(12) United States Patent (10) Patent No.: US 9,555,031 B2 Wang Et Al

USO09555031B2

(12) United States Patent (10) Patent No.: US 9,555,031 B2 Wang et al. (45) Date of Patent: Jan. 31, 2017

(54) THERAPEUTIC USES OF SELECTED (56) References Cited PYRROLOPYRIMIDINE COMPOUNDS WITH ANT-MERTYROSNE KNASE ACTIVITY U.S. PATENT DOCUMENTS (71) Applicant: The University of North Carolina at 5,958,930 A 9/1999 Gangjee et al. 7,217,710 B2 5/2007 Adams et al. Chapel Hill, Chapel Hill, NC (US) 7,589,086 B2 9, 2009 Bondavelli et al. (72) Inventors: Xiaodong Wang, Chapel Hill, NC 7,897,607 B2 3/2011 Gyorkos et al. 7.956,060 B2 6/2011 Arai et al. (US); Weihe Zhang, Vestavia, AL (US); 7.998,978 B2 8/2011 Huang et al. Stephen Frye, Chapel Hill, NC (US) 8.324,225 B2 12/2012 Brain et al. 8,362,023 B2 1/2013 Liu et al. (73) Assignee: The University of North Carolina at 8,415,361 B2 4/2013 Lemke et al. Chapel Hill, Chapel Hill, NC (US) 8,513,242 B2 8/2013 Chiang et al. 2004/02098.95 A1 10/2004 Luecking et al. (*) Notice: Subject to any disclaimer, the term of this 2006.0025383 A1 2/2006 Wishart et al. patent is extended or adjusted under 35 2007/OO78140 A1 4/2007 Borzilleri et al. 2007/0105874 A1 5/2007 Zhang et al. U.S.C. 154(b) by 0 days. 2007/0225.306 A1 9, 2007 Choi et al. (21) Appl. No.: 14/678,905 2007/0275984 A1 11/2007 Imogai et al. 2008/024804.6 A1 10/2008 Ni et al. (22) Filed: Apr. 3, 2015 2008/0267887 A1 10/2008 Yuan et al. 2009/0012060 A1 1/2009 Arai et al. (65) Prior Publication Data 2010.0137313 A1 6/2010 Boriack-Sjodin et al. 2010, O247554 A1 9/2010 Lemke et al. US 2015/O29O.197 A1 Oct. 15, 2015 2010/0266604 A1 10/2010 Rothlin et al. 2011 (0281867 A1 1 1/2011 Kalman et al. 2011/0319267 A1 12/2011 Ekwuribe et al. Related U.S. Application Data 2012, 0035.194 A1 2/2012 Huang et al. 2012fO2O7763 A1 8, 2012 Brain et al. (60) Provisional application No. 61/978.268, filed on Apr. 2012fO2O7764 A1 8, 2012 Terrett et al. 11, 2014, provisional application No. 61/978,281, 2012/0219559 A1 8, 2012 Chen et al. filed on Apr. 11, 2014, provisional application No. (Continued) 61/978,290, filed on Apr. 11, 2014, provisional application No. 61/978,443, filed on Apr. 11, 2014, FOREIGN PATENT DOCUMENTS provisional application No. 61/978.485, filed on Apr. 11, 2014, provisional application No. 61/978,513, CA 2492319 A1 4/2004 filed on Apr. 11, 2014, provisional application No. EP 1710246 A1 10, 2006 61/978,321, filed on Apr. 11, 2014, provisional (Continued) application No. 61/994,384, filed on May 16, 2014, provisional application No. 62/088,159, filed on Dec. OTHER PUBLICATIONS 5, 2014. U.S. Appl. No. 13/641,729. The University of North Carolina at (51) Int. Cl. Chapel Hill, filed Nov. 9, 2012. AOIN 43/90 (2006.01) U.S. Appl. No. 14/348,805. The University of North Carolina at A 6LX 3/59 (2006.01) Chapel Hill, filed Mar. 31, 2014. A6 IK3I/506 (2006.01) U.S. Appl. No. 14/384,789. The University of North Carolina at A 6LX 3/5.377 (2006.01) Chapel Hill, filed Sep. 12, 2014. A 6LX 3L/505 (2006.01) U.S. Appl. No. 14436,356, The University of North Carolina at A6 IK3I/55 (2006.01) Chapel Hill, filed Apr. 16, 2015. A6 IK3I/55 (2006.01) U.S. Appl. No. 14/647,733, The University of North Carolina at A 6LX 3/553 (2006.01) Chapel Hill, filed May 27, 2015. A6 IK 45/06 (2006.01) U.S. Appl. No. 14/678,830. The University of North Carolina at CO7D 487/04 (2006.01) Chapel Hill, filed Apr. 3, 2015. CO7D 40/04 (2006.01) (Continued) CO7D 40/4 (2006.01) CO7D 487/08 (2006.01) Primary Examiner — Jeffrey H Murray (52) U.S. Cl. (74) Attorney, Agent, or Firm — Myers Bigel, P.A. CPC ...... A6 IK3I/506 (2013.01); A61K 3 1/505 (2013.01); A61 K3I/519 (2013.01); A61 K (57) ABSTRACT 31/5377 (2013.01); A61 K3I/55 (2013.01); Uses of pyrrolopyrimidines with anti-Mer tyrosine kinase A6 IK3I/551 (2013.01); A61 K3I/5513 activity as anti-infective agents, immunostimulatory and (2013.01); A61K 45/06 (2013.01); C07D immunomodulatory agents, anti-cancer agents (including 401/04 (2013.01); C07D 401/14 (2013.01); against MerTK-/- tumors and ITD and TKD mutant forms C07D 487/04 (2013.01); C07D 487/08 of Acute Myeloid Leukemia (AML)), and as adjunctive (2013.01) agents in combination with chemotherapeutic, radiation or (58) Field of Classification Search other standard of care for neoplasms. None See application file for complete search history. 12 Claims, 55 Drawing Sheets US 9,555,031 B2 Page 2

(56) References Cited Aly et al. “Heteroannelations with o-amino aldehyde and o-amino cyano of some pyrazole derivatives' Afinidad, Barcelona, ES(2004) U.S. PATENT DOCUMENTS 61:510-515. Angelillo-Scherrer et al. “Role of Gas6 receptors in platelet signal 2012fO230991 A1 9/2012 Graham et al. 2013, OO29993 A1 1/2013 Stadtmueller ing during thrombus stabilization and implications for 2013.0034862 A1 2/2013 Fantlet al. antithrombotic therapy'. J. Clin. Invest. (2005) 115(2):237-246. 2013,0059836 A1 3/2013 Wang et al. Bernsmeier, et al. "Patients with Acute-on-Chronic Liver Failure 2013,007 2382 A1 3/2013 Trullinger et al. Have Increased Numbers of Regulatory Immune Cells Expressing 2013/01O2587 A1 4/2013 Evans et al. the Receptor Tyrosine Kinase MERTK'. Gastroenterology (2015), 2013/O137708 A1 5, 2013 Garske et al. 1-13. 2013, O150368 A1 6, 2013 Ashcraft et al. 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WO PCT/US2O15,024301 4/2015 Meertens, L. et al. “The TIM and TAM families of WO PCT/US2O15,024328 4/2015 phosphatidylserine receptors mediate dengue virus entry. Cell Host WO PCT/US2O15,02438O 4/2015 Microbe (2012) 12:544-557. WO PCT/US2O15,024381 4/2015 Mercer, J. & Helenius, A. Vaccinia virus uses macropinocytosis WO PCT/US2O15,024393 4/2015 and apoptotic mimicry to enter host cells'. Science (2008) 320: WO PCT/US2O15,024.395 4/2015 531-535. WO PCT/US2O15,024396 4/2015 Morizono, et al. “The Soluble Serum Protein Gas6 Bridges Virion Envelope Phosphatidylserine to the TAM Receptor Tyrosine Kinase OTHER PUBLICATIONS Axl to mediate Viral Entry”. Cell Host & Microbe (2011) 9:286 298. U.S. Appl. No. 14/678,678, The University of North Carolina at Morizono and Chen, “Role of Phosphatidyl Receptors in Enveloped Chapel Hill, filed Apr. 3, 2015. Virus Infection”. J. Virology (2014) 88(8):4275-4290. U.S. Appl. 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(56) References Cited European Search Report corresponding to European Application No. 13793.925.2 dated Nov. 30, 2015. OTHER PUBLICATIONS Banker et al. Modern Pharmaceuticals p. 596 (1996). Wolff at al. “Burger's Medicinal Chemistry and Drug Discovery', Powell et al. "Optimization of highly selective 2,4- John Wiley & Sons. Inc. 5' Ed vol. 1:975-977 (1995). diaminopyridine-5-carboxamide inhibitors of Sky kinase”, Bioorg. Database CAPLUS in STN, Ace. No. 2007: 1144983, Guillemont et Med. Chem. Lett. (2013) 23:1051-1055. al., WO 2007/113254. A 1 (Oct. 11, 2007) (abstract). Sather, et al. “A soluble form of the Mer receptor tyrosine kinase European Search Report corresponding to European Application inhibits macrophage clearance of apoptotic cells and platelet aggre No. 13858929.6 dated May 3, 2016. gation”. Blood (2007) 109(3): 1026-1033. European Search Report corresponding to European Application Schlegel et al. “MER receptor tyrosine kinase is a therapeutic target No. 13847985.2 dated May 24, 2016. in melanoma” J. Clin. Invest. (2013) 123(5): 2257-67. Database CAPLUS Online—Chemical Abstracts Service, Colum Shimojima, et al. “Tyro3 Family-mediated Cell Entry of Ebola and bus, Ohio, US; 2004, Ismail, M.A.: “Efficient synthesis of 5-(5- Marburg Viruses”,Journal of Virology (2006) 80(20): 10.109-10116. aryl-2-furyl)pyrimidine derivitive”. Database accession No. Zhang, W., et al. “Discovery of Mer specific tyrosine kinase 2004:55.1368; & ISMAIL, M.A.: “Efficient synthesis of 5-(5-aryl inhibitors for the treatment and prevention of thrombosis”. J. Med. 2-furyl)pyrimidine derivatives'. Mansoura Science Bulletin, A: Chem. (2013) 56:9693-9700. Chemistry, vol. 30, No. 2, 2003, pp. 157-172 (Abstract Only) Zhang, W., et al. “Pseudo-cyclization through intramolecular hydro Ishida et al. “Novel and orally active 5-(1,3,4-oxadiazol-2- gen bond enables discovery of pyridine Substituted pyrimidines as yl)pyrimidine derivatives as selective FLT3 inhibitors'. Bioorangic new Merkinase inhibitors”, J. Med. Chem. (2013) 56:9683-9692. & Medicinal Chemistry Letters 18:5471-5477 (2008). Extended European Search Report, EP 11783985.2, mailed Oct. 15, Kiyoi et al. “A Novel FLT3 Inhibitor FI-700 Selectively Suppresses 2013. the Growth of Leukemia Cells with FLT3 Mutations', Clin Cancer Extended European Search Report, EP 12839069.7, mailed May 4, Res 13(15):4575-4582 (2007). 2015. Pawar et al. “Synthesis of 2,4,5-Trisubstituted Pyrimidines”, Indian International Search Report and Written Opinion, PCT/US2011/ Journal of Heterocyclic Chemistry 20012):133-136 (2010). 036215, mailed Aug. 16, 2011. 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Notification Concerning Transmittal of Copy of International Pre International Preliminary Report on Patentability, PCT/US2013/ liminary Report on Patentability corresponding to International 0651.92, Apr. 30, 2015. Application No. PCT/US2015/024381 mailed Oct. 20, 2016. International Search Report and Written Opinion, PCT/US2013/ Notification Concerning Transmittal of Copy of International Pre 07 1409, mailed Mar. 31, 2014. liminary Report on Patentability corresponding to International International Preliminary Report on Patentability, PCT/US2013/ Application No. PCT/US2015/024362 mailed Oct. 20, 2016. 07 1409, mailed Jun. 11, 2015. Notification Concerning Transmittal of Copy of International Pre International Search Report and Written Opinion, PCT/US2015/ liminary Report on Patentability corresponding to International 24258, mailed Jun. 24, 2015. Application No. PCT/US2015/024328 mailed Oct. 20, 2016. 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Tyro-3/Axl/Mer NH

FIG. A

Gas6/protein S Gladomain

open ALG2E. domain NH- SPY mCOOH

FIG. 1B U.S. Patent Jan. 31, 2017 Sheet 2 of 55 US 9,555,031 B2

FIG. C

U.S. Patent Jan. 31, 2017 Sheet 3 Of 55 US 9,555,031 B2

MMTV-PyVmt mammary tumors 1 OO the MerTKN-17 mln MerTKN-15 BO -- MerTKN=17 SO PC OOOO1 40 2O O O 50 OO 150 200 days FIG. 2A

B1 6: F1 O intradema tumors 100 the Merik N=10 80 to MerTK NO h C 60 P. C. O.OO1 E 40 3 20 A O O 1 O2O3O4O SO days FIG. 2B

c t O E 3.

E o s SS

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U.S. Patent US 9,555,031 B2

U.S. Patent Jan. 31, 2017 Sheet 6 of 55 US 9,555,031 B2

Patient 10510 Mer, Fit3-TD

Patient 123009 Merp, Fit39

to -

(OMSO) UNC1888

FIG. 4D U.S. Patent Jan. 31, 2017 Sheet 7 Of 55 US 9,555,031 B2

Patient Mer, FH3-ITD 1Cori

(CESO) JNCES

FIG. 4E

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g t d :

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U.S. Patent Jan. 31, 2017 Sheet 17 Of 55 US 9,555,031 B2

FIG. 7B U.S. Patent Jan. 31, 2017 Sheet 18 Of 55 US 9,555,031 B2

SEC 100 80 all Vehicle an MRX-6313 S. 60 - MTX MRX-6313-M TX A 40 E S. 20 0 & 20 40 60 80 100 Days Post-Transplant

FIG. 7C

Treatment Mediar

Survival Vehicle

75 mg/kg MRX-6313 + 1 mg/kg MTX

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FIG. 9A

FIG. 9B

FIG. 9C U.S. Patent Jan. 31, 2017 Sheet 22 of 55 US 9,555,031 B2

+ Gas6 + Gass (200 nM) (200 nM) MRX-6313 (nM) 100500 0 100500 0 100500 0 100500 pStat6 Stat6

ha 15C 8

2 s s 3 ? MRX6313 (nM)

FIG. 9E U.S. Patent Jan. 31, 2017 Sheet 23 Of 55 US 9,555,031 B2

J774 PyVmT 250

FIG 10A

1000 3. 800 --50mg/kgb-Saline qd MRX-6313 qd

600 in E 6 $ 400 p < 0.001

200 P

15.0 17.5 20.0 22.5 25.0 27.5 30.0 Days Post-Tumor injection

FIG. 10B U.S. Patent Jan. 31, 2017 Sheet 24 Of 55 US 9,555,031 B2

U.S. Patent Jan. 31, 2017 Sheet 25 Of 55 US 9,555,031 B2

* & 2.

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DAY 7 DAY 14 DAY 21 DAY 28 DAY 35 DAY 42 DAY 49 DAY 56 DAY 63

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H1299 SiNTV siAX1 siAx12 a a a

MRX6313; 2 5 S 8 8 8 S 3 pMer

Mer

pSTAT6 pAkt

FIG, 16B U.S. Patent Jan. 31, 2017 Sheet 34 of 55 US 9,555,031 B2

2N S C O O as SS sew

a O O O Sis

FIG. 17A U.S. Patent Jan. 31, 2017 Sheet 35 of 55 US 9,555,031 B2

S y o O& S &5 E5 o> N Da 55

37 kDa- pERK

ERK 37 kDa -

50 kDa - Tubulin

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U.S. Patent Jan. 31, 2017 Sheet 38 of 55 US 9,555,031 B2

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U.S. Patent Jan. 31, 2017 Sheet 40 of 55 US 9,555,031 B2

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FIG. 22 U.S. Patent Jan. 31, 2017 Sheet 42 of 55 US 9,555,031 B2

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U.S. Patent Jan. 31, 2017 Sheet 45 of 55 US 9,555,031 B2

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s koku Ongkg AO220. . . . . 8 x 50rgkg wrX2843 2s so is the 2s so horseereeeeeeeeeeeeeeeeeOtherapy pays Post-fraspiant G. 25A FT3-Dt Patient Sample in NSG nice

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U.S. Patent Jan. 31, 2017 Sheet 49 of 55 US 9,555,031 B2

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O835Y 80 on Saire 83: « Origikg AC22 2. x SOrgkg MRX28-3 488 88xx883 : &:::: s * : x 8.388: as sit is to as ic Days ost-raisgist w On Therapy

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U.S. Patent Jan. 31, 2017 Sheet 52 of 55 US 9,555,031 B2

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pCO.01 1225O5 &OOO1 10

Control 2025 LD ADP HDADPi LD ADP - 2025 FIG. 29A

2 O

Control 2025 LOADP HD ADP LD ADP + 2025 FIG. 29B U.S. Patent Jan. 31, 2017 Sheet 54 of 55 US 9,555,031 B2

100 P42 (p<0.001

80 HDADPi

4 O

2 O

10 20 30 Time (Minutes) FIG. 29C

5 | 10 5

Control 2025 LD ADP LD ADPi HD ADPi Abx + 2025

FIG, 29D U.S. Patent Jan. 31, 2017 Sheet 55 of 55 US 9,555,031 B2

100

Control 2025 AOPis A

FIG. 29E US 9,555,031 B2 1. 2 THERAPEUTIC USES OF SELECTED As described in more detail below, ligand-bound MerTK PYRROLOPYRIMIDINE COMPOUNDS WITH can complex with phosphatidyl serine and it binds apoptotic ANT-MERTYROSINE KNASE ACTIVITY cells which triggers ingestion and Suppresses inflammatory cytokines. It is aberrantly expressed in certain cancers (for CROSS-REFERENCE TO RELATED example, acute leukemia (ALL and AML) and some solid APPLICATIONS tumors (for example melanoma, breast cancer, colon cancer, non-Small cell lung carcinoma, glioblastoma and others). This application claims the benefit of U.S. Provisional The MerTK ligands include growth arrest-specific 6 pro Application No. 61/978,268 filed Apr. 11, 2014, U.S. Pro tein (GAS6; Chen, et al: Oncogene (1997) 14, 2033-2039), visional Application No. 61/978.281 filed Apr. 11, 2014, 10 protein-S, tubby and tubby-like protein-1 (TULP1), and U.S. Provisional Application No. 61/978,290 filed Apr. 11, galectin-3. Several of these ligands are present in serum and 2014, U.S. Provisional Application No. 61/978,321 filed expressed locally in a number of tissues. These ligands bind Apr. 11, 2014, U.S. Provisional Application No. 61/978,443 to the extracellular domain of MerTK, resulting in tyrosine filed Apr. 11, 2014, U.S. Provisional Application No. kinase activation. 61/978,485 filed Apr. 11, 2014, U.S. Provisional Application 15 Since the discovery of MerTK in the Earp laboratory in No. 61/978,513 filed Apr. 11, 2014, U.S. Provisional Appli 1994, there has been a growing body of literature and patents cation No. 61/994,384 filed May 16, 2014, and U.S. Provi that suggest the possibility of MerTK as a druggable target sional Application No. 62/088,159 filed Dec. 5, 2014. The for a number of indications. entirety of each of these applications is hereby incorporated TAM receptor tyrosine kinases have been investigated for by reference for all purposes. their involvement in certain infectious diseases. Shimojima, et al., reported the involvement of members of the Tyro3 GOVERNMENT INTEREST receptor tyrosine kinase family, Axl, Dkt and MerTK, in the The U.S. Government has rights in this invention by cell entry of filoviruses Ebolavirus and Marburgvirus, and virtue of support under Contract No. HHSN261200800001E concluded that each Tyro3 family member is likely a cell awarded by the National Cancer Institute, National Institute 25 entry factor in the infection (“Tyro3 Family-mediated Cell of Health. Entry of Ebola and Marburg, Viruses’ Journal of Virology, October 2006 p. 10109-10116). STATEMENT REGARDING ELECTRONIC U.S. Pat. No. 8,415,361 to Lemke, et al. (claiming priority FILING OF A SEQUENCE LISTING to a Nov. 9, 2007 provisional application), assigned to The 30 Salk Institute for Biological Studies, describes the use of A Sequence Listing in ASCII text format, submitted under TAM receptor inhibitors as antimicrobials. In particular, the 37 C.F.R. S1.821, entitled 5470-693 ST25.txt, 1,804 bytes 361 patent reports that inhibition of the TAM pathway in in size, generated on Jun. 2, 2015 and filed via EFS-Web, is virally infected macrophages from TAM triple knock-out provided in lieu of a paper copy. This Sequence Listing is mice leads to reduced levels of infection with a variety of incorporated by reference into the specification for its dis 35 pseudotyped viruses with either filoviral, retroviral or rhab closures. doviral glycoproteins. Brindley, et al., reported that in a bioinformatics-based screen for cellular genes that enhance FIELD OF THE INVENTION Zaire ebolavirus (ZEBOV) transduction, AXL mRNA The present invention is directed to the use of selected expression strongly correlated with ZEBOV infection (“Ty pyrrolopyrimidine compounds having Mer tyrosine kinase 40 rosine kinase receptor Axl enhances entry of Zaire ebolavi (MerTK) inhibitory activity as anti-infective agents, immu rus without direct interactions with the viral glycoprotein’ nostimulatory and immunomodulatory agents, anti-cancer Virology, 415 (2011) 83-84). agents (including against MerTK -f- tumors and ITD and Morizono, et al, published that Gas6 mediates binding of TKD mutant forms of Acute Myeloid Leukemia (AML)). the virus to target cells by bridging virion envelope phos and as adjunctive agents in combination with chemothera 45 phatidyl serine to Axl on the target cells. Replication of peutic, radiation or other standard of care for neoplasms. vaccinia virus, which was previously reported to use apop totic mimicry to enter cells, is enhanced by Gas6, and BACKGROUND OF THE INVENTION Morizono asserts that these results reveal an alternative molecular mechanism of viral entry that can broaden host MerTK is a member of a receptor tyrosine kinase (RTK) 50 range and enhance infectivity of enveloped viruses (“The family known as TAM, which also includes AXL and Soluble Serum Protein Gasó Bridges Virion Envelope Phos TYRO3. Each member of the TAM family contains an phatidylserine to the TAM Receptor Tyrosine Kinase Axl to extracellular domain, a transmembrane domain and a con mediate Viral Entry”. Cell Host & Microbe 9, 286-298, served intracellular kinase domain. MerTK was first discov 2011). In 2014, Morizono and Chen reported that virus ered in the laboratory of H. Shelton Earp at the University binding by viral envelope phosphatidyl serine is a viral entry of North Carolina in 1994 (Graham et al., Cloning and 55 mechanism generalized to a number of families of viruses mRNA expression analysis of a novel human proto-onco (Morizono and Chen, “Role of Phosphatidyl Receptors in gene, c-mer. Cell Growth Differ 5, 647-657 (1994)). The Enveloped Virus Infection”, J. Virology Vol 88(8), 4275 TAM family members undergo ligand-induced homodi 4290 (Jan. 29, 2014)). merization, followed by catalytic tyrosine kinase activation WO2013/124324 filed by Amara et al. (priority date Feb. and intracellular signaling. Cross-phosphorylation has also 60 21, 2012), and assigned to Institut National De La Sante et been demonstrated within this RTK family, Suggesting het De La Recherche Medicale, reports that Dengue virus is erodimerization can occur also. These RTKs are widely mediated by the interaction between phosphatidylserine at expressed in many epithelial tissues and in cells of the the surface of the Dengue viral envelope and TAM receptors immune, nervous, and reproductive systems. MerTK was present at the surface of the host cell, and that such inter given its name by the Earp laboratory because it was found 65 action can be blocked, thereby inhibiting entry of Dengue to be expressed in monocytes and in tissues of epithelial and into host cells. They also report that the interaction between reproductive tissue. phosphatidyl serine and TAM receptors is used by other US 9,555,031 B2 3 4 flaviviruses such as Yellow Fever, West Nile and perhaps In November 2013, Dr. Stephen Frye presented data Chikungunya. Amara focuses on antisense, siRNA and anti showing the inhibitory effects of a pyrrolopyrimidine com body approaches. pound (UNC2025) in non-small cell lung cancer cell lines, Similarly, Bhattacharayya et al., reports that several MerTK-expressing AML cell lines, and MerTK-negative human viruses, for example Ebola, Dengue, and HIV, exter AML cell lines. In addition, the effect of UNC2025 was nalize PtdSer on their capsid during budding and use phos analyzed in an ALL 697 cell line xenograft model and a phatidylserine to bind to and activate TAM RTKs in the FLT3-ITD AML patient xenograft model. Frye, S. “Aca presence of TAM ligands, allowing entry of the virus into demic Drug Discovery and Chemical Biology”. Presentation cells and furthermore, activation of MerTK in macrophages at the Northwestern 18th Annual Drug Discovery Sympo in response to viral particles expressing PtdSer stimulates an 10 sium. November 2013. The structure of the pyrrolopyrimi anti-inflammatory cytokine profile as if apoptotic material dine compound UNC2025 is: was being ingested, thereby inhibiting the anti-viral immune response. Bhattacharayya et al observe that TAM receptors are engaged by viruses to attenuate type 1 interferon sig naling (“Enveloped viruses disable innate immune 15 responses in dendritic cells by direct activation of TAM receptors', Cell Host & Microbe 14, 136-147 (2013)). See also Meertens, L. et al. The TIM and TAM families of phosphatidylserine receptors mediate dengue virus entry. Cell Host Microbe 12, 544-557, doi:10.1016/ j.chom.2012.08.009 (2012). Mercer, J. & Helenius, A. Vac cinia virus uses macropinocytosis and apoptotic mimicry to enter host cells. Science 320, 531-535, doi:10.1126/sci N1 N N ence. 1155164 (2008). MerTK is ectopically expressed or overexpressed in a 25 ----- N number of hematologic and epithelial malignant cells. H Expression of MerTK and GAS6 correlates with poor prog nosis and/or chemoresistance in these tumor types. The mechanisms by which increased MerTK signaling in tumor cells contributes to tumor malignancy, however, remain 30 unclear. OH WO2013/052417 titled “Pyrrolopyrimidine Compounds for the Treatment of Cancer filed by Wang, et al., and assigned to the University of North Carolina describe pyr WO2011/146313 and WO2014/062774, both titled “Pyra rolopyrimidines with MerTK inhibitory activity for the 35 Zolopyrimidine Compounds for the Treatment of Cancer' treatment of tumors such as myeloid leukemia, lymphoblas filed by Wang, et al., and assigned to the University of North tic leukemia, melanoma, breast, lung, colon, liver, gastric, Carolina describe pyrazolopyrimidines with MerTK inhibi kidney, ovarian, uterine and brain cancer, wherein the pyr tory activity for the treatment of tumors such as myeloid rolopyrimidines have the general structures below, with R leukemia, lymphoblastic leukemia, melanoma, breast, lung, Substituents as defined in the those applications: 40 colon, liver, gastric, kidney, ovarian, uterine and brain cancer, wherein the pyrazolopyrimidines have the general structures below, with R substituents as defined in the those (I) applications: R4 R1 I 45 (I) N1S-X R4 R1 l 2 2X R5 R3 N X V R2 50 1. N N (LA) N M R3 N NV R2

55 WO2014/062774 further discloses pyrazolopyrimidine compounds for use in a method of treating or inhibiting blood clot formation. In January 2012, Liu, J, et al., published a comparison of (IB) the activity of forty four pyrazolopyrimidine compounds R1 60 against MerTK, Axl and Tyro3 kinases. One of these com pounds (UNC569) was tested for inhibition of MerTK autophosphorylation in human B-ALL cells (“Discovery of Novel Small Molecule Mer Kinase Inhibitors for the Treat C2 Y-Rs R3 N N ment of Pediatric Acute Lymphoblastic Leukemia. ACS R2 65 Med Chem Lett. 2012 Feb. 9; 3(2):129-134). In May 2013, Schlegel, et al., published results on the pyrazolopyrimidine compound UNC1062, which reduced activation of MERTK US 9,555,031 B2 5 6 mediated downstream signaling, induced apoptosis in cul lineage cells where it acts to Suppress pro-inflammatory ture, reduced colony formation in soft agar, and inhibited cytokines following ingestion of apoptotic material. It was invasion of melanoma cells (“MER receptor tyrosine kinase found that MerTK -/- leukocytes exhibit lower tumor is a therapeutic target in melanoma. J Clin Invest. 2013 cell-induced expression of wound healing cytokines (IL-10 May: 123(5):2257-67). and GAS6) and enhanced expression of acute inflammatory In December 2013, Zhang, W., et al., also published a cytokines (IL-12 and IL-6). Further, intratumoral CD8+ comparison of the activity of forty six 5-arylpyrimidine lymphocytes are increased. The loss of MerTK in the tumor based compounds for treatment of tumors (“Pseudo-cycl microenvironment in Mer-f- mice slowed the establish ization through intramolecular hydrogen bond enables dis ment, growth, and metastasis of mammary tumors and covery of pyridine substituted pyrimidines as new Mer 10 melanomas in immune competent, Syngeneic mice. Cook, R. kinase inhibitors.” J Med. Chem., vol. 56:9683-9692, 2013). S. et al., MerTK inhibition in tumor leukocytes decreases These pyrimidine compounds were identified using a tumor growth and metastasis, J. Clin Invest 123, 3231-3242 pseudo-ring replacement strategy based on the previously (2013). identified pyrazolopyrimidine MerTK inhibitor, UNC569. Linger et al. have also presented data demonstrating In July 2013, Liu, J, et al. published the first evidence of 15 increased MerTK expression in E2A-PBX11 and other cyto anti-tumor activity mediated by a member of this novel class genetic Subgroups of B-acute lymphoblastic leukemia of inhibitors. Specifically, the pyrazolopyrimidine com (B-ALL), and that MerTK inhibition may attenuate prosur pound UNC1062 inhibited MerTK phosphorylation and vival and proliferation signaling. Linger et al., Mer receptor colony formation in soft agar (“UNC1062, a new and potent tyrosine kinase is a therapeutic target in pre-B-cell acute Mer inhibitor.” Eur J Med Chem. 2013 July; 65.83-93). In lymphoblastic leukemia, Blood, vol. 122(9): 1599-1609, November 2013, Christoph, S. et al., published effects of a 2013. Lee-Sherick, et al. (“Efficacy of a Mer and Flt3 pyrazolopyrimidine (UNC569) in ALL and ATRT (atypical tyrosine kinase small molecule inhibitor, UNC1666, in acute teratoid/rhabdoid tumors (ATRT) (“UNC569, a novel small myeloid leukemia. Oncotarget, Advance Publications 2015 molecule Mer inhibitor with efficacy against acute lympho Feb. 10, 2015) have reported that UNC1666 (a pyrrolopy blastic leukemia in vitro and in vivo.” Mol Cancer Ther: 25 2013 November; 12(11):2367-77). The MerTK inhibitors rimidine) decreases oncogenic signaling and myeloid Sur UNC569 and UNC1062 have the following structures: vival in AML. TAM (Tyro3-Axl-Mer) receptor tyrosine kinases have UNC569 also been investigated for their involvement in platelet F aggregation. In 2004, Chen et al., from the Johnson & 30 Johnson Pharmaceutical Research and Development, pub lished that MerTK, presumably through activation by its ligand Gas6, participates in the regulation of platelet func tion in vitro and platelet-dependent thrombosis in vivo. Chen, et al., “Mer Receptor tyrosine Kinase Signaling Par 35 ticipates in Platelet Function'. Arterioscler. ThromV. Vase. N N \ and Biol. 1118-1123 June 2004. Chen reported that PtdSer on aggregating platelets activates MerTK, helping to stabilize 1N1N N lelN 2 N clot formation. MerTK knockout mice have decreased plate H let aggregation while maintaining normal bleeding times and 40 coagulation parameters. Consequently, these mice appear to ''NH be protected from thrombosis without concomitant increased spontaneous bleeding (see also Angelillo-Scherrer UNC1062 A et al., Role of Gas6 receptors in platelet signaling during thrombus stabilization and implications for antithrombotic 45 therapy. J. Clin. Invest. 2005, 115 (2), 237-246). In 2007, Sather, et al., reported that membrane-bound MerTK is cleaved in the extracellular domain via a metal loproteinase to produce a soluble MerTK that decreased 50 platelet aggregation in vitro and prevented fatal collagen/ epinephrine-induced thromboembolism. “A soluble form of the Mer receptor tyrosine kinase inhibits macrophage clear ance of apoptotic cells and platelet aggregation', Blood. Vol 109(3): 1026-1033). 55 Paolino et al. have reported on the treatment of wild-type NK cells with a newly developed small molecule TAM kinase inhibitor, LDC1267, that conferred therapeutic poten tial and efficiently enhancing anti-metastatic NK cell activity in vivo. Oral or intraperitoneal administration using this 60 TAM inhibitor markedly reduced murine mammary cancer and melanoma metastases dependent on NK cells. See, Paolino, M., et al. The E3 ligase Cbl-b and TAM receptors OH regulate cancer metastasis via natural killer cells, Nature, vol. 507:508-512, 2014. LDC1267 is a highly selective An important observation was made in 2013 that MerTK 65 TAM kinase inhibitor with ICs of <5 nM, 8 nM, and 29 nM -/- knock-out mice are less Susceptible to tumor growth for MerTK, Tyro3, and Axl, respectively, and has the chemi than normal mice. MerTK is normally expressed in myeloid cal structure: US 9,555,031 B2 7 8 Paramyxoviridae viruses, for example Respiratory syncytial LDC1267 virus (RSV), measles and mumps; and Caliciviridae viruses, including Lagovirus, Vesivirus, and Sapovirus and Norovi rus (Norwalk-like virus), and Lentiviruses, for example, HIV. In one embodiment, the virus is an enveloped virus. In O another embodiment, the virus is a non-enveloped virus. e It has also been discovered that an effective amount of the H N pyrrolopyrimidine compounds described in Formulas I, IA, F N S. M. N F IB, II, IIA and IIB below can be used to treat a host bearing a bacterial infection. In one embodiment, the bacteria treated O 10 is, for example, a Gram-negative bacilli (GNB), especially O Escherichia coli, Gram-positive cocci (GPC), Staphylococ O cus aureus, Enterococcus faecalis, or Streptococcus pneu 1 N moniae. In one embodiment, the bacterial infection is asso ciated with liver failure. In one embodiment, an active 2 compound disclosed herein is administered in combination No N 15 with an antibiotic or another anti-bacterial agent. It has also been discovered that the compounds described herein can be used as immunomodulatory agents that reverse Bernsmeier, et al., have noted that characteristics of the MerTK-induced suppression of pro-inflammatory cytok decompensated cirrhosis and acute-on-chronic liver failure ines such as wound healing cytokines (IL-10 and GAS6) and (ACLF) include susceptibility to infection, immune paresis enhance the expression of acute inflammatory cytokines and monocyte dysfunction. The authors found that the (IL-12 and IL-6). In this way, the pyrrolopyrimidine com number of monocytes and macrophages that expressed pounds can “re-normalize' or “re-program’ the host MerTK was greatly increased in circulation, livers and microenvironment in the diseased tissue area to attack the lymph nodes of patients with ACLF. They found that addi diseased cells. tion of a substituted pyrazolopyrimidine UNC569 (see WO Taking advantage of the immunostimulatory activity of 2011/146313 filed by Wang, et al., and assigned to Univer 25 the compounds described herein, or a pharmaceutically sity of North Carolina at Chapel Hill, page 25) restored acceptable composition, salt, isotopic analog, or prodrug production of inflammatory cytokines. Bernsmeier, et al., thereof, may be used for the treatment of a MERTK-negative “Patients with Acute-on-Chronic Liver Failure Have (-/-) tumor or cancer, for example MERTK-negative (-/-) Increased Numbers of Regulatory Immune Cells Expressing breast cancer. the Receptor Tyrosine Kinase MERTK. Gastroenterology 30 As part of the invention, one or more of the compounds 2015: 1-13. disclosed herein can be used as adjunctive antineoplastic It is an object of the invention to identify new methods therapy for its immunostimulatory effect as a means to and compositions for the treatment of infectious diseases. increase the efficacy of the antineoplastic standard of care It is another object of the invention to identify new therapies, such as chemotherapeutic compounds or radia methods and compositions for the treatment of thrombosis. 35 tion. It is another object of the invention to identify new Some of these pyrrolopyrimidine compounds have dual methods and compositions for the treatment of a tumor, Mer/Flt-3 inhibitory activity, as discussed in more detail cancer or other neoplasm. below, and thus are useful in the treatment of tumors It is yet another object of the invention to identify new mediated by FLT-3 or which exhibit drug resistance or ITD methods and compositions for the treatment of disorders that and TKD mutations, such as certain forms of Acute Myeloid can be treated with immunosuppression, or which would 40 Leukemia (AML). benefit from immunostimulatory therapy. The compounds described as useful in the present inven tions were first described in WO 2013/052417, which is SUMMARY OF THE INVENTION incorporated by reference for all purposes. The present invention describes for the first time that these compounds The present invention is directed to the use of selected 45 are useful for medical applications not described in or pyrrolopyrimidine compounds having Mer tyrosine kinase flowing from these earlier published applications. Specifi (MerTK) inhibitory activity as anti-infective agents, immu cally, MerTK inhibitors useful in treating a disorder nostimulatory agents, anti-cancer agents (including against described herein have the structure of Formula I, IA, IB, II, MerTK -f- tumors and ITD and TKD mutant forms of IIA, or IIB: Acute Myeloid Leukemia (AML)), and as adjunctive agents 50 in combination with chemotherapeutic, radiation or other standard of care for neoplasms. (I) An effective amount of the pyrrolopyrimidine compounds R1 described in Formulas I, IA, IB, II, IIA and IIB below or M other active compounds as otherwise provided herein can be 55 N21 X used to treat a host bearing any virus-related infection where the virus has a virion envelope phosphatidyl serine that N t complexes with MerTK to achieve viral entry or is otherwise R 3 J. N J.X V " facilitated by MerTK in the infectious process. Nonlimiting R2 examples of Such viruses include, but are not limited to, (IA) Flaviviridae viruses, including Flavivirus (such as Yellow 60 Fever, West Nile and Dengue), Hepacivirus (Hepatitis C virus, “HCV), Pegivirus and Pestivirus (Bovine viral diar rhea virus); Filoviridae viruses, including Ebola viruses: Togaviridae viruses, including Chikungunya virus; Corona viruses, such as SARS (Severe acute respiratory syndrome) 65 and MERS (Middle East respiratory syndrome); Orthomyxoviridae viruses, for example influenza; US 9,555,031 B2 10 -continued heterocyclo. —(CH), NH(CH), aryl, -(CH2), NH (IB) (CH-) heteroaryl, -(CH2)NH(CH)N(alkyl), alk enylamino, alkynylamino, haloalkylamino, cycloalky lamino, cycloalkylalkylamino, arylamino, arylalkylamino, heterocycloamino, heterocycloalkylamino, disubsti tutedamino, acylamino, acyloxy, ester, amide, S(O),OR". CONHNH, cyano, nitro, aminosulfonyl, COOH, sulfona mide, urea, alkoxyacylamino, aminoacyloxy, —C(CH2)

(II) 10 R', and wherein R' is optionally substituted one, two or R 14 R11 three times; / m=0, 1, 2 or 3: N1S-X n=0, 1 or 2; X R15 R'' is R'R'', where R' is a covalent bond or C to C. 15 alkyl and R' is cycloalkyl, cycloalkylalkyl, heterocyclo, --- /V heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, R12 hydroxyalkyl, alkoxyalkyl, or alkyl, and wherein R' is (ILA) optionally substituted one, two or three times; R" is NR7R, where; R'' is selected from the group consisting of H, alkyl, hydroxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, heterocyclo, heterocycloalkyl, alkylheterocycloalkyl, het eroaryl, heteroarylalkyl, and alkoxyalkyl, each of which is optionally substituted one, two or three times (typically R'7 (IIB) 25 is H): R 14 R11 R" is selected from the group consisting of H, alkyl, hydroxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, N1 N heterocyclo, heterocycloalkyl, alkylheterocycloalkyl, het l N R15 eroaryl, heteroarylalkyl, and alkoxyalkyl, each of which is 2 30 R13 N NV optionally substituted one, two or three times; R12 O R7 and R' together with the nitrogen to which they are bonded can form a heterocyclic group that can be optionally wherein: substituted; one of X and X" is N and the other of X and X" is C; 35 R" is H. loweralkyl, halo, or loweralkoxy; one of the dashed lines in Formula I is a single bond and R" is H. loweralkyl, halo, or loweralkoxy; the other of the dashed lines is a double bond (e.g., as shown R’ is selected from alkyl, alkenyl, alkynyl, aryl, arylal in Formulas IA and IB); kyl, cycloalkyl, cycloalkylalkyl, heterocyclo, heterocy R" is aryl: cloalkyl, heteroaryl, or heteroarylalkyl; R’ is RR, where R is a covalent bond or C1 to C3 40 or a pharmaceutically acceptable composition, salt, iso alkyl and R is cycloalkyl, heterocycloalkyl, aryl, heteroaryl topic analog, or prodrug thereof. or alkyl, and wherein R is optionally substituted from one Illustrative additional examples of compounds that to two times with independently selected polar groups; exhibit the activities described herein, have a structure R is NR7R, where R7 and Rare each independently selected from: selected from H. alkyl, arylalkyl cycloalkylalkyl, heterocy 45 cloalkylalkyl, heteroarylalkyl, and alkoxyalkyl, each of which is optionally substituted one, two or three times with independently selected polar groups (typically one of R or NH, R is H): 50 R is H. loweralkyl, halo, or loweralkoxy; R is H. loweralkyl, halo, or loweralkoxy; R'' is R(R'), where R is alkyl, alkenyl, -alkylaryl, heterocyclo, aryl, heteroaryl and R' is hydrogen, alkyl, haloalkyl, alkoxyalkyl, —O-alkylaryl, hydroxyalkyl, alk 55 enyl, alkenyloxy, alkynyl, alkynyloxy, cycloalkyl, N N cycloalkylalkyl, cycloalkoxy, cycloalkylalkyloxy, heterocy N clo, heterocycloalkyl, alkylheterocycloalkyl, heterocy 2 --- N N clooxy, heterocyclolalkyloxy, aryl, arylalkyl, aryloxy, aryl H alkyloxy, heteroaryl, alkylheteroaryl, halo, hydroxyl, 60 alkoxy, haloalkoxy, mercapto, alkyl-S(O), , haloalkyl-S (O), , alkenyl-S(O), , alkynyl-S(O), , cycloalkyl-S (O) , cycloalkylalkyl-S(O), , aryl-S(O), , arylalkyl S(O) , heterocyclo-S(O), ... heterocycloalkyl-S(O), . , H amino, carboxy, alkylamino, -(CH), NHalkyl, 65 —(CH2), N(alkyl). —(CH), NH(CH),OH, UNC4308A —(CH2), NH(CH2)cycloalkyl, -(CH2), NH(CH2).

US 9,555,031 B2 13 14 -continued -continued

OH UNC3908A

, H or a pharmaceutically acceptable composition, salt, isotopic UNC4291A analog, or prodrug thereof. The present invention thus provides at least the following: 25 (a) Use of one or more of the compounds disclosed herein in an effective immunostimulatory dosage for use as an anti-infective agent. (b) Use of one or more of the compounds disclosed herein in an effective immunostimulatory dosage for use as an 30 anti-viral agent. (c) Use of one or more of the compounds disclosed herein in an effective immunostimulatory dosage for use as an anti-bacterial agent. N N (d) Use of one or more of the compounds disclosed herein N 35 in an effective immunostimulatory dosage for use as an N anti-infective agent, in combination with an additional -----H anti-infective agent. (e) Use of one or more of the compounds disclosed herein in an effective immunostimulatory dosage for use as an 40 anti-viral agent, in combination with an additional anti viral agent. , (f) Use of one or more of the compounds disclosed herein in UNC4292A an effective immunostimulatory dosage for use as an 45 anti-bacterial agent, in combination with an additional anti-bacterial agent. (g) Use of any of the active compounds described herein, or a pharmaceutically acceptable composition, salt, isotopic analog, or prodrug thereof, for the treatment or prevention 50 of an infection that gains entry into the cell via phospha tidyl serine or another mechanism mediated by MerTK, or which infection is otherwise mediated by MerTK, for example a viral or bacterial infection, as further described herein. 55 (h) Use of any of the active compounds described herein, or a pharmaceutically acceptable composition, salt, isotopic analog, or prodrug thereof, to treat a host that has an immunosuppressed microenvironment Surrounding dis eased tissue, by re-programming the microenvironment to 60 a pro-inflammatory environment. As one example, the host is in need of treatment because it has tumor associ ated macrophages that are protecting tumor cells. (i) Use of one or more of the compounds disclosed herein in , H an effective immunostimulatory dosage for adjunctive UNC431 OA 65 antineoplastic therapy as a means to increase the efficacy of the antineoplastic standard of care therapies, such as chemotherapeutic compounds or radiation. US 9,555,031 B2 15 16 (j) Use of one or more of the compounds disclosed herein in UNC4310A, UNC4311A, UNC4319A, UNC4320A, and an effective immunostimulatory dosage for adjunctive UNC4321A, and pharmaceutically acceptable salts and antineoplastic therapy as a means to increase the efficacy prodrugs thereof, together with a pharmaceutically of the antineoplastic standard of care therapies, such as acceptable carrier or diluent. chemotherapeutic compounds or radiation, in combina 5 (dd) Processes for the manufacture of UNC3908A, tion with an additional chemotherapeutic agent. UNC4218A, UNC4291A, UNC4292A, UNC4308A, (k) Use of one or more of the compounds as described herein UNC4309A, UNC4310A, UNC4311A, UNC4319A, in an effective dosage to treat a host with a tumor, UNC4320A, and UNC4321A, and salts, compositions, including cancer. and dosage forms thereof. (1) Use of one or more of the compounds as described herein 10 (ee) Processes for the preparation of therapeutic products in an effective dosage to treat a host with a selected that contain an effective amount of UNC3908A, MerTK (+/+) tumor, including cancer. UNC4218A, UNC4291A, UNC4292A, UNC4308A, (m) Use of one or more of the compounds as described UNC4309A, UNC4310A, UNC4311A, UNC4319A, herein in an effective dosage to treat a host with a selected UNC4320A, and UNC4321A, as described herein. MerTK (-/-) tumor, including cancer. 15 (n) Use of one or more of the compounds disclosed herein BRIEF DESCRIPTION OF FIGURES to treat a host with acute myeloid leukemia (including FLT3-ITDAML, FLT3-TKDAML, or AML having both FIG. 1A illustrates the Ig-like domain, FNIII domain and FLT3-ITD and FLT3-TKD mutations). kinase domain in Tyro-3, Axl and MerTK. FIG. 1B illus (o) Use of one or more of the compounds disclosed herein trates the Gla domain, EGF repeat, LG1 domain and LG2 in combination with a second chemotherapeutic agent in domain in MerTK. The Gasó/protein S loop region is also a subject undergoing a therapeutic regime to treat a tumor, illustrated. FIG. 1C and FIG. 1D are scanning EM illustrat including cancer. ing the binding of apoptotic thymocytes to MerTK" and (p) Use of any of the active compounds described herein, to MerTK macrophages. Wild-type macrophages ingest; treat a host with a thrombotic or clotting disorder. 25 MerTK do not. (q) A compound selected from the group consisting of FIG. 2A illustrates the results obtained when MMTV UNC3908A, UNC4218A, UNC4291A, UNC4292A, PVmT mammary tumors were implanted into MerTK", UNC4308A, UNC4309A, UNC4310A, UNC4311A, MerTK' and MerTK' mice. Tumors that were implanted UNC4319A, UNC4320A, and UNC4321A, and pharma into MerTK mice were almost 75% tumor free after 200 ceutically acceptable compositions, salts, isotopic ana 30 days. FIG. 2B illustrates the results when B16:F10 intrad logs, and prodrugs thereof. ermal tumors were implanted in MerTK" or MerTK (r) A compound as described herein, for use in the manu mice. MerTK mice were tumor free for 40 days and facture of a medicament for use in treating an infectious MerTK' mice were tumor free for approximately 28 days. disease, including a viral disease or a bacterial disease. FIG. 2C is a graph showing the number of lung metastases (s) A compound as described herein, for use in the manu 35 per mouse verses the genotype of mice transplanted with facture of a medicament for treatment of a tumor, includ MMTV-PVVmT or B16:F10 tumor lines. ing cancer. FIG. 3: MerTK is a dual target in cancer. MerTK is over (t) A compound as described herein, for use in the manu expressed in tumor cells Such as lung, melanoma and GBM facture of a medicament for treatment of a MerTK+/+ and sends a survival signal. MerTK inhibitors inhibit tumor tumor, including cancer. 40 cell survival and chemoresistance. In addition, MerTK is (u) A compound as described herein, for use in the manu expressed in tumor-associated macrophages (e.g., breast, facture of a medicament for treatment of a MerTK-f- melanoma and lung cancer) and Suppresses tumor immunity. tumor, including cancer. MerTK inhibitors stimulate innate anti-tumor immunity. (v) A compound as described herein, for use in the manu FIG. 4A and FIG. 4B demonstrate that UNC1666 abro facture of a medicament for acute myeloid leukemia 45 gates MerTK and Flt3 kinase phosphorylation and down (including FLT3-ITDAML, FLT3-TKDAML, or AML stream signaling in leukemic blasts isolated from a patient having both FLT3-ITD and FLT3-TKD mutations). with acute myeloid leukemia at concentrations of 50, 100 (w) A compound as described herein, for use in the manu and 300 nM. FIGS. 4C and 4D illustrate the percent apop facture of a medicament for immunostimulatory therapy. totic and necrotic cells in when leukemic blasts isolated (X) A compound as described herein, for use in the manu 50 from patients with AMLS expressing MerTK and/or a FLT3 facture of a medicament for immunomodulatory therapy. ITD were treated with UNC1666 at concentrations of 50, (y) A compound as described herein, for use in the manu 100 and 300 nM. FIGS. 4E and 4F are graphs of the relative facture of a medicament for immunostimulatory therapy number of colonies when AML cells isolated from patients in combination with chemotherapeutic or radiation stan were grown in the presence of UNC1666 at concentrations dard of care. 55 of 50, 100 and 300 nM. See Example 10. (Z) A compound as described herein, for use in the manu FIG.5A: MRX6313/UNC2025 is a potent Mer/FLT3 dual facture of a medicament for immunomodulatory therapy TK inhibitor. The compound has a K–0.16 nM against in combination with chemotherapeutic or radiation stan MerTK, a K-0.71 nM against FLT3, a K-15 nM against dard of care. Axl and a K-5.1 nM against Tyro3. Mice were dosed (iv (aa) A compound as described herein, for use in the manu 60 and po) with 3 mg/kg MRX-6313. The graph illustrates the facture of a medicament for the treatment of a thrombotic plasma concentration of MRX-6313 in ng/mL verses time in or clotting disorder. hours. FIG. 5B illustrates the pharmacokinetic parameters (bb) A process for manufacturing a medicament as described for MRX6313/UNC2025. See Example 8. in (r) through (aa). FIG. 6A and FIG. 6B show reduced tumor burden mea (cc) A pharmaceutical formulation comprising an effective 65 Sured by bioluminescent imaging in response to treatment host-treating amount of UNC3908A, UNC4218A, with MRX6313/UNC2025 relative to mice treated with UNC4291A, UNC4292A, UNC4308A, UNC4309A, vehicle in orthotopic B-ALL xenograft models of estab US 9,555,031 B2 17 18 lished disease (A) and minimal residual disease (B). FIG. 6C FIG. 11 is a graph illustrating percent change in mela shows mean bioluminescence intensity verses day post noma tumor Volume in a genetically-engineered mouse transplant in mice receiving saline qd or 100 mg/kg (GEM) model (TRIA) after 21 days of treatment with MRX6313/UNC2025 qd starting at day 12 post-transplant in various drugs and combinations of drugs. MEK plus P13K the B-ALL xenograft model of established disease. FIG. 6D (AZD6244/BEZ235) was the only regimen to show efficacy is a Kaplan Meier plot showing percent Survival verses days in the model. This combination is not tolerated in humans. post-transplant for mice receiving either saline or 100 mg/kg FIG. 12A is a graph illustrating tumor volume (mm) MRX6313/UNC2025 in the B-ALL xenograft model of verses days when in TRIA mice treated with MRX6313/ established disease. FIG. 6E shows mean bioluminescence UNC2025 or vehicle. FIG. 12B is a Kaplan Meier plot intensity verses day post-transplant in mice receiving saline 10 showing percent survival verses days on MRX6313/ qd or 75 mg/kg MRX6313/UNC2025 qd starting at day 1 in UNC2025 therapy in the TRIA GEM model. FIG. 12C is a the B-ALL xenograft model of minimal residual disease. Kaplan Meier plot of percent survival verses days on therapy FIG. 6F is a Kaplan Meier plot showing percent survival verses no treatment in the TRIA GEM model. Mice with verses days post-transplant for mice receiving either saline melanoma were treated with MRX6313/UNC2025, or 75 mg/kg MRX6313/UNC2025 in the B-ALL xenograft 15 AZD6244/BEZ235 or given no treatment. model of minimal residual disease. FIGS. 6G-6H show FIG. 13 is a waterfall plot showing percent change in median Survival for mice receiving saline, 100 mg/kg tumor volumes verses days of treatment in the TRIA GEM MRX6313/UNC2025 qd starting at day 12, or 75 mg/kg model of melanoma. Mice were treated with UNC2025, MRX6313/UNC2025 qd starting at day 1. See Example 8. AZD6244, CarboTaxol or received no treatment. The best FIG. 7A is a graph illustrating the average biolumines response was mediated by UNC2025. cence intensity (x10° photons/sec) verses days post-trans FIG. 14 is a Kaplan Meier plot showing percent survival plant in mice treated with 75 mg/kg MRX6313/UNC2025, verses days on therapy in TRIA mice with melanoma treated 1 mg/kg methotrexate (MTX) or 75 mg/kg MRX6313/ with PD1, UNC2025, UNC2025 in combination with PD1 UNC2025+1 mg/kg methotrexate in a B-ALL xenograft or received no treatment. model. FIG. 7B is a graph showing tumor burden 88 days 25 FIG. 15A is a graph illustrating percent change in tumor post-transplant in individual mice treated with 75 mg/kg volume in TRIA mice with melanoma treated with MRX6313/UNC2025+1 mg/kg methotrexate in the experi UNC2025 or AZD6244 verses no treatment. AZD6244 is a ment shown in 7A. FIG. 7C is Kaplan Meier plot illustrating MEK inhibitor that was administered in mouse chow at a % leukemia-free survival verses days post-transplant for predicted dose of 37 mg/kg (MTD). UNC2025 was admin mice treated with 75 mg/kg MRX6313/UNC2025, 1 mg/kg 30 istered in chow at a predicted dose of 120 mg/kg (MTD). methotrexate (MTX) or 75 mg/kg MRX6313/UNC2025+1 FIG. 15B is a Kaplan Meier plot illustrating percent survival mg/kg methotrexate in the B-ALL xenograft model. FIG. 7D verses days of treatment when TRIA mice with melanoma is a table illustrating median survival when mice were dosed were treated with no drug, UNC2025 or AZD6244. with 75 mg/kg MRX-6313 QD starting at d12, 1 mg/kg AZD6244 is a MEK inhibitor that was dosed in mouse chow MTX QDx2d/wkx7 cycles starting at d14, or 75 mg/kg 35 at a predicted dose of 37 mg/kg (MTD). UNC2025 was MRX6313/UNC2025 d12 and 1 mg/kg MTX d14 (n=5). See dosed in chow at a predicted dose of 120 mg/kg (MTD). See Example 8. Example 6. FIG. 8A shows reduced tumor volume in response to FIG. 16A is a graph illustrating tumor volume verses days treatment with 50 mg/kg MRX6313/UNC2025 in a subcu treated. Colo699 tumor cells were subcutaneously implanted taneous xenograft model of NSCLC established using 40 in mice. Mice subsequently received either saline or MerTK+, FGFR+ Colo699 cells. FIG. 8B: H226 (MerTK+, MRX6313/UNC2025, 50 mg/kg, qd. FIG. 16B is an immu FGFR+) NSCLC cells were cultured for 14 days in soft agar noblot of pMer and downstream signaling proteins in the in the presence of MRX6313/UNC2025 and/or AZD-4547, NSCLC cell line H1299 after 24 h pre-treatment with Axl alone or in combination, and colonies were stained and siRNA and MRX6313/UNC2025 treatment for one hour. counted. See Example 7 and Example 9. 45 See Example 9. FIGS. 9A, 9B and 9C show MerTK protein expression FIG. 17A illustrates the number of colonies (H226) in a detected by immunocytochemistry in melanocytes (S100 Soft agar assay after two weeks of treatment. Colonies were positive) in nevus (A), primary melanoma (B), and meta treated with MRX6313/UNC2025 and AZD4547 at concen static melanoma (C) samples. FIG.9D is an immunoblot that trations ranging from 0 to 100 nM. FIG. 17B is an immu shows that MRX6313/UNC2025 abrogates signaling down 50 noblot of signaling proteins downstream of MerTK in the stream of MerTK in the melanoma cell lines HMCB and NSCLC cell line H226 after 4 h treatment with DMSO, G361. FIG.9E is a graph illustrating relative colony number AZD4547, MRX6313/UNC2025, or AZD4547 and when HMCB and G361 cells were dosed with MRX6313/ MRX6313/UNC2O25. UNC2025 at 25, 50, 100, 300 and 500 nM. FIG. 18A is a graph of tumor volume (mm) verses days. FIG. 10A is an immunoblot showing the presence of 55 This is treatment of the intact GEMM. FIG. 18B is a graph MerTK in J774 murine macrophage and absence in PyVmT illustrating the results from TRIA injected into NSG mice. murine mammary tumor cells. FIGS. 10B and 10C illustrate The mice were then treated with no drug or UNC2025. the results from an immune-competent orthotopic model of Tumor volumes were significantly reduced when mice were MerTK-negative breast cancer. Mice were transplanted with treated with UNC2025 verses control. In FIGS. 18A and PyVmT mammary tumor cells and were treated with 50 60 18B, both treated slopes were statistically significant com mg/kg MRX6313/UNC2025 or vehicle qd starting 2 days pared to untreated slopes using linear regression p(0.001. before transplant. FIG. 10B is a graph showing tumor FIG. 18C; Pten/Braf genetically engineered mice were volume (mm) verses days post-tumor injection. FIG. 10C treated with no drug or UNC2025. The graph illustrates illustrates proinflammatory signaling pathway components tumor volumes (mm) verses days on treatment. that exhibit altered expression in tumor-associated macro 65 FIG. 19A is a timeline illustrating a mouse model using phages following treatment with MRX6313/UNC2025 PyVmT cells. Mice were treated with 3 mg/kg MRX6313/ determined by RNA sequencing. See Example 11. UNC2025 or saline twice daily by oral gavage. Mice were US 9,555,031 B2 19 20 dosed from day -2 to day 28. At day zero, 1x10° PyVmT FIG. 25G is a graph illustrating peripheral blasts (%) at cells were implanted into the inguinal mammary fatpad of day 57 of the study in a Molm 14 (FLT3-ITD) parental vs. mice. Tumor volumes were measured at days 16, 19, 21, 23. Molm14 (FLT3-ITD) D835Y mutations (with or without 26 and 28. Day 28 was the end of the study. FIG. 19B is a treatment of AC220). graph illustrating tumor volume (mm) verses days post FIG. 25H is a graph illustrating peripheral blasts (%) at tumor injection. RNA-sequence data indicate that day 100 of the study in a Molm 14 (FLT3-ITD) parental vs. MRX6313/UNC2025 treatment increases pro-inflammatory Molm14 (FLT3-ITD) D835Y mutations (with or without cytokines in CD11b" cells and activates CD8"T cell effector treatment of AC220). function. See Example 11. FIG. 26A: MRX-2843/UNC2371 prolongs survival in a 10 study of a Molm 14 xenograft model of FLT3-ITD AML FIG. 20A illustrates a Mer spleen verses a wild type containing a mutation in the FLT3 tyrosine kinase domain spleen. FIG. 20B illustrates an enlarged Mer lymph node. (F691L) that confers resistance to the FLT3 inhibitor quizar FIG.20C is a picture of cells from a Mer, lymph node. FIG. tinib (AC220). 20D shows MerTK expression in pediatric ALL patients FIG. 26B is a table summarizing the median survival detected by RT-PCR. FIGS. 20E and 20F illustrate the 15 times in a study of a Molm 14 xenograft model of FLT3-ITD percent of adult and pediatric patients with acute myeloid AML containing a mutation in the FLT3 tyrosine kinase leukemias that are MerTK positive, MerTK Dim, or MerTK domain (F691L) that confers resistance to the FLT3 inhibitor negative. See, Graham, Armistead et al. Oncogene, 2013. quizartinib (AC220). FIG. 21 is the chemical structure of UNC1666. FIG. 27A: MRX-2843/UNC2371 prolongs survival in a FIG. 22 is the chemical structure of UNC2025/ study of a patient-derived xenograft model of FLT3-ITD MRX6313. AML containing a mutation in the FLT3 tyrosine kinase FIG. 23A: Immunoprecipitation of FLT3-ITD positive domain (D835Y) that confers resistance to the FLT3 inhibi AML cell lines after 1 h treatment with MRX-2843/ tor quizartinib (AC220). UNC2371 demonstrates decreased phosphorylation of FLT3 FIG. 27B is a table summarizing median survival times in (pFLT3) in comparison to total FLT3. See Example 12. 25 a study of a patient-derived xenograft model of FLT3-ITD FIG. 23B: Treatment of AML cell lines with increasing AML containing a mutation in the FLT3 tyrosine kinase doses of MRX-2843/UNC2371 leads to decreased phospho domain (D835Y) that confers resistance to the FLT3 inhibi rylation of downstream signaling proteins STAT5, AKT, and tor quizartinib (AC220). ERK 1/2 in comparison to DMSO and control TKI. FIG. 27C is a graph of splenic blasts (%) in a patient FIG. 24A: AML cell lines treated for 72 h with MRX 30 derived xenograft model of FLT3-ITD AML containing a mutation in the FLT3 tyrosine kinase domain (D835Y) that 2843/UNC2371 demonstrate significantly increased apop confers resistance to the FLT3 inhibitor quizartinib (AC220) tosis after staining with Yo-Pro-1 iodide and propidium at day 15 post-treatment with saline, AC220, or MRX2843/ iodide and undergoing flow cytometric analysis. See UNC2371. Example 13 and Example 14. 35 FIG. 27D is a graph of spleen weight (mg) in a patient FIG. 24B: FLT3-ITDAML cell lines colony formation in derived xenograft model of FLT3-ITD AML containing a soft agar is inhibited by treatment with MRX-2843/ mutation in the FLT3 tyrosine kinase domain (D835Y) that UNC2371; colony number is relative to vehicle-treated confers resistance to the FLT3 inhibitor quizartinib (AC220) cells. See Example 14. at day 15 post-treatment with saline, AC220, or MRX2843/ FIG. 25A: Daily treatment with MRX-2843/UNC2371 or 40 UNC2371. AC220 via oral gavage significantly prolongs Survival in FIG. 27E is a graph of bone marrow blasts (%) in a AML Molm 14 xenograft model containing FLT3-ITD. See patient-derived xenograft model of FLT3-ITD AML con Example 15. taining a mutation in the FLT3 tyrosine kinase domain FIG. 25B: MRX-2843/UNC2371 prolongs survival in a (D835Y) that confers resistance to the FLT3 inhibitor pilot study of a patient-derived xenograft model of FLT3 45 quizartinib (AC220) at day 15 post-treatment with saline, ITD AML. See Example 16. AC220, or MRX2843/UNC2371. FIG. 25C: MRX-2843/UNC2371 prolongs survival in a FIG. 28: Chemical structures of FLT3 inhibitors. study of a patient-derived xenograft model of FLT3-ITD Examples of FLT3 inhibitors include, but are not limited to, AML containing a mutation in the FLT3 tyrosine kinase AC220 (quizartinib), CEP-701 (lestaurtinib), MLN-518 domain (D835Y) that confers resistance to the FLT3 inhibi 50 (tandutinib), PKC-412 (midostaurin), CGP-52421 (mi dostaurin metabolite), Sorafenib, and Sunitinib. tor quizartinib (AC220). See Example 18. FIG. 29A. Gas6/TAM antagonists mediate synergistic FIG. 25D: MRX-2843/UNC2371 survival analysis in a inhibition of arterial/venous thrombosis and platelet aggre study of a Molm 14 xenograft model of FLT3-ITD AML gation when combined with ADP/PY inhibitors. Arterial containing a mutation in the FLT3 tyrosine kinase domain 55 and venous thrombosis models as in FIG. 4 above and (F691L) that confers resistance to the FLT3 inhibitor quizar platelet aggregation as in FIG. 1 above. TTFO in mice tinib (AC220). treated with vehicle (negative control), 3 mg/kg UNC2025, FIG. 25E is a Table summarizing the median survival low-dose (1.5 mg/kg) ADP inhibitors (LD ADPi), high dose times of AML xenograft mice containing FLT3-ITD (3 mg/kg) ADP inhibitors (HDADPi), a combination of LD (Molm14), FLT3-ITD with the D835Y mutation, or FLT3 60 ADPi and UNC2025, or Abx (positive control). FeCl ITD with the F691 L. mutation. Mice were treated with either application induced longer TTFO in mice pre-treated with 10 mg/kg saline, 10 mg/kg AC220 or 50 mg/kg MRX-2843/ HD ADPis, n=3, 9.8+/- 1.1 min, p<0.05) or 3 mg/kg UNC UNC2371. Mer TKI (n=12, 7.7+/-0 3 minutes, p<0.05), compared to FIG. 25F is a graph illustrating peripheral blasts (%) at the vehicle control (n=24., 6.6+/-0.2 minutes). Mice pre-treated end of the study in a Molm 14 (FLT3-ITD) parental vs. 65 with (LD ADPis, however, exhibited shorter TTFO (n=5, Molm 14 (FLT3-ITD) D835Y mutations (with or without 7.5+/-0.2 minutes, p=NS). Combination of 3 mg/kg UNC treatment of AC220). Mer TKI and the LD ADPis (n=6, 10.5 +/- 1.9 minutes, US 9,555,031 B2 21 22 p-0.001), however, recapitulated the longer TTFO seen with tion and does not pose a limitation on the scope of the the HD ADPis. See Example 20. invention unless otherwise claimed. FIG. 29B. DOO of artery in mice from the same groups. Isotopic Substitution FeCls application induced shorter total DOO in mice pre In one embodiment, the present invention includes com treated with HD ADPis (n=3, 11.4+/-2.2 min, p<0.0001) or pounds of Formula I, Formula IA, Formula IB, Formula II, 3 mg/kg UNC MerTKI (n=12, 42.2+/-4.7 minutes, p<0.05), Formula IIA, or Formula IIB and additional active com compared to vehicle control (n=24, 53.2+/-0.4 minutes). pounds described herein, and the use of these compounds Mice pre-treated with LD ADPis, however, exhibited longer with at least one desired isotopic Substitution of an atom, at DOO (n=5, 52.7+/-0.2 minutes, p=NS). Combination of 3 an amount above the natural abundance of the isotope, i.e., mg/kg UNC Mer TKI and the LD ADPis (n-6, 31.6+/-9.2 10 minutes, p<0.001), however, recapitulated the longer TTFO enriched. Isotopes are atoms having the same atomic num seen with the HD ADPis. See Example 20. ber but different mass numbers, i.e., the same number of FIG. 29C. Survival curve (minutes) after collagen/epi protons but a different number of neutrons. nephrine injection in mice from the same groups, after which Examples of isotopes that can be incorporated into com Survival time was recorded, with significance determined by 15 pounds of the invention include isotopes of hydrogen, car Mantel-Cox logrank test. Survival times following venous bon, nitrogen, oxygen, phosphorous, fluorine, and chlorine, injection of collagen and epinephrine significantly differed such as H *H, IC, 13C, 14C, 15N, 18F 3P. 32p, 35S, 36C1, 125 between mice treated with HD ADPis (n=5, 19.4+/-4.4 respectively. The invention includes various isotopically minutes, p<0.001) or 3 mg/kg UNC Mer TKI (n=9, 19.9+/- labeled compounds as defined herein, for example those into 4.9 minutes, p<0.05), compared to vehicle control (n=21, which radioactive isotopes, such as H, C, and ''C, are 3.21+/-2.4 minutes). Mice treated with LD ADPis, however, present. Such isotopically labelled compounds are useful in exhibited shorter survival times (n=6, 11.9+/-5.0 minutes). metabolic studies (with 'C), reaction kinetic studies (with, Interestingly, combination of 3 mg/kg UNC Mer TKI and for example H or H), detection or imaging techniques, LD ADPis recapitulated the longer survival times seen with Such as positron emission tomography (PET) or single the HD ADPis (n=7, 25.9+/-3.8 minutes). No significant 25 photon emission computed tomography (SPECT) including difference in survival times was noted between any of the drug or Substrate tissue distribution assays, or in radioactive groups of drug-treated mice. See Example 20. treatment of patients. In particular, an 'Flabeled compound FIG. 29D. Tail bleeding times were compared in mice may be particularly desirable for PET or SPECT studies. from the same groups. No significant differences were found Isotopically labeled compounds of this invention and prod in bleeding times except in HD LDPi-treated mice compared 30 rugs thereof can generally be prepared by carrying out the to vehicle-treated controls. procedures disclosed in the schemes or in the examples and FIG. 29E: Mean maximum aggregation in 1 uM preparations described below by substituting a readily avail UNC2025-treated samples (n=7, 68.9+/-2.2%, p<0.05), dif able isotopically labeled reagent for a non-isotopically fered significantly from vehicle-treated controls (n=7. labeled reagent. 79.7+/- 1.6%) and from null TKI-treated controls (n=7. 35 76.7+/-1.8%, p<0.01). 100 uM ADP/P2Y inhibitor By way of general example and without limitation, iso treated samples (n=7) exhibited a mean maximum aggrega topes of hydrogen, for example, deuterium (H) and tritium tion of 62+/-5.2% (p<0.01), and samples treated with a (H) may be used anywhere in described structures. Alter combination of 100 uM each of ADP/P2Y inhibitors and natively or in addition, isotopes of carbon, e.g., C and ''C, 1 uM UNC2025 had a maximum aggregation of 31.3+/- 40 may be used. A typical isotopic Substitution is deuterium for 7.7% (n=7, p=0.001). See Example 20. hydrogen at one or more locations on the molecule to improve the performance of the drug, for example, the 1. TERMINOLOGY pharmacodynamics, pharmacokinetics, biodistribution, half life, stability, AUC, Tmax, Cmax, etc. For example, the Compounds are described using standard nomenclature. 45 deuterium can be bound to carbon in a location of bond Unless defined otherwise, all technical and scientific terms breakage during metabolism (an O-deuterium kinetic isotope used herein have the same meaning as is commonly under effect) or next to or near the site of bond breakage (a stood by one of skill in the art to which this invention B-deuterium kinetic isotope effect). belongs. Isotopic Substitutions, for example deuterium Substitu The compounds in any of the Formulas described herein 50 tions, can be partial or complete. Partial deuterium substi include enantiomers, mixtures of enantiomers, diastereom tution means that at least one hydrogen is Substituted with ers, tautomers, racemates and other isomers, such as rotam deuterium. In certain embodiments, the isotope is 90, 95 or ers, as if each is specifically described. 99% or more enriched in an isotope at any location of The terms 'a' and “an do not denote a limitation of interest. In one embodiments deuterium is 90, 95 or 99% quantity, but rather denote the presence of at least one of the 55 enriched at a desired location. Unless otherwise stated, the referenced item. The term “or” means “and/or”. Recitation enrichment at any point is above natural abundance and of ranges of values are merely intended to serve as a enough to alter a detectable property of the drug in a human. shorthand method of referring individually to each separate In one embodiment, the Substitution of a hydrogen atom value falling within the range, unless otherwise indicated for a deuterium atom occurs within an R group when at least herein, and each separate value is incorporated into the 60 one of the variables within the R group is hydrogen (e.g., H specification as if it were individually recited herein. The or D) or alkyl (e.g., CD). For example, when any of R endpoints of all ranges are included within the range and groups are, or contain for example through substitution, independently combinable. All methods described herein methyl or ethyl, the alkyl residue is typically deuterated, can be performed in a suitable order unless otherwise e.g., CD, CHCD or CDCD. In certain other embodi indicated herein or otherwise clearly contradicted by con 65 ments, when any of the above mentioned R groups are text. The use of examples, or exemplary language (e.g., hydrogen, the hydrogen may be isotopically enriched as “such as'), is intended merely to better illustrate the inven deuterium (i.e., H). US 9,555,031 B2 23 24 A dash (“-”) that is not between two letters or symbols is nyl, 4-pentenyl, 3-pentenyl, 2-hexenyl, 3-hexenyl, 2.4-hep used to indicate a point of attachment for a substituent. For tadiene, and the like. The term “alkenyl' or “loweralkenyl example, —(C=O)NH is attached through carbon of the is intended to include both substituted and unsubstituted keto (C=O) group. alkenyl and loweralkenyl unless otherwise indicated and “Alkyl as used herein alone or as part of another group, these groups may be substituted with groups as described in refers to a straight or branched chain hydrocarbon contain connection with alkyl and loweralkyl above. ing from 1 to 10 carbon atoms. In one embodiment, the alkyl “Alkynyl' as used herein alone or as part of another contains from 1 to about 10 carbon atoms, more generally group, refers to a straight or branched chain hydrocarbon from 1 to about 6 carbon atoms or from 1 to about 4 carbon containing from 1 to 10 carbon atoms (or in loweralkynyl 1 atoms. In certain embodiments, the alkyl is C-C or C-Cs. 10 to 4 carbonatoms) which include 1 triple bond in the normal The specified ranges as used herein indicate an alkyl group chain. Representative examples of alkynyl include, but are having each member of the range described as an indepen not limited to, 2-propynyl, 3-butynyl, 2-butynyl, 4-pentynyl, dent species. For example, the term C-C alkyl as used 3-pentynyl, and the like. The term “alkynyl' or “loweralky herein indicates a straight or branched alkyl group having nyl is intended to include both substituted and unsubsti from 1, 2, or 3 carbon atoms and is intended to mean that 15 tuted alkynyl or loweralkynyl unless otherwise indicated and each of these is described as an independent species. For these groups may be substituted with the same groups as set example, the term C-C alkyl as used herein indicates a forth in connection with alkyl and loweralkyl above. straight or branched alkyl group having from 1, 2, or 3 “Cycloalkyl as used herein alone or as part of another carbon atoms and is intended to mean that each of these is group, refers to a saturated or partially unsaturated cyclic described as an independent species. Representative hydrocarbon group containing from 3, 4 or 5 to 6, 7 or 8 examples of alkyl include, but are not limited to, methyl, carbons (which carbons may be replaced in a heterocyclic ethyl, n-propyl, iso-propyl. n-butyl, Sec-butyl, iso-butyl, group as discussed below). Representative examples of tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl, 3-meth cycloalkyl include, cyclopropyl, cyclobutyl, cyclopentyl, ylhexyl, 2.2-dimethylpenty1, 2,3-dimethylpentyl, n-heptyl, cyclohexyl, cycloheptyl, and cyclooctyl. These rings may be n-octyl, n-nonyl, n-decyl, and the like. "Lower alkyl as 25 optionally substituted with additional substituents as used herein, is a Subset of alkyl, in some embodiments described herein such as halo or loweralkyl. The term typically, and refers to a straight or branched chain hydro “cycloalkyl is generic and intended to include heterocyclic carbon group containing from 1 to 4 carbon atoms. Repre groups as discussed below unless specified otherwise. In one sentative examples of lower alkyl include, but are not embodiment, as used herein, the term “cycloalkyl refers to limited to, methyl, ethyl, n-propyl, iso-propyl. n-butyl, iso 30 a saturated or unsaturated hydrocarbon mono- or multi-ring, butyl, tert-butyl, and the like. The term “alkyl or “lower e.g., fused, bridged, or spiro rings system having 3 to 15 alkyl” is intended to include both substituted and unsubsti carbon atoms (e.g., C.-Co). Examples of cycloalkyl tuted alkyl or loweralkyl unless otherwise indicated and include, but are not limited to, cyclopropyl, cyclobutyl, these groups may be substituted with groups selected from cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, and ada halo (e.g., haloalkyl), alkyl, haloalkyl, hydroxyalkyl, alk 35 manty1. In another embodiment, the term “cycloalkyl refers enyl, alkynyl, cycloalkyl (including spiroalkyl, e.g., to a saturated or partially unsaturated, monocyclic, fused —C(CH2) spiroalkyl), cycloalkylalkyl, aryl, arylalkyl, bicyclic or bridged polycyclic ring assembly containing heterocyclo, heterocycloalkyl, alkylheterocycloalkyl, het from 3 to 12 ring atoms, or the number of atoms indicated. eroaryl, alkylheteroaryl, hydroxyl, alkoxy (thereby creating Cycloalkyl can include any number of carbons. Such as C. a polyalkoxy Such as polyethylene glycol), alkenyloxy, 40 C4-6. CS-6. C-8. Cas: Cs-s, and Co-s: Saturated monocyclic alkynyloxy, haloalkoxy, cycloalkoxy, cycloalkylalkyloxy, cycloalkyl rings include, for example, cyclopropyl, cyclobu aryloxy, arylalkyloxy, heterocyclooxy, heterocyclolalky tyl, cyclopentyl, cyclohexyl, and cyclooctyl. Saturated bicy loxy, mercapto, alkyl-S(O), haloalkyl-S(O), alkenyl clic and polycyclic cycloalkyl rings include, for example, S(O), alkynyl-S(O), cycloalkyl-S(O), cycloalkylalkyl-S norbornane, 2.2.2 bicyclooctane, decahydronaphthalene (O), aryl-S(O), arylalkyl-S(O), heterocyclo-S(O), het 45 and adamantane. Cycloalkyl groups can also be partially erocycloalkyl-S(O), amino, carboxy, alkylamino, unsaturated, having one or more double bonds in the ring. —(CH), NH(CH), CH, —(CH), NH(CH),OH, Representative cycloalkyl groups that are partially unsatu alkenylamino, alkynylamino, halo alkylamino, cycloalky rated include, but are not limited to, cyclobutene, cyclopen lamino, cycloalkylalkylamino, arylamino, arylalkylamino, tene, cyclohexene, cyclohexadiene (1.3- and 1.4-isomers), heterocycloamino, heterocycloalkylamino, disubstituted 50 cycloheptene, cycloheptadiene, cyclooctene, cyclooctadiene amino, acylamino, acyloxy, ester, amide, Sulfonamide, urea, (1.3-, 1.4- and 1.5-isomers), norbornene, and norbornadiene. alkoxyacylamino, aminoacyloxy, nitro or cyano where m=0, These groups may be substituted with groups as described in 1, 2 or 3. In one embodiment, alkyl or loweralkyl can be connection with alkyl and loweralkyl above. Substituted with groups selected from a polar group, “Heterocyclic group' or "heterocyclo” as used herein —(CH), N(R'), —(CH), NH(CH),R', 55 alone or as part of another group, refers to an aliphatic (e.g., —(CH),NH(CH)N(R), –S(O),OR, fully or partially saturated heterocyclo) or aromatic (e.g., —CONHNHR', aminosulfonyl –C(CH) R' wherein heteroaryl) monocyclic- or a bicyclic-ring system. In some each R" is independently selected from hydrogen, alkyl, embodiments, monocyclic ring systems are exemplified by alkenyl, alkynyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, any 7 membered ring containing 1, 2, 3, or 4 heteroatoms heterocyclo, heterocycloalkyl, heteroaryl, or heteroarylal 60 independently selected from oxygen, nitrogen and Sulfur. kyl. Monocyclic ring systems are exemplified by any 5 or 6 “Alkenyl as used herein alone or as part of another membered ring containing 1, 2, 3, or 4 heteroatoms inde group, refers to a straight or branched chain hydrocarbon pendently selected from oxygen, nitrogen and Sulfur. The 5 containing from 1 to 10 carbon atoms (or in loweralkenyl 1 membered ring has from 0-2 double bonds and the 6 to 4 carbon atoms) which include 1 to 4 double bonds in the 65 membered ring has from 0-3 double bonds. Representative normal chain. Representative examples of alkenyl include, examples of monocyclic ring systems include, but are not but are not limited to, vinyl, 2-propenyl, 3-butenyl, 2-bute limited to, aZetidine, azepine, aziridine, diazepine, 1.3- US 9,555,031 B2 25 26 dioxolane, dioxane, dithiane, furan, imidazole, imidazoline, tuted and unsubstituted aryl unless otherwise indicated and imidazolidine, isothiazole, isothiazoline, isothiazolidine, these groups may be substituted with the same groups as set isoxazole, isoxazoline, isoxazolidine, morpholine, oxadiaz forth in connection with alkyl and loweralkyl above. ole, oxadiazoline, oxadiazolidine, oxazole, oxazoline, "Arylalkyl as used herein alone or as part of another oxazolidine, piperazine, piperidine, pyran, pyrazine, pyra group, refers to an aryl group, as defined herein, appended Zole, pyrazoline, pyrazolidine, pyridine, pyrimidine, to the parent molecular moiety through an alkyl group, as pyridazine, pyrrole, pyrroline, pyrrolidine, tetrahydrofuran, defined herein. Representative examples of arylalkyl tetrahydrothiophene, tetrazine, tetrazole, thiadiazole, thiadi include, but are not limited to, benzyl, 2-phenylethyl, 3-phe aZoline, thiadiazolidine, thiazole, thiazoline, thiazolidine, nylpropyl 2-naphth-2-ylethyl, and the like. thiophene, thiomorpholine, thiomorpholine Sulfone, thiopy 10 ran, triazine, triazole, trithiane, and the like. Bicyclic ring “Heteroaryl as used herein is as described in connection systems are exemplified by any of the above monocyclic with heterocyclo above. ring systems fused to an aryl group as defined herein, a "Alkoxy” as used herein alone or as part of another group, cycloalkyl group as defined herein, or another monocyclic refers to an alkyl or loweralkyl group, as defined herein (and ring system as defined herein. Representative examples of 15 thus including Substituted versions such as polyalkoxy), bicyclic ring systems include but are not limited to, for appended to the parent molecular moiety through an oxy example, benzimidazole, benzothiazole, benzothiadiazole, group, —O—. Representative examples of alkoxy include, benzothiophene, benzoxadiazole, benzoxazole, benzofuran, but are not limited to, methoxy, ethoxy, propoxy. 2-propoxy, benzopyran, benzothiopyran, benzodioxine, 1,3-benzodiox butoxy, tert-butoxy, pentyloxy, hexyloxy and the like. ole, cinnoline, indazole, indole, indoline, indolizine, naph "Halo' as used herein refers to any suitable halogen, thyridine, isobenzofuran, isobenzothiophene, isoindole, including —F. —Cl, —Br, and —I. isoindoline, isoquinoline, phthalazine, purine, pyranopyri “Mercapto' as used herein refers to an —SH group. dine, quinoline, quinolizine, quinoxaline, quinazoline, tet “AZido” as used herein refers to an —N group. rahydroisoquinoline, tetrahydroquinoline, thiopyranopyri “Cyano” as used herein refers to a —CN group. dine, and the like. These rings include quaternized 25 “Formyl as used herein refers to a C(O)H group. derivatives thereof and may be optionally substituted with “Carboxylic acid as used herein refers to a C(O)CH groups selected from halo, alkyl, haloalkyl, alkenyl, alkynyl, group. cycloalkyl, cycloalkylalkyl, aryl, arylalkyl, heterocyclo, het “Hydroxyl as used herein refers to an —OH group. erocycloalkyl, hydroxyl, alkoxy, alkenyloxy, alkynyloxy, "Nitro” as used herein refers to an —NO, group. haloalkoxy, cycloalkoxy, cycloalkylalkyloxy, aryloxy, aryl 30 alkyloxy, heterocyclooxy, heterocyclolalkyloxy, mercapto, “Acyl as used herein alone or as part of another group alkyl-S(O), haloalkyl-S(O), alkenyl-S(O), alkynyl refers to a C(O)R radical, where R is any suitable sub S(O), cycloalkyl-S(O), cycloalkylalkyl-S(O), aryl stituent Such as aryl, alkyl, alkenyl, alkynyl, cycloalkyl or S(O), arylalkyl-S(O), heterocyclo-S(O), heterocy other suitable substituent as described herein. cloalkyl-S(O), amino, alkylamino. —(CH), NH(CH), 35 “Alkylthio' as used herein alone or as part of another CH, -(CH2), NH(CH), OH alkenylamino, alky group, refers to an alkyl group, as defined herein, appended nylamino, haloalkylamino, cycloalkylamino, cycloalkylal to the parent molecular moiety through a thio moiety, as kylamino, arylamino, arylalkylamino, heterocycloamino, defined herein. Representative examples of alkylthio heterocycloalkylamino, disubstituted-amino, acylamino, include, but are not limited, methylthio, ethylthio, tert acyloxy, ester, amide, Sulfonamide, urea, alkoxyacylamino, 40 butylthio, hexylthio, and the like. aminoacyloxy, nitro or cyano where m=0, 1, 2 or 3. In some “Amino” as used herein means the radical NH. embodiments, the heterocyclo groups can be substituted “Alkylamino” as used herein alone or as part of another with groups as described in connection with alkyl and group means the radical —NHR, where R is an alkyl group. loweralkyl above. In another embodiment, the term “het "Arylalkylamino” as used herein alone or as part of erocyclo” refers to a saturated or unsaturated nonaromatic 45 another group means the radical —NHR, where R is an 3-8 membered monocyclic, 7-12 membered bicyclic (fused, arylalkyl group. bridged, or spiro rings), or 11-14 membered tricyclic ring “Disubstituted-amino” as used herein alone or as part of system (fused, bridged, or Spiro rings) having one or more another group means the radical —NRR, where R and R. heteroatoms (such as O, N, or S), unless specified otherwise. are independently selected from the groups hydrogen, alkyl, Examples of heterocyclo groups include, but are not limited 50 haloalkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, to, piperidinyl, piperazinyl, pyrrolidinyl, dioxanyl, tetrahy aryl, arylalkyl, heterocyclo, heterocycloalkyl. drofuranyl, isoindolinyl, indolinyl, imidazolidinyl, pyrazo “Acylamino” as used herein alone or as part of another lidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahy group means the radical —NRR, where R is an acyl group rofuranyl, oxiranyl, aZetidinyl, oxetanyl, thietanyl, 1.2.3,6- as defined herein and R, is selected from the groups hydro tetrahydropyridinyl, tetrahydropyranyl, dihydropyranyl. 55 gen, alkyl, haloalkyl, alkenyl, alkynyl, cycloalkyl, pyranyl, morpholinyl, 1,4-diazepanyl, 1,4-oxazepanyl. cycloalkylalkyl, aryl, arylalkyl, heterocyclo, heterocy 2-oxa-5-azabicyclo[2.2.1]heptanyl. 2,5-diazabicyclo[2.2.1 cloalkyl. heptanyl, 2-oxa-6-azaspiro3.3 heptanyl. 2,6-diazaspiro “Acyloxy” as used herein alone or as part of another 3.3 heptanyl, 1,4-dioxa-8-azaspiro4.5 decanyl and the group means the radical —OR, where R is an acyl group as like. These groups may be substituted with groups as 60 defined herein. described in connection with alkyl and loweralkyl above. "Ester” as used herein alone or as part of another group "Aryl as used herein alone or as part of another group, refers to a —C(O)OR radical, where R is any suitable refers to a monocyclic carbocyclic ring system or a bicyclic Substituent Such as alkyl, cycloalkyl, alkenyl, alkynyl or carbocyclic fused ring system having one or more aromatic aryl. rings. Representative examples of aryl include, aZulenyl, 65 “Amide' as used herein alone or as part of another group indanyl, indenyl, naphthyl, phenyl, tetrahydronaphthyl, and refers to a —C(O)NRR, radical, where R and R, are any the like. The term “aryl' is intended to include both substi Suitable Substituent Such as alkyl, cycloalkyl, alkenyl, alky US 9,555,031 B2 27 28 nyl or aryl. In some embodiments, R., and R, together with —CONHNHR', aminosulfonyl –C(CH) R' wherein the nitrogen to which they are bonded form a heterocyclic each R is independently selected from hydrogen, alkyl, r1ng. alkenyl, alkynyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, "Sulfoxyl as used herein refers to a compound of the heterocyclo, heterocycloalkyl, heteroaryl, or heteroarylal formula —S(O)R, where R is any suitable substituent such kyl. as alkyl, cycloalkyl, alkenyl, alkynyl or aryl. “Polar group’ as used herein refers to a group wherein the "Sulfonyl as used herein refers to a compound of the nuclei of the atoms covalently bound to each other to form formula —S(O)(O)R, where R is any suitable substituent the group do not share the electrons of the covalent bond(s) Such as amino, alkyl, cycloalkyl, alkenyl, alkynyl or aryl. joining them equally; that is the electron cloud is denser "Sulfonate” as used herein refers to a compound of the 10 about one atom than another. This results in one end of the formula —S(O)(O)OR, where R is any suitable substituent Such as alkyl, cycloalkyl, alkenyl, alkynyl or aryl. covalent bond(s) being relatively negative and the other end "Sulfonic acid' as used herein refers to a compound of the relatively positive; i.e., there is a negative pole and a positive formula - S(O)(O)OH. pole. Examples of polar groups include, without limitations, "Sulfonamide as used herein alone or as part of another 15 halo, hydroxy, alkoxy, carboxy, nitro, cyano, amino (pri group refers to a —S(O)NRR, radical, where R and R. mary, secondary and tertiary), amido, ureido, Sulfonamido, are any suitable Substituent Such as H, alkyl, cycloalkyl, sulfinyl, sulfhydryl, silyl S-sulfonamido, N-sulfonamido, alkenyl, alkynyl or aryl. In some embodiments, R., and R. C-carboxy, O-carboxy, C-amido, N-amido, sulfonyl, N-tert are any suitable Substituent such as hydrogen, alkyl, alkenyl, butoxycarbonyl (or “t-BOC) groups, phosphono, mor alkynyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, hetero pholino, piperazinyl, tetrazolo, and the like. See, e.g., U.S. cyclo, heterocycloalkyl, heteroaryl, or heteroarylalkyl and Pat. No. 6,878,733, as well as alcohol, thiol, polyethylene each R, and R, can be optionally Substituted one, two or glycol, polyol (including Sugar, aminosugar, uronic acid). three times. In some embodiments, R., and R, together with sulfonamide, carboxamide, hydrazide, N-hydroxycarbox the nitrogen to which they are bonded form a heterocyclic amide, urea, metal chelates (including macrocyclic ligand or ring that can be optionally Substituted one, two or three 25 crown ether metal chelates). The polar group can be an ionic times. group. “Urea' as used herein alone or as part of another group “Ionic group’ as used herein includes anionic and cationic refers to an N(R)C(O)NRR, radical, where R. R. and groups, and includes groups (sometimes referred to as R are any Suitable Substituent Such as H, alkyl, cycloalkyl, “ionogenic groups) that are uncharged in one form but can alkenyl, alkynyl or aryl. In some embodiments, R., and R. 30 be easily converted to ionic groups (for example, by proto together with the nitrogen to which they are bonded form a nation or deprotonation in aqueous solution). Examples heterocyclic ring. include but are not limited to carboxylate, sulfonate, phos "Alkoxyacylamino” as used herein alone or as part of phate, amine, N-oxide, and ammonium (including quater another group refers to an —N(R)C(O)OR radical, where nized heterocyclic amines such as imidazolium and pyri R. R., are any suitable substituent such as H. alkyl, 35 dinium) groups. See, e.g., U.S. Pat. Nos. 6,478,863; 6,800, cycloalkyl, alkenyl, alkynyl or aryl. 276; and 6,896,246. Additional examples include uronic “Aminoacyloxy' as used herein alone or as part of acids, carboxylic acid, Sulfonic acid, amine, and moieties another group refers to an —OC(O)NRR, radical, where R. Such as guanidinium, phosphoric acid, phosphonic acid, and R, are any Suitable Substituent such as H, alkyl, phosphatidylcholine, phosphonium, borate, Sulfate, etc. cycloalkyl, alkenyl, alkynyl or aryl. In some embodiments, 40 “Deuterium' as used herein alone or as part of another R, and R, together with the nitrogen to which they are group, refers to H, which has one proton and one neutron bonded form a heterocyclic ring. in the nucleus. It is a safe, non-radioactive isotope of "Optionally substituted as used herein refers to the hydrogen. Any hydrogen in a group or Substituent described optionally Substitution of a chemical moiety. These moieties above may be replaced with deuterium to provide a “deu can be substituted with groups selected from, but not limited 45 terated” compound, in Some embodiments to modify and/or to, halo (e.g., haloalkyl), alkyl, haloalkyl, hydroxyalkyl, improve metabolic stability, resulting in better safety, toler alkenyl, alkynyl, cycloalkyl (including spiroalkyl, e.g., ability and/or efficacy. —C(CH2)4-spiroalkyl), cycloalkylalkyl, aryl, arylalkyl, "Linking group’ as used herein are generally bivalent aryl substituted heteroaryl, heterocyclo, heterocycloalkyl, aromatic, aliphatic, or mixed aromatic and aliphatic groups. alkylheterocycloalkyl, heteroaryl, heteroarylalkyl, hydroxyl, 50 Thus linking groups include linear or branched, Substituted alkoxy (thereby creating a polyalkoxy such as polyethylene or unsubstituted aryl, alkyl, alkylaryl, or alkylarylalkyl glycol), alkenyloxy, alkynyloxy, haloalkoxy, cycloalkoxy, linking groups, where the alkyl groups are saturated or cycloalkylalkyloxy, aryloxy, arylalkyloxy, heterocyclooxy, unsaturated, and where the alkyl and aryl groups optionally heterocyclolalkyloxy, mercapto, alkyl-S(O), haloalkyl-S containing independently selected heteroatoms such as 1, 2, (O), alkenyl-S(O), alkynyl-S(O), cycloalkyl-S(O), 55 3 or 4 heteroatoms selected from the group consisting of N. cycloalkylalkyl-S(O), aryl-S(O), arylalkyl-S(O), hetero O, and S. In some embodiments, linking groups containing cyclo-S(O), heterocycloalkyl-S(O), amino, carboxy, from 2 to 20 carbon atoms are preferred. Numerous alkylamino, -(CH2), NH(CH2)CH, -(CH2), NH examples of Suitable linking groups are known, including (CH), OH, alkenylamino, alkynylamino, haloalkylamino, but not limited to those described in, U.S. Pat. Nos. 8,247, cycloalkylamino, cycloalkylalkylamino, arylamino, arylal 60 572; 8,097,609; 6,624,317; 6,613,345; 6,596,935; and kylamino, heterocyclo amino, heterocycloalkylamino, dis 6.420,377, the disclosures of which are incorporated by ubstituted-amino, acylamino, acyloxy, ester, amide, Sulfo reference herein in their entirety. namide, urea, alkoxyacylamino, aminoacyloxy, nitro, polar “Treat' as used herein refers to any type of treatment that group or cyano where m=0, 1, 2 or 3. In one embodiment, imparts a benefit to a patient afflicted with a disease, alkyl or loweralkyl can be substituted with groups selected 65 including improvement in the condition of the patient (e.g., from a polar group, —(CH2), N(R'), -(CH2), NH in one or more symptoms), delay in the progression of the (CH) R', -(CH),NH(CH)N(R), S(O).OR', disease, delay in onset of the disease, etc. US 9,555,031 B2 29 30 “Pharmaceutically acceptable' as used herein means that excipient that is acceptable for veterinary use as well as the compound or composition is suitable for administration human pharmaceutical use. A "pharmaceutically acceptable to a subject to achieve the treatments described herein, excipient as used in the present application includes both without unduly deleterious side effects in light of the sever one and more than one Such excipient. ity of the disease and necessity of the treatment. Compounds of the present invention may optionally be A "dosage form' means a unit of administration of an administered in conjunction with other compounds. The active agent. Examples of dosage forms include tablets, other compounds may optionally be administered concur capsules, injections, Suspensions, liquids, emulsions, rently. As used herein, the word “concurrently’ means sufficiently close in time to produce a combined effect (that implants, particles, spheres, creams, ointments, supposito is, concurrently may be simultaneously, or it may be two or ries, inhalable forms, transdermal forms, buccal, Sublingual, 10 more events occurring within a short time period before or topical, gel, mucosal, and the like. after each other). "Pharmaceutical compositions are compositions com The present invention is primarily focused on the treat prising at least one active agent, such as a compound or salt ment of a human Subject or host, but the invention may be of Formula I, Formula IA, Formula IB, Formula II, Formula used to treat animals, such as mammalian Subjects such as IIA, or Formula IIB, and at least one other substance, such 15 mice, rats, dogs, cats, livestock and horses for veterinary as a carrier. “Pharmaceutical combinations' are combina purposes, and for drug screening and drug development tions of at least two active agents which may be combined purposes. Subjects may be of any age, including infant, in a single dosage form or provided together in separate juvenile, adolescent, adult, and geriatric Subjects. dosage forms with instructions that the active agents are to be used together to treat any disorder described herein. 2. DETAILED DESCRIPTION OF ACTIVE “Pharmaceutically acceptable salts' includes derivatives COMPOUNDS of the disclosed compounds in which the parent compound is modified by making inorganic and organic, non-toxic, acid The present invention is directed to the use of selected or base addition salts thereof. The salts of the present pyrrolopyrimidine compounds having Mer tyrosine kinase compounds can be synthesized from a parent compound that 25 (MerTK) inhibitory activity as antinfective agents, immu nostimulatory agents, anti-cancer agents (including against contains a basic or acidic moiety by conventional chemical MerTK-f- tumors and ITD and TKD mutant forms of Acute methods. Generally, Such salts can be prepared by reacting Myeloid Leukemia (AML)), and as adjunctive agents in free acid forms of these compounds with a stoichiometric combination with chemotherapeutic, radiation or other stan amount of the appropriate base (such as Na, Ca, Mg, or K dard of care for neoplasms, or as anti-thrombotic agents. hydroxide, carbonate, bicarbonate, or the like), or by react 30 The majority of the compounds described as useful in the ing free base forms of these compounds with a stoichiomet present invention were first described in WO 2013/052417, ric amount of the appropriate acid. Such reactions are which is incorporated by reference for all purposes. The typically carried out in water or in an organic solvent, or in present invention describes for the first time that these a mixture of the two. Generally, non-aqueous media like compounds, and the additional compounds described herein ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are 35 that are not in WO 2013/052417, are useful for medical typical, where practicable. Salts of the present compounds applications not described in these earlier published appli further include solvates of the compounds and of the com cations. pound salts. In one embodiment, the MerTK inhibitors useful in treat Examples of pharmaceutically acceptable salts include, ing a disorder described herein have the structure of Formula but are not limited to, mineral or organic acid salts of basic 40 residues such as amines; alkali or organic salts of acidic I, IA, or IB: residues such as carboxylic acids; and the like. The phar maceutically acceptable salts include the conventional non (I) 4 toxic salts and the quaternary ammonium salts of the parent R R1 compound formed, for example, from non-toxic inorganic or 45 M organic acids. For example, conventional non-toxic acid salts include those derived from inorganic acids such as N21 X hydrochloric, hydrobromic, Sulfuric, Sulfamic, phosphoric, N t 3 J. J.X " nitric and the like; and the salts prepared from organic acids R N V Such as acetic, propionic, Succinic, glycolic, Stearic, lactic, 50 R2 malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxyma (IA) leic, phenylacetic, glutamic, benzoic, Salicylic, mesylic, esylic, besylic, Sulfanilic, 2-acetoxybenzoic, fumaric, tolu enesulfonic, methanesulfonic, ethane disulfonic, oxalic, ise thionic, HOOC-(CH2), COOH where n is 0-4, and the 55 like. Lists of additional Suitable salts may be found, e.g., in Remington's Pharmaceutical Sciences, 17th ed., Mack Pub lishing Company, Easton, Pa., p. 1418 (1985). The term “carrier applied to pharmaceutical composi (IB) tions/combinations of the invention refers to a diluent, 60 excipient, or vehicle with which an active compound is provided. A "pharmaceutically acceptable excipient’ means an excipient that is useful in preparing a pharmaceutical com position/combination that is generally safe, non-toxic and 65 neither biologically nor otherwise inappropriate for admin istration to a host, and includes, in one embodiment, an US 9,555,031 B2 31 32 wherein: amino, carboxy, alkylamino, -(CH2), NHalkyl, one of X and X" is N and the other of X and X" is C; —(CH), N(alkyl). —(CH), NH(CH),OH, one of the dashed lines is a single bond (between a ring —(CH2), NH(CH2)cycloalkyl, -(CH2), NH(CH2). carbon atom and a ring nitrogen atom) and the other of the 3heterocyclo. —(CH2), NH(CH), aryl, -(CH2), NH dashed lines is a double bond (between two ring carbon 5 (CH2)-heteroaryl, -(CH2)NH(CH2)N(alkyl), alk atoms); enylamino, alkynylamino, halo alkylamino, R" is aryl: cycloalkylamino, cycloalkylalkylamino, arylamino, arylal R’ is RR, where R is a covalent bond or C1 to C3 kylamino, heterocycloamino, heterocycloalkylamino, disub alkyl and R is cycloalkyl, heterocycloalkyl, aryl, heteroaryl stitutedamino, acylamino, acyloxy, ester, amide, S(O).OR', or alkyl, and wherein R is optionally substituted from one 10 CONHNH, cyano, nitro, aminosulfonyl, COOH, sulfona to two times with independently selected polar groups; mide, urea, alkoxyacylamino, aminoacyloxy, —C(CH2) R is NR7R, where R7 and Rare each independently R', and wherein R' is optionally substituted one, two or selected from H, alkyl, arylalkyl, cycloalkylalkyl, heterocy three times; cloalkylalkyl, heteroarylalkyl, and alkoxyalkyl, each of m=0, 1, 2 or 3: n=0, 1 or 2; which is optionally substituted one, two or three times with 15 R'' is R'R'', where R' is a covalent bond or C to C. independently selected polar groups (typically one of R or alkyl and R' is cycloalkyl, cycloalkylalkyl, heterocyclo, R is H); and heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, R is H. loweralkyl, halo, or loweralkoxy; hydroxyalkyl, alkoxyalkyl, or alkyl, and wherein R' is R is H. loweralkyl, halo, or loweralkoxy; optionally Substituted one, two or three times; or a pharmaceutically acceptable composition, salt, iso R" is NR7R, where; topic analog, or prodrug thereof. R'' is selected from the group consisting of H, alkyl, In one embodiment, the MerTK inhibitors useful in treat hydroxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, ing a disorder described herein have the structure of Formula heterocyclo, heterocycloalkyl, alkylheterocycloalkyl, het II, IIA, or IIB: eroaryl, heteroarylalkyl, and alkoxyalkyl, each of which is 25 optionally substituted one, two or three times (typically R' is H): 14 (II) R" is selected from the group consisting of H, alkyl, R R11 hydroxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, X heterocyclo, heterocycloalkyl, alkylheterocycloalkyl, het N1 N 30 eroaryl, heteroarylalkyl, and alkoxyalkyl, each of which is l 2 /X R 15 optionally Substituted one, two or three times; or 13 X R'' and R' together with the nitrogen to which they are R N V bonded can form a heterocyclic group that can be optionally R12 substituted; (ILA) R" is H. loweralkyl, halo, or loweralkoxy; 35 R" is H. loweralkyl, halo, or loweralkoxy; R’ is selected from alkyl, alkenyl, alkynyl, aryl, arylal kyl, cycloalkyl, cycloalkylalkyl, heterocyclo, heterocy cloalkyl, heteroaryl, or heteroarylalkyl; or a pharmaceutically acceptable composition, salt, iso 40 topic analog, or prodrug thereof. In some embodiments of the foregoing, R is phenyl or 14 (IIB) pyridyl, which phenyl or pyridyl is unsubstituted or substi R R11 tuted from 1 to 3 times with halo, amino, nitro, alkyl, alkoxyl, haloalkyl, cycloalkyl, heterocycloalkyl, aryl, or N1 N N 45 heteroaryl. l R15 In some embodiments of the foregoing R is hydrogen or 13 2 N methyl. In some embodiments of the foregoing, R is C-Cs R N V alkyl, C-C cycloalkyl, or C-C alkyl aryl. R12 In some embodiments of the foregoing, R is cyclohexyl. 50 In some embodiments of the foregoing, R is substituted wherein: once with amino. one of X and X" is N and the other of X and X" is C; In some embodiments of the foregoing, R is H. one of the dashed lines is a single bond (between a ring In some embodiments of the foregoing, R is loweralkyl. carbon atom and a ring nitrogen atom) and the other of the In some embodiments of the foregoing, R is H. dashed lines is a double bond (between two ring carbon In some embodiments of the foregoing, R' is C-Cs atoms); 55 alkyl, C-C cycloalkyl, or C-C alkyl aryl. R'' is R(R'), where R is alkyl, alkenyl, -alkylaryl, In some embodiments of the foregoing, R' is cyclohexyl. heterocyclo, aryl, heteroaryl and R' is hydrogen, alkyl, In some embodiments of the foregoing, R' is substituted haloalkyl, alkoxyalkyl, —O-alkylaryl, hydroxyalkyl, alk once with amino. enyl, alkenyloxy, alkynyl, alkynyloxy, cycloalkyl, In some embodiments of the foregoing, R7 is H. cycloalkylalkyl, cycloalkoxy, cycloalkylalkyloxy, heterocy 60 In some embodiments of the foregoing, R' is loweralkyl. clo, heterocycloalkyl, alkylheterocycloalkyl, heterocy In some embodiments of the foregoing, R'' is H. clooxy, heterocyclolalkyloxy, aryl, arylalkyl, aryloxy, aryl In some embodiments, structures are provided including alkyloxy, heteroaryl, alkylheteroaryl, halo, hydroxyl, Formula I, wherein R and R7 or R and R can form a alkoxy, haloalkoxy, mercapto, alkyl-S(O), , haloalkyl-S linking group. (O), , alkenyl-S(O), , alkynyl-S(O), , cycloalkyl-S 65 In some embodiments, structures are provided including (O) , cycloalkylalkyl-S(O), , aryl-S(O), , arylalkyl Formulas II, wherein R'' and R7 or R'' and R' can form S(O) , heterocyclo-S(O), ... heterocycloalkyl-S(O), . a linking group. US 9,555,031 B2 33 34 In some embodiments, structures are provided including is NR'R''. R' is phenyl, R'' is cyclohexyl, and R' is Formulas IIA and IIB, wherein R', R', and R7 are H, R' butyl, any of which can be optionally substituted. is NR'R'', R'' is aryl, R' is cycloalkyl, and R is In some embodiments, structures are provided including loweralkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR'R'', R'' is phenyl, R' is para-hydroxy cyclohexyl, Formulas IIA and IIB, wherein R'', R', and R7 are H. R' and R' is butyl, any of which can be optionally substituted. is NR7R, R is aryl, R' is cyclohexyl, and R' is In some embodiments, structures are provided including loweralkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR7R, R is aryl, R' is cycloalkyl, and R' is Formulas IIA and IIB, wherein R'', R', and R7 are H. R' 10 cycloalkylalkyl, any of which can be optionally substituted. is NR'R''. R'' is aryl, R' is para-hydroxy cyclohexyl, and In some embodiments, structures are provided including R" is loweralkyl, any of which can be optionally substi Formulas IIA and IIB, wherein R', and R7 are H, R' is tuted. NR7R, R is aryl, R' is cyclohexyl, and R is In some embodiments, structures are provided including cycloalkylalkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R', R', and R7 are H, R' In some embodiments, structures are provided including is NR'R''. R' is heteroaryl, R' is cycloalkyl, and R' is 15 Formulas IIA and IIB, wherein R'', R', and R7 are H. R' loweralkyl, any of which can be optionally substituted. is NR'R''. R'' is aryl, R' is para-hydroxy cyclohexyl, and In some embodiments, structures are provided including R" is cycloalkylalkyl, any of which can be optionally Formulas IIA and IIB, wherein R', R', and R7 are H, R' substituted. is NR'R''. R' is heteroaryl, R' is cyclohexyl, and R' is In some embodiments, structures are provided including loweralkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R', R', and R7 are H, R' In some embodiments, structures are provided including is NR'R''. R' is heteroaryl, R' is cycloalkyl, and R' is Formulas IIA and IIB, wherein R', R', and R7 are H, R' cycloalkylalkyl, any of which can be optionally substituted. is NR'R''. R'' is heteroaryl, R' is para-hydroxy cyclo In some embodiments, structures are provided including hexyl, and R' is loweralkyl, any of which can be optionally Formulas IIA and IIB, wherein R'', Rand R7 are H, R' substituted. 25 is NR'R''. R' is heteroaryl, R'' is cyclohexyl, and R' is In some embodiments, structures are provided including cycloalkylalkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR'R''. R'' is phenyl, R' is cycloalkyl, and R is Formulas IIA and IIB, wherein R', R', and R7 are H, R' loweralkyl, any of which can be optionally substituted. is NR'R''. R'' is heteroaryl, R' is para-hydroxy cyclo In some embodiments, structures are provided including 30 hexyl, and R' is cycloalkylalkyl, any of which can be Formulas IIA and IIB, wherein R'', R', and R7 are H. R' optionally substituted. is NR7R, R'' is phenyl, R' is cyclohexyl, and R is In some embodiments, structures are provided including loweralkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR'R''. R' is phenyl, R' is cycloalkyl, and R' is Formulas IIA and IIB, wherein R'', R', and R7 are H. R' cycloalkylalkyl, any of which can be optionally substituted. is NR'R'', R'' is phenyl, R'' is para-hydroxy cyclohexyl, 35 In some embodiments, structures are provided including and R' is loweralkyl, any of which can be optionally Formulas IIA and IIB, wherein R'', R', and R7 are H. R' substituted. is NR'R''. R' is phenyl, R'' is cyclohexyl, and R' is In some embodiments, structures are provided including cycloalkylalkyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R', R', and R7 are H, R' In some embodiments, structures are provided including is NR'R''. R'' is aryl, R' is cycloalkyl, and R' is butyl, 40 Formulas IIA and IIB, wherein R'', R', and R7 are H. R' any of which can be optionally substituted. is NR'R''. R' is phenyl, R' is para-hydroxy cyclohexyl, In some embodiments, structures are provided including and R' is cycloalkylalkyl, any of which can be optionally Formulas IIA and IIB, wherein R', R', and R7 are H, R' substituted. is NR'R''. R' is aryl, R' is cyclohexyl, and R' is butyl, In some embodiments, structures are provided including any of which can be optionally substituted. 45 Formulas IIA and IIB, wherein R'', R'' and R'' are H. R' In some embodiments, structures are provided including is NR'R''. R' is aryl, R' is cycloalkyl, and R' is aryl, Formulas IIA and IIB, wherein R', R', and R7 are H, R' any of which can be optionally substituted. is NR'R'', R'' is aryl, R' is para-hydroxy cyclohexyl, and In some embodiments, structures are provided including R" is butyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including 50 is NR'R'', R' is aryl, R' is cyclohexyl, and R is aryl, Formulas IIA and IIB, wherein R', R', and R7 are H, R' any of which can be optionally substituted. is NR'R''. R' is heteroaryl, R' is cycloalkyl, and R' is In some embodiments, structures are provided including butyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR'R''. R'' is aryl, R' is para-hydroxy cyclohexyl, and Formulas IIA and IIB, wherein R', R', and R7 are H, R' R" is aryl, any of which can be optionally substituted. is NR'R''. R' is heteroaryl, R' is cyclohexyl, and R' is 55 In some embodiments, structures are provided including butyl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR'R''. R'' is heteroaryl, R' is cycloalkyl, and R is Formulas IIA and IIB, wherein R', R', and R7 are H, R' aryl, any of which can be optionally substituted. is NR'R''. R'' is heteroaryl, R' is para-hydroxy cyclo In some embodiments, structures are provided including hexyl, and R' is butyl, any of which can be optionally 60 Formulas IIA and IIB, wherein R'', R', and R7 are H. R' substituted. is NR'R''. R'' is heteroaryl, R'' is cyclohexyl, and R is In some embodiments, structures are provided including aryl, any of which can be optionally substituted. Formulas IIA and IIB, wherein R'', R', and R7 are H. R' In some embodiments, structures are provided including is NR'R''. R'' is phenyl, R' is cycloalkyl, and R is Formulas IIA and IIB, wherein R'', R', and R7 are H. R' butyl, any of which can be optionally substituted. 65 is NR'R''. R'' is heteroaryl, R' is para-hydroxy cyclo In some embodiments, structures are provided including hexyl, and R' is aryl, any of which can be optionally Formulas IIA and IIB, wherein R'', R', and R7 are H. R' substituted. US 9,555,031 B2 35 36 In some embodiments, structures are provided including In one embodiment, the FLT3 and/or dual MER/FLT-3 Formulas IIA and IIB, wherein R'', R' and R7 are H, R' TKI inhibitor is Formula IV having the structure depicted is NR'R''. R'' is phenyl, R' is cycloalkyl, and R' is aryl, below: any of which can be optionally substituted. In some embodiments, structures are provided including Formulas IIA and IIB, wherein R'', R', and R7 are H. R' is NR'R''. R' is phenyl, R' is cyclohexyl, and R' is aryl, any of which can be optionally substituted. In some embodiments, structures are provided including Formulas IIA and IIB, wherein R'', R', and R7 are H. R' 10 is NR'R'', R'' is phenyl, R'' is para-hydroxy cyclohexyl, and R' is aryl, any of which can be optionally substituted. In some embodiments, structures are provided including Formulas IIA and IIB, wherein R', R', and R7 are H, R' is NR'R'', R' is aryl, R'' is cycloalkyl, and R' is phenyl, 15 any of which can be optionally substituted. In some embodiments, structures are provided including Formulas IIA and IIB, wherein R'', R', and R7 are H. R' is NR'R''. R' is aryl, R'' is cyclohexyl, and R' is phenyl, any of which can be optionally substituted. In some embodiments, structures are provided including Formulas IIA and IIB, wherein R'', R', and R7 are H. R' is NR'R''. R'' is aryl, R' is para-hydroxy cyclohexyl, and OH R" is phenyl, any of which can be optionally substituted. 25 In some embodiments, structures are provided including Particular examples of compounds of the present inven Formulas IIA and IIB, wherein R'', R' and R7 are H, R' tion include but are not limited to those set forth in Tables is NR'R''. R' is heteroaryl, R' is cycloalkyl, and R' is 1-6 and Examples 2-5 below. In one embodiment, the phenyl, any of which can be optionally Substituted. present invention is directed to the use of selected pyrrolo In some embodiments, structures are provided including 30 pyrimidine compounds having Mer tyrosine kinase Formulas IIA and IIB, wherein R'', R'' and R'' are H. R' (MerTK) inhibitory activity as antinfective agents, immu is NR'R'', R'' is heteroaryl, R' is cyclohexyl, and R is nostimulatory agents, anti-cancer agents (including against phenyl, any of which can be optionally Substituted. MerTK -f- tumors and ITD and TKD mutant forms of In some embodiments, structures are provided including Acute Myeloid Leukemia (AML)), and as adjunctive agents Formulas IIA and IIB, wherein R', R', and R7 are H, R' 35 in combination with chemotherapeutic, radiation or other is NR'R''. R'' is heteroaryl, R' is para-hydroxy cyclo standard of care for neoplasms, or as anti-thrombotic agents, hexyl, and R' is phenyl, any of which can be optionally wherein the compound is selected from those in Tables 1 to substituted. 3. The compounds of Tables 1 to 3 have been previously In one embodiment, the inhibitors useful in the present disclosed in WO2013/052417. In one embodiment, the invention are dual MER/FLT-3 TKIs. In one embodiment, 40 compound is selected from UNC2025A, UNC2371A, and the inhibitors are dual FLT3/Axl TKIS. UNC2142A, In one embodiment, the inhibitor and/or dual MER/FLT-3 In another aspect, new pyrrolopyrimidine compounds TKI has the structure of Formula III: having the uses described herein have a structure selected from: 45 III

NH,

55 23 s CO4. N N N N 2 R22 --- N N H 60

, H , H wherein R is heterocycle; 65 R’ and R are each independently hydrogen, alkyl, UNC4308A cycloalkyl, or cycloalkylalkyl.

US 9,555,031 B2 39 40 -continued -continued

OH UNC3908A

or a pharmaceutically acceptable composition, salt, isotopic , H analog, or prodrug thereof. UNC4291A Active compounds may be provided as pharmaceutically 25 acceptable prodrugs, which are those prodrugs of the active compounds of the present invention which are, within the Scope of sound medical judgment, Suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, commen 30 Surate with a reasonable risk/benefit ratio, and effective for their intended use, as well as the Zwitterionic forms, where possible, of the compounds of the invention. The term “prodrug” refers to compounds that are transformed, some times rapidly in vivo to yield the parent compound of the N N 35 above formulae, for example, by hydrolysis in blood. A N thorough discussion is provided in T. Higuchi and V. Stella, ----- N Prodrugs as Novel delivery Systems, Vol. 14 of the A.C.S. H Symposium Series and in Edward B. Roche, ed., Biorevers ible Carriers in Drug Design, American Pharmaceutical 40 Association and Pergamon Press, 1987, both of which are incorporated by reference herein. See also U.S. Pat. No. 6,680.299 Examples include a prodrug that is metabolized in Vivo by a subject to an active drug having an activity of , active compounds as described herein, wherein the prodrug UNC4292A 45 is an ester of an alcohol or carboxylic acid group, if Such a group is present in the compound; an acetal or ketal of an alcohol group, if Such a group is present in the compound; an N-Mannich base or an imine of an amine group, if Such a group is present in the compound; or a Schiffbase, oxime, 50 acetal, enol ester, oxazolidine, or thiazolidine of a carbonyl group, if such a group is present in the compound, such as described in U.S. Pat. No. 6,680,324 and U.S. Pat. No. 6,680,322. The active compounds disclosed herein can, as noted 55 above, be provided in the form of their pharmaceutically acceptable salts. Pharmaceutically acceptable salts are salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects. Nonlimiting examples of such salts are (a) acid addition salts 60 formed with inorganic acids, for example hydrochloric acid, hydrobromic acid, Sulfuric acid, phosphoric acid, nitric acid and the like; and salts formed with organic acids such as, for example, acetic acid, oxalic acid, tartaric acid. Succinic acid, , H maleic acid, fumaric acid, gluconic acid, citric acid, malic 65 acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, UNC431 OA alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-toluenesulfonic acid, naphthalene US 9,555,031 B2 41 42 disulfonic acid, polygalacturonic acid, and the like; (b) salts in association with a suitable pharmaceutical excipient. formed from elemental anions such as chlorine, bromine, Typical unit dosage forms include prefilled, premeasured and iodine, and (c) salts derived from bases, such as ammo ampules or syringes of the liquid compositions or pills, nium salts, alkali metal salts such as those of sodium and tablets, capsules or the like in the case of Solid compositions. potassium, alkaline earth metal salts such as those of cal In Such compositions, the compound is usually a minor cium and magnesium, and salts with organic bases Such as component (as a nonlimiting example, from about 0.1 to dicyclohexylamine and N-methyl-D-glucamine. about 50% by weight or preferably from about 1 to about Active compounds as described herein can be prepared in 40% by weight) with the remainder being various vehicles accordance with known procedures, or variations thereof or carriers and processing aids helpful for forming the that will be apparent to those skilled in the art. 10 desired dosing form. In one embodiment, the compound is present from about 1% to about 10% by weight. 3. PHARMACEUTICAL COMPOSITIONS AND Liquid forms suitable for oral administration may include DOSAGES FOR ALL INDICATIONS a suitable aqueous or nonaqueous vehicle with buffers, Suspending and dispensing agents, colorants, flavors and the The active compounds described above may be formu 15 like. Solid forms may include, for example, any of the lated for administration in a pharmaceutical carrier in accor following ingredients, or compounds of a similar nature: a dance with known techniques. See, e.g., Remington, The binder Such as microcrystalline cellulose, gum tragacanth or Science And Practice of Pharmacy (9" Ed. 1995). In the gelatin; an excipient Such as starch or lactose, a disintegrat manufacture of a pharmaceutical formulation according to ing agent Such as alginic acid, Primogel, or corn starch; a the invention, the active compound (including the physi lubricant such as magnesium Stearate; a glidant such as ologically acceptable salts thereof) is typically admixed colloidal silicon dioxide; a Sweetening agent such as Sucrose with, inter alia, an acceptable carrier. The carrier must, of or saccharin; or a flavoring agent such as peppermint, methyl course, be acceptable in the sense of being compatible with salicylate, or orange flavoring. any other ingredients in the formulation and must not be Formulations suitable for oral administration may be deleterious to the patient. The carrier may be a solid or a 25 presented in discrete units, such as capsules, cachets, loZ liquid, or both, and is preferably formulated with the com enges, or tablets, each containing a predetermined amount of pound as a unit-dose formulation, for example, a tablet, the active compound; as a powder or granules; as a Solution which may contain from 0.01 or 0.5% to 95% or 99% by or a suspension in an aqueous or non-aqueous liquid; or as weight of the active compound. One or more active com an oil-in-water or water-in-oil emulsion. Such formulations pounds may be incorporated in the formulations of the 30 may be prepared by any suitable method of pharmacy which invention, which may be prepared by any of the well-known includes the step of bringing into association the active techniques of pharmacy comprising admixing the compo compound and a suitable carrier (which may contain one or nents, optionally including one or more accessory ingredi more accessory ingredients as noted above). In general, the entS. formulations of the invention are prepared by uniformly and In one aspect, the invention provides a pharmaceutical 35 intimately admixing the active compound with a liquid or composition comprising a pharmaceutically effective finely divided solid carrier, or both, and then, if necessary, amount of an active compound as described herein and a shaping the resulting mixture. For example, a tablet may be pharmaceutically acceptable carrier. prepared by compressing or molding a powder or granules The compounds provided herein are administered for containing the active compound, optionally with one or medical therapy in a therapeutically effective amount. The 40 more accessory ingredients. Compressed tablets may be amount of the compounds administered will typically be prepared by compressing, in a Suitable machine, the com determined by a physician, in the light of the relevant pound in a free-flowing form, Such as a powder or granules circumstances, including the condition to be treated, the optionally mixed with a binder, lubricant, inert diluent, chosen route of administration, the compound administered, and/or Surface active/dispersing agent(s). Molded tablets the age, weight, and response of the individual patient, the 45 may be made by molding, in a suitable machine, the pow severity of the patient’s symptoms, and the like. dered compound moistened with an inert liquid binder. In The formulations of the invention include those suitable one embodiment, the compounds are administered in a for oral, rectal, topical, buccal (e.g., Sub-lingual), vaginal, controlled release formulation. parenteral (e.g., Subcutaneous, intramuscular, intradermal, Formulations Suitable for buccal (Sub-lingual) adminis or intravenous), topical (i.e., both skin and mucosal Surfaces, 50 tration include lozenges comprising the active compound in including airway Surfaces), transdermal administration, and a flavored base, usually Sucrose and acacia or tragacanth; intraventricular injection (injection into a ventricle of the and pastilles comprising the compound in an inert base Such brain, e.g., by an implanted catheter or Ommaya reservoir, as gelatin and glycerin or Sucrose and acacia. Such as in the case of morbid obesity), ocular (via injection, Formulations of the present invention suitable for paren implantation or by reservoir), and intranasal, although the 55 teral administration comprise sterile aqueous and non-aque most Suitable route in any given case will depend on the ous injection solutions of the active compound, which nature and severity of the condition being treated and on the preparations are preferably isotonic with the blood of the nature of the particular active compound which is being intended recipient. These preparations may contain anti used. oxidants, buffers, bacteriostats and solutes which render the The compositions for oral administration can take the 60 formulation isotonic with the blood of the intended recipi form of bulk liquid solutions or Suspensions, or bulk pow ent. Aqueous and non-aqueous sterile Suspensions may ders. Typically, the compositions are presented in unit dos include Suspending agents and thickening agents. The for age forms to facilitate accurate dosing. The term “unit mulations may be presented in unit\dose or multi-dose dosage forms’ refers to physically discrete units suitable as containers, for example sealed ampoules and vials, and may unitary dosages for human Subjects and other mammals, 65 be stored in a freeze-dried (lyophilized) condition requiring each unit containing a predetermined quantity of active only the addition of the sterile liquid carrier, for example, material calculated to produce the desired therapeutic effect, saline or water-for-injection immediately prior to use. US 9,555,031 B2 43 44 Extemporaneous injection Solutions and Suspensions may be Other pharmaceutical compositions may be prepared prepared from sterile powders, granules and tablets of the from the water-insoluble compounds disclosed herein, or kind previously described. For example, in one aspect of the salts thereof. Such as aqueous base emulsions. In Such an present invention, there is provided an injectable, stable, instance, the composition will contain a sufficient amount of sterile composition comprising a compound of Formula I, pharmaceutically acceptable emulsifying agent to emulsify Formula IA, Formula IB, Formula II, Formula IIA, Formula the desired amount of the compound or salt thereof. Par IIB or a salt thereof, in a unit dosage form in a sealed ticularly useful emulsifying agents include phosphatidylcho container. The compound or salt is provided in the form of lines, and lecithin. a lyophilizate which is capable of being reconstituted with a In addition to compounds of Formula I, Formula IA, Suitable pharmaceutically acceptable carrier to form a liquid 10 Formula IB, Formula II, Formula IIA, or Formula IIB or other active compounds described herein, or their salts, the composition suitable for injection thereof into a subject. The pharmaceutical compositions may contain other additives, unit dosage form typically comprises from about 10 mg to Such as pH-adjusting additives. In particular, useful pH about 10 grams of the compound or salt. When the com adjusting agents include acids, such as hydrochloric acid, pound or salt is substantially water-insoluble, a Sufficient 15 bases or buffers, such as Sodium lactate, sodium acetate, amount of emulsifying agent which is physiologically Sodium phosphate, sodium citrate, sodium borate, or Sodium acceptable may be employed in Sufficient quantity to emul gluconate. Further, the compositions may contain microbial Sify the compound or salt in an aqueous carrier. One Such preservatives. Useful microbial preservatives include meth useful emulsifying agent is phosphatidylcholine. ylparaben, propylparaben, and benzyl alcohol. The micro Injectable compositions are typically based upon inject bial preservative is typically employed when the formulation able sterile saline or phosphate-buffered saline or other is placed in a vial designed for multidose use. Of course, as injectable carriers known in the art. indicated, the pharmaceutical compositions of the present Formulations suitable for rectal administration are pref invention may be lyophilized using techniques well known erably presented as unit dose Suppositories. These may be in the art. prepared by admixing the active compound with one or 25 The Mer TKI compound of this invention can also be more conventional Solid carriers, for example, cocoa butter, administered in Sustained release forms or from Sustained and then shaping the resulting mixture. release drug delivery systems. A description of representa Formulations suitable for topical application to the skin tive Sustained release materials can be found in Remington's preferably take the form of an ointment, cream, lotion, paste, Pharmaceutical Sciences. gel, spray, aerosol, or oil. Carriers which may be used 30 In certain embodiments, the formulation comprises water. include petroleum jelly, lanoline, polyethylene glycols, alco In another embodiment, the formulation comprises a cyclo hols, transdermal enhancers, and combinations of two or dextrin derivative. In certain embodiments, the formulation more thereof. comprises hexapropyl-3-cyclodextrin. In a more particular Formulations Suitable for transdermal administration may embodiment, the formulation comprises hexapropyl-3-cy be presented as discrete patches adapted to remain in inti 35 clodextrin (10-50% in water). mate contact with the epidermis of the recipient for a The present invention also includes pharmaceutically prolonged period of time. Formulations Suitable for trans acceptable acid addition salts of compounds of the com dermal administration may also be delivered by iontopho pounds of the invention. The acids which are used to prepare resis (see, for example, Pharmaceutical Research 3 (6):318 the pharmaceutically acceptable salts are those which form (1986)) and typically take the form of an optionally buffered 40 non-toxic acid addition salts, i.e. salts containing pharma aqueous solution of the active compound. Suitable formu cologically acceptable anions such as the hydrochloride, lations comprise citrate or bis\tris buffer (pH 6) or ethanol/ hydroiodide, hydrobromide, nitrate, sulfate, bisulfate, phos water and contain from 0.1 to 0.2M active ingredient. phate, acetate, lactate, citrate, tartrate. Succinate, maleate, Further, the present invention provides liposomal formu fumarate, benzoate, para-toluenesulfonate, and the like. lations of the compounds disclosed herein and salts thereof. 45 The above-described components for pharmaceutical The technology for forming liposomal suspensions is well compositions are merely representative. Other materials as known in the art. When the compound or salt thereof is an well as processing techniques and the like are set forth in aqueous-soluble salt, using conventional liposome technol Part 8 of Remington's Pharmaceutical Sciences, 17th edi ogy, the same may be incorporated into lipid vesicles. In tion, 1985, Mack Publishing Company, Easton, Pa., which is Such an instance, due to the water Solubility of the com 50 incorporated herein by reference. pound or salt, the compound or salt will be substantially As noted above, the present invention provides pharma entrained within the hydrophilic center or core of the lipo ceutical formulations comprising the active compounds (in Somes. The lipid layer employed may be of any conventional cluding the pharmaceutically acceptable salts thereof), in composition and may either contain cholesterol or may be pharmaceutically acceptable carriers for oral, rectal, topical, cholesterol-free. When the compound or salt of interest is 55 buccal, parenteral, intramuscular, intradermal, or intrave water-insoluble, again employing conventional liposome nous, and transdermal administration. formation technology, the salt may be substantially The therapeutically effective dosage of any specific com entrained within the hydrophobic lipid bilayer which forms pound, the use of which is in the scope of present invention, the structure of the liposome. In either instance, the lipo will vary somewhat from compound to compound, and Somes which are produced may be reduced in size, as 60 patient to patient, and will depend upon the condition of the through the use of standard Sonication and homogenization patient and the route of delivery. As a general proposition, a techniques. dosage from about 0.1 to about 50 mg/kg will have thera Of course, the liposomal formulations containing the peutic efficacy, with all weights being calculated based upon compounds disclosed herein or salts thereof, may be the weight of the active compound, including the cases lyophilized to produce a lyophilizate which may be recon 65 where a salt is employed. Toxicity concerns at the higher stituted with a pharmaceutically acceptable carrier, Such as level may restrict intravenous dosages to a lower level Such water, to regenerate a liposomal Suspension. as up to about 10 mg/kg, with all weights being calculated US 9,555,031 B2 45 46 based upon the weight of the active base, including the cases mg, about 140 mg, about 150, about 175, or about 200 mg. where a salt is employed. The duration of the treatment can In another embodiment, the dose is between about 200 mg be once per day for a period of two to three weeks or until and 1250 mg. In one embodiment, the dose is about 200 mg. the condition is essentially controlled. about 225 mg, about 250 mg, about 275 mg, about 300 mg. The therapeutically effective dosage of any active com about 325 mg, about 350 mg, about 375 mg, about 400 mg. pound described herein will be determined by the health care about 425 mg, about 450 mg, about 475 mg, about 500 mg. practitioner depending on the condition, size and age of the about 525 mg, about 550 mg, about 575 mg, about 600 mg. patient as well as the route of delivery. In one non-limited about 625 mg, about 650 mg, about 675 mg, about 700 mg. embodiment, a dosage from about 0.1 to about 200 mg/kg about 725 mg, about 750 mg, about 775 mg, about 800 mg. has therapeutic efficacy, with all weights being calculated 10 about 825 mg, about 850 mg, about 875 mg, about 900 mg. based upon the weight of the active compound, including the about 925 mg, about 950 mg, about 975 mg, about 1000 mg cases where a salt is employed. In some embodiments, the O. O. dosage can be the amount of compound needed to provide In one embodiment, the compounds described herein are a serum concentration of the active compound of up to combined with an additional anti-tumor agent, anti-neoplas between about 1 and 5, 10, 20, 30, or 40 uM. In some 15 tic agent, anti-cancer agent, immunomodulatory agent, embodiments, a dosage from about 10 mg/kg to about 50 immunostimulatory agent, anti-infective agents, anti-throm mg/kg can be employed for oral administration. Typically, a botic, and/or anti-clotting agent. The dosage administered to dosage from about 0.5 mg/kg to 5 mg/kg can be employed the host can be similar to that as administered during for intramuscular injection. In some embodiments, dosages monotherapy treatment, or may be lower, for example, can be from about 1 umol/kg to about 50 umol/kg, or, between about 0.5 mg and about 150 mg. In one embodi optionally, between about 22 umol/kg and about 33 umol/kg ment, the dose is at least about 1 mg, about 2 mg, about 3 of the compound for intravenous or oral administration. An mg, about 4 mg, about 5 mg, about 10 mg, about 12 mg, oral dosage form can include any appropriate amount of about 15 mg, about 20 mg, about 25 mg, about 30 mg, about active material, including for example from 5 mg to, 50, 100, 35 mg, about 40 mg, about 45 mg, about 50 mg, about 55 200, or 500 mg per tablet or other solid dosage form. 25 mg, about 60 mg, about 65 mg, about 70 mg, about 75 mg. Active compounds may be administered as pharmaceuti about 80 mg, about 85 mg, about 90 mg, about 95 mg, about cally acceptable prodrugs, which are those prodrugs of the 100 mg, about 110 mg, about 125 mg, about 140 mg. or active compounds of the present invention which are, within about 150 mg. the scope of Sound medical judgment, Suitable for use in In one embodiment, for the case of the co-administration contact with the tissues of humans and lower animals 30 of an active compound in combination with an additional without undue toxicity, irritation, allergic response and the anti-tumor agent, anti-neoplastic agent, anti-cancer agent, like, commensurate with a reasonable risk/benefit ratio, and immunomodulatory agent, immunostimulatory agent, anti effective for their intended use, as well as the Zwitterionic infective agents, anti-thrombotic, and/or anti-clotting agent, forms, where possible, of the compounds of the invention. as otherwise described herein, the amount of the compound The term “prodrug” refers to compounds that are rapidly 35 according to the present invention to be administered ranges transformed in vivo to yield the parent compound of the from about 0.01 mg/kg of the patient to about 50 mg/kg or above formulae, for example, by hydrolysis in blood. A more of the patient or considerably more, depending upon thorough discussion is provided in T. Higuchi and V. Stella, the second compound to be co-administered, the condition Prodrugs as Novel delivery Systems, Vol. 14 of the A.C.S. of the patient, severity of the disease to be treated, and the Symposium Series and in Edward B. Roche, ed., Biorevers 40 route of administration. In one embodiment, the additional ible Carriers in Drug Design, American Pharmaceutical anti-tumor agent, anti-neoplastic agent, anti-cancer agent, Association and Pergamon Press, 1987, both of which are immunomodulatory agent, immunostimulatory agent, anti incorporated by reference herein. See also U.S. Pat. No. infective agents, anti-thrombotic, and/or anti-clotting agent 6,680,299 Examples include a prodrug that is metabolized in may, for example, be administered in amounts ranging from Vivo by a Subject to an active drug having an activity of 45 about 0.01 mg/kg to about 500 mg/kg. In one embodiment, active compounds as described herein, wherein the prodrug for oral dosing, Suitable daily dosages are, for example, is an ester of an alcohol or carboxylic acid group, if Such a between about 0.1-4000 mg administered orally once-daily, group is present in the compound; an acetal or ketal of an twice-daily, or three times-daily, continuous (every day) or alcohol group, if Such a group is present in the compound; intermittently (e.g., 3-5 days a week). an N-Mannich base or an imine of an amine group, if Such 50 a group is present in the compound; or a Schiffbase, oxime, Methods of Use of the Active Compounds acetal, enol ester, oxazolidine, or thiazolidine of a carbonyl group, if such a group is present in the compound, Such as 4. ANTI-INFECTIVE AGENTS described in U.S. Pat. No. 6,680,324 and U.S. Pat. No. 6,680,322. 55 It has been discovered that an effective amount of the In one aspect of the invention, a method is provided to pyrrolopyrimidine compounds described in Formulas I, IA, treat a host by administering a daily amount of a Mer TKI IB, II, IIA and IIB below or as otherwise provided herein, including active compounds of the present invention, which can be administered as an immunomodulatory agent to may be provided in dosages once or more a day. In one stimulate the innate immune system. This immunostimula embodiment, the Mer TKI dose is between about 0.5 mg and 60 tory activity can be used therapeutically to treat a host with about 200 mg. In one embodiment, the dose is at least about an infection. In one embodiment, the infection is a viral 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg. infection. In one embodiment, the infection is a bacterial about 10 mg, about 12 mg, about 15 mg, about 20 mg, about infection. In an alternative embodiment, an effective amount 25 mg, about 30 mg, about 35 mg, about 40 mg, about 45 of the pyrrolopyrimidine compounds described in Formulas mg, about 50 mg, about 55 mg, about 60 mg, about 65 mg. 65 I, IA, IB, II, IIA and IIB below or as otherwise provided about 70 mg, about 75 mg, about 80 mg, about 85 mg, about herein can be used to treat a host bearing any virus-related 90 mg, about 95 mg, about 100 mg, about 110 mg, about 125 infection where the virus has a virion envelope phosphatidyl US 9,555,031 B2 47 48 serine that complexes with MerTK to achieve viral entry or Onyongnyong virus, Ross River virus, Semliki Forest is otherwise facilitated by MerTK in the infectious process virus, Sindbis, Venezuelan equine encephalitis or Western or maintenance. equine encephalitis virus. Viral Infections. In one embodiment, the host is infected with Chikungu The virus may be an enveloped virus or a non-enveloped nya virus. In one embodiment, the host is infected with virus. In one embodiment, the host is infected or threatened Ebola virus. In one embodiment, an active compound or Mer to become infected with a virus selected from, for example, TKI as described herein is used in combination with brin Flaviviridae viruses, including Flavivirus (such as Yellow cidofovir (CMX001). Fever, West Nile and Dengue), Hepacivirus (Hepatitis C In another particular embodiment, the host is infected 10 with a non-enveloped virus, such as, but not limited to, virus, “HCV), Pegivirus and Pestivirus (Bovine viral diar viruses of the following families: Adenoviridae, Arenaviri rhea virus); Filoviridae viruses, including Ebola viruses: dae, Birnaviridae, Calciviridae, Iridoviridae, Ophioviridae Togaviridae viruses, including Chikungunya virus; Corona Parvoviradae, Papillomaviridae, Papovaviridae, Picornaviri viruses, such as SARS (Severe acute respiratory syndrome) dae, and Reoviridae. Examples of viruses from the Adeno and MERS (Middle East respiratory syndrome); 15 viridae family include, but are not limited to adenoviruses. Orthomyxoviridae viruses, for example influenza; Examples of viruses from the Arenaviradae family include, Paramyxoviridae viruses, for example Respiratory syncytial but are not limited to, hemorrhagic fever viruses such as virus (RSV), measles and mumps; and Caliciviridae viruses, Guanarito, LCMV, Lassa, Junin, and Machupo. Examples of including Lagovirus, Vesivirus, and Sapovirus and Norovi viruses from the Iridoviridae family include, but are not rus (Norwalk-like virus), and Lentiviruses, for example, limited to, African swine fever virus. Examples of viruses HIV. In one embodiment, an active compound disclosed from the Papillomavirus family include, but are not limited herein is administered in combination or alternation with to, papillomaviruses. Examples of viruses from the Papova another anti-viral agent for combination therapy. In one viridae family include, but are not limited to, polyoma embodiment, the compound administered is selected from viruses such as BK virus and JC virus. Examples of viruses UNC2025A, UNC2142A and UNC2371A. 25 from the Parvoviridae family include, but are not limited to, More broadly, the host to be treated may be infected with parvoviruses such as human bocavirus and adeno-associated an enveloped virus including, but not limited to, viruses of virus. Examples of viruses from the Picornaviridae family the following families: Bornaviridae, Bunyaviridae, Coro include, but are not limited to, aptoviruses, cardioviruses, naviridae, Filoviridae, Flaviviridae, Hepadnaviridae, Her coxsackieviruses, echoviruses, enteric viruses, enterovi pesviridae, Nyamiviridae, Orthomyxoviridae, Paramyxo 30 ruses, foot and mouth disease virus, hepatitis A virus, hepatoviruses, Poliovirus, and rhinovirus. Examples of viridae, Poxviridae, Retroviridae, Rhabdoviridae, and viruses from the Reoviradae family include, but are not Togaviridae. Examples of viruses form the Bunyaviridae limited to, orbiviruses, reoviruses and rotaviruses. family include, but are not limited to, bunya viruses Such as In another embodiment, a host is infected with a virus La Crosse virus and Hantaan. Examples of viruses from the 35 Such as an astroviruses, caliciviruses including but not Coronaviridae family include, but are not limited to, coro limited to, Norovirus and Norwalk, and Hepeviruses includ naviruses such as SARS virus or Toroviruses. Examples of ing, but not limited to, Hepatitis E. viruses from the Filoviridae family include, but are not As described above, a compound described herein can be limited to, Ebola and Marburg. Examples of viruses from the administered to a host Suffering from a viral infection in Flaviviridae family include, but are not limited to, dengue, 40 combination with another anti-viral or anti-infective com encephalitis viruses including West Nile virus, Japanese pound. Antiviral compounds that can be used in combination encephalitis virus and yellow fever virus and Hepatitis C with the compounds described herein include, but are not virus. Examples of viruses from the Hepadnaviridae family limited to, abacavir, acyclovir, adefovir, amantadine, ampre include, but are not limited to, Hepatitis B. Examples of navir, ampligen, arbitol, atazanavir, balavir, boceprevir, viruses from the Herpesviridae family include, but are not 45 boceprevirertet, cidofovir, dolutegravir, darunavir, delavir limited to, cytomegalovirus, herpes simplex viruses 1 and 2. dine, didanosine, docosanol, edoxudine, efavirenz, emitric HHV-6, HHV-7, HHV-8, pseudorabies virus, and varicella itabine, epivir, enfuvirtide, entecavir, famciclovir, fomi Zoster virus. Examples of viruses from the Orthomyxoviri Virsen, fosamprenavir, foScarnet, fosfonet, ganciclovir, dae family include, but are not limited to, influenza virus. ibacitabine, imunovir, idoxuridine, imiquimod, indinavir, Examples of viruses from the Paramyxoviridae family 50 lamivudine, lopinavir, loviride, maraviroc, moroxydine, nel include, but are not limited to, measles, metapneumovirus, finavir, nevirapine, nexavir, oseltamivir, penciclovir, mumps, parainfluenza, respiratory syncytial virus, and sen peramivir, pleconaril, podophyllotoxin, raltegravir, ribavi dai. Examples of viruses from the Poxviridae family include, rin, rilpivirine, rimantadine, pyramidine, saquinavir, but are not limited to, pox viruses such as Smallpox, monkey simeprevir, Sofosbuvir, Stavudine, telaprevir, tenofovir, tip poX, and Molluscum contagiosum virus, variola viruses, 55 ranavir, trifluridine, trizivir, tromantadine, traporved, tru vaccinia virus, and yatapox viruses such as Tanapox and vada, Valaciclovir, Valganciclovir, Vicriviroc, Vidarabine, Yabapox. Examples of viruses from the Retroviridae family Viramidine, Zalcitabine, Zanamivir, and Zidovudine. include, but are not limited to, Coltiviruses such as CTFV In one embodiment, a host is infected with a human and Banna virus, human immunodeficiency viruses such as immunodeficiency virus and is administered a compound HIV-1 and HIV-2, murine leukemia virus, simian immuno 60 described herein in combination with the anti-HIV combi deficiency virus, feline immunodeficiency virus, human nation drug. Such as Atripla R or other drug that includes T-cell leukemia viruses 1 and 2, and XMRV. Examples of emtricitabine. In another embodiment, the patient with the viruses from the Rhabdoviridae family include, but are not human immunodeficiency virus can be treated with ataza limited to, Vesicular stomatitis and rabies. Examples of navir, ritonavir, or Truvada(R) in combination with a com viruses from the Togaviridae family include, but are not 65 pound described herein. In another embodiment, the patient limited to, rubella viruses or alpha viruses such as Chikun infected with human immunodeficiency virus can be treated gunya virus, Eastern equine encephalitis virus, with the combination of dolutegravir, TruvadaR) and a US 9,555,031 B2 49 50 compound described herein. In another embodiment, human ment, a host infected with hepatitis C genotype 6 is treated immunodeficiency virus can be treated with the combination with SovaldiTM, ribavirin, pegylated interferon, and a com dolutegravir, Epzicom R and a compound described herein. pound described herein for 12 weeks. In one embodiment, a In another embodiment, a host infected with human immu host infected with hepatitis C genotype 6 is treated with nodeficiency virus can be treated with a combination of 5 ribavirin, pegylated interferon, and a compound described raltegravir, Truvada(R) and a compound described herein. In herein for 48 weeks. another embodiment, a host infected with human immuno In one embodiment, a host infected with hepatitis C deficiency virus can be treated with the combination of genotype 1 is treated with SovaldiTM, OlysioTM, ribavirin, CompleraR) and a compound described herein. It will be and a compound described herein for 12 weeks. In another appreciated by one skilled in the art that a host infected with 10 embodiment, a host infected with hepatitis C genotype 1 is HIV can be treated with a number of combinations of drugs treated with SovaldiTM, ribavirin, and a compound described depending on the mutation pattern of the virus. The patient herein for 24 weeks. In one embodiment, a host infected can be treated with an appropriate combination of drugs in with hepatitis C genotype 2 is treated with SovaldiTM, combination with a compound described herein. ribavirin, and a compound described herein for 12 weeks. In In one embodiment, the host is infected with a hepatitis C 15 one embodiment, a host infected with hepatitis C genotype virus and is treated with an anti-hepatitis C drug in addition 3 is treated with SovaldiTM, ribavirin, and a compound to the active compound described herein. For example, the described herein for 24 weeks. In one embodiment, a patient patient can be treated with a combination of SovaldiTM, infected with hepatitis C genotype 4 is treated with HarvoniR, ribavirin, and/or a pegylated interferon and a SovaldiTM, ribavirin, and a compound described herein for compound described herein. In one embodiment the pegy 24 weeks. lated interferon is Peglintron(R). In another embodiment, the In one embodiment, a host infected with papilloma virus pegylated interferon is PegasySR. In one embodiment, the is treated with Imiquimod and a compound described herein. host infected with hepatitis C virus is treated with SovaldiTM, In another embodiment, a host infected with papilloma virus ribavirin and a compound described herein. In one embodi is treated with cryotherapy and a compound described ment, the host infected with hepatitis C virus is treated with 25 herein. In another embodiment, papilloma virus is Surgically HarvoniR, ribavirin and a compound described herein. In removed from a host and the host is treated with a compound one embodiment, a host infected with hepatitis C virus is described herein. In one embodiment, the host receives a treated with a combination of OlysioTM, ribavirin, a pegy compound described herein prior to, during, and post lated interferon and a compound described herein. In one Surgery. In one embodiment, the patient receives a com embodiment the pegylated interferon is Peglintron(R). In 30 pound described herein post-Surgery. another embodiment, the pegylated interferon is PegasyS(R). In one embodiment a host infected with herpes simplex In one embodiment, the host is infected with a hepatitis C type 2 is treated with Famvir R and a compound described virus and is treated with a combination of ABT-267, ABT herein. In one embodiment a host infected with herpes 333 and ABT-450/ritonavir, in addition to an active com simplex type 1 is treated with acyclovir and a compound pound described herein. In one embodiment, the host is 35 described herein. In another embodiment, a host infected infected with a hepatitis C virus and is treated with a with herpes simplex type 2 is treated with acyclovir and a combination of MK-5172 and MK-8742, in addition to an compound described herein. In one embodiment, a host active compound described herein. infected with herpes simplex type 1 is treated with ValtrexR) In one embodiment, a host infected with hepatitis C and a compound described herein. In another embodiment, genotype 1 is treated with a combination of SovaldiTM, 40 a host infected with herpes simplex type 2 is treated with ribavirin, a pegylated interferon and a compound described Valtrex R and a compound described herein. In one embodi herein for 12 weeks. In another embodiment, a host infected ment, a host infected with herpes simplex type 1 virus with hepatitis. C genotype 1 is treated with SovaldiTM and a receives a compound described herein for 7 days prior to compound described herein for 12 weeks followed by riba treatment with acyclovir. In one embodiment, a host infected Virin, pegylated interferon and a compound described herein 45 with herpes simplex type 2 virus receives a compound for 24 weeks. In one embodiment, a host infected with described herein for 7 days prior to treatment with acyclovir. hepatitis C genotype 2 is treated with SovaldiTM, ribavirin, In one embodiment, a host infected with herpes simplex type and a compound described herein for 12 weeks. In one 1 virus receives a compound described herein for 7 days embodiment, a host infected with hepatitis C genotype 3 is prior to treatment with Valtrex R. In one embodiment, a host treated with SovaldiTM, ribavirin, and a compound described 50 infected with herpes simplex type 2 virus receives a com herein for 24 weeks. In another embodiment, a host infected pound described herein for 7 days prior to treatment with with hepatitis C genotype 3 is treated with SovaldiTM, Valtrex(R). ribavirin, pegylated interferon, and a compound described In one embodiment a host infected with varicella Zoster herein for 12 weeks. In one embodiment, a host infected virus, VZV. is treated with acyclovir and a compound with hepatitis C genotype 4 is treated with SovaldiTM, 55 described herein. In another embodiment a host infected ribavirin, pegylated interferon, and a compound described with varicella Zoster virus, VZV, is treated with Valtrex R. herein for 12 weeks. In another embodiment, a host infected and a compound described herein. In one embodiment, a with hepatitis C genotype 4 is treated with a combination of host infected with varicella Zoster virus, VZV, is treated with OlysioTM, and a compound described herein for 12 weeks famciclovir and a compound described herein. In another followed by ribavirin, pegylated interferon and a compound 60 embodiment a host infected with varicella Zoster virus, VZV. described herein for 24-28 weeks. is treated with foscarnet and a compound described herein. In one embodiment, a host infected with hepatitis C In one embodiment, a host infected with varicella Zoster genotype 5 is treated with SovaldiTM, ribavirin, pegylated virus is treated with a compound described herein prior to interferon, and a compound described herein for 12 weeks. vaccination with Zostavax(R). In another embodiment, a host In one embodiment, a host infected with hepatitis C geno 65 infected with varicella Zoster virus is treated with a com type 5 is treated with ribavirin, pegylated interferon, and a pound described herein prior to and post vaccination with compound described herein for 48 weeks. In one embodi Zostavax(R). US 9,555,031 B2 51 52 In one embodiment a host infected with influenza virus is ment, the compound administered is selected from treated with Relenza R) and a compound described herein. In UNC2025A, UNC2142A and UNC2371A. another embodiment a host infected with influenza virus is In one embodiment, a patient is suffering from acute-on treated with TamifluR) and a compound described herein. In chronic liver failure (ACLF). In one embodiment, a patient another embodiment a host is infected with influenza virus is suffering from acute liver failure. In one embodiment, a and is treated with amantadine and a compound described patient is suffering from chronic liver failure. In one embodi herein. In another embodiment, a host infected with influ ment, the liver failure is caused by a disease or condition enza virus is treated with rimantadine and a compound selected from alcoholic liver disease, chronic viral hepatitis described herein. type C, chronic viral hepatitis type B, chronic bile duct In one embodiment, a host infected with cytomegalovirus 10 blockage, Wilson's disease, hemochromatosis, exposure to is treated with Valganciclovir and a compound described drug and toxins, autoimmune hepatitis, cystic fibrosis, alpha herein. In another embodiment, a host infected with cyto antitrypsin deficiency, obesity or Schistosomiasis. megalovirus is treated with ganciclovir and a compound In one embodiment, an active compound disclosed herein described herein. In one embodiment, a host infected with is administered in combination with an antibiotic for the cytomegalovirus is treated with foscarnet and a compound 15 prevention or treatment of bacterial infections. Examples of described herein. In another embodiment, a host infected antibiotics include, but are not limited to, cefotaxime (Cla with cytomegalovirus is treated with cidofovir and a com foran), ofloxacin (Floxin), norfloxacin (Noroxin) or pound described herein. trimethoprim/sulfamethoxazole (Bactrim, Septra). In one embodiment, a host infected with hepatitis B virus is treated with lamivudine and a compound described herein. 5. IMMUNOMODULATORY AND In another embodiment, a host infected with hepatitis B IMMUNOSTIMULATORY AGENTS virus is treated with adefovir and a compound described herein. It has also been discovered that the compounds described In one embodiment, a host infected with hepatitis B virus herein can be used as immunomodulatory agents that reverse is treated with tenofovir and a compound described herein. 25 the MerTK-induced suppression of proinflammatory cytok In another embodiment, a host infected with hepatitis B ines such as wound healing cytokines (IL-10 and GAS6) and virus is treated with telbivudine and a compound described enhance the expression of acute inflammatory cytokines herein. (IL-12 and IL-6). In this way, the pyrrolopyrimidine com Bacterial Infections. pounds can “re-normalize' or “re-program’ the host In one embodiment of the present invention, a compound 30 microenvironment in the diseased tissue area to attack the of Formula I, Formula IA, Formula IB, Formula II, Formula diseased cells. This immunostimulatory activity can be used IIA, or Formula IIB, or other active compound described therapeutically to treat a host with a tumor, cancer or other herein, is used in an effective amount to treat a host infected neoplasm, or alternatively, to treat a host with an infection, with a bacterial infection. In one embodiment, the bacteria for example, a viral or bacterial infection. treated is, for example, a Gram-negative bacilli (GNB), 35 Taking advantage of the immunostimulatory activity of especially Escherichia coli, Gram-positive cocci (GPC), the compounds described herein, or a pharmaceutically Staphylococcus aureus, Enterococcus faecalis, or Strepto acceptable composition, salt, isotopic analog, or prodrug coccus pneumoniae. In one embodiment, the bacterial infec thereof, may be used for the treatment of a MERTK-negative tion may be caused, for example, by a Gram-negative (-/-) tumor or cancer. In one embodiment, the cancer is a bacteria, including, but not limited to Escherichia coli, 40 MERTK-negative (-/-) breast cancer. Salmonella, and other Enterobacteriaceae, Pseudomonas, Therefore, as part of the invention, one or more of the Moraxella, Helicobacter, Stenotrophomonas, Bdellovibrio, compounds disclosed herein can be used as adjunctive acetic acid bacteria, Legionella, Staphylococcus aureus, therapy for its immunostimulatory effect as a means to Hemophilus influenzae, Klebsiella pneumoniae, Legionella increase the efficacy of the antineoplastic standard of care pneumophila, Pseudomonas aeruginosa, Vibrio cholerae, 45 therapies, such as chemotherapeutic compounds or radia Proteus mirabilis, Enterobacter cloacae, Serratia marc tion. escens, Clostridium tetani, Helicobacter pylori, Salmonella In another aspect of the invention, one or more of the enteritidis, Salmonella typhi, Shigella flexneri, or Acineto compounds disclosed herein can be used as adjunctive bacter baumanii. In one embodiment, the bacterial infection therapy for its immunostimulatory effect as a means to may be caused, for example, by a Gram-positive species 50 increase the efficacy of the antiviral or antibacterial standard from the following genera: Bacillus, Listeria, Staphylococ of care therapies. cus, Enterococcus, Lactobacillus, Lactococcus, Leuconos For example, a compound of Formula I, Formula IA, to C, Pedicoccus, Streptococcus, Acetobacterium, Formula IB, Formula II, Formula IIA, or Formula IIB, or Clostridium, Eubacterium, Heliobacterium, Heliospirillum, another compound as described herein, is administered to a Megasphaera, Pectinatus, Selenomonas, Zymophilus, 55 host in an immunomodulatory effective amount to inhibit Sporomusa, Mycoplasma, Spiroplasma, Ureaplasma, or Mer tyrosine kinase activity in the host's tumor associated Erysipelothrix. macrophage to suppress tumor immunity. In one embodi In one embodiment, the bacterial infection is associated ment, the dosage of the Mer TKI administered as an immu with liver failure. In one embodiment, an active compound nomodulatory agent to stimulate innate anti-tumor immunity disclosed herein is administered in combination with an 60 is lower than a dosage of a Mer TKI administered to a host antibiotic or another anti-bacterial agent. In one embodi as a direct anti-cancer agent. In one embodiment, the Mer ment, the compound administered is selected from TKI is administered at a dosage which exhibits immuno UNC2025A, UNC2142A and UNC2371A. modulatory but not direct cytotoxic effect. In one embodiment, the bacterial infection is associated In one embodiment, the cancer is a MERTK-negative with liver failure. In one embodiment, an active compound 65 (-/-) cancer. In one embodiment, the MerTK inhibitory disclosed herein is administered in combination with an compound administered is selected from UNC2025A, antibiotic or another anti-bacterial agent. In one embodi UNC2142A and UNC2371A. US 9,555,031 B2 53 54 Without wanting to be bound by any particular theory, it Formula IIB, or other active compound as described herein, is believed that the administration of a chemotherapeutic is capable of direct anti-cancer effects by inhibiting Mer agent results in the apoptosis of tumor cells, exposing tyrosine kinase within tumor cells. In one embodiment, the antigenic tumor proteins. The hosts innate immune system cancer treated overexpresses MerTK. In one embodiment, is thus stimulated to recognize the antigenic apoptotic com the cancer which overexpresses MerTK is selected from the ponents from the tumor cells after chemotherapy or ionizing group consisting of acute myeloid leukemia, T-cell acute radiation and mount an immune response. In one embodi lymphoid leukemia, B-cell acute lymphoid leukemia, lung ment, the administration of a chemotherapeutic agent or cancer, glioma, melanoma, prostate cancer, Schwannoma, ionizing radiation, before, with or subsequently followed by mantle cell lymphoma, and rhabdomyosarcoma. In an alter the administration of a Mer TKI is carried out using the normal standard of care chemotherapeutic protocol. In 10 native embodiment, the cancer ectopically expresses another embodiment, the standard of care protocol of the MerTK. In one embodiment, the compound administered is chemotherapeutic is changed in a manner that causes less selected from UNC2025A, UNC2142A and UNC2371A. toxicity to the host due to the adjunctive or synergistic In one embodiment, the cancer treated has a mutation in activity of the Mer TKI. the amino acid sequence of the MerTK extracellular or In one embodiment, a method for the treatment of a tumor 15 transmembrane domain selected from P40S (melanoma), is provided that includes administering an effective amount S159F (lung), E204K (urinary tract) S428G (gastric), I431F of a Mer TKI to inhibit TK signaling in a tumor associated (lung), A446G (kidney), N454S (liver), W485S/C (lym macrophage, without inhibiting the Survival signal in the phoma), and V486I (melanoma). In one embodiment the tumor itself. In this way, the Mer TKI can be used to ramp cancer treated has a mutation in the amino acid sequence of up the immune response to the tumor by inhibiting macro the MerTK cytosolic domain mutation selected from L586F phage tumorigenic tolerance during normal tumor chemo (urinary tract), G594R (breast), S626C (urinary tract), therapeutic agent. The immunomodulatory dosage of the P672S (lung), L688M (colon), A7085 (head and neck), Mer TKI can be given prior to, with or after chemothera N718Y (lung), R722stop (colon), M790V (lung), P802S peutic therapy and can be used simultaneously with or (melanoma), V873I (liver), S905F (lung), K923R (mela intermittently with the chemotherapeutic therapy. In one 25 noma), P958L (kidney), D983N (liver), and D990N (colon). embodiment, less chemotherapeutic therapy is needed than In one embodiment, the compound administered is selected the normal standard of care defined for that chemotherapeu from UNC2025A, UNC2142A and UNC2371A. tic agent, due to the increased efficacy of the immune In one embodiment of the invention, a compound of response in the Surrounding tumor microenvironment. In Formula I, Formula IA, Formula IB, Formula II, Formula one embodiment, a dose of Mer TKI including active 30 IIA, or Formula IIB, as described herein, is administered to compounds of the present invention (for example 0.5 to 150 a host with a cancer in combination with one or more mg/dose) is given as a type of adjunctive therapy with the additional chemotherapeutic agents, resulting in a synergis chemotherapeutic agent. tic anti-cancer effect and the prolonged Survival of a host In one aspect of the invention, a Mer TKI is administered compared to treatment with either a compound described to a host having a cancer as an immunomodulatory agent to 35 herein or chemotherapeutic agent alone. In one embodiment, inhibit Mer tyrosine kinase activity in a tumor associated the use of a MerTKIcompound described herein in combi macrophage in order to suppress tumor immunity. In one nation with a chemotherapeutic agent provides for increased embodiment, the dosage of the Mer TKI administered as an anti-tumor effects without an increase in the standard of care immunomodulatory agent to stimulate innate anti-tumor dosage of the chemotherapeutic agent. In one embodiment, immunity is lower than a dosage of a MerTKI administered 40 the use of a MerTKIcompound described herein in combi to a host as a direct anti-cancer agent. In one embodiment, nation with a chemotherapeutic provides for equivalent or the Mer TKI is administered at a dosage which exhibits increased anti-tumor effects utilizing a lower dosage of a immunomodulatory but not direct cytotoxic effects on the chemotherapeutic agent than the standard of care dosage. CaCC. In one embodiment, a compound of Formula I. Formula In one embodiment, the dose associated with the immu 45 IA, Formula IB, Formula II, Formula IIA, or Formula IIB, nomodulatory effect of an active compound of the present as described herein, is provided for use in treating a non invention is about 2-fold, about 3-fold, about 4-fold, about small cell lung carcinoma (NSCLC). In one embodiment, a 5-fold, about 6-fold, about 7-fold, about 8-fold, about 9-fold, method is provided to treat a host with non-small cell lung about 10-fold or greater lower than the dose associated with carcinoma (NSCLC) comprising administering to the host a direct Survival-signal inhibiting anti-tumor or cytotoxic 50 an effective amount of a compound of Formula I, Formula effect, or the direct antiviral or antibacterial effect. In one IA, Formula IB, Formula II, Formula IIA, or Formula IIB in embodiment, the dose used to induce an immunomodulatory combination with one or more additional chemotherapeutic effect in a host is between about 0.5 mg and about 150 mg. agents. In one embodiment of the invention, a method is In one embodiment, the dose is about 1 mg, about 2 mg, provided to treat a host with cancer comprising administer about 3 mg, about 4 mg, about 5 mg, about 10 mg, about 12 55 ing to the host an effective amount of a Mer TKI including mg, about 15 mg, about 20 mg, about 25 mg, about 30 mg. active compounds of the present invention in combination about 35 mg, about 40 mg, about 45 mg, about 50 mg, about with another tyrosine kinase inhibitor. In one embodiment, 55 mg, about 60 mg, about 65 mg, about 70 mg, about 75 the tyrosine kinase inhibitor is a fibroblast growth factor mg, about 80 mg, about 85 mg, about 90 mg, about 95 mg. receptor (FGFR) inhibitor. In one embodiment, the FGFR about 100 mg, about 110 mg, about 125 mg, about 140 mg. 60 inhibitor is AZD-4547. In one embodiment, the cancer is or about 150 mg. non-small cell lung carcinoma (NSCLC). In some embodi ments of the invention, a method is provided to treat a host 6. ANTI-TUMORAGENTS, INCLUDING with non-Small cell lung carcinoma (NSCLC) comprising ANTI-CANCERAGENTS administering to the host an effective amount of a Mer TKI 65 including active compounds of the present invention in In one aspect of the invention, a compound of Formula I, combination with an additional tyrosine kinase inhibitor, Formula IA, Formula IB, Formula II, Formula IIA, or wherein the Mer TKI is selected from the group consisting US 9,555,031 B2 55 56 of UNC2025A, UNC2142A and UNC2371A, and wherein tumor effects utilizing a lower dosage of a chemotherapeutic the additional tyrosine kinase inhibitor is selected from the agent than the standard of care dosage. group consisting of gefitinib and crizotinib. In one aspect of the invention, the Mer TKI including In one embodiment, a compound of Formula I. Formula compounds of the present invention can be administered to IA, Formula IB, Formula II, Formula IIA, or Formula IIB, a host with a cancer prior to, during, or after administration as described herein, is provided for use in treating a mela with a chemotherapeutic agent or exposure to ionizing noma. In one embodiment, the administration of the Mer radiation. In one embodiment, a host is administered an TKI compound described herein is combined with a che effective amount of a chemotherapeutic agent or ionizing motherapeutic agent. In one embodiment, the chemothera radiation and subsequently administered a Mer TKI. peutic agent is an anti-programmed cell death -1 (PD-1) 10 In one embodiment, a method is provided to treat a host agent. In one embodiment, the chemotherapeutic agent is a with cancer comprising administering to the host an effec B-RAF inhibitor. In one embodiment, the B-RAF inhibitor tive amount of a compound of Formula I, Formula IA, is vemurafenib. In one embodiment, the host does not have Formula IB, Formula II, Formula IIA, or Formula IIB in a melanoma with a B-RAF mutation. In one embodiment, combination with an immunomodulatory agent. In one the host has a melanoma with a B-RAF mutation. In one 15 embodiment, the immunomodulatory agent is selected from embodiment, the host has a melanoma with a RAS mutation. the group consisting of a CTLA-4 inhibitor, PD-1 or anti In one embodiment, the melanoma over-expresses MerTK. PD-1 ligand, IFN-alpha, IFN-beta, and a vaccine, for In one embodiment, the melanoma has metastasized. In one example, a cancer vaccine. In one embodiment, a method is embodiment, the MerTK inhibitory compound administered provided to treat a host with cancer comprising administer is selected from UNC2025A, UNC2142A and UNC2371A. ing to the host an effective amount of a Mer TKI including In one embodiment, a compound of Formula I. Formula active compounds of the present invention in combination IA, Formula IB, Formula II, Formula IIA, or Formula IIB, with Keytruda R (pembrolizumab). In one embodiment, a as described herein, is provided for use in treating Acute method is provided to treat a host with cancer comprising Lymphoblastic Leukemia (ALL). In one embodiment, a administering to the host an effective amount of a Mer TKI method is provided to treat a host with ALL comprising 25 including active compounds of the present invention in administering to the host an effective amount of a compound combination with Opdivo (nivolumab). In one embodiment, of Formula I, Formula IA, Formula IB, Formula II, Formula a method is provided to treat a host with cancer comprising IIA, or Formula IIB in combination with methotrexate. In administering to the host an effective amount of a Mer TKI one embodiment, the MerTK inhibitory compound admin including active compounds of the present invention in istered is selected from UNC2025A, UNC2142A and 30 combination with Yervoy(R) (ipilimumab). In some embodi UNC2371A. ments, a method is provided to treat a host with cancer In one embodiment, a compound of Formula I, Formula comprising administering to the host an effective amount of IA, Formula IB, Formula II, Formula IIA, or Formula IIB, a Mer TKI including active compounds of the present as described herein, is provided for use in treating Acute invention in combination with an immunomodulatory agent Myeloid Leukemia (AML). In one embodiment, the AML 35 selected from the group consisting of pembrolizumab and contains a wild type FLT3 protein. In one embodiment, the ipilimumab, wherein the Mer TKI is selected from the group replication of the AML cells are dependent on FLT3 expres consisting of UNC2025A, UNC2142A and UNC2371A, sion. In one embodiment, the AML contains a FLT3-ITD wherein the cancer is melanoma. mutation. In one embodiment, the AML contains a FLT3 In one embodiment, the Mer TKIs useful in the present TKD mutation. In one embodiment, the AML contains both 40 invention, including active compounds of the present inven a FLT3-ITD and FLT3-TKD mutation. In one embodiment, tion, are dual MER/FLT-3 TKIs. In one embodiment, the a FLT3 or dual MER/FLT3 inhibitor described herein is MerTKIs are dual MER/Axl TKIs. In one embodiment, the administered to a host suffering from AML, wherein the Mer TKIs are MER-specific TKIs. AML contains a mutation within the FLT3-TKD at amino Tumors. acid F691 or D835. In one embodiment, the MerTK inhibi 45 The active compounds and methods described herein are tory compound administered is selected from UNC2025A, useful for the treatment of tumors. As contemplated herein, UNC2142A and UNC2371A. the cancer treated can be a primary tumor or a metastatic In one embodiment, a tumor Survival-signal inhibiting tumor. In one aspect, the methods described herein are used amount (for example 0.5 to 150 mg/dose) of Mer TKI to treat a solid tumor, for example, melanoma, lung cancer including compounds of the present invention is adminis 50 (including lung adenocarcinoma, basal cell carcinoma, tered to a host alone or in combination with a chemothera squamous cell carcinoma, large cell carcinoma, bronchi peutic agent and/or anti-cancer targeted agent. In an alter oloalveolar carcinoma, bronchiogenic carcinoma, non native embodiment, a tumor Survival-signal inhibiting Small-cell carcinoma, Small cell carcinoma, mesothelioma); amount (for example, at least 150 mg/dose, and in some breast cancer (including ductal carcinoma, lobular carci embodiments, at least 200, 250, 300, 350, 400, 450, or 500 55 noma, inflammatory breast cancer, clear cell carcinoma, mg/dosage or more) of Mer TKI including active com mucinous carcinoma, serosal cavities breast carcinoma); pounds of the present invention is administered to a host colorectal cancer (colon cancer, rectal cancer, colorectal alone or in combination with a chemotherapeutic agent adenocarcinoma); anal cancer; pancreatic cancer (including and/or anti-cancer targeted agent. In one embodiment, the pancreatic adenocarcinoma, islet cell carcinoma, neuroen MerTKI and the chemotherapeutic agent act synergistically. 60 docrine tumors); prostate cancer, prostate adenocarcinoma; In one embodiment, the use of a Mer TKI in combination ovarian carcinoma (ovarian epithelial carcinoma or Surface with a chemotherapeutic agent provides for increased anti epithelial-stromal tumor including serous tumor, endometri tumor effects without an increase in the standard of care oid tumor and mucinous cystadenocarcinoma, sex-cord dosage of the chemotherapeutic agent. stromal tumor); liver and bile duct carcinoma (including In one embodiment, the use of a Mer TKI including 65 hepatocellular carcinoma, cholangiocarcinoma, heman compounds of the present invention in combination with a gioma); esophageal carcinoma (including esophageal adeno chemotherapeutic provides for equivalent or increased anti carcinoma and squamous cell carcinoma); oral and oropha US 9,555,031 B2 57 58 ryngeal squamous cell carcinoma; Salivary gland adenoid pituitary cancer. In one embodiment, the cancer is a prostate cystic carcinoma; bladder cancer; bladder carcinoma; car cancer. In one embodiment, the cancer is a skeletal muscle cinoma of the uterus (including endometrial adenocarci cancer. In one embodiment, the cancer is a skin cancer. In noma, ocular, uterine papillary serous carcinoma, uterine one embodiment, the cancer is a stomach cancer. In one clear-cell carcinoma, uterine sarcomas and leiomyosarco embodiment, the cancer is a thyroid cancer. In one embodi mas, mixed mullerian tumors); glioma, glioblastoma, ment, the cancer is a neuroendocrine cancer. In one embodi medulloblastoma, and other tumors of the brain; kidney ment, the cancer is a gastroesophageal cancer. In one cancers (including renal cell carcinoma, clear cell carci embodiment, the cancer is a renal cell cancer. In one noma, Wilm's tumor); cancer of the head and neck (includ embodiment, the cancer is a head and neck cancer. In some ing squamous cell carcinomas); cancer of the stomach 10 embodiments, the Mer TKI used to treat a host having a (gastric cancers, stomach adenocarcinoma, gastrointestinal cancer is selected from the group consisting of UNC2025A, stromal tumor); testicular cancer, germ cell tumor; neuroen UNC2142A and UNC2371A. docrine tumor, cervical cancer, carcinoids of the gastroin In one embodiment, the methods described herein are testinal tract, breast, and other organs; signet ring cell useful for treating a host Suffering from a lymphoma or carcinoma; mesenchymal tumors including sarcomas, fibro 15 lymphocytic or myelocytic proliferation disorder or abnor sarcomas, haemangioma, angiomatosis, haemangiopericy mality. For example, the Mer TKIs as described herein can toma, pseudoangiomatous stromal hyperplasia, myofibro be administered to a Subject Suffering from a Hodgkin blastoma, fibromatosis, inflammatory myofibroblastic Lymphoma of a Non-Hodgkin Lymphoma. For example, the tumor, lipoma, angiolipoma, granular cell tumor, neurofi Subject can be suffering from a Non-Hodgkin Lymphoma broma, Schwannoma, angiosarcoma, liposarcoma, rhab such as, but not limited to: an AIDS-Related Lymphoma; domyosarcoma, osteosarcoma, leiomyoma, leiomysarcoma, Anaplastic Large-Cell Lymphoma; Angioimmunoblastic skin, including melanoma, cervical, retinoblastoma, head Lymphoma; Blastic NK-Cell Lymphoma; Burkitt's Lym and neck cancer, pancreatic, brain, thyroid, testicular, renal, phoma; Burkitt-like Lymphoma (Small Non-Cleaved Cell bladder, Soft tissue, adenal gland, urethra, cancers of the Lymphoma); Chronic Lymphocytic Leukemia/Small Lym penis, myxosarcoma, chondrosarcoma, osteosarcoma, chor 25 phocytic Lymphoma; Cutaneous T-Cell Lymphoma; Diffuse doma, malignant fibrous histiocytoma, lymphangiosarcoma, Large B-Cell Lymphoma; Enteropathy-Type T-Cell Lym mesothelioma, squamous cell carcinoma, epidermoid carci phoma; Follicular Lymphoma; Hepatosplenic Gamma-Delta noma, malignant skin adnexal tumors, adenocarcinoma, T-Cell Lymphoma; Lymphoblastic Lymphoma; Mantle Cell hepatoma, hepatocellular carcinoma, renal cell carcinoma, Lymphoma; Marginal Zone Lymphoma; Nasal T-Cell Lym hypernephroma, cholangiocarcinoma, transitional cell car 30 phoma; Pediatric Lymphoma; Peripheral T-Cell Lympho cinoma, choriocarcinoma, seminoma, embryonal cell carci mas; Primary Central Nervous System Lymphoma; T-Cell noma, glioma anaplastic; glioblastoma multiforme, neuro Leukemias; Transformed Lymphomas; Treatment-Related blastoma, medulloblastoma, malignant meningioma, T-Cell Lymphomas; or Waldenstrom's Macroglobulinemia. malignant Schwannoma, neurofibrosarcoma, parathyroid Alternatively, the subject may be suffering from a Hodg carcinoma, medullary carcinoma of thyroid, bronchial car 35 kin Lymphoma, such as, but not limited to: Nodular Scle cinoid, pheochromocytoma, Islet cell carcinoma, malignant rosis Classical Hodgkin’s Lymphoma (CHL); Mixed Cellu carcinoid, malignant paraganglioma, melanoma, Merkel cell larity CHL; Lymphocyte-depletion CHL; Lymphocyte-rich neoplasm, cystosarcoma phylloide, Salivary cancers, thymic CHL; Lymphocyte Predominant Hodgkin Lymphoma; or carcinomas, and cancers of the vagina among others. Nodular Lymphocyte Predominant HL. In some embodiments, a method is provided to treat a host 40 In one embodiment, the methods as described herein may with a glioblastoma comprising administering to the host an be useful to treat a host suffering from a specific T-cell, a effective amount of a Mer TKI including active compounds B-cell, or a NK-cell based lymphoma, proliferative disorder, of the present invention in combination with temozolomide, or abnormality. For example, the Subject can be suffering wherein the Mer TKI is selected from the group consisting from a specific T-cell or NK-cell lymphoma, for example, of UNC2025A, UNC2142A and UNC2371A. In some 45 but not limited to: Peripheral T-cell lymphoma, for example, embodiments, a method is provided to treat a host with a peripheral T-cell lymphoma and peripheral T-cell lymphoma breast cancer comprising administering to the host an effec not otherwise specified (PTCL-NOS); anaplastic large cell tive amount of a Mer TKI including active compounds of the lymphoma, for example anaplastic lymphoma kinase (ALK) present invention in combination with trastuzumab, wherein positive, ALK negative anaplastic large cell lymphoma, or the Mer TKI is selected from the group consisting of 50 primary cutaneous anaplastic large cell lymphoma; angioim UNC2025A, UNC2142A and UNC2371A. munoblastic lymphoma; cutaneous T-cell lymphoma, for In one embodiment, the cancer is NSCLC. In one embodi example mycosis fungoides, Sezary syndrome, primary ment, the cancer is a melanoma. In one embodiment, the cutaneous anaplastic large cell lymphoma, primary cutane cancer is breast cancer. In one embodiment, the cancer is a ous CD30+ T-cell lymphoproliferative disorder; primary glioblastoma. In one embodiment, the cancer is a bone 55 cutaneous aggressive epidermotropic CD8+ cytotoxic T-cell cancer. In one embodiment, the cancer is a brain cancer. In lymphoma; primary cutaneous gamma-delta T-cell lym one embodiment, the cancer is a colon cancer. In one phoma; primary cutaneous Small/medium CD4+ T-cell lym embodiment, the cancer is a rectal cancer. In one embodi phoma. and lymphomatoid papulosis; Adult T-cell Leuke ment, the cancer is an endometrial cancer. In one embodi mia/Lymphoma (ATLL); Blastic NK-cell Lymphoma; ment, the cancer is an esophageal cancer. In one embodi 60 Enteropathy-type T-cell lymphoma; Hematosplenic gamma ment, the cancer is a cancer of the gastrointestinal tract. In delta T-cell Lymphoma; Lymphoblastic Lymphoma; Nasal one embodiment, the cancer is a kidney cancer. In one NK/T-cell Lymphomas; Treatment-related T-cell lympho embodiment, the cancer is a liver cancer. In one embodi mas; for example lymphomas that appear after Solid organ or ment, the cancer is a lung cancer. In one embodiment, the bone marrow transplantation; T-cell prolymphocytic leuke cancer is a mantle cell lymphoma. In one embodiment, the 65 mia; T-cell large granular lymphocytic leukemia; Chronic cancer is an ovarian cancer. In one embodiment, the cancer lymphoproliferative disorder of NK-cells; Aggressive NK is a pancreatic cancer. In one embodiment, the cancer is a cell leukemia: Systemic EBV+ T-cell lymphoproliferative US 9,555,031 B2 59 60 disease of childhood (associated with chronic active EBV one embodiment, the AML contains a FLT3-TKD mutation. infection); Hydroa vacciniforme-like lymphoma; Adult In one embodiment, the AML contains both a FLT3-ITD and T-cell leukemia/lymphoma; Enteropathy-associated T-cell FLT3-TKD mutation. lymphoma; Hepatosplenic T-cell lymphoma; or Subcutane FLT3-ITD mutations are well known in the art. FLT3 ous panniculitis-like T-cell lymphoma. TKD mutations are also well known in the art. In one Alternatively, the subject may be suffering from a specific embodiment, a FLT3 or dual MER/FLT3 inhibitor is admin B-cell lymphoma or proliferative disorder such as, but not istered to a host suffering from AML, wherein the AML limited to: multiple myeloma; Diffuse large B cell lym contains a mutation within the FLT3-TKD at amino acid phoma; Follicular lymphoma; Mucosa-Associated Lym F691 or D835. In one embodiment, the FLT3-TKD mutation phatic Tissue lymphoma (MALT); Small cell lymphocytic 10 is selected from D835H, D835N, D835Y, D835A, D835V, lymphoma; Mantle cell lymphoma (MCL); Burkitt lym D835V, D835E, I836F, I836L, I836V, I836D, I836H, phoma; Mediastinal large B cell lymphoma; Waldenström I836M, and F691 L. In one embodiment, the host is suffering macroglobulinemia; Nodal marginal Zone B cell lymphoma from the FLT3-TKD mutation D835Y. In one embodiment, (NMZL); Splenic marginal Zone lymphoma (SMZL); Intra the host is suffering from the FLT3-TKD mutation F691 L. vascular large B-cell lymphoma; Primary effusion lym 15 In one embodiment, the host is suffering from acute phoma; or Lymphomatoid granulomatosis; Chronic lympho promyelocytic leukemia (a Subtype of AML); a minimally cytic leukemia/small lymphocytic lymphoma; B-cell differentiated AML (MO); myeloblastic leukemia (M1; with/ prolymphocytic leukemia; Hairy cell leukemia; Splenic without minimal cell maturation); myeloblastic leukemia lymphoma/leukemia, unclassifiable: Splenic diffuse red pulp (M2; with cell maturation); promyelocytic leukemia (M3 or small B-cell lymphoma; Hairy cell leukemia-variant; Lym M3 variant M3V); myelomonocytic leukemia (M4 or M4 phoplasmacytic lymphoma; Heavy chain diseases, for variant with eosinophilia M4E); monocytic leukemia example, Alpha heavy chain disease, Gamma heavy chain (M5); erythroleukemia (M6); or megakaryocytic leukemia disease, Mu heavy chain disease; Plasma cell myeloma; (M7). In one embodiment, the host is suffering from AML Solitary plasmacytoma of bone; Extraosseous plasmacy that has relapsed or become refractory to previous treat toma; Primary cutaneous follicle center lymphoma; T cell/ 25 ments. In one embodiment, the host has previously been histiocyte rich large B-cell lymphoma; DLBCL associated treated with a FLT3 inhibitor or other chemotherapeutic with chronic inflammation; Epstein-Barr virus (EBV)+ agent. DLBCL of the elderly; Primary mediastinal (thymic) large In one embodiment, the FLT3 inhibitors are efficacious B-cell lymphoma; Primary cutaneous DLBCL, leg type: against AML having both FLT3-ITD and FLT3-TKD muta ALK+ large B-cell lymphoma; Plasmablastic lymphoma; 30 tions, wherein resistance to other FLT3 inhibitors, for Large B-cell lymphoma arising in HHV8-associated multi example, AC220, has been established. centric: Castleman disease: B-cell lymphoma, unclassifi In one embodiment, the host has an Acute Myeloid able, with features intermediate between diffuse large B-cell Leukemia (AML) comprising a FLT3 mutation, wherein the lymphoma and Burkitt lymphoma; B-cell lymphoma, mutation confers resistance to a FLT3 inhibitor other than unclassifiable, with features intermediate between diffuse 35 the FLT3 inhibitors described herein. In one embodiment, large B-cell lymphoma and classical Hodgkin lymphoma; the host has a AML comprising a FLT3 mutation, wherein Nodular Sclerosis classical Hodgkin lymphoma; Lympho the mutation has conferred resistance to quizartinib (AC220) cyte-rich classical Hodgkin lymphoma; Mixed cellularity or other FLT3 inhibitor selected from lestaurtinib, Sunitinib, classical Hodgkin lymphoma; or Lymphocyte-depleted clas Sorafenib, tandutinib, midostaurin, amuvatinib crenolanib, sical Hodgkin lymphoma. 40 dovitinib, ENMD-2076 (Entremed), or KW-2449 (Kyowa In one embodiment, the methods described herein can be Hakko Kirin), or a combination thereof. used to a subject Suffering from a leukemia. For example, the Chemotherapeutic Agents. Subject may be suffering from an acute or chronic leukemia In one embodiment, an active compound or Mer TKI as of a lymphocytic or myelogenous origin, such as, but not described herein is used in combination or alternation with limited to: Acute lymphoblastic leukemia (ALL); Acute 45 a chemotherapeutic agent. Such agents may include, but are myelogenous leukemia (AML); Chronic lymphocytic leu not limited to, tamoxifen, midazolam, letrozole, bortezomib, kemia (CLL); Chronic myelogenous leukemia (CML); juve anastrozole, goserelin, an mTOR inhibitor, a PI3 kinase nile myelomonocytic leukemia (JMML); hairy cell leukemia inhibitors, dual mTOR-PI3K inhibitors, MEK inhibitors, (HCL); acute promyelocytic leukemia (a subtype of AML); RAS inhibitors, ALK inhibitors, HSP inhibitors (for T-cell prolymphocytic leukemia (TPLL); large granular 50 example, HSP70 and HSP 90 inhibitors, or a combination lymphocytic leukemia; or Adult T-cell chronic leukemia; thereof). Examples of mTOR inhibitors include but are not large granular lymphocytic leukemia (LGL). In one embodi limited to rapamycin and its analogs, everolimus (Afinitor), ment, the patient Suffers from an acute myelogenous leuke temsirolimus, ridaforolimus, sirolimus, and deforolimus. mia, for example an undifferentiated AML (MO); myeloblas Examples of P13 kinase inhibitors include but are not tic leukemia (M1; with/without minimal cell maturation); 55 limited to Wortmannin, demethoxyviridin, perifosine, idela myeloblastic leukemia (M2; with cell maturation); promy lisib, PX-866, IPI-145, BAY 80-6946, BEZ235, RP6503, elocytic leukemia (M3 or M3 variant M3V); myelomono TGR 1202 (RP5264), MLN1117 (INK1117), Pictilisib, cytic leukemia (M4 or M4 variant with eosinophilia M4E); Buparlisib, SAR245408 (XL147), SAR245409 (XL765), monocytic leukemia (M5); erythroleukemia (M6); or mega Palomid 529, ZSTK474, PWT33597, RP6530, CUDC-907, karyoblastic leukemia (M7). 60 and AEZS-136. Examples of MEK inhibitors include but are Acute Myeloid Leukemia. not limited to Tametinib, Selumetinib, MEK162, GDC-0973 In one embodiment, the methods described herein can be (XL518), and PD0325901. Examples of RAS inhibitors used to treat a host suffering from Acute Myeloid Leukemia include but are not limited to Reolysin and siC 12D LODER. (AML). In one embodiment, the AML contains a wild type Examples of ALK inhibitors include but are not limited to FLT3 protein. In one embodiment, the replication of the 65 Crizotinib, AP26113, and LDK378. HSP inhibitors include AML cells are dependent on FLT3 expression. In one but are not limited to Geldanamycin or 17-N-Allylamino embodiment, the AML contains a FLT3-ITD mutation. In 17-demethoxygeldanamycin (17AAG), and Radicicol. In US 9,555,031 B2 61 62 one embodiment, the chemotherapeutic agent is an anti carmustine implant, porfimer sodium, procaine, procarba programmed cell death -1 (PD-1) agent, for example, Zine HCL, propranolol, rituximab, Sargramostim, streptozo nivolumab, pembrolizumab, BMS936559, lambrolizumab, tocin, tamoxifen, taxol, teniposide, tenoposide, testolactone, MPDL3280A, pidilizumab, AMP-244, and MEDI4736. In tetracaine, thioepa chlorambucil, thioguanine, thiotepa, one embodiment, the chemotherapeutic agent is a B-RAF topotecan HCL, toremifene citrate, trastuzumab, tretinoin, inhibitor, for example, Vemurafenib or Sorafenib. In one valrubicin, vinblastine sulfate, Vincristine sulfate, and embodiment, the chemotherapeutic agent is a FGFR inhibi Vinorelbine tartrate. In one embodiment, an active com tor, for example, but not limited to, AZD4547, dovitinib, pound or Mer TKI as described herein is used in combina BGJ398, LY2874455, and ponatinib. In one embodiment, an tion with oligomycin A. active compound or Mer TKI as described herein is used in 10 Additional therapeutic agents that can be administered in combination with crizotinib. combination with a compound disclosed herein can include In certain aspects, the additional therapeutic agent is an bevacizumab, Sutinib, Sorafenib, 2-methoxyestradiol or anti-inflammatory agent, a chemotherapeutic agent, a radio 2ME2, finasunate, Vatalanib, vandetanib, aflibercept, therapeutic, an additional therapeutic agent, or an immuno volociximab, etaracizumab (MEDI-522), cilengitide, erlo Suppressive agent. 15 tinib, cetuximab, panitumumab, gefitinib, trastuzumab, Suitable chemotherapeutic agents include, but are not dovitinib, figitumumab, atacicept, rituximab, alemtuzumab, limited to, radioactive molecules, toxins, also referred to as aldesleukine, atlizumab, tocilizumab, temsirolimus, everoli cytotoxins or cytotoxic agents, which includes any agent mus, lucatumumab, dacetuzumab, HLL1, huN901-DM1, that is detrimental to the viability of cells, agents, and atiprimod, natalizumab, bortezomib, carfilzomib, mari liposomes or other vesicles containing chemotherapeutic Zomib, tanespimycin, saquinavir mesylate, ritonavir, nelfi compounds. General anticancer pharmaceutical agents navir meSylate, indinavir Sulfate, belinostat, panobinostat, include: Vincristine (Oncovin R) or liposomal Vincristine mapatumumab, lexatumumab, dulanermin, ABT-737, (MarqiboR), Daunorubicin (daunomycin or Cerubidine(R) oblimersen, plitidepsin, talmapimod, P276-00, enzastaurin, or doxorubicin (Adriamycin R), Cytarabine (cytosine arab tipifarnib, perifosine, imatinib, dasatinib, lenalidomide, tha inoside, ara-C, or Cytosar R), L-asparaginase (Elspar R) or 25 lidomide, simvastatin, ABT-888, temozolomide, erlotinib, PEG-L-asparaginase (pegaspargase or Oncaspar R), Etopo lapatinib, Sunitinib, FTS, AZD6244, BEZ235, and cele side (VP-16), Teniposide (VumonR), 6-mercaptopurine coxib. In one embodiment, an active compound or Mer TKI (6-MP or PurinetholR), Methotrexate, Cyclophosphamide as described herein is used in combination with gefitinib. (Cytoxan R), Prednisone, Dexamethasone (Decadron), ima In one embodiment, a FLT3 or dual MER/FLT3 inhibitor tinib (GleevecR), dasatinib (Sprycel(R), nilotinib (Ta 30 described herein is used in combination with a chemothera signaR), bosutinib (BosulifR), and ponatinib (IclusigTM). peutic agent for the treatment of AML. Such agents may Examples of additional suitable chemotherapeutic agents include, but are not limited to, cytarabine (ara-C), anthra include but are not limited to 1-dehydrotestosterone, 5-fluo cycline drugs including but not limited to, daunorubicin, rouracil decarbazine, 6-mercaptopurine, 6-thioguanine, idarubicin; cladribine, fludarabine, Gleevec R (imatinib), actinomycin D, adriamycin, aldesleukin, alkylating agents, 35 Sprycel(R) (dasatinib), adriamycin, arsenic trioxide, ceru allopurinol Sodium, altretamine, amifostine, anastroZole, bidine, clafen, cyclophosphamide, cytarabine, daunorubicin, anthramycin (AMC)), anti-mitotic agents, cis-dichlorodi doxorubicin, Vincristine, and topotecan. Some of the other amine platinum (II) (DDP) cisplatin), diamino dichloro chemo drugs that may be used to treat AML include: platinum, anthracyclines, antibiotics, antimetabolites, etoposide (VP-16), 6-thioguanine (6-TG), hydroxyurea (Hy asparaginase, BCG live (intravesical), betamethasone 40 dreaR), Corticosteroid drugs, such as prednisone or dexam Sodium phosphate and betamethasone acetate, bicalutamide, ethasone (Decadron(R), methotrexate (MTX), 6-mercap bleomycin Sulfate, buSulfan, calcium leucouorin, cali topurine (6-MP), azacitidine (VidazaR), and decitabine cheamicin, capecitabine, carboplatin, lomustine (CCNU), (DacogenR). In one embodiment, a FLT3 or dual MER/ carmustine (BSNU), Chlorambucil, Cisplatin, Cladribine, FLT3 inhibitor described herein is used in combination with Colchicin, conjugated estrogens, Cyclophosphamide, 45 cytarabine. Cyclothosphamide, Cytarabine, Cytarabine, cytochalasin B, In one embodiment, a FLT3 or dual MER/FLT3 inhibitor Cytoxan, Dacarbazine, Dactinomycin, dactinomycin (for described herein is used in combination with an additional merly actinomycin), daunirubicin HCL, daunorucbicin cit FLT3 inhibitor to treat with a host suffering from AML. rate, denileukin diftitox, Dexrazoxane, Dibromomannitol, Additional FLT3 inhibitors for use in combination with the dihydroxy anthracin dione, Docetaxel, dolasetron mesylate, 50 FLT3 or dual MER/FLT3 inhibitors described herein include doxorubicin HCL, dronabinol, E. coli L-asparaginase, lestaurtinib, Sunitinib, Sorafenib, tandutinib, midostaurin, emetine, epoetin-C. Erwinia L-asparaginase, esterified estro crenolanib, dovitinib, ENMD-2076 (Entremed), amuvatinib, gens, estradiol, estramustine phosphate Sodium, ethidium or KW-2449 (Kyowa Hakko Kirin). bromide, ethinyl estradiol, etidronate, etoposide citrororum In one embodiment, a FLT3 or dual MER/FLT3 inhibitor factor, etoposide phosphate, filgrastim, floXuridine, flucon 55 described herein is used in combination with a Ras inhibitor. azole, fludarabine phosphate, fluorouracil, flutamide, folinic Examples of RAS inhibitors include but are not limited to acid, gemcitabine HCL, glucocorticoids, goserelin acetate, Reolysin, FusOn-H2, and siC12D LODER. gramicidin D. granisetron HCL, hydroxyurea, idarubicin In one embodiment, a FLT3 or dual MER/FLT3 inhibitor HCL, ifosfamide, interferon C-2b, irinotecan HCL, letro described herein is used in combination with a Phosphoino Zole, leucovorin calcium, leuprolide acetate, levamisole 60 sitide 3-kinase inhibitor (PI3K inhibitor). PI3K inhibitors HCL, lidocaine, lomustine, maytansinoid, mechlorethamine that may be used in the present invention are well known. HCL, medroxyprogesterone acetate, megestrol acetate, mel Examples of PI3K inhibitors include but are not limited to phalan HCL, mercaptipurine, mesna, methotrexate, methyl Wortmannin, demethoxyviridin, perifosine, idelalisib, Pic testosterone, mithramycin, mitomycin C, mitotane, mitox tilisib, Palomid 529, ZSTK474, PWT33597, CUDC-907, antrone, nilutamide, octreotide acetate, oligomycin A, 65 AEZS-136, PX-866, IPI-145, RP6503, SAR245408 ondansetron HCL, paclitaxel, pamidronate disodium, pen (XL147), duvelisib, GS-9820, GDC-0032 (2-4-2-(2-Iso to statin, pilocarpine HCL, plimycin, polifeprosan 20 with propyl-5-methyl-1,2,4-triazol-3-yl)-5,6-dihydroimidazol, US 9,555,031 B2 63 64 2-d1.4benzoxazepin-9-ylpyrazol-1-yl)-2-methylpro In one embodiment, a FLT3 or dual MER/FLT3 inhibitor panamide), MLN-1117 ((2R)-1-Phenoxy-2-butanyl described herein is used in combination with a modulator of hydrogen (S)-methylphosphonate; or Methyl(oxo) {(2R)- the STAT5 pathway. Compounds which modulate the Janus 1-phenoxy-2-butanyloxyphosphonium)), BYL-719 Kinase 2 (JAK2)—Signal Transducer and Activator of Tran ((2S) N1-4-Methyl-5-2-(2.2.2-trifluoro-1,1-dimethyl ethyl)-4-pyridinyl-2-thiazolyl-1,2-pyrrolidinedicarboxam scription 5 (STAT5) pathway include but are not limited to ide), GSK2126458 (2,4-Difluoro-N-(2-(methyloxy)-5-4- Lestaurtinib, Ruxolitinib, SB1518, CYT387, LY3009 104, (4-pyridzinyl)-6-quinolinyl-3- INC424, LY2784544, BMS-911543, NS-018, and pyridinylbenzenesulfonamide), TGX-221 ((+)-7-Methyl-2- TG 101348. (morpholin-4-yl)-9-(1-phenylaminoethyl)-pyrido 1,2-a- In one embodiment, a FLT3 or dual MER/FLT3 inhibitor pyrimidin-4-one), GSK2636771 (2-Methyl-1-(2-methyl-3- 10 described herein is used in combination with an AKT (trifluoromethyl)benzyl)-6-morpholino-1H-benzod inhibitor, including but not limited to, MK-2206, imidazole-4-carboxylic acid dihydrochloride), KIN-193 GSK690693, Perifosine, (KRX-0401), GDC-0068, Tricirib ((R)-2-((1-(7-methyl-2-morpholino-4-oxo-4H-pyrido 1,2-a ine, AZD5363, Honokiol, PF-0469 1502, and Miltefosine. pyrimidin-9-yl)ethyl)amino)benzoic acid), TGR-1202/ Immunomodulatory Combination Agents. RP5264, GS-9820 ((S)-1-(4-((2-(2-aminopyrimidin-5-yl)-7- 15 Active compounds as described herein used in a dosage methyl-4-mohydroxypropan-1-one), GS-1101 (5-fluoro-3- for direct effect on the diseased cell can be used in combi phenyl-2(S)-1-9H-purin-6-ylamino-propyl)-3H nation with one or more immunotherapy agents for additive quinazolin-4-one), AMG-319, GSK-2269557, SAR245409 or synergistic efficacy against Solid tumors. In one embodi (N-(4-(N-(3-((3,5-dimethoxyphenyl)amino)quinoxalin-2- ment, a tumor associated macrophage MerTK inhibiting yl)sulfamoyl)phenyl)-3-methoxy-4 methylbenzamide), amount of a Mer TKI is used in combination or alternation BAY 80-6946 (2-amino-N-(7-methoxy-8-(3-morpholino with the immunomodulatory agent. In another embodiment, propoxy)-2,3-dihydroimidazo[1,2-cquinaz), AS 252424 (5- a host tumor Survival-signal inhibiting, antiviral or antibac 1-5-(4-Fluoro-2-hydroxy-phenyl)-furan-2-yl)-meth-(Z)- terial amount of a Mer TKI is used in combination or ylidene-thiazolidine-2,4-dione). CZ 24832 (5-(2-amino-8- alternation with the immunomodulatory agent. fluoro-1,2,4-triazolo 1.5-appidin-6-yl)-N-tert butylpyridine-3-sulfonamide), Buparlisib (5-2,6-DiG4 25 Immunomodulators are Small molecules or biologic morpholinyl)-4-pyrimidinyl)-4-(trifluoromethyl)-2- agents that treat a disease by inducing, enhancing or Sup pyridinamine), GDC-0941 (2-(1H-Indazol-4-yl)-6-4- pressing the host's immune system. In the present applica (methylsulfonyl)-1-piperazinylmethyl-4-(4-morpholinyl) tion, one or more immunomodulators are selected that thieno 3.2-dpyrimidine), GDC-0980 ((S)-1-(4-((2-(2- induce or enhance the host’s immune system. Some immu aminopyrimidin-5-yl)-7-methyl-4-morpholinothieno3.2-d 30 nomodulators boost the host’s immune system and others pyrimidin-6 yl)methyppiperazin-1-yl)-2-hydroxypropan-1- help train the host’s immune system to better attack tumor one (also known as RG7422)), SF1126 (8S, 14S,17S)-14 cells. Other immunomodulators target proteins that help (carboxymethyl)-8-(3-guanidinopropyl)-17 cancer grOW. (hydroxymethyl)-3,6,9,12,15-pentaoxo-1-(4-(4-oxo-8- Three general categories of immunotherapies are antibod phenyl-4H-chromen-2-yl)morpholino-4-ium)-2-oxa-7.10, 35 ies, cancer vaccines, and non-specific immunotherapies. 13,16-tetra azaoctadecan-18-oate), PF-05212384 (N-4-4- Antibodies are typically administered as monoclonals, (Dimethylamino)-1-piperidinylcarbonylphenyl)-N'-[4-(4. although that is not required. “Naked monoclonal antibod 6-di-4-morpholinyl-1,3,5-triazin-2-yl)phenylurea), ies' work by attaching to antigens on tumor cells. Some LY3023414, BEZ235 (2-Methyl-2-4-3-methyl-2-oxo-8- antibodies can act as a marker for the body's immune system (quinolin-3-yl)-2,3-dihydro-1H-imidazo 4.5-cquinolin-1- 40 to destroy the tumor cells. Others block signaling agents for ylphenylpropanenitrile), XL-765 (N-(3-(N-(3-(3,5-dime tumor cells. Antibodies can generally be used to bind to any thoxyphenylamino)cquinoxalin-2-yl)sulfamoyl)phenyl)-3- signaling or metabolic agent that directly or indirectly methoxy-4-methylbenzamide), and GSK105.9615 (5-4-(4- facilitates tumor growth. Examples are alemtuzumab (Cam Pyridinyl)-6-quinolinyl)methylene-2,4-thiazolidenedione), path) which binds to CD52 antigen, and trastuzumab (Her PX886 ((3 aR,6E.9S.9aR,10R, 11 aS)-6-bis(prop-2-enyl) 45 ceptin), which binds to the HER2 protein. aminomethylidene-5-hydroxy-9-(methoxymethyl)-9a,11a In another embodiment, an antibody can be used that is dimethyl-1,4,7-trioxo-2.3.3a,9,10,11-hexahydroindeno4. conjugated to another moiety that increases it delivery or 5hisochromen-10-yl)acetate (also known as Sonolisib)). efficacy. For example, the antibody can be connected to a and the structure described in WO2014/071109 having the formula: cytotoxic drug or a radiolabel. Conjugated antibodies are 50 sometimes referred to as "tagged, labeled or loaded. Radio labeled antibodies have small radioactive particles attached to them. Examples are Zevalin, which is an antibody against Compound 292 CD20 used to treatlymphoma. Chemolabeled antibodies are C O antibodies that have cytotoxic agents attached to them. 55 Examples are Adcetris, which targets CD30, and Kadcyla, N which targets HER2. Ontak, while not an antibody, is similar in that it is interleukin-2 attached to a toxin from diphtheria. 21 Another category of immunotherapy that can be used in the present invention is a cancer Vaccine. Most cancer sh 60 vaccines are prepared from tumor cells, parts of tumor cells or pure antigens. The vaccine can be used with an adjuvant to help boost the immune response. An example is Provenge, N21 N which is the first cancer vaccine approved by the US FDA. y The vaccine can for example be a dendritic cell vaccine or sus 65 a vector-based vaccine Nonspecific tumor immunotherapies and adjuvants include compounds that stimulate the immune system to do US 9,555,031 B2 65 66 a better job at attacking the tumor cells. Such immunothera from UNC2025A, UNC2142A and UNC2371A, including a pies include cytokines, interleukins, interferons (C. primarily pharmaceutically acceptable composition, salt, isotopic ana but can be also for Y). Specific agents include granulocyte log or prodrug thereof. macrophage colony-stimulating factor (GM-CSF), IL-12, In one embodiment, the treatment of blood clot formation IL-7, IL-21, drugs that target CTLA-4 (such as Yervoy, is in, for example, a Subject with coronary artery disease, which is Ipilimumab) and drugs that target PD-1 or PDL-1 peripheral vascular disease, or cerebrovascular disease, or (such as for example, nivolumab (BMS), pembrolizumab the treatment is given prior to any medical or Surgical (Merck), pidilizumab (CureTech/Teva), AMP-244 (Am procedure in which diminished coagulation potential is plimmune/GSK), BMS-936559 (BMS), and MEDI4736 desirable. Coronary artery disease includes, for example, (Roche/Genentech)). 10 any coronary dysfunction (pathological state) resulting from Other drugs that boost the immune system are thalido coronary artherosclerosis, i.e. partial or total occlusion of mide, lenalidomide, pomalidomide, the Bacille Calmette coronary vessels. The term also includes a range of various Gurin bacteria and Imiquimod. Additional therapeutic acute and chronical pathological states comprising stable agents that can be used in combination with the MerTK and unstable angina pectoris (SAP and UAP respectively), inhibitor include bispecific antibodies, chimeric antigen 15 left ventricular dysfunction LVD, (congestive) heart failure receptor (CAR) T-cell therapy and tumor-infiltrating lym CHF, myocardial death. Peripheral vascular disease phocytes. includes, for example, occlusive or functional peripheral In one aspect of the present invention, a compound arterial disease (PAD). Examples of occlusive PAD include described herein can be combined with at least one immu peripheral arterial occlusion, which may be acute, and nosuppressive agent. The immunosuppressive agent is pref Buerger's disease (thomboangiitis obliterans). Examples of erably selected from the group consisting of a calcineurin functional PAD include Raynaud's disease, Raynaud's phe inhibitor, e.g. a cyclosporin or an ascomycin, e.g. nomenon, and acrocyanosis. Cerebrovascular disease Cyclosporin A (NEORAL(R), FK506 (tacrolimus), pime includes, for example, any abnormality of the brain resulting crolimus, a mTOR inhibitor, e.g. rapamycin or a derivative from a pathologic process of a blood vessel. In one embodi thereof, e.g. Sirolimus (RAPAMUNE(R), Everolimus (Cer 25 ment, the cerebrovascular disease is selected from cerebral tican(R), temsirolimus, Zotarolimus, biolimus-7, biolimus-9, ischemia, cerebral hemorrhage, ischemic stroke, hemor a rapalog, e.g. ridaforolimus, azathioprine, campath 1H, a rhagic stroke, or ischemic reperfusion injury resulting from S1P receptor modulator, e.g. fingolimod or an analogue reintroduction of blood flow following cerebral ischemia or thereof, an anti IL-8 antibody, mycophenolic acid or a salt ischemic stroke. In one non-limiting embodiment, the medi thereof, e.g. sodium salt, or a prodrug thereof, e.g. Myco 30 cal or Surgical procedure is pulmonary vein ablation. phenolate Mofetil (CELLCEPTR), OKT3 (ORTHOCLONE In one embodiment, the treatment of blood clot formation OKT3(R), Prednisone, ATGAMR, THYMOGLOBULINR, is in a host having thrombi in blood vessels from pathologies Brequinar Sodium, OKT4, T10B9.A-3A, 33B3.1, 15-deox or treatments including, for example, myocardial infarction, yspergualin, tresperimus, Leflunomide ARAVAR, CTLAI unstable angina, atrial fibrillation, stroke, renal damage, Ig, anti-CD25, anti-IL2R, Basiliximab (SIMULECTR), 35 percutaneous translumenal coronary angioplasty, athreoscle Daclizumab (ZENAPAX(R), mizorbine, methotrexate, dex rosis, disseminated intravascular coagulation, sepsis, endo amethasone, ISAtX-247, SDZ ASM 981 (pimecrolimus, toxemia (i.e., the presence of endotoxins in the blood), Elidel(R). CTLA41 g (Abatacept), belatacept, LFA31g, etan pulmonary embolism and deep vein thrombosis. In one ercept (sold as Enbrel(R) by Immunex), adalimumab (Hu embodiment, the compounds described herein are adminis miraR), infliximab (Remicade(R), an anti-LFA-1 antibody, 40 tered to a host having blood clots on the surfaces of artificial natalizumab (Antegren(R), Enlimomab, gavilimomab, anti organs, shunts and prostheses (for example, artificial heart thymocyte immunoglobulin, Siplizumab, Alefacept efali valves that are implanted into a patient), and in patients that Zumab, pentasa, mesalazine, asacol, codeine phosphate, have received an intracoronary stent. In one embodiment, a benorylate, fenbufen, naprosyn, diclofenac, etodolac and host is administered an effective amount of a compound indomethacin, aspirin and ibuprofen. 45 described herein due to the formation of clots resulting from Some pathological conditions (for example, genetic mutation 7. ANTI-PLATELET AGENTS of VWF cleaving protease, ADAMT13), which may cause spontaneous binding of VWF to platelets resulting in for In another embodiment, a compound described herein is mation of microthrombi in blood vessels leading to throm used in the treatment of blot clot (thrombus) formation in a 50 botic thrombocytopenic purpura and other microangiopathy. host in need thereof. In one embodiment, the host is suffer Microangiopathy is a disease of blood vessels in which the ing from coronary artery disease, peripheral vascular dis walls of very small blood vessels (capillaries) become so ease, or cerebrovascular disease. In one embodiment, a thick and weak that they bleed, leak protein, and slow the compound described herein is administered to a host prior to flow of blood. In one embodiment, the treatment is in a any medical or Surgical procedure in which diminished 55 patient with hemolytic uremic syndrome. coagulation potential is desirable. In one embodiment, an In one embodiment, an active compound disclosed herein active compound disclosed herein is administered in com is administered in combination with an additional anti bination with another anti-thrombotic or anti-clotting agent. platelet agent. Examples of anti-platelet agents include, but In one embodiment, a compound of Formula I. Formula are not limited to, aspirin, tirofiban (Aggrastat), Aggrenox, IA, Formula IB, Formula II, Formula IIA, or Formula IIB, 60 Agrylin, triflusal (Disgren), Flolan, eptifibatide (Integrilin), or another compound, as described herein, is provided for dipyridamole (Presantine), cilostazol (Pletal), abciximab use in treating blot clot (thrombus) formation in a Subject in (ReoPro), and Terutroban. In one embodiment, a compound need thereof, comprising administering an active compound selected from UNC2025A, UNC2142A and UNC237A1 is as described herein, or a pharmaceutically acceptable com administered in combination with an additional anti-platelet position, salt, isotopic analog, or prodrug thereof. In one 65 agent. In one embodiment, the Mer TKI and the additional embodiment, the compound for use in treating blot clot anti-platelet agent act synergistically. In one embodiment, (thrombus) formation in a subject in need thereof is selected the use of a Mer TKI in combination with an additional US 9,555,031 B2 67 68 anti-platelet agent provides for increased anti-thrombotic or crystalline alpha form can be created and preserved. By anti-clotting effects without an increase in the standard of doing this, the SLN carrier has a built in trigger mechanism care dosage. as lipids transform from the alpha to beta form and conse In one embodiment, the additional anti-platelet agent is an quently control drug release. Drug release profiles can be adenosine diphosphate (ADP) receptor inhibitor. Examples 5 modified according to the composition of the lipid matrix, of ADP receptor inhibitors include, but are not limited to, Surfactant concentration and production parameters. See, clopidogrel (Plavix), prasugrel (Effient), ticagrelor (Bril Muller, R. H., et al., Solid lipid nanoparticles (SLN) for inta), ticlopidine (Ticlid), N6-methyl-T-deoxyadenosine-3', controlled drug delivery—a review of the state of the art, 5'-bisphosphate (MRS2179; PY1 inhibitor), and 2-methyl Eur. H. Pharm. Biopharm., 50:161-177, 2000. Consien et al. thioadenosine 5'-monophosphate triethylammonium salt 10 have recently disclosed lipid nanoparticles having novel (2-Me-SAMP: PY12 inhibitor). amino-lipids that form lipid nanoparticles and their use for In one embodiment, an active compound disclosed herein the intracellular delivery of biologically active compounds, is administered in combination with multiple anti-platelet e.g., nucleic acids. See, U.S. Pat. No. 8,691,750 to Consien agents. In one non-limiting embodiment, an active com et al. pound disclosed herein is administered in combination with 15 N6-methyl-2'-deoxyadenosine-3',5'-bisphosphate and In regard to controlled release, Kanwar has recently 2-methylthioadenosine 5'-monophosphate triethylammo disclosed alginate adsorbed chitosan adsorbed lactoferrin nium salt. adsorbed calcium phosphate nanoparticles and the con In one embodiment, an active compound disclosed herein trolled release of lactoferrin from the nanoparticles. See, is administered in combination with an anti-coagulant. In WO 2012/145801 to Kanwar. In addition, Armes et al. have one embodiment, the anti-coagulant is a heparin composi recently disclosed polymer-templated core-shell nanopar tion. In one embodiment, the heparin composition is a low ticles adapted to facilitate controlled release of at least one molecular weight heparin composition. Low molecular active agent into a system in response to controlled changes weight heparin compositions are well known to those of skill in the pH of the system. See, U.S. Pat. No. 8,580,311 to in the art and include, but are not limited to, tinzaparin, 25 Armes, S. et al. incorporated by reference herein. certoparin, pamaparin, nadroparin, ardeparin, enoxaparin, Petros and DeSimone have recently reviewed strategies in reviparin, dalteparin, and fraxiparin. Additional examples of the design of nanoparticles. In addition, the authors anti-coagulants include, but are not limited to, warfarin reviewed their PRINT (particle replication in non-wetting (Coumadin), Fragmin, Hep-Lock, Lovenox, and Miradon. In templates) technology for generating microparticles and one embodiment, a compound selected from UNC2025A, 30 nanoparticles. See, Petros, R. A. and DeSimone, J. M., UNC2142A and UNC2371A is administered in combination Strategies in the design of nanoparticles for therapeutic with an anti-coagulant. applications, Nature Reviews/Drug Discovery, vol. 9:615 627, 2010. Importantly, the authors disclosed the production 8. NANOPARTICLE COMPOSITIONS OR of nanoparticles in which a single parameter (shape or size) CARRIERS 35 can be altered independently of all other particle attributes. The authors concluded their paper by outlining several In one aspect of the present invention, an effective amount particle characteristics that have emerged as being central to of an active compound as described herein is incorporated the function of engineered nanoparticles. These parameters into nanoparticles, e.g. for convenience of delivery and/or include particle size, particle shape, Surface characteristics extended release delivery. The use of materials in nanoscale 40 and the ability to release therapeutics. Additional nanopar provides one the ability to modify fundamental physical ticle fabrication methods can also be found in U.S. Pat. No. properties such as solubility, diffusivity, blood circulation 8,465,775, U.S. Pat. No. 8,444,899, U.S. Pat. No. 8,420,124, half-life, drug release characteristics, and immunogenicity. U.S. Pat. No. 8,263,129, U.S. Pat. Nos. 8,158,728 and In the last two decades, a number of nanoparticle-based 8.268,446 all hereby incorporated by reference. therapeutic and diagnostic agents have been developed for 45 Nanoparticles may be prepared using a wide variety of the treatment of cancer, diabetes, pain, asthma, allergy, and methods known in the art. For example, nanoparticles can be infections. These nanoscale agents can provide more effec formed by methods as nanoprecipitation, flow focusing tive and/or more convenient routes of administration, lower fluidic channels, spray drying, single and double emulsion therapeutic toxicity, extend the product life cycle, and ulti Solvent evaporation, Solvent extraction, phase separation, mately reduce health-care costs. As therapeutic delivery 50 milling, microemulsion procedures, microfabrication, nano systems, nanoparticles allow targeted delivery and con fabrication, sacrificial layers, simple and complex coacer trolled release. vation, and other methods well known to those of ordinary In addition, nanoparticle-based drug delivery can be used skill in the art. Alternatively or additionally, aqueous and to release drugs at a Sustained rate and thus lower the organic solvent syntheses for monodisperse semiconductor, frequency of administration, deliver drugs in a target manner 55 conductive, magnetic, organic, and other nanomaterials have to minimize systemic side effects, or deliver two or more been described (Pellegrino et al., 2005, Small, 1:48; Murray drugs simultaneously for combination therapy to generate a et al., 2000, Ann. Rev. Mat. Sci., 30:545; and Trindade et al., synergistic effect and Suppress drug resistance. To date, a 2001, Chem. Mat. 13:3843). Additional methods have been number of nanotechnology-based therapeutic products have described in the literature (see, e.g., Doubrow, Ed., “Micro been approved for clinical use. Among these products, 60 capsules and Nanoparticles in Medicine and Pharmacy.” liposomal drugs and polymer-based conjugates account for CRC Press, Boca Raton, 1992; Mathiowitz et al., 1987, J. more than 80% of the products. See, Zhang, L., et al., Control. Release, 5:13; Mathiowitz et al., 1987, Reactive Nanoparticles in Medicine: Therapeutic Applications and Polymers, 6:275; and Mathiowitz et al., 1988, J. Appl. Developments, Clin. Pharm. and Ther. 83(5):761-769, Polymer Sci., 35:755; U.S. Pat. Nos. 5,578,325 and 6,007, 2008. 65 845; P. Paolicelli et al., “Surface-modified PLGA-based Optimal solid lipid nanoparticles (SLN) can be produced Nanoparticles that can Efficiently Associate and Deliver in a controlled fashion when a fraction of lipid in the Virus-like Particles' Nanomedicine. 5(6):843-853 (2010)). US 9,555,031 B2 69 70 In some embodiments, the compounds described herein diacylglycerol; diacylglycerolsuccinate; diphosphatidyl are associated with a nanoparticle. Such as a polymeric glycerol (DPPG); hexanedecanol; fatty alcohols such as nanoparticle. Nanoparticles may comprise natural polymers, polyethylene glycol (PEG); polyoxyethylene-9-lauryl ether; including but not limited to chitosan, alginate, dextran, a surface active fatty acid, Such as palmitic acid or oleic acid; gelatin, and albumin, and synthetic polymers such as, but not fatty acids; fatty acid monoglycerides; fatty acid diglycer limited to, poly(lactide-co-glycolide) (PLGA), (3-hydroxy ides; fatty acid amides; sorbitan trioleate (Span R85) glyco butyrate-co-3-hydroxyvalerate) (PHBV), poly(sebacic cholate; sorbitan monolaurate (SpanR20); polysorbate 20 anhydride), poly(s-caprolactone), polystyrene, thermo (Tween R.20): polysorbate 60 (Tween R60); polysorbate 65 responsive (i.e., NIPA Am and CMCTS-g-PDEA) and pH (Tween R65); polysorbate 80 (Tween R80); polysorbate 85 10 (Tween R.85); polyoxyethylene monostearate; surfactin; a responsive (i.e., Eudragit L100, Eudragit S and AQOAT poloXomer, a Sorbitan fatty acid ester Such as Sorbitan AS-MG) polymers. trioleate; lecithin; lysolecithin; phosphatidylserine; phos In one embodiment, the polymeric particle is between phatidylinositol; sphingomyelin; phosphatidylethanolamine about 0.1 nm to about 10000 nm, between about 1 nm to (cephalin); cardiolipin; phosphatidic acid; cerebro sides; about 1000 nm, between about 10 nm and 1000 nm, between dicetylphosphate: dipalmitoylphosphatidylglycerol; about 100 nm and 800 nm, between about 400 nm and 600 15 Stearylamine; dodecylamine; hexadecyl-amine; acetyl nm, or about 500 nm. In one embodiment, the micro palmitate; glycerol ricinoleate; hexadecyl sterate; isopropyl particles are about 0.1 nm, 0.5 nm, 1.0 nm, 5.0 nm, 10 nm, myristate; tyloxapol; poly(ethylene glycol).5000-phosphati 25 nm, 50 nm, 75 nm, 100 nm, 150 nm, 200 nm, 250 nm, dylethanolamine; poly(ethylene glycol)400-monostearate; 300 nm, 400 nm, 450 nm, 500 nm, 550 nm, 600 nm, 650 nm, phospholipids; synthetic and/or natural detergents having 700 nm, 750 nm, 800 nm, 850 nm, 900 nm, 950 nm, 1000 high Surfactant properties; deoxycholates; cyclodextrins; nm, 1250 nm, 1500 nm, 1750 nm, or 2000 nm. In one chaotropic salts; ion pairing agents; and combinations embodiment, the compounds described herein are covalently thereof. An amphiphilic entity component may be a mixture coupled to a polystyrene particle, PLGA particle, PLA of different amphiphilic entities. Those skilled in the art will particle, or other nanoparticle. recognize that this is an exemplary, not comprehensive, list In some embodiments, the nanoparticle can be solid or 25 of Substances with Surfactant activity. Any amphiphilic hollow and can comprise one or more layers. In some entity may be used in the production of nanoparticles to be embodiments, each layer has a unique composition and used in accordance with the present invention. unique properties relative to the other layer(s). To give but In Some embodiments, a nanoparticle may optionally one example, the nanoparticle may have a core/shell struc comprise one or more carbohydrates. Carbohydrates may be ture, wherein the core is one layer (e.g. a polymeric core) 30 natural or synthetic. A carbohydrate may be a derivatized and the shell is a second layer (e.g. a lipid bilayer or natural carbohydrate. In certain embodiments, a carbohy monolayer). In some embodiments, the nanoparticle may drate comprises monosaccharide or disaccharide, including comprise a plurality of different layers. In some embodi but not limited to glucose, fructose, galactose, ribose, lac ments, the compounds described herein can be incorporated tose, Sucrose, maltose, trehalose, cellbiose, mannose, Xylose, into or Surrounded by one or more layers. arabinose, glucoronic acid, galactoronic acid, mannuronic In some embodiments, the nanoparticles comprising the 35 acid, glucosamine, galatosamine, and neuramic acid. In compounds described herein may optionally comprise one certain embodiments, a carbohydrate is a polysaccharide, or more lipids. In some embodiments, a nanoparticle may including but not limited to pullulan, cellulose, microcrys comprise a liposome. In some embodiments, a nanoparticle talline cellulose, hydroxypropyl methylcellulose (HPMC), may comprise a lipid bilayer. In some embodiments, a hydroxycellulose (HC), methylcellulose (MC), dextran, nanoparticle may comprise a lipid monolayer. In some 40 cyclodextran, glycogen, hydroxyethylstarch, carageenan, embodiments, a nanoparticle may comprise a micelle. In glycon, amylose, chitosan, N.O-carboxylmethylchitosan, Some embodiments, a nanoparticle may comprise a core algin and alginic acid, starch, chitin, inulin, konjac, glucom comprising a polymeric matrix Surrounded by a lipid layer mannan, pustulan, heparin, hyaluronic acid, curdlan, and (e.g., lipid bilayer, lipid monolayer, etc.). In some embodi Xanthan. In some embodiments, the nanoparticle does not ments, a nanoparticle may comprise a non-polymeric core 45 comprise (or specifically exclude) carbohydrates, such as a (e.g., metal particle, quantum dot, ceramic particle, bone polysaccharide. In certain embodiments, the carbohydrate particle, viral particle, proteins, nucleic acids, carbohy may comprise a carbohydrate derivative such as a Sugar drates, etc.) Surrounded by a lipid layer (e.g., lipid bilayer, alcohol, including but not limited to mannitol, Sorbitol, lipid monolayer, etc.). xylitol, erythritol, maltitol, and lactitol. In other embodiments, the nanoparticle may comprise 50 In some embodiments, the associated nanoparticle can metal particles, quantum dots, ceramic particles, etc. In comprise one or more polymers. In some embodiments, the Some embodiments, a non-polymeric nanoparticle is an nanoparticle comprises one or more polymers that are a aggregate of non-polymeric components, such as an aggre non-methoxy-terminated, pluronic polymer. In some gate of metal atoms (e.g., gold atoms). embodiments, at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, In some embodiments, nanoparticles may optionally com 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, prise one or more amphiphilic entities. In some embodi 55 70%, 75%, 80%, 85%, 90%. 95%, 97%, or 99% (weight/ ments, an amphiphilic entity can promote the production of weight) of the polymers that make up the nanoparticles are nanoparticles with increased Stability, improved uniformity, non-methoxy-terminated, pluronic polymers. In some or increased viscosity. In some embodiments, amphiphilic embodiments, all of the polymers that make up the nano entities can be associated with the interior surface of a lipid particle are non-methoxy-terminated, pluronic polymers. In membrane (e.g., lipid bilayer, lipid monolayer, etc.). Many 60 Some embodiments, the nanoparticle comprises one or more amphiphilic entities known in the art are suitable for use in polymers that are a non-methoxy-terminated polymer. In making nanoparticles useful in the present invention. Such some embodiments, at least 1%, 2%, 3%, 4%, 5%, 10%, amphiphilic entities include, but are not limited to, phos 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, phoglycerides; phosphatidylcholines; dipalmitoyl phospha 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% tidylcholine (DPPC); dioleylphosphatidyl ethanolamine 65 (weight/weight) of the polymers that make up the nanopar (DOPE); dioleyloxypropyltriethylammonium (DOTMA); ticles are non-methoxy-terminated polymers. In some dioleoylphosphatidylcholine; cholesterol: cholesterol ester; embodiments, all of the polymers that make up the nano US 9,555,031 B2 71 72 particle are non-methoxy-terminated polymers. In some include, for example, acrylic acid and methacrylic acid embodiments, the nanoparticle comprises one or more poly copolymers, methyl methacrylate copolymers, ethoxyethyl mers that do not comprise pluronic polymer. In some methacrylates, cyanoethyl methacrylate, aminoalkyl meth embodiments, at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, acrylate copolymer, poly(acrylic acid), poly(methacrylic 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, acid), methacrylic acid alkylamide copolymer, poly(methyl 70%, 75%, 80%, 85%, 90%. 95%, 97%, or 99% (weight/ methacrylate), poly(methacrylic acid anhydride), methyl weight) of the polymers that make up the nanoparticle do not methacrylate, polymethacrylate, poly(methyl methacrylate) comprise pluronic polymer. In some embodiments, all of the copolymer, polyacrylamide, aminoalkyl methacrylate copo polymers that make up the nanoparticles do not comprise lymer, glycidyl methacrylate copolymers, polycyanoacry pluronic polymer. In some embodiments, such a polymer 10 lates, and combinations comprising one or more of the can be surrounded by a coating layer (e.g., liposome, lipid foregoing polymers. The acrylic polymer may comprise monolayer, micelle, etc.). In some embodiments, various fully-polymerized copolymers of acrylic and methacrylic elements of the nanoparticle can be coupled with the poly acid esters with a low content of quaternary ammonium C. groups. Other examples of polymers include, but are not limited In some embodiments, polymers can be cationic poly to polyethylenes, polycarbonates (e.g. poly(1,3-dioxan 15 mers. In general, cationic polymers are able to condense Zone)), polyanhydrides (e.g. poly(sebacic anhydride)), poly and/or protect negatively charged strands of nucleic acids propylfumerates, polyamides (e.g. polycaprolactam), poly (e.g. DNA, or derivatives thereof). Amine-containing poly acetals, polyethers, polyesters (e.g., polylactide, mers such as poly(lysine) (Zauner et al., 1998, Adv. Drug polyglycolide, polylactide-co-glycolide, polycaprolactone, Del. Rev. 30:97; and Kabanov et al., 1995, Bioconjugate polyhydroxyacid (e.g. poly(3-hydroxyalkanoate))), poly Chem. 6:7), poly(ethylene imine) (PEI; Boussif et al., 1995, (orthoesters), polycyanoacrylates, polyvinyl alcohols, poly Proc. Natl. Acad. Sci., USA, 1995, 92:7297), and poly urethanes, polyphosphaZenes, polyacrylates, polymethacry (amidoamine) dendrimers (Kukowska-Latallo et al., 1996, lates, polyureas, polystyrenes, and polyamines, polylysine, Proc. Natl. Acad. Sci., USA, 93:4897; Tang et al., 1996, polylysine-PEG copolymers, and poly(ethyleneimine), poly Bioconjugate Chem., 7.703; and Haensler et al., 1993, (ethylene imine)-PEG copolymers. 25 Bioconjugate Chem., 4:372) are positively-charged at physi In some embodiments, nanoparticles include polymers ological pH, form ion pairs with nucleic acids, and mediate which have been approved for use in humans by the U.S. transfection in a variety of cell lines. In embodiments, the Food and Drug Administration (FDA) under 21 C.F.R. nanoparticles may not comprise (or may exclude) cationic S177.2600, including but not limited to polyesters (e.g., polymers. polylactic acid, poly(lactic-co-glycolic acid), polycaprolac 30 In some embodiments, polymers can be degradable poly tone, polyvalerolactone, poly(1,3-dioxan-2One)); polyanhy esters bearing cationic side chains (Putnam et al., 1999, drides (e.g., poly(sebacic anhydride)), polyethers (e.g., poly Macromolecules, 32:3658: Barrera et al., 1993, J. Am. ethylene glycol); polyurethanes; polymethacrylates; Chem. Soc., 115:11010; Kwon et al., 1989, Macromol polyacrylates; and polycyanoacrylates. ecules, 22:3250; Lim et al., 1999, J. Am. Chem. Soc., In some embodiments, polymers can be hydrophilic. For 121:5633; and Zhou et al., 1990, Macromolecules, 23:3399). example, polymers may comprise anionic groups (e.g., 35 Examples of these polyesters include poly(L-lactide-co-L- phosphate group, Sulphate group, carboxylate group); cat lysine) (Barrera et al., 1993, J. Am. Chem. Soc., 115:11010), ionic groups (e.g., quaternary amine group); or polar groups poly(serine ester) (Zhou et al., 1990, Macromolecules, (e.g., hydroxyl group, thiol group, amine group). In some 23:3399), poly(4-hydroxy-L-proline ester) (Putnam et al., embodiments, a nanoparticles comprising a hydrophilic 1999, Macromolecules, 32:3658; and Lim et al., 1999, J. polymeric matrix generates a hydrophilic environment 40 Am. Chem. Soc., 121:5633), and poly(4-hydroxy-L-proline within the nanoparticle. In some embodiments, polymers ester) (Putnam et al., 1999, Macromolecules, 32:3658; and can be hydrophobic. In some embodiments, a nanoparticles Lim et al., 1999, J. Am. Chem. Soc., 121:5633). comprising a hydrophobic polymeric matrix generates a The properties of these and other polymers and methods hydrophobic environment within the nanoparticle. Selection for preparing them are well known in the art (see, for of the hydrophilicity or hydrophobicity of the polymer may 45 example, U.S. Pat. Nos. 6,123,727; 5,804,178; 5,770,417: have an impact on the nature of materials that are incorpo 5,736,372; 5,716.404; 6,095,148; 5,837,752; 5,902,599; rated (e.g., coupled) within the nanoparticle. 5,696,175: 5,514,378; 5,512,600: 5,399.665; 5,019,379; In some embodiments, polymers may be modified with 5,010,167; 4.806,621; 4,638.045; and 4.946,929; Wang et one or more moieties and/or functional groups. A variety of al., 2001, J. Am. Chem. Soc., 123:9480; Lim et al., 2001, J. moieties or functional groups can be used in accordance 50 Am. Chem. Soc., 123:2460; Langer, 2000. Acc. Chem. Res., with the present invention. In some embodiments, polymers 33:94: Langer, 1999, J. Control. Release, 62:7; and Uhrich may be modified with polyethylene glycol (PEG), with a et al., 1999, Chem. Rev.,99:3181). More generally, a variety carbohydrate, and/or with acyclic polyacetals derived from of methods for synthesizing certain Suitable polymers are polysaccharides (Papisov, 2001, ACS Symposium Series, described in Concise Encyclopedia of Polymer Science and 786:301). Certain embodiments may be made using the Polymeric Amines and Ammonium Salts, Ed. by Goethals, general teachings of U.S. Pat. No. 5,543,158 to Gref et al., 55 Pergamon Press, 1980; Principles of Polymerization by or WO publication WO2009/051837 by Von Andrian et al. Odian, John Wiley & Sons, Fourth Edition, 2004; Contem In some embodiments, polymers may be modified with a porary Polymer Chemistry by Allcock et al., Prentice-Hall, lipid or fatty acid group. In some embodiments, a fatty acid 1981: Deming et al., 1997, Nature, 390:386; and in U.S. Pat. group may be one or more of butyric, caproic, caprylic, Nos. 6,506,577, 6,632,922, 6,686,446, and 6,818,732. capric, lauric, myristic, palmitic, Stearic, arachidic, behenic, 60 Polymers can be linear or branched polymers. In some or lignoceric acid. In some embodiments, a fatty acid group embodiments, polymers can be dendrimers. In some may be one or more of palmitoleic, oleic. Vaccenic, linoleic, embodiments, polymers can be substantially cross-linked to alpha-linoleic, gamma-linoleic, arachidonic, gadoleic, one another. In some embodiments, polymers can be Sub arachidonic, eicosapentaenoic, docosahexaenoic, or erucic stantially free of cross-links. In some embodiments, poly acid. 65 mers can be used without undergoing a cross-linking step. It In some embodiments, polymers may be one or more is further to be understood that a nanoparticle may comprise acrylic polymers. In certain embodiments, acrylic polymers block copolymers, graft copolymers, blends, mixtures, and/ US 9,555,031 B2 73 74 or adducts of any of the foregoing and other polymers. Those In regard to polymers used for the production of nano skilled in the art will recognize that the polymers listed particles, several reviews are available. See, for example, herein represent an exemplary, not comprehensive, list of Soppimath, K. S., et al., Biodegradable polymeric nanopar polymers that can be of use in accordance with the present ticles as drug delivery devices, J. Controlled Release, 70: 1 invention. 20, 2001, Agnihotri, S. A., et al., Recent advances on The compounds of the present invention can be coupled chitosan-based micro- and nanoparticle delivery, J. Con to a nanoparticle by any of a number of methods. Generally, trolled Release, 100(1):5-28, 2004, Ganta, S, et al. A review the coupling can be a result of bonding between the com of stimuli-responsive nanocarriers for drug and gene deliv pound and the nanoparticle. This bonding can result in the ery, J. Controlled Release, 126(3):187-204, 2008, Danhier, compound being attached to the Surface of the nanoparticle 10 F. et al., PLGA-based nanoparticles: An overview of bio and/or contained within (encapsulated) the nanoparticle. In medical applications, J. Controlled Release, 161(2):505 522, 2012, Some embodiments, however, the compounds are encapsu In one embodiment, nanoparticles are comprised of lated by the nanoparticle as a result of the structure of the L-glutamic acid copolymers and a compound described nanoparticle rather than bonding to the nanoparticle. In herein. In another embodiment, nanoparticles are comprised Some embodiments, the nanoparticle comprises a polymeras 15 provided herein, and the compounds described herein are of L-alanine copolymers and a compound described herein. coupled to the nanoparticle. The compounds described In one embodiment, nanoparticles are comprised of L-lysine herein may be encapsulated into nanoparticles as desirable copolymers and a compound described herein. In another using a variety of methods including but not limited to C. embodiment, nanoparticles are comprised of L-tyrosine Astete et al., “Synthesis and characterization of PLGA copolymers and a compound described herein. In other nanoparticles' J. Biomater. Sci. Polymer Edn, Vol. 17, No. embodiment, nanoparticles are comprised of poly(lactic-co 3, pp. 247-289 (2006); K. Avgoustakis “Pegylated Poly glycolic acid) and a compound described herein. In another (Lactide) and Poly(Lactide-Co-Glycolide) Nanoparticles: embodiment, nanoparticles are comprised of methoxy-PEG Preparation, Properties and Possible Applications in Drug poly(D.L-lactide) and a compound described herein. In Delivery” Current Drug Delivery 1:321-333 (2004); C. Reis another embodiment, nanoparticles are comprised of HPMA et al., “Nanoencapsulation I. Methods for preparation of 25 copolymer and a compound described herein. In one drug-loaded polymeric nanoparticles' Nanomedicine 2:8-21 embodiment, nanoparticles are comprised of polycyclodex tran and a compound described herein. In one embodiment, (2006); P. Paolicelli et al., “Surface-modified PLGA-based nanoparticles are comprised of polyglutamate and a com Nanoparticles that can Efficiently Associate and Deliver pound described herein. In another embodiment, nanopar Virus-like Particles' Nanomedicine. 5(6):843-853 (2010). ticles are comprised of poly(iso-hexyl-cyanoacrylate) and a Other methods suitable for encapsulating the compounds 30 described herein may be used, including without limitation compound described herein. In one embodiment, nanopar methods disclosed in U.S. Pat. No. 6,632,671 to Unger Oct. ticles are comprised of poly-L-lysine and a compound 14, 2003. described herein. In another embodiment, nanoparticles are In certain embodiments, nanoparticles are prepared by a comprised of PEG and a compound described herein. In one nanoprecipitation process or spray drying. Conditions used embodiment, nanoparticles are made of combinations of in preparing nanoparticles may be altered to yield particles 35 polymers and a compound described herein. of a desired size or property (e.g., hydrophobicity, hydro In one embodiment, a compounds described herein is philicity, external morphology, 'stickiness,” shape, etc.). released from a nanoparticle over a period of between about The method of preparing the nanoparticles and the condi 1 and about 90 days. In one embodiment, the compound is tions (e.g., Solvent, temperature, concentration, air flow rate, released over a period of about 3 to 28 days. In one etc.) used may depend on the materials to be coupled to the 40 embodiment, the compound is released over a period of nanoparticles and/or the composition of the polymer matrix. about 5 to 21 days. If particles prepared by any of the above methods have a size EXAMPLES range outside of the desired range, particles can be sized, for The present invention is explained in greater detail in the example, using a sieve. following non-limiting Examples. In one embodiment of the present invention, PRINT 45 technology is used to manufacture nanoparticles comprising Example 1 a compound described herein. Syntheses of Active Compounds In another embodiment, provided herein are liposome based nanoparticles comprising a compound described General Schemes herein. In another embodiment, a liposome based nanopar 50 Scheme 1 illustrates a general procedure for preparing a ticle comprises a compound described hereinformulated for compound of the present invention. Structure 1-1 can be controlled-release. prepared by alkylating a desired 7H-pyrrolo2,3-dipyrimi In one embodiment, provided herein are polymer based dine with a desired R-LGs, LG, is a leaving group, com nanoparticles comprising a compound described herein. In pound according to methods known in the art. The R moiety another embodiment, provided herein are polymer based can be protected and deprotected by one skilled in the art to nanoparticles comprising a compound described herein for 55 generate compounds of Formula I. See, for example, mulated for controlled-release. Greene, T. W. and Wuts, P. G. M., Protective Groups in In one embodiment, nanoparticles are comprised of albu Organic Synthesis, 2" Ed., New York, John Wiley and Sons, min and a compound described herein. In another embodi Inc., 1991. For example, Structure 1-1 can be prepared by ment, nanoparticles are comprised of a polysaccharide and treating a desired 7H-pyrrolo2,3-dipyrimidine with a a compound described herein. In one embodiment, nano 60 desired alkyl halide, for example, tert-butyl trans-4-(iodom particles are comprised of a metal and a compound ethyl)cyclohexylcarbamate in the presence of a base, for described herein. In another embodiment, nanoparticles are example, potassium carbonate in the presence of organic comprised of gold and a compound described herein. In solvent(s), for example dimethyl sulfoxide and tetrahydro another embodiment, nanoparticles are comprised of iron furan optionally in a microwave apparatus optionally at an oxide and a compound described herein. In one embodi 65 elevated temperature. In one embodiment, X" is nitrogen and ment, nanoparticles are comprised of silicon and a com X is C. In one embodiment, LG is a leaving group. In one pound described herein. embodiment, LG is chloride. In one embodiment, LG is a US 9,555,031 B2 75 76 leaving group. In one embodiment, LG is bromide. Struc Scheme 2 illustrates a general procedure for preparing a ture 1-2 can be prepared by aminating a desired 7H-pyrrolo compound of the present invention. Structure 2-1 can be 2,3-dipyrimidine, Structure 1-1, with a desired amine in an prepared by alkylating a desired 7H-pyrrolo2,3-dipyrimi organic solvent(s), for example, dimethyl sulfoxide and dine with a desired R'-LGs, LG, is a leaving group, tetrahydrofuran, in the presence of a base, for example, compound according to methods known in the art. The R' potassium carbonate optionally at an elevated temperature in 5 moiety can be protected and deprotected by one skilled in a sealed tube. Structure 1-3 can be prepared by treating a the art to generate compounds of Formula II. See, for desired 7H-pyrrolo[2,3-dipyrimidine with a desired R'-LG example, Greene, T. W. and Wuts, P. G. M., Protective compound according to methods known in the art. For Groups in Organic Synthesis, 2" Ed., New York, John Wiley example, Structure 1-3 can be prepared by treating Structure and Sons, Inc., 1991. For example, Structure 2-1 can be 1-2 with a desired boronic acid, an organometallic reagent, 10 prepared by treating a desired 7H-pyrrolo2,3-dipyrimidine a base and a mixture of Solvents optionally in a microwave with a desired alkyl halide, for example, tert-butyl trans-4- apparatus optionally at an elevated temperature of about (iodomethyl)cyclohexylcarbamate in the presence of a base, 120° C. In one embodiment, the boronic acid is 4-fluoro for example, potassium carbonate in the presence of organic phenylboronic acid. In one embodiment, the organometallic solvent(s), for example dimethyl sulfoxide and tetrahydro reagent is tetrakis(triphenylphosphine)palladium. In one 15 furan optionally in a microwave apparatus optionally at an embodiment, the base is potassium carbonate. In one elevated temperature. In one embodiment, X" is nitrogen and embodiment, the mixture of solvents comprises dioxane and X is C. In one embodiment, LG is a leaving group. In one water. A compound of Formula I can be prepared by treating embodiment, LG is chloride. In one embodiment, LG is a Structure 1-3 with an acid and an organic solvent. In one leaving group. In one embodiment, LG is bromide. Struc embodiment, the acid is trifluoroacetic acid. In one embodi ture 2-2 can be prepared by aminating a desired 7H-pyrrolo ment, the organic solvent is dichloromethane. This chemis 2,3-dipyrimidine, Structure 2-1, with a desired amine in an try is illustrated in Scheme 1. organic solvent(s), for example, dimethyl sulfoxide and tetrahydrofuran, in the presence of a base, for example, Scheme 1 potassium carbonate optionally at an elevated temperature in R4 a sealed tube. Structure 2-3 can be prepared by treating a LG2 25 desired 7H-pyrrolo[2,3-dipyrimidine with a desired R'- M R-LG LG compound according to methods known in the art. For N N X - - example, Structure 2-3 can be prepared by treating Structure 2-2 with a desired boronic acid, an organometallic reagent, us 2 X-Ri Step 1 LG1 N X a base and a mixture of Solvents optionally in a microwave R4 30 apparatus optionally at an elevated temperature of about LG2 120° C. In one embodiment, the boronic acid is 4-fluoro M phenylboronic acid. In one embodiment, the organometallic N1S-X reagent is tetrakis(triphenylphosphine)palladium. In one /w R5 --Step 2 embodiment, the base is potassium carbonate. In one 2 i embodiment, the mixture of solvents comprises dioxane and LG N X 35 water. A compound of Formula II can be prepared by R2 treating Structure 2-3 with an acid and an organic solvent. In 1-1 one embodiment, the acid is trifluoroacetic acid. In one R4 embodiment, the organic solvent is dichloromethane. This LG2 chemistry is illustrated in Scheme 2. M 40 N1S-X R-LG4 l /} R Step 3 Scheme 2 2 i R 3 N XM R 14 R2 45 J.G. 1-2 N1S-X R2-LG l 2 R15 Step 1 4 2 i R R1 LG N X M 50 R 14 LG2 N1S-X W R5 Hops M us / Step 4 N1S-X } -e- R3 4. XV l / R15 Step 2 55 LG 4. XV R12 2-1 R 14 R4 RI LG2 / M N1S-X 60 N1N X R-LG l 2 Xy-R 5 /W R 15 HerStep 3 R3 N X R13 4. X V V R2 R12 65 Formula I 2-2 US 9,555,031 B2 77 78 -continued -continued R4 R 14 R11 LG2 / M

N1S-X -e- N1S-X X 15 Step 4 /w R5 HeStep 2 l 2 / R 2 i R 13 N XV LG N X R12 R2 2 3 10 R4 3-1 R 14 R11 LG2 M / N1S-X R-LG4 N1S-X w R5 -- X R 15 l / Step 3 R3 4. X R 13 N XV 15 V R12 R2 Formula II R-2 R / Scheme 3 illustrates a general procedure for preparing a N1S-X compound of the present invention. Structure 3-1 can be /W R5 --Step 4 prepared by alkylating a desired 7H-pyrrolo2,3-dipyrimi R3 4. X dine with a desired R-LGs compound according to methods V known in the art. The R moiety can be protected and R2 deprotected by one skilled in the art to generate compounds 25 3-3 R4 RI of Formula I. See, for example, Greene, T. W. and Wuts, P. G. M., Protective Groups in Organic Synthesis, 2" 2 Ed., / New York, John Wiley and Sons, Inc., 1991. For example, N1S-X Structure 3-1 can be prepared by treating a desired 7H-pyr 2 i rolo2,3-dipyrimidine with a desired alcohol, for example, 30 3 X2 cis-4-(tert-butyldimethylsilyloxy)cyclohexanol in the pres R N V ence of a phosphorane, for example, (cyanomethylene) R2 trimethylphosphorane in the presence of organic solvent(s), Formula I for example toluene and tetrahydrofuran. In one embodi ment, X" is nitrogen and X is C. In one embodiment, LG is Scheme 4 illustrates a general procedure for preparing a a leaving group. In one embodiment, LG is chloride. In one 35 compound of the present invention. Structure 4-1 can be embodiment, LG is a leaving group. In one embodiment, prepared by alkylating a desired 7H-pyrrolo2,3-dipyrimi LG is bromide. Structure 3-2 can be prepared by aminating dine with a desired R'-LGs, LG, is a leaving group, a desired 7H-pyrrolo2,3-dipyrimidine, Structure 3-1, with a compound according to methods known in the art. The R' desired amine in an organic solvent, for example, 2-propa moiety can be protected and deprotected by one skilled in nol, optionally at an elevated temperature in a microwave 40 the art to generate compounds of Formula II. See, for example, Greene, T. W. and Wuts, P. G. M., Protective apparatus. Structure 3-3 can be prepared by treating a Groups in Organic Synthesis, 2" Ed., New York, John Wiley desired 7H-pyrrolo[2,3-dipyrimidine with a desired R'-LG and Sons, Inc., 1991. For example, Structure 4-1 can be compound according to methods known in the art. For prepared by treating a desired 7H-pyrrolo2,3-dipyrimidine example, Structure 3-3 can be prepared by treating Structure with a desired alcohol, for example, cis-4-(tert-butyldimeth 3-2 with a desired boronic acid, an organometallic reagent, 45 ylsilyloxy)cyclohexanol in the presence of a phosphorane, a base and a mixture of Solvents optionally in a microwave for example, (cyanomethylene)trimethylphosphorane in the apparatus optionally at an elevated temperature of about presence of organic solvent(s), for example toluene and 150° C. In one embodiment, the boronic acid is (4-fluoro tetrahydrofuran. In one embodiment, X" is nitrogen and X is phenyl)boronic acid. In one embodiment, the organometallic C. In one embodiment, LG is a leaving group. In one reagent is Pd(PPh3)4. In one embodiment, the base is potas 50 embodiment, LG is chloride. In one embodiment, LG is a sium carbonate. In one embodiment, the mixture of Solvents leaving group. In one embodiment, LG is bromide. Struc comprises tetrahydrofuran and water. A compound of For ture 4-2 can be prepared by aminating a desired 7H-pyrrolo mula I can be prepared by treating Structure 3-3 with an acid 2,3-dipyrimidine, Structure 4-1, with a desired amine in an and an organic solvent. In one embodiment, the acid is 1% organic solvent, for example, 2-propanol, optionally at an concentrated hydrochloric acid. In one embodiment, the 55 elevated temperature in a microwave apparatus. Structure organic solvent is methanol. This chemistry is illustrated in 4-3 can be prepared by treating a desired 7H-pyrrolo2,3- Scheme 3. dpyrimidine with a desired R'-LG compound according to methods known in the art. LG is a leaving group. For example, Structure 4-3 can be prepared by treating Structure Scheme 3 60 4-2 with a desired boronic acid, an organometallic reagent, R4 a base and a mixture of Solvents optionally in a microwave LG2 apparatus optionally at an elevated temperature of about X R-LG 150° C. In one embodiment, the boronic acid is (4-fluoro N N w - - phenyl)boronic acid. In one embodiment, the organometallic reagent is Pd(PPh3)4. In one embodiment, the base is potas l 2 X-Ri Step 1 65 sium carbonate. In one embodiment, the mixture of solvents LG1 N X comprises tetrahydrofuran and water. A compound of For mula II can be prepared by treating Structure 4-3 with an US 9,555,031 B2 79 acid and an organic solvent. In one embodiment, the acid is -continued 1% concentrated hydrochloric acid. In one embodiment, the organic solvent is methanol. This chemistry is illustrated in 14 Scheme 4. R R11 / Scheme 4

R 14 l 2 Xi R 15 J.G. R 13 N XV N1,N-X R-LG R2 10 l 2 R 15 Step 1 Formula II 2 i LG1 N X R 14 LG2 M Compounds of Formula I or Formula II can be metabo N1N X, 15 lized to generate pyrrolopyrimidine compounds. In one / R15 Step 2 2 X embodiment, a compound of Formula I or Formula II can be LG N V dealkylated. For example, a compound of Formula I can be R12 dealkylated at R to generate R=NH. In one embodiment, 4-1 a compound of Formula II can be dealkylated. For example, R 14 a compound of Formula II can be dealkylated at R' to LG2 M generate R'—NH2. In one embodiment, a compound of N N X RI-LG Formula I comprising a methylated amine can be demeth w R15 -es / Step 3 25 ylated. In another embodiment, a compound of Formula II comprising a methylated amine can be demethylated. In one R13 4. XM R12 embodiment, a compound of Formula I or Formula II can be oxidized. For example, a compound of Formula I or Formula 4-2 14 II comprising a piperazine group can be oxidized to generate R R11 30 a piperazine N-oxide. In another embodiment, a compound N1 N X of Formula I or Formula II comprising a piperazine group Aw R 15 -e-Step 4 can be oxidized twice to generate a piperazine bis-N-oxide. In another embodiment, a compound of Formula I or For R13 4. X V 35 mula II can be oxidized to generate a pyrrolopyrimidine R12 N-oxide. The metabolic pathways described above are illus 4-3 trated below, in Scheme 5, with the example compound UNC2371A.

Scheme 5

dealkylation

demethylation -e-

UNC2371 o N US 9,555,031 B2 81 82 -continued ON -NN -CH3 -N KCH

2 N N No.

15 Example 2 Tert-Butyl trans-4-((5-bromo-2-(butylamino)-7H pyrrolo2,3-dipyrimidin-7-yl)methyl)cyclohexylcar 7-((Trans-4-aminocyclohexyl)methyl)-N-butyl-5-(4- bamate fluorophenyl)-7H-pyrrolo2,3-dipyrimidin-2-amine Br General Procedure A

I 1) K2CO3 25 BHN CO4. N Br DMSO:THF = 1:2 MW, 80° C., 100 l -- 2) BuNH, MW, ''NHBoc 150° C., 1.5 h C OS4. N 30 A 10 mL microwave tube was charged with 5-bromo-2- NHBoc chloro-7H-pyrrolo2,3-dipyrimidine (0.23 g, 1.0 mmol), Br tert-butyl trans-4-(iodomethyl)cyclohexylcarbamate (0.51 g, 1.5 mmol), KCO (0.28g, 2.0 mmol), DMSO (1.5 mL) and THF (3 mL). The mixture was heated at 150° C. for 100 min (HO)2B O 35 an OSN in microwave. After the reaction mixture was cooled to Pd(PPh3)4, KCO ambient temperature, n-butylamine (0.18 g, 2.5 mmol) was dioxane, H2O added. The mixture was heated at 150° C. for 90 min in O. NHBoc 120° C., 10 min microwave. After cooling to ambient temperature, the reac F tion was poured into water and extracted with EtOAc (3x). 40 The combined organic layer was dried (Na2SO4) and con centrated. The crude mixture was purified by Isco to provide tert-butyl trans-4-((5-bromo-2-(butylamino)-7H-pyrrolo2, 3-dipyrimidin-7-yl)methyl)cyclohexylcarbamate (0.35 g, 73%) as a white solid. MS m/z 480.2 M+H". TFA 45 1S-\ -e- 7-((Trans-4-aminocyclohexyl)methyl)-N-butyl-5-(4- fluorophenyl)-7H-pyrrolo2,3-dipyrimidin-2-amine BHN 1,1-N O NHBoc 50 F

N1 N N N1 N N N 60 BHN --- l 2 N BHN N SO 65 O A 10 mL microwave tube was charged with tert-butyl trans-4-((5-bromo-2-(butylamino)-7H-pyrrolo2,3-dpy