United States Patent 10) Patent No.: US 9.656,9999 9 B2 Cianchetta Et Al

USOO9656999B2

12 United States Patent 10) Patent No.: US 9.656,9999 9 B2 Cianchetta et al. (45) Date of Patent: May 23, 2017

(54) THERAPEUTICALLY ACTIVE COMPOUNDS 8.465,673 B2 6, 2013 Yasuda et al. AND THER METHODS OF USE 2003.0109527 A1 6/2003 Jin et al. 2003/0213405 A1 11/2003 Harada et al. 2006, OO84645 A1 4/2006 Pal et al. (71) Applicant: Agios Pharmaceuticals, Inc., 2007/0244088 A1 10, 2007 Brickmann et al. Cambridge, MA (US) 2009/0093526 A1 4, 2009 Miller et al. 2009,0163508 A1 6/2009 Kori et al. (72) Inventors: Giovanni Cianchetta, Waltham, MA 2009,0163545 A1 6, 2009 Goldfarb (US); Byron DeLaBarre, Arlington 2010/0129350 A1 5/2010 Zacharie et al. MA US : J ta. P . ML s 2010, O144722 A1 6/2010 Alexander et al. (US); Janeta Popovici-Muller, 2011/0073.007 A1 3f2011 Yasuda et al. Waltham, MA (US); Francesco G. 2011/0288065 A1 11/2011 Fujihara et al. Salituro, Marlborough, MA (US); 2012/0164143 A1 6/2012 Teeling et al. Jeffrey O. Saunders, Lincoln, MA 2012/02028.18 A1 8, 2012 Tao et al. (US); Jeremy Travins, Southborough, 2012fO238576 A1 9, 2012 Tao et al. MA (US);(US): ShungSh i YYan, Irvine,Irvi CA,CA 2012,02772332013/0035329 A1 11/20122/2013 TaoSaunders et al. et al. (US); Tao Guo, Dayton, NJ (US); Li 2013,0183281 A1 7, 2013 Su et al. Zhang, Shanghai (CN) 2013/0184222 A1 7/2013 Popovici-Muller et al. 2013, O190249 A1 T/2013 Lemieux et al. (73) Assignee: Agios Pharmaceuticals, Inc., 2013, O190287 A1 7/2013 Cianchetta et al. Cambridge, MA (US) 2013, O197106 A1 8, 2013 Fantin et al. 2C, 2013,0316385 A1 11/2013 Cantley et al. - 2014/0187435 A1 7/2014 Dang et al. (*) Notice: Subject to any disclaimer, the term of this 2014/0206673 A1 7/2014 Cao et al. patent is extended or adjusted under 35 2014/0213580 A1 7, 2014 Cao et al. U.S.C. 154(b) by 0 days. 2015,0018328 A1 1/2015 Konteatis et al. 2015.OO31627 A1 1/2015 Lemieux et al. 2015,00876OO A1 3/2015 Popovici-Muller et al. (21) Appl. No.: 15/337,683 2015/0240286 A1 8/2015 Dang et al. (22) Filed: Oct. 28, 2016 FOREIGN PATENT DOCUMENTS (65) Prior Publication Data CN 101575408 A 11, 2009 CN 102659765 A 9, 2012 US 2017/OO44139 A1 Feb. 16, 2017 CN 103097340 A 5, 2013 DE 3314663 A1 10, 1983 Related U.S. Application Data DE 3512630 A1 10, 1986 EP O945446 A1 9, 1999 (63) Continuation of application No. 15/173,519, filed on (Continued) Jun. 3, 2016, now Pat. No. 9,512,107, which is a continuation of application No. 13/735,467, filed on Jan. 7, 2013. OTHER PUBLICATIONS (60) Provisional application No. 61/584.214, filed on Jan. Ansell et al. “The interactions of artificial coenzymes with alcohol 6, 2012. dehydrogenase and other NAD(P)(H) dependent enzymes' Journal of Molecular Catalysis B: Enzymatic (1999) vol. 6, No. 1-2, pp. (51) Int. C. 111-123. CO7D 40/4 (2006.01) Bhushan et al. "Reversed-phase liquid chromatographic resolution A6 IK3I/53 (2006.01) of diastereomers of protein and non-protein amino acids prepared CO7D 25L/8 (2006.01) with newly synthesized chiral derivatizing reagents based on (52) U.S. C. cyanuric chloride” Amino Acids (2011) vol. 40, pp. 403-409. CPC ...... C07D 401/14 (2013.01); A61 K3I/53 Braun et al. “Triazine-based polymers: 4. MALDI-MS of triazine based polyamines' Polymer (1996) vol. 37, No. 5, pp. 777-783. (2013.01); C07D 251/18 (2013.01) Cairns et al. “Oncogenic Isocitrate Dehydrogenase Mutations: (58) Field of Classification Search Mechanisms, Models, and Clinical Opportunities' Cancer Discov None ery (2013) vol. 3, Iss 7, pp. 730-741. See application file for complete search history. Cecil Textbook of Medicine, edited by Bennet and Plum, (1997) 20th edition, vol. 1, pp. 1004-1010. (56) References Cited (Continued) U.S. PATENT DOCUMENTS Primary Examiner — Savitha Rao 2,390,529 A 12/1945 Friedheim Assistant Examiner — Gregg Polansky 3,755,322 A 8, 1973 Winter et al. (74) Attorney, Agent, or Firm — Jones Day 3,867,383 A 2, 1975 Winter 4,084,053 A 4, 1978. Desai et al. 4,693,726 A 9/1987 Meininger et al. (57) ABSTRACT 5,160,346 A 11/1992 Fusa et al. Provided are compounds useful for treating cancer and 5,489,591 A 2/1996 Kobayashi et al. 6,274,620 B1 8/2001 Labrecque et al. methods of treating cancer comprising administering to a 7,173,025 B1 2/2007 Stocker et al. subject in need thereof a compound described herein. 7,858,782 B2 12/2010 Tao et al. 8,133,900 B2 3/2012 Hood et al. 4 Claims, No Drawings US 9,656.999 B2 Page 2

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CLAIM OF PRIORITY 5

This application is a continuation of U.S. application Ser. No. 15/173,519, filed Jun. 3, 2016, which is a continuation of U.S. application Ser. No. 13/735,467, filed Jan. 7, 2013, which claims priority from U.S. Ser. No. 61/584,214, filed 10 Jan. 6, 2012 each of which is incorporated herein by reference in its entirety. wherein: ring A is an optionally Substituted 5-6 member monocy clic aryl or monocyclic heteroaryl; BACKGROUND OF INVENTION 15 ring B is an optionally Substituted 5-6 member monocy clic aryl or monocyclic heteroaryl; Isocitrate dehydrogenases (IDHs) catalyze the oxidative R" and Rare each independently selected from hydrogen, decarboxylation of isocitrate to 2-oxoglutarate (i.e., C.-keto C-C alkyl, C-C haloalkyl, —O-C-C alkyl, and glutarate). These enzymes belong to two distinct Subclasses, CN, wherein any alkyl portion of R is optionally one of which utilizes NAD(+) as the electron acceptor and substituted with —OH, NH, NH(C-C alkyl), or the other NADP(+). Five isocitrate dehydrogenases have N(C-C alkyl); been reported: three NAD(+)-dependent isocitrate dehydro R is selected from: —(C-C alkyl). —(C-C alkenyl or genases, which localize to the mitochondrial matrix, and two alkynyl), —(C-C alkylene)-N(R)-(C-C alky NADP(+)-dependent isocitrate dehydrogenases, one of as lene)-O (C-C alkyl), —(C-C alkylene)-N(R)— which is mitochondrial and the other predominantly cyto (Co-C alkylene)-Q, —(C-C alkylene)-N(R)(R), solic. Each NADP(+)-dependent isozyme is a homodimer. —(C-C alkylene)-N(R)—S(O), (C-C alkyl). IDH2 (isocitrate dehydrogenase 2 (NADP+), mitochon —(C-C alkylene)-N(R)-S(O)-2-(Co-Co alkyl)-Q, drial) is also known as IDH: IDP; IDHM; IDPM; ICD-M; or —(C-C alkylene)-S(O), N(R)(R), —(C-C, mNADP-IDH. The protein encoded by this gene is the 30 alkylene)-S(O), N(R)—(C-C, alkylene)-Q, NADP(+)-dependent isocitrate dehydrogenase found in the —C(O)N(R)-(C-C alkylene)-C(O)—(Co-Co alky mitochondria. It plays a role in intermediary metabolism and lene)-O (C-C alkyl), C(O)N(R)-(C-C alky energy production. This protein may tightly associate or lene)-C(O)—(C-C alkylene)-O-(C-C alkylene)- interact with the pyruvate dehydrogenase complex. Human Q. —(C-C alkylene)-O-C(O)—(C-C alkyl). IDH2 gene encodes a protein of 452 amino acids. The 35 —(C-C alkylene)-O-C(O)—(Co-Co alkyl)-Q, nucleotide and amino acid sequences for IDH2 can be found —(C-C alkylene)-O-(C-C alkyl). —(C-C alky as GenBank entries NM 002168.2 and NP 002159.2 lene)-O-(C-C alkylene)-Q, —(Co-Co alkylene)-C respectively. The nucleotide and amino acid sequence for (O)—(Co-Co alkylene)-O-(C-C alkyl). —(Co-C human IDH2 are also described in, e.g., Huh et al., Submit alkylene)-C(O)—(C-C alkylene)-O-(C-C alky ted (NOV-1992) to the EMBL/GenBank/DDBJ databases: 40 lene)-Q, —(C-C alkylene)-O-C(O)—(C-C alkyl). and The MGC Project Team, Genome Res. 14:2121-2127 —(C-C alkylene)-O-C(O)—(Co-C alkylene)-Q, (2004). —(Co-Calkylene)-C(O)N(R)—(C-C alkyl). —(Co Non-mutant, e.g., wild type, IDH2 catalyzes the oxidative Calkylene)-C(O)N(R)-(Co-Co alkylene)-Q, —(C- decarboxylation of isocitrate to C.-ketoglutarate (C-KG) C alkylene)-N(R)C(O)—(C-C alkyl). —(C-C, thereby reducing NAD" (NADP") to NADH (NADPH), alkylene)-N(R)C(O)—(Co-C alkylene)-Q, —(Co-C e.g., in the forward reaction: alkylene)-S(O) (C-C alkyl). —(Co-C alkylene)- S(O) (C-C alkylene)-Q, —(C-C alkylene)-N Isocitrate+NAD"(NADP)->C-KG+CO+NADH (NADPH)+H". (R) C(O) N(R)-(C-C alkyl). —(Co-C alky 50 lene)-Q, —(Co-C alkylene)-C(O)—(C-C alkyl). It has been discovered that mutations of IDH2 present in —(C-C alkylene)-C(O)—(C-C alkylene)-Q, certain cancer cells result in a new ability of the enzyme to wherein: catalyze the NAPH-dependent reduction of C.-ketoglutarate any alkyl or alkylene moiety present in R is optionally to R(-)-2-hydroxyglutarate (2HG). 2HG is not formed by substituted with one or more —OH, - O(C-C alkyl) wild-type IDH2. The production of 2HG is believed to 55 or halo: contribute to the formation and progression of cancer (Dang, any terminal methyl moiety present in R is optionally Let al, Nature 2009, 462:739-44). replaced with —CH2OH. CF, —CHF, —CHCl, The inhibition of mutant IDH2 and its neoactivity is C(O)CH, C(O)CF, CN, or COH: therefore a potential therapeutic treatment for cancer. each R is independently selected from hydrogen and Accordingly, there is an ongoing need for inhibitors of IDH2 60 C-C alkyl; and mutants having alpha hydroxyl neoactivity. Q is selected from aryl, heteroaryl, carbocyclyl and het erocyclyl, any of which is optionally substituted; or R" and Rare optionally taken together with the carbon to SUMMARY OF INVENTION which they are attached to form C(=O); or 65 R" and R are optionally taken together to form substi Described herein are compounds of Structural Formula I, tuted carbocyclyl, optionally substituted heterocyclyl or a pharmaceutically acceptable salt or hydrate thereof: or optionally substituted heteroaryl, wherein: US 9,656,999 B2 3 4 a. when ring A is unsubstituted phenyl, and ring B is 2-chloro-4-(methylsulfonyl)-N-4-(phenylamino)-6-(2- phenyl substituted by methoxy or ethoxy; then said pyridinyl)-1,3,5-triazin-2-yl)-benzamide, phenyl of ring B is not further substituted by oxazolyl; N'-(2-methoxyethyl)-N'-phenyl-6-5-6-(2,2,2-trifluoroeth b. when ring A is optionally substituted phenyl or option oxy)-3-pyridinyl-1,2,4-oxadiazol-3-yl-1,3,5-triazine-2, ally substituted pyridyl, and ring B is optionally sub- 5 4-diamine, stituted phenyl; then the portion of the compound N'-(2-furanylmethyl)-6-phenyl-N'-[3-(trifluoromethyl)phe represented by NH C(R)(R)(R) is not NH nyl-1,3,5-triazine-2,4-diamine, (CH)-aryl; 6-(3-methoxyphenyl)-N'-methyl-N'-(3-nitrophenyl)-1,3,5- c. when ring A is optionally Substituted phenyl, and ring triazine-2,4-diamine, B is optionally substituted phenyl or pyrrolyl; then the 10 N-butyl-N'-(4-methylphenyl)-6-phenyl-1,3,5-triazine-2,4- portion of the compound represented by NH-C(R') diamine, and (R)(R) is not NH(CH)C(O)NH: 4-4-(5-chloro-2-methylphenyl)-6-(methylamino)-1,3,5- d. when ring A is phenyl substituted with 2 or more triazin-2-ylamino-benzenemethanol. hydroxyl or methoxy, and ring B is optionally substi The compound of Formula I or II or as described in any tuted phenyl; then the portion of the compound repre 15 one of the embodiments herein inhibits mutant IDH2, par sented by NH C(R)(R)(R) is not NH-cyclo ticularly mutant IDH2 having alpha hydroxyl neoactivity. heptyl: Also described herein are pharmaceutical compositions e. when ring A is optionally Substituted phenyl and ring B comprising a compound of Formula I and methods of using is optionally substituted phenyl; then R' and R do not Such compositions to treat cancers characterized by the form 2.2.6.6.-tetramethylpiperidin-4-yl; presence of a mutant IDH2. f, when ring A and ring B are optionally substituted phenyl; then the portion of the compound represented DETAILED DESCRIPTION by NH COR')(R)(R) is not cysteine, optionally substituted phenylalanine or leucine or methyl ester The details of construction and the arrangement of com thereof; 25 ponents set forth in the following description or illustrated in g. when ring A is phenyl or pyridin-3-yl optionally the drawings are not meant to be limiting. Other embodi Substituted with one or more substituents selected from ments and different ways to practice the invention are halo, methyl or CF, and ring B is phenyl optionally expressly included. Also, the phraseology and terminology Substituted with one or more substituents selected from used herein is for the purpose of description and should not halo, methyl, CF, methoxy, CH=C(phenyl)CN; then 30 be regarded as limiting. The use of “including.” “compris the portion of the compound represented by NHC ing,” or “having.” “containing”, “involving, and variations (R')(R)(R) is other than -NH(C-C alkylene)-N thereof herein, is meant to encompass the items listed (R)(R), NH-1-(aminomethyl)cyclopentylmethyl, thereafter and equivalents thereof as well as additional —NH-4-(aminomethyl)cyclohexylmethyl, wherein items. each R" is hydrogen, C-C alkyl or two R's are taken 35 together with the nitrogen to which they are commonly DEFINITIONS bound to form morpholin-4-yl or pipieridin-1-yl: h. when ring A is phenyl, 4-chlorophenyl or 4-methyl The term “halo' or “halogen refers to any radical of phenyl and ring B is 4-chlorophenyl or 3,4-dichloro fluorine, chlorine, bromine or iodine. phenyl; then the portion of the compound represented 40 The term “alkyl refers to a fully saturated or unsaturated by NHC(R')(R)(R) is not NH-isopropyl: hydrocarbon chain that may be a straight chain or branched i. when ring A is unsubstituted phenyl and the portion of chain, containing the indicated number of carbon atoms. For the compound represented by NHC(R')(R)(R) is example, C-C alkyl indicates that the group may have —NH CHCHN(CH), NH CHCH-morpho from 1 to 12 (inclusive) carbon atoms in it. The term lin-4-yl or —NH CHCH-OH; then ring B is other 45 “haloalkyl refers to an alkyl in which one or more hydrogen than oxadiazole, imidazole, thiazole or oxazole each of atoms are replaced by halo, and includes alkyl moieties in which is substituted with –C(O)NHR', wherein R is which all hydrogens have been replaced by halo (e.g., isopropyl, cyclopropyl or 2-chloro-6-methylphenyl; perfluoroalkyl). The terms “arylalkyl or “aralkyl refer to j. when ring A is phenyl substituted with SOOH or an alkyl moiety in which an alkyl hydrogen atom is replaced SONa and ring B is phenyl, or when ring B is phenyl 50 by an aryl group. Aralkyl includes groups in which more substituted with SOOH and ring A is substituted than one hydrogen atom has been replaced by an aryl group. phenyl; then the portion of the compound represented Examples of “arylalkyl or “aralkyl include benzyl, 2-phe by NHC(R')(R)(R) is not NH(CH)OH or nylethyl, 3-phenylpropyl, 9-fluorenyl, benzhydryl, and trityl NH(CH)CH(OH)CH; and groups. The term “alkyl includes “alkenyl' and “alkynyl'. k. the compound is other than: 55 The term “alkylene' refers to a divalent alkyl, e.g., (E)-3-(4-((4-((3-(diethylamino)propyl)amino)-6-phenyl-1, —CH2—, —CH2CH2—, —CH2CH2CH2— and —CHCH 3,5-triazin-2-yl)amino)-2-methoxyphenyl)-2-phenylacry (CH)CH2—. lonitrile, The term “alkenyl refers to a straight or branched hydro 4-((4-((furan-2-ylmethyl)amino)-6-(pyridin-4-yl)-1,3,5-tri carbon chain containing 2-12 carbon atoms and having one azin-2-yl)amino)phenol, 3-(4-((5-aminopentyl)amino)-6- 60 or more double bonds. Examples of alkenyl groups include, ((3-fluorophenyl)amino)-1,3,5-triazin-2-yl)phenol, but are not limited to, allyl, propenyl, 2-butenyl, 3-hexenyl N,6-bis(3-fluorophenyl)-N'-(piperidin-3-yl)-1,3,5-triaz and 3-octenyl groups. One of the double bond carbons may ine-2,4-diamine, optionally be the point of attachment of the alkenyl sub N-butyl-6-phenyl-N'-(p-tolyl)-1,3,5-triazine-2,4-diamine, stituent. N'-cyclohexyl-N,6-diphenyl-1,3,5-triazine-2,4-diamine, 65 The term “alkynyl refers to a straight or branched (R)-3-((4-(3-chlorophenyl)-6-(pyrrolidin-3-ylamino)-1,3,5- hydrocarbon chain containing 2-12 carbon atoms and char triazin-2-yl)amino)-4-methylbenzamide, acterized in having one or more triple bonds. Examples of US 9,656,999 B2 5 6 alkynyl groups include, but are not limited to, ethynyl, tuted at one or more Substitutable atoms with, unless speci propargyl, and 3-hexynyl. One of the triple bond carbons fied otherwise, substituents independently selected from: may optionally be the point of attachment of the alkynyl halo, -C=N, C-C alkyl, =O, —OR. -OR', SR, substituent. —SR, -(C-C alkyl)-N(R)(R), —(C-C alkyl)-N(R) The term “alkoxy' refers to an —O-alkyl radical. The (R), N(R)(R), N(R)(R), O (C-C alkyl)-N term “haloalkoxy' refers to an alkoxy in which one or more (R')(R), O (C-C alkyl)-N(R)(R), (C-C alkyl)- hydrogen atoms are replaced by halo, and includes alkoxy O (C-C alkyl)-N(R)(R), —(C-C alkyl)-O (C-C, moieties in which all hydrogens have been replaced by halo alkyl)-N(R)(R), C(O) N(R)(R), —(C-C alkyl)-C (e.g., perfluoroalkoxy). (O) N(R)(R), —(C-C alkyl)-C(O) N(R)(R), Unless otherwise specified, the term “aryl refers to a 10 —OR, R = C(O)(C-C alkyl), C(O)R’ –C(O)N fully aromatic monocyclic, bicyclic, or tricyclic hydrocar (R)(R), N(R)C(O)(R), N(R)C(O)(R), N(R) bon ring system. Examples of aryl moieties are phenyl, SO.(R), SON(R)(R), N(R)SO.(R), and SON naphthyl, and anthracenyl. Unless otherwise specified, any (R')(R'), wherein any alkyl substituent is optionally further ring atom in an aryl can be substituted by one or more substituted with one or more of OH, - O (C-C alkyl). Substituents. The term "monocyclic aryl' means a monocy 15 halo. —NH2, —NH(C-C alkyl), or —N(C-C alkyl); clic fully romatic hydrocarbon ring system, optionally Sub each R is independently selected from hydrogen, and stituted by one or more substituents which can not form a —C-C alkyl, or fused bicyclic or tricyclic ring. two R's are taken together with the nitrogen atom to The term “carbocyclyl refers to a non-aromatic, mono which they are bound to form a 4- to 8-membered cyclic, bicyclic, or tricyclic hydrocarbon ring system. Car heterocyclyl optionally comprising one additional het bocyclyl groups include fully saturated ring systems (e.g., eroatom selected from N. S., and O; and cycloalkyls), and partially saturated ring systems. each R is independently selected from C-C, carbocy The term "cycloalkyl as employed herein includes satu clyl phenyl, heteroaryl, and heterocyclyl, wherein one rated cyclic, bicyclic, tricyclic, or polycyclic hydrocarbon or more Substitutable positions on said phenyl, groups having 3 to 12 carbons. Any ring atom can be 25 cycloalkyl, heteroaryl or heterocycle substituent is Substituted (e.g., by one or more substituents). Examples of optionally further substituted with one or more of cycloalkyl moieties include, but are not limited to, cyclo —(C-C alkyl). —(C-C fluoroalkyl). —OH, -O- propyl, cyclohexyl, methylcyclohexyl, adamanty1, and nor (C-C alkyl), —O—(C-C fluoroalkyl), halo. —NH, bornyl. —NH(C-C alkyl), or —N(C-C alkyl). Unless otherwise specified, the term "heteroaryl” refers to 30 Heterocyclyl groups, either alone or as part of a group, are a fully aromatic 5-8 membered monocyclic, 8-12 membered optionally substituted on one or more any substitutable bicyclic, or 11-14 membered tricyclic ring system having nitrogen atom with oxo. —C-C alkyl, or fluoro-substituted 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, C-C alkyl. or 1-9 heteroatoms if tricyclic, said heteroatoms selected The term “substituted” refers to the replacement of a from O, N, or S (or the oxidized forms such as N' O, S(O) 35 hydrogen atom by another group. and S(O)). The term “monocyclic heteroaryl' means a As used herein, the term "elevated levels of 2HG' means monocyclic fully romatic ring system having 1-3 heteroa 10%, 20% 30%, 50%, 75%, 100%, 200%, 500% or more toms, optionally substituted by one or more Substituents 2HG then is present in a subject that does not carry a mutant which can not form a fused bicyclic or tricyclic ring. IDH2 allele. The term “elevated levels of 2HG” may refer to The term "heterocyclyl refers to a nonaromatic, 3-10 40 the amount of 2HG within a cell, within a tumor, within an membered monocyclic, 8-12 membered bicyclic, or 11-14 organ comprising a tumor, or within a bodily fluid. membered tricyclic ring system having 1-3 heteroatoms if The term “bodily fluid includes one or more of amniotic monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms fluid Surrounding a fetus, aqueous humour, blood (e.g., if tricyclic, said heteroatoms selected from O, N, or S (or the blood plasma), serum, Cerebrospinal fluid, cerumen, chyme, oxidized forms such as N' O, S(O) and S(O)). The 45 Cowper's fluid, female ejaculate, interstitial fluid, lymph, heteroatom may optionally be the point of attachment of the breast milk, mucus (e.g., nasal drainage or phlegm), pleural heterocyclyl substituent. Examples of heterocyclyl include, fluid, pus, saliva, sebum, semen, serum, Sweat, tears, urine, but are not limited to, tetrahydrofuranyl, tetrahydropyranyl, vaginal Secretion, or vomit. piperidinyl, morpholino, pyrrolinyl, pyrimidinyl, and pyrro As used herein, the terms “inhibit or “prevent include lidinyl. Heterocyclyl groups include fully saturated ring 50 both complete and partial inhibition and prevention. An systems, and partially saturated ring systems. inhibitor may completely or partially inhibit the intended Bicyclic and tricyclic ring systems containing one or more target. heteroatoms and both aromatic and non-aromatic rings are The term “treat’ means decrease, Suppress, attenuate, considered to be heterocyclyl or heteroaryl groups. Bicyclic diminish, arrest, or stabilize the development or progression or tricyclic ring systems where an aryl or a heteroaryl is 55 of a disease? disorder (e.g., a cancer), lessen the severity of fused to a carbocyclyl or heterocyclyl and the point of the disease/disorder (e.g., a cancer) or improve the Symp attachment from the ring system to the rest of the molecule toms associated with the disease/disorder (e.g., a cancer). is through an aromatic ring are considered to be aryl or As used herein, an amount of a compound effective to heteroaryl groups, respectively. Bicyclic or tricyclic ring treat a disorder, or a “therapeutically effective amount systems where an aryl or a heteroaryl is fused to a carbo 60 refers to an amount of the compound which is effective, cyclyl or heterocyclyl and the point of attachment from the upon single or multiple dose administration to a subject, in ring system to the rest of the molecule is through the treating a cell, or in curing, alleviating, relieving or improv non-aromatic ring are considered to be carbocyclyl (e.g., ing a subject with a disorder beyond that expected in the cycloalkyl) or heterocyclyl groups, respectively. absence of Such treatment. Aryl, heteroaryl, carbocyclyl (including cycloalkyl), and 65 As used herein, the term “subject' is intended to include heterocyclyl groups, either alone or a part of a group (e.g., human and non-human animals. Exemplary human Subjects the aryl portion of an aralkyl group), are optionally Substi include a human patient (referred to as a patient) having a US 9,656,999 B2 7 8 disorder, e.g., a disorder described herein or a normal R" and Rare optionally taken together with the carbon to subject. The term “non-human animals” of one aspect of the which they are attached to form C(=O); or invention includes all vertebrates, e.g., non-mammals (such R" and R are optionally taken together to form an as chickens, amphibians, reptiles) and mammals, such as optionally substituted carbocyclyl, optionally Substi non-human primates, domesticated and/or agriculturally tuted heterocyclyl or optionally substituted heteroaryl; useful animals, e.g., sheep, dog, cat, cow, pig, etc. wherein: Compounds a. when ring A is unsubstituted phenyl, and ring B is Provided is a compound of Structural Formula I, or a phenyl substituted by methoxy or ethoxy; then said pharmaceutically acceptable salt or hydrate thereof: phenyl of ring B is not further substituted by oxazolyl; 10 b. when ring A is optionally substituted phenyl or option ally Substituted pyridyl, and ring B is optionally Sub (I) stituted phenyl; then the portion of the compound represented by NH C(R)(R)(R) is not NH (CH)-aryl; 15 c. when ring A is optionally Substituted phenyl, and ring N1 NN R1 B is optionally substituted phenyl or pyrrolyl; then the portion of the compound represented by NH-C(R) Ou 2 R2, N N N R3 (R)(R) is not NH(CH)C(O)NH: H H d. when ring A is phenyl substituted with 2 or more hydroxyl or methoxy, and ring B is optionally substi wherein: tuted phenyl; then the portion of the compound repre ring A is an optionally Substituted 5-6 member monocy sented by NH-C(R')(R)(R) is not NH-cyclo clic aryl or monocyclic heteroaryl; heptyl: 25 e. when ring A is optionally Substituted phenyl and ring B ring B is an optionally Substituted 5-6 member monocy is optionally substituted phenyl; then R' and R do not clic aryl or monocyclic heteroaryl; form 2.2.6.6.-tetramethylpiperidin-4-yl; R" and Rare each independently selected from hydrogen, f, when ring A and ring B are optionally Substituted C-C alkyl, C-C haloalkyl, -O-C-C alkyl, and CN. phenyl; then the portion of the compound represented wherein any alkyl portion of R' is optionally substituted 30 by NH C(R)(R)(R) is not cysteine, optionally with —OH, NH, NH(C-C alkyl), or N(C-C alkyl); substituted phenylalanine or leucine or methyl ester R is selected from: —(C-C alkyl), —(C-C alkenyl or thereof; alkynyl), —(C-C alkylene)-N(R)-(C-C alkylene)-O- g. when ring A is phenyl or pyridin-3-yl optionally (C-C alkyl). —(C-C alkylene)-N(R)-(Co-Co alky Substituted with one or more substituents selected from lene)-Q, —(C-C alkylene)-N(R)(R), —(C-C alky 35 halo, methyl or CF, and ring B is phenyl optionally lene)-N(R)-S(O)-2-(C-C alkyl). —(C-C alkylene)- Substituted with one or more substituents selected from N(R)-S(O)12 (Co-Co alkyl)-Q, —(C-C alkylene)-S halo, methyl, CF, methoxy, CH=C(phenyl)CN; then (O), N(R)(R), —(C-C alkylene)-S(O), N(R)— the portion of the compound represented by NHC (C-C alkylene)-Q, —C(O)N(R)-(C-C alkylene)-C (R')(R)(R) is other than -NH(C-C alkylene)-N (O) (C-C alkylene)-O (C-C alkyl), —C(O)N(R)— 40 (R)(R), NH-1-(aminomethyl)cyclopentylmethyl, (C-C alkylene)-C(O)—(Co-C alkylene)-O-(Co-Co —NH-4-(aminomethyl)cyclohexylmethyl, wherein alkylene)-Q, —(C-C alkylene)-O—C(O)—(C-C alkyl). each R" is hydrogen, C-C alkyl or two R's are taken —(C-C alkylene)-O-C(O)—(Co-Co alkyl)-Q, —(C-C, together with the nitrogen to which they are commonly alkylene)-O-(C-C alkyl). —(C-C alkylene)-O-(C-C, bound to form morpholin-4-yl or pipieridin-1-yl: alkylene)-Q, —(Co-Co alkylene)-C(O)—(Co-C alkylene)- 45 h. when ring A is phenyl, 4-chlorophenyl or 4-methyl O—(C-C alkyl). —(C-C alkylene)-C(O)—(Co-C alky phenyl and ring B is 4-chlorophenyl or 3,4-dichloro lene)-O-(C-C alkylene)-Q, —(C-C alkylene)-O-C phenyl; then the portion of the compound represented (O)—(C-C alkyl). —(C-C alkylene)-O-C(O)—(Co-Co by NHC(R')(R)(R) is not NH-isopropyl: alkylene)-Q, —(C-C alkylene)-C(O)N(R)-(C-C, i. when ring A is unsubstituted phenyl and the portion of alkyl), —(Co-Co alkylene)-C(O)N(R)-(Co-Co alkylene)- 50 the compound represented by NHC(R')(R)(R) is Q. —(C-C alkylene)-N(R)C(O)—(C-C alkyl), —(C- —NH CHCHN(CH), NH CHCH-morpho C alkylene)-N(R)C(O)—(Co-C alkylene)-Q, —(Co-Co lin-4-yl or —NH CHCH-OH; then ring B is other alkylene)-S(O)o (C-C alkyl). —(Co-Co alkylene)- than oxadiazole, imidazole, thiazole or oxazole each of S(O) (Co-C alkylene)-Q, —(C-C alkylene)-N(R)— which is substituted with –C(O)NHR', wherein R is C(O) N(R)-(C-C alkyl), —(Co-Co alkylene)-Q, 55 isopropyl, cyclopropyl or 2-chloro-6-methylphenyl; —(C-C alkylene)-C(O)—(C-C alkyl). —(C-C alky j. when ring A is phenyl substituted with SOOH or lene)-C(O)—(C-C alkylene)-Q, wherein: SONa and ring B is phenyl, or when ring B is phenyl any alkyl or alkylene moiety present in R is optionally substituted with SOOH and ring A is substituted substituted with one or more —OH, - O(C-C alkyl) or phenyl; then the portion of the compound represented halo; 60 by NHC(R')(R)(R) is not NH(CH)OH or any terminal methyl moiety present in R is optionally NH(CH)CH(OH)CH; and replaced with —CH2OH. CF, —CHF, —CH2C1, C(O) k. the compound is other than: CH, C(O)CF, CN, or COH: (E)-3-(4-((4-((3-(diethylamino)propyl)amino)-6-phenyl-1, each R is independently selected from hydrogen and 3.5-triazin-2-yl)amino)-2-methoxyphenyl)-2-phenylacry C-C alkyl; and 65 lonitrile, Q is selected from aryl, heteroaryl, carbocyclyl and het 4-((4-((furan-2-ylmethyl)amino)-6-(pyridin-4-yl)-1,3,5-tri erocyclyl; and Q is optionally Substituted; or azin-2-yl)amino)phenol,

US 9,656,999 B2 11 12 substituted with –C(O)NHR', wherein R is isopro In some embodiments, ring A is selected from phenyl, pyl, cyclopropyl or 2-chloro-6-methylphenyl: pyrazolyl, oxazolyl, isoxazolyl pyridinyl, pyrimidinyl, j. when ring A is phenyl substituted with SOOH or pyrazinyl, and thiazolyl, wherein ring A is optionally Sub SONa, and ring B is phenyl; then the portion of the stituted with up to two substituents independently selected compound represented by NHC(R')(R)(R) is not from halo. —C-C alkyl, -C-C haloalkyl, -C-C, - NH(CH)OH or -NH(CH)CH(OH)CH; and hydroxyalkyl, - NH S(O)—(C-C alkyl). —S(O)NH k. the compound is other than: (C-C alkyl). —CN. —S(O) (C-C alkyl), C-C, (E)-3-(4-(4-((3-(diethylamino)propyl)amino)-6-phenyl alkoxy, NH(C-C alkyl). —OH, —CN, and —NH. 1.3.5-triazin-2-yl)amino)-2-methoxyphenyl)-2-phenylacry In some embodiments, ring B is selected from phenyl, lonitrile, 4-(4-((furan-2-ylmethyl)amino)-6-(pyridin-4-yl)- 10 pyrazolyl, oxazolyl, isoxazolyl, thiazolyl pyridinyl, pyrim 1.3.5-triazin-2-yl)amino)phenol, 3-(4-((5-aminopentyl) idinyl, pyridazinyl, and pyrazinyl, wherein ring B is option amino)-6-((3-fluorophenyl)amino)-1,3,5-triazin-2-yl) ally substituted with up to two substituents independently selected from halo. —C-C alkyl, -C-C alkynyl, —C- phenol, N,6-bis(3-fluorophenyl)-N'-(piperidin-3-yl)-1,3,5- C haloalkyl, -C-C hydroxyalkyl, C-C cycloalkyl, triazine-2,4-diamine, N-butyl-6-phenyl-N'-(p-tolyl)-1,3,5- 15 —(Co-C alkylene)-O-C-C alkyl, —O—(C-C alky triazine-2,4-diamine, N'-cyclohexyl-N,6-diphenyl-1,3,5- lene)-C-C cycloalkyl, -NH S(O) (C-C alkyl). triazine-2,4-diamine, and (R)-3-((4-(3-chlorophenyl)-6- —S(O)NH(C-C, alkyl). —S(O). NH (C-C, (pyrrolidin-3-ylamino)-1,3,5-triazin-2-yl)amino)-4- cycloalkyl). —S(O)-(saturated heterocyclyl), —CN. methylbenzamide. —S(O) (C-C alkyl). —NH(C-C alkyl). —N(C-C, In some embodiments, R' is independently selected from alkyl). —OH, C(O)—O—(C-C alkyl), saturated hetero hydrogen, —CH, —CHCH. —CH-OH, CN, or R' and R' cyclyl, and —NH. are taken together to form —O. In another embodiment, the compound is a compound In some embodiments, R' and R are taken together to having Structural Formula II: form carbocyclyl or heterocyclyl, either of which is option ally substituted with up to 3 substituents independently 25 selected from halo. C-C alkyl, C-C haloalkyl, C-C, alkoxy, —CN, =O. —OH, and —C(O)C-C alkyl. In some embodiments, R is —(C-C alkyl) optionally substituted with fluoro or —OH: —(C-C alkylene)-O- (C-C alkyl). —(Co-C, alkylene)-N(R)-(C-C alkyl). 30 —(Co-C alkylene)-Q, and —O—(Co-C alkylene)-Q. N n N R1a wherein Q is optionally substituted with up to 3 substituents GD I 2 R2a, independently selected from C-C alkyl, C-C haloalkyl, N N N R3a C-C alkoxy, =O. —C(O)—C-C alkyl, —CN, and halo. H H In one aspect of these embodiments, Q is selected from 35 pyridinyl, tetrahydrofuranyl, cyclobutyl, cyclopropyl, phe or a pharmaceutically acceptable salt thereof, wherein: nyl, pyrazolyl, morpholinyl and oxetanyl, wherein Q is Ring A' is selected from phenyl and pyridin-2-yl, wherein optionally substituted with up to 2 substituents indepen ring A' is optionally substituted with one or two substituents dently selected from C-C alkyl, C-C haloalkyl, =O. independently selected from chloro, fluoro. —CF, —CHF fluoro, chloro, and bromo. In another aspect of these 40 —CH, —CHCH. —CFCH —OH, —OCH, embodiments, Q is selected from pyridinyl, tetrahydrofura —OCHCH —NH —NH(CH), and —N(CH): nyl, cyclobutyl, cyclopropyl, phenyl, pyrazolyl, morpholinyl Ring B' is selected from pyridin-3-yl pyridin-4-yl, isox and oxetanyl, wherein Q is optionally substituted with up to aZoly-4-yl, isoxazol-3-yl, thiazol-5-yl, pyrimidin-5-yl and 2 substituents independently selected from —CH and —O. pyrazol-4-yl, wherein ring B' is optionally substituted with In some embodiments, R' and R are taken together to 45 one to two substituents independently selected from halo: form cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, tet —CN; —OH: C-C alkyl optionally substituted with halo, rahydrofuranyl, tetrahydropyranyl, oxetanyl, bicyclo2.2.1 CN or —OH: —S(O), C-C alkyl:—S(O)—C-C alkyl: heptanyl, Oxobicyclo3.1.0 hexanyl, azetidinyl, phenyl and —S(O). NH-C-C alkyl; —S(O), N(C-C alkyl); pyridinyl, any of which is optionally substituted with up to —S(O)-azetidin-1-yl; —O—C-C alkyl; —CH2—O— 2 substituents independently selected from C-C alkyl, 50 CH, morpholin-4-yl, cyclopropyl. —S(O). NH-cyclopro C-C alkoxy, C-C cycloalkyl, -OH, -C(O)CH, fluoro, pyl; —C(O)—O—CH; and and chloro. —C(R')(R)(R) is selected from C-C alkyl option In some embodiments, ring A is an optionally substituted ally substituted with halo or —OH: —(C-C alkylene)- 6-membered monocyclic aryl. In some embodiments, ring A cycloalkyl, wherein the alkylene is optionally substituted is an optionally substituted 5-6 membered heteroaryl. In 55 with methyl and the cycloalkyl is optionally substituted with Some embodiments, ring A is an optionally Substituted 6 halo, —OCH or methyl; saturated heterocyclyl optionally membered heteroaryl. substituted with halo or methyl; —C(O)—O C-C alkyl; In some embodiments, ring A is selected from phenyl, —C(O)—(Co-C alkylene)-cyclopropyl; and C(O)-benzyl. pyrazolyl, oxazolyl, isoxazolyl pyridinyl, pyrimidinyl, In certain embodiments of Formula II, ring A' is selected pyrazinyl, and thiazolyl, wherein ring A is optionally Sub 60 from 2-chlorophenyl, 2-fluorophenyl, 2-methoxyphenyl, stituted with up to two substituents independently selected 3-hydroxyphenyl, 6-aminopyridin-2-yl, 6-chloropyridin-2- from halo. —C-C alkyl, -C-C haloalkyl, -C-C, y1, 6-trifluoromethylpyridin-2-yl, and phenyl. hydroxyalkyl, - NH S(O) (C-C alkyl). —S(O)NH In certain embodiments of Formula II, ring B' is selected (C-C alkyl). —CN. —S(O) (C-C alkyl), C-C, from 2-(morpholin-4-yl)pyridin-4-yl, 2-dimethylaminopyri alkoxy, NH(C-C alkyl). —OH, - OCF. —CN, NH, 65 din-4-yl, 3-(2-methyoxyethyl)phenyl, 3,5-difluorophenyl, —C(O)NH2. —C(O)NH(C-C alkyl), —C(O)—N(C-C, 3-chlorophenyl, 3-cyanomethylphenyl, 3-cyanophenyl, alkyl), and cyclopropyl optionally substituted with OH. 3-cyclopropylaminosulfonylphenyl, 3-dimethylaminosulfo

US 9,656,999 B2

TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

5 Cmpd Cmpd No Structure No Structure

103 112 10 1.HN s 15 als N l Nals N 1. N NH H H

20 113 108 CN

25 1.n - - - N N N N N H H 114 NN

109 35 2

V/S n N1 N N N

40 NN N N N

N N N 115 O N 45 110 -A n es O.C.-l

116 N 55

65 US 9,656,999 B2 19 20 TABLE 1-continued TABLE 1-continued

Representative Compounds

Cmpd No Structure

117 C

l Nals 118

l Nals

119 126

120 128 45

50 1.

121 129

65 US 9,656,999 B2 21 22 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 130 139 10

CN 15

132 140

133 30

OH 141 35

40 135

45 143

55 137 145

65 US 9,656,999 B2 23 24 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

146 151

Ns uCl N 1. 15 /\, N l, H

147 20 154 s ls ses N N

148 N 30 / 155 HN a ses 35 40

149 156

C 50

55 150 158 C

65 US 9,656,999 B2 25 26 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

159 168 ls 10 es ON HN 15 es- O N N H

160

169

162 170

35 1 - C

16S 172 45

55 173 167

65 US 9,656,999 B2 27 28 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds 5 Cmpd Cmpd No No Structure 179 174 O u) 10 es 2 CuON N H

181

175

1. 25

Nals N O H 30

182 176

177

HN 1. 183

als N 50 Ns N -Cl s1'N,

55 178

HN 1. 184 es 60

Nals N F H

65 US 9,656,999 B2 29 30 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd No

185

Na N 1C-l 186

2 C C N JC, 187

21 C C S JCIC 188

2 C N JClu?

189

N21 C C N JCX JCl 190

21 C C N US 9,656,999 B2

TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

5 Cmpd Cmpd No Structure No Structure

2O3 198 10

NC N1 NN N1 NN 15 - als 1.12 - H 1N 4 N N N H H

199 20 204 H O C N4 No n 25 N1 NN

30 2OO 205

O 1No 1-4M 35 no N21 NN N1 NN

N 40

45 1. O HO S. --- 50 ---

65 US 9,656,999 B2 33 34 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure Structure 208

- N als l Nals 209 C C JCl 1. C C US 9,656,999 B2 35 36 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 223 218

/ N N 1. l als >A 15 H JC H N N N H H 224 219

\/ 1. US 9,656,999 B2 37 38 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds

Cmpd 5 Cmpd No No Structure

229 234

230

235

30 231

rsN HO 2

35 236

N N N H H 40

232

45 237 HN es O 50

233 55

238

65 US 9,656,999 B2 39 40 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 244

239 10

N Nals H N

OH 245 240

N l als OH N r 30

241 246 N 35

l als 40 N 1

242 45 247

l 50 N

243 55

248

65 US 9,656,999 B2 41 42 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Structure No Structure

249

l Nals N N l Nals H H

250

l als N N s H us Nals

251

N l Nals H l Nals N H

252

253 US 9,656,999 B2 43 44 TABLE 1-continued TABLE 1-continued

Cmpd No

259

260

261

262 abs

21 N O-on

263

N21 N US 9,656,999 B2 45 46 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd No Structure Structure

269

l als N N N OS l Nals H H

270 275

271 276 35

OH 40

45 272 277

273 278

OH 65 US 9,656,999 B2 47 48 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure

279

21 N 21 N

S N N l Nals N H H -Q

28O

Z 21 S N 21 N

281 OH

N 1. H

N 282

283 abs

iOH US 9,656,999 B2 49 50 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

290 295

l Nals ZEI: l

296 291

297 292 35

1. 40

298 45 293

50 s 55 299 294

65 US 9,656,999 B2 51 52 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd No Structure

3OO

Nals N H 301 C

Nals N l, Cl-l H 3O2 C

Nals N Cl H 303 C

ul Nals N C-l H 3O4 C -- H

305

C s l Nals US 9,656,999 B2 53 54 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

3.18 313 10 F F

N n / N N 1 is 1. 15 usual-O S N N N H H H H 319 314 2O

CF3 F N21 NN N21 N1 SN 1. 25 Null-l N S H 's--H H OH

320 315 35 F F 1 is N& H--- H H

45 316 321

CN F 50 21 N sus-s-s NS1 ----- H H H 55 317 322 N O F 2N N4 -o 60 N1 NN sus-s-sOl CD 65 H H US 9,656,999 B2 55 56 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd No

323

r Nr S. -D

324 CF3 21al

N C

325 r N ---(~(_---(---(5--(--( 21al -O |O-OO-OO-OE

326

O M SO \ N 5ZEI:ZIz-EERZZIZIZEI: 1. ClN 327

CF3 N21N 1. Nr US 9,656,999 B2 57 58 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure Cmpd No Structure 335 342 10 CF

N 15

O O

343

25 *--()© 30 ---(---(O!!!% 35 344 O-O ZI£ZEI: 40 45 340 /~{ŽT,/~{

341 US 9,656,999 B2 59 60 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 353

347

10 r N&

348 C N21 N

30 CN

350 N 35

356

351 45 N

357

OH 55 352 abs 358

o 65 US 9,656,999 B2 61 62 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

364 |IZ / 359 10 /

365 360

366

361 35

367 362 45

55 363 368

Nin OH 65 US 9,656,999 B2 63 64 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure 5 No Structure

369 377

CN 10

21 N N C O N l N Pl als 1. l N 15 OF N N N N 370 378 C

N 2 N C. O N l l N l 25 N N 371 379 C

N d NC N l -U 35 N l N N

372 380 CF 3

CF 40 21 C. NN l 45 C N l N U H N 374 381

50 1 NC. NN l 55 rN l

376

SEO 60 n N 1. 65 r 1. N l N N US 9,656,999 B2 65 66 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

383 C 388 N C N 10 2N F 2N

N NN 21 N NN 15 NS N& N N 11. N --- 1. H H H H OH US 9,656,999 B2 67 68 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds 5 Cmpd Cmpd No Structure No Structure 398 N NH2 393 N 10 N F 2 F 2N

N21 NN F N N N O 15 oucH H Nussels 399 C

394 rsN s1' F 2 CF 2N 21 N1 NN 21 N1 NN 25 N l als H H NS N N N r

30 395 400 C

O \\NN / rsN 35 N.Zo 2

N N N 40 H H

396 s1''' 45 401 N CF CF 2 N CN 2 N21 N1 NN 21 N1 NN N lu-llN N H H N N N l Nals N 1. H H 397 55 402 N CF N N 2N F 2

60 N21 NN S S N l Nals

/\, H 65 US 9,656,999 B2 69 70 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds 5 Cmpd Cmpd No Structure No Structure 408 N CF 403 N 10 CN 2N CN 2N N21 N NN N nN. 15 S N - als N N H H N --- N H H

404 409

CN 25 CF3 N21 N 30 OH

40S

CN 35 410

NS 40 OH

406 45 411 CF3

50 NS OH

55 CF N 412

OH 65 US 9,656,999 B2 71 72 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd No Structure

413

O N

Z N21

l als S N N N N H JC H H

414

ul Nals N H

415

O YséNo F s l als N l N N H H

416

l Nals N l H c

450

F F

N l Nals Sa N l ZIZEI:ZIZIC)- H H US 9,656,999 B2 73 74 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure Cmpd No Structure 458 463 10

2O 459 464

460 465

466 45 461

55 467

462

65 US 9,656,999 B2 75 76 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd No Structure

468

F F

N l H

469

F F

N N N l H

470 F

F l N H 471 Y

-sels c 472

2 -sels to US 9,656,999 B2 77 78 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No No Structure

478 483 C C 10

479 20 484

485

481 486 45

55 487

482 HO N F

65 US 9,656,999 B2 79 80 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

488 493 10

494

489

30 495

490 F F HO S 35 F l N21 N1 NN N 40

N ---N N H H 496 C

491 rs s-N: 45 F F 2N l F r is Na NN 50 N N l Nals N ls us H H N N 1< HO F

55 497 F 492 N-N'- l HO 60 N21 NN N21 N -----N N H 65 US 9,656,999 B2 81 82 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

503 Cl 498 FIZ

SO4 499 2O

25 Nin

30 505 500

40 Nin

SO1 SO6

OH N

502 55 507

N21 N NN

N N - N - 65 US 9,656,999 B2

TABLE 1-continued TABLE 1-continued Representative Compounds - Representative Compounds Cmpd Cmpd 5 No Structure No Structure 513 C 21 SO8 F F N N 21 F 10

21 NN AO 15 N N N N l 2. S14 C Sa N N 2 N N H H F F N 509 F 2O 2 F es r is 1. F N-N 25 S --->

Na N1 NN O 515 N C S. ---1. N 30 HO 2N H H

510 F F N21 NN

35 Null-l-lN N N

S16 N

40 F 2N

511 F F ---, F 45 H H

21 F 517 N

N-N F F 2N 50 N1 NN O F - als N21 N N1 NN 4N H 55 N! N - N 1 N

512 21 C S18 N

F N-N 60 F F 2N F 21 NN AO N21 NN alsN - Nals N 65 N! N - Nals N US 9,656,999 B2 85 86 TABLE 1-continued TABLE 1-continued

Representative Compounds

Cmpd Structure No F

519 N

2 N

l als N N H

521 F

2 N

l als N ON H 522 F

2 N

OH l Nals N H 523 F

als N N H 524

2 N

lsh O US 9,656,999 B2 87 88 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 535 F F 531 10 rN\, CN N C N N21 NN 15 N N N N H H

536 F F rN\, Na2N 532 25 F 21 N1 CNN

N S. N l Nals N 1. H H 30 537 F F

533 40 N N H

538 F F

45 21 F N N F

50 r is N N N N H H

S4O F 534 55 F

rs,N F 2 60 F 21 N1 NN

65 US 9,656,999 B2 89 90 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure Cmpd No Structure 541 S46

S42

547

30 543 N

S48 40

544

545 55 549

65 US 9,656,999 B2 91 92 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 555 F 550 F 10 rs, F 2N

F N 15 N? N

556

551 F F

F lN F 25 Sr

557 F r is 1s 30 F nus-s-s N H H rs, 35 2N

552 F

s 40 l als N Nrty O

558 F 45 F N F 2N OH 50

l Nals N 1 N 554 H 55 559 F F rts, 60 O 2N rk Na N1 NN US 9,656,999 B2 93 94 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure 5 No Structure

S60 565 F F 10 N F 2N F

15 N21 N1 NN

F N lull)AN Nals N H H

566 F S61 F 2O F

rs,N OESEO 2 25 s C N N N 30 H H 567 S62 F F

568 563 F F 45

rts,2N 50 r is N N N N H H 55 569 F S64 F F F N F N F 2N 2N 60 N1 SN N21 N1 NN

N N l N 2.2 N -k 65 4N H trans OH H H US 9,656,999 B2 95 96 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure 5 No Structure 570 F F 576 N F O 10 Os 1. 2N F F N1 NN 15 N21 F N 4. N H H N 571 F F 20 577 F N F F

O O N N F sia 2

30 572 578 rs N1 NF 2N 35 N C 2 O NN ls 40 als N N H

573 S8O F F 45 F

50 1\1 N \,

55 581 F 574 F F F N F N F 2N O 2N 60 N21 N1 NN 1. N l --- 65 N 's- H US 9,656,999 B2 97 98 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd No Structure Cmpd

582 No Structure

587 F 10 F

15 O

583 N H

S88 F F 25 F

N H OH 35

589 F 40 F F

585

S86 55 590 lN

N1 NN

- N - 65 US 9,656,999 B2 99 100 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure Cmpd No Structure

596 10

F F

15 N21 N 592

597 F F 25 N F F F F 2N

30 593 in r 4N ls N N H H 35

598 F 40 F

594 rns,N F 2

F N - N els N H H 50

599 F 595 55 F

rs,N OESEO 2 60 N1 NN 2 65 ------, US 9,656,999 B2 101 102 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure

600 60S

N n N N21 15 N l C N --- -k ZI H H

N H

US 9,656,999 B2 103 104 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd Cmpd 5 No Structure No Structure 614

610 10 Nsa' NoS.

15 C

615

2O Nsa 611 so 25

30 616

35 Nsa' noS.

612 40 F

617 F F N F 45 2 2 N

N21 Na NN

50 N N lN N l N H H

618 613 55 F

60 N21

65 US 9,656,999 B2 105 106 TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds Cmpd Cmpd No Structure No Structure 625

619

N& 15

626

621

627

30 OH

622

628

623 45

629

50 N

630

65 US 9,656,999 B2 107 108 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds Cmpd No Structure Structure 631

NN F

21 N l Nals N H NS ul als 632 N N AO ZEI: H

l als F N N N NN O H

633 l Nals N H

21 C 634 HO N l Nals N 1s H

635 21 N s l Nals N 1. H

636 US 9,656,999 B2 109 110 TABLE 1-continued TABLE 1-continued

Representative Compounds

Cmpd No

642 HO OH 10

US 9,656,999 B2 111 112 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

Cmpd Cmpd No Structure No Structure

1. US 9,656,999 B2

TABLE 1-continued TABLE 1-continued Representative Compounds Representative Compounds

Cmpd 5 Cmpd No Structure No Structure

667 673 F

10 N F

F F 2 N N1 NN N1 Boc - als 15 r N1 NN 1. N N N 669 F H H F 674 F r F 2O F N F NC 2N HO 2N N21 NN 25 l als 1. N 21 N n N N N N N l als N N N N 670 F 30 H H F 675

rts,2N C 35 F F F 21 N1 NN

N N l 2els OH N21 N N N H H 40 N

671 F 676 F F F N F 45 N F NC 2N F 2N

N21 nN. 50 N21 N1 NN

N N l Nals N 1. N N l 4Nels 1. H H H H

672 F 55 677 F F

NC rts,2N 60 N21 N1SN

65 US 9,656,999 B2 115 116 TABLE 1-continued TABLE 1-continued

R epresentativetative UompoundsC d Representative Compounds Cmpd 5 No Structure Cmpd No Structure 678 F F 683 O

CN rts,N NSN 2 2N O F 21 n F F N l N 15 Na h N N Nals N OH lsN 1. N H H H

679 684 NH

68O 685

681 O N N 45 686 O

2N O F F 2N O

N 21 N 50 ls ls N21 Na NN s Hr N N lsN ls N 1. H H 55 682 H N O 687 NH N N N 2

2N O 2N F 60 O. N21 N N21 h F N s N N N H H 65 US 9,656,999 B2 117 118 TABLE 1-continued TABLE 1-continued

Representative Compounds Representative Compounds

5 Cmpd Cmpd No Structure No Structure 694 689

691

692

693 US 9,656,999 B2 119 120 TABLE 1-continued and step (2) reacting

Representative Compounds

Cmpd No Structure n NH N N R 699 N 2 10 R with NH2. C 4. N R 2N H 3 F Na NN 15 In other embodiments, the preceding methods comprise step (1) reacting ---.S.--> -C ...

- Included herein are also methods for making compounds C Cl with NH2 of Formula I or a compound of any one of the embodiments described herein comprising reacting to give 25 C 1s, R R2

30 C 4. N R 3. N1 N N R. W.ith NH.2 H

C ul N els2 N uk R3 stepp (2) reactin9. H C

" N1- NN R R2 with B(OH)2 2 In some embodiments, the preceding methods comprise step C N NH R3 (1) reacting 40 to give

n R N1 NN R N N R R3 els -k R - als2 50 C N2 N R3; C N Cl with NH2 H and step (3) reacting to give 55

60 N1 SN R ul 2 uk with NH2. N NN R C N N R3 2 -k C N lukN R3: 65 Also included are methods for making compounds of Formula I or a compound of any one of the embodiments described herein comprising reacting US 9,656,999 B2 121 122 with NH to give

R2 N1 NN with R1 R3.

N Nals C NH 10 N H 2 N JCl NH2: H In some embodiments, the preceding methods comprise step (1) reacting 15 and step (2) reacting

2O N1 NN N1 SN l es with NH2 l els2 C 4. C N N NH2

25 to give with RC(O)C1 or RC(O)OMe. Also included are methods for making compounds of Formula I or a compound of any one of the embodiments described herein comprising reacting 30 C

n 1. N R N l els2 uk - als, 35 N N N R3 with O-BOH). H s In some embodiments, the preceding methods comprise step and step (2) reacting (1) reacting 40 C es R 2 R C ul N els N uk R3 with GD-NH, NN with 's- 45 - als C NH2 to give C In other embodiments, the preceding methods wherein R' 50 N11. NN R and R are taken together with the carbon atom to form l els k C(=O), comprise step (1) reacting N 4. N R3 H H 55 and step (2) reacting C

N 1. N R n 2 N N NH N NH R3 with O-BOH). N Nals C 65 Also included are methods for making compounds of Formula I or a compound of any one of the embodiments described herein comprising reacting US 9,656,999 B2 123 124 to give

NH NH RI

N ls N l N -k R2;R3 N1 NN R H H H ul els2 k HN N N R3 with O-hide. and step (2) reacting 10

In some embodiments, the preceding methods comprise step NH NH R1 (1) reacting l l k with O N N N N 15 H H O

N1 NN R In other embodiments, the preceding methods comprise step R (1) converting 2 C N N R3 H NH ls CN with NH to give NH2 to N N 1 25 H H step (2) reacting

30 R1 R2 NH2 N N CN with H H R3

35 and step (2) reacting to give

NH NH RI 40 N1 NN R N ls N ls N -k R3R2; H H H ul 22. k HN N N R3 with O-hide. and step (3) reacting 45

Also included are methods for making compounds of NH NH RI Formula I or a compound of any one of the embodiments R2 described herein comprising reacting with N N N R3 50 H H H

NH NH RI R with O ON

O O 55 The compounds of one aspect of this invention may contain one or more asymmetric centers and thus occur as In some embodiments, the preceding methods comprise step racemates, racemic mixtures, scalemic mixtures, and diaste (1) reacting reomeric mixtures, as well as single enantiomers or indi 60 vidual stereoisomers that are substantially free from another possible enantiomer or stereoisomer. The term “substantially NH R1 free of other stereoisomers' as used herein means a prepa R2 NH2 ration enriched in a compound having a selected Stereo N N -CN with chemistry at one or more selected Stereocenters by at least H H R3 65 about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%. The term “enriched' means that at least the designated percentage of a preparation is the compound US 9,656,999 B2 125 126 having a selected Stereochemistry at one or more selected phorsulfonic, cinnamic, citric, edetic, ethanedisulfonic, eth Stereocenters. Methods of obtaining or synthesizing an indi anesulfonic, fumaric, glucoheptonic, gluconic, glutamic, vidual enantiomer or Stereoisomer for a given compound are glycolic, hydroxymaleic, hydroxynaphthalene carboxylic, known in the art and may be applied as practicable to final isethionic, lactic, lactobionic, lauric, maleic, malic, meth compounds or to starting material or intermediates. anesulfonic, mucic, oleic, oxalic, palmitic, pamoic, pantoth In certain embodiments, the compound of Formula I or II enic, phenylacetic, phenylsulfonic, propionic, pyruvic, Sali is enriched for a structure or structures having a selected cylic, Stearic, succinic, Sulfanilic, tartaric, toluenesulfonic, Stereochemistry at one or more carbon atoms. For example, and Valeric. Mesylates of each compound in Table 1 are the compound is enriched in the specific stereoisomer by at explicitly included herein. Examples of suitable polymeric least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 10 organic anions include, but are not limited to, those derived 96%, 97%, 98%, or 99%. from the following polymeric acids: tannic acid, carboxym The compounds of Formula I or II may also comprise one ethyl cellulose. or more isotopic Substitutions. For example, H may be in any The compounds provided herein therefore include the isotopic form, including 'H, H (D or deuterium), and H (T compounds themselves, as well as their salts, hydrates and or tritium); C may be in any isotopic form, including 'C, 15 their prodrugs, if applicable. The compounds provided 'C, and ''C: O may be in any isotopic form, including 'O herein may be modified and converted to prodrugs by and 'O; and the like. For example, the compound is appending appropriate functionalities to enhance selected enriched in a specific isotopic form of H, C and/or O by at biological properties, e.g., targeting to a particular tissue. least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, Such modifications (i.e., prodrugs) are known in the art and 96%, 97%, 98%, or 99%. include those which increase biological penetration into a Unless otherwise indicated when a disclosed compound is given biological compartment (e.g., blood, lymphatic sys named or depicted by a structure without specifying the tem, central nervous system), increase oral availability, Stereochemistry and has one or more chiral centers, it is increase solubility to allow administration by injection, alter understood to represent all possible stereoisomers of the metabolism and alter rate of excretion. Examples of prod compound. 25 rugs include esters (e.g., phosphates, amino acid (e.g., The compounds of one aspect of this invention may also valine) esters), carbamates and other pharmaceutically be represented in multiple tautomeric forms, in Such acceptable derivatives, which, upon administration to a instances, one aspect of the invention expressly includes all Subject, are capable of providing active compounds. Cal tautomeric forms of the compounds described herein, even cium and sodium phosphates of each compound in Table 1, though only a single tautomeric form may be represented 30 if applicable, are explicitly included herein. Amino acid (e.g., alkylation of a ring system may result in alkylation at (e.g., valine) esters of each compound in Table 1, if appli multiple sites, one aspect of the invention expressly includes cable, are explicitly included herein. all Such reaction products; and keto-enol tautomers). All Compositions and Routes of Administration Such isomeric forms of Such compounds are expressly The compounds utilized in the methods described herein included herein. 35 may be formulated together with a pharmaceutically accept It may be convenient or desirable to prepare, purify, able carrier or adjuvant into pharmaceutically acceptable and/or handle a corresponding salt of the active compound, compositions prior to be administered to a Subject. In for example, a pharmaceutically-acceptable salt. Examples another embodiment, such pharmaceutically acceptable of pharmaceutically acceptable salts are discussed in Berge compositions further comprise additional therapeutic agents et al., 1977, “Pharmaceutically Acceptable Salts.” J. Pharm. 40 in amounts effective for achieving a modulation of disease Sci. Vol. 66, pp. 1.-19. or disease symptoms, including those described herein. For example, if the compound is anionic, or has a func The term “pharmaceutically acceptable carrier or adju tional group which may be anionic (e.g., -COOH may be vant” refers to a carrier or adjuvant that may be administered —COO), then a salt may be formed with a suitable cation. to a Subject, together with a compound of one aspect of this Examples of Suitable inorganic cations include, but are not 45 invention, and which does not destroy the pharmacological limited to, alkali metal ions such as Na" and K", alkaline activity thereof and is nontoxic when administered in doses earth cations such as Ca" and Mg", and other cations such Sufficient to deliver a therapeutic amount of the compound. as Al". Examples of suitable organic cations include, but Pharmaceutically acceptable carriers, adjuvants and are not limited to, ammonium ion (i.e., NH) and substituted vehicles that may be used in the pharmaceutical composi ammonium ions (e.g., NHR", NHR", NHR", NR"). 50 tions of one aspect of this invention include, but are not Examples of Some Suitable Substituted ammonium ions are limited to, ion exchangers, alumina, aluminum Stearate, those derived from: ethylamine, diethylamine, dicyclohex lecithin, self-emulsifying drug delivery systems (SEDDS) ylamine, triethylamine, butylamine, ethylenediamine, etha Such as d-C-tocopherol polyethyleneglycol 1000 Succinate, nolamine, diethanolamine, piperazine, benzylamine, phe Surfactants used in pharmaceutical dosage forms such as nylbenzylamine, choline, meglumine, and tromethamine, as 55 Tweens or other similar polymeric delivery matrices, serum well as amino acids, such as lysine and arginine. An example proteins, such as human serum albumin, buffer Substances of a common quaternary ammonium ion is N(CH). Such as phosphates, glycine, Sorbic acid, potassium Sorbate, If the compound is cationic, or has a functional group that partial glyceride mixtures of Saturated vegetable fatty acids, may be cationic (e.g., -NH2 may be —NH), then a salt water, salts or electrolytes, such as protamine Sulfate, diso may be formed with a suitable anion. Examples of suitable 60 dium hydrogen phosphate, potassium hydrogen phosphate, inorganic anions include, but are not limited to, those Sodium chloride, Zinc salts, colloidal silica, magnesium derived from the following inorganic acids: hydrochloric, trisilicate, polyvinyl pyrrolidone, cellulose-based sub hydrobromic, hydroiodic, Sulfuric, Sulfurous, nitric, nitrous, stances, polyethylene glycol, Sodium carboxymethylcellu phosphoric, and phosphorous. lose, polyacrylates, waxes, polyethylene-polyoxypropylene Examples of Suitable organic anions include, but are not 65 block polymers, polyethylene glycol and wool fat. limited to, those derived from the following organic acids: Cyclodextrins such as C.-, 3-, and Y-cyclodextrin, or chemi 2-acetyoxybenzoic, acetic, ascorbic, aspartic, benzoic, cam cally modified derivatives such as hydroxyalkylcyclodex US 9,656,999 B2 127 128 trins, including 2- and 3-hydroxypropyl-3-cyclodextrins, or Solid at room temperature but liquid at the rectal temperature other solubilized derivatives may also be advantageously and therefore will melt in the rectum to release the active used to enhance delivery of compounds of the formulae components. Such materials include, but are not limited to, described herein. cocoa butter, beeswax and polyethylene glycols. The pharmaceutical compositions of one aspect of this Topical administration of the pharmaceutical composi invention may be administered orally, parenterally, by inha tions of one aspect of this invention is useful when the lation spray, topically, rectally, nasally, buccally, vaginally desired treatment involves areas or organs readily accessible or via an implanted reservoir, preferably by oral adminis by topical application. For application topically to the skin, tration or administration by injection. The pharmaceutical the pharmaceutical composition should be formulated with compositions of one aspect of this invention may contain 10 any conventional non-toxic pharmaceutically-acceptable a Suitable ointment containing the active components Sus carriers, adjuvants or vehicles. In some cases, the pH of the pended or dissolved in a carrier. Carriers for topical admin formulation may be adjusted with pharmaceutically accept istration of the compounds of one aspect of this invention able acids, bases or buffers to enhance the stability of the include, but are not limited to, mineral oil, liquid petroleum, formulated compound or its delivery form. The term paren 15 white petroleum, propylene glycol, polyoxyethylene poly teral as used herein includes Subcutaneous, intracutaneous, oxypropylene compound, emulsifying wax and water. Alter intravenous, intramuscular, intraarticular, intraarterial, intra natively, the pharmaceutical composition can be formulated synovial, intrasternal, intrathecal, intralesional and intracra with a suitable lotion or cream containing the active com nial injection or infusion techniques. pound suspended or dissolved in a carrier with suitable The pharmaceutical compositions may be in the form of emulsifying agents. Suitable carriers include, but are not a sterile injectable preparation, for example, as a sterile limited to, mineral oil, Sorbitan monostearate, polysorbate injectable aqueous or oleaginous Suspension. This suspen 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, sion may be formulated according to techniques known in benzyl alcohol and water. The pharmaceutical compositions the art using Suitable dispersing or wetting agents (such as, of one aspect of this invention may also be topically applied for example, Tween 80) and Suspending agents. The sterile 25 to the lower intestinal tract by rectal suppository formulation injectable preparation may also be a sterile injectable solu or in a Suitable enema formulation. Topically-transdermal tion or Suspension in a non-toxic parenterally acceptable patches are also included in one aspect of this invention. diluent or solvent, for example, as a solution in 1,3-butane The pharmaceutical compositions of one aspect of this diol. Among the acceptable vehicles and solvents that may invention may be administered by nasal aerosol or inhala be employed are mannitol, water, Ringer's Solution and 30 tion. Such compositions are prepared according to tech isotonic sodium chloride solution. In addition, sterile, fixed niques well-known in the art of pharmaceutical formulation oils are conventionally employed as a solvent or suspending and may be prepared as solutions in saline, employing medium. For this purpose, any bland fixed oil may be benzyl alcohol or other suitable preservatives, absorption employed including synthetic mono- or diglycerides. Fatty promoters to enhance bioavailability, fluorocarbons, and/or acids, Such as oleic acid and its glyceride derivatives are 35 other solubilizing or dispersing agents known in the art. useful in the preparation of injectables, as are natural phar When the compositions of one aspect of this invention maceutically-acceptable oils, such as olive oil or castor oil, comprise a combination of a compound of the formulae especially in their polyoxyethylated versions. These oil described herein and one or more additional therapeutic or Solutions or Suspensions may also contain a long-chain prophylactic agents, both the compound and the additional alcohol diluent or dispersant, or carboxymethyl cellulose or 40 agent should be present at dosage levels of between about 1 similar dispersing agents which are commonly used in the to 100%, and more preferably between about 5 to 95% of the formulation of pharmaceutically acceptable dosage forms dosage normally administered in a monotherapy regimen. Such as emulsions and or Suspensions. Other commonly The additional agents may be administered separately, as used Surfactants such as Tweens or Spans and/or other part of a multiple dose regimen, from the compounds of one similar emulsifying agents or bioavailability enhancers 45 aspect of this invention. Alternatively, those agents may be which are commonly used in the manufacture of pharma part of a single dosage form, mixed together with the ceutically acceptable Solid, liquid, or other dosage forms compounds of one aspect of this invention in a single may also be used for the purposes of formulation. composition. The pharmaceutical compositions of one aspect of this The compounds described herein can, for example, be invention may be orally administered in any orally accept 50 administered by injection, intravenously, intraarterially, Sub able dosage form including, but not limited to, capsules, dermally, intraperitoneally, intramuscularly, or Subcutane tablets, emulsions and aqueous Suspensions, dispersions and ously; or orally, buccally, nasally, transmucosally, topically, solutions. In the case of tablets for oral use, carriers which in an ophthalmic preparation, or by inhalation, with a dosage are commonly used include lactose and corn starch. Lubri ranging from about 0.5 to about 100 mg/kg of body weight, cating agents. Such as magnesium Stearate, are also typically 55 alternatively dosages between 1 mg and 1000 mg/dose, added. For oral administration in a capsule form, useful every 4 to 120 hours, or according to the requirements of the diluents include lactose and dried corn starch. When aque particular drug. The methods herein contemplate adminis ous Suspensions and/or emulsions are administered orally, tration of an effective amount of compound or compound the active ingredient may be suspended or dissolved in an composition to achieve the desired or stated effect. Typi oily phase is combined with emulsifying and/or Suspending 60 cally, the pharmaceutical compositions of one aspect of this agents. If desired, certain Sweetening and/or flavoring and/or invention will be administered from about 1 to about 6 times coloring agents may be added. per day or alternatively, as a continuous infusion. Such The pharmaceutical compositions of one aspect of this administration can be used as a chronic or acute therapy. The invention may also be administered in the form of Supposi amount of active ingredient that may be combined with the tories for rectal administration. These compositions can be 65 carrier materials to produce a single dosage form will vary prepared by mixing a compound of one aspect of this depending upon the host treated and the particular mode of invention with a suitable non-irritating excipient which is administration. A typical preparation will contain from about US 9,656,999 B2 129 130 5% to about 95% active compound (w/w). Alternatively, embodiment, the R140X mutation is a R140L, mutation. In such preparations contain from about 20% to about 80% another aspect of this embodiment, the mutant IDH2 has an active compound. R172X mutation. In another aspect of this embodiment, the Lower or higher doses than those recited above may be R172X mutation is a R172K mutation. In another aspect of required. Specific dosage and treatment regimens for any 5 this embodiment, the R172X mutation is a R172G mutation. particular Subject will depend upon a variety of factors, A cancer can be analyzed by sequencing cell samples to including the activity of the specific compound employed, determine the presence and specific nature of (e.g., the the age, body weight, general health status, sex, diet, time of changed amino acid presentat) a mutation at amino acid 140 administration, rate of excretion, drug combination, the and/or 172 of IDH2. severity and course of the disease, condition or symptoms, 10 Without being bound by theory, applicants believe that the Subject's disposition to the disease, condition or symp mutant alleles of IDH2 wherein the IDH2 mutation results in toms, and the judgment of the treating physician. a new ability of the enzyme to catalyze the NAPH-depen Upon improvement of a subjects condition, a mainte dent reduction of O-ketoglutarate to R(-)-2-hydroxyglut nance dose of a compound, composition or combination of arate, and in particular R140O and/or R172K mutations of one aspect of this invention may be administered, if neces 15 IDH2, characterize a subset of all types of cancers, without sary. Subsequently, the dosage or frequency of administra regard to their cellular nature or location in the body. Thus, tion, or both, may be reduced, as a function of the symptoms, the compounds and methods of one aspect of this invention to a level at which the improved condition is retained when are useful to treat any type of cancer that is characterized by the symptoms have been alleviated to the desired level. the presence of a mutant allele of IDH2 imparting such Subjects may, however, require intermittent treatment on a activity and in particular an IDH2 R140O and/or R172K long-term basis upon any recurrence of disease symptoms. mutation. The pharmaceutical compositions described above com In one aspect of this embodiment, the efficacy of cancer prising a compound of Structural Formula I or II or a treatment is monitored by measuring the levels of 2HG in compound described in any one of the embodiments herein, the subject. Typically levels of 2HG are measured prior to may further comprise another therapeutic agent useful for 25 treatment, wherein an elevated level is indicated for the use treating cancer. of the compound of Formula I or II or a compound described Methods of Use in any one of the embodiments described herein to treat the The inhibitory activities of the compounds provided cancer. Once the elevated levels are established, the level of herein against IDH2 mutants (e.g., IDH2R140O and 2HG is determined during the course of and/or following IDH2R172K) can be tested by methods described in 30 termination of treatment to establish efficacy. In certain Example 12 or analogous methods. embodiments, the level of 2HG is only determined during Provided is a method for inhibiting a mutant IDH2 the course of and/or following termination of treatment. A activity comprising contacting a Subject in need thereof with reduction of 2HG levels during the course of treatment and a compound of Structural Formula I or II, a compound following treatment is indicative of efficacy. Similarly, a described in any one of the embodiments herein, or a 35 determination that 2HG levels are not elevated during the pharmaceutically acceptable salt thereof. In one embodi course of or following treatment is also indicative of effi ment, the cancer to be treated is characterized by a mutant cacy. Typically, the these 2HG measurements will be utilized allele of IDH2 wherein the IDH2 mutation results in a new together with other well-known determinations of efficacy of ability of the enzyme to catalyze the NAPH-dependent cancer treatment, such as reduction in number and size of reduction of C.-ketoglutarate to R(-)-2-hydroxyglutarate in a 40 tumors and/or other cancer-associated lesions, improvement subject. In one aspect of this embodiment, the mutant IDH2 in the general health of the subject, and alterations in other has an R140X mutation. In another aspect of this embodi biomarkers that are associated with cancer treatment effi ment, the R140X mutation is a R140O mutation. In another cacy. aspect of this embodiment, the R140X mutation is a R140W 2HG can be detected in a sample by LC/MS. The sample mutation. In another aspect of this embodiment, the R140X 45 is mixed 80:20 with methanol, and centrifuged at 3,000 rpm mutation is a R140L, mutation. In another aspect of this for 20 minutes at 4 degrees Celsius. The resulting Superna embodiment, the mutant IDH2 has an R172X mutation. In tant can be collected and stored at -80 degrees Celsius prior another aspect of this embodiment, the R172X mutation is to LC-MS/MS to assess 2-hydroxyglutarate levels. A variety a R172K mutation. In another aspect of this embodiment, of different liquid chromatography (LC) separation methods the R172X mutation is a R172G mutation. 50 can be used. Each method can be coupled by negative Also provided are methods of treating a cancer charac electrospray ionization (ESI, -3.0 kV) to triple-quadrupole terized by the presence of a mutant allele of IDH2 compris mass spectrometers operating in multiple reaction monitor ing the step of administering to Subject in need thereof (a) a ing (MRM) mode, with MS parameters optimized on compound of Structural Formula I or II, a compound infused metabolite standard solutions. Metabolites can be described in any one of the embodiments herein, or a 55 separated by reversed phase chromatography using 10 mM pharmaceutically acceptable salt thereof, or (b) a pharma tributyl-amine as an ion pairing agent in the aqueous mobile ceutical composition comprising (a) and a pharmaceutically phase, according to a variant of a previously reported acceptable carrier. method (Luo et al. J Chromatogr A 1147, 153-64, 2007). In one embodiment, the cancer to be treated is character One method allows resolution of TCA metabolites: t—0, 50% ized by a mutant allele of IDH2 wherein the IDH2 mutation 60 B; t—5, 95% B; t-7, 95% B; t—8, 0% B, where B refers to results in a new ability of the enzyme to catalyze the an organic mobile phase of 100% methanol. Another method NAPH-dependent reduction of O-ketoglutarate to R(-)-2- is specific for 2-hydroxyglutarate, running a fast linear hydroxyglutarate in a patient. In one aspect of this embodi gradient from 50%-95% B (buffers as defined above) over 5 ment, the mutant IDH2 has an R140X mutation. In another minutes. A Synergi Hydro-RP 100 mmx2 mm, 2.1 um aspect of this embodiment, the R140X mutation is a R140O 65 particle size (Phenomonex) can be used as the column, as mutation. In another aspect of this embodiment, the R140X described above. Metabolites can be quantified by compari mutation is a R140W mutation. In another aspect of this Son of peak areas with pure metabolite standards at known US 9,656,999 B2 131 132 concentration. Metabolite flux studies from C-glutamine 2017-22 (2003)), potentially contributing to an increased can be performed as described, e.g., in Munger et al. Nat risk of cancer. The ability of 2HG to act as an NMDA Biotechnol 26, 1179-86, 2008. receptor agonist may contribute to this effect (Kolker, S. et In one embodiment 2HG is directly evaluated. al. EurJ Neurosci 16, 21-8 (2002)). 2HG may also be toxic In another embodiment a derivative of 2HG formed in 5 to cells by competitively inhibiting glutamate and/or CKG process of performing the analytic method is evaluated. By utilizing enzymes. These include transaminases which allow way of example such a derivative can be a derivative formed utilization of glutamate nitrogen for amino and nucleic acid in MS analysis. Derivatives can include a salt adduct, e.g., biosynthesis, and CKG-dependent prolyl hydroxylases Such a Na adduct, a hydration variant, or a hydration variant as those which regulate Hif1-alpha levels. which is also a salt adduct, e.g., a Na adduct, e.g., as formed 10 Thus, according to another embodiment, one aspect of the in MS analysis. invention provides a method of treating 2-hydroxyglutaric In another embodiment a metabolic derivative of 2HG is aciduria, particularly D-2-hydroxyglutaric aciduria, in a evaluated. Examples include species that build up or are patient by administering to the patient a compound of elevated, or reduced, as a result of the presence of 2HG, such Structural Formula I or II or a compound described in any as glutarate or glutamate that will be correlated to 2HG, e.g., 15 one of the embodiments described herein. R-2HG. Treatment methods described herein can additionally Exemplary 2HG derivatives include dehydrated deriva comprise various evaluation steps prior to and/or following tives such as the compounds provided below or a salt adduct treatment with a compound of Structural Formula I or II or thereof: a compound described in any one of the embodiments described herein. In one embodiment, prior to and/or after treatment with a compound of Structural Formula I or II or a compound described in any one of the embodiments described herein, the method further comprises the step of evaluating the 25 growth, size, weight, invasiveness, stage and/or other phe notype of the cancer. In one embodiment, prior to and/or after treatment with a compound of Formula I or II or a compound described in any one of the embodiments described herein, the method 30 further comprises the step of evaluating the IDH2 genotype of the cancer. This may be achieved by ordinary methods in the art, such as DNA sequencing, immuno analysis, and/or evaluation of the presence, distribution or level of 2HG. In one embodiment the cancer is a tumor wherein at least In one embodiment, prior to and/or after treatment with a 30, 40, 50, 60, 70, 80 or 90% of the tumor cells carry an 35 compound of Formula I or II or a compound described in IDH2 mutation, and in particular an IDH2 R140O, R140W. any one of the embodiments described herein, the method or R140L and/or R172K or R172G mutation, at the time of further comprises the step of determining the 2HG level in diagnosis or treatment. the Subject. This may be achieved by spectroscopic analysis, In another embodiment, one aspect of the invention e.g., magnetic resonance-based analysis, e.g., MRI and/or provides a method of treating a cancer selected from glio 40 MRS measurement, sample analysis of bodily fluid, such as blastoma (glioma), myelodysplastic syndrome (MDS). serum or spinal cord fluid analysis, or by analysis of Surgical myeloproliferative neoplasm (MPN), acute myelogenous material, e.g., by mass-spectroscopy. leukemia (AML), sarcoma, melanoma, non-small cell lung Combination Therapies cancer, chondrosarcoma, cholangiocarcinomas or angioim In some embodiments, the methods described herein munoblastic lymphoma in a patient by administering to the 45 comprise the additional step of co-administering to a subject patient a compound of Formula I or Formula II in an amount in need thereof a second therapy e.g., an additional cancer effective to treat the cancer. In a more specific embodiment therapeutic agent or an additional cancer treatment. Exem the cancer to be treated is glioma, myelodysplastic Syn plary additional cancer therapeutic agents include for drome (MDS), myeloproliferative neoplasm (MPN), acute example, chemotherapy, targeted therapy, antibody thera myelogenous leukemia (AML), melanoma, chondrosar 50 pies, immunotherapy, and hormonal therapy. Additional coma, or angioimmunoblastic non-Hodgkin’s lymphoma cancer treatments include, for example: Surgery, and radia (NHL). tion therapy. Examples of each of these treatments are 2HG is known to accumulate in the inherited metabolic provided below. disorder 2-hydroxyglutaric aciduria. This disease is caused The term “co-administering as used herein with respect by deficiency in the enzyme 2-hydroxyglutarate dehydroge 55 to an additional cancer therapeutic agents means that the nase, which converts 2HG to C-KG (Struys, E. A. et al. Am additional cancer therapeutic agent may be administered J. Hum Genet 76,358-60 (2005)). Patients with 2-hydroxy together with a compound of one aspect of this invention as glutarate dehydrogenase deficiencies accumulate 2HG in the part of a single dosage form (such as a composition of one brain as assessed by MRI and CSF analysis, develop leu aspect of this invention comprising a compound of one koencephalopathy, and have an increased risk of developing 60 aspect of the invention and an second therapeutic agent as brain tumors (Aghili, M., Zahedi, F. & Rafiee. J Neurooncol described above) or as separate, multiple dosage forms. 91,233-6 (2009): Kolker, S., Mayatepek, E. & Hoffmann, G. Alternatively, the additional cancer therapeutic agent may be F. Neuropediatrics 33,225-31 (2002); Wajner, M., Latini, A., administered prior to, consecutively with, or following the Wyse, A. T. & Dutra-Filho, C. S. J. Inherit Metab Dis 27, administration of a compound of one aspect of this inven 427-48 (2004)). Furthermore, elevated brain levels of 2HG 65 tion. In Such combination therapy treatment, both the com result in increased ROS levels (Kolker, S. et al. Eur J pounds of one aspect of this invention and the second Neurosci 16, 21-8 (2002); Latini, A. et al. EurJ Neurosci 17, therapeutic agent(s) are administered by conventional meth US 9,656,999 B2 133 134 ods. The administration of a composition of one aspect of compounds (such as hexamethylene bisacetamide this invention, comprising both a compound of one aspect of ((HMBA)); vitamin D; and cytokines (such as colony the invention and a second therapeutic agent, to a subject stimulating factors including G-CSF and GM-CSF, and does not preclude the separate administration of that same interferons). therapeutic agent, any other second therapeutic agent or any In some embodiments the additional cancer therapeutic compound of one aspect of this invention to said subject at agent is a targeted therapy agent. Targeted therapy consti another time during a course of treatment. The term "co tutes the use of agents specific for the deregulated proteins administering as used herein with respect to an additional of cancer cells. Small molecule targeted therapy drugs are cancer treatment means that the additional cancer treatment generally inhibitors of enzymatic domains on mutated, over may occur prior to, consecutively with, concurrently with or 10 following the administration of a compound of one aspect of expressed, or otherwise critical proteins within the cancer this invention. cell. Prominent examples are the tyrosine kinase inhibitors In some embodiments, the additional cancer therapeutic such as Axitinib, Bosutinib, Cediranib, dasatinib, erlotinib, agent is a chemotherapy agent. Examples of chemothera imatinib, gefitinib, lapatinib, Lestaurtinib, Nilotinib, Semax peutic agents used in cancer therapy include, for example, 15 anib, Sorafenib, Sunitinib, and Vandetanib, and also cyclin antimetabolites (e.g., folic acid, purine, and pyrimidine dependent kinase inhibitors such as Alvocidib and Seliciclib. derivatives), alkylating agents (e.g., nitrogen mustards, Monoclonal antibody therapy is another strategy in which nitrosoureas, platinum, alkyl Sulfonates, hydrazines, tri the therapeutic agent is an antibody which specifically binds aZenes, aziridines, spindle poison, cytotoxic agents, topoi to a protein on the Surface of the cancer cells. Examples Somerase inhibitors and others), and hypomethylating agents include the anti-HER2/neu antibody trastuzumab (HER (e.g., decitabine (5-aza-deoxycytidine), Zebularine, isothio CEPTINR) typically used in breast cancer, and the anti cyanates, azacitidine (5-azacytidine), 5-flouro-2'-deoxycyti CD20 antibody rituximab and Tositumomab typically used dine, 5,6-dihydro-5-azacytidine and others). Exemplary in a variety of B-cell malignancies. Other exemplary anti agents include Aclarubicin, Actinomycin, Alitretinoin, bodies include Cetuximab, Panitumumab, Trastuzumab, Altretamine, Aminopterin, Aminolevulinic acid, Amrubicin, 25 Alemtuzumab, Bevacizumab, Edrecolomab, and Gemtu Amsacrine, Anagrelide, Arsenic trioxide, Asparaginase, Zumab. Exemplary fusion proteins include Aflibercept and Atrasentan, Belotecan, Bexarotene, bendamustine, Bleomy Denileukin diftitox. In some embodiments, the targeted cin, Bortezomib, Busulfan, Camptothecin, Capecitabine, therapy can be used in combination with a compound Carboplatin, Carboquone, Carmofur, Carmustine, Cele described herein, e.g., a biguanide Such as metformin or coxib, Chlorambucil, Chlormethine, Cisplatin, Cladribine, 30 phenformin, preferably phenformin. Clofarabine, Crisantaspase, Cyclophosphamide, Cytarabine, Targeted therapy can also involve Small peptides as "hom Dacarbazine, Dactinomycin, Daunorubicin, Decitabine, ing devices” which can bind to cell surface receptors or Demecolcine, Docetaxel, Doxorubicin, Efaproxiral, Eles affected extracellular matrix surrounding the tumor. Radio clomol, Elsamitrucin, Enocitabine, Epirubicin, Estramus nuclides which are attached to these peptides (e.g., RGDs) tine, Etoglucid, Etoposide, Floxuridine, Fludarabine, Fluo 35 eventually kill the cancer cell if the nuclide decays in the rouracil (5FU), Fotemustine, Gemcitabine, Gliadel implants, vicinity of the cell. An example of such therapy includes Hydroxycarbamide, Hydroxyurea, Idarubicin, Ifosfamide, BEXXARCR). Irinotecan, Irofulven, IXabepilone, Larotaxel, Leucovorin, In some embodiments, the additional cancer therapeutic Liposomal doxorubicin, Liposomal daunorubicin, agent is an immunotherapy agent. Cancer immunotherapy Lonidamine, Lomustine, Lucanthone, Mannosulfan, Maso 40 refers to a diverse set of therapeutic strategies designed to procol, Melphalan, Mercaptopurine, Mesna, Methotrexate, induce the Subjects own immune system to fight the tumor. Methyl aminolevulinate, Mitobronitol, MitoguaZone, Mito Contemporary methods for generating an immune response tane, Mitomycin, Mitoxantrone, Nedaplatin, Nimustine, against tumors include intravesicular BCG immunotherapy Oblimersen, Omacetaxine, Ortataxel, Oxaliplatin, Pacli for superficial bladder cancer, and use of interferons and taxel, Pegaspargase, Pemetrexed, Pentostatin, Pirarubicin, 45 other cytokines to induce an immune response in renal cell Pixantrone, Plicamycin, Porfimer sodium, Prednimustine, carcinoma and melanoma Subjects. Procarbazine, Raltitrexed, Ranimustine, Rubitecan, Sapac Allogeneic hematopoietic stem cell transplantation can be itabine, Semustine, Sitimagene ceradenovec, Strataplatin, considered a form of immunotherapy, since the donors Streptozocin, Talaporfin, Tegafur-uracil, Temoporfin, Temo immune cells will often attack the tumor in a graft-versus Zolomide, Teniposide, Tesetaxel, Testolactone, Tetranitrate, 50 tumor effect. In some embodiments, the immunotherapy Thiotepa, Tiazofurine, Tioguanine, Tipifarnib, Topotecan, agents can be used in combination with a compound or Trabectedin, Triaziquone, Triethylenemelamine, Triplatin, composition described herein. Tretinoin, Treosulfan, Trofosfamide, Uramustine, Valrubi In some embodiments, the additional cancer therapeutic cin, Verteporfin, Vinblastine, Vincristine, Vindesine, Vinflu agent is a hormonal therapy agent. The growth of some nine, Vinorelbine, Vorinostat, Zorubicin, and other cytostatic 55 cancers can be inhibited by providing or blocking certain or cytotoxic agents described herein. hormones. Common examples of hormone-sensitive tumors Because some drugs work better together than alone, two include certain types of breast and prostate cancers. Remov or more drugs are often given at the same time. Often, two ing or blocking estrogen or testosterone is often an important or more chemotherapy agents are used as combination additional treatment. In certain cancers, administration of chemotherapy. 60 hormone agonists, such as progestogens may be therapeu In some embodiments, the additional cancer therapeutic tically beneficial. In some embodiments, the hormonal agent is a differentiation agent. Such differentiation agent therapy agents can be used in combination with a compound includes retinoids (such as all-trans-retinoic acid (ATRA), or a composition described herein. 9-cis retinoic acid, 13-cis-retinoic acid (13-cRA) and 4-hy Other possible additional therapeutic modalities include droxy-phenretinamide (4-HPR)); arsenic trioxide; histone 65 imatinib, gene therapy, peptide and dendritic cell vaccines, deacetylase inhibitors HDACs (such as azacytidine (Vidaza) synthetic chlorotoxins, and radiolabeled drugs and antibod and butyrates (e.g., sodium phenylbutyrate)); hybrid polar 1CS US 9,656,999 B2 135 EXAMPLES Scheme 1 Abbreviations C anhy.—anhydrous dt—doublet of triplets N11. SN HerPhMgBr aq.—aqueous CHCl chloroform THF min minute(s) DCM dichloromethane 2 mL milliliter DMF dimethylformamide C N C mmol millimole(s) EtO—diethyl ether 1 mol mole(s) EtOH ethyl alcohol 10 MS mass spectrometry EtOAc—ethyl acetate NMR nuclear magnetic resonance MeOH methyl alco hol NH2 -e- TLC thin layer chromatography MeCN acetonitrile THF.r.t HPLC high-performance liquid PE petroleum ether 15 chromatography THF tetrahydrofuran HZ hertz, AcOH-acetic acid - als Ö—chemical shift HCl hydrochloric acid C N C J—coupling constant H2SO -sulfuric acid 2 s—singlet NHCl-ammonium chloride d—doublet KOH potassium hydroxide t—triplet NaOH sodium hydroxide q-quartet KCO potassium carbonate 4 -- m—multiplet NaCO Sodium carbonate 25 Procedure br—broad TFA trifluoroacetic acid N1SN A, B, or C qd-quartet of doublets Na2SO -sodium Sulfate dquin doublet of quintets NaBH sodium borohydride C N N dd doublet of doublets NaHCO, sodium bicarbonate H LiHMDS lithium hexamethyldisilylamide mide 30 3 NaHMDS sodium hexamethyldisilylamide HOBt—1-hy droxybenzotriazole LAH lithium aluminum hydride HATU— NaBH sodium borohydride O-(7-azabenzotriazol-1-yl)- 35 N,N,N',N'-tetra LDA lithium diisopropylamide methyluronium EtN triethylamine BINAP– DMAP 4-(dimethylamino)pyridine 2,2'-bis(diphenylphos phanyl)-1,1'-binaphth 40 O------DIPEA N,N-diisopropylethylamine y1 Formula I NHOH ammonium hydroxide EDCI 1-ethyl-3-(3-dimethylaminopropyl)carbodii Example 1, Step 1: Preparation of In the following examples, reagents were purchased from 45 2,4-dichloro-6-phenyl-1,3,5-triazine (2) commercial sources (including Alfa, Acros, Sigma Aldrich, TCI and Shanghai Chemical Reagent Company), and used without further purification. Nuclear magnetic resonance To a solution of 2,4,6-trichloro-1,3,5 triazine (1, 120g, (NMR) spectra were obtained on a Brucker AMX-400 NMR 0.652 mol) in anhydrous THF (1200 mL) was added phe (Brucker, Switzerland). Chemical shifts were reported in 50 nylmagnesium bromide (217 mL, 0.651 mol, 3 M in ether) parts per million (ppm, 8) downfield from tetramethylsilane. dropwise at -10 to -0° C. under N protection. After the Mass spectra were run with electrospray ionization (ESI) addition, the mixture was warmed to room temperature and from a Waters LCT TOF Mass Spectrometer (Waters, USA). stirred for 2 hrs. The reaction was cooled to 0° C. and For exemplary compounds disclosed in this section, the quenched by addition of saturated NHCl (200 mL), then specification of a stereoisomer (e.g., an (R) or (S) stereoi 55 extracted with ethyl acetate. The organic layer was dried, Somer) indicates a preparation of that compound Such that concentrated and purified via column chromatography the compound is enriched at the specified Stereocenter by at (eluted with petroleum ether) to afford 2,4-dichloro-6-phe least about 90%, 95%, 96%, 97%, 98%, or 99%. The nyl-1,3,5-triazine as a white solid. "H NMR (CDC1) & chemical name of each of the exemplary compound 7.51-7.55 (m, 2H), 7.64-7.67 (m. 1H), 8.49-8.63 (m, 2H). described below is generated by ChemDraw software. 60 Example 1, Step 2: Preparation of 4-chloro-N-iso Example 1. Preparation of Compounds of Formula propyl-6-phenyl-1,3,5-triazin-2-amine (3) I Wherein Ring a is Phenyl, and C(R)(R)(R) is Isopropyl To a solution of 2,4-dichloro-6-phenyl-1,3,5-triazine (2: 65 20 g, 0.089 mol) in anhydrous THF (150 mL) was added The compounds of this Example are prepared by general dropwise a solution of isopropylamine (5.25 g, 0.089 mol) Scheme 1, set forth below. in THF (10 mL) at room temperature via syringe under N.

US 9,656,999 B2 155 156 -continued F

5 N N N l N1 CN H H

10 H NMR (DMSO-d4) & 7.42 (s. 2H), 7.85-8.01 (m. 1H), 8.24 (s, 1H), 8.38 (s, 1H). Formula I 1-3-chloro-pyridin-2-cyanoguanidine as a pale gray solid.

Example 2, Step 1: Preparation of 15 C 1-phenyl-2-cyanoguanidine (5) 21 NH To a solution of NaN(CN), (50 g., 0.5618 mol) in water (430 mL) at 80°C. was added a solution of aniline (26.2 g, N N N l N 1 CN 0.28 mol) in water and conc. HCl (132 mL/23.5 mL). The H H mixture was heated to 90° C. for 16 hours. The mixture was cooled to room temperature and quenched by adding Satu rated sodium bicarbonate (317 mL). The mixture was fil H NMR (DMSO-d4) & 8.06 (s, 1H), 8.29 (s, 1H), 8.47 (s, tered and the filter cake was dried via vacuum to afford 1H). 1-phenyl-2-cyanoguanidine as a white solid. 25 1-2-fluoro-pyridin-2-cyanoguanidine as a brown solid.

F 21 NH

30 N l CN N l N1 CN Sa N N1 H H H H

"H NMR (DMSO-d4) & 6.95 (s. 2H), 7.02-7.06 (m, 1H), H NMR (DMSO-d4) & 7.10-7.20 (m, 1H), 7.95-7.99 (m, 7.26-7.32 (m, 4H), 9.00 (s, 1H). 35 1H), 8.15 (s, 1H). The procedure set forth in Example 2, step 1 was used to 1-3,5-difluoro-phenyl-2-cyano-guanidine as white solid, produce the following intermediates (5) using the appropri which was directly used in the next step without further ate starting material 4. purification. 1-(3-cyanophenyl-2-cyanoguanidine as a brown solid. 40

45 N usesN1 NH H H

N lesN1 H H LC-MS: m/z 196.8 (M+H)". 50 Example 2, Step 2: Preparation of LC-MS: m/z 185.9 (M+H)". 1-phenyl-2-isopropylamine-diguanidine(7) 1-methanesulfonyl-benzenyl-2-cyanoguanidine as a pale gray Solid. To a mixture of 1-phenyl-2-cyanoguanidine (5.0 g, 0.031 55 mol) in ethanol/water (46 mL/18.4 mL) was added O CuSO4.5HO (3.91 g, 0.01563 mol), followed by isopropyl Il-O amine (5.53 g, 0.03975 mol). The mixture was heated to Ng4 reflux for 16 hours. To the mixture was added water (137 mL) and aq.HCl (15.5 mL in 93 mL of water) at 25-30° C. NH 60 The resultant mixture was stirred at r.t. for 30 mm. Then NaS (12.4 g in 62 mL of water) was added and stirred for another 30 mm. The insoluble CuS was filtered off. The N ls N1in H H filtrate was cooled to 10° C. and added aqueous NaOH (7 g NaOH in 50 mL water) dropwise. The mixture was extracted 65 with dichloromethane (100 mLX3). The organic layer was LC-MS: m/z 238.8 (M+H)". combined, dried over NaSO and concentrated to give 1-3-fluoro-pyridin-2-cyanoguanidine as a pale Solid. 1-phenyl-2-isopropylamine-diguanidine as a brown solid. US 9,656,999 B2 157 158 s1' C l 5 d NH NH "Ne NN N& ---O

NS --- 10 LC-MS: m/z 267 (M+H)". 1-2-fluoro-pyridin-2-cyclobutyl-diguanidine as a red solid. "H NMR (DMSO-d4) & 1.25 (d. J=4.8 Hz, 6H), 4.91-4.97 (m. 1H), 7.17-7.39 (m, 5H). The procedure set forth in Example 2, step 2 was used to 15 produce the following intermediates (7) using the appropri ate intermediate 5 and the appropriate amine 6. O NH NH 1-3-cyanophenyl-2-isopropylamine-diguanidine as a Nan !--- brown solid. LC-MS: m/z 250.8 (M+H)". 1-3,5-difluoropneyl-2-isopropyl-diguanidine as a brown solid, which was used in the next step without further 25 purification.

F 30 o NH NH 1. F H ---,H H

LC-MS: m/z 245 (M+H)". 35 1-methanesulfonyl-2-isopropyl-diguanidine as a pale LC-MS: m/z 256 (M+H)". solid. Example 2, Step 3: Preparation of Compound 214 N-Isopropyl-N'-phenyl-6-pyridin-2-yl-1,3,5 40 triazine-2,4-diamine N S420 To a mixture of N-isopropyl-N'-phenyl-6-pyridin-2-yl-1, 3.5 triazine-2,4-diamine (0.5g, 2.28 mmol) and pyridine-2- carboxylic acid methyl ester (0.312 g, 2.28 mmol) in metha O NH NH nol (7 mL) was added NaOMe (0.25 g, 4.56 mmol). The --- mixture was stirred at r,t. for 16 hours. The mixture was poured into water and extracted with ethyl acetate (50 mL), dried over NaSO, concentrated and purified by a standard method to afford N-isopropyl-N'-phenyl-6-pyridin-2-yl-1, 50 3.5 triazine-2,4-diamine. LC-MS: m/z 298 (M+H)". 1-3-fluoro-pyridin-2-cyclobutyl-diguanidine as a red solid. 55

F Nand ill-ONH NH 60 H NMR (METHANOL-d) & 8.72-8.73 (d. 1H), 8.47 LC-MS: m/z 251 (M+H)". 65 8.49 (d. 1H), 7.97-8.01 (t, 1H), 7.77-7.79 (d. 2H), 7.56-7.59 1-3-chloro-pyridin-2-cyclobutyl-diguanidine as a red (t, 1H), 7.31-7.35 (t, 2H), 7.04-7.07 (t, 1H), 4.40-4.45 (m, solid. 1H), 1.30-1.31 (d. 6H). LC-MS: m/z 3.07.0 (M+H)".

US 9,656,999 B2 169 170 -continued Example 3, Step 2: Preparation of 6-(6-chloropyridin-2-yl)-1,3,5-triazine-2,4-dione as saR4 O To a solution of Na (32 g, 0.16 mol) in ethanol (500 mL) NH2 was added methyl 6-chloropicolinate (32 g, 0.16 mol) and 2 4 biuret (5.3.g., 0.052 mol). The mixture was heated to reflux Hs for 1 hour. Then concentrated to give residue which was N1 NN RI poured to water and added SatNaHCO, solution to adjust R2 pH to 7, the precipitated solid was collected by filtration and 2 10 dried to give 6-(6-chloropyridin-2-yl)-1,3,5-triazine-2,4-di C N N R3 H one as a white Solid. 13 R4 C. % 15 N 2N 2N

N1 NN RI n R2 2 2O 1. 1. N N N R3 O N O H H Formula I 25 LC-MS: m/z 225 (M+H)". The procedure set forth in Example 3, step 2 was used to Example 3, Step 1: Preparation of produce the following intermediates (11) starting with 6-chloro-pyridine-2-carboxylic acid methyl ester appropriate intermediate 10. (10) 30 To a solution of 6-chloro-pyridine-2-carboxylic acid (48 g, 0.31 mol) in methanol (770 ml) was added concentrated 6-(6-trifluoromethyl-pyridin-2-yl)-1H-1,3,5-triazine-2,4- HCl (6 ml). The mixture was stirred at 80° C. for 48 hours dione as a pale white Solid. then concentrated to remove the volatile. The crude product 35 was diluted with ethyl acetated and washed with Sat. NaHCO, solution. The organic layer was dried with anhy F drous Na2SO and concentrated to give 6-chloro-pyridine F 2-carboxylic acid methyl ester as a white solid. N F 40 2N

HN1 NN

45 O1. N 1.O H

LC-MS: m/z. 172.0 (M+H)". The procedure set forth in Example 3, step 1 was used to 50 LC-MS: m/z 259 (M+H)". produce the following intermediates (10) using the appro 6-pyridin-2-yl-1H-1,3,5-triazine-2,4-dione. priate starting material 9. 6-trifluoromethyl-pyridine-2-carboxylic acid methyl ester. 55

F F N F

2N 60 O1. N 1sO H

O o1 65 "H NMR (DMSO-d4): 8 11.9-12.5 (s, 1H), 11.3-11.6 (s, 1H), 8.7-8.9 (m. 1H), 8.2-8.4 (m. 1H), 8.0-8.2 (m, 1H), LC-MS: m/z. 206 (M+H)". 7.6-7.8 (m, 1H). US 9,656,999 B2 171 172 Example 3, Step 3: Preparation of 2,4-dichloro-6- was stirred at room temperature for 1 hour. The mixture was (6-chloropyridin-2-yl)-1,3,5-triazine quenched by water and extracted with ethyl acetate. The organic layer was dried over anhydrous Na2SO4 and con To a solution of 6-(pyridin-2-yl)-1,3,5-triazine-2,4(1H, centrated to give 4-chloro-6-(6-chloropyridin-2-yl)-N-iso 3H)-dione (3.0 g. 013 mol) in POC1 (48 mL) was added 5 propyl-1,3,5-triazin-2-amine which was used directly in the PC1s (23 g, 0.1 mol). The mixture was stirred at 100° C. for next step. 2 hours then concentrated to remove the volatile. The residue was diluted with ethyl acetated and washed with SatNaHCO solution. The organic layer was dried over anhydrous Na2SO4 and concentrated to give 2,4-dichloro 10 6-(6-chloropyridin-2-yl)-1,3,5-triazine as a brown solid.

N1 NN s --- C l Nals C LC-MS: m/z 221.1 (M+H)". LC-MS: m/z 260.9 (M+H)". The procedure set forth in Step 4 using the appropriate The procedure set forth in Example 3, step 3 together with 25 intermediate 12 and amine 6 was used to produce the the appropriate starting intermediate 11 was used to produce following intermediates (13). the following intermediates (12). 4-Chloro-6-(6-trifluoromethyl-pyridin-2-yl)-1, 3, 5 tri 2,4-dichloro-6-(6-trifluoromethyl-pyridin-2-yl)-1,3,5-tri azin-2-yl-isopropyl-amine. azine as light yellow solid. 30

F N F. F l 35 F rs,2N N n N 40 N1 NN C l Nals C LC-MS: m/z 294.9 (M+H)". --- 2,4-Dichloro-6-pyridin-2-yl-1,3,5 triazine (1.0 g, 80%) 45 as brown solid. LC-MS: m/z. 318.1 (M+H)". 4-Chloro-6-pyridin-2-yl-1,3,5 triazin-2-yl)-isopropyl amine. N 50 2 N

N n N 55 N C Nals C. 2N LC-MS: m/z 227.0 (M+H)". 60 Example 3, Step 4: Preparation of 4-chloro-6-(6- chloropyridin-2-yl)-N-isopropyl-1,3,5-triazin-2- amine ---

To a solution of 2,4-dichloro-6-(pyridin-2-yl)-1,3,5-triaz 65 LC-MS: m/z 249.9 (M+H)". ine (2.0 g, 0.0077 mol) in anhydrous THF (20 mL) was 4-chloro-6-(6-chloropyridin-2-yl)-N-(oxetan-3-yl)-1,3,5- added isopropyl amine (0.45 g, 0.0077 mol). The mixture triazin-2-amine, which was used directly in the next step.

US 9,656,999 B2 189 190 -continued 1-(4,6-Dichloro-1,3,5 triazin-2-ylamino)-2-methyl-pro R4 pan-2-ol, which was directly used in the next step.

Y, O NH2 C 21 4

Procedure A, B, or C N1 NN R1 R2 10 C. 2 C N N R3 H 15 R4 LCMS: m/z 237.0 (M+H)". SA 15 4,6-dichloro-N-isobutyl-1,3,5-triazin-2-amine, which was directly used in the next step. 2

C N1 NN RI R2 2 N N N R3 H H C. Formula I 25 ----- Example 4, Step 1: Preparation of H NMR (CDC1) & 0.85 (d. J=8.6 Hz, 6H), 1.75-194 (m, 4,6-dichloro-N-isopropyl-1,3,5-triazin-2-amine 1H), 3.30-3.33 (m, 2H), 6.29 (br. 1H). 30 To a solution of 2,4,6-trichloro-1,3,5-triazine (4.0 g, 0.0217 mol) in THF (25 mL) was added isopropyl amine (1.27 g., 0.0217 mmol) at 0°C. The mixture was stirred at room temperature for 12 hours. The mixture was adjusted Example 4, Step 2: Preparation of 1-4-chloro-6-(2- pH 7 by aq NaHCO and extracted with ethyl acetate (100 35 fluoro-phenyl)-1.3.5 triazin-2-ylamino-2-methyl mL*2). The combined organic layer was dried over NaSO, propan-2-ol concentrated and purified by column chromatography to give 4,6-dichloro-N-isopropyl-1,3,5-triazin-2-amine as a To a mixture of 4,6-dichloro-N-isopropyl-1,3,5-triazin-2- colorless oil. 40 amine (1.0 g, 4.83 mmol), 3-fluorophenylboronic acid (0.671 g, 0.00483 mol) and CsCO, (3.15g, 0.00966 mol) C in dioxane?water (12 mL/2.4 mL) was added Pd(PPh.) (0.56 g. 483 mmol). The mixture was heated to 80°C. for 2 hours. The mixture was concentrated and purified by SiO, 1s, chromatography to give 1-4-chloro-6-(2-fluoro-phenyl)-1, 45 3.5 triazin-2-ylamino-2-methyl-propan-2-ol as a white --- solid.

H NMR (CDC1) & 1.24-1.27 (m, 6H), 4.21-4.26 (m, 50 1H), 5.68 (brs, 1H). The following intermediates (13) were prepared follow ing the procedure of Step 1 using the appropriate amine 6. 4,6-dichloro-N-(oxetan-3-yl)-1,3,5-triazin-2-amine, which was directly used in the next step. 55 N

C - Nals N C es 60

--- LCMS: m/z 297.1 (M+H)". 65 Additional intermediates 15 were prepared by the method H NMR (CDC1) & 1.71-1.83 (m, 2H), 1.90-2.04 (m, of Example 4, step 2 using the appropriate boronic acid 14 2H), 2.37-2.46 (m, 2H), 4.46-4.56 (m. 1H), 6.04 (br. 1H). and the appropriate starting intermediate 13.

US 9,656,999 B2 193 194 The following compound was also made using the pro (15 mL) was stirred at 80° C. under N for 2 hrs. Cooled to cedure of Step 3 and the appropriate amine 4. room temperature and water was added. Extracted with ethyl acetate and the organic layer was washed with brine, dried Compound 226—6-(2-chlorophenyl)-N-isopropyl over sodium sulfate and filtered. The filtrate was concen N'-(pyridin-4-yl)-1,3,5-triazine-2,4-diamine trated in vacuo and the residue was purified by a standard method to obtain N-cyclobutyl-6-(2-fluoro-phenyl)-N'-(5- fluoro-pyridin-3-yl)-1.3.5 triazine-2,4-diamine.

C F F 15 21 N1 NN OJO.N ----- N& - - -D H NMR (METHANOL-d) 8: 8.31 (t, J=6.2 Hz, 2H), 7.87 (t, J=6.2 Hz, 2H), 7.74-7.65 (m, 1H), 7.50-7.37 (m, H NMR (METHANOL-d) 8: 8.73-8.44 (m, 2H), 8.08 3H), 4.31-4.26 (m. 1H), 1.30-1.24 (m, 6H). LC-MS: m/z (d. J=13.1 Hz, 2H), 7.53 (br.s., 1H), 7.28-7.19 (m, 2H), 341.0 (M+H)". 4.58-4.51 (m, 1H), 2.42 (br.s., 2H), 2.09 (t, J=9.6 Hz, 2H), 1.80 (br.s., 2H). LC-MS: m/z. 355.2 (M+H)". Example 4, Step 3 (Procedure B): Compound 25 The following compounds were analogously made 317 N°-cyclobutyl-6-(2-fluorophenyl)-N'-(3- according to Example 4, step 3 (procedure C) using the (methylsulfonyl)phenyl)-1,3,5-triazine-2,4-diamine appropriate intermediate 15 and the appropriate amine 4 A mixture of 4-chloro-6-(2-fluoro-phenyl)-1.3.5 triazin Compound 184—6-(3-fluorophenyl)-N-isopropyl 2-yl)-cyclobutyl-amine (150 mg, 0.538 mmol) and 3-meth N'-(pyridin-4-yl)-1,3,5-triazine-2,4-diamine anesulfonyl-phenylamine (111 mg, 0.648 mmol) in anhy 30 drous THF (10 mL) was stirred at 80° C. for 8 hrs. TLC (petroleum ether?ethyl acetate 10/1) indicated the reaction was complete and water was added. The mixture was F extracted with ethyl acetate and the organic layer was 35 washed with brine, dried over sodium sulfate. Filtered and the filtrate was concentrated in vacuo to give crude N-cy clobutyl-6-(2-fluoro-phenyl)-N'-(3-methane-sulfonyl-phe nyl)1.3.5 triazine-2,4-diamine, which was purified a stan dard method to give pure N-cyclobutyl-6-(2-fluoro-phenyl)- N21 NN N'-(3-methanesulfonyl-phenyl)-1.3.5 triazine-2,4-diamine. 40 N ----- H H

45 H NMR (METHANOL-d) 8: 8,35-8.31 (m, 2H), 8.26 O 8.20 (m, 1H), 8.10 (t, J=8.9 Hz, 1H), 7.90 (t, J=6.9 Hz, 2H), 7.55-7.47 (m. 1H), 7.30-7.24 (m, 1H), 4.43-4.24 (m, 1H), O 1.30 (d. J=6.9 Hz, 6H). LC-MS: m/z 325.0 (M+H)". 1n Compound 185-6-(3-chlorophenyl)-N-isopropyl --- 50 N'-(pyridin-4-yl)-1,3,5-triazine-2,4-diamine

"H NMR (METHANOL-d) 8: 9.00-8.61 (m. 1H), 8.16 C 7.76 (m, 1H), 7.62-7.52 (m, 3H), 7.30-7.18 (m, 2H), 4.67 55 4.61 (m. 1H), 3.16 (s.3H), 2.52-2.38 (m, 2H), 2.10-2.01 (m, 2H), 1.88-1.76 (m, 2H). LC-MS: m/z. 414.3 (M+H)". Example 4, Step 3 (Procedure C): Synthesis of Compound 318 N-Cyclobutyl-6-(2-fluoro-phenyl)- 60 N'-(5-fluoro-pyridin-3-yl)-1.3.5 triazine-2,4-di amine OJO.N ------A mixture of 4-chloro-6-(2-fluoro-phenyl)-1.3.5 triazin 2-yl)-cyclobutyl-amine (300 mg, 1.08 mmol), 5-fluoro-pyri 65 H NMR (METHANOL-d) 8: 8.38-8.30 (m, 4H), 7.91 din-3-ylamine (145 mg, 1.29 mmol) Pd(dppf)Cl(80 mg. 7.87(m, 2H), 7.53-743 (m, 2H), 4.41-4.23 (m. 1H), 1.30 (d. 0.11 mmol) and t-BuONa (208 mg, 2.17 mmol) in dioxane J=6.2 Hz, 6H). LC-MS: m/z 340.9 (M+H)".