formula III: Formula Va. R3 55 Formula III N R (R): -- (P(R): \ . . N1 N. 21

N N-a->e re-OulN 4. O

N N N O Q H Q 65 wherein s1 is 0 to 4 and ring B. R. R. R. Q and r are described previously. US 8,372,970 B2 27 28 In another embodiment is a compound having the structure -continued of Formula Vb:

O Formula Vb 5 N-4 O 2N N

N N N 10 (R) l 2 N N N O H /oH Q 15 wherein ring B, R. R. R. Q and rare described previously. In one embodiment is a compound of Formula I, II, III, IV. V. Va., or Vb wherein R is selected from pyrrole, furan, thiophene, pyrazole, imidazole, isoxazole, oxazole, isothiaz ole, thiazole, 1,2,3-triazole, 1.3,4-triazole, 1-Oxa-2,3-diazole, 1-Oxa-2,4-diazole, 1-oxa-2,5-diazole, 1-Oxa-3,4-diazole, 1-thia-2,3-diazole, 1-thia-2,4-diazole, 1-thia-2,5-diazole, 1-thia-3,4-diazole, tetrazole, pyridine, pyridazine, pyrimi dine, and pyrazine. 25 In another embodiment, is a compound of Formula I, II, III, IV, V, Va., or Vb wherein R is selected from

US 8,372,970 B2 29 30 In a further embodiment is a compound of Formula I, II, III, In one embodiment is a compound of Formula I, II, III, IV. IV, V, Va, or Vb, wherein V. Va, or Vb, wherein at least one R is NR'S(=O).R. —S(=O)N(R'), N(R'), C(=O)N(R'), NRC(=O)R'', NRC(=O)CR'', NRC(=O)N (R'), or a substituted or unsubstituted heterocycloalkyl. In one embodiment is a compound of Formula I, II, III, IV. V. Va, or Vb, wherein at least one R is N(R'), or a substituted or unsubstituted heterocycloalkyl. In a further is: 10 embodiment is a compound of Formula I, II, III, IV, V, Va., or Vb wherein at least one of R is a substituted or unsubstituted piperazine, a Substituted or unsubstituted piperidine, a Sub N N1 N. stituted or unsubstituted pyrrolidine, or a substituted or (R5). H s (R) s unsubstituted morpholine. In one embodiment is a compound 21 21N 2 15 of Formula I, II, III, IV, V, Va, or Vb, wherein at least one R H is —OR''. In another embodiment is a compound of Formula O N I, II, III, IV, V, Va., or Vb, wherein R is independently halo (R)- (R)- / gen, —CN, —OH, - OCF. —OCF, —OCF.H. —CF, 2 2 —SR, a substituted or unsubstituted alkyl, or a substituted or unsubstituted alkoxy. (RS) N N. (RS) ?y N. In one embodiment is a compound of Formula I, II, III, IV. 21 A N-4N, V, Va., or Vb, whereins is zero. H In a further embodiment is a compound of Formula I, II, III, 25 IV, V, Va., or Vb, wherein Q is a substituted or unsubstituted (RS) (). (RS) 1NY. alkyl, or a substituted or unsubstituted heteroalkyl. In another Q-U^ S2 N/ embodiment is a compound of Formula I, II, III, IV, V, Va., or S N Vb, wherein Q is a substituted or unsubstituted cycloalkyl, or 5 - || N-V 5 1st a substituted or unsubstituted heterocycloalkyl. In a further 30 (R)-i 2 N. (R)- 21 7 embodiment is a compound of Formula I, II, III, IV, V, Va., or H H Vb, wherein Q is a substituted or unsubstituted cycloalkyla N N lkyl, or a substituted or unsubstituted heterocycloalkylalkyl. (R) 1st- s e? s In one embodiment is a compound of Formula I, II, III, IV. V. -N/ N-IN/ 35 Va., or Vb, wherein Q is a substituted or unsubstituted aryl, or a substituted or unsubstituted heteroaryl. s- Ns - In one embodiment is a compound of Formula I, II, III, IV. V. Va, or Vb, wherein Q is a substituted or unsubstituted 4. 4. arylalkyl, or a substituted or unsubstituted heteroarylalkyl. s s 40 In another embodiment is a compound of Formula I, II, III, e-f ?i\ IV or V, wherein Q is selected from: * Na2 7 , (R) 2 A s H H 1s-N 1s-N 45 (R) tract (R) 50

S (R) ? EX (R), n N 2 2n.2 55 . . . , N1N1 N N N1 N (R)- , (R)- or (R)-H 2n 21 N4 N4 60 In another embodiment is a compound of Formula I, II, III, IV. V. Va., or Vb, where R is halogen, —CN, OH, a substi , , , tuted or unsubstituted alkyl, -OR', NR'S(=O).R. –S(=O)N(R'), N(R'), C(O)N(R'), NRC 65 (—O)R'9, NRC(=O)CR9, NRC(=O)N(R0), or a substituted or unsubstituted heterocycloalkyl. US 8,372,970 B2 31 32 -continued unsubstituted heteroalkyl, substituted or unsubsti tuted cycloalkyl or substituted or unsubstituted het erocycloalkyl, R is H or substituted or unsubstituted alkyl: R is substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubsti tuted aryl or substituted or unsubstituted heteroaryl each R' is independently H, substituted or unsubsti tuted alkyl, substituted or unsubstituted cycloalkyl, 10 substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl, or two R' together with the atoms to which they are attached form a hetero cycle; ring B is aryl or heteroaryl substituted with R: 15 each R is independently halogen, —CN, NO, OH, SR, S(–O)R, S(—O).R, NR'S (=O),R, S(=O)N(R'), C(=O)R, OC Also provided herein, in some embodiments, are com (=O)R, COR', N(R'), C(=O)N(R'), pounds having the structure of Formula VI or pharmaceuti 2O NRC(O)R'9, NRC(O)OR, NRC cally acceptable salt or N-oxide thereof: (=O)N(R'), substituted or unsubstituted alkyl, substituted or unsubstituted alkoxy, substituted or unsubstituted heteroalkyl, substituted or unsubsti Formula VI tuted cycloalkyl or substituted or unsubstituted het R6 25 erocycloalkyl, 7 r is 0-8. N1N1 N R In one embodiment, is a compound having the structure of Formula VI or pharmaceutically acceptable salt or N-oxide 2 thereof wherein: (R-OulN N O 30 W is a bond; H R is CN, -OH, substituted or unsubstituted alkoxy, W. - N(R'), substituted or unsubstituted heteroalkyl, No substituted or unsubstituted cycloalkyl, substituted or unsubstituted aryl or substituted or unsubstituted het wherein: 35 eroaryl; W is a bond; R’ is halogen, —CN, OH, substituted or unsubstituted R is —CN, -OH, substituted or unsubstituted alkoxy, alkoxy, C(=O)N(R'), COR', N(R'), acyl, N(R'), substituted or unsubstituted heteroalkyl, substituted or unsubstituted heteroalkyl, substituted or substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted unsubstituted aryl or substituted or unsubstituted het 40 heterocycloalkyl, substituted or unsubstituted aryl or eroaryl; substituted or unsubstituted heteroaryl; R’ is halogen, —CN, -OH, substituted or unsubstituted Q substituted or unsubstituted heteroalkyl, substituted or alkoxy, —C(=O)N(R'), COR', N(R'), acyl, unsubstituted heterocycloalkyl, substituted or unsubsti substituted or unsubstituted heteroalkyl, substituted or tuted cycloalkyl, substituted or unsubstituted cycloalky 45 lalkyl, substituted or unsubstituted heterocycloalkyla unsubstituted cycloalkyl, substituted or unsubstituted lkyl, substituted or unsubstituted aryl, substituted or heterocycloalkyl, substituted or unsubstituted aryl or unsubstituted arylalkyl, substituted or unsubstituted het substituted or unsubstituted heteroaryl; eroaryl, substituted or unsubstituted heteroarylalkyl; Q is substituted or unsubstituted alkyl, substituted or ring A is substituted or unsubstituted aryl or heteroaryl unsubstituted heteroalkyl, substituted or unsubstituted 50 substituted with 0-4 R: heterocycloalkyl, substituted or unsubstituted each R is independently halogen, —CN, NO, cycloalkyl, substituted or unsubstituted cycloalkylalkyl, OH, SR, S(=O)R. S(=O).R. NR'S substituted or unsubstituted heterocycloalkylalkyl, sub (=O).R., S(=O)N(R'), C(=O)R, OC stituted or unsubstituted aryl, substituted or unsubsti (=O)R, COR, N(R'), C(=O)N(R'), tuted arylalkyl, substituted or unsubstituted heteroaryl, 55 NRC(O)R'9, NRC(O)OR, NRC substituted or unsubstituted heteroarylalkyl, or substi (=O)N(R'), substituted or unsubstituted alkyl, tuted or unsubstituted cycloalkyl or heterocycloalkyl substituted or unsubstituted alkoxy, substituted or fused to ring A: unsubstituted heteroalkyl, substituted or unsubsti ring A is substituted or unsubstituted aryl or heteroaryl tuted cycloalkyl or substituted or unsubstituted het substituted with 0-4 R: 60 erocycloalkyl, each R is independently halogen, —CN, NO, R is H or substituted or unsubstituted alkyl: OH, SR, S(=O)R. S(=O).R. NR'S R is substituted or unsubstituted alkyl, substituted or (=O),R, S(=O)N(R'), C(=O)R, OC unsubstituted cycloalkyl, substituted or unsubsti (=O)R, COR', N(R'), C(=O)N(R'), tuted aryl or substituted or unsubstituted heteroaryl NRC(O)R'9, NRC(O)OR, NRC 65 each R" is independently H, substituted or unsubsti (=O)N(R'), substituted or unsubstituted alkyl, tuted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted alkoxy, substituted or substituted or unsubstituted aryl or substituted or US 8,372,970 B2 33 34 unsubstituted heteroaryl, or two R' together with In yet another embodiment is a compound of structure of the atoms to which they are attached form a hetero- Formula VI or pharmaceutically acceptable salt or N-oxide cycle; thereof wherein: ring B is aryl or heteroaryl substituted with R: W is a bond; each R is independently halogen, —CN, NO. 5 R is CN, -OH, substituted or unsubstituted alkoxy, - N(R'), substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted aryl or substituted or unsubstituted het eroaryl; (=O)N(R'), substituted or unsubstituted alkyl, R7 is halogen, —CN, OH, substituted or unsubstituted substituted or unsubstituted alkoxy, substituted or alkoxy, C(=O)N(R'), COR', N(R'), acyl, unsubstituted heteroalkyl, substituted or unsubsti- substituted or unsubstituted heteroalkyl, substituted or tuted cycloalkyl or substituted or unsubstituted het- unsubstituted cycloalkyl, substituted or unsubstituted erocycloalkyl, 15 heterocycloalkyl, substituted or unsubstituted aryl or r is 0-8. substituted or unsubstituted heteroaryl; In another embodiment is a compound of structure of For- Q is a substituted alkyl: mula VI or pharmaceutically acceptable salt or N-oxide ring A is substituted or unsubstituted aryl or heteroaryl thereof wherein: substituted with 0-4 R: W is a bond; 2O each R is independently halogen, —CN, NO, R is —CN, OH, substituted or unsubstituted alkoxy, -OH, -SR, S(=O)R’, S(=O),R, NR'S - N(R'), substituted or unsubstituted heteroalkyl, (=O).R., S(=O)N(R'), C(=O)R, OC substituted or unsubstituted cycloalkyl, substituted or (=O)R, COR', N(R'), C(=O)N(R'), unsubstituted aryl or substituted or unsubstituted het- NRC(O)R 9, NRC(O)OR, NRC eroaryl; 25 (=O)N(R'), substituted or unsubstituted alkyl, R’ is halogen, —CN, OH, substituted or unsubstituted substituted or unsubstituted alkoxy, substituted or alkoxy, —C(=O)N(R') - COR', N(R'), acyl, unsubstituted heteroalkyl, substituted or unsubsti substituted or unsubstituted heteroalkyl, substituted or tuted cycloalkyl or substituted or unsubstituted het unsubstituted cycloalkyl, substituted or unsubstituted erocycloalkyl heterocycloalkyl, substituted or unsubstituted aryl or " R. is Hor substituted or unsubstituted alkyl: substituted or unsubstituted heteroaryl; RS substituted or unsubstituted alkyl, substituted or Q is an unsubstituted alkyl; unsubstituted cycloalkyl, substituted or unsubsti tuted aryl or substituted or unsubstituted heteroaryl ring A is substituted or 4.unsubstituted aryl or heteroaryl each R'LO is independently H, substituted or unsubsti substituted4 : with: 0-4 R: 35 tutedaled alkyl, substituted or unsubstituted cycloalkyl, each R" is independently halogen, —CN, NO, bstituted or unsubstituted arvl or substituted or OH, 9 SR, S(=O)R.O S(=O).R. 8 NR'S unsubstitutedsubsutu heteroaryl, or tworye, R' together with (=O).R. —S(=O)N(R'), C(=O)R, OC the atoms to which they are attached form a hetero (=O)R, COR, N(R'), C(=O)N(R'), cycle; NRC(=O)R'', NRC(=O)CR', NRC 40 ring B is aryl or heteroaryl substituted with R: (=O)N(R'), substituted or unsubstituted alkyl, each R is independently halogen, —CN, NO, substituted or unsubstituted alkoxy, substituted or OH, SR, S(–O)R, S(—O).R, NR unsubstituted heteroalkyl, substituted or unsubsti- (=O).R., S(=O)N(R'), C(=O)R, OC tuted cycloalkyl or substituted or unsubstituted het- (—O)R’, COR', N(R'), C(=O)N(R'), erocycloalkyl, 45 NRC(O)R 9, NRC(O)OR, NRC R is H or substituted or unsubstituted alkyl: (=O)N(R'), substituted or unsubstituted alkyl, R is substituted or unsubstituted alkyl, substituted or substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubsti unsubstituted heteroalkyl, substituted or unsubsti tuted aryl or substituted or unsubstituted heteroaryl tuted cycloalkyl or substituted or unsubstituted het each R" is independently H, substituted or unsubsti- 50 erocycloalkyl, tuted alkyl, substituted or unsubstituted cycloalkyl, r is 0-8. substituted or unsubstituted aryl or substituted or Provided herein, in Some embodiments, are compounds unsubstituted heteroaryl, or two R' together with having the structure of Formula VII or pharmaceutically the atoms to which they are attached form a hetero acceptable salt or N-oxide thereof: cycle; 55 ring B is aryl or heteroaryl substituted with R: each R is independently halogen, —CN, NO, Formula VII OH, SR, S(–O)R’, S(—O).R, NR'S R6 (=O).R., S(=O)N(R'), C(=O)R, OC (=O)R, COR', N(R'), C(=O)N(R'), 60 N NRC(O)R 9, NRC(O)OR, NRC (=O)N(R'), substituted or unsubstituted alkyl, substituted or unsubstituted alkoxy, substituted or unsubstituted heteroalkyl, substituted or unsubsti- W. tuted cycloalkyl or substituted or unsubstituted het- 65 Q erocycloalkyl, r is 0-8. US 8,372,970 B2 35 36 wherein: Provided herein, in Some embodiments, are compounds W is a bond; having the structure of Formula VIII or pharmaceutically R is substituted or unsubstituted heteroalkyl, substituted acceptable salt or N-oxide thereof: or unsubstituted cycloalkyl, substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl; R’ is H, halogen, —CN, -OH, substituted or unsubsti Formula VIII tuted alkyl, substituted or unsubstituted alkoxy, R6 —C(=O)N(R'), COR', N(R'), acyl, substi R7 tuted or unsubstituted heteroalkyl, substituted or unsub N1 N1 N stituted cycloalkyl, substituted or unsubstituted hetero 10 cycloalkyl, substituted or unsubstituted aryl or (R)-O N us N 2 N O substituted or unsubstituted heteroaryl; H Q is substituted or unsubstituted alkyl, substituted or W. unsubstituted heteroalkyl, substituted or unsubstituted n Q heterocycloalkyl, substituted or unsubstituted 15 cycloalkyl, substituted or unsubstituted cycloalkylalkyl, substituted or unsubstituted heterocycloalkylalkyl, sub wherein: stituted or unsubstituted aryl, substituted or unsubsti W is a bond; tuted arylalkyl, substituted or unsubstituted heteroaryl, R is H, or halogen; substituted or unsubstituted heteroarylalkyl: R’ is acyl, substituted or unsubstituted heteroalkyl, substi ring A is substituted or unsubstituted aryl or heteroaryl tuted or unsubstituted cycloalkyl, substituted or unsub substituted with 0-4 R: stituted heterocycloalkyl or substituted or unsubstituted each R is independently halogen, —CN, NO, heteroaryl; OH, SR, S(=O)R. S(=O).R. NR'S Q is substituted or unsubstituted alkyl, substituted or (=O).R., S(=O)N(R'), C(=O)R, OC 25 unsubstituted heteroalkyl, substituted or unsubstituted (=O)R, COR, N(R'), C(=O)N(R'), heterocycloalkyl, substituted or unsubstituted NRC(O)R'9, NRC(O)OR, NRC cycloalkyl, substituted or unsubstituted cycloalkylalkyl, (=O)N(R'), substituted or unsubstituted alkyl, substituted or unsubstituted heterocycloalkylalkyl, sub substituted or unsubstituted alkoxy, substituted or stituted or unsubstituted aryl, substituted or unsubsti unsubstituted heteroalkyl, substituted or unsubsti 30 tuted arylalkyl, substituted or unsubstituted heteroaryl, tuted cycloalkyl or substituted or unsubstituted het substituted or unsubstituted heteroarylalkyl: erocycloalkyl: ring A is substituted or unsubstituted aryl or heteroaryl R is H or substituted or unsubstituted alkyl: substituted with 0-4 R: R is substituted or unsubstituted alkyl, substituted or each R is independently halogen, —CN, NO, unsubstituted cycloalkyl, substituted or unsubsti 35 -OH, -SR, S(=O)R’, S(=O),R, NR'S tuted aryl or substituted or unsubstituted heteroaryl (=O).R., S(=O)N(R'), C(=O)R, OC each R" is independently H, substituted or unsubsti (=O)R, COR', N(R'), C(=O)N(R'), tuted alkyl, substituted or unsubstituted cycloalkyl, NRC(O)R'9, NRC(O)OR, NRC substituted or unsubstituted aryl or substituted or (=O)N(R'), substituted or unsubstituted alkyl, unsubstituted heteroaryl, or two R' together with 40 substituted or unsubstituted alkoxy, substituted or the atoms to which they are attached form a hetero unsubstituted heteroalkyl, substituted or unsubsti cycle; tuted cycloalkyl or substituted or unsubstituted het ring B is aryl or heteroaryl substituted with R: erocycloalkyl, each R is independently halogen, —CN, NO, R is H or substituted or unsubstituted alkyl: OH, SR, S(–O)R’, S(—O).R, NRS 45 R is substituted or unsubstituted alkyl, substituted or (=O).R., S(=O)N(R'), C(=O)R, OC unsubstituted cycloalkyl, substituted or unsubsti (=O)R, COR, N(R'), C(=O)N(R'), tuted aryl or substituted or unsubstituted heteroaryl NRC(O)R'9, NRC(O)OR, NRC each R" is independently H, substituted or unsubsti (=O)N(R'), substituted or unsubstituted alkyl, tuted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted alkoxy, substituted or 50 substituted or unsubstituted aryl or substituted or unsubstituted heteroalkyl, substituted or unsubsti unsubstituted heteroaryl, or two R' together with tuted cycloalkyl or substituted or unsubstituted het the atoms to which they are attached form a hetero erocycloalkyl, cycle; r is 0-8. ring B is aryl or heteroaryl substituted with R: In one embodiment is a compound of Formula VII wherein 55 each R is independently halogen, —CN, NO, Q is substituted or unsubstituted alkyl. In a further embodi OH, SR, S(=O)R, S(=O).R, NRS ment is a compound of Formula VII wherein Q is a substituted (=O).R., S(=O)N(R'), C(=O)R, OC alkyl. In yet another embodiment is a compound of Formula (=O)R, COR', N(R'), C(=O)N(R'), VII wherein Q is an unsubstituted alkyl. In a further embodi NRC(O)R 9, NRC(O)OR, NRC ment is a compound of Formula VII wherein Q is substituted 60 (=O)N(R'), substituted or unsubstituted alkyl, or unsubstituted heteroalkyl, substituted or unsubstituted het substituted or unsubstituted alkoxy, substituted or erocycloalkyl, substituted or unsubstituted cycloalkyl, sub unsubstituted heteroalkyl, substituted or unsubsti stituted or unsubstituted cycloalkylalkyl, substituted or tuted cycloalkyl or substituted or unsubstituted het unsubstituted heterocycloalkylalkyl, substituted or unsubsti erocycloalkyl, tuted aryl, substituted or unsubstituted arylalkyl, substituted 65 r is 0-8. or unsubstituted heteroaryl, substituted or unsubstituted het In one embodiment is a compound of Formula VIII eroarylalkyl. wherein Q is substituted or unsubstituted alkyl. In a further US 8,372,970 B2 37 38 embodiment is a compound of Formula VIII wherein Q is a (=O)R, COR', N(R'), C(=O)N(R'), Substituted alkyl. In yet another embodiment is a compound NRC(O)R 9, NRC(O)OR, NRC of Formula VIII wherein Q is an unsubstituted alkyl. In a (=O)N(R'), substituted or unsubstituted alkyl, further embodiment is a compound of Formula VIII wherein substituted or unsubstituted alkoxy, substituted or Q is substituted or unsubstituted heteroalkyl, substituted or unsubstituted heteroalkyl, substituted or unsubsti unsubstituted heterocycloalkyl, substituted or unsubstituted tuted cycloalkyl or substituted or unsubstituted het cycloalkyl, substituted or unsubstituted cycloalkylalkyl, sub erocycloalkyl, stituted or unsubstituted heterocycloalkylalkyl, substituted or r is 0-8. unsubstituted aryl, substituted or unsubstituted arylalkyl, In one embodiment is a compound of Formula IX wherein substituted or unsubstituted heteroaryl, substituted or unsub 10 Q is substituted or unsubstituted alkyl. In a further embodi stituted heteroarylalkyl. ment is a compound of Formula IX wherein Q is a substituted Also provided herein, in some embodiments, are com alkyl. In yet another embodiment is a compound of Formula pounds having the structure of Formula IX or pharmaceuti IX wherein Q is an unsubstituted alkyl. In a further embodi cally acceptable salt or N-oxide thereof: 15 ment is a compound of Formula IX wherein Q is substituted or unsubstituted heteroalkyl, substituted or unsubstituted het erocycloalkyl, substituted or unsubstituted cycloalkyl, sub Formula IX stituted or unsubstituted cycloalkylalkyl, substituted or R6 unsubstituted heterocycloalkylalkyl, substituted or unsubsti tuted aryl, substituted or unsubstituted arylalkyl, substituted N1 N1 N or unsubstituted heteroaryl, substituted or unsubstituted het eroarylalkyl. R-O ul Provided herein, in Some embodiments, are compounds N N O H having the structure of Formula X or pharmaceutically WQ 25 acceptable salt or N-oxide thereof:

Formula X wherein: R6 W is a bond; R is substituted or unsubstituted alkyl: 30 R7 R’ is substituted or unsubstituted heteroalkyl, substituted N1 N1 N or unsubstituted cycloalkyl, or substituted or unsubsti 5 tuted heterocycloalkyl; (R -O N l N 2 O Q is substituted or unsubstituted alkyl, substituted or H unsubstituted heteroalkyl, substituted or unsubstituted 35 W. heterocycloalkyl, substituted or unsubstituted No cycloalkyl, substituted or unsubstituted cycloalkylalkyl, substituted or unsubstituted heterocycloalkylalkyl, sub wherein: stituted or unsubstituted aryl, substituted or unsubsti W is a bond; tuted arylalkyl, substituted or unsubstituted heteroaryl, 40 R is H: substituted or unsubstituted heteroarylalkyl: R7 is ring A is substituted or unsubstituted aryl or heteroaryl substituted with 0-4 R: each R is independently halogen, —CN, NO, (R), OH, SR, S(=O)R. S(=O).R. NR'S 45 (=O).R., S(=O)N(R'), C(=O)R, OC (=O)R, COR, N(R'), C(=O)N(R'), R3 NRC(O)R'9, NRC(O)OR, NRC (=O)N(R'), substituted or unsubstituted alkyl, substituted or unsubstituted alkoxy, substituted or 50 ring T is aryl, heteroaryl, cycloalkyl or heterocycloalkyl unsubstituted heteroalkyl, substituted or unsubsti substituted with RandR': tuted cycloalkyl or substituted or unsubstituted het R is a substituted or unsubstituted aryl, substituted or erocycloalkyl, unsubstituted heteroaryl, substituted or unsubstituted R is H or substituted or unsubstituted alkyl: cycloalkyl or substituted or unsubstituted heterocy R is substituted or unsubstituted alkyl, substituted or 55 cloalkyl attached to ring T via a carbon atom; unsubstituted cycloalkyl, substituted or unsubsti Q is substituted or unsubstituted alkyl, substituted or tuted aryl or substituted or unsubstituted heteroaryl unsubstituted heteroalkyl, substituted or unsubstituted each R" is independently H, substituted or unsubsti heterocycloalkyl, substituted or unsubstituted tuted alkyl, substituted or unsubstituted cycloalkyl, cycloalkyl, substituted or unsubstituted cycloalkylalkyl, substituted or unsubstituted aryl or substituted or 60 substituted or unsubstituted heterocycloalkylalkyl, sub unsubstituted heteroaryl, or two R' together with stituted or unsubstituted aryl, substituted or unsubsti the atoms to which they are attached form a hetero tuted arylalkyl, substituted or unsubstituted heteroaryl, cycle; substituted or unsubstituted heteroarylalkyl: ring B is aryl or heteroaryl substituted with R: ring A is substituted or unsubstituted aryl or heteroaryl each R is independently halogen, —CN, NO, 65 substituted with 0-4 R: OH, SR, S(–O)R’, S(—O).R, NRS each R is independently halogen, —CN, NO, (=O).R., S(=O)N(R'), C(=O)R, OC OH, SR, S(=O)R. S(=O).R. NR'S US 8,372,970 B2 39 40 (=O).R., S(=O)N(R'), C(=O)R, OC substituted or unsubstituted heterocycloalkylalkyl, sub (=O)R, COR, N(R'), C(=O)N(R'), stituted or unsubstituted aryl, substituted or unsubsti NRC(O)R 9, NRC(O)OR, NRC tuted arylalkyl, substituted or unsubstituted heteroaryl, (=O)N(R'), substituted or unsubstituted alkyl, or substituted or unsubstituted heteroarylalkyl: substituted or unsubstituted alkoxy, substituted or ring B is aryl or heteroaryl substituted with R: unsubstituted heteroalkyl, substituted or unsubsti each R is independently halogen, —CN, NO, tuted cycloalkyl or substituted or unsubstituted het OH, SR, S(–O)R, S(—O).R, NR'S erocycloalkyl, (=O),R, S(=O)N(R'), C(=O)R, OC R is H or substituted or unsubstituted alkyl: (=O)R, COR', N(R'), C(=O)N(R'), R is substituted or unsubstituted alkyl, substituted or 10 NRC(O)R'9, NRC(O)OR, NRC unsubstituted cycloalkyl, substituted or unsubsti (=O)N(R'), substituted or unsubstituted alkyl, tuted aryl or substituted or unsubstituted heteroaryl substituted or unsubstituted alkoxy, substituted or each R' is independently H, substituted or unsubsti unsubstituted heteroalkyl, substituted or unsubsti tuted alkyl, substituted or unsubstituted cycloalkyl, tuted cycloalkyl or substituted or unsubstituted het substituted or unsubstituted aryl or substituted or 15 erocycloalkyl, unsubstituted heteroaryl, or two R' together with r is 0-8: the atoms to which they are attached form a hetero R is H. halogen, —CN, -OH, substituted or unsubsti cycle; tuted alkyl, substituted or unsubstituted alkoxy, substi s is 0-4: ring B is aryl or heteroaryl substituted with R: tuted or unsubstituted heteroalkyl, - N(R'), substi each R is independently halogen, —CN, NO, tuted or unsubstituted cycloalkyl, substituted or OH, SR, S(–O)R’, S(—O).R, NR unsubstituted aryl or substituted or unsubstituted het (=O),R, S(=O)N(R'), C(=O)R, OC eroaryl; (=O)R, COR', N(R'), C(=O)N(R'), R’ is H. halogen, —CN, OH, acyl, substituted or unsub NRC(O)R 9, NRC(O)OR, NRC 25 stituted alkyl, substituted or unsubstituted alkoxy, (=O)N(R'), substituted or unsubstituted alkyl, C(=O)N(R'), COR, N(R'), substituted substituted or unsubstituted alkoxy, substituted or or unsubstituted heteroalkyl, substituted or unsubsti unsubstituted heteroalkyl, substituted or unsubsti tuted cycloalkyl, substituted or unsubstituted heterocy tuted cycloalkyl or substituted or unsubstituted het cloalkyl, substituted or unsubstituted aryl or substituted erocycloalkyl, 30 or unsubstituted heteroaryl. r is 0-8. In one embodiment is a compound of Formula XI wherein In one embodiment is a compound of Formula X wherein Q is substituted or unsubstituted alkyl. In a further embodi Q is substituted or unsubstituted alkyl. In a further embodi ment is a compound of Formula XI wherein Q is a substituted ment is a compound of Formula X wherein Q is a substituted alkyl. In yet another embodiment is a compound of Formula alkyl. In yet another embodiment is a compound of Formula 35 XI wherein Q is an unsubstituted alkyl. In a further embodi X wherein Q is an unsubstituted alkyl. In a further embodi ment is a compound of Formula XI wherein Q is substituted ment is a compound of Formula X wherein Q is substituted or or unsubstituted heteroalkyl, substituted or unsubstituted het unsubstituted heteroalkyl, substituted or unsubstituted het erocycloalkyl, substituted or unsubstituted cycloalkyl, sub erocycloalkyl, substituted or unsubstituted cycloalkyl, sub stituted or unsubstituted cycloalkylalkyl, substituted or stituted or unsubstituted cycloalkylalkyl, substituted or 40 unsubstituted heterocycloalkylalkyl, substituted or unsubsti unsubstituted heterocycloalkylalkyl, substituted or unsubsti tuted aryl, substituted or unsubstituted arylalkyl, substituted tuted aryl, substituted or unsubstituted arylalkyl, substituted or unsubstituted heteroaryl, substituted or unsubstituted het or unsubstituted heteroaryl, substituted or unsubstituted het eroarylalkyl. eroarylalkyl. 45 In a further aspect is a compound having the structure of Provided herein, in some embodiments, are compounds Formula XII: having the structure of Formula XI or pharmaceutically acceptable salt or N-oxide thereof: Formula XII R6 50 Formula XI R7 R6 N1 N1 N R7 N1 N1 N ( R5 -O l 2 N N O R5 55 ( -O N ls N 2 O l H 31

W. 4 No YN y5 60 (R), wherein: W is N. R'': wherein: R'' is H or substituted or unsubstituted alkyl: each ofY, Y and Y are independently N. R', CRR, Q is substituted or unsubstituted alkyl, substituted or SO, or C=O: unsubstituted heteroalkyl, substituted or unsubstituted 65 R" is H or substituted or unsubstituted alkyl: heterocycloalkyl, substituted or unsubstituted R" and Rare each independently H or substituted or unsub cycloalkyl, substituted or unsubstituted cycloalkylalkyl, stituted alkyl. US 8,372,970 B2 41 42 In some embodiments, a compound of Formula XI has the R" and Rare each independently H or substituted or unsub structure of formula XIII: stituted alkyl. In some embodiments, the compound of Formula XI has the structure of Formula XVA, Formula XVB, Formula XVC Formula XIII 5 or Formula XVD:

Formula XVA R6 R7 N1 N1 N. 2 (R-O N l N N O 15 (R), (R)-W / \ In some embodiments, a compound of Formula XI has the structure of formula XIV: 2O (R), Formula XVB Formula XIV R6 N1 N. R7 25 N 2 R-O N l N N O

(RID1) 7S,A wherein: 35 Formula XVC p is 1, 2 or 3: R" and R are each independently H or substituted or R6 unsubstituted alkyl; or R' and R together with the car bon to which they are attached form a C-C cycloalkyl N N1 N. R7 r1ng. 40 In some embodiments of Formula XVI, ring A is a het 2 eroaryl ring. In some embodiments of Formula XVI, ring A is (R-O N l N N O an aryl ring. In some embodiments of Formula XVI, ring A is l a heterocycloalkyl ring. In some embodiments of Formula 1N1s XVI, ring A is a cycloalkyl ring. 45 In some embodiments, the compound of Formula XI has (RD1 ax1. the structure of Formula XV: (R), Formula XVD R6 Formula XV so N N1 N. R7

2 (R-O N l N N O 55 - (R) 1. 21 ex 60 N X (R), (R),

wherein: each of Y.Y. and Y are independently N. R', CR'R'', 65 wherein: SO, or C=O: each R'' is independently H, halogen, substituted or R" is H or substituted or unsubstituted alkyl; unsubstituted alkyl, substituted or unsubstituted alkoxy, US 8,372,970 B2 43 44 or two R' together with the carbonatom to which they -continued are attached form C=O; and N k is 1-4. C y s In a further aspect is a compound having the structure: 5 r S N - C N1N1N Ny N l 4n O C -> F S 10 N N- N N N N O, C N 1.2N S^ O 15 N- N1 n1n l C y 2O N N S N O N1 N. n C M OJ--- N NO 25 N-- N1 N. N

30

2 35 s^ v 40

N- N1 n1n -C, N N N N O N 45 2 CF

50

55 y

2 l 2 C N 65 N US 8,372,970 B2 45 46 -continued -continued

79. le

F N

N1 N1 N 2

N - N - N O

O

O U2

N1N1N

NS C US 8,372,970 B2 47 48 -continued -continued O Y O- S.O-O N \ 5 O a O1 N N N O N Sv F N NSN 10 N \ Z s N1 N. --- N O 15 NN

-N Sk F O- N1N1N NY F O 2O C 2 V

N1 N1 N N1 N 2N N N N O 30

35 N

d 40 I NS

N1 N1 n 45

N - N - N O () N

s 50 O7s

() US 8,372,970 B2 49 50 -continued -continued N O

CS s sy N1 N1 N S l 2 N1 N1 n N N N O 10 l 2 N N N N -N1 15 N /\, C D O CC. c.V a S^loc

O 30

C O 2 N1N1 N l 2 C N N N O

50 c) Coldl

- " N US 8,372,970 B2 51 52 -continued -continued N S C y N C S^ 5 N- N1 n1n 21 N1 N.

--- N O --- N O N 10 N S O C 2

n1 N. --- N O S 2 O N N X N CF3 C / s

--- N O X. 30 N S

35

45

55 N N N O

65 N US 8,372,970 B2 53 54 -continued -continued

N21 N1N1N 1s1s-1S - - CF3 N N.- N.2 N. O F 10 N

N 2

N1 N1 N 15 N N S

N - - l N l N N NN O

O

N1 N1 N 25 N - - us C Oc N N N O N l N 30

N1N1 N n N 35 C - N - N l 2 Co. N N N O N N 40

N O n n N N n l 2 F 45 l 2 C o, N l O N N NN O

50

N1 N1 N n N CF3 2 C - - N l N N O o, N l O 55

N N1 N1 N - - CF3 O N N N O N N 65 US 8,372,970 B2 55 56 -continued -continued

r s 5 r N 1s1s1S N N1 N. - - C N N N O so N --- N 10 r r N 1s1s1S 15 N - - C N1 N1 N N N N O us N N N 2 2O

N N21 s

N1 N. N 25 - - C r N N l O N N1 N1 N - - 30 N N N O r F s N- N1 N1 N - - C 35 N N l O S^ Nu N1 N1 N

40 Ol -sels, O Oc N N N -se l O F 45 N S^ r 50 Nu N1 N1 N N N N1 N. Ol 11, O l 2 C N N l O 55 N N r o S^ N N1s1s1S N N1 N1 N - - F N N Ol - als, O 65 N US 8,372,970 B2 57 58 -continued -continued y S^ s O S N So ---N1 N1N N Oc --N s' 2n-n C ls N N y r S S^Solo 15 N

n / is ^ N s Sr. le 25 N- to C N-S-S ------D - - N. N. N. on-n \ /h. N N- N1N1N S D ( 35 N 4n 1so s^ 2. N N- N1 N1 N s S^ N O, OCCC.N C. 1N -->4 N1so N X- 45 S^ N N, S N N1N1 N S S^ le Nu N1 N1 N so N

OCC O n N

N21 N 1n O S^ N N N- OC-N-N-N-" N Y N N N N N N NO N 65 N

US 8,372,970 B2 63 64 -continued -continued

N1 N. N1N1N O N 1 N - N --- l 10

15 S^N

2O

25

30 S

35

40

45 O N

* 50

65

US 8,372,970 B2 67 68 -continued -continued e N, y N N NJ O N1N1 N 21 N - - C N N N 2 10 N1 N1 N

N - N - N O

15 N. rN K) N 2N, N SN - - C \-2 OC N N N O 25

N1 N1 N F 30 2 N N N O

Cl, 35 N N N

40 O --- N O N 1N1 45 MV N N O O O N. 50

N

Na 55 S. NSN N

O \ 4 60 N1 N1N

N - N - N O N

US 8,372,970 B2 71 72 -continued -continued n

-N S. C N1 n1n N s 1.2 5 NN O N N N NO - N1 N1N N O N l N 2 N O 10 -Nns1AV N 1. S O O \-/ N O N ls 15 N s

O- N1N1N 20 N.O- Na S O l a C C N N N S.

usO 25 Sk F

N 30 S N N le N1 N1N N N NN. O F 35 NO- C N1 N1 N S. S 2

N N1 N1N C. C O 2 N1 N. 50 --- N O F O N N N s 55 1N N N- y r) . ()

US 8,372,970 B2 75 76 -continued -continued N e S, y F F \ S. 5 S F S. N1 N. N1 N N

O -se N O --- N O C 10

O () 15 N-N-1 ^ N

M -2 N

N1 N1 N

N - N - N O 25

30

35 Y-N.M 40 N C | MN. N V 45 N1 N1 N C N N O 50 Sk F

55

65 US 8,372,970 B2 77 78 -continued -continued

N O -QN F N1'N4 O- N

a Cirr--- N O N N N O r 10 N. N N ( ) O2/N7 15 N, N Z \ 20 -N O N1N1 n N / S. -se N O N

CS \/SN 7 SOO N1 N.

2 30

US 8,372,970 B2 79 80 -continued -continued

10

15

20

25

30

Cl,

35

40

N 45 o?2N.

O 50

)- Na 55 1s1s1s

N N NO 60

65 US 8,372,970 B2 81 82 -continued -continued

O N y S -N 10 C C - N1 N1- N M N N l O 15 1ns-1 W \,

25

NN N s N 30

N1N 35 2 o N N F O 40

45

50

55

60

65 US 8,372,970 B2 83 84 -continued -continued y F F -\, s 5 S F S. N1 N. N1 N1 N O 10

s

N y

C 15 -QN F ( -(). 2O C. ---c. l O a C) N1 N1 N N -N 30 Oc--- N O s1 s

35

l 2 o%N US 8,372,970 B2 85 86 -continued -continued

US 8,372,970 B2 87 88 -continued -continued N

r s N1s oncesco oc,O Sv 10 N 1ns1N N 15 c/ Y

1.2 2O s N N N O

-S O- N N Nav =N 25 O --- OO ... O t

| N. N le y

C N 1 N S-C--- N O 45

O ( ) 50

N 55 N y

S- N1 n1n N-N2 N - - N1 N1 N1 - N. N N N YO 60 -----, X-so

F 65 US 8,372,970 B2 89 90 -continued -continued Nav O, O, S. N

N N1 N.

2 C - N N O 10

15

()

1. O, N S O

25

30

35

40

45

50

55 Cl,

60

65 US 8,372,970 B2 91 92 -continued -continued N F N1 N \ y F F F N N / Q- N 5 N 2 N N1 N1N 21 S1s1S N

- N a N O -se N O 10

r), F N, S -Qu 21 s N 2O Sa r&uN y -----soN n N C. N1 n1 N 25 S --- N O N 7 N d -Ns1A M 30 C Ns O O S N1 N n 35 --- N1 NO 1. S. N S O 1.2 40 \—/ N N

N N

O O 50 occo y F F C S- N N N 55 --- V Coc, K) US 8,372,970 B2 93 94 -continued -continued N s N N I C N M NS O- V 5 N s

N - N - N O C C 1s-1s-N4 N 10 N % N O

Q C Cl, to c

-N 65 O US 8,372,970 B2 95 96 -continued -continued

10 N s C sN M

N1 N1 N 2 N O

25 s C sN

N1 n1n 2 N N O

35

45

55

Ns 65 US 8,372,970 B2 97 98 -continued -continued

US 8,372,970 B2 99 100 -continued -continued

Cl, 5 N

N1 N1 N 2 10 - N N O s 15 O

25

30

35

40

N1 N.

2 45 N. N.

F 50 F F

55

N1 N.

2 N. N. 60

1. 65 US 8,372,970 B2 101 102 -continued -continued

/ N N SV C N 5 Q

OrrC C. N c.N N O US 8,372,970 B2 103 104 -continued N. N. -continued N YN N S. 2 N 5 V y 1s-1s-1s-N Or--- N O -se N O 10 N. %in 15

y 2NN S S.

O --- N O 25

F F F

N 35 N2\ \ N1s1s N-KDN --- t 40

-N1 45 /\,

N Ns 50

\N Cl N

N 55 N1 N1 N N l \ N 4. O 60 US 8,372,970 B2 105 106 -continued -continued

US 8,372,970 B2 107 108 -continued -continued N O d

Q F N s?"N1 N 2 O r N O, Cu 4n O r )- N N C ( ) 15

N C 1s1 S s N 21 - as O 25 N -N O

O O Y 30 N1 N1 in, N N N1 n1n 35 N1 N. -- a N1 YO - - Ns N N N O NA 40 O O

a C- N1 N. Ny --- N O 50 s N

55

65 Sv US 8,372,970 B2 109 110 -continued -continued

US 8,372,970 B2 113 114

-continued -continued US 8,372,970 B2 115 116 -continued -continued / Q. le 5 O- 21 N1 N -N C N,N's -se N1 YO -N1 N1- N. N\ 10 es N N N O \=/

N 15 r o2n N- N y O 2O N1 N. N s --- N1 YO N2 N- 25 N Na- 1N S N1s1S ------, ()

O

N1 N. A

N 4. N O

N

rs21 US 8,372,970 B2 117 118 -continued -continued N-N NS. \ --On O- S 2 S- O - - C C. N 4nr. O N N N O

15 N

O /SN \ s 2O Oro N1 N1N Z N l 4\ O 25 N 1N

N

N 2 N

35 O- cos.N O O y O 2N N W 40 y y N S- 2 N A s

S- F NN 45 O N1 N N-N N1 N1N M -se N1 YO --- N O 1. 50 F % Ns F

N 55 N N1\. so. C O, r S N1 N. N1)-1s-1SN N 60 --- N O 2 N F N Sk F 65 1. ns1A V O O US 8,372,970 B2 119 120 -continued -continued N NN

5 N1N -NN 1s1s1N1 O, C N % N O F 10 Sk F F

15 N N1

25

30 N Cl,

35 - ins1s-l.

40

45

- sel-lo 50

N y 55

N1 N. 4N1so F

65 US 8,372,970 B2 121 122 -continued -continued

N O N 2\N N 5 -Crock - O) sN --- N O N N N N1 N. \ 4 N -N - 10 ( ) N N N O

15 e N O N1 N N N s O Q N-1N1 '' - rv- N1N1N 2N N N N O

N 4n O 25

C) OS 30 | N y S 2 N

35 N N N O N NN -QN F N Sy N1N1N 21 40 l 2 -N N N N1 YO N N,

N 45 O- N1 n1n N -Ns1A V C l 2

50 SkF

N s C 55 N=N

60 l N N 4. N O

US 8,372,970 B2 125 126 -continued -continued

N s 1s1s1sO-O 5 y --- N O

10 on D. or a pharmaceutically acceptable salt, Solvate or N-oxide thereof. 15 In some embodiments, a PAK inhibitoris a small molecule. As referred to herein, a 'small molecule' is an organic, mol ecule that is less than about 5 kilodaltons (kDa) in size. In Some embodiments, the Small molecule is less than about 4 N1 N. kDa, 3 kDa, about 2 kDa, or about 1 kDa. In some embodi ments, the small molecule is less than about 800 daltons (Da), --- N O about 600 Da, about 500 Da, about 400 Da, about 300 Da, about 200 Da, or about 100 Da. In some embodiments, a small molecule is less than about 4000 g/mol, less than about 3000 25 g/mol, 2000 g/mol, less than about 1500 g/mol, less than about 1000 g/mol, less than about 800 g/mol, or less than 1N about 500 g/mol. In some embodiments, small molecules are non-polymeric. Typically, Small molecules are not proteins, polypeptides, polynucleotides, oligonucleotides, polysac 30 charides, glycoproteins, or proteoglycans, but includes pep N 2 tides of up to about 40 amino acids. A derivative of a small molecule refers to a molecule that shares the same structural core as the original, Small molecule, but which is prepared by a series of chemical reactions from the original Small mol 35 ecule. As one example, a pro-drug of a small molecule is a derivative of that Small molecule. An analog of a small mol ecule refers to a molecule that shares the same or similar structural core as the original Small molecule, and which is synthesized by a similar or related route, or art-recognized 40 variation, as the original Small molecule. In certain embodiments, compounds described herein, have one or more chiral centers. As such, all Stereoisomers are envisioned herein. In various embodiments, compounds described herein are present in optically active or racemic 45 forms. It is to be understood that the compounds described herein encompass racemic, optically-active, regioisomeric and stereoisomeric forms, or combinations thereof that pos sess the therapeutically useful properties described herein. 2 N N O Preparation of optically active forms is achieve in any suitable 50 manner, including by way of non-limiting example, by reso lution of the racemic form by recrystallization techniques, by synthesis from optically-active starting materials, by chiral synthesis, or by chromatographic separation using a chiral stationary phase. In some embodiments, mixtures of one or 55 more isomer is utilized as the therapeutic compound described herein. In certain embodiments, compounds described herein contains one or more chiral centers. These compounds are prepared by any means, including enantiose lective synthesis and/or separation of a mixture of enanti N1N1 N 60 omers and/or diastereomers. Resolution of compounds and isomers thereof is achieved by any means including, by way 2 of non-limiting example, chemical processes, enzymatic pro N N O cesses, fractional crystallization, distillation, chromatogra phy, and the like. 65 In various embodiments, pharmaceutically acceptable salts described herein include, by way of non-limiting example, a nitrate, chloride, bromide, phosphate, Sulfate, US 8,372,970 B2 127 128 acetate, hexafluorophosphate, citrate, gluconate, benzoate, TABLE A propionate, butyrate, Sulfosalicylate, maleate, laurate, malate, fumarate. Succinate, tartrate, amsonate, pamoate, Examples of Covalent Linkages and Precursors Thereof p-toluenenesulfonate, mesylate and the like. Furthermore, Covalent Linkage Product Electrophile Nucleophile pharmaceutically acceptable salts include, by way of non Carboxamides Activated esters amines?anilines limiting example, alkaline earth metal salts (e.g., calcium or Carboxamides acyl azides amines?anilines magnesium), alkali metal salts (e.g., sodium-dependent or Carboxamides acyl halides amines?anilines potassium), ammonium salts and the like. Esters acyl halides alcoholsphenols Compounds described herein also include isotopically-la Esters acyl nitriles alcoholsphenols 10 Carboxamides acyl nitriles amines?anilines beled compounds wherein one or more atoms is replaced by Imines Aldehydes amines?anilines an atom having the same atomic number, but an atomic mass Hydrazones aldehydes or ketones Hydrazines or mass number different from the atomic mass or mass Oximes aldehydes or ketones Hydroxylamines Alkylamines alkyl halides amines?anilines number usually found in nature. Examples of isotopes Suit Esters alkyl halides carboxylic acids able for inclusion in the compounds described herein include Thioethers alkyl halides Thiols 15 Ethers alkyl halides alcoholsphenols and are not limited to H, H, C, C, C, CI, F, 'I, Thioethers alkylsulfonates Thiols I, N, N, O, 7O, O, ?PS or the like. In some Esters alkylsulfonates carboxylic acids embodiments, isotopically-labeled compounds are useful in Ethers alkylsulfonates alcoholsphenols Esters Anhydrides alcoholsphenols drug and/or Substrate tissue distribution studies. In some Carboxamides Anhydrides amines?anilines embodiments, Substitution with heavier isotopes such as deu Thiophenols aryl halides Thiols terium affords certain therapeutic advantages resulting from Aryl amines aryl halides Amines greater metabolic stability (for example, increased in vivo Thioethers AZindines Thiols Boronate esters Boronates Glycols half-life or reduced dosage requirements). In some embodi Carboxamides carboxylic acids amines?anilines ments, Substitution with positron emitting isotopes, such as Esters carboxylic acids Alcohols 'C, F, 'O and 'N, is useful in Positron Emission Topog 25 hydrazines Hydrazides carboxylic acids N-acylureas or Anhydrides carbodiimides carboxylic acids raphy (PET) studies for examining substrate receptor occu Esters diazoalkanes carboxylic acids pancy. Isotopically-labeled compounds are prepared by any Thioethers Epoxides Thiols Suitable method or by processes using an appropriate isoto Thioethers haloacetamides Thiols pically-labeled reagent in place of the non-labeled reagent Ammotriazines halotriazines amines?anilines 30 Triazinyl ethers halotriazines alcoholsphenols otherwise employed. Amidines imido esters amines?anilines The compounds described herein, and other related com Ureas socyanates amines?anilines pounds having different Substituents are synthesized using Urethanes Socyanates alcoholsphenols Thioureas isothiocyanates amines?anilines techniques and materials described herein and as described, Thioethers Maleimides Thiols for example, in Fieser and Fieser’s Reagents for Organic 35 Phosphite esters phosphoramidites Alcohols Synthesis, Volumes 1-17 (John Wiley and Sons, 1991); Sillyl ethers silyl halides Alcohols Alkylamines sulfonate esters amines?anilines Rodd's Chemistry of Carbon Compounds, Volumes 1-5 and Thioethers sulfonate esters Thiols Supplementals (Elsevier Science Publishers, 1989); Organic Esters sulfonate esters carboxylic acids Reactions, Volumes 1-40 (John Wiley and Sons, 1991), Ethers sulfonate esters Alcohols Sulfonamides sulfonylhalides amines?anilines Larock's Comprehensive Organic Transformations (VCH 40 Sulfonate esters sulfonylhalides phenols, alcohols Publishers Inc., 1989), March, ADVANCED ORGANIC CHEMISTRY 4' Ed., (Wiley 1992); Carey and Sundberg, ADVANCED ORGANIC CHEMISTRY 4" Ed., Vols. A and B (Plenum 2000, Use of Protecting Groups 2001), and Green and Wuts, PROTECTIVE GROUPS IN ORGANIC In the reactions described, it is necessary to protect reactive SYNTHESIS 3' Ed. (Wiley 1999) (all of which are incorporated 45 functional groups, for example hydroxy, amino, imino, thio or by reference for such disclosure). General methods for the carboxy groups, where these are desired in the final product, preparation of compound as described herein are modified by in order to avoid their unwanted participation in reactions. the use of appropriate reagents and conditions, for the intro Protecting groups are used to block Some or all of the reactive duction of the various moieties found in the formula as pro moieties and prevent Such groups from participating in vided herein. As a guide the following synthetic methods are 50 chemical reactions until the protective group is removed. In utilized. Some embodiments it is contemplated that each protective Compounds described herein are synthesized using any group be removable by a different means. Protective groups Suitable procedures starting from compounds that are avail that are cleaved under totally disparate reaction conditions able from commercial sources, or are prepared using proce fulfill the requirement of differential removal. dures described herein. 55 In some embodiments, protective groups are removed by Formation of Covalent Linkages by Reaction of an Electro acid, base, reducing conditions (such as, for example, hydro phile with a Nucleophile genolysis), and/or oxidative conditions. Groups such as trityl, The compounds described herein are modified using vari dimethoxytrityl, acetal and t-butyldimethylsilyl are acid ous electrophiles and/or nucleophiles to form new functional labile and are used to protect carboxy and hydroxy reactive groups or substituents. Table A entitled “Examples of Cova 60 moieties in the presence of amino groups protected with Cbz lent Linkages and Precursors Thereof lists selected non groups, which are removable by hydrogenolysis, and Fmoc limiting examples of covalent linkages and precursor func groups, which are base labile. Carboxylic acid and hydroxy tional groups which yield the covalent linkages. Table A is reactive moieties are blocked with base labile groups such as, used as guidance toward the variety of electrophiles and but not limited to, methyl, ethyl, and acetyl in the presence of nucleophiles combinations available that provide covalent 65 amines blocked with acid labile groups such as t-butyl car linkages. Precursor functional groups are shown as electro bamate or with carbamates that are both acid and base stable philic groups and nucleophilic groups. but hydrolytically removable. US 8,372,970 B2 129 130 In some embodiments carboxylic acid and hydroxy reac -continued tive moieties are blocked with hydrolytically removable pro H3C CH3 tective groups such as the benzyl group, while amine groups Y/ capable of hydrogen bonding with acids are blocked with (CH3)3C Y y base labile groups such as Fmoc. Carboxylic acid reactive moieties are protected by conversion to simple ester com TBDMS pounds as exemplified herein, which include conversion to O alkyl esters, or are blocked with oxidatively-removable pro H Si tective groups such as 2,4-dimethoxybenzyl, while co-exist (CH3)4C1 O ing amino groups are blocked with fluoride labile silyl car 10 bamates. Allyl blocking groups are useful in the presence of acid Teoc and base-protecting groups since the former are stable and are O Subsequently removed by metal or pi-acid catalysts. For 15 1. example, anallyl-blocked carboxylic acid is deprotected with (CH3)3C a Pd-catalyzed reaction in the presence of acid labile t-butyl O carbamate or base-labile acetate amine protecting groups. Yet Boc another form of protecting group is a resin to which a com H pound or intermediate is attached. As long as the residue is attached to the resin, that functional group is blocked and does not react. Once released from the resin, the functional group is available to react. H3CO Typically blocking/protecting groups are selected from: PMB 25 cates, trityl 30 O

35 acetyl

HC-O 40 Q) 45

Other protecting groups, plus a detailed description of techniques applicable to the creation of protecting groups and 50 their removal are described in Greene and Wuts, Protective Groups in Organic Synthesis, 3rd Ed., John Wiley & Sons, New York, N.Y., 1999, and Kocienski, Protective Groups, Thieme Verlag, New York, N.Y., 1994, which are incorpo rated herein by reference for such disclosure. 55 Certain Definitions As used herein the term “Treatment”, “treat’, or “treating includes achieving atherapeutic benefit and/or a prophylactic benefit. Therapeutic benefit is meant to include eradication or amelioration of the underlying disorder or condition being 60 treated. For example, in an individual with Huntington's dis ease, therapeutic benefit includes alleviation or partial and/or complete halting of the progression of the disease, or partial or complete reversal of the disease. Also, a therapeutic benefit is achieved with the eradication or amelioration of one or 65 more of the physiological or psychological symptoms asso ciated with the underlying condition Such that an improve ment is observed in the patient, notwithstanding the fact that US 8,372,970 B2 131 132 the patient is still affected by the condition. For example, in an organism is considered to be biologically active. In particular individual suffering from epilepsy, therapeutic benefit embodiments, where a protein or polypeptide is biologically includes alleviation or partial and/or complete halting of sei active, a portion of that protein or polypeptide that shares at Zures, or reduction in frequency of seizures. A prophylactic least one biological activity of the protein or polypeptide is benefit of treatment includes prevention of a condition, 5 typically referred to as a “biologically active' portion. retarding the progress of a condition, or decreasing the like As described herein, a CNS disorder is a disorder that can lihood of occurrence of a condition. As used herein, “treat', affect either the spinal cord or brain. By way of example only, “treating or “treatment includes prophylaxis. CNS disorder include Schizophrenia, Psychotic disorder, As used herein, the phrase "abnormal spine size” refers to schizoaffective disorder, schizophreniform, Alzheimer's dis dendritic spine Volumes or dendritic spine Surface areas (e.g., 10 ease, Age-related cognitive decline, Mild cognitive impair Volumes or Surface areas of the spine heads and/or spine ment, cognitive decline associated with menopause, Parkin necks) associated with CNS disorders that deviate signifi son's Disease, Huntington's Disease, Substance abuse and cantly relative to spine Volumes or Surface areas in the same Substance dependence, Fragile X, Rett's syndrome, Angel brain region (e.g., the CA1 region, the prefrontal cortex) in a man Syndrome, Asperger's Syndrome, Autism, Autism Spec normal individual (e.g., a mouse, rat, or human) of the same 15 trum Disorders, Neurofibromatosis I, Neurofibromatosis II, age; Such abnormalities are determined as appropriate, by Tuberous sclerosis, Clinical Depression, Bipolar Disorder, methods including, e.g., tissue samples, relevant animal mod Mania, Epilepsy, Mental retardation, Down's syndrome, els, post-mortem analyses, or other model systems. Niemann-Pick disease, Spongiform encephalitis, Lafora dis The phrase “defective spine morphology” or "abnormal ease, Maple syrup urine disease, maternal phenylketonuria, spine morphology' or "aberrant spine morphology” refers to atypical phenylketonuria, Generalized Anxiety Disorder, abnormal dendritic spine shapes, Volumes, Surface areas, Turner Syndrome, Lowe Syndrome, Obsessive-compulsive length, width (e.g., diameter of the neck), spine head diam disorder, Panic disorder, Phobias, Posttraumatic Stress Dis eter, spine head volume, spine head Surface area, spine den order, Anorexia Nervosa, and Bulimia Nervosa. sity, ratio of mature to immature spines, ratio of spine Volume As used herein, Mental retardation is a disorder character to spine length, or the like that is associated with a CNS 25 ized by significantly impaired cognitive function and deficits disorder relative to the dendritic spine shapes, Volumes, Sur in adaptive behaviors. By way of example only, mental retar face areas, length, width (e.g., diameter of the neck), spine dation is Down's syndrome, Fetal alcohol syndrome, density, ratio of mature to immature spines, ratio of spine Klinefelter's syndrome, congenital hypothyroidism, Will volume to spine length, or the like observed in the same brain iams syndrome, Smith-Lemli-Opitz syndrome, Prader-Willi region in a normal individual (e.g., a mouse, rat, or human) of 30 syndrome Phelan-McDermid syndrome, Mowat-Wilson syn the same age; Such abnormalities or defects are determined as drome, ciliopathy or Lowe syndrome. appropriate, by methods including, e.g., tissue samples, rel As used herein, the term "subcortical dementia' refers to evant animal models, post-mortem analyses, or other model symptoms related to Huntington's disease (e.g., deficits in systems. executive functions such as planning, cognitive flexibility, The phrase "abnormal spine function' or “defective spine 35 abstract thinking, rule acquisition, initiating appropriate function” or “aberrant spine function” refers to a defect of actions, inhibiting inappropriate actions; memory deficits dendritic spines to undergo stimulus-dependent morphologi Such as short-term memory deficits, long-term memory dif cal or functional changes (e.g., following activation of AMPA ficulties, deficits in episodic (memory of one’s life), proce and/or NMDA receptors, LTP LTD, etc) associated with CNS dural (memory of the body of how to performan activity) and disorders as compared to dendritic spines in the same brain 40 working memory, and the like). In some instances, progres region in a normal individual of the same age. The “defect” in sion toward dementia' is identified, monitored or diagnosed spine function includes, e.g., a reduction in dendritic spine by neuropsychological or behavioral testing. In other plasticity, (e.g., an abnormally small change in dendritic instances, “progression toward dementia” is identified, moni spine morphology or actin re-arrangement in the dendritic tored or diagnosed by neuroimaging or brain scans. spine), or an excess level of dendritic plasticity, (e.g., an 45 As used herein, the term “effective amount” is an amount, abnormally large change in dendritic spine morphology or which when administered systemically, is sufficient to effect actin re-arrangement in the dendritic spine). Such abnormali beneficial or desired results, such as beneficial or desired ties or defects are determined as appropriate, by methods clinical results, or enhanced cognition, memory, mood, or including, e.g., tissue samples, relevant animal models, post other desired effects. An effective amount is also an amount mortem analyses, or other model systems. 50 that produces a prophylactic effect, e.g., an amount that The phrase "abnormal spine motility” refers to a significant delays, reduces, or eliminates the appearance of a pathologi low or high movement of dendritic spines associated with a cal or undesired condition associated with a CNS disorder. An CNS disorder as compared to dendritic spines in the same effective amount is optionally administered in one or more brain region in a normal individual of the same age. Any administrations. In terms of treatment, an “effective amount defect in spine morphology (e.g., spine length, density or the 55 of a composition described herein is an amount that is suffi like) or synaptic plasticity or synaptic function (e.g., LTP, cient to palliate, alleviate, ameliorate, stabilize, reverse or LTD or the like) or spine motility occurs in any region of the slow the progression of a CNS disorder e.g., cognitive decline brain, including, for example, the frontal cortex, the hippoc toward dementia, mental retardation or the like. An "effective ampus, the amygdala, the CA1 region, the prefrontal cortex or amount includes any PAK inhibitor used alone or in con the like. Such abnormalities or defects are determined as 60 junction with one or more agents used to treat a disease or appropriate, by methods including, e.g., tissue samples, rel disorder. An "effective amount of a therapeutic agent as evant animal models, post-mortem analyses, or other model described herein will be determined by a patients attending systems. physician or other medical care provider. Factors which influ As used herein, the phrase “biologically active' refers to a ence what a therapeutically effective amount will be include, characteristic of any Substance that has activity in a biological 65 the absorption profile (e.g., its rate of uptake into the brain) of system and/or organism. For instance, a Substance that, when the PAK inhibitor, time elapsed since the initiation of disease, administered to an organism, has a biological effect on that and the age, physical condition, existence of other disease US 8,372,970 B2 133 134 states, and nutritional status of an individual being treated. PAK inhibitors described herein increase dendritic spine den Additionally, other medication the patient is receiving, e.g., sity. In some embodiments, PAK inhibitors described herein antidepressant drugs used in combination with a PAK inhibi decrease dendritic spine density. In some embodiments, PAK tor, will typically affect the determination of the therapeuti inhibitors described herein increase the number of mushroom cally effective amount of the therapeutic agent to be admin shaped spines. In some embodiments, PAK inhibitors istered. described herein decrease the number of mushroom shaped As used herein, the term “inhibitor” refers to a molecule spines. which is capable of inhibiting (including partially inhibiting In some embodiments, a PAK inhibitor suitable for the or allosteric inhibition) one or more of the biological activi methods described herein is a direct PAK inhibitor. In some ties of a target molecule, e.g., a p21-activated kinase. Inhibi 10 embodiments, a PAK inhibitor suitable for the methods tors, for example, act by reducing or Suppressing the activity described herein is an indirect PAK inhibitor. In some of a target molecule and/or reducing or Suppressing signal embodiments, a PAK inhibitor suitable for the methods transduction. In some embodiments, a PAK inhibitor described herein decreases PAK activity relative to a basal described herein causes substantially complete inhibition of level of PAK activity by about 1.1 fold to about 100 fold, e.g., one or more PAKs. In some embodiments, the phrase “partial 15 to about 1.2 fold, 1.5 fold, 1.6 fold, 1.7 fold, 2.0 fold, 3.0 fold, inhibitor refers to a molecule which can induce a partial 5.0 fold, 6.0 fold, 7.0 fold, 8.5 fold, 9.7 fold, 10 fold, 12 fold, response for example, by partially reducing or Suppressing 14 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 the activity of a target molecule and/or partially reducing or fold, 90 fold, 95 fold, or by any other amount from about 1.1 Suppressing signal transduction. In some instances, a partial fold to about 100 fold relative to basal PAK activity. In some inhibitor mimics the spatial arrangement, electronic proper embodiments, the PAK inhibitoris a reversible PAK inhibitor. ties, or some other physicochemical and/or biological prop In other embodiments, the PAK inhibitor is an irreversible erty of the inhibitor. In some instances, in the presence of PAK inhibitor. Direct PAK inhibitors are optionally used for elevated levels of an inhibitor, a partial inhibitor competes the manufacture of a medicament for treating a CNS disorder. with the inhibitor for occupancy of the target molecule and In some embodiments, a PAK inhibitor used for the meth provides a reduction in efficacy, relative to the inhibitor alone. 25 ods described herein has in vitro EDso for PAK activation of In some embodiments, a PAK inhibitor described herein is a less than 100 uM (e.g., less than 10 uM, less than 5uM, less partial inhibitor of one or more PAKs. In some embodiments, than 4 M, less than 3 uM, less than 1 M, less than 0.8 uM, a PAK inhibitor described herein is an allosteric modulator of less than 0.6 uM, less than 0.5uM, less than 0.4 uM, less than PAK. In some embodiments, a PAK inhibitor described 0.3 uM, less than less than 0.2 uM, less than 0.1 uM, less than herein blocks the p21 binding domain of PAK. In some 30 0.08M, less than 0.06 uM, less than 0.05uM, less than 0.04 embodiments, a PAK inhibitor described herein blocks the uM, less than 0.03 uM, less than less than 0.02 uM, less than ATP binding site of PAK. In some embodiments, a PAK 0.01 uM, less than 0.0099 uM, less than 0.0098 uM, less than inhibitor is a “Type II kinase inhibitor. In some embodiment 0.0097 uM, less than 0.0096 uM, less than 0.0095 uM, less a PAK inhibitor stabilizes PAK in its inactive conformation. than 0.0094 uM, less than 0.0093 uM, less than 0.00092 uM, In some embodiments, a PAK inhibitor stabilizes the “DFG 35 or less than 0.0090 uM). out conformation of PAK. In some embodiments, a PAK inhibitor used for the meth In some embodiments, PAK inhibitors reduce, abolish, ods described herein has in vitro EDso for PAK activation of and/or remove the binding between PAK and at least one of its less than 100 uM (e.g., less than 10 uM, less than 5uM, less natural binding partners (e.g., Cdc42 or Rac). In some than 4 M, less than 3 uM, less than 1 M, less than 0.8 uM, instances, binding between PAK and at least one of its natural 40 less than 0.6 uM, less than 0.5uM, less than 0.4 uM, less than binding partners is stronger in the absence of a PAK inhibitor 0.3 uM, less than less than 0.2 uM, less than 0.1 uM, less than (by e.g., 90%, 80%, 70%, 60%, 50%, 40%, 30% or 20%) than 0.08M, less than 0.06 uM, less than 0.05uM, less than 0.04 in the presence of a PAK inhibitor. Alternatively or addition uM, less than 0.03 uM, less than less than 0.02 uM, less than ally, PAK inhibitors inhibit the phosphotransferase activity of 0.01 uM, less than 0.0099 uM, less than 0.0098 uM, less than PAK, e.g., by binding directly to the catalytic site or by 45 0.0097 uM, less than 0.0096 uM, less than 0.0095 uM, less altering the conformation of PAK such that the catalytic site than 0.0094 uM, less than 0.0093 uM, less than 0.00092 uM, becomes inaccessible to Substrates. In some embodiments, or less than 0.0090 uM). PAK inhibitors inhibit the ability of PAK to phosphorylate at As used herein, synaptic function refers to synaptic trans least one of its target substrates, e.g., LIM kinase 1 (LIMK1), mission and/or synaptic plasticity, including stabilization of myosin light chain kinase (MLCK), cortactin; or itself. PAK 50 synaptic plasticity. As used herein, “defect in synaptic plas inhibitors include inorganic and/or organic compounds. ticity” or “aberrant synaptic plasticity” refers to abnormal In some embodiments, PAK inhibitors described herein synaptic plasticity following stimulation of that synapse. In increase dendritic spine length. In some embodiments, PAK Some embodiments, a defect in synaptic plasticity is a inhibitors described herein decrease dendritic spine length. In decrease in LTP. In some embodiments, a defect in synaptic some embodiments, PAK inhibitors described herein increase 55 plasticity is an increase in LTD. In some embodiments, a dendritic neck diameter. In some embodiments, PAK inhibi defect in Synaptic plasticity is erratic (e.g., fluctuating, ran tors described herein decrease dendritic neck diameter. In domly increasing or decreasing) synaptic plasticity. In some some embodiments, PAK inhibitors described herein increase instances, measures of synaptic plasticity are LTP and/or LTD dendritic spine head diameter. In some embodiments, PAK (induced, for example, by theta-burst stimulation, high-fre inhibitors described herein decrease dendritic spine head 60 quency stimulation for LTP. low-frequency (e.g., e.g., 1 Hz) diameter. In some embodiments, PAK inhibitors described stimulation for LTD) and LTP and/or LTD after stabilization. herein increase dendritic spine head volume. In some In some embodiments, stabilization of LTP and/or LTD embodiments, PAK inhibitors described herein decrease den occurs in any region of the brain including the frontal cortex, dritic spine head volume. In some embodiments, PAK inhibi the hippocampus, the prefrontal cortex, the amygdala or any tors described herein increase dendritic spine Surface area. In 65 combination thereof. some embodiments, PAK inhibitors described herein As used herein “stabilization of synaptic plasticity” refers decrease dendritic spine Surface area. In some embodiments, to stable LTP or LTD following induction (e.g., by theta-burst US 8,372,970 B2 135 136 stimulation, high-frequency stimulation for LTP, low-fre lowering of aberrant synaptic plasticity where the aberrant quency (e.g., e.g., 1 Hz) stimulation for LTD). synaptic plasticity is higher than the synaptic plasticity of a Aberrant stabilization of synaptic transmission' (for normal individual or to that predicted from an animal model example, aberrant stabilization of LTP or LTD), refers to for a normal individual. In some embodiments, normalization failure to establish a stable baseline of synaptic transmission or partial normalization of aberrant synaptic plasticity in an following an induction paradigm (e.g., by theta-burst stimu individual Suffering from, Suspected of having, or pre-dis lation, high-frequency stimulation for LTP, low-frequency posed to a CNS disorder is an increase in aberrant synaptic (e.g., 1 Hz) stimulation for LTD) or an extended period of plasticity where the aberrant synaptic plasticity is lower than Vulnerability to disruption by pharmacological or electro the synaptic plasticity of a normal individual or to that pre physiological means 10 dicted from an animal model for a normal individual. In some As used herein “synaptic transmission' or “baseline syn embodiments, normalization or partial normalization of syn aptic transmission” refers to the EPSP and/or IPSP amplitude aptic plasticity in an individual Suffering from, Suspected of and frequency, neuronal excitability or population spike having, or pre-disposed to a CNS disorder is a change from an thresholds of a normal individual (e.g., an individual not erratic (e.g., fluctuating, randomly increasing or decreasing) suffering from a CNS disorder) or that predicted for an animal 15 synaptic plasticity to a normal (e.g. stable) or partially normal model for a normal individual. As used herein “aberrant syn (e.g., less fluctuating) synaptic plasticity compared to the aptic transmission' or “defective synaptic transmission” synaptic plasticity of a normal individual or to that predicted refers to any deviation in synaptic transmission compared to from an animal model for a normal individual. In some synaptic transmission of a normal individual or that predicted embodiments, normalization or partial normalization of syn for an animal model for a normal individual. In some embodi aptic plasticity in an individual Suffering from, Suspected of ments, an individual suffering from a CNS disorder has a having, or pre-disposed to a CNS disorder is a change from a defect in baseline synaptic transmission that is a decrease in non-stabilizing synaptic plasticity to a normal (e.g., stable) or baseline synaptic transmission compared to the baseline Syn partially normal (e.g., partially stable) synaptic plasticity aptic transmission in a normal individual or that predicted for compared to the synaptic plasticity of a normal individual or an animal model for a normal individual. In some embodi 25 to that predicted from an animal model for a normal indi ments, an individual suffering from a CNS disorder has a vidual. defect in baseline synaptic transmission that is an increase in As used herein, “normalization of aberrant baseline Syn baseline synaptic transmission compared to the baseline Syn aptic transmission” refers to a change in aberrant baseline aptic transmission in a normal individual or that predicted for synaptic transmission in an individual Suffering from, Sus an animal model for a normal individual. 30 pected of having, or pre-disposed to a CNS disorder to a level As used herein “sensorimotor gating is assessed, for of baseline synaptic transmission that is Substantially the example, by measuring prepulse inhibition (PPI) and/or same as the baseline synaptic transmission of a normal indi habituation of the human startle response. In some embodi vidual or to that predicted from an animal model for a normal ments, a defect in sensorimotor gating is a deficit in sen individual. As used herein, Substantially the same means, for Sorimotor gating. In some embodiments, a defect in sen 35 example, about 90% to about 110% of the measured baseline Sorimotor gating is an enhancement of sensorimotor gating. synaptic transmission in a normal individual or to that pre As used herein, “normalization of aberrant synaptic plas dicted from an animal model for a normal individual. In other ticity' refers to a change in aberrant synaptic plasticity in an embodiments, Substantially the same means, for example, individual Suffering from, Suspected of having, or pre-dis about 80% to about 120% of the measured baseline synaptic posed to a CNS disorder to a level of synaptic plasticity that is 40 transmission in a normal individual or to that predicted from Substantially the same as the synaptic plasticity of a normal an animal model for a normal individual. In yet other embodi individual or to that predicted from an animal model for a ments, Substantially the same means, for example, about 70% normal individual. As used herein, Substantially the same to about 130% of the measured baseline synaptic transmis means, for example, about 90% to about 110% of the mea Sionin a normal individual or to that predicted from an animal Sured synaptic plasticity in a normal individual or to that 45 model for a normal individual. As used herein, “partial nor predicted from an animal model for a normal individual. In malization of aberrant baseline synaptic transmission” refers other embodiments, Substantially the same means, for to any change inaberrant baseline synaptic transmission in an example, about 80% to about 120% of the measured synaptic individual Suffering from, Suspected of having, or pre-dis plasticity in a normal individual or to that predicted from an posed to a CNS disorder that trends towards baseline synaptic animal model for a normal individual. In yet other embodi 50 transmission of a normal individual or to that predicted from ments, Substantially the same means, for example, about 70% an animal model for a normal individual. As used herein to about 130% of the synaptic plasticity in a normal individual "partially normalized baseline synaptic transmission” or or to that predicted from an animal model for a normal indi "partially normal baseline synaptic transmission' is, for vidual. As used herein, “partial normalization of aberrant example, tabout 25%, tabout 35%, about 45%, tabout synaptic plasticity' refers to any change in aberrant synaptic 55 55%, about 65%, or about 75% of the measured baseline plasticity in an individual Suffering from, Suspected of hav synaptic transmission of a normal individual or to that pre ing, or pre-disposed to a CNS disorder that trends towards dicted from an animal model for a normal individual. In some synaptic plasticity of a normal individual or to that predicted embodiments, normalization or partial normalization of aber from an animal model for a normal individual. As used herein rant baseline synaptic transmission in an individual Suffering “partially normalized synaptic plasticity' or “partially nor 60 from, suspected of having, or pre-disposed to a CNS disorder mal synaptic plasticity' is, for example, tabout 25%, about is lowering of aberrant baseline synaptic transmission where 35%, about 45%, about 55%, about 65%, or about 75% the aberrant baseline synaptic transmission is higher than the of the synaptic plasticity of a normal individual or to that baseline synaptic transmission of a normal individual or to predicted from an animal model for a normal individual. In that predicted from an animal model for a normal individual. Some embodiments, normalization or partial normalization of 65 In some embodiments, normalization or partial normalization aberrant synaptic plasticity in an individual Suffering from, of aberrant baseline synaptic transmission in an individual suspected of having, or pre-disposed to a CNS disorder is Suffering from, Suspected of having, or pre-disposed to a CNS US 8,372,970 B2 137 138 disorder is an increase in aberrant baseline synaptic transmis mal (e.g. stable) or partially normal (e.g., less fluctuating) sion where the aberrant baseline synaptic transmission is synaptic function compared to the synaptic function of a lower than the baseline synaptic transmission of a normal normal individual or to that predicted from an animal model individual or to that predicted from an animal model for a for a normal individual. In some embodiments, normalization normal individual. In some embodiments, normalization or or partial normalization of aberrant synaptic function in an partial normalization of baseline synaptic transmission in an individual Suffering from, Suspected of having, or pre-dis individual Suffering from, Suspected of having, or pre-dis posed to a CNS disorder is a change from a non-stabilizing posed to a CNS disorder is a change from an erratic (e.g., synaptic function to a normal (e.g., stable) or partially normal fluctuating, randomly increasing or decreasing) baseline Syn (e.g., partially stable) synaptic function compared to the Syn aptic transmission to a normal (e.g. stable) or partially normal 10 aptic function of a normal individual or to that predicted from (e.g., less fluctuating) baseline synaptic transmission com an animal model for a normal individual. pared to the baseline synaptic transmission of a normal indi As used herein, “normalization of aberrant long term vidual or to that predicted from an animal model for a normal potentiation (LTP) refers to a change in aberrant LTP in an individual. In some embodiments, normalization or partial individual Suffering from, Suspected of having, or pre-dis normalization of aberrant baseline synaptic transmission in 15 posed to a CNS disorder to a level of LTP that is substantially an individual Suffering from, Suspected of having, or pre the same as the LTP of a normal individual or to that predicted disposed to a CNS disorder is a change from a non-stabilizing from an animal model for a normal individual. As used herein, baseline synaptic transmission to a normal (e.g., stable) or substantially the same means, for example, about 90% to partially normal (e.g., partially stable) baseline synaptic about 110% of the LTP in a normal individual or to that transmission compared to the baseline synaptic transmission predicted from an animal model for a normal individual. In of a normal individual or to that predicted from an animal other embodiments, Substantially the same means, for model for a normal individual. example, about 80% to about 120% of the LTP in a normal As used herein, “normalization of aberrant synaptic func individual or to that predicted from an animal model for a tion” refers to a change in aberrant synaptic function in an normal individual. In yet other embodiments, substantially individual Suffering from, Suspected of having, or pre-dis 25 the same means, for example, about 70% to about 130% of the posed to a CNS disorder to a level of synaptic function that is LTP in a normal individual or to that predicted from an animal Substantially the same as the synaptic function of a normal model for a normal individual. As used herein, “partial nor individual or to that predicted from an animal model for a malization of aberrant LTP refers to any change in aberrant normal individual. As used herein, Substantially the same LTP in an individual suffering from, suspected of having, or means, for example, about 90% to about 110% of the synaptic 30 pre-disposed to a CNS disorder that trends towards LTP of a function in a normal individual or to that predicted from an normal individual or to that predicted from an animal model animal model for a normal individual. In other embodiments, for a normal individual. As used herein "partially normalized substantially the same means, for example, about 80% to LTP” or “partially normal LTP is, for example, about 25%, about 120% of the synaptic function in a normal individual or about 35%, about 45%, about 55%, about 65%, or to that predicted from an animal model for a normal indi 35 +about 75% of the measured LTP of a normal individual or to vidual. In yet other embodiments, substantially the same that predicted from an animal model for a normal individual. means, for example, about 70% to about 130% of the synaptic In some embodiments, normalization or partial normalization function in a normal individual or to that predicted from an ofaberrant LTP in an individual suffering from, suspected of animal model for a normal individual. As used herein, “partial having, or pre-disposed to a CNS disorder is lowering of normalization of aberrant synaptic function” refers to any 40 aberrant LTP where the aberrant LTP is higher than the LTP of change in aberrant synaptic function in an individual Suffer a normal individual or to that predicted from an animal model ing from, Suspected of having, or pre-disposed to a CNS for a normal individual. In some embodiments, normalization disorder that trends towards synaptic function of a normal or partial normalization of aberrant LTP in an individual individual or to that predicted from an animal model for a Suffering from, Suspected of having, or pre-disposed to a CNS normal individual. As used herein “partially normalized syn 45 disorder is an increase in aberrant LTP where the aberrant aptic function” or “partially normal synaptic function' is, for LTP is lower than the LTP of a normal individual or to that example, tabout 25%, tabout 35%, about 45%, tabout predicted from an animal model for a normal individual. In 55%, tabout 65%, or about 75% of the measured synaptic Some embodiments, normalization or partial normalization of function of a normal individual or to that predicted from an LTP in an individual suffering from, suspected of having, or animal model for a normal individual. In some embodiments, 50 pre-disposed to a CNS disorder is a change from an erratic normalization or partial normalization of aberrant synaptic (e.g., fluctuating, randomly increasing or decreasing) LTP to function in an individual Suffering from, Suspected of having, a normal (e.g. stable) or partially normal (e.g., less fluctuat or pre-disposed to a CNS disorder is lowering of aberrant ing) LTP compared to the LTP of a normal individual or to that synaptic function where the aberrant synaptic function is predicted from an animal model for a normal individual. In higher than the synaptic function of a normal individual or to 55 Some embodiments, normalization or partial normalization of that predicted from an animal model for a normal individual. aberrant LTP in an individual suffering from, suspected of In some embodiments, normalization or partial normalization having, or pre-disposed to a CNS disorder is a change from a of aberrant synaptic function in an individual Suffering from, non-stabilizing LTP to a normal (e.g., stable) or partially Suspected of having, or pre-disposed to a CNS disorder is an normal (e.g., partially stable) LTP compared to the LTP of a increase in aberrant synaptic function where the aberrant 60 normal individual or to that predicted from an animal model synaptic function is lower than the synaptic function of a for a normal individual. normal individual or to that predicted from an animal model As used herein, “normalization of aberrant long term for a normal individual. In some embodiments, normalization depression (LTD) refers to a change in aberrant LTD in an or partial normalization of synaptic function in an individual individual Suffering from, Suspected of having, or pre-dis Suffering from, Suspected of having, or pre-disposed to a CNS 65 posed to a CNS disorder to a level of LTD that is substantially disorder is a change from an erratic (e.g., fluctuating, ran the same as the LTD of a normal individual or to that predicted domly increasing or decreasing) synaptic function to a nor from an animal model for a normal individual. As used herein, US 8,372,970 B2 139 140 substantially the same means, for example, about 90% to tially normalized sensorimotor gating or “partially normal about 110% of the LTD in a normal individual or to that sensorimotor gating is, for example, tabout 25%, tabout predicted from an animal model for a normal individual. In 35%, about 45%, about 55%, about 65%, or about 75% other embodiments, Substantially the same means, for of the measured sensorimotorgating of a normal individual or example, about 80% to about 120% of the LTD in a normal to that predicted from an animal model for a normal indi individual or to that predicted from an animal model for a vidual. In some embodiments, normalization or partial nor normal individual. In yet other embodiments, substantially malization of aberrant sensorimotor gating in an individual the same means, for example, about 70% to about 130% of the Suffering from, Suspected of having, or pre-disposed to a CNS LTD in a normal individual or to that predicted from an disorder is lowering of aberrant sensorimotor gating where animal model for a normal individual. As used herein, “partial 10 the aberrant sensorimotor gating is higher than the sen normalization of aberrant LTD” refers to any change in aber Sorimotor gating of a normal individual or to that predicted rant LTD in an individual Suffering from, Suspected of having, from an animal model for a normal individual. In some or pre-disposed to a CNS disorder that trends towards LTD of embodiments, normalization or partial normalization of aber a normal individual or to that predicted from an animal model rant sensorimotor gating in an individual Suffering from, Sus for a normal individual. As used herein “partially normalized 15 pected of having, or pre-disposed to a CNS disorder is an LTD or “partially normal LTD is, for example, about 25%, increase in aberrant sensorimotor gating where the aberrant about 35%, about 45%, about 55%, about 65%, or sensorimotor gating is lower than the sensorimotor gating of +about 75% of the measured LTD of a normal individual or to a normal individual or to that predicted from an animal model that predicted from an animal model for a normal individual. for a normal individual. In some embodiments, normalization In some embodiments, normalization or partial normalization or partial normalization of sensorimotor gating in an indi ofaberrant LTD in an individual suffering from, suspected of vidual Suffering from, Suspected of having, or pre-disposed to having, or pre-disposed to a CNS disorder is lowering of a CNS disorder is a change from an erratic (e.g., fluctuating, aberrant LTD where the aberrant LTD is higher than the LTD randomly increasing or decreasing) sensorimotor gating to a of a normal individual or to that predicted from an animal normal (e.g. stable) or partially normal (e.g., less fluctuating) model for a normal individual. In some embodiments, nor 25 sensorimotorgating compared to the sensorimotorgating of a malization or partial normalization of aberrant LTD in an normal individual or to that predicted from an animal model individual Suffering from, Suspected of having, or pre-dis for a normal individual. In some embodiments, normalization posed to a CNS disorder is an increase inaberrant LTD where or partial normalization of aberrant sensorimotorgating in an the aberrant LTD is lower than the LTD of a normal individual individual Suffering from, Suspected of having, or pre-dis or to that predicted from an animal model for a normal indi 30 posed to a CNS disorder is a change from a non-stabilizing vidual. In some embodiments, normalization or partial nor sensorimotor gating to a normal (e.g., stable) or partially malization of LTD in an individual suffering from, suspected normal (e.g., partially stable) sensorimotor gating compared of having, or pre-disposed to a CNS disorder is a change from to the sensorimotor gating of a normal individual or to that an erratic (e.g., fluctuating, randomly increasing or decreas predicted from an animal model for a normal individual. ing) LTD to a normal (e.g. stable) or partially normal (e.g., 35 As used herein, "expression' of a nucleic acid sequence less fluctuating) LTD compared to the LTD of a normal indi refers to one or more of the following events: (1) production vidual or to that predicted from an animal model for a normal ofan RNA template from a DNA sequence (e.g., by transcrip individual. In some embodiments, normalization or partial tion); (2) processing of an RNA transcript (e.g., by splicing, normalization of aberrant LTD in an individual suffering editing, 5' cap formation, and/or 3' end formation); (3) trans from, suspected of having, or pre-disposed to a CNS disorder 40 lation of an RNA into a polypeptide or protein; (4) post is a change from a non-stabilizing LTD to a normal (e.g., translational modification of a polypeptide or protein. stable) or partially normal (e.g., partially stable) LTD com As used herein the term “PAK polypeptide' or “PAK pro pared to the LTD of a normal individual or to that predicted tein' or “PAK’ refers to a protein that belongs in the family of from an animal model for a normal individual. p21-activated serine/threonine protein kinases. These include As used herein, “normalization of aberrant sensorimotor 45 mammalian isoforms of PAK, e.g., the Group I PAK proteins gating refers to a change in aberrant sensorimotor gating in (sometimes referred to as Group A PAK proteins), including an individual Suffering from, Suspected of having, or pre PAK1, PAK2, PAK3, as well as the Group II PAK proteins disposed to a CNS disorder to a level of sensorimotor gating (sometimes referred to as Group B PAK proteins), including that is Substantially the same as the sensorimotor gating of a PAK4, PAK5, and/or PAK6 Also included as PAK polypep normal individual or to that predicted from an animal model 50 tides or PAK proteins are lower eukaryotic isoforms, such as for a normal individual. As used herein, substantially the the yeast Step 20 (Leberter et al., 1992, EMBO J., 11:4805; same means, for example, about 90% to about 110% of the incorporated herein by reference) and/or the Dictyostelium sensorimotorgating in a normal individual or to that predicted single-headed myosin I heavy chain kinases (Wu et al., 1996, from an animal model for a normal individual. In other J. Biol. Chem.,271:31787; incorporated herein by reference). embodiments, Substantially the same means, for example, 55 Representative examples of PAK amino acid sequences about 80% to about 120% of the sensorimotor gating in a include, but are not limited to, human PAK1 (GenBank normal individual or to that predicted from an animal model Accession Number AAA65441), human PAK2 (GenBank for a normal individual. In yet other embodiments, substan Accession Number AAA65442), human PAK3 (GenBank tially the same means, for example, about 70% to about 130% Accession Number AAC36097), human PAK 4 (GenBank of the sensorimotor gating in a normal individual or to that 60 Accession Numbers NP 005875 and CAA09820), human predicted from an animal model for a normal individual. As PAK5 (GenBank Accession Numbers CAC18720 and used herein, partial normalization of aberrant sensorimotor BAA94194), human PAK6 (GenBank Accession Numbers gating refers to any change in aberrant sensorimotor gating NP 064553 and AAF82800), human PAK7 (GenBank in an individual Suffering from, Suspected of having, or pre Accession Number Q9P286), C. elegans PAK (GenBank disposed to a CNS disorder that trends towards sensorimotor 65 Accession Number BAA 11844), D. melanogaster PAK gating of a normal individual or to that predicted from an (GenBank Accession Number AAC47094), and rat PAK1 animal model for a normal individual. As used herein par (GenBank Accession Number AAB95646). In some embodi US 8,372,970 B2 141 142 ments, a PAK polypeptide comprises an amino acid sequence programs, the default parameters of the respective programs that is at least 70% to 100% identical, e.g., at least 75%, 80%, (e.g., XBLAST and NBLAST) are used. See the website of 85%. 86%, 87%, 88%, 90%, 91%, 92%, 94%, 95%, 96%, the National Center for Biotechnology Information for fur 97%, 98%, or any other percent from about 70% to about ther details (on the world wide web at ncbi.nlm.nih.gov). 100% identical to sequences of GenBank Accession Numbers 5 Proteins suitable for use in the methods described herein also AAA65441, AAA65442, AAC36097, NP 005875, includes proteins having between 1 to 15 amino acid changes, CAAO9820, CAC18720, BAA94194, NP 064553, e.g., 1,2,3,4,5,6,7,8,9, 10, 11, 12, 13, 14, or 15 amino acid AAF82800, Q9P286, BAA 11844, AAC47094, and/or Substitutions, deletions, or additions, compared to the amino AAB95646. In some embodiments, a Group I PAK polypep acid sequence of any protein PAK inhibitor described herein. tide comprises an amino acid sequence that is at least 70% to 10 In other embodiments, the altered amino acid sequence is at 100% identical, e.g., at least 75%, 80%, 85%. 86%, 87%, least 75% identical, e.g., 77%, 80%, 82%, 85%, 88%, 90%, 88%, 90%, 91%, 92%, 94%, 95%, 96%, 97%, 98%, or any 92%, 95%, 97%, 98%, 99%, or 100% identical to the amino other percent from about 70% to about 100% identical to acid sequence of any protein PAK inhibitor described herein. sequences of GenBank Accession Numbers AAA65441, Such sequence-variant proteins are Suitable for the methods AAA65442, and/or AAC36097. 15 described herein as long as the altered amino acid sequence Representative examples of PAK genes encoding PAK pro retains sufficient biological activity to be functional in the teins include, but are not limited to, human PAK1 (GenBank compositions and methods described herein. Where amino Accession Number U24152), human PAK2 (GenBank acid Substitutions are made, the Substitutions should be con Accession Number U24153), human PAK3 (GenBank servative amino acid Substitutions. Among the common Accession Number AF068864), human PAK4 (GenBank amino acids, for example, a “conservative amino acid Substi Accession Number AJO11855), human PAK5 (GenBank tution' is illustrated by a Substitution among amino acids Accession Number AB040812), and human PAK6 (GenBank within each of the following groups: (1) glycine, alanine, Accession Number AF276893). In some embodiments, a Valine, leucine, and isoleucine, (2) phenylalanine, tyrosine, PAK gene comprises a nucleotide sequence that is at least and tryptophan, (3) serine and threonine, (4) aspartate and 70% to 100% identical, e.g., at least 75%, 80%, 85%. 86%, 25 glutamate, (5) glutamine and asparagine, and (6) lysine, argi 87%, 88%, 90%, 91%, 92%, 94%, 95%, 96%, 97%, 98%, or nine and histidine. The BLOSUM62 table is an amino acid any other percent from about 70% to about 100% identical to substitution matrix derived from about 2,000 local multiple sequences of GenBank Accession Numbers U24152, alignments of protein sequence segments, representing U24153, AF068864, AJO1 1855, AB040812, and/or highly conserved regions of more than 500 groups of related AF276893. In some embodiments, a Group I PAK gene com 30 proteins (Henikoff et al (1992), Proc. Natl. Acad. Sci. USA, prises a nucleotide sequence that is at least 70% to 100% 89:10915-10919). Accordingly, the BLOSUM62 substitution identical, e.g., at least 75%, 80%, 85%. 86%, 87%, 88%, frequencies are used to define conservative amino acid sub 90%, 91%, 92%, 94%. 95%, 96%, 97%, 98%, or any other stitutions that may be introduced into the amino acid percent from about 70% to about 100% identical to sequences sequences described or described herein. Although it is pos of GenBank Accession Numbers U24152, U24153, and/or 35 sible to design amino acid Substitutions based solely upon AFO68864. chemical properties (as discussed above), the language “con To determine the percent homology of two amino acid servative amino acid substitution' preferably refers to a sub sequences or of two nucleic acids, the sequences are aligned stitution represented by a BLOSUM62 value of greater than for optimal comparison purposes (e.g., gaps can be intro -1. For example, an amino acid substitution is conservative if duced in the sequence of a first amino acid or nucleic acid 40 the substitution is characterized by a BLOSUM62 value of 0. sequence for optimal alignment with a second amino or 1, 2, or 3. According to this system, preferred conservative nucleic acid sequence). The amino acid residues or nucle amino acid substitutions are characterized by a BLOSUM62 otides at corresponding amino acid positions or nucleotide value of at least 1 (e.g., 1, 2 or 3), while more preferred positions are then compared. When a position in the first conservative amino acid Substitutions are characterized by a sequence is occupied by the same amino acid residue or 45 BLOSUM62 value of at least 2 (e.g., 2 or 3). nucleotide as the corresponding position in the second As used herein, the term “PAK activity.” unless otherwise sequence, then the molecules are identical at that position. specified, includes, but is not limited to, at least one of PAK The percent homology between the two sequences is a func protein-protein interactions, PAK phosphotransferase activ tion of the number of identical positions shared by the ity (intermolecular or intermolecular), translocation, etc of sequences (i.e., 9% identity—it of identical positions/total it of 50 one or more PAK isoforms. positions (e.g., overlapping positions)x100). In one embodi As used herein, a “PAK inhibitor refers to any molecule, ment the two sequences are the same length. compound, or composition that directly or indirectly To determine percent homology between two sequences, decreases the PAK activity. In some embodiments, PAK the algorithm of and Altschul (1990) Proc. Natl. Acad. Sci. inhibitors inhibit, decrease, and/or abolish the level of a PAK USA 87:2264-2268, modified as in Karlin and Altschul 55 mRNA and/or protein or the half-life of PAK mRNA and/or (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877 is used. protein, Such inhibitors are referred to as "clearance agents'. Such an algorithm is incorporated into the NBLAST and In some embodiments, a PAK inhibitor is a PAK antagonist XBLAST programs of Altschul, et al. (1990) J. Mol. Biol. that inhibits, decreases, and/or abolishes an activity of PAK. 215:403-410. BLAST nucleotide searches are performed In some embodiments, a PAK inhibitor also disrupts, inhibits, with the NBLAST program, score=100, wordlength=12 to 60 or abolishes the interaction between PAK and its natural obtain nucleotide sequences homologous to a nucleic acid binding partners (e.g., a Substrate for a PAK kinase, a Rac molecules described or disclose herein. BLAST protein protein, a cdc42 protein, LIM kinase) or a protein that is a searches are performed with the XBLAST program, binding partner of PAK in a pathological condition, as mea score=50, wordlength=3. To obtain gapped alignments for Sured using standard methods. In some embodiments, the comparison purposes, Gapped BLAST is utilized as 65 PAK inhibitor is a Group I PAK inhibitor that inhibits, for described in Altschul et al. (1997) Nucleic Acids Res. example, one or more Group I PAK polypeptides, for 25:3389-3402. When utilizing BLAST and Gapped BLAST example, PAK1, PAK2, and/or PAK3. In some embodiments, US 8,372,970 B2 143 144 the PAK inhibitor is a PAK1 inhibitor. In some embodiments, methionine, phenylalanine, proline, serine, threonine, tryp the PAK inhibitor is a PAK2 inhibitor. In some embodiments, tophan, tyrosine, and valine) and pyrolysine and selenocys the PAK inhibitor is a PAK3 inhibitor. In some embodiments, teine. Amino acid analogs refers to compounds that have the the PAK inhibitor is a mixed PAK1/PAK3 inhibitor. In some same basic chemical structure as a naturally occurring amino embodiments, the PAK inhibitor inhibits all three Group I acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl PAK isoforms (PAK1, PAK2 and PAK3) with equal or similar group, an amino group, and an R group, Such as, homoserine, potency. In some embodiments, the PAK inhibitor is a Group norleucine, methionine Sulfoxide, methionine methyl Sulfo II PAK inhibitor that inhibits one or more Group II PAK nium. Such analogs have modified R groups (such as, norleu polypeptides, for example PAK4, PAK5, and/or PAK6. In cine) or modified peptide backbones, but retain the same some embodiments, the PAK inhibitor is a PAK4 inhibitor. In 10 basic chemical structure as a naturally occurring amino acid. some embodiments, the PAK inhibitor is a PAK5 inhibitor. In Amino acids may be referred to herein by either their some embodiments, the PAK inhibitor is a PAK6 inhibitor. In commonly known three letter symbols or by the one-letter some embodiments, the PAK inhibitor is a PAK7 inhibitor. As symbols recommended by the IUPAC-IUB Biochemical used herein, a PAK5 polypeptide is substantially homologous Nomenclature Commission. Nucleotides, likewise, may be to a PAK7 polypeptide. 15 referred to by their commonly accepted single-letter codes. In some embodiments, PAK inhibitors reduce, abolish, The term “nucleic acid refers to deoxyribonucleotides, and/or remove the binding between PAK and at least one of its deoxyribonucleosides, ribonucleosides, or ribonucleotides natural binding partners (e.g., Cdc42 or Rac). In some and polymers thereof in either single- or double-stranded instances, binding between PAK and at least one of its natural form. Unless specifically limited, the term encompasses binding partners is stronger in the absence of a PAK inhibitor nucleic acids containing known analogues of natural nucle (by e.g., 90%, 80%, 70%, 60%, 50%, 40%, 30% or 20%) than otides which have similar binding properties as the reference in the presence of a PAK inhibitor. In some embodiments, nucleic acid and are metabolized in a manner similar to natu PAK inhibitors prevent, reduce, or abolish binding between rally occurring nucleotides. Unless specifically limited oth PAK and a protein that abnormally accumulates or aggregates erwise, the term also refers to oligonucleotide analogs includ in cells or tissue in a disease state. In some instances, binding 25 ing PNA (peptidonucleic acid), analogs of DNA used in between PAK and at least one of the proteins that aggregates antisense technology (phosphorothioates, phosphoroami or accumulates in a cell or tissue is stronger in the absence of dates, and the like). Unless otherwise indicated, a particular a PAK inhibitor (by e.g., 90%, 80%, 70%, 60%, 50%, 40%, nucleic acid sequence also implicitly encompasses conserva 30% or 20%) than in the presence of an inhibitor. tively modified variants thereof (including but not limited to, An “individual' or an “individual,” as used herein, is a 30 degenerate codon Substitutions) and complementary mammal. In some embodiments, an individual is an animal, sequences as well as the sequence explicitly indicated. Spe for example, a rat, a mouse, a dog or a monkey. In some cifically, degenerate codon substitutions may be achieved by embodiments, an individual is a human patient. In some generating sequences in which the third position of one or embodiments an “individual' or an “individual' is a human. more selected (or all) codons is substituted with mixed-base In some embodiments, an individual suffers from a CNS 35 and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. disorder or is suspected to be suffering from a CNS disorder 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605 or is pre-disposed to a CNS disorder. 2608 (1985); and Cassol et al. (1992); Rossolini et al., Mol. In some embodiments, a pharmacological composition Cell. Probes 8:91-98 (1994)). comprising a PAK inhibitor is “administered peripherally” or The terms "isolated and “purified’ refer to a material that “peripherally administered.” As used herein, these terms refer 40 is Substantially or essentially removed from or concentrated to any form of administration of an agent, e.g., a therapeutic in its natural environment. For example, an isolated nucleic agent, to an individual that is not direct administration to the acid is one that is separated from the nucleic acids that nor CNS, i.e., that brings the agent in contact with the non-brain mally flank it or other nucleic acids or components (proteins, side of the blood-brain barrier. “Peripheral administration.” lipids, etc.) in a sample. In another example, a polypeptide is as used herein, includes intravenous, intra-arterial, Subcuta 45 purified if it is substantially removed from or concentrated in neous, intramuscular, intraperitoneal, transdermal, by inha its natural environment. Methods for purification and isola lation, transbuccal, intranasal, rectal, oral, parenteral, Sublin tion of nucleic acids and proteins are documented method gual, or trans-nasal. In some embodiments, a PAK inhibitor is ologies. administered by an intracerebral route. The term “antibody” describes an immunoglobulin The terms “polypeptide.” and “protein’ are used inter 50 whether natural or partly or wholly synthetically produced. changeably herein to refer to a polymer of amino acid resi The term also covers any polypeptide or protein having a dues. That is, a description directed to a polypeptide applies binding domain which is, or is homologous to, an antigen equally to a description of a protein, and vice versa. The terms binding domain. CDR grafted antibodies are also contem apply to naturally occurring amino acid polymers as well as plated by this term. amino acid polymers in which one or more amino acid resi 55 The termantibody as used herein will also be understood to dues is a non-naturally occurring amino acid, e.g., an amino mean one or more fragments of an antibody that retain the acid analog. As used herein, the terms encompass amino acid ability to specifically bind to an antigen, (see generally, Hol chains of any length, including full length proteins (i.e., anti liger et al., Nature Biotech. 23 (9) 1126-1129 (2005)). Non gens), wherein the amino acid residues are linked by covalent limiting examples of Such antibodies include (i) a Fab frag peptide bonds. 60 ment, a monovalent fragment consisting of the VL, VH, CL The term “amino acid refers to naturally occurring and and CH1 domains; (ii) a F(ab')2 fragment, a bivalent fragment non-naturally occurring amino acids, as well as amino acid comprising two Fab fragments linked by a disulfide bridge at analogs and amino acid mimetics that function in a manner the hinge region; (iii) a Fd fragment consisting of the VHand similar to the naturally occurring amino acids. Naturally CH1 domains; (iv) a Fv fragment consisting of the VL and VH encoded amino acids are the 20 common amino acids (ala 65 domains of a single arm of an antibody, (v) a dAb fragment nine, arginine, asparagine, aspartic acid, cysteine, glutamine, (Ward et al., (1989) Nature 341:544546), which consists of a glutamic acid, glycine, histidine, isoleucine, leucine, lysine, VH domain; and (vi) an isolated complementarity determin US 8,372,970 B2 145 146 ing region (CDR). Furthermore, although the two domains of which enables the sRv to form the desired structure for anti the Fv fragment, VL and VH, are coded for by separate genes, gen binding. For a review of sv see, e.g., Pluckthun in The they are optionally joined, using recombinant methods, by a Pharmacology of Monoclonal Antibodies, Vol. 113, Rosen synthetic linker that enables them to be made as a single burg and Moore eds. Springer-Verlag, New York, pp. 269315 protein chain in which the VL and VH regions pair to form (1994). monovalent molecules (known as single chain FV (ScPV); see A “chimeric' antibody includes an antibody derived from e.g., Bird et al. (1988) Science 242:423 426; and Huston et al. a combination of different mammals. The mammal is, for (1988) Proc. Natl. Acad. Sci. USA 85:5879 5883; and example, a rabbit, a mouse, a rat, a goat, or a human. The Osbournet al. (1998) Nat. Biotechnol. 16:778). Such single combination of different mammals includes combinations of chain antibodies are also intended to be encompassed within 10 fragments from human and mouse sources. the termantibody. Any VHandVL sequences of specific schv In some embodiments, an antibody described or described is optionally linked to human immunoglobulin constant herein is a monoclonal antibody (MAb), typically a chimeric region cDNA or genomic sequences, in order to generate human-mouse antibody derived by humanization of a mouse expression vectors encoding complete IgG molecules or monoclonal antibody. Such antibodies are obtained from, other isotypes. VH and VL are also optionally used in the 15 e.g., transgenic mice that have been “engineered to produce generation of Fab., Fv or other fragments of immunoglobulins specific human antibodies in response to antigenic challenge. using either protein chemistry or recombinant DNA technol In this technique, elements of the human heavy and light ogy. Otherforms of single chain antibodies, such as diabodies chain locus are introduced into strains of mice derived from are also encompassed. embryonic stem cell lines that contain targeted disruptions of “F(ab')2 and “Fab' moieties are optionally produced by the endogenous heavy chain and light chain loci. In some treating immunoglobulin (monoclonal antibody) with a pro embodiments, the transgenic mice synthesize human anti tease such as pepsin and papain, and includes an antibody bodies specific for human antigens, and the mice are used to fragment generated by digesting immunoglobulin near the produce human antibody-secreting hybridomas. disulfide bonds existing between the hinge regions in each of The term “optionally substituted' or “substituted” means the two H chains. For example, papain cleaves IgG upstream 25 that the referenced group substituted with one or more addi of the disulfide bonds existing between the hinge regions in tional group(s). In certain embodiments, the one or more each of the two H chains to generate two homologous anti additional group(s) are individually and independently body fragments in which an L chain composed of VL (L chain selected from amide, ester, alkyl, cycloalkyl, heteroalkyl, variable region) and CL (L chain constant region), and an H aryl, heteroaryl, heteroalicyclic, hydroxy, alkoxy, aryloxy, chain fragment composed of VH (H chain variable region) 30 alkylthio, arylthio, alkylsulfoxide, arylsulfoxide, ester, alkyl and CHY 1 (y1 region in the constant region of H chain) are Sulfone, arylsulfone, cyano, halogen, alkoyl, alkoyloxo, iso connected at their C terminal regions through a disulfide cyanato, thiocyanato, isothiocyanato, nitro, haloalkyl, bond. Each of these two homologous antibody fragments is haloalkoxy, fluoroalkyl, amino, alkyl-amino, dialkyl-amino, called Fab'. Pepsin also cleaves IgG downstream of the dis amido. ulfide bonds existing between the hinge regions in each of the 35 An “alkyl group refers to an aliphatic hydrocarbon group. two H chains to generate an antibody fragment slightly larger Reference to an alkyl group includes “saturated alkyl and/or than the fragment in which the two above-mentioned Fab' are “unsaturated alkyl. The alkyl group, whether saturated or connected at the hinge region. This antibody fragment is unsaturated, includes branched, straight chain, or cyclic called F(ab')2. groups. By way of example only, alkyl includes methyl, ethyl, The Fab fragment also contains the constant domain of the 40 propyl, iso-propyl. n-butyl, iso-butyl, Sec-butyl, t-butyl, pen light chain and the first constant domain (CH1) of the heavy tyl, iso-pentyl, neo-pentyl, and hexyl. In some embodiments, chain. Fab' fragments differ from Fab fragments by the addi alkyl groups include, but are in no way limited to, methyl, tion of a few residues at the carboxyl terminus of the heavy ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, chain CH1 domain including one or more cysteine(s) from the hexyl, ethenyl, propenyl, butenyl, cyclopropyl, cyclobutyl, antibody hinge region. Fab'-SH is the designation herein for 45 cyclopentyl, cyclohexyl, and the like. A “lower alkyl is a Fab' in which the cysteine residue(s) of the constant domains C-C alkyl. A "heteroalkyl group substitutes any one of the bear a free thiol group. F(ab')2 antibody fragments originally carbons of the alkyl group with a heteroatom having the were produced as pairs of Fab' fragments which have hinge appropriate number of hydrogen atoms attached (e.g., a CH2 cysteines between them. Other chemical couplings of anti group to an NH group or an Ogroup). body fragments are documented. 50 An “alkoxy' group refers to a (alkyl)O— group, where “Fv' is the minimum antibody fragment which contains a alkyl is as defined herein. complete antigen-recognition and antigen-binding site. This The term “alkylamine” refers to the N(alkyl), H, group, region consists of a dimer of one heavy chain and one light wherein alkyl is as defined herein and X and y are selected chain variable domain in tight, non-covalent association. It is from the group x=1, y=1 and x=2... y–0. When x=2, the alkyl in this configuration that the three hyperVariable regions of 55 groups, taken together with the nitrogen to which they are each variable domain interact to define an antigen-binding attached, optionally form a cyclic ring system. site on the surface of the VH-VL dimer. Collectively, the six An "amide' is a chemical moiety with formula C(O)NHR hyperVariable regions confer antigen-binding specificity to or NHC(O)R, where R is selected from alkyl, cycloalkyl, aryl, the antibody. However, even a single variable domain (or half heteroaryl (bonded through a ring carbon) and heteroalicyclic of an Fv comprising only three hyperVariable regions specific 60 (bonded through a ring carbon). for an antigen) has the ability to recognize and bind antigen, The term “ester refers to a chemical moiety with formula although at a lower affinity than the entire binding site. —C(=O)CR, where R is selected from the group consisting “Single-chain Fv' or “sv' antibody fragments comprise a of alkyl, cycloalkyl, aryl, heteroaryl and heteroalicyclic. VH, a VL, or both a VH and VL domain of an antibody, As used herein, the term “aryl” refers to an aromatic ring wherein both domains are present in a single polypeptide 65 wherein each of the atoms forming the ring is a carbon atom. chain. In some embodiments, the Fv polypeptide further com Aryl rings described herein include rings having five, six, prises a polypeptide linker between the VH and VL domains seven, eight, nine, or more than nine carbon atoms. Aryl US 8,372,970 B2 147 148 groups are optionally substituted. Examples of aryl groups tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl. include, but are not limited to phenyl, and naphthalenyl. piperidino, morpholino, thiomorpholino, thioxanyl, piperazi The term “cycloalkyl refers to a monocyclic or polycyclic nyl, aziridinyl, azetidinyl, oxetanyl, thietanyl, homopiperidi non-aromatic radical, wherein each of the atoms forming the nyl, oxepanyl, thiepanyl, oxazepinyl, diazepinyl, thiazepinyl, ring (i.e. skeletal atoms) is a carbon atom. In various embodi 1.2.3,6-tetrahydropyridinyl, 2-pyrrolinyl, 3-pyrrolinyl, ments, cycloalkyls are Saturated, or partially unsaturated. In indolinyl, 2H-pyranyl, 4H-pyranyl, dioxanyl, 1,3-dioxolanyl. Some embodiments, cycloalkyls are fused with an aromatic pyrazolinyl, dithianyl, dithiolanyl, dihydropyranyl, dihy ring. Cycloalkyl groups include groups having from 3 to 10 drothienyl, dihydrofuranyl, pyrazolidinyl, imidazolinyl, imi ring atoms. Illustrative examples of cycloalkyl groups dazolidinyl, 3-azabicyclo[3.1.0 hexanyl, 3-azabicyclo4.1.0 include, but are not limited to, the following moieties: 10 heptanyl, 3H-indolyl and quinolizinyl. Examples of aromatic heterocyclic groups are pyridinyl, imidazolyl pyrimidinyl, pyrazolyl, triazolyl pyrazinyl, tetrazolyl, furyl, thienyl, isox azolyl, thiazolyl, oxazolyl, isothiazolyl pyrrolyl, quinolinyl, isoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinno 15 linyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazi nyl, isoindolyl, pteridinyl, purinyl, oxadiazolyl, thiadiazolyl, furazanyl, benzofurazanyl, benzothiophenyl, benzothiazolyl, benzoxazolyl, quinazolinyl, quinoxalinyl, naphthyridinyl, and furopyridinyl. The terms "heteroaryl' or, alternatively, "heteroaromatic' refers to an aryl group that includes one or more ring heteroa toms selected from nitrogen, oxygen and Sulfur. An N-con taining "heteroaromatic' or "heteroaryl moiety refers to an 25 aromatic group in which at least one of the skeletal atoms of the ring is a nitrogen atom. In certain embodiments, het eroaryl groups are monocyclic or polycyclic. Examples of monocyclic heteroaryl groups include and are not limited to: 30

35 pyrrole (pyrrolyl) and the like. Monocyclic cycloalkyls include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 40 cycloheptyl, and cyclooctyl. Dicylclic cycloalkyls include, furan but are not limited to tetrahydronaphthyl, indanyl, tetrahydro (furanyl) pentalene or the like. Polycyclic cycloalkyls include adaman tane, norbornane or the like. The term cycloalkyl includes "unsaturated nonaromatic carbocyclyl or “nonaromatic 45 unsaturated carbocyclyl groups both of which refer to a nonaromatic carbocycle, as defined herein, that contains at thiophene least one carbon carbon double bond or one carbon carbon (thiophenyl) triple bond. The term "heterocyclo” refers to heteroaromatic and het 50 eroalicyclic groups containing one to four ring heteroatoms each selected from O, S and N. In certain instances, each \ heterocyclic group has from 4 to 10 atoms in its ring system, pyrazole and with the proviso that the ring of said group does not (pyrazolyl contain two adjacent O or Satoms. Non-aromatic heterocy 55 clic groups include groups having 3 atoms in their ring sys tem, but aromatic heterocyclic groups must have at least 5 atoms in their ring system. The heterocyclic groups include benzo-fused ring systems. An example of a 3-membered het imidazole erocyclic group is aziridinyl (derived from aziridine). An 60 (imidazolyl) example of a 4-membered heterocyclic group is aZetidinyl (derived from azetidine). An example of a 5-membered het ON erocyclic group is thiazolyl. An example of a 6-membered N heterocyclic group is pyridyl, and an example of a 10-mem bered heterocyclic group is quinolinyl. Examples of non 65 isoxazole aromatic heterocyclic groups are pyrrolidinyl, tetrahydro (isoxazolyl) furanyl. dihydrofuranyl, tetrahydrothienyl,

US 8,372,970 B2 153 154 -continued -continued S

thiarane )thiaranyl) OS 1,4-oxathiane (i.4-oxathianyl)

aziridine (aziridinyl) 10 H

Oxetane OO (oxetanyl) 15 morpholine S (morpholinyl)

thiatane (thiatanyl) OS " 1,4-dithiane aZetidine (1,4-dithianyl) (aZetidinyl) K) 25 tetrahydrofuran (tetrahydrofuranyl) O piperazine () 30 (piperazinyl) tetrahydrothiaphene (tetrahydrothiaphenyl) 35 S 1,4-azathiane (1,4-azathianyl) () O pyrrollidine (pyrrollidinyl) 40

oxepane (oxepanyl) O 45 tetrahydropyran S (tetrahydropyranyl)

50 thiepane O (thiepanyl) tetrahydrothiopyran (tetrahydrothiopyranyl)

55

azepane piperidine (azepanyl) (piperidinyl) 60 O

O O 1,4-dioxepane 1,4-dioxane 65 (1,4-dioxypanyl) (i,4-dioxanyl) US 8,372,970 B2 155 156 -continued -continued O H N

S N 1,4-oxathiepane 1,2,5,6-tetrahydropyridine (1,4-oxathiepanyl) (1,2,5,6-tetrahydropyridinyl) O 10 Other illustrative examples of heterocyclo groups, also referred to as non-aromatic heterocycles, include: 1,4-oxaazepane (1,4-oxaazepanyl) S 15

S , , , , , 1,4-dithiepane (1,4-dithiepanyl) S (, CC CO NH 25 1,4-thieaZapane (14-thieaZapanyl) (a DC COO

30

NH 1,4-diazepane H H OOOC.O 47 (1,4-diazepanyl) 35 N-S=O, M

NH 40 tropane (tropanyl) OOOOOO O O O Examples of partially unsaturated heterocyclyl groups as S V/ include

CN D CN H H 50 or the like. 3,4-dihydro-2H-pyran The term heteroalicyclic also includes all ring forms of the (3,4-dihydro-2H-pyranyl) carbohydrates, including but not limited to the monosaccha O rides, the disaccharides and the oligosaccharides. 55 The term “halo” or, alternatively, “halogen' means fluoro, chloro, bromo and iodo. N The terms “haloalkyl, and “haloalkoxy' include alkyl and 5,6-dihydro-2H-pyran alkoxy structures that are substituted with one or more halo (5,6-dihydro-2H-pyranyl) 60 gens. In embodiments, where more than one halogen is O included in the group, the halogens are the same or they are different. The terms “fluoroalkyland “fluoroalkoxy' include haloalkyl and haloalkoxy groups, respectively, in which the 2 halo is fluorine. 2H-pyran 65 The term "heteroalkyl include optionally substituted (2H-pyranyl) alkyl, alkenyl and alkynyl radicals which have one or more skeletal chain atoms selected from an atom other than carbon, US 8,372,970 B2 157 158 e.g., oxygen, nitrogen, Sulfur, phosphorus, silicon, or combi the core, for example by alkylation with a halogen containing nations thereof. In certain embodiments, the heteroatom(s) is Q forms substituted compound III. Oxidation of the sulfanyl placed at any interior position of the heteroalkyl group. compound III using an oxidizing agent Such as for example, Examples include, but are not limited to. —CH2—O—CH, chloroperbenzoic acid gives sulfinyl compound IV. Addition CH, CH, O CH, CH-NH CH, CH of the B-ring (V) results in compounds of Formula VI. Addi CH-NH CH, CH N(CH)—CH, CH tion of the Tring (VIII) where M represents a group such a CH-NH CH, —CH, CH, N(CH)—CH, boronic acid, boronic ester, alkyl tin, Zinc atom or other CH, S CH, CH, CH, CH, S(O)-CH, similar moieties generates compound IX. Alternatively, VI —CH, CH, S(O), CH, —CH=CH-O CH, -Si can be converted to its boronic acid VIII and ring T (X) can be (CH), —CH2—CH=N OCH and —CH=CH-N 10 attached via a halogen atom to generate IX. The procedures (CH)—CH. In some embodiments, up to two heteroatoms described herein are given merely as an example and should are consecutive, such as, by way of example, —CH2—NH- in no way limit the methods of making the compounds OCH and —CH2—O—Si(CH). described herein. A “cyano' group refers to a CN group. Methods An "isocyanato' group refers to a NCO group. 15 Provided herein are methods for treating CNS disorders A “thiocyanato' group refers to a CNS group. comprising administration of a therapeutically effective An “isothiocyanato' group refers to a NCS group. amount of a p21-activated kinase inhibitor (e.g., a compound Alkoyloxy' refers to a RC(=O)C)—group. of Formula I-XV) to an individual in need thereof. In some Alkoyl” refers to a RC(=O)—group. embodiments of the methods provided herein, administration Synthesis of Compounds 20 of a p21-activated kinase inhibitor alleviates or reverses one In some embodiments, compounds of Formula I, II, III, IV. or more behavioral symptoms (e.g., Social withdrawal, dep V. Va, or Vb are synthesized according to procedures ersonalization, loss of appetite, loss of hygiene, delusions, described in Scheme 1 and in the Examples section. hallucinations, depression, blunted affect, avolition, anhe

Scheme 1 N1 N1 n N1 N1 N Br Ns CC4. N O - NsUCCC 4. N O

I II Br N1 N1 n -e- 2 V Ns N O CCC4. O Q O Q III IV R3 R3

N N N Br (R')s N N N (R), (R),5 2 - V - (R),ps 2 N N N O N N N O H H Q Q VI DX

OH

N1 N1 N1 no R (R)-G) l 2 3 NH N N O Br () Q (R), VII

Generally, compounds of Formula IX described herein are 65 donia, alogia, the sense of being controlled by outside forces synthesized by conversion of (methylthio)-pyridopyrimidi or the like) of the CNS disorder (e.g. negative symptoms of none, I, to its bromo derivative II. Substitution at the NH of Schizophrenia). In some embodiments of the methods pro US 8,372,970 B2 159 160 vided herein, administration of a p21-activated kinase inhibi term depression (LTD) in the temporal lobe, parietal lobe, the tor (e.g., a compound of Formula I-XV) alleviates or reverses frontal cortex, the cingulate gyrus, the prefrontal cortex, the one or more negative symptoms and/or cognition impairment cortex, or the hippocampus or any other region in the brain or associated with a CNS disorder (e.g., impairment in executive a combination thereof. function, comprehension, inference, decision-making, plan In some embodiments of the methods described herein, ning, learning or memory associated with Schizophrenia, administration of a PAK inhibitor reverses defects in synaptic Alzheimer's disease, FXS, autism or the like). function (i.e. synaptic transmission and/or synaptic plasticity, Also provided herein are methods for modulation of den induced by soluble Abeta dimers or oligomers. In some dritic spine morphology and/or synaptic function comprising embodiments of the methods described herein, administra administering to an individual in need thereof (e.g., an indi 10 vidual Suffering from or Suspected of having schizophrenia, tion of a PAK inhibitor reverses defects in synaptic function Parkinson's disease, Alzheimer's disease, epilepsy or the (i.e. synaptic transmission and/or synaptic plasticity, induced like) a therapeutically effective amount of a PAK inhibitor by insoluble Abeta oligomers and/or Abeta-containing (e.g., a compound of Formula I-XV). In some embodiments, plaques. modulation of dendritic spine morphology and/or synaptic 15 Provided herein are methods for stabilization of synaptic functionalleviates or reverses negative symptoms and/or cog plasticity comprising administering to an individual in need nitive impairment associated with a CNS disorder. In some thereof (e.g., an individual Suffering from or Suspected of embodiments, modulation of dendritic spine morphology having a CNS disorder) a therapeutically effective amount of and/or synaptic function halts or delays further deterioration a PAK inhibitor (e.g., a compound of Formula I-XV). In some of symptoms associated with a CNS disorder (e.g., progres embodiments of the methods described herein, administra sion of cognitive impairments and/or loss of bodily func tion of a PAK inhibitor stabilizes LTP or LTD following tions). In some embodiments, modulation of dendritic spine induction (e.g., by theta-burst stimulation, high-frequency morphology and/or synaptic function stabilizes or reverses stimulation for LTP. low-frequency (e.g., 1 Hz) stimulation symptoms of disease (e.g., reduces frequency of epileptic for LTD). seizures, stabilizes mild cognitive impairment and prevents 25 Provided herein are methods for stabilization of synaptic progression to early dementia). In some embodiments of the transmission comprising administering to an individual in methods provided herein, administration of a p21-activated need thereof (e.g., an individual Suffering from or Suspected kinase inhibitor halts or delays progressive loss of memory of having a CNS disorder) a therapeutically effective amount and/or cognition associated with a CNS disorder (e.g., Alzhe of a PAK inhibitor (e.g., a compound of Formula I-XV). In imer's disease). 30 some embodiments of the methods described herein, admin Provided herein are methods for modulation of synaptic istration of a PAK inhibitor stabilizes LTP or LTD following function or synaptic plasticity comprising administering to an induction (e.g., by theta-burst stimulation, high-frequency individual in need thereof (e.g., an individual Suffering from stimulation for LTP. low-frequency (e.g., 1 Hz) stimulation or suspected of having any CNS disorder described herein) a for LTD). therapeutically effective amount of a PAK inhibitor (e.g., a 35 Also provided herein are methods for alleviation or rever compound of Formula I-XV). Modulation of synaptic func sal of cortical hypofrontality during performance of a cogni tion or plasticity includes, for example, alleviation or reversal tive task comprising administering to an individual in need of defects in LTP LTD or the like. thereof (e.g., an individual Suffering from or Suspected of Defects in LTP include, for example, an increase in LTP or having a CNS disorder) a therapeutically effective amount of a decrease in LTP in any region of the brain in an individual 40 a PAK inhibitor (e.g., a compound of Formula I-XV). In some suffering from or suspected of having a CNS disorder. embodiments of the methods described herein, administra Defects in LTD include for example a decrease in LTD or an tion of a PAK inhibitor to an individual suffering from or increase in LTD in any region of the brain (e.g., the temporal suspected of having a CNS disorder alleviates deficits in the lobe, parietal lobe, the frontal cortex, the cingulate gyrus, the frontal cortex, for example deficits in frontal cortical activa prefrontal cortex, the cortex, or the hippocampus or any other 45 tion, during the performance of a cognitive task (e.g., a Wis region in the brain or a combination thereof) in an individual consin Card Sort test, Mini-Mental State Examination suffering from or suspected of having a CNS disorder. (MMSE), MATRICS cognitive battery, BACS score, Alzhe In some embodiments of the methods, administration of a imer's disease Assessment Scale-Cognitive Subscale PAK inhibitor (e.g., a compound of Formula I-XV) modu (ADAS-Cog), Alzheimer's disease Assessment Scale-Be lates synaptic function (e.g., synaptic transmission and/or 50 havioral Subscale (ADAS-Behav), Hopkins Verbal Learning plasticity) by increasing long term potentiation (LTP) in an Test-Revised or the like) and improves cognition scores of the individual suffering from or suspected of having a CNS dis individual. order. In some embodiments of the methods described herein, Provided herein are methods for reversing abnormalities in administration of a PAK inhibitor (e.g., a compound of For dendritic spine morphology or synaptic function that are mula I-XV) to an individual in need thereof modulates syn 55 caused by mutations in high-risk genes (e.g. mutations in aptic function (e.g., synaptic transmission and/or plasticity) Amyloid Precursor Protein (APP), mutations in presenilin 1 by increasing long term potentiation (LTP) in the prefrontal and 2, the epsilon4 allele, the 91 bp allele in the telomeric cortex, or the cortex, or the hippocampus or any other region region of 12q, Apollipoprotein E-4 (APOE4) gene, SORL1 in the brain or a combination thereof. In some embodiments gene, reelin gene, DISC1 gene, or any other high-risk allele) of the methods described herein, administration of a PAK 60 comprising administering to an individual in need thereof a inhibitor modulates synaptic function (e.g., synaptic trans therapeutically effective amount of a PAK inhibitor (e.g., a mission and/or plasticity) by decreasing long term depression compound of Formula I-XV). In some embodiments of the (LTD) in an individual suffering from or suspected of having methods described herein, prophylactic administration of a a CNS disorder. In some embodiments of the methods PAK inhibitor to an individual at a high risk for developing a described herein, administration of a PAK inhibitor to an 65 CNS disorder (e.g., a mutation in a DISC1 gene pre-disposes individual in need thereof modulates synaptic function (e.g., the individual to schizophrenia, a mutation in an APOE4 gene synaptic transmission and/or plasticity) by decreasing long pre-disposes the individual to Alzheimer's disease) reverses US 8,372,970 B2 161 162 abnormalities in dendritic spine morphology and/or synaptic individual suffering from or suspected of having a CNS dis function and prevents development of the CNS disorder. order (e.g., Alzheimer's disease, Parkinson's disease or the Provided herein are methods for stabilizing, reducing or like) stabilizes, alleviates or reverses neuronal withering and/ reversing abnormalities in dendritic spine morphology or or atrophy and/or degeneration in the temporal lobe, parietal synaptic function that are caused by increased activation of 5 lobe, the frontal cortex, the cingulate gyms or the like. In PAK at the synapse, comprising administration of a therapeu some embodiments of the methods described herein, admin tically effective amount of a PAK inhibitor (e.g., a compound istration of a PAK inhibitor to an individual suffering from or of Formula I-XV) to an individual in need thereof (e.g., an suspected of having a CNS disorder stabilizes, reduces or individual suffering from or suspected of having a CNS dis reverses deficits in memory and/or cognition and/or control of order). In some embodiments of the methods described 10 bodily functions. herein, increased activation of PAK at the synapse is caused In some instances, a CNS disorder is associated with a by Abeta. In some instances, increased activation of PAK at decrease in dendritic spine density. In some embodiments of the synapse is caused by redistribution of PAK from the the methods described herein, administration of a PAK cytosol to the synapse. In some embodiments of the methods inhibitor increases dendritic spine density. In some instances, described herein, administration ofatherapeutically effective 15 a CNS disorder is associated with an increase in dendritic amount of a PAK inhibitor (e.g., a compound of Formula spine length. In some embodiments of the methods described I-XV) to an individual in need thereof (e.g., an individual herein, administration of a PAK inhibitor decreases dendritic suffering from or suspected of having a CNS disorder) spine length. In some instances, a CNS disorder is associated reduces or prevents redistribution of PAK from the cytosol to with a decrease in dendritic spine neck diameter. In some the synapse in neurons, thereby stabilizing, reducing or embodiments of the methods described herein, administra reversing abnormalities in dendritic spine morphology or tion of a PAK inhibitor increases dendritic spine neck diam synaptic function that are caused by increased activation of eter. In some instances, a CNS disorder is associated with a PAK at the synapse. decrease in dendritic spine head diameter and/or dendritic Provided herein are methods for delaying the onset of a spine head Surface area and/or dendritic spine head volume. CNS disorder comprising administering to an individual in 25 In some embodiments of the methods described herein, need thereof (e.g., an individual with a high-risk allele for a administration of a PAK inhibitor increases dendritic spine NC) a therapeutically effective amount of a PAK inhibitor head diameter and/or dendritic spine head volume and/or (e.g., a compound of Formula I-XV). Provided herein are dendritic spine head Surface area. methods for delaying the loss of dendritic spine density com In some instances, a CNS disorder is associated with an prising administering to an individual in need thereof (e.g., an 30 increase in immature spines and a decrease in mature spines. individual with a high-risk allele for a CNS disorder) a thera In some embodiments of the methods described herein, peutically effective amount of a PAK inhibitor. Provided administration of a PAK inhibitor modulates the ratio of herein are methods for modulation of spine density, shape, immature spines to mature spines. In some instances, a CNS spine length, spine head volume, or spine neck diameter or the disorder is associated with an increase in Stubby spines and a like comprising administering to an individual in need thereof 35 decrease in mushroom-shaped spines. In some embodiments (e.g., an individual Suffering from or Suspected of having a of the methods described herein, administration of a PAK CNS disorder) a therapeutically effective amount of a PAK inhibitor modulates the ratio of stubby spines to mushroom inhibitor (e.g., a compound of Formula I-XV). Provided shaped spines. herein are methods of modulating the ratio of mature den In some embodiments of the methods described herein, dritic spines to immature dendritic spines comprising admin 40 administration of a PAK inhibitor modulates a spine:head istering to an individual in need thereof (e.g., an individual ratio, e.g., ratio of the volume of the spine to the volume of the suffering from or suspected of having a CNS disorder) a head, ratio of the length of a spine to the head diameter of the therapeutically effective amount of a PAK inhibitor. Provided spine, ratio of the Surface area of a spine to the Surface area of herein are methods of modulating the ratio of dendritic spines the head of a spine, or the like, compared to a spine:head ratio head volume to dendritic spines length comprising adminis 45 in the absence of a PAK inhibitor. In certain embodiments, a tering to an individual in need thereof (e.g., an individual PAK inhibitor suitable for the methods described herein suffering from or suspected of having a CNS disorder) a modulates the volume of the spine head, the width of the spine therapeutically effective amount of a PAK inhibitor (e.g., a head, the Surface area of the spinehead, the length of the spine compound of Formula I-XV). shaft, the diameter of the spine shaft, or a combination In some embodiments of the methods described herein, 50 thereof. In some embodiments, provided herein is a method of administration of a PAK inhibitor (e.g., a maintenance dose of modulating the Volume of a spine head, the width of a spine a PAK inhibitor) reduces the incidence of recurrence of one or head, the Surface area of a spine head, the length of a spine more symptoms or pathologies in an individual (e.g., recur shaft, the diameter of a spine shaft, or a combination thereof, rence of psychotic episodes, epileptic seizures or the like). In by contacting a neuron comprising the dendritic spine with an some embodiments of the methods described herein, admin 55 effective amount of a PAK inhibitor described herein. In istration of a PAK inhibitor causes substantially complete specific embodiments, the neuron is contacted with the PAK inhibition of PAK and restores dendritic spine morphology inhibitor in vivo. and/or synaptic function to normal levels. In some embodi Also described herein are methods for treating cancer in a ments of the methods described herein, administration of a Subject comprising administering to a Subject in need thereof PAK inhibitor causes partial inhibition of PAK and restores 60 atherapeutically effective amount of a compound of Formula dendritic spine morphology and/or synaptic function to nor I-XV. As used herein, "cancer includes any malignant mal levels. growth or tumor caused by abnormal and uncontrolled cell Provided herein are methods for stabilizing, reducing or division. Examples of cancers include pancreatic cancer, gas reversing neuronal withering and/or atrophy or nervous tissue trointestinal Stromal tumors, lung cancer, stomach cancer, and/or degeneration of nervous tissue that is associated with 65 brain cancer, kidney cancer, breast cancer, head and neck a CNS disorder. In some embodiments of the methods cancer, myeloma, leukemia, lymphoma, adenocarcinoma, described herein, administration of a PAK inhibitor to an melanoma or the like. US 8,372,970 B2 163 164 In one embodiment is a method for treating cancer in a used to detect brain morphological changes in individuals Subject comprising administering to a Subject in need thereof prior to the onset of disease (see, e.g., Toga etal (2006), TINS, a therapeutically effective amount of a compound of Formula 29(3): 148-159). For example, in some instances, the typical I wherein the cancer is selected from ovarian, breast, colon, age of onset for schizophrenia is post-puberty. In some brain, neurofibromatosis, CML, renal cell carcinoma, gastric, instances, the typical age of onset for Schizophrenia is leukemia, NSCLC, CNS, melanoma, prostate, T-cell lym between 20-28 for males and 26-32 for females. For example, phoma, heptocellular, bladder and glioblastoma. In one in some instances, a typical age of onset for Alzheimer's embodiment, the breast cancer is tamoxifen-resistant or intol disease is about 55-80 years. Accordingly, in some embodi erant breast cancer. In another embodiment, the CML is ima ments, a PAK inhibitor is administered prophylactically to an tinib resistant or intolerant CML. 10 individual at risk between about 1 to about 10 years, e.g., 1, 2, In one embodiment, is a method for modulating a p21 3, 4, 5, 6, 7, 8, 9, or 10 years prior to an established and/or activated kinase comprising contacting a compound of For typical age range of onset for a CNS disorder. mula I-XV with a p21 activated kinase such that PAK expres In prophylactic applications, compounds or compositions sion or activation has been altered. PAK kinases have been containing compounds described herein are administered to identified as key regulators of cancer-cell signaling networks 15 an individual susceptible to or otherwise at risk of a particular where they regulate essential biological processes. These pro disease, disorder or condition. In certain embodiments of this cesses include cytoskeletal dynamics, energy homeostasis, use, the precise amounts of compound administered depend cell Survival, differentiation, anchorage-independent growth, on an individual’s state of health, weight, and the like. Fur mitosis, and hormone dependence. Dysregulation of these thermore, in Some instances, when a compound or composi processes by alterations in PAK expression or activation have tion described herein is administered to an individual, effec been reported in numerous human cancers. See, e.g., Kumar tive amounts for this use depend on the severity and course of R. Gururaj A E, Barnes C J, p21-activated kinases in cancer, the disease, disorder or condition, previous therapy, an indi Nat Rev Cancer, 2006; 6: 459-471, which is incorporated by viduals health status and response to the drugs, and the reference herein to the extent it is relevant. judgment of the treating physician. In another embodiment is a method for treating cancer in a 25 In certain instances, wherein following administration of a Subject comprising administering to a Subject in need thereof selected dose of a compound or composition described a therapeutically effective amount of a compound of Formula herein, an individual’s condition does not improve, upon the I-XV wherein the cancer is selected from pancreatic cancer, doctor's discretion the administration of a compound or com gastrointestinal stromal tumors, lung cancer, stomach cancer, position described herein is optionally administered chroni brain cancer, kidney cancer, breast cancer, head and neck 30 cally, that is, for an extended period of time, including cancer, myeloma, leukemia, lymphoma, adenocarcinoma, throughout the duration of an individuals life in order to bone cancer, cutaneous or intraocular melanoma, uterine can ameliorate or otherwise control or limit the symptoms of an cer, ovarian cancer, rectal cancer, cancer of the anal region, individual’s disorder, disease or condition. stomach cancer, colon cancer, carcinoma of the fallopian In certain embodiments, an effective amount of a given tubes, carcinoma of the endometrium, carcinoma of the cer 35 agent varies depending upon one or more of a number of vix, carcinoma of the vagina, carcinoma of the Vulva, factors such as the particular compound, disease or condition Hodgkin’s Disease, cancer of the esophagus, cancer of the and its severity, the identity (e.g., weight) of an individual or Small intestine, cancer of the endocrine system, cancer of the host in need of treatment, and is determined according to the thyroid gland, cancer of the parathyroid gland, cancer of the particular circumstances Surrounding the case, including, adrenal gland, sarcoma of Soft tissue, cancer of the urethra, 40 e.g., the specific agent being administered, the route of cancer of the penis, prostate cancer, lymphocytic lymphomas, administration, the condition being treated, and an individual cancer of the bladder, renal cell carcinoma, carcinoma of the or host being treated. In some embodiments, doses adminis renal pelvis, neoplasms of the central nervous system (CNS), tered include those up to the maximum tolerable dose. In primary CNS lymphoma, spinal axis tumors, brain stem certain embodiments, about 0.02 to about 5000 mg per day, glioma, pituitary adenoma, or a combination of one or more 45 from about 1 to about 1500 mg per day, about 1 to about 100 of the foregoing cancers. mg/day, about 1 to about 50 mg/day, or about 1 to about 30 In certain embodiments, a compound or a composition mg/day, or about 5 to about 25 mg/day of a compound comprising a compound described herein is administered for described herein is administered. In various embodiments, prophylactic and/or therapeutic treatments. In therapeutic the desired dose is conveniently be presented in a single dose applications, the compositions are administered to an indi 50 or in divided doses administered simultaneously (or over a vidual already Suffering from a disease or condition, in an short period of time) or at appropriate intervals, for example amount Sufficient to cure or at least partially arrest the Symp as two, three, four or more Sub-doses per day. toms of the disease or condition. In various instances, In certain instances, there are a large number of variables in amounts effective for this use depend on the severity and regard to an individual treatment regime, and considerable course of the disease or condition, previous therapy, an indi 55 excursions from these recommended values are considered vidual’s health status, weight, and response to the drugs, and within the scope described herein. Dosages described herein the judgment of the treating physician. are optionally altered depending on a number of variables In some embodiments, a composition containing a thera Such as, by way of non-limiting example, the activity of the peutically effective amount of a PAK inhibitor is adminis compound used, the disease or condition to be treated, the tered prophylactically to an individual that while not overtly 60 mode of administration, the requirements of an individual, the manifesting symptoms of a CNS disorder has been identified severity of the disease or condition being treated, and the as having a high risk of developing a CNS disorder, e.g., an judgment of the practitioner. individual is identified as being a carrier of a mutation or Toxicity and therapeutic efficacy of Such therapeutic regi polymorphism associated with a higher risk to develop a CNS mens are optionally determined by pharmaceutical proce disorder (see, e.g., Hall et al (2006), Nat Neurosci., 9(12): 65 dures in cell cultures or experimental animals, including, but 1477-8), or an individual that is from a family that has a high not limited to, the determination of the LDs (the dose lethal incidence of CNS disorders. In some embodiments, MRI is to 50% of the population) and the EDs (the dose therapeuti US 8,372,970 B2 165 166 cally effective in 50% of the population). The dose ratio liver enzyme that degrades the PAK inhibitor) thereby between the toxic and therapeutic effects is the therapeutic increasing efficacy of a PAK inhibitor. In some embodiments, index and it can be expressed as the ratio between LDso and administration of a combination of a PAK inhibitor and a EDso. Compounds exhibiting high therapeutic indices are second therapeutic agent (e.g. a second agent that modulates preferred. In certain embodiments, data obtained from cell dendritic spine morphology (e.g., minocyline)) improves the culture assays and animal studies are used in formulating a therapeutic index of a PAK inhibitor. range of dosage for use in human. In specific embodiments, Agents for Treating Psychotic Disorders the dosage of compounds described herein lies within a range Where a subject is suffering from or at risk of suffering of circulating concentrations that include the EDs with mini from a psychotic disorder (e.g., Schizophrenia), a PAK inhibi mal toxicity. The dosage optionally varies within this range 10 depending upon the dosage form employed and the route of tor composition described herein is optionally used together administration utilized. with one or more agents or methods for treating a psychotic Combination Therapy disorder in any combination. Alternatively, a PAK inhibitor In some embodiments, one or more PAK inhibitors are composition described herein is administered to a patient who used in combination with one or more other therapeutic 15 has been prescribed an agent for treating a psychotic disorder. agents to treat an individual suffering from a CNS disorder. In some embodiments, administration of a PAK inhibitor in The combination of PAK inhibitors with a second therapeutic combination with an antipsychotic agent has a synergistic agent (e.g., a typical or atypical antipsychotic agent, an effect and provides an improved therapeutic outcome com mGluR1 antagonist, an mGluR5 antagonist, an mGluR5 pared to monotherapy with antipsychotic agent or mono potentiator, a mGluR2 agonist, an alpha7 nicotinic receptor therapy with PAK inhibitor. Alternatively, a PAK inhibitor agonist or potentiator, an antioxidant, a neuroprotectant, a composition described herein is administered to a patient who trophic factor, an anticholinergic, a beta-secretase inhibitor or is non-responsive to, or being unsatisfactorily treated with an the like) allows a reduced dose of both agents to be used antipsychotic agent. thereby reducing the likelihood ofside effects associated with In some embodiments, a PAK inhibitor composition higher dose monotherapies. In one embodiment, the dose of a 25 described herein is administered in combination with an second active agent is reduced in the combination therapy by antipsychotic having 5-HT2A antagonist activity. In some at least 50% relative to the corresponding monotherapy dose, embodiments, a PAK inhibitor composition described herein whereas the PAK inhibitor dose is not reduced relative to the is administered in combination with a selective 5-HT2A monotherapy dose; in further embodiments, the reduction in antagonist. dose of a second active agent is at least 75%; in yet a further 30 Examples of therapeutic agents/treatments for treating a embodiment, the reduction in dose of a second active agent is at least 90%. In some embodiments, the second therapeutic psychotic disorder include, but are not limited to, any of the agent is administered at the same dose as a monotherapy dose, following: typical antipsychotics, e.g., Chlorpromazine (Lar and the addition of a PAK inhibitor to the treatment regimen gactil, Thorazine), Fluphenazine (Prolixin), Haloperidol alleviates symptoms of a CNS disorder that are not treated by 35 (Haldol, Serenace), Molindone. Thiothixene (Navane), monotherapy with the second therapeutic agent. Symptoms Thioridazine (Mellaril), Trifluoperazine (Stelazine), Loxap and diagnostic criteria for all of the conditions mentioned ine, Perphenazine, Prochlorperazine (Compazine, Bucca above are described in detail in the Diagnostic and Statistical stem, Stemetil), Pimozide (Orap), Zuclopenthixol; and atypi Manual of Mental Disorders, fourth edition, American Psy cal antipsychotics, e.g., LY2140023, Clozapine, Risperidone, chiatric Association (2005) (DSM-IV). 40 Olanzapine, Quetiapine, Ziprasidone, Aripiprazole, Paliperi In some embodiments, the combination of a PAK inhibitor done, Asenapine, Iloperidone, Sertindole, Zotepine, Amisul and a second therapeutic agent is synergistic (e.g., the effect pride, Bifeprunox, and Melperone. of the combination is better than the effect of each agent Agents for Treating Mood Disorders alone). In some embodiments, the combination of a PAK Where a subject is suffering from or at risk of suffering inhibitor and a second therapeutic agent is additive (e.g., the 45 from a mood disorder (e.g., clinical depression), a PAK effect of the combination of active agents is about the same as inhibitor composition described herein is optionally used the effect of each agent alone). In some embodiments, an together with one or more agents or methods for treating a additive effect is due to the PAK inhibitor and the second mood disorder in any combination. Alternatively, a PAK therapeutic agent modulating the same regulatory pathway. In inhibitor composition described herein is administered to a some embodiments, an additive effect is due to the PAK 50 patient who has been prescribed an agent for treating a mood inhibitor and the second therapeutic agent modulating differ disorder. Alternatively, a PAK inhibitor composition ent regulatory pathways. In some embodiments, an additive described herein is administered to a patient who is non effect is due to the PAK inhibitor and the second therapeutic responsive to or being unsatisfactorily treated with an agent agent treating different symptom groups of the CNS disorder for treating a mood disorder. (e.g., a PAK inhibitor treats negative symptoms and the sec 55 Examples of therapeutic agents/treatments for treating a ond therapeutic agent treats positive symptoms of Schizo mood disorder include, but are not limited to, any of the phrenia). In some embodiments, administration of a second following: selective serotonin reuptake inhibitors (SSRIs) therapeutic agent treats the remainder of the same or different Such as citalopram (Celexa), escitalopram (Lexapro, symptoms or groups of symptoms that are not treated by Esipram), fluoxetine (Prozac), paroxetine (Paxil, Seroxat), administration of a PAK inhibitor alone. 60 Sertraline (Zoloft), fluvoxamine (Luvox); serotonin-norepi In some embodiments, administration of a combination of nephrine reuptake inhibitors (SNRIs) such as Venlafaxine a PAK inhibitor and a second therapeutic agentalleviates side (Effexor), desvenlafaxine, nefazodone, milnacipran, dulox effects that are caused by the second therapeutic agent (e.g., etine (Cymbalta), bicifadine; tricyclic antidepressants such as side effects caused by an antipsychotic agent or a nootropic amitriptyline, amoxapine, butriptyline, clomipramine, agent). In some embodiments, administration of the second 65 desipramine, do Sulepin, doxepin, impramine, lofepramine, therapeutic agent inhibits metabolism of an administered nortriptyline; monoamine oxidase inhibitors (MAOIs) such PAK inhibitor (e.g., the second therapeutic agent blocks a as isocarboxazid, lineZolid, moclobemide, nialamide, US 8,372,970 B2 167 168 phenelZine, selegiline, tranylcypromine, trimipramine; and mGluRantagonists allows a reduced dose of both agents to be other agents such as mirtazapine, reboxetine, Viloxazine, mal used thereby reducing the likelihood ofside effects associated protiline, and bupropion. with higher dose monotherapies. Agents for Treating Epilepsy In some embodiments, reduction of signaling from a Group Where a subject is suffering from or at risk of suffering I mGluR (mGluR5) in vivo by genetic engineering (using from epilepsy, a PAK inhibitor composition described herein mGluR5 knock-out heterozygote animals) leads to a reversal is optionally used together with one or more agents or meth of the dendritic spine and behavioral defects. In some ods for treating epilepsy in any combination. Alternatively, a instances, where an individual is suffering from or at risk of PAK inhibitor composition described herein is administered suffering from a CNS disorder, a PAK inhibitor composition to a patient who has been prescribed an agent for treating 10 described herein is optionally used together with one or epilepsy. Alternatively, a PAK inhibitor composition Group I mGluR antagonists. Group I mGluR antagonists described herein is administered to a patient who is refractory include antagonists that are mGluR1-selective antagonists, to or being unsatisfactorily treated with an agent for treating mGluR5-selective antagonists, orantagonists that antagonize epilepsy. both mGluR1 and mGluR5. In some embodiments, a PAK Examples of therapeutic agents/treatments for treating epi 15 inhibitor composition is used in combination with an lepsy include, but are not limited to, any of the following: mGluR5-selective antagonist. In some embodiments, a PAK carbamazepine, clobazam, clonazepam, ethoSuximide, fel inhibitor composition is used in combination with an bamate, fosphenyloin, gabapentin, lamotrigine, levetirac mGluR1-selective antagonist. In some embodiments, a PAK etam, oXcarbazepine, phenobarbital, phenyloin, pregabalin, inhibitor composition is used in combination with a Group I primidone, sodium valproate, tiagabine, topiramate, val mGluR antagonist that antagonizes both mGluR1 and proate semisodium, Valproic acid, vigabatrin, and Zonisa mGluR5 (i.e., an antagonist that is not selective for mGluR1 mide. or mGluR5). As used herein, the term “selective antagonist' Agents for Treating Huntington's Disease indicates that the antagonist has an EDs for antagonizing a Where a subject is suffering from or at risk of suffering first receptor (e.g., mGluR5) that is at least about 10 fold to from Huntington's disease, a PAK inhibitor composition 25 about 1000 fold lower, e.g., 11, 20, 30, 40, 50, 100, 105,125, described herein is optionally used together with one or more 135, 150, 200,300,400, 500, 600, 700, 800,900, or any other agents or methods for treating Huntington's disease in any fold lower from about 10 fold to about 1000 fold lower than combination. Alternatively, a PAK inhibitor composition the EDso for antagonism of a second receptor (e.g., mGluR1). described herein is administered to a patient who has been Examples of Group I mGluRantagonists include, but are prescribed an agent for treating Huntington's disease. Alter 30 not limited to, any of the following (E)-6-methyl-2-styryl natively, a PAK inhibitor composition described herein is pyridine (SIB 1893), 6-methyl-2-(phenylazo)-3-pyridinol, . administered to a patient who is refractory to or being unsat alpha.-methyl-4-carboxyphenylglycine (MCPG), or 2-me isfactorily treated with an agent for treating Huntington's thyl-6-(phenylethynyl)pyridine (MPEP). Examples of Group disease. I mGluR antagonists also include those described in, e.g., Examples of therapeutic agents/treatments for treating 35 U.S. patent application Ser. Nos. 10/076,618; 10/211,523; Huntington's disease include, but are not limited to, any of the and 10/766,948. Examples of mGluR5-selective antagonists following: omega-3 fatty acids, miraxion, Haloperidol. include, but are not limited to those described in, e.g., U.S. dopamine receptor blockers, creatine, cystamine, cysteam Pat. No. 7,205,411 and U.S. patent application Ser. No. ine, clonazepam, clozapine, Coenzyme Q10, minocycline, 1 1/523,873. Examples of mGluR1-selective antagonists antioxidants, antidepressants (notably, but not exclusively, 40 include, but are not limited to, those described in, e.g., U.S. selective serotonin reuptake inhibitors SSRIs, such assertra Pat. No. 6,482,824. line, fluoxetine, and paroxetine), select dopamine antago In some embodiments, the mGluR Group I antagonist is nists. Such as tetrabenazine; and RNAi knockdown of mutant AIDA (1-aminoindan-1,5-dicarboxylic acid); ACDPP huntingtin (mHtt). (3-Amino-6-chloro-5-dimethylamino-N-2-pyridinylpyrazi Agents for Treating Parkinson's Disease 45 necarboxamide hydrochloride; DL-AP3 (DL-2-Amino-3- Where a subject is suffering from or at risk of suffering phosphonopropionic acid); BAY-36-7620 ((3aS,6aS)- from Parkinson's Disease, a PAK inhibitor composition Hexahydro-5-methylene-6a-(2-naphthalenylmethyl)-1H described herein is optionally used together with one or more cyclopentacfuran-1-one): Fenobam; 4 CPG ((S)-4- agents or methods for treating Parkinson's disease in any carboxyphenylglycine): (S)-4C3HPG ((S)-4-carboxy-3- combination. Alternatively, a PAK inhibitor composition 50 hydroxyphenylglycine); CPCCOEt described herein is administered to a patient who has been (7-hydroxyiminocyclopropanbchromen-la-carboxylic prescribed an agent for treating Parkinson's disease. Alterna acid ethyl ester); LY367385 (S)-(+)-a-Amino-4-carboxy-2- tively, a PAK inhibitor composition described herein is methylbenzeneacetic acid); LY 456236 hydrochloride administered to a patient who is refractory to or being unsat (6-methoxy-N-(4-methoxyphenyl)cquinazolin-4-amine, isfactorily treated with an agent for treating Parkinson's dis 55 MPMQ hydrochloride); 3-MATIDA (a-Amino-5-carboxy-3- CaSC. methyl-2-thiopheneacetic acid); MCPG (C.-methyl-4-car Examples of therapeutic agents/treatments for treating Par boxyphenylglycine); MPEP (2-methyl-6-(phenylethynyl)- kinson's Disease include, but are not limited to any of the pyridine); (MTEP) 3-(2-methyl-1,3-thiazol-4-yl)ethynyl following: L-dopa, carbidopa, benserazide, tolcapone, enta pyridine; PHCCC(N-Phenyl-7-(hydroxyimino)cyclopropa capone, bromocriptine, pergolide, pramipexole, ropinirole, 60 bchromen-1a-carbox amide: SIB 1757 (6-Methyl-2- cabergoline, apomorphine, lisuride, selegiline, or rasagiline. (phenylazo)-3-pyridinol; SIB 1893 (2-Methyl-6-(2- Group I mGluR Antagonists phenylethenyl)pyridine: YM 2.98198 hydrochloride In some embodiments, one or more PAK inhibitors are (6-Amino-N-cyclohexyl-N,3-dimethylthiazolo 3.2-abenz used in combination with one or more Group I metabotropic imidazole-2-carboxamidehydrochloride); (YM-193167 glutamate receptor (mGluR) antagonists (e.g., mGluR5 65 (6-amino-N-cyclohexyl-N,3-dimethylthiazolo 3.2-abenz antagonists) to treat an individual suffering from a CNS dis imidazole-2-carboxamide); (NPS 2390 (Quinoxaline-2-car order. The combination of PAK inhibitors with Group I boxylic acid adamantan-1-ylamide); 3-(5-(pyridin-2-yl)-2H US 8,372,970 B2 169 170 tetrazol-2-yl)benzonitrile, 3-3-fluoro-5-(5-pyridin-2-yl-2H 4-dicarboxyphenylglycine); (RS)-4-phosphonophenylgly tetrazol-2-yl)phenyl-4-methylpyridine; 3-fluoro-5-(5- cine ((RS)PPG); AMN082 (N'-bis(diphenylmethyl)-1,2- pyridin-2-yl-2H-tetrazol-2-yl)benzonitrile; N-cyclohexyl-6- ethanediamine dihydrochloride); DCG-IV ((2S,2R,3R)-2- {(2-methoxyethyl)(methyl)aminomethyl-N- (2',3'-dicarboxycyclopropyl)glycine) or the like. In some methylthiazolo 3.2-abenzimidazole-2-carboxamide (YM embodiments, an mGluR1 agonist is AMN082. In some 202074): Desmethyl-YM298198 (6-Amino-N-cyclohexyl embodiments, a second therapeutic agent is a mGluR2/3 ago 3-methylthiazolo 3.2-abenzimidazole-2-carboxamide nist or mGluR2/3 potentiator. Examples of mGluR2/3 ago hydrochloride); MPEP hydrochloride (2-Methyl-6-(phenyl nists include and are not limited to LY389795 ((-)-2-thia-4- ethynyl)pyridine hydrochloride); (S)-MCPG ((S)-a-Methyl aminobicyclo-hexane-4,6-dicarboxylate); LY379268 ((-)-2- 4-carboxyphenylglycine); (RS)-MCPG ((RS)-a-Methyl-4- 10 oxa-4-aminobicyclo-hexane-4,6-dicarboxylate); LY354740 carboxyphenylglycine); E4CPG ((RS)-a-Ethyl-4- ((+)-2-aminobicyclo-hexane-2,6dicarboxylate); DCG-IV carboxyphenylglycine); Hexylhomoibotenic acid (a-Amino ((2S,2R,3R)-2-(2',3'-dicarboxycyclopropyl)glycine); 4-hexyl-2,3-dihydro-3-oxo-5-isoxazolepropanoic acid; 2R4R-APDC (2R,4R-4-aminopyrrolidine-2,4-dicarboxy HexylHIBO): (S)-Hexylhomoibotenic acid ((S)-a-Amino-4- late), (S)-3C4HPG ((S)-3-carboxy-4-hydroxyphenylgly hexyl-2,3-dihydro-3-oxo-5-isoxazolepropanoic acid: (S)- 15 cine): (S)-4C3HPG ((S)-4-carboxy-3-hydroxyphenylgly HexylHIBO); EMQMCM (3-ethyl-2-methyl-quinolin-6-yl)- cine); L-CCG-I ((2S,1'S,2S)-2-(carboxycyclopropyl) (4-methoxy-cyclohexyl)-methanone methanesulfonate); JNJ glycine); and/or combinations thereof. Examples of mGluR2 16259685; R214127 (1-(3,4-dihydro-2H-pyrano 2,3-b agonists or mGluR2 potentiators include and are not limited quinolin-7-yl)-2-phenyl-1-ethanone): (S)-3-Carboxy-4-hy to positive allosteric modulators of mGluR2, including droxyphenylglycine (S)-3C4HPG); Anti-mClu5 blocking ADX71149 (Addex Partner). Examples of mGluR5 agonists peptide (K-SSPKYDTLIIRDYTQSSSSL); DFB (3,3'-Dif or mGluR5 potentiators include and are not limited to MPEP. luorobenzaldazine); DMeOB ((3-Methoxyphenyl)methyl (RS)-2-chloro-5-hydroxyphenylglycine (CHPG), 1S,3R-1- enehydrazone-3-methoxybenzaldehyde); Anti-mClus amino-1,3-cyclopentanedicarboxylate (ACPD) or the like. ((K-SSPKYDTLIIRDYTQSSSSL); reluzole; or combina Apha7 Nicotinic Receptor Modulators tions thereof. 25 In some embodiments, one or more PAK inhibitors are In some embodiments, the modulator of a Group I mGluR used in combination with one or more alpha7 nicotinic recep is S-(4-Fluorophenyl)-3-3-(4-fluoro-phenyl)-1,2,4-oxa tor modulators to treat an individual suffering from a CNS diazol-5-yl)-piperidin-1-yl)-methanone (ADX47273) (Posi disorder. Alpha7 nicotinic receptor modulators include tive allosteric modulator): 4-1-(2-fluoropyridin-3-yl)-5-me alpha7 nicotinic receptor agonists, alpha7 nicotinic receptor thyl-1H-1,2,3-triazol-4-yl)-N-isopropyl-N-methyl-3,6- 30 antagonists, and/or alpha7 nicotinic receptor modulators dihydropyridine-1 (2H)-carboxamide (FTIDC); 6-(3- positive allosteric potentiators. The combination of PAK methoxy-4-(pyridin-2-yl)phenyl)imidazole.2.1-bithiazole; inhibitors with alpha7 nicotinic receptor modulators allows a 2-(2-methoxy-4-(4-(pyridin-2-yl)oxazol-2-yl)phenyl)aceto reduced dose of both agents to be used thereby reducing the nitrile, 2-(4-(benzodoxazol-2-yl)-2-methoxyphenyl)aceto likelihood of side effects associated with higher dose mono nitrile: 2-(4-(2,3-dihydro-1H-inden-2-ylamino)4a,5,6,7,8, 35 therapies. 8a-hexahydroquinazolin-2-ylthio)ethanol; or combinations Examples of alpha7 nicotinic receptoragonists include and thereof. are not limited to (+)-N-(1-azabicyclo[2.2.2]oct-3-yl)benzo In some embodiments, where a Group I mGluRantagonist bifuran-2-carboxamide, PHA-709829, PNU-282,987, (e.g., an mGluR5 antagonist) is administered in combination A-582941, TC-1698, TC-5619, GTS-21, SSR180711, tro with a PAK inhibitor, the dose of the Group I mGluRantago 40 pisetron or the like. Examples of alpha7 nicotinic receptor nist ranges from about 0.001 mg/kg/day to about 30.0 mg/kg/ antagonists include C-conotoxin, quinolizidine or the like. day, e.g., about 0.005 mg/kg/day, 0.009 mg/kg/day, 0.010 Alpha7 nicotinic receptor allosteric potentiators include mg/kg/day, 0.050 mg/kg/day, 0.20 mg/kg/day, 0.50 mg/kg/ PNU-120596, NS-1738, XY4083, A-867744, EVP-6124 day, 0.75 mg/kg/day, 1.0 mg/kg/day, 2.0 mg/kg/day, 3.5 (Envivo), or the like. mg/kg/day, 4.5 mg/kg/day, 5.0 mg/kg/day, 6.2 mg/kg/day, 6.8 45 Cholinesterase Inhibitors mg/kg/day, 7.0 mg/kg/day, 10.0 mg/kg/day, 15 mg/kg/day, 20 Where a subject is suffering from or at risk of suffering mg/kg/day, 25 mg/kg/day, or any other dose from about 0.001 from Alzheimer's disease, a PAK inhibitor composition mg/kg/day to about 10.0 mg/kg/day, from about 0.001 mg/kg/ described herein is optionally used together with one or more day to about 20.0 mg/kg/day, or from about 0.01 mg/kg/day to agents or methods for treating Alzheimer's disease in any about 20.0 mg/kg/day. 50 combination. In some embodiments, a PAK inhibitor compo In some embodiments, the combination treatment com sition described herein is administered to a patient who has prises administering a combined dosage form that is a phar been prescribed an acetylcholinesterase inhibitor. In some macological composition comprising a therapeutically effec embodiments, administration of a PAK inhibitor in combina tive amount of a PAK inhibitor and a Group I mGluR tion with an acetylcholinesterase inhibitor has a synergistic antagonist (e.g., an mGluR5-selective antagonist) as 55 effect and provides an improved therapeutic outcome com described herein. In some embodiments, the pharmacological pared to monotherapy with acetylcholinesterase inhibitors or composition comprises a PAK inhibitor compound and an monotherapy with PAK inhibitor. Alternatively, a PAK mGluR5-selective antagonist selected from U.S. Pat. No. inhibitor composition described herein is administered to an 7,205,411. individual who is non-responsive to, or being unsatisfactorily mGluRAgonists 60 treated with an acetylcholinesterase inhibitor. Example of In some embodiments, a second therapeutic agent used in acetylcholinesterase inhibitors include donepezil (Aricept), combination with a PAK inhibitor is a Group I mGluR1 galantamine (Razadyne), rivastigmine (Exelon and Exelon agonist. Examples of mGluR1 agonists and/or mGluR1 Patch). potentiators include and are not limited to ACPT-I ((1S,3R, Muscarinic Modulators 4S)-1-aminocyclopentane-1,3,4-tricarboxylic acid); L-AP4 65 In some embodiments, a PAK inhibitor composition (L-(+)-2-Amino-4-phosphonobutyric acid): (S)-3,4-DCPG described herein is administered to a patient in combination ((S)-3,4-dicarboxyphenylglycine); (RS)-3,4-DCPG ((RS)-3, with a muscarinic receptor modulator. In some embodiments, US 8,372,970 B2 171 172 the muscarinic receptor modulator is a M1 muscarinic recep Beta-Secretase Inhibitors tor agonist. In some embodiments, the muscarinic receptor Where a subject is suffering from or at risk of suffering modulator is AF102B, AF150(S), AF267B, N-(1-3-(3-oxo from a CNS disorder (e.g., Alzheimer's disease), a PAK 2,3-dihydrobenzo[1,4]oxazin-4-yl)propylpiperidin-4-yl)- inhibitor composition described herein is optionally used together with one or more agents or methods for treating the 2-phenylacetamide, BRL-55473, NXS-292, NXS-267, CNS disorder in any combination. In some embodiments, a MCD-386, AZD-6088, N-Desmethylclozapine or a similar PAK inhibitor composition described herein is administered compound. In some embodiments, the muscarinic receptor to a patient who has been prescribed a beta secretase inhibitor. modulator is a positive allosteric modulator of M1 muscarinic Examples of beta secretase inhibitors useful in the methods receptors. Examples of positive allosteric M1 muscarinic and compositions described herein include and are not lim receptor modulators include, but are not limited to, 10 ited to LY450139, 2-Aminoquinazolines compounds VUO119498, VU0027414, VU0090157, VU0029767, described in J. Med. Chem. 50 (18): 4261-4264, beta secre BQCA, TBPB or 77-LH-28-1. In some embodiments, the tase inhibitors described therein are incorporated herein by muscarinic receptor modulator is a M4 muscarinic receptor reference, or the like. Gamma Secretase Inhibitors agonist. In some embodiments, the muscarinic receptor 15 Where a subject is suffering from or at risk of suffering modulator is a positive allosteric modulator of M4 muscarinic from a CNS disorder (e.g., Alzheimer's disease), a PAK receptors. Examples for positive allosteric M4 muscarinic inhibitor composition described herein is optionally used receptor modulators include, but are not limited to, together with one or more agents or methods for treating the VUO010010, VUO152099, VU0152100, or LY2033298. CNS disorder in any combination. In some embodiments, a NMDA Receptor Antagonists PAK inhibitor composition described herein is administered Where a subject is suffering from or at risk of suffering to a patient who has been prescribed a beta secretase inhibitor. from Alzheimer's disease, a PAK inhibitor composition Examples of beta secretase inhibitors useful in the methods described herein is optionally used together with one or more and compositions described herein include and are not lim agents or methods for treating Alzheimer's disease in any ited to LY-41 1575, (2S)-2-hydroxy-3-methyl-N-((1S)-1-me combination. In some embodiments, a PAK inhibitor compo 25 thyl-2-(1S)-3-methyl-2-oxo-2,3,4,5-tetrahydro-1H-3-ben sition described herein is administered to a patient who has Zazepin-1-yl)amino-2-oxoethyl)butanamide been prescribed an NMDA receptor antagonist. Examples of (Semagacestat), (R)-2-(3-Fluoro-4-phenylphenyl)propanoic NMDA receptor antagonists useful in the methods and com acid (Tarenflurbil), or the like. positions described herein include and are not limited to Antibodies memantine. 30 Where a subject is suffering from or at risk of suffering Neuroprotectants from a CNS disorder (e.g., Alzheimer's disease), a PAK In some embodiments, a PAK inhibitor or a composition inhibitor composition described herein is optionally used thereof described herein is administered in combination with together with one or more agents or methods for treating the a neuroprotectant such as, for example, minocycline, resvera CNS disorder in any combination. In some embodiments, a trol or the like. 35 PAK inhibitor composition described herein is administered Trophic Factors to a patient who has been prescribed an Abeta antibody. In some embodiments, a PAK inhibitor or a composition Examples of antibodies useful in the methods and composi thereof described herein is administered in combination with tions described herein include and are not limited an Abeta a trophic agent including, by way of example, glial derived antibody (e.g., bapineuZumab), PAK antibodies (e.g., nerve factor (GDNF), brain derived nerve factor (BDNF) or 40 ABIN237914) or the like. the like. Other Agents Antioxidants In some embodiments, one or more PAK inhibitors are Where a subject is suffering from or at risk of suffering used in combination with one or more agents that modulate from a CNS disorder (e.g., Alzheimer's disease, Mild Cog dendritic spine morphology or synaptic function. Examples nitive Impairment), a PAK inhibitor composition described 45 of agents that modulate dendritic spine morphology include herein is optionally used together with one or more agents or minocycline, trophic factors (e.g., brain derived neutrophic methods for treating the CNS disorder in any combination. In factor, glial cell-derived neurtrophic factor), or anesthetics some embodiments, a PAK inhibitor composition described that modulate spine motility, or the like. In some embodi herein is administered to a patient who is taking or has been ments, one or more PAK inhibitors are used in combination prescribed an antioxidant. Examples of antioxidants useful in 50 with one or more agents that modulate cognition. In some the methods and compositions described herein include and embodiments, a second therapeutic agent is a nootropic agent are not limited to ubiquinone, aged garlic extract, curcumin, that enhances cognition. Examples of nootropic agents lipoic acid, beta-carotene, melatonin, resveratrol, Ginkgo include and are not limited to piracetam, pramiracetam, biloba extract, vitamin C, vitamin E or the like. oxiracetam, and aniracetam. Metal Protein Attenuating Compounds 55 Blood Brain Barrier Facilitators Where a subject is suffering from or at risk of suffering In some instances, a PAK inhibitor is optionally adminis from a CNS disorder (e.g., Alzheimer's disease, Parkinson's tered in combination with a blood brain barrier facilitator. In disease), a PAK inhibitor composition described herein is certain embodiments, an agent that facilitates the transport of optionally used together with one or more agents or methods a PAK inhibitor is covalently attached to the PAK inhibitor. In for treating the CNS disorder in any combination. In some 60 some instances, PAK inhibitors described hereinare modified embodiments, a PAK inhibitor composition described herein by covalent attachment to a lipophilic carrier or co-formula is administered to a patient who has been prescribed a Metal tion with a lipophilic carrier. In some embodiments, a PAK Protein Attenuating agent. Examples of Metal Protein inhibitor is covalently attached to a lipophilic carrier, Such as Attenuating agents useful in the methods and compositions e.g., DHA, or a fatty acid. In some embodiments, a PAK described herein include and are not limited to 8-Hydrox 65 inhibitor is covalently attached to artificial low density lipo yduinoline, iodochlorhydroxyquin or the like and derivatives protein particles. In some instances, carrier systems facilitate thereof. the passage of PAK inhibitors described herein across the US 8,372,970 B2 173 174 blood-brain barrier and include but are not limited to, the use 70%, 75%, 80%, 85%, 90%, 92%, 93%, 95%, 96%, 97%, of a dihydropyridine pyridinium salt carrier redox system for 98%, 99%, or any other percent from about 60% to about delivery of drug species across the blood brain barrier. In 100% identical the following amino acid sequence: PPVI some instances a PAK inhibitor described herein is coupled to APREHTKSVYTRS as described in, e.g., Zhao et al (2006), a lipophilic phosphonate derivative. In certain instances, PAK Nat Neurosci, 9(2):234-242. In some embodiments, the pep inhibitors described herein are conjugated to PEG-oligomers/ tide sequence further comprises a PTD amino acid sequence polymers or aprotinin derivatives and analogs. In some as described above. instances, an increase in influx of a PAK inhibitor described In some embodiments, compounds of Formula I-XV are herein across the blood brain barrier is achieved by modifying optionally administered in combination with a polypeptide A PAK inhibitor described herein (e.g., by reducing or 10 comprising an amino acid sequence at least 80% to 100%, increasing the number of charged groups on the compound) e.g., 85%, 90%, 92%, 93%. 95%, 96%, 97%, 98%, 99%, or and enhancing affinity for a blood brain barrier transporter. In any other percent from about 80% to about 100% identical to certain instances, a PAK inhibitor is co-administered with an the FMRP1 protein (GenBank Accession No. Q06787), agent that reduces or inhibits efflux across the blood brain where the polypeptide is able to bind with a PAK (for barrier, e.g. an inhibitor of P-glycoprotein pump (PGP) medi 15 example, PAK1, PAK2, PAK3, PAK4, PAK5 and/or PAK6). ated efflux (e.g., cyclosporin, SCH66336 (lonafarnib, Scher In some embodiments compounds of Formula I-XV are ing)). optionally administered in combination with a polypeptide In some embodiments, compounds of Formula I-XV are comprising an amino acid sequence at least 80% to 100%, optionally administered in combination with, e.g., com e.g., 85%, 90%, 92%, 93%. 95%, 96%, 97%, 98%, 99%, or pounds described in U.S. Pat. Nos. 5,863,532, 6,191,169, any other percent from about 80% to about 100% identical to 6,248.549, and 6,498,163: U.S. Patent Applications the FMRP1 protein (GenBank Accession No. Q06787), 200200045564, 2002008.6390, 20020106690, 20020142325, where the polypeptide is able to bind with a Group I PAK, 20030.124107, 20030166623, 20040091992, 2004.0102623, such as, for example PAK1 (see, e.g., Hayashi et al (2007), 20040208880, 2005.00203114, 20050037965, 20050080002, Proc Natl Acad Sci USA, 104(27): 11489-11494. In some and 20050233.965, 20060088897: EP Patent Publication 25 embodiments, compounds of Formula I-XV are optionally 1492871; PCT patent publication WO9902701; PCT patent administered in combination with a polypeptide comprising a publication WO 2008/047307; Kumaret al., (2006), Nat. Rev. fragment of human FMRP1 protein with an amino acid Cancer, 6:459; and Eswaran et al., (2007), Structure, 15:201 sequence at least 80% to 100%, e.g., 85%, 90%, 92%, 93%, 213, all of which are incorporated herein by reference for 95%, 96%,97%.98%, 99%, or any other percent from about disclosure of kinase inhibitors and/or PAK inhibitors 30 80% to about 100% identical to the sequence of amino acids described therein. 207-425 of the human FMRP1 protein (i.e., comprising the In some embodiments, compounds of Formula I-XV are KH1 and KH2 domains), where the polypeptide is able to optionally administered in combination with compounds bind to PAK1. including and not limited to BMS-387032: SNS-032: CHI4 In some embodiments, compounds of Formula I-XV are 258; TKI-258: EKB-569; JNJ-7706621; PKC-412: stauro 35 optionally administered in combination with a polypeptide sporine; SU-14813; Sunitinib.; N-(3-chloro-4-fluoro-phenyl)- comprising an amino acid sequence at least 80% to 100%, 7-methoxy-6-(3-morpholin-4-ylpropoxy)guinazolin-4- e.g., 85%, 90%, 92%, 93%. 95%, 96%, 97%, 98%, 99%, or amine (gefitinib), VX-680; MK-0457; combinations thereof; any other percent from about 80% to about 100% identical to or salts, prodrugs thereof. at least five, at least ten at least twenty, at least thirty, at least In some embodiments, compounds of Formula I-XV are 40 forty, at least fifty, at least sixty, at least seventy, at least optionally administered in combination with a polypeptide eighty, at least ninety contiguous amino acids of the hunting comprising an amino acid sequence about 80% to about tin (htt) protein (GenBank Accession No. NP 002102, gi 100% identical, e.g., 85%, 90%, 92%.93%, 95%,96%.97%, 90903231), where the polypeptide is able to bind to a Group 98%, 99%, or any other percent from about 80% to about 1 PAK (for example, PAK1, PAK2, and/or PAK3). In some 100% identical the following amino acid sequence: 45 embodiments, compounds of Formula I-XV are optionally administered in combination with a polypeptide comprising an amino acid sequence at least 80% to 100%, e.g., 85%, HTIHVGFDAVTGEFTGMPEOWARLLOTSNITKSEOKKNPOAVLDVLEFY 90%, 92%, 93%. 95%, 96%, 97%, 98%, 99%, or any other NSKKTSNSO KYMSFTDKS percent from about 80% to about 100% identical to at least a 50 portion of the huntingtin (htt) protein (GenBank Accession The above sequence corresponds to the PAK autoinhibi No. NP 002102, gi90903231), where the polypeptide is able tory domain (PAD) polypeptide amino acids 83-149 of PAK1 to bind to PAK1. In some embodiments, compounds of For polypeptide as described in, e.g., Zhao et al (1998). In some mula I-XV are optionally administered in combination with a embodiments, the PAK inhibitor is a fusion protein compris polypeptide comprising a fragment of human huntingtin pro ing the above-described PAD amino acid sequence. In some 55 tein with an amino acid sequence at least 80% to 100%, e.g., embodiments, in order to facilitate cell penetration the fusion 85%, 90%, 92%, 93%, 95%, 96%, 97%, 98%, 99%, or any polypeptide (e.g., N-terminal or C-terminal) further com other percent from about 80% to about 100% identical to a prises a polybasic protein transduction domain (PTD) amino sequence of at least five, at least ten, at least twenty, at least acid sequence, e.g.: RKKRRQRR:YARAAARQARA:THR thirty, at least forty, at least fifty, at least sixty, at least seventy, LPRRRRRR: or GGRRARRRRRR. 60 at least eighty, at least ninety, or at least 100 contiguous amino In some embodiments, in order to enhance uptake into the acids of the human huntingtin protein that is outside of the brain, the fusion polypeptide further comprises a human insu sequence encoded by exon 1 of the htt gene (i.e., a fragment lin receptor antibody as described in U.S. patent application that does not contain poly glutamate domains), where the Ser. No. 1 1/245,546. polypeptide binds a PAK. In some embodiments, compounds In some embodiments, compounds of Formula I-XV are 65 of Formula I-XV are optionally administered in combination optionally administered in combination with a peptide inhibi with a polypeptide comprising a fragment of human hunting tor comprising a sequence at least 60% to 100%, e.g., 65%, tin protein with an amino acid sequence at least 80% identical US 8,372,970 B2 175 176 to a sequence of the human huntingtin protein that is outside Adenosine receptor modulators include, by way of of the sequence encoded by exon 1 of the htt gene (i.e., a example, theophylline, 8-Cyclopentyl-1,3-dimethylxanthine fragment that does not contain poly glutamate domains), (CPX), 8-Cyclopentyl-1,3-dipropylxanthine (DPCPX), where the polypeptide binds PAK1. 8-Phenyl-1,3-dipropylxanthine, PSB 36, istradefylline, Upstream Regulators of p21 Activated Kinases SCH-58261, SCH-442,416, ZM-241,385, CVT-6883, MRS In certain embodiments, compounds of Formula I-XV are 1706, MRS-1754, PSB-603, PSB-0788, PSB-1115, MRS optionally administered in combination with an indirect PAK 1191, MRS-1220, MRS-1334, MRS-1523, MRS-3777, modulator (e.g., an indirect PAK inhibitor) that affects the MRE3008F20, PSB-10, PSB-11, VUF-5574, N6-Cyclopen activity of a molecule that acts in a signaling pathway tyladenosine, CCPA,2'-MeCCPA, GR79236, SDZ WAG 99, upstream of PAK (upstream regulators of PAK). Upstream 10 ATL-146e, CGS-21680, Regadenoson, 5'-N-ethylcarboxa midoadenosine, BAY 60-6583, LUF-5835, LUF-5845, 2-(1- effectors of PAK include, but are not limited to: TrkB recep Hexynyl)-N-methyladenosine, CF-101 (IB-MECA), 2-Cl tors; NMDA receptors; EphB receptors; adenosine receptors: IB-MECA, CP-532,903, MRS-3558, Rosuvastatin, estrogen receptors; integrins; FMRP; Rho-family GTPases, KW-3902, SLV320, mefloquine, regadenoson, or the like. including Cdc42, Rac (including but not limited to Rac1 and 15 In some embodiments, compounds reducing PAK levels Rac2), CDK5, PI3 kinases, NCK, PDK1, EKT, GRB2, Chp, decrease PAK transcription or translation or reduce RNA or TC10, Tcl, and Wrch-1; guanine nucleotide exchange factors protein levels. In some embodiments, a compound that (“GEFs), such as but not limited to GEFT, members of the decreases PAK levels is an upstream effector of PAK. In some Dbl family of GEFs, p21-activated kinase interacting embodiments, exogenous expression of the activated forms of exchange factor (PIX), DEF6, Zizimin1, Vavl, Vav2, Dbs, the Rho family GTPases Chp and cdc42 in cells leads to members of the DOCK180 family, Kalirin-7, and Tiam1; G increased activation of PAK while at the same time increasing protein-coupled receptor kinase-interacting protein 1 (GIT1). turnover of the PAK protein, significantly lowering its level in CIB1, filamin A, Etk/Bmx, and sphingosine. the cell (Hubsman et al. (2007) Biochem. J. 404: 487-497). Modulators of NMDA receptor include, but are not limited PAK clearance agents include agents that increase expression to, 1-aminoadamantane, dextromethorphan, dextrorphan, 25 of one or more Rho family GTPases and/or one or more ibogaine, ketamine, nitrous oxide, phencyclidine, riluzole, guanine nucleotide exchange factors (GEFs) that regulate the tiletamine, memantine, neramexane, dizocilpine, aptiganel, activity of Rho family GTPases, in which overexpression of a remacimide, 7-chlorokynurenate, DCKA (5,7-dichlo Rho family GTPase and/or a GEF results in lower levels of rokynurenic acid), kynurenic acid, 1-aminocyclopropanecar PAK protein in cells. PAK clearance agents also include ago boxylic acid (ACPC), AP7 (2-amino-7-phosphonoheptanoic 30 nists of Rho family GTPases, as well as agonists of GTP acid), APV (R-2-amino-5-phosphonopentanoate), CPPene exchange factors that activate Rho family GTPases, such as (3-(R)-2-carboxypiperazin-4-yl)-prop-2-enyl-1-phospho but not limited to agonists of GEFs of the Dbl family that nic acid); (+)-(1S,2S)-1-(4-hydroxy-phenyl)-2-(4-hydroxy activate Rho family GTPases. 4-phenylpiperidino)-1-pro-panol: (1S,2S)-1-(4-hydroxy-3- Overexpression of a Rho family GTPase is optionally by methoxyphenyl)-2-(4-hydroxy-4-phenylpiperi-dino)-1- 35 means of introducing a nucleic acid expression construct into propanol: (3R,4S)-3-(4-(4-fluorophenyl)-4- the cells or by administering a compound that induces tran hydroxypiperidin-1-yl-)chroman-4,7-diol: (1R,2R)-1-(4- Scription of the endogenous gene encoding the GTPase. In hydroxy-3-methylphenyl)-2-(4-(4-fluoro-phenyl)-4- some embodiments, the Rho family GTPase is Rac (e.g., hydroxypiperidin-1-yl)-propan-1-ol-mesylate; and/or Rac1, Rac2, or Rac3), cdc42, Chp, TC10, Tcl, or Wrinch-1. combinations thereof. 40 For example, a Rho family GTPase includes Rac1, Rac2. Modulators of estrogen receptors include, and are not lim Rac3, or cdc42. A gene introduced into cells that encodes a ited to, PPT (4,4',4'-(4-Propyl-1H-pyrazole-1,3,5-triyl) Rho family GTPase optionally encodes a mutant form of the trisphenol); SKF-82958 (6-chloro-7,8-dihydroxy-3-allyl-1- gene, for example, a more active form (for example, a con phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine); estrogen; stitutively active form, Hubsman et al. (2007) Biochem. J. estradiol; estradiol derivatives, including but not limited to 45 404: 487-497). In some embodiments, a PAK clearance agent 17-13 estradiol, estrone, estriol, ERB-131, phytoestrogen, is, for example, a nucleic acid encoding a Rho family GTPase, MK 101 (bioNovo); VG-1010 (bioNovo); DPN (diarylpropi in which the Rho family GTPase is expressed from a consti olitrile); ERB-041; WAY-202196; WAY-214156; genistein: tutive or inducible promoter. PAK levels in some embodi estrogen; estradiol; estradiol derivatives, including but not ments are reduced by a compound that directly or indirectly limited to 17-B estradiol, estrone, estriol, benzopyrans and 50 enhances expression of an endogenous gene encoding a Rho triazolo-tetrahydrofluorenones, disclosed in U.S. Pat. No. family GTPase. 7.279,499, and Parker et al., Bioorg. & Med. Chem. Ltrs. 16: In some embodiments, compounds of Formula I-XV are 4652-4656 (2006), each of which is incorporated herein by optionally administered in combination with a PAK clearance reference for such disclosure. agent. Modulators of TrkB include by way of example, neutor 55 In some embodiments, compounds of Formula I-XV are ophic factors including BDNF and GDNF. Modulators of optionally administered in combination with a compound that EphB include XL647 (Exelixis), EphB modulator com directly or indirectly decreases the activation or activity of the pounds described in WO/2006081418 and US Appl. Pub. No. upstream effectors of PAK. For example, in some embodi 200803.00245, incorporated herein by reference for such dis ments a compound that inhibits the GTPase activity of the closure, or the like. 60 small Rho-family GTPases such as Rac and cdc42 thereby Modulators of integrins include by way of example, ATN reduce the activation of PAK kinase. In some embodiments, 161, PF-04605412, MEDI-522, Volociximab, natalizumab, the compound that decreases PAK activation is by secramine Volociximab, Ro 27-2771, Ro 27-2441, etaracizumab, that inhibits cac42 activation, binding to membranes and CNTO-95, JSM6427, cilengitide, R411 (Roche), EMD GTP in the cell (Pelish et al. (2005) Nat. Chem. Biol. 2: 121974, integrin antagonist compounds described in J. Med. 65 39-46). In some embodiments, PAK activation is decreased Chem., 2002, 45 (16), pp 3451-3457, incorporated herein by by EHT 1864, a small molecule that inhibits Rac1, Rac1b. reference for such disclosure, or the like. Rac2 and Rac3 function by preventing binding to guanine US 8,372,970 B2 177 178 nucleotide association and engagement with downstream is in some embodiments a mutant GEF, for example a mutant effectors (Shutes et al. (2007) J. Biol. Chem. 49: 35666 having enhanced activity with respect to wild type. 35678). In some embodiments, PAK activation is also The clearance agent is optionally a bacterial toxin such as decreased by the NSC23766 small molecule that binds Salmonella typhinmurium toxin SpoE that acts as a GEF to directly to Rac1 and prevents its activation by Rac-specific promote cdc42 nucleotide exchange (Buchwald et al. (2002) RhoGEFs (Gao et al. (2004) Proc. Natl. Acad. Sci. U.S.A. EMBO.J. 21:3286-3295; Schlumberger et al. (2003).J. Bio 101: 7618-7623). In some embodiments, PAK activation is logical Chem. 278: 27149-27159). Toxins such as Soph, frag also decreased by the 16 kDa fragment of prolactin (16 k ments thereof, or peptides or polypeptides having an amino PRL), generated from the cleavage of the 23 kDa prolactin acid sequence at least 80% to 100%, e.g., 85%, 90%, 92%, 10 93%, 95%, 96%, 97%, 98%,99° A, or any other percent from hormone by matrix metalloproteases and cathepsin D in Vari about 80% to about 100% identical to a sequence of at least ous tissues and cell types. 16 k PRL down-regulates the five, at least ten, at least twenty, at least thirty, at least forty, at Ras-Tiam1-Rac1-Pak1 signaling pathway by reducing Rac1 least fifty, at least sixty, at least seventy, at least eighty, at least activation in response to cell stimuli such as wounding (Lee et ninety, or at least 100 contiguous amino acids of the toxin are al. (2007) Cancer Res 67: 11045-11053). In some embodi 15 also optionally used as downregulators of PAK activity. The ments, PAK activation is decreased by inhibition of NMDA toxin is optionally produced in cells from nucleic acid con and/or AMPA receptors. Examples of modulators of AMPA structs introduced into cells. receptors include and are not limited to ketamine, MK801, Modulators of Upstream Regulators of PAKs CNQX (6-cyano-7-nitroquinoxaline-2,3-dione); NBQX In some embodiments, compounds of Formula I-XV are (2,3-dihydroxy-6-nitro-7-sulfamoyl-benzof duinoxaline-2, optionally administered in combination with a modulator of 3-dione); DNQX (6,7-dinitroquinoxaline-2,3-dione); an upstream regulator of PAKS. In some embodiments, a kynurenic acid; 2,3-dihydroxy-6-nitro-7-sulfamoylbenzo-f modulator of an upstream regulator of PAKS is an indirect quinoxaline: PCP or the like. In some embodiments, PAK inhibitor of PAK. In certain instances, a modulator of an activation is decreased by inhibition of TrkB activation. In upstream regulator of PAKs is a modulator of PDK1. In some some embodiments, PAK activation is decreased by inhibi 25 instances, a modulator of PDK1 reduces of inhibits the activ tion of BDNF activation of TrkB. In some embodiments, ity of PDK1. In some instances a PDK1 inhibitor is an anti compounds of Formula I-XV are optionally administered in sense compound (e.g., any PDK1 inhibitor described in U.S. combination with an antibody to BDNF. In some embodi Pat. No. 6,124,272, which PDK1 inhibitor is incorporated ments, PAK activation is decreased by inhibition of TrkB herein by reference). In some instances, a PDK1 inhibitor is a receptors; NMDA receptors; EphB receptors; adenosine 30 compound described in e.g., U.S. Pat. Nos. 7,344,870, and receptors; estrogen receptors; integrins; Rho-family 7,041,687, which PDK1 inhibitors are incorporated herein by GTPases, including Cdc42, Rac (including but not limited to reference. In some embodiments, an indirect inhibitor of PAK Rac1 and Rac2), CDK5, PI3 kinases, NCK, PDK1, EKT, is a modulator of a PI3 kinase. In some instances a modulator GRB2. Chp, TC10, Tcl, and Wrch-1; guanine nucleotide of a PI3 kinase is a PI3 kinase inhibitor. In some instances, a exchange factors (“GEFs), such as but not limited to GEFT, 35 PI3 kinase inhibitor is an antisense compound (e.g., any PI3 members of the Dbl family of GEFs, p21-activated kinase kinase inhibitor described in WO 2001/018023, which PI3 interacting exchange factor (PIX), DEF6, Zizimin1, Vav 1. kinase inhibitors are incorporated herein by reference). In Vav2, Dbs, members of the DOCK180 family, Kalirin-7, and some instances, an inhibitor of a PI3 kinase is 3-morpholino Tiaml; G protein-coupled receptor kinase-interacting protein 5-phenylnaphthalen-1 (4H)-one (LY294.002), or a peptide 1 (GIT1), CIB1, filamin A, Etk/Bmx, and/or binding to 40 based covalent conjugate of LY294.002, (e.g., SF1126, Sema FMRP and/or sphingosine. phore pharmaceuticals). In certain embodiments, an indirect In some embodiments, compounds of Formula I-XV are inhibitor of PAK is a modulator of Cdc42. In certain embodi optionally administered in combination with a compound that ments, a modulator of Cdc42 is an inhibitor of Cdc42. In decreases PAK levels in the cell, e.g., a compound that certain embodiments, a Cdc42 inhibitor is an antisense com directly or indirectly increases the activity of a guanine 45 pound (e.g., any Cdc42 inhibitor described in U.S. Pat. No. exchange factor (GEF) that promotes the active state of a Rho 6.410.323, which Cdc42 inhibitors are incorporated herein by family GTPase, such as an agonist of a GEF that activates a reference). In some instances, an indirect inhibitor of PAK is Rho family GTPase, such as but not limited to, Rac or cdc42. a modulator of GRB2. In some instances, a modulator of Activation of GEFs is also effected by compounds that acti GRB2 is an inhibitor of GRB2. In some instances a GRB2 vate TrkB, NMDA, or EphB receptors. 50 inhibitor is a GRb2 inhibitor described in e.g., U.S. Pat. No. In some embodiments, a PAK clearance agent is a nucleic 7.229,960, which GRB2 inhibitor is incorporated by refer acid encoding a GEF that activates a Rho family GTPase, in ence herein. In certain embodiments, an indirect inhibitor of which the GEF is expressed from a constitutive or inducible PAK is a modulator of NCK. In certain embodiments, an promoter. In some embodiments, a guanine nucleotide indirect inhibitor of PAK is a modulator of ETK. In some exchange factor (GEF), such as but not limited to a GEF that 55 instances, a modulator of ETK is an inhibitor of ETK. In some activates a Rho family GTPase is overexpressed in cells to instances an ETK inhibitor is a compound e.g., C.-Cyano-(3. increase the activation level of one or more Rho family 5-di-t-butyl-4-hydroxy)thiocinnamide (AG879). GTPases and thereby lower the level of PAK in cells. GEFs In some embodiments, indirect PAK inhibitors act by include, for example, members of the Dbl family of GTPases, decreasing transcription and/or translation of PAK. An indi such as but not limited to, GEFT, PIX (e.g., alphaPIX, 60 rect PAK inhibitor in some embodiments decreases transcrip betaPIX), DEF6, Zizimin1, Vav 1, Vav2, Dbs, members of the tion and/or translation of a PAK. For example, in some DOCK180 family, hPEM-2, FLJ00018, kalirin, Tiam1, embodiments, modulation of PAK transcription or translation STEF, DOCK2, DOCK6, DOCK7, DOCKS, Asf, EhCEF3, occurs through the administration of specific or non-specific or GEF-1. In some embodiments, PAKlevels are also reduced inhibitors of PAK transcription or translation. In some by a compound that directly or indirectly enhances expres 65 embodiments, proteins or non-protein factors that bind the sion of an endogenous gene encoding a GEF. A GEF upstream region of the PAK gene or the 5' UTR of a PAK expressed from a nucleic acid construct introduced into cells mRNA are assayed for their affect on transcription or trans US 8,372,970 B2 179 180 lation using transcription and translation assays (see, for cal structures are also introduced into cells to inhibit tran example, Baker, et al. (2003) J. Biol. Chem. 278: 17876 scription of the PAK gene (Helene (1991) Anticancer Drug 17884; Jiang et al. (2006).J. Chromatography A 1133: 83-94: Des. 6:569-584). Novoa et al. (1997) Biochemistry 36: 7802-78.09: Brandietal. For example, a clearance agent is in Some embodiments an (2007) Methods Enzymol. 431: 229-267). PAK inhibitors RNAi molecule or a nucleic acid construct that produces an include DNA or RNA binding proteins or factors that reduce RNAi molecule. An RNAi molecule comprises a double the level of transcription or translation or modified versions stranded RNA of at least about seventeen bases having a 2-3 thereof. In other embodiments, compounds of Formula I-XV nucleotide single-stranded overhangs on each end of the are optionally administered in combination with an agent that double-stranded structure, in which one strand of the double is a modified form (e.g., mutant form or chemically modified 10 stranded RNA is substantially complementary to the target form) of a protein or other compound that positively regulates PAK RNA molecule whose downregulation is desired. “Sub transcription or translation of PAK, in which the modified stantially complementary' means that one or more nucle form reduces transcription or translation of PAK. In yet other otides within the double-stranded region are not complemen embodiments, a transcription or translation inhibitor is an tary to the opposite strand nucleotide(s). Tolerance of antagonist of a protein or compound that positively regulates 15 mismatches is optionally assessed for individual RNAi struc transcription or translation of PAK, or is an agonist of a tures based on their ability to downregulate the target RNA or protein that represses transcription or translation. protein. In some embodiments, RNAi is introduced into the Regions of a gene other than those upstream of the tran cells as one or more short hairpin RNAs (“shRNAs) or as one scriptional start site and regions of an mRNA other than the 5' or more DNA constructs that are transcribed to produce one UTR (such as but not limited to regions 3' of the gene or in the or more shRNAs, in which the shRNAs are processed within 3' UTR of an mRNA, or regions within intron sequences of the cell to produce one or more RNAi molecules. either a gene or mRNA) also include sequences to which Nucleic acid constructs for the expression of siRNA, effectors of transcription, translation, mRNA processing, shRNA, antisense RNA, ribozymes, or nucleic acids for gen mRNA transport, and mRNA stability bind. In some embodi erating triple helical structures are optionally introduced as ments, compounds of Formula I-XV are optionally adminis 25 RNA molecules or as recombinant DNA constructs. DNA tered in combination with a clearance agent comprising a constructs for reducing gene expression are optionally polypeptide having homology to an endogenous protein that designed so that the desired RNA molecules are expressed in affects mRNA processing, transport, or stability, or is an the cell from a promoter that is transcriptionally active in antagonist or agonist of one or more proteins that affect mammalian cells, such as, for example, the SV40 promoter, mRNA processing, transport, or turnover, Such that the 30 the human cytomegalovirus immediate-early promoter inhibitor reduces the expression of PAK proteinby interfering (CMV promoter), or the pol III and/or pol II promoter using with PAK mRNA transport or processing, or by reducing the known methods. For some purposes, it is desirable to use viral half-life of PAK mRNA. A PAK clearance agents in some or plasmid-based nucleic acid constructs. Viral constructs embodiments interferes with transport or processing of a PAK include but are not limited to retroviral constructs, lentiviral mRNA, or by reducing the half-life of a PAK mRNA. 35 constructs, or based on a pox virus, aherpes simplex virus, an For example, PAK clearance agents decrease RNA and/or adenovirus, or an adeno-associated virus (AAV). protein half-life of a PAK isoform, for example, by directly In other embodiments, compounds of Formula I-XV are affecting mRNA and/or protein stability. In certain embodi optionally administered in combination with a polypeptide ments, PAK clearance agents cause PAK mRNA and/or pro that decreases the activity of PAK. Protein and peptide inhibi tein to be more accessible and/or Susceptible to nucleases, 40 tors of PAKare optionally based on natural substrates of PAK, proteases, and/or the proteasome. In some embodiments, e.g., Myosin light chain kinase (MLCK), regulatory Myosin compounds of Formula I-XV are optionally administered in light chain (R-MLC), Myosins I heavy chain, myosin II heavy combination with agents that decrease the processing of PAK chain, Myosin VI, Caldesmon, Desmin, Op.18/stathmin, Mer mRNA thereby reducing PAK activity. For example, PAK lin, Filamin A. LIM kinase (LIMK), cortactin, cofilin, Ras, clearance agents function at the level of pre-mRNA splicing, 45 Raf, Mek, p47(phox), BAD, caspase 3, estrogen and/or 5' end formation (e.g. capping), 3' end processing (e.g. cleav progesterone receptors, NET1, GCZ, phosphoglycerate age and/or polyadenylation), nuclear export, and/or associa mutase-B, RhoGDI, prolactin, p41 Arc, cortactin and/or tion with the translational machinery and/or ribosomes in the Aurora-A. In some embodiments, compounds of Formula cytoplasm. In some embodiments, PAK clearance agents I-XV are optionally administered in combination with an cause a decrease in the level of PAK mRNA and/or protein, 50 agent that is based on a sequence of PAK itself, for example, the half-life of PAK mRNA and/or protein by at least about the autoinhibitory domain in the N-terminal portion of the 5%, at least about 10%, at least about 20%, at least about 30%, PAK protein that binds the catalytic domain of a partner PAK at least about 40%, at least about 50%, at least about 60%, at molecule when the PAK molecule is in its homodimeric state least about 80%, at least about 90%, at least about 95%, or (Zhao et al. (1998) Mol. Cell Biol. 18:2153-2163: Knaus et al. substantially 100%. 55 (1998) J. Biol. Chem. 273: 21512-21518; Hofman et al. In some embodiments, the clearance agent comprises one (2004).J. Cell Sci. 117: 4343-4354). In some embodiments, or more RNAi or antisense oligonucleotides directed against polypeptide inhibitors of PAK comprise peptide mimetics, in one or more PAK isoform RNAs. In some embodiments, which the peptide has binding characteristics similar to a compounds of Formula I-XV are optionally administered in natural binding partner or substrate of PAK. combination with agent that comprise one or more ribozymes 60 In some embodiments, provided herein are compounds that directed against one or more PAK isoform RNAs. The design, downregulate PAK protein level. In some embodiments, the synthesis, and use of RNAi constructs, antisense oligonucle compounds described herein activate or increase the activity otides, and ribozymes are found, for example, in Dykxhoorn of an upstream regulator or downstream target of PAK. In et al. (2003) Nat. Rev. Mol. Cell. Biol. 4:457-467: Hannonet Some embodiments, compounds described herein downregu al. (2004) Nature 431:371-378; Sarver et al. (1990) Science 65 late protein level of a PAK. In some instances compounds 247: 1222-1225; Been et al. (1986) Cell 47:207-216). In some described herein reduce at least one of the symptoms related embodiments, nucleic acid constructs that induce triple heli a CNS disorder by reducing the amount of PAK in a cell. In US 8,372,970 B2 181 182 Some embodiments a compound that decreases PAK protein embodiments a compound that increases PAKactivity in cells levels in cells also decreases the activity of PAK in the cells. decreases PAK protein levels in the cells. In some embodiments a compound that decreases PAK pro In some instances, compounds of Formula I-XV are tein levels does not have a substantial impact on PAK activity optionally administered in combination with a polypeptide in cells. In some embodiments a compound that increases that is delivered to one or more brain regions of an individual PAK activity in cells decreases PAK protein levels in the cells. by administration of a viral expression vector, e.g., an AAV In some embodiments, a compound that decreases the vector, a lentiviral vector, an adenoviral vector, or a HSV amount of PAK protein in cells decreases transcription and/or vector. A number of viral vectors for delivery of therapeutic translation of PAK or increases the turnover rate of PAK proteins are described in, e.g., U.S. Pat. Nos. 7.244.423, mRNA or protein by modulating the activity of an upstream 10 6,780,409, 5,661,033. In some embodiments, the PAK inhibi effector or downstream regulator of PAK. In some embodi tor polypeptide to be expressed is under the control of an ments, PAK expression or PAK levels are influenced by feed inducible promoter (e.g., a promoter containing a tet-opera back regulation based on the conformation, chemical modi tor). Inducible viral expression vectors include, for example, fication, binding status, or activity of PAK itself. In some those described in U.S. Pat. No. 6,953,575. Inducible expres embodiments, PAK expression or PAK levels are influenced 15 sion of a PAK inhibitor polypeptide allows for tightly con by feedback regulation based on the conformation, chemical trolled and reversible increases of PAK inhibitor polypeptide modification, binding status, or activity of molecules directly expression by varying the dose of an inducing agent (e.g., or indirectly acted on by PAK signaling pathways. As used tetracycline) administered to an individual. herein “binding status' refers to any or a combination of Anti-Cancer Agents whether PAK, an upstream regulator of PAK, or a down Where the subject is suffering from or at risk of suffering stream effector of PAK is in a monomeric state or in an from a B-cell proliferative disorder (e.g., plasma cell oligomeric complex with itself, or whetherit is bound to other myeloma), the Subjected in Some embodiments is treated with polypeptides or molecules. For example, a downstream target a compound of Formula I-XV in any combination with one or of PAK, when phosphorylated by PAK, in some embodiments more other anti-cancer agents. In some embodiments, one or directly or indirectly downregulates PAK expression or 25 more of the anti-cancer agents are proapoptotic agents. decrease the half-life of PAK mRNA or protein. Downstream Examples of anti-cancer agents include, but are not limited to, targets of PAK include but are not limited to: Myosin light any of the following: gossyphol, genasense, polyphenol E. chain kinase (MLCK), regulatory Myosin light chain Chlorofusin, all trans-retinoic acid (ATRA), bryostatin, (R-MLC), Myosins I heavy chain, myosin II heavy chain, tumor necrosis factor-related apoptosis-inducing ligand Myosin VI, Caldesmon, Desmin, Op.18/stathmin, Merlin, Fil 30 (TRAIL), 5-aza-2'-deoxycytidine, all trans retinoic acid, aminA, LIM kinase (LIMK), Ras, Raf, Mek, p47", BAD, doxorubicin, Vincristine, etoposide, gemcitabine, imatinib caspase 3, estrogen and/or progesterone receptors, NET1, (Gleevec(R), geldanamycin, 17-N-Allylamino-17 GCZ, phosphoglycerate mutase-B, RhoGDI, prolactin, Demethoxygeldanamycin (17-AAG), flavopiridol, p41", cortactin and/or Aurora-A. Downregulators of PAK LY294.002, bortezomib, trastuzumab, BAY 1 1-7082, levels include downstream targets of PAK or fragments 35 PKC412, or PD184352, TaxolTM, also referred to as “pacli thereof in a phosphorylated State and downstream targets of taxel, which is an anti-cancer drug which acts by enhancing PAK or fragments thereof in a hyperphosphorylated state. and stabilizing microtubule formation, and analogs of A fragment of a downstream target of PAK includes any TaxolTM, such as Taxoteret M. Compounds that have the basic fragment with an amino acid sequence at least 80% to 100%, taxane skeleton as a commonstructure feature, have also been e.g., 85%, 90%, 92%, 93%. 95%, 96%, 97%, 98%, 99%, or 40 shown to have the ability to arrest cells in the G2-M phases any other percent from about 80% to about 100% identical to due to stabilized microtubules and in some embodiments are a sequence of at least five, at least ten, at least twenty, at least useful for treating cancer in combination with the compounds thirty, at least forty, at least fifty, at least sixty, at least seventy, described herein. at least eighty, at least ninety, or at least 100 contiguous amino Further examples of anti-cancer agents for use in combi acids of the downstream regulator, in which the fragment of 45 nation with a compound of Formula I-XV include inhibitors the downstream target of PAK is able to downregulate PAK of mitogen-activated protein kinase signaling, e.g., U0126, mRNA or protein expression or increase turnover of PAK PD98059, PD184352, PD0325901, ARRY-142886, mRNA or protein. In some embodiments, the fragment of a SB239063, SP600 125, BAY 43-9006, wortmannin, or downstream regulator of PAK comprises a sequence that LY294.002; Syk inhibitors; mTOR inhibitors; and antibodies includes a phosphorylation site recognized by PAK, in which 50 (e.g., rituxan). the site is phosphorylated. Other anti-cancer agents that can be employed in combi In some embodiments, compounds of Formula I-XV are nation with an irreversible Btk inhibitor compound include optionally administered in combination with a compound that Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cispl decreases the level of PAK including a peptide, polypeptide, atin, acivicin; aclarubicin; acodazole hydrochloride; acro or small molecule that inhibits dephosphorylation of a down 55 nine; adoZelesin; aldesleukin; altretamine; ambomycin; stream target of PAK, such that phosphorylation of the down ametantrone acetate; aminoglutethimide; amsacrine; anastro stream target remains at a level that leads to downregulation Zole; anthramycin; asparaginase; asperlin; azacitidine; of PAK levels. aZetepa; azotomycin; batimastat; benzodepa; bicalutamide; In some embodiments, PAKactivity is reduced or inhibited bisantrene hydrochloride; bisnafide dimesylate; bizelesin; via activation and/or inhibition of an upstream regulator and/ 60 bleomycin Sulfate; brequinar Sodium; bropirimine; buSulfan; or downstream target of PAK. In some embodiments, the cactinomycin; calusterone; caracemide; carbetimer; carbopl protein expression of a PAK is downregulated. In some atin: carmustine; carubicin hydrochloride; carzelesin: cedef embodiments, the amount of PAK in a cell is decreased. In ingol; chlorambucil; cirolemycin; cladribine; crisinatol mesy Some embodiments a compound that decreases PAK protein late; cyclophosphamide; cytarabine; dacarbazine; levels in cells also decreases the activity of PAK in the cells. 65 daunorubicin hydrochloride; decitabine; dexormaplatin: In some embodiments a compound that decreases PAK pro deZaguanine; deZaguanine mesylate; diaziquone, doxorubi tein levels does not decrease PAK activity in cells. In some cin: doxorubicin hydrochloride; droloxifene; droloxifene cit US 8,372,970 B2 183 184 rate; dromostanolone propionate; duaZomycin; ediatrexate; rin, cladribine; clomifene analogues; clotrimazole; eflornithine hydrochloride; elsamitrucin; enloplatin; enpro collismycin A; collismycin B; combretastatin A4, combret mate; epipropidine; epirubicin hydrochloride; erbulozole; astatin analogue; conagenin, crambescidin 816; crisinatol; esorubicin hydrochloride; estramustine; estramustine phos cryptophycin 8; cryptophycin Aderivatives; curacin A; cyclo phate sodium; etanidazole; etoposide; etoposide phosphate: pentanthraquinones; cycloplatam, cypemycin; cytarabine etoprine; fadrozole hydrochloride; fazarabine; fenretinide; ocfosfate; cytolytic factor; cytostatin; dacliximab, decitab floxuridine; fludarabine phosphate; fluorouracil; fluorocitab ine; dehydrodidemnin B; deslorelin; dexamethasone; dexi ine; fosquidone; fostriecin Sodium; gemcitabine; gemcitab fosfamide; dexraZOxane; dexVerapamil; diaziquone; didem ine hydrochloride; hydroxyurea; idarubicin hydrochloride: nin B; didox; diethylnorspermine; dihydro-5-azacytidine: ifosfamide; ilmofosine; interleukin II (including recombinant 10 9-dioxamycin; diphenyl spiromustine; docosanol; dolas interleukin II, or rIL2), interferon alfa-2a: interferon alfa-2b: etron: doxifluridine; droloxifene; dronabinol; duocarmycin interferon alfa-n1; interferon alfa-n3; interferon beta-1a: SA; ebselen; ecomustine; edelfosine; edrecolomab; eflomith interferon gamma-1b; iproplatin; irinotecan hydrochloride; ine; elemene; emitefur, epirubicin; epristeride; estramustine lanreotide acetate; letrozole; leuprolide acetate; liarozole analogue; estrogen agonists; estrogen antagonists; etanida hydrochloride; lometrexol Sodium, lomustine; losoxantrone 15 Zole; etoposide phosphate; exemestane; fadrozole; faZara hydrochloride; masoprocol; maytansine; mechlorethamine bine; fenretinide; filgrastim; fmasteride; flavopiridol; fle hydrochloride; megestrol acetate; melengestrol acetate; mel Zelastine; fluasterone; fludarabine; fluorodaunorunicin phalan; menogaril; mercaptopurine; methotrexate; methotr hydrochloride; forfenimex; formestane; fostriecin: fotemus exate Sodium; metoprine; meturedepa; mitindomide; mito tine; gadolinium texaphyrin; gallium nitrate; galocitabine; carcin, mitocromin, mitogillin, mitomalcin, mitomycin; ganirelix; gelatinase inhibitors; gemcitabine; glutathione mitosper, mitotane; mitoxantrone hydrochloride; mycophe inhibitors; hepsulfam; heregulin; hexamethylene bisaceta nolic acid; nocodazole; nogalamycin; ormaplatin; oxisuran: mide; hypericin; ibandronic acid; idarubicin; idoxifene; idra pegaspargase; peliomycin; pentamustine; peplomycin Sul mantone; ilmofosine; illomastat; imidazoacridones; imiqui fate; perfosfamide; pipobroman; piposulfan, piroXantrone mod; immunostimulant peptides; insulin-like growth factor-1 hydrochloride; plicamycin; plomestane; porfimer Sodium; 25 receptor inhibitor; interferon agonists; interferons; interleu porfiromycin; prednimustine; procarbazine hydrochloride; kins; iobenguane; iododoxorubicin; ipomeanol, 4-, iroplact; puromycin; puromycin hydrochloride; pyrazofurin: ribo irsogladine, isobengaZole; isohomohalicondrin B; itasetron; prine; rogletimide: Safingol; Safingol hydrochloride: Semus jasplakinolide; kahalalide F. lamellarin-N triacetate; lan tine; simtraZene; sparfosate Sodium; sparsomycin; Spiroger reotide; leinamycin; lenograstim; lentinan Sulfate; leptolsta manium hydrochloride; spiromustine; spiroplatin: 30 tin; letrozole; leukemia inhibiting factor, leukocyte alpha streptonigrin: Streptozocin, Sulofenur; talisomycin; tecogalan interferon; leuprolide+estrogen-progesterone; leuprorelin; sodium; tegafur; teloxantrone hydrochloride; temoporfin; levamisole; liarozole; linear polyamine analogue; lipophilic teniposide; teroxirone; testolactone; thiamiprine; thiogua disaccharide peptide; lipophilic platinum compounds; lisso nine; thiotepa; tiazofurin; tirapazamine; toremifene citrate; clinamide 7: lobaplatin; lombricine; lometrexol; lonidamine: trestolone acetate; triciribine phosphate; trimetrexate; trime 35 losoxantrone; lovastatin; loxoribine; lurtotecan; lutetium trexate glucuronate; triptorelin; tubulozole hydrochloride; texaphyrin; lysofylline; lytic peptides; maitansine; mannosta uracil mustard; uredepa; vapreotide; verteporfin; vinblastine tin A; marimastat; masoprocol; maspin; matrilysin inhibitors; sulfate; Vincristine sulfate; Vindesine; vindesine sulfate; vine matrix metalloproteinase inhibitors; menogaril; merbarone; pidine Sulfate; Vinglycinate Sulfate; Vinleurosine Sulfate; meterelin; methioninase; metoclopramide; MIF inhibitor; vinorelbine tartrate; Vinrosidine sulfate; Vinzolidine sulfate; 40 mifepristone; miltefosine; mirimostim; mismatched double Vorozole; Zeniplatin: Zinostatin: Zorubicin hydrochloride. Stranded RNA, mitoguaZone; mitolactol, mitomycin ana Other anti-cancer agents that in some embodiments are logues; mitonafide; mitotoxin fibroblast growth factor-sa employed in combination with a compound of Formula I-XV porin; mitoxantrone; mofarotene; molgramostim; mono include: 20-epi-1, 25 dihydroxyvitamin D3; 5-ethynyluracil; clonal antibody, human chorionic gonadotrophin; abiraterone; aclarubicin; acylfulvene; adecypenol; adoZe 45 monophosphoryl lipid A+myobacterium cell wall sk; mopi lesin; aldesleukin; ALL-TKantagonists; altretamine; amba damol; multiple drug resistance gene inhibitor, multiple mustine; amidox; amifostine; aminolevulinic acid; amrubi tumor Suppressor 1-based therapy; mustard anticancer agent; cin; amsacrine; anagrelide; anastrozole; andrographolide; my caperoxide B; mycobacterial cell wall extract; myriapor angiogenesis inhibitors; antagonist D; antagonist G, antar one; N-acetyldinaline; N-substituted benzamides; nafarelin; elix; anti-dorsalizing morphogenetic protein-1, antiandro 50 nagrestip; naloxone-pentazocine; napavin; naphterpin, nar gen, prostatic carcinoma, antiestrogen; antineoplaston; anti tograstim; nedaplatin: nemorubicin; neridronic acid; neutral sense oligonucleotides; aphidicolinglycinate; apoptosis gene endopeptidase; nilutamide; nisamycin; nitric oxide modula modulators; apoptosis regulators; apurinic acid; ara-CDP tors; nitroxide antioxidant; nitrullyn; O6-benzylguanine; oct DL-PTBA, arginine deaminase; asulacrine; atamestane; atri reotide; okicenone; oligonucleotides; onapristone; mustine; axinastatin 1; axinastatin2; axinastatin3; aZasetron; 55 ondansetron; ondansetron; oracin; oral cytokine inducer, aZatoxin; azatyrosine; baccatin III derivatives; balanol; bati ormaplatin: osaterone; oxaliplatin: Oxaunomycin; palaua mastat; BCR/ABL antagonists; benzochlorins; benzoylstau mine; palmitoylrhizoxin; pamidronic acid; panaxytriol: rosporine; beta lactam derivatives; beta-alethine; betaclamy panomifene; parabactin; paZelliptine; pegaspargase; cin B; betulinic acid; bFGF inhibitor; bicalutamide: peldesine; pentosan polysulfate sodium; pentostatin: pentro bisantrene; bisaziridinylspermine; bisnafide; bistratene A: 60 Zole; perflubron; perfosfamide; perillyl alcohol; phenazino bizelesin; breflate; bropirimine; budotitane; buthionine sul mycin; phenylacetate; phosphatase inhibitors; picibanil; pilo foXimine; calcipotriol; calphostin C; camptothecin deriva carpine hydrochloride; pirarubicin; piritrexim; placetin A; tives; canarypox IL-2; capecitabine; carboxamide-amino placetin B; plasminogen activator inhibitor; platinum com triazole; carboxyamidotriazole; CaRest M3; CARN 700; plex; platinum compounds; platinum-triamine complex; por cartilage derived inhibitor, carZelesin; casein kinase inhibi 65 fimer Sodium; porfiromycin; prednisone; propyl bis-acri tors (ICOS); castanospermine; cecropin B; cetrorelix; chlor done; prostaglandin J2, proteasome inhibitors; protein ins; chloroquinoxaline Sulfonamide; cicaprost, cis-porphy A-based immune modulator, protein kinase C inhibitor, pro US 8,372,970 B2 185 186 tein kinase C inhibitors, microalgal; protein tyrosine phos limited to, adrenocorticosteroids (e.g., prednisone), phatase inhibitors; purine nucleoside phosphorylase inhibi progestins (e.g., hydroxyprogesterone caproate, megestrol tors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin acetate, medroxyprogesterone acetate), estrogens (e.g., polyoxyethylerie conjugate; raf antagonists; raltitrexed: diethly stilbestrol, ethinyl estradiol), antiestrogen (e.g., ramosetron; ras farnesyl protein transferase inhibitors; ras 5 tamoxifen), androgens (e.g., testosterone propionate, flu inhibitors: ras-GAP inhibitor; retelliptine demethylated; rhe oxymesterone), antiandrogen (e.g., flutamide), gonadotropin nium Re 186 etidronate; rhizoxin: ribozymes; R.Sub. 11 reti releasing hormone analog (e.g., leuprolide). Other agents that namide; rogletimide; rohitukine; romurtide; roquinimex: can be used in the methods and compositions described rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarco herein for the treatment or prevention of cancer include plati phytol A. Sargramostim; Sdi 1 mimetics; Semustine; senes- 10 num coordination complexes (e.g., cisplatin, carboblatin), cence derived 1; sense oligonucleotides; signal transduction anthracenedione (e.g., mitoxantrone), Substituted urea (e.g., inhibitors; signal transduction modulators; single chain anti hydroxyurea), methyl hydrazine derivative (e.g., procarba gen-binding protein; sizofuran; Sobuzoxane; sodium boroc Zine), adrenocortical Suppressant (e.g., mitotane, aminoglu aptate; sodium phenylacetate; Solverol; somatomedin bind tethimide). ing protein; Sonermin; Sparfosic acid; spicamycin D; 15 Examples of anti-cancer agents which act by arresting cells spiromustine; splenopentin; spongistatin 1; squalamine; stem in the G2-M phases due to stabilized microtubules and which cell inhibitor; stem-cell division inhibitors; stipiamide: in other embodiments are used in combination with a com stromelysin inhibitors; sulfinosine; Superactive vasoactive pound of Formula I-XV include without limitation the fol intestinal peptide antagonist; Suradista; Suramin; Swainso lowing marketed drugs and drugs in development: ErbuloZole nine; synthetic glycosaminoglycans; tallimustine; tamoxifen 20 (also known as R-55 104), Dolastatin 10 (also known as DLS methiodide; tauromustine; tazarotene; tecogalan Sodium; 10 and NSC-376128), Mivobulin isethionate (also known as tegafur, tellurapyrylium; telomerase inhibitors; temoporfin; CI-980), Vincristine, NSC-639829, Discodermolide (also temozolomide; teniposide; tetrachlorodecaoxide; tetraZom known as NVP-XX-A-296), ABT-751 (Abbott, also known ine; thaliblastine; thiocoraline; thrombopoietin; thrombopoi as E-7010). Altorhyrtins (such as Altorhyrtin A and Altorhyr etin mimetic; thymalfasin; thymopoietin receptor agonist; 25 tin C), Spongistatins (such as Spongistatin 1, Spongistatin 2, thymotrinan; thyroid stimulating hormone; tin ethyl etiopur Spongistatin 3, Spongistatin 4, Spongistatin 5, Spongistatin purin; tirapazamine; titanocene bichloride; top sentin; 6, Spongistatin 7, Spongistatin 8, and Spongistatin9), Cema toremifene; totipotent stem cell factor; translation inhibitors: dotin hydrochloride (also known as LU-103793 and NSC-D- tretinoin; triacetyluridine; triciribine; trimetrexate; triptore 669356), Epothilones (such as Epothilone A, Epothilone B, lin; tropisetron; turosteride; tyrosine kinase inhibitors; tyr- 30 Epothilone C (also known as desoxyepothilone A or dEpoA), phostins; UBC inhibitors: ubenimex: urogenital sinus-de Epothilone D (also referred to as KOS-862, dEpoB, and des rived growth inhibitory factor; urokinase receptor oxyepothilone B), Epothilone E. Epothilone F, Epothilone B antagonists; vapreotide; variolin B; vector system, erythro N-oxide, Epothilone A N-oxide, 16-aza-epothilone B. cyte gene therapy; Velaresol; Veramine; Verdins; verteporfin; 21-aminoepothilone B (also known as BMS-310705), 21-hy Vinorelbine; Vinxaltine; vitaxin; Vorozole; Zanoterone; Zeni- 35 droxyepothilone D (also known as Desoxyepothilone F and platin: Zilascorb; and Zinostatin stimalamer. dEpoF), 26-fluoroepothilone), Auristatin PE (also known as Yet other anticancer agents that in further embodiments are NSC-654663), Soblidotin (also known as TZT-1027), employed in combination with a compound of Formula I-XV LS-4559-P (Pharmacia, also known as LS-4577), LS-4578 include alkylating agents, antimetabolites, natural products, (Pharmacia, also known as LS-477-P), LS-4477 (Pharmacia), or hormones, e.g., nitrogen mustards (e.g., mechloroet- 40 LS-4559 (Pharmacia), RPR-112378 (Aventis), Vincristine hamine, cyclophosphamide, chlorambucil, etc.), alkyl Sul sulfate, DZ-3358 (Daiichi), FR-182877 (Fujisawa, also fonates (e.g., buSulfan), nitrosoureas (e.g., carmustine, known as WS-9885B), GS-164 (Takeda), GS-198 (Takeda), lomusitne, etc.), or triaZenes (decarbazine, etc.). Examples of KAR-2 (Hungarian Academy of Sciences), BSF-223651 antimetabolites include but are not limited to folic acid analog (BASF, also known as ILX-651 and LU-223651), (e.g., methotrexate), or pyrimidine analogs (e.g., Cytarabine), 45 SAH-49960 (Lilly/Novartis), SDZ-268970 (Lilly/Novartis), purine analogs (e.g., mercaptopurine, thioguanine, pentosta AM-97 (Armad/Kyowa Hakko), AM-132 (Armad), AM-138 tin). (Armad/Kyowa Hakko), IDN-5005 (Indena), Cryptophycin Examples of natural products useful in combination with a 52 (also known as LY-355703), AC-7739 (Ajinomoto, also compound of Formula I-XV include but are not limited to known as AVE-8063A and CS-39.HCl), AC-7700 (Ajino Vinca alkaloids (e.g., vinblastin, Vincristine), epipodophyllo- 50 moto, also known as AVE-8062, AVE-8062A, CS-39-L-Ser toxins (e.g., etoposide), antibiotics (e.g., daunorubicin, doxo .HCl, and RPR-258062A), Vitilevuamide, Tubulysin A, rubicin, bleomycin), enzymes (e.g., L-asparaginase), or bio Canadensol, Centaureidin (also known as NSC-106969), logical response modifiers (e.g., interferon C). T-138067 (Tularik, also known as T-67, TL-138067 and Examples of alkylating agents that in further embodiments TI-138067), COBRA-1 (Parker Hughes Institute, also known are employed in combination with a compound of Formula 55 as DDE-261 and WHI-261), H10 (Kansas State University), I-XV include, but are not limited to, nitrogen mustards (e.g., H16 (Kansas State University). Oncocidin A1 (also known as mechloroethamine, cyclophosphamide, chlorambucil, mel BTO-956 and DIME), DDE-313 (Parker Hughes Institute), phalan, etc.), ethylenimine and methylmelamines (e.g., hex Fijianolide B. Laulimalide, SPA-2 (Parker Hughes Institute), amethlymelamine, thiotepa), alkyl Sulfonates (e.g., buSul SPA-1 (Parker Hughes Institute, also known as SPIKET-P), fan), nitrosoureas (e.g., carmustine, lomusitne, Semustine, 60 3-IAABU (Cytoskeleton/Mt. Sinai School of Medicine, also streptozocin, etc.), or triaZenes (decarbazine, etc.). Examples known as MF-569), Narcosine (also known as NSC-5366), of antimetabolites include, but are not limited to folic acid Nascapine, D-24851 (Asta Medica), A-105972 (Abbott), analog (e.g., methotrexate), or pyrimidine analogs (e.g., fluo Hemiasterlin, 3-BAABU (Cytoskeleton/Mt. Sinai School of rouracil, floXuridine, Cytarabine), purine analogs (e.g., mer Medicine, also known as MF-191), TMPN (Arizona State captopurine, thioguanine, pentostatin. 65 University), Vanadocene acetylacetonate, T-138026 (Tu Examples of hormones and antagonists useful in combina larik), Monsatrol, Inanocine (also known as NSC-698666), tion with a compound of Formula I-XV include, but are not 3-1AABE (Cytoskeleton/Mt. Sinai School of Medicine), US 8,372,970 B2 187 188 A-204197 (Abbott), T-607 (Tuiarik, also known as more than Zero weeks to less than four weeks. In addition, the T-900607), RPR-115781 (Aventis), Eleutherobins (such as combination methods, compositions and formulations are not Desmethyleleutherobin, Desaetyleleutherobin, Isoeleuther to be limited to the use of only two agents; the use of multiple obin A, and Z-Eleutherobin), Caribaeoside, Caribaeolin, therapeutic combinations are also envisioned. Halichondrin B, D-64131 (Asta Medica), D-68144 (Asta 5 The pharmaceutical agents which make up the combina Medica), Diazonamide A, A-293620 (Abbott), NPI-2350 tion therapy disclosed herein are optionally a combined dos (Nereus), Taccalonolide A, TUB-245 (Aventis), A-259754 age form or in separate dosage forms intended for Substan (Abbott), DioZostatin, (-)-Phenylahistin (also known as tially simultaneous administration. The pharmaceutical NSCL-96F037), D-68838 (Asta Medica), D-68836 (Asta agents that make up the combination therapy are optionally Medica), Myoseverin B, D-43411 (Zentaris, also known as 10 also be administered sequentially, with either therapeutic D-81862), A-289099 (Abbott), A-318315 (Abbott), HTI-286 compound being administered by a regimen calling for two (also known as SPA-1 10, trifluoroacetate salt) (Wyeth), step administration. The two-step administration regimen D-82317 (Zentaris), D-82318 (Zentaris), SC-12983 (NCI), optionally calls for sequential administration of the active Resverastatin phosphate sodium, BPR-OY-007 (National agents or spaced-apart administration of the separate active Health Research Institutes), and SSR-250411 (Sanofi). 15 agents. The time period between the multiple administration Any combination of one or more PAK inhibitors and a steps ranges from, a few minutes to several hours, depending second therapeutic agent is compatible with any method upon the properties of each pharmaceutical agent, Such as described herein. The PAK inhibitor compositions described potency, solubility, bioavailability, plasma half-life and herein are also optionally used in combination with other kinetic profile of the pharmaceutical agent. Circadian varia therapeutic reagents that are selected for their therapeutic 20 tion of the target molecule concentration are optionally used value for the condition to be treated. In general, the compo to determine the optimal dose interval. sitions described herein and, in embodiments where combi In addition, a PAK inhibitor is optionally used in combi national therapy is employed, other agents do not have to be nation with procedures that provide additional or synergistic administered in the same pharmaceutical composition, and, benefit to the patient. By way of example only, patients are because of different physical and chemical characteristics, 25 expected to find therapeutic and/or prophylactic benefit in the are optionally administered by different routes. The initial methods described herein, wherein pharmaceutical composi administration is generally made according to established tion of a PAK inhibitor and/or combinations with other thera protocols, and then, based upon the observed effects, the peutics are combined with genetic testing to determine dosage, modes of administration and times of administration whether that individual is a carrier of a mutant gene that is Subsequently modified. 30 correlated with certain diseases or conditions. In certain instances, it is appropriate to administer at least A PAK inhibitor and the additional therapy(ies) are option one PAK inhibitor composition described herein in combina ally administered before, during or after the occurrence of a tion with another therapeutic agent. By way of example only, disease or condition, and the timing of administering the if one of the side effects experienced by a patient upon receiv composition containing a PAK inhibitor varies in some ing one of the PAK inhibitor compositions described herein is 35 embodiments. Thus, for example, the PAK inhibitor is used as nausea, then it is appropriate to administer an anti-nausea a prophylactic and administered continuously to individuals agent in combination with the initial therapeutic agent. Or, by with a propensity to develop conditions or diseases in order to way of example only, the therapeutic effectiveness of a PAK prevent the occurrence of the disease or condition. The PAK inhibitor is enhanced by administration of an adjuvant (i.e., inhibitors and compositions are optionally administered to an by itself the adjuvant has minimal therapeutic benefit, but in 40 individual during or as soon as possible after the onset of the combination with another therapeutic agent, the overall thera symptoms. The administration of the compounds are option peutic benefit to the patient is enhanced). Or, by way of ally initiated within the first 48 hours of the onset of the example only, the benefit experienced by a patient is symptoms, preferably within the first 48 hours of the onset of increased by administering a PAK inhibitor with another the symptoms, more preferably within the first 6 hours of the therapeutic agent (which also includes atherapeutic regimen) 45 onset of the symptoms, and most preferably within 3 hours of that also has therapeutic benefit. In any case, regardless of the the onset of the symptoms. The initial administration is disease, disorder or condition being treated, the overall ben optionally via any route practical, such as, for example, an efit experienced by the patient is either simply additive of the intravenous injection, a bolus injection, infusion over 5 min two therapeutic agents or the patient experiences a synergistic utes to about 5 hours, a pill, a capsule, transdermal patch, benefit. 50 buccal delivery, and the like, or combination thereof. A PAK Therapeutically-effective dosages vary when the drugs are inhibitor is optionally administered as soon as is practicable used in treatment combinations. Suitable methods for experi after the onset of a disease or condition is detected or Sus mentally determining therapeutically-effective dosages of pected, and for a length of time necessary for the treatment of drugs and other agents include, e.g., the use of metronomic the disease, Such as, for example, from about 1 month to about dosing, i.e., providing more frequent, lower doses in order to 55 3 months. The length of treatment optionally varies for each minimize toxic side effects. Combination treatment further individual, and the length is then determined using the known includes periodic treatments that start and stop at various criteria. For example, the PAK inhibitor or a formulation times to assist with the clinical management of the patient. containing the PAK inhibitor is administered for at least 2 In any case, the multiple therapeutic agents (one of which weeks, preferably about 1 month to about 5 years, and more is a PAK inhibitor described herein) is administered in any 60 preferably from about 1 month to about 3 years. order, or even simultaneously. If simultaneously, the multiple In some embodiments, the particular choice of compounds therapeutic agents are optionally provided in a single, unified depends upon the diagnosis of the attending physicians and form, or in multiple forms (by way of example only, either as their judgment of the condition of an individual and the a single pill or as two separate pills). In some embodiments, appropriate treatment protocol. The compounds are option one of the therapeutic agents is given in multiple doses, or 65 ally administered concurrently (e.g., simultaneously, essen both are given as multiple doses. If not simultaneous, the tially simultaneously or within the same treatment protocol) timing between the multiple doses optionally varies from or sequentially, depending upon the nature of the disease, US 8,372,970 B2 189 190 disorder, or condition, the condition of an individual, and the age Forms, Marcel Decker, New York, N.Y., 1980; and Phar actual choice of compounds used. In certain instances, the maceutical Dosage Forms and Drug Delivery Systems, Sev determination of the order of administration, and the number enth Ed. (Lippincott Williams & Wilkins, 1999). of repetitions of administration of each therapeutic agent Provided herein are pharmaceutical compositions that during a treatment protocol, is based on an evaluation of the include one or more PAK inhibitors and a pharmaceutically disease being treated and the condition of an individual. acceptable diluent(s), excipient(s), or carrier(s). In addition, In some embodiments, therapeutically-effective dosages the PAK inhibitor is optionally administered as pharmaceu vary when the drugs are used in treatment combinations. tical compositions in which it is mixed with other active Methods for experimentally determining therapeutically-ef ingredients, as in combination therapy. In some embodi fective dosages of drugs and other agents for use in combi 10 ments, the pharmaceutical compositions includes other nation treatment regimens are described in the literature. In some embodiments of the combination therapies medicinal orpharmaceutical agents, carriers, adjuvants. Such described herein, dosages of the co-administered compounds as preserving, stabilizing, wetting or emulsifying agents, vary depending on the type of co-drug employed, on the Solution promoters, salts for regulating the osmotic pressure, specific drug employed, on the disease or condition being 15 and/or buffers. In addition, the pharmaceutical compositions treated and so forth. In addition, when co-administered with also contain other therapeutically valuable Substances. one or more biologically active agents, the compound pro A pharmaceutical composition, as used herein, refers to a vided herein is optionally administered either simultaneously mixture of a PAK inhibitor with other chemical components, with the biologically active agent(s), or sequentially. In cer Such as carriers, stabilizers, diluents, dispersing agents, Sus tain instances, if administered sequentially, the attending pending agents, thickening agents, and/or excipients. The physician will decide on the appropriate sequence of thera pharmaceutical composition facilitates administration of the peutic compound described herein in combination with the PAK inhibitor to an organism. In practicing the methods of additional therapeutic agent. treatment or use provided herein, therapeutically effective The multiple therapeutic agents (at least one of which is a amounts of a PAK inhibitor are administered in a pharmaceu therapeutic compound described herein) are optionally 25 tical composition to a mammal having a condition, disease, or administered in any order or even simultaneously. If simulta disorder to be treated. Preferably, the mammal is a human. A neously, the multiple therapeutic agents are optionally pro therapeutically effective amount varies depending on the vided in a single, unified form, or in multiple forms (by way severity and stage of the condition, the age and relative health of example only, either as a single pillor as two separate pills). of an individual, the potency of the PAK inhibitor used and In certain instances, one of the therapeutic agents is option 30 other factors. The PAK inhibitor is optionally used singly or ally given in multiple doses. In other instances, both are in combination with one or more therapeutic agents as com optionally given as multiple doses. If not simultaneous, the ponents of mixtures. timing between the multiple doses is any suitable timing, e.g., The pharmaceutical formulations described herein are from more than Zero weeks to less than four weeks. In some optionally administered to an individual by multiple admin embodiments, the additional therapeutic agent is utilized to 35 istration routes, including but not limited to, oral, parenteral achieve reversal or amelioration of symptoms of a CNS dis (e.g., intravenous, Subcutaneous, intramuscular), intranasal, order, whereupon the therapeutic agent described herein (e.g., buccal, topical, rectal, or transdermal administration routes. a compound of any one of Formula I-XV is Subsequently By way of example only, Example 26a is describes a administered. In addition, the combination methods, compo parenteral formulation, Example 26f describes a rectal for sitions and formulations are not to be limited to the use of only 40 mulation. The pharmaceutical formulations described herein two agents; the use of multiple therapeutic combinations are include, but are not limited to, aqueous liquid dispersions, also envisioned (including two or more compounds described self-emulsifying dispersions, Solid solutions, liposomal dis herein). persions, aerosols, Solid dosage forms, powders, immediate In certain embodiments, a dosage regimento treat, prevent, release formulations, controlled release formulations, fast or ameliorate the condition(s) for which relief is sought, is 45 melt formulations, tablets, capsules, pills, delayed release modified in accordance with a variety of factors. These fac formulations, extended release formulations, pulsatile release tors include the disorder from which an individual suffers, as formulations, multiparticulate formulations, and mixed well as the age, weight, sex, diet, and medical condition of an immediate and controlled release formulations. individual. Thus, in various embodiments, the dosage regi The pharmaceutical compositions will include at least one men actually employed varies and deviates from the dosage 50 PAK inhibitor, as an active ingredient in free-acid or free-base regimens set forth herein. form, or in a pharmaceutically acceptable Salt form. In addi Examples of Pharmaceutical Compositions and Methods of tion, the methods and pharmaceutical compositions Administration described herein include the use of N-oxides, crystalline Provided herein, in certain embodiments, are compositions forms (also known as polymorphs), as well as active metabo comprising a therapeutically effective amount of any com 55 lites of these PAK inhibitors having the same type of activity. pound described herein (e.g., a compound of Formula I-XV. In some situations, PAK inhibitors exist as tautomers. All Pharmaceutical compositions are formulated using one or tautomers are included within the scope of the compounds more physiologically acceptable carriers including excipients presented herein. Additionally, the PAK inhibitor exists in and auxiliaries which facilitate processing of the active com unsolvated as well as solvated forms with pharmaceutically pounds into preparations which are used pharmaceutically. 60 acceptable solvents such as water, ethanol, and the like. The Proper formulation is dependent upon the route of adminis solvated forms of the PAK inhibitors presented herein are also tration chosen. A Summary of pharmaceutical compositions considered to be disclosed herein. is found, for example, in Remington: The Science and Prac "Carrier materials' include any commonly used excipients tice of Pharmacy, Nineteenth Ed (Ea histon, Pa...: Mack Pub in pharmaceutics and should be selected on the basis of com lishing Company, 1995); Hoover, John E., Remington’s Phar 65 patibility with compounds disclosed herein, such as, a PAK maceutical Sciences, Mack Publishing Co., Easton, Pa. 1975; inhibitor, and the release profile properties of the desired Liberman, H. A. and Lachman, L., Eds. Pharmaceutical Dos dosage form. Exemplary carrier materials include, e.g., bind US 8,372,970 B2 191 192 ers, Suspending agents, disintegration agents, filling agents, a powder (including a sterile packaged powder, a dispensable Surfactants, solubilizers, stabilizers, lubricants, wetting powder, or an effervescent powder) a capsule (including both agents, diluents, and the like. Soft or hard capsules, e.g., capsules made from animal-de Moreover, the pharmaceutical compositions described rived gelatin or plant-derived HPMC, or “sprinkle capsules”), herein, which include a PAK inhibitor, are formulated into 5 Solid dispersion, Solid solution, bioerodible dosage form, any suitable dosage form, including but not limited to, aque controlled release formulations, pulsatile release dosage ous oral dispersions, liquids, gels, syrups, elixirs, slurries, forms, multiparticulate dosage forms, pellets, granules, oran Suspensions and the like, for oral ingestion by a patient to be aerosol. By way of example, Example 26b describes a solid treated, solid oral dosage forms, aerosols, controlled release dosage formulation that is a capsule. In other embodiments, formulations, fast melt formulations, effervescent formula 10 the pharmaceutical formulation is in the form of a powder. In tions, lyophilized formulations, tablets, powders, pills, drag still other embodiments, the pharmaceutical formulation is in ees, capsules, delayed release formulations, extended release the form of a tablet, including but not limited to, a fast-melt formulations, pulsatile release formulations, multiparticulate tablet. Additionally, pharmaceutical formulations of a PAK formulations, and mixed immediate release and controlled inhibitor are optionally administered as a single capsule or in release formulations. In some embodiments, a formulation 15 multiple capsule dosage form. In some embodiments, the comprising a PAK inhibitor is a solid drug dispersion. A Solid pharmaceutical formulation is administered in two, or three, dispersion is a dispersion of one or more active ingredients in or four, capsules or tablets. an inert carrier or matrix at Solid state prepared by the melting In another aspect, dosage forms include microencapsu (or fusion), solvent, or melting-solvent methods. (Chiou and lated formulations. In some embodiments, one or more other Riegelman, Journal of Pharmaceutical Sciences, 60, 1281 compatible materials are present in the microencapsulation (1971)). The dispersion of one or more active agents in a solid material. Exemplary materials include, but are not limited to, diluent is achieved without mechanical mixing. Solid disper pH modifiers, erosion facilitators, anti-foaming agents, anti sions are also called solid-state dispersions. In some embodi oxidants, flavoring agents, and carrier materials such as bind ments, any compound described herein (e.g., a compound of ers, Suspending agents, disintegration agents, filling agents, Formula I-XV is formulated as a spray dried dispersion 25 Surfactants, Solubilizers, stabilizers, lubricants, wetting (SDD). An SDD is a single phase amorphous molecular dis agents, and diluents. persion of a drug in a polymer matrix. It is a Solid Solution Exemplary microencapsulation materials useful for delay prepared by dissolving the drug and a polymer in a solvent ing the release of the formulations including a PAK inhibitor, (e.g., acetone, methanol or the like) and spray drying the include, but are not limited to, hydroxypropyl cellulose ethers solution. The solvent rapidly evaporates from droplets which 30 (HPC) such as Klucel(R) or Nisso HPC, low-substituted rapidly Solidifies the polymer and drug mixture trapping the hydroxypropyl cellulose ethers (L-HPC), hydroxypropyl drug in amorphous form as an amorphous molecular disper methylcellulose ethers (HPMC) such as Seppifilm-LC, Phar Sion. In some embodiments, such amorphous dispersions are macoat(R), Metolose SR, Methocel(R)-E, Opadry YS, Prima filled in capsules and/or constituted into oral powders for Flo, Benecel MP824, and Benecel MP843, methylcellulose reconstitution. Solubility of an SDD comprising a drug is 35 polymers such as Methocel(R-A, hydroxypropylmethylcellu higher than the solubility of a crystalline form of a drug or a lose acetate stearate Aqoat (HF-LS, HF-LG, HF-MS) and non-SDDamorphous form of a drug. In some embodiments Metolose(R), Ethylcelluloses (EC) and mixtures thereof such of the methods described herein, PAK inhibitors are admin as E461, Ethocel(R), Aqualon(R)-EC, Surelease.R., Polyvinyl istered as SDDS constituted into appropriate dosage forms alcohol (PVA) such as Opadry AMB, hydroxyethylcelluloses described herein. 40 such as Natrosol(R), carboxymethylcelluloses and salts of car Pharmaceutical preparations for oral use are optionally boxymethylcelluloses (CMC) such as Aqualon(R)-CMC, obtained by mixing one or more solid excipient with a PAK polyvinyl alcohol and polyethylene glycol co-polymers such inhibitor, optionally grinding the resulting mixture, and pro as Kollicoat IRR, monoglycerides (Myverol), triglycerides cessing the mixture of granules, after adding suitable auxil (KLX), polyethylene glycols, modified food starch, acrylic iaries, if desired, to obtain tablets or dragee cores. Suitable 45 polymers and mixtures of acrylic polymers with cellulose excipients include, for example, fillers such as Sugars, includ ethers such as EudragitR) EPO, EudragitR) L30D-55, ing lactose, Sucrose, mannitol, or Sorbitol; cellulose prepara Eudragit R FS 30D EudragitR) L100-55, EudragitR) L100, tions such as, for example, maize starch, wheat starch, rice Eudragit R 5100, Eudragit R. RD100, EudragitR) E100, starch, potato starch, gelatin, gum tragacanth, methylcellu Eudragit R L 12.5, Eudragit R 512.5, Eudragit R NE30D, and lose, microcrystalline cellulose, hydroxypropylmethylcellu 50 Eudragit(R) NE 40D, cellulose acetate phthalate, sepifilms lose, sodium carboxymethylcellulose; or others such as: such as mixtures of HPMC and stearic acid, cyclodextrins, polyvinylpyrrolidone (PVP or povidone) or calcium phos and mixtures of these materials. phate. If desired, disintegrating agents are added, such as the The pharmaceutical Solid oral dosage forms including for cross linked croScarmellose sodium, polyvinylpyrrolidone, mulations described herein, which include a PAK inhibitor, agar, oralginic acid or a salt thereof Such as sodium alginate. 55 are optionally further formulated to provide a controlled Dragee cores are provided with suitable coatings. For this release of the PAK inhibitor. Controlled release refers to the purpose, concentrated Sugar Solutions are generally used, release of the PAK inhibitor from a dosage form in which it is which optionally contain gum arabic, talc, polyvinylpyrroli incorporated according to a desired profile over an extended done, carbopol gel, polyethylene glycol, and/or titanium period of time. Controlled release profiles include, for dioxide, lacquer Solutions, and Suitable organic solvents or 60 example, Sustained release, prolonged release, pulsatile Solvent mixtures. Dyestuffs or pigments are optionally added release, and delayed release profiles. In contrast to immediate to the tablets or dragee coatings for identification or to char release compositions, controlled release compositions allow acterize different combinations of active compound doses. delivery of an agent to an individual over an extended period In some embodiments, the solid dosage forms disclosed of time according to a predetermined profile. Such release herein are in the form of a tablet, (including a suspension 65 rates provide therapeutically effective levels of agent for an tablet, a fast-melt tablet, a bite-disintegration tablet, a rapid extended period of time and thereby provide a longer period disintegration tablet, an effervescent tablet, or a caplet), a pill, of pharmacologic response while minimizing side effects as