WO2016161282A1 - Heterocyclic compounds as lsd1 inhibitors - Google Patents

Heterocyclic compounds as lsd1 inhibitors Download PDF

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Publication number
WO2016161282A1
WO2016161282A1 PCT/US2016/025550 US2016025550W WO2016161282A1 WO 2016161282 A1 WO2016161282 A1 WO 2016161282A1 US 2016025550 W US2016025550 W US 2016025550W WO 2016161282 A1 WO2016161282 A1 WO 2016161282A1
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Prior art keywords
pyrimidin
imidazo
benzonitrile
alkyl
methoxy
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PCT/US2016/025550
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French (fr)
Inventor
Chunhong He
Zhenwu Li
Liangxing Wu
Wenqing Yao
Fenglei Zhang
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Incyte Corporation
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Priority to EA201792205A priority Critical patent/EA201792205A1/en
Priority to AU2016243939A priority patent/AU2016243939B2/en
Application filed by Incyte Corporation filed Critical Incyte Corporation
Priority to KR1020177031860A priority patent/KR102659373B1/en
Priority to SG11201708047UA priority patent/SG11201708047UA/en
Priority to NZ735998A priority patent/NZ735998A/en
Priority to CA2981661A priority patent/CA2981661C/en
Priority to MX2017012699A priority patent/MX2017012699A/en
Priority to MYPI2017001449A priority patent/MY191796A/en
Priority to ES16726215T priority patent/ES2757948T3/en
Priority to BR112017021114-9A priority patent/BR112017021114B1/en
Priority to JP2017551636A priority patent/JP6995623B2/en
Priority to CN201680021455.9A priority patent/CN107660205B/en
Priority to CR20170500A priority patent/CR20170500A/en
Priority to EP16726215.3A priority patent/EP3277689B1/en
Priority to EP19190014.1A priority patent/EP3626720A1/en
Priority to UAA201710636A priority patent/UA122688C2/en
Publication of WO2016161282A1 publication Critical patent/WO2016161282A1/en
Priority to IL254736A priority patent/IL254736B/en
Priority to PH12017501817A priority patent/PH12017501817A1/en
Priority to ZA2017/06710A priority patent/ZA201706710B/en
Priority to CONC2017/0011216A priority patent/CO2017011216A2/en
Priority to HK18109396.1A priority patent/HK1249905A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
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    • A61P13/00—Drugs for disorders of the urinary system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P15/00—Drugs for genital or sexual disorders; Contraceptives
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/08—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
    • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
    • C07D471/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D519/00—Heterocyclic compounds containing more than one system of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring system not provided for in groups C07D453/00 or C07D455/00

Definitions

  • the present invention is directed to heterocyclic compounds and compostions thereof which are LSD1 inhibitors useful in the treatment of diseases such as cancer.
  • LSD1 lysine specific demethylase-1
  • the N-terminal SWIRM which functions in nucleosome targeting
  • the tower domain which is involved in protein-protein interaction, such as transcriptional co-repressor, co-repressor of RE1-silencing transcription factor (CoREST), and lastly the C terminal catalytic domain whose sequence and structure share homology with the flavin adenine dinucleotide (FAD)-dependent monoamine oxidases (i.e., MAO-A and MAO-B)
  • FAD flavin adenine dinucleotide
  • MAO-A and MAO-B flavin adenine dinucleotide
  • MAO-A and MAO-B flavin adenine dinucleotide
  • MAO-A and MAO-B flavin adenine dinucleotide
  • MAO-A and MAO-B flavin adenine dinucleotide
  • MAO-A and MAO-B flavin adenine dinucleotide
  • LSD1 also shares a fair degree of homology with another lysine specific demethylase (LSD2) (Karytinos, A., et al., A novel mammalian flavin-dependent histone demethylase. J Biol Chem, 2009.284(26): p.17775- 82). Although the biochemical mechanism of action is conserved in two isoforms, the substrate specificities are thought to be distinct with relatively small overlap.
  • LSD2 lysine specific demethylase
  • LSD1 and LSD2 are dependent on the redox process of FAD and the requirement of a protonated nitrogen in the methylated lysine is thought to limit the activity of LSD1/2 to mono- and di-methylated lysines at the position of 4 or 9 of histone 3 (H3K4 or H3K9).
  • Jumonji domain containing family that can demethylate mono-, di-, and tri-methylated lysines through alpha-ketoglutarate dependent reactions (Kooistra, S.M. and K. Helin, Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell Biol, 2012.13(5): p.297-311; Mosammaparast, N. and Y. Shi, Reversal of histone
  • Methylated histone marks on H3K4 and H3K9 are generally coupled with transcriptional activation and repression, respectively.
  • corepressor complexes e.g., CoREST
  • LSD1 has been reported to demethylate H3K4 and repress transcription
  • LSD1 in nuclear hormone receptor complex (e.g., androgen receptor)
  • LSD1 in nuclear hormone receptor complex (e.g., androgen receptor)
  • LSD1 in nuclear hormone receptor complex
  • LSD1 may demethylate H3K9 to activate gene expression
  • Metzger, E., et al. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription.
  • LSD1 may demethylate non-histone proteins. These include p53 (Huang, J., et al., p53 is regulated by the lysine demethylase LSD1.
  • E2F Kontaki, H. and I. Talianidis, Lysine methylation regulates E2F1-induced cell death. Mol Cell, 2010.39(1): p. 152-60
  • STAT3 Yamamoto, J., et al., Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes. Proc Natl Acad Sci U S A, 2010.107(50): p.21499-504
  • Tat Sakane, N., et al., Activation of HIV transcription by the viral Tat protein requires a
  • LSD1 also associates with other epigenetic regulators, such as DNA methyltransferase 1 (DNMT1) (Wang, J., et al., The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat Genet, 2009.41(1): p.125-9) and histone deacetylases (HDACs) complexes (Hakimi, M.A., et al., A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. Proc Natl Acad Sci U S A, 2002.99(11): p.
  • DNMT1 DNA methyltransferase 1
  • HDACs histone deacetylases
  • LSD1 has been reported to contribute to a variety of biological processes, including cell proliferation, epithelial-mesenchymal transition (EMT), and stem cell biology (both embryonic stem cells and cancer stem cells) or self-renewal and cellular transformation of somatic cells (Chen, Y., et al., Lysine-specific histone demethylase 1 (LSD1): A potential molecular target for tumor therapy. Crit Rev Eukaryot Gene Expr, 2012.22(1): p.53-9; Sun, G., et al., Histone demethylase LSD1 regulates neural stem cell proliferation. Mol Cell Biol, 2010.30(8): p.1997-2005; Adamo, A., M.J. Barrero, and J.C.
  • cancer stem cells or cancer initiating cells have some pluripotent stem cell properties that contribute to the heterogeneity of cancer cells. This feature may render cancer cells more resistant to conventional therapies, such as chemotherapy or radiotherapy, and then develop recurrence
  • LSD1 was reported to maintain an undifferentiated tumor initiating or cancer stem cell phenotype in a spectrum of cancers (Zhang, X., et al., Pluripotent Stem Cell Protein Sox2 Confers Sensitivity to LSD1 Inhibition in Cancer Cells.
  • Acute myeloid leukemias are an example of neoplastic cells that retain some of their less differentiated stem cell like phenotype or leukemia stem cell (LSC) potential.
  • LSD1 may regulate a subset of genes involved in multiple oncogenic programs to maintain LSC (Harris, W.J., et al., The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells. Cancer Cell, 2012.21(4): p.473-87; Schenk, T., et al., Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia. Nat Med, 2012.18(4): p.605-11). These findings suggest potential therapeutic benefit of LSD1 inhibitors targeting cancers having stem cell properties, such as AMLs.
  • LSD1 Overexpression of LSD1 is frequently observed in many types of cancers, including bladder cancer, NSCLC, breast carcinomas, ovary cancer, glioma, colorectal cancer, sarcoma including chondrosarcoma, Ewing’s sarcoma, osteosarcoma, and rhabdomyosarcoma, neuroblastoma, prostate cancer, esophageal squamous cell carcinoma, and papillary thyroid carcinoma.
  • studies found over-expression of LSD1 was significantly associated with clinically aggressive cancers, for example, recurrent prostate cancer, NSCLC, glioma, breast, colon cancer, ovary cancer, esophageal squamous cell carcinoma, and neuroblastoma.
  • LSD1 Lysine-specific demethylase 1
  • CD86 expression is a marker of maturation of dendritic cells (DCs) which are involved in antitumor immune response.
  • DCs dendritic cells
  • CD86 functions as a co-stimulatory factor to activate T cell proliferation (Greaves, P. and J.G. Gribben, The role of B7 family molecules in hematologic malignancy. Blood, 2013.121(5): p.734-44; Chen, L. and D.B. Flies, Molecular mechanisms of T cell co-stimulation and co-inhibition. Nat Rev Immunol, 2013.13(4): p.227-42).
  • LSD1 activity has also been associated with viral pathogenesis.
  • LSD1 activity appears to be linked with viral replications and expressions of viral genes.
  • LSD1 functions as a co-activator to induce gene expression from the viral immediate early genes of various type of herpes virus including herpes simplex virus (HSV), varicella zoster virus (VZV), and ⁇ -herpesvirus human
  • HSV herpes simplex virus
  • VZV varicella zoster virus
  • cytomegalovirus Liang, Y., et al., Targeting the JMJD2 histone demethylases to
  • fetal globin gene would be potentially therapeutically beneficial for the disease of ⁇ -globinopathies, including ⁇ -thalassemia and sickle cell disease where the production of normal ⁇ -globin, a component of adult hemoglobin, is impaired (Sankaran, V.G. and S.H. Orkin, The switch from fetal to adult hemoglobin. Cold Spring Harb Perspect Med, 2013. 3(1): p. a011643; Bauer, D.E., S.C. Kamran, and S.H. Orkin, Reawakening fetal hemoglobin: prospects for new therapies for the beta-globin disorders. Blood, 2012.120(15): p.2945-53).
  • LSD1 inhibition may potentiate other clinically used therapies, such as hydroxyurea or azacitidine. These agents may act, at least in part, by increasing ⁇ -globin gene expression through different mechanisms.
  • LSD1 contributes to tumor development by altering epigenetic marks on histones and non-histone proteins. Accumulating data have validated that either genetic depletion or pharmacological intervention of LSD1 normalizes altered gene expressions, thereby inducing differentiation programs into mature cell types, decreasing cell proliferation, and promoting apoptosis in cancer cells. Therefore, LSD1 inhibitors alone or in combination with established therapeutic drugs would be effective to treat the diseases associated with LSD1 activity.
  • the present invention is directed to, inter alia, a compound of Formula I:
  • the present invention is further directed to a pharmaceutical composition
  • a pharmaceutical composition comprising a compound of Formula I and at least one pharmaceutically acceptable carrier.
  • the present invention is further directed to a method of inhibiting LSD1 comprising contacting the LSD1 with a compound of Formula I.
  • the present invention is further directed to a method of modulating LSD1 comprising contacting the LSD1 with a compound of Formula I.
  • the present invention is further directed to a method of mediating LSD1 comprising contacting the LSD1 with a compound of Formula I.
  • the present invention is further directed to a method of modulating LSD1 signaling comprising contacting the LSD1 with a compound of Formula I.
  • the present invention is further directed to a method of treating an LSD1-mediated disease in a patient comprising administering to the patient a therapeutically effective amount of a compound of Formula I.
  • the present invention provides, inter alia, LSD1-inhibiting compounds such as a compound of Formula I:
  • ring A is C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, or 4-10 membered heterocycloalkyl, wherein the 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the C3-10 cycloalkyl or 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group;
  • X is N or CR X , wherein R X is H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C 1-4 haloalkoxy, NHC 1-4 alkyl, N(C 1-4 alkyl) 2 or C 1-4 alkylthio;
  • R U is N or CR U , wherein R U is H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C 1-4 haloalkoxy, NHC 1-4 alkyl, N(C 1-4 alkyl) 2 or C 1-4 alkylthio;
  • Y is N or CR 4 ;
  • Z is N or CR 5 ;
  • L 1 is a bond, -O-, -NR 9 -, -C(O)NH-, -NHC(O)-, C1-4 alkylene; wherein R 9 is H, C1-6 alkyl, -C(O)C 1-6 alkyl or–C(O)OC 1-6 alkyl;
  • L 2 is a bond, -C(O)-, C1-4 alkylene, -O-C1-4 alkylene-, -C1-4 alkylene-O-, -C1-4 alkylene-NR 9 -, or–NR 9 -C 1-4 alkylene-;
  • R 2 is independently selected from H, OH, CN, halo, NH2, C1-4 alkyl, C 1-4 alkoxy, C 1-4 haloalkyl, C 1-4 haloalkoxy, NHC 1-4 alkyl, N(C 1-4 alkyl) 2 , and C 1-4 alkylthio;
  • R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 5- or 6-membered heterocycloalkyl ring, a fused C 3-6 cycloalkyl ring, or a fused 5- or 6-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected R A substituents, wherein a ring carbon of the fused 5- or 6- membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring is optionally replaced by a carbonyl group;
  • R 6 is 5- to 10-membered heteroaryl, 5- to 10-membered heteroaryl-C1-4 alkyl, 4- to 10- membered heterocycloalkyl, or 4- to 10-membered heterocycloalkyl-C 1-4 alkyl, each of which is optionally substituted with 1, 2, 3 or 4 independently selected R A substituents;
  • R 7 and R 8 together with the nitrogen atom to which they are attached form 4- to 10- membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R 7 and R 8 , wherein a ring-forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected R B substituents;
  • each R A is independently selected from H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C 1-6 haloalkyl, C 1-6 haloalkoxy, Cy 2 , C 3-10 cycloalkyl-C 1-4 alkyl, 5-10 membered heteroaryl- C1-4 alkyl, 4-10 membered heterocycloalkyl-C1-4 alkyl, CN, NO2, OR a4 , SR a4 , C(O)R b4 , C(O)NR c4 R d4 , C(O)OR a4 , OC(O)R b4 , OC(O)NR c4 R d4 , NR c4 R d4 , NR c4 C(O)R b4 ,
  • each R B is independently selected from H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C 1-6 haloalkyl, C 1-6 haloalkoxy, Cy 3 , C 3-10 cycloalkyl-C 1-4 alkyl, 5-10 membered heteroaryl- C1-4 alkyl, 4-10 membered heterocycloalkyl-C1-4 alkyl, CN, NO2, OR a5 , SR a5 , C(O)R b5 , C(O)NR c5 R d5 , C(O)OR a5 , OC(O)R b5 , OC(O)NR c5 R d5 , NR c5 R d5 , NR c5 C(O)R b5 ,
  • each Cy 1 , Cy 2 , Cy 3 , and Cy 4 is independently selected from C 6-10 aryl, C 3-10 cycloalkyl, 5-10 membered heteroaryl, and 4-10 membered heterocycloalkyl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R Cy ;
  • each R Cy is independently selected from H, halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, C2-6 alkenyl, C2-6 alkynyl, phenyl, C3-7 cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl, phenyl-C 1-4 alkyl-, C 3-7 cycloalkyl-C 1-4 alkyl-, (5-6 membered heteroaryl)-C1-4 alkyl-, and (4-7 membered heterocycloalkyl)-C1-4 alkyl-, oxo, CN, NO2, OR a4 , SR a4 , C(O)R b4 , C(O)NR c4 R d4 , C(O)OR a4 , OC(O)R b4 , OC(O)NR c4 R d4 ,
  • each R a1 , R b1 , R c1 , and R d1 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C 1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C 1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C 6-10 aryl-C 1-4 alkyl-, C 3-10
  • each R a2 , R b2 , R c2 , and R d2 is independently selected from H, C 1-6 alkyl, C 1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C 6-10 aryl-C 1-4 alkyl-, C 3-10 cycloalkyl-C 1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 6-10 aryl, C 3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3
  • each R a3 , R b3 , R c3 , and R d3 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C 6-10 aryl-C 1-4 alkyl-, C 3-10 cycloalkyl-C 1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 6-10 aryl, C 3-10 cycloalkyl, 5-10 membered
  • heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C 1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C 1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C 1-4 alkyl, C 1-4 haloalkyl, C 1-4 cyanoalkyl, halo, CN, OR a5 , SR a5 , C(O)R b5 , C(O)NR c5 R d5 , C(O)OR a5 , OC(O)R b5 , OC(O)NR c5 R d5 , NR c5 R d5 , NR c5 C(O)R b5 , NR c5 C(O)OR a5 ,
  • each R a4 , R b4 , R c4 , and R d4 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C 2-6 alkenyl, and C 2-6 alkynyl, wherein said C 1-6 alkyl, C 2-6 alkenyl, and C 2-6 alkynyl are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C 1-4 alkyl, C 1-4 haloalkyl, C 1-4 cyanoalkyl, halo, CN, OR a5 , SR a5 , C(O)R b5 , C(O)NR c5 R d5 , C(O)OR a5 , OC(O)R b5 , OC(O)NR c5 R d5 , NR c5 R d5 , NR c5 C(O)R b5 ,
  • R c4 and R d4 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C 1-6 alkyl, C 1-6 haloalkyl, halo, CN, OR a5 , SR a5 , C(O)R b5 , C(O)NR c5 R d5 , C(O)OR a5 , OC(O)R b5 , OC(O)NR c5 R d5 , NR c5 R d5 , NR c5 C(O)R b5 ,
  • each R a5 , R b5 , R c5 , and R d5 is independently selected from H, C1-4 alkyl, C1-4 haloalkyl, C 2-4 alkenyl, and C 2-4 alkynyl, wherein said C 1-4 alkyl, C 2-4 alkenyl, and C 2-4 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from OH, CN, amino, halo, C 1-4 alkyl, C 1-4 alkoxy, C 1-4 alkylthio, C 1-4 alkylamino, di(C 1-4 alkyl)amino, C 1-4 haloalkyl, and C1-4 haloalkoxy;
  • each R e1 , R e2 , R e3 , R e4 , and R e5 is independently selected from H, C 1-4 alkyl, and CN; the subscript m is 1 or 2; and
  • the subscript n is 1, 2, 3 or 4.
  • the compounds of the invention have Formula II:
  • U is CR U .
  • the compounds of the invention have Formula IIIb:
  • U is N.
  • h m n f h in n i n h ve Formula IIIa h m n f h in n i n h ve Formula IIIa:
  • Y is N.
  • Y is CR 4 .
  • Z is N.
  • Z is CR 5 .
  • Y and Z are each CH.
  • U, Y and Z are each N; (ii) U and Z are N and Y is CR 4 ; (iii) U and Y are N and Z is CR 5 ; (iv) U is N, Y is CR 4 , and Z is CR 5 ; (v) U is CR U and both Yand Z are N; (vi) U is CR U , Y is N, and Z is CR 5 ; or (vii) U is CR U , Y is CR 4 , and Z is N.
  • U, Y and Z are each N.
  • U and Z are N and Y is CR 4 .
  • U and Y are N and Z is CR 5 .
  • U is N
  • Y is CR 4
  • Z is CR 5 .
  • U is CR U and both Yand Z are N.
  • U is CR U
  • Y is N
  • Z is CR 5 .
  • U is CR U
  • Y is CR 4
  • Z is N.
  • two of U, Y, and Z are N.
  • one of U, Y, and Z are N.
  • ring A is C6-10 aryl, 5-10 membered heteroaryl, or 4-10 membered heterocycloalkyl, wherein the 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group.
  • ring A is phenyl, 5-6 membered heteroaryl, or 4-7 membered heterocycloalkyl, wherein the 5-6 membered heteroaryl or 4-7 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group.
  • ring A is C6-10 aryl.
  • ring A is phenyl
  • ring A is 5-10 membered heteroaryl. In some embodiments, ring A is 5-6 membered heteroaryl. In some embodiments, ring A is 6 membered heteroaryl. In some embodiments, ring A is 5 membered heteroaryl.
  • ring A is pyridyl, 1H-indazolyl, 1H-pyrrolo[2,3-b]pyridinyl, or 1H-benzo[d]imidazolyl.
  • ring A is pyridyl
  • ring A is 4-10 membered heterocycloalkyl having at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized, and wherein a ring-forming carbon atom is optionally substituted by oxo to form a carbonyl group.
  • ring A is 4-7 membered heterocycloalkyl having at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S optionally oxidized, and wherein a ring-forming carbon atom is optionally substituted by oxo to form a carbonyl group.
  • ring A is 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro- 1,3-benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; 1H-pyrazolo[3,4-b]pyridinyl; 3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin- 7-yl; 2-oxo-2,3-dihydro-1H-benzimidazolyl; 1H-benzimidazolyl; 2-oxo-2,3- dihydro[1,3]oxazolo[4,5-b]pyridinyl, or 2,3-dihydro-1-benzofuranyl.
  • ring A is 2,3-dihydro-1H-indolyl; 2,3-dihydro-1,3- benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3,4-dihydro-2H-1,4-benzoxazinyl; or 2,3-dihydro-1-benzofuran.
  • ring A is 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro- 1,3-benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; or 2,3-dihydro-1-benzofuran.
  • ring A is phenyl; 2,3-dihydro-1,4-benzodioxine; 2,3-dihydro- 1H-pyrrolo[2,3-b]pyridin-5-yl; 5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl; 2-oxo-1,2,3,4- tetrahydroquinolin-7-yl; pyridyl; 2-oxo-2,3-dihydro-1,3-benzoxazolyl; 1,3-benzothiazol-5-yl; 2,3-dihydro-1H-inden-5-yl; 1H-pyrrolo[2,3-b]pyridinyl; 8-quinoxalin-6-yl; 2-oxo-1,2,3,4- tetrahydroquinolin-6-yl; or 1H-pyrazolo[3,4-b]pyridinyl.
  • ring A is phenyl; pyridyl; 1H-indazolyl; 1H-pyrrolo[2,3- b]pyridinyl; 1H-benzo[d]imidazolyl; 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro-1,3- benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; 1H-pyrazolo[3,4-b]pyridinyl; 3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin- 7-yl; 2-oxo-2,3-dihydro-1H-benzimidazolyl; 1H-benzimidazolyl; 2-oxo-2,3- diphenyl;
  • R 3 is independently selected from Cy 2 , C1- 6 alkyl, CN, OR a2 , C(O)NR c2 R d2 , and NR c2 R d2 ; wherein said C 1-6 alkyl is optionally substituted with 1, 2, or 3 substituents independently selected from Cy 2 , C(O)R b2 , and C(O)NR c2 R d2 .
  • R 3 is, at each occurrence, CN, methyl, methoxy, 1- pyrrolidinyl, 2-oxo-1-pyrrolidinyl, -C(O)N(CH 3 ) 2 , dimethylamino, 4- methylpiperazinylmethyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl,
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 5- or 6-membered heterocycloalkyl ring, a fused C 3-6 cycloalkyl ring, or a fused 5- or 6-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected R A substituents; wherein a ring
  • carbon of the fused 5- or 6-membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring is optionally replaced by a carbonyl group;
  • two R A substituents attached to the same carbon of the fused 5- or 6-membered heterocycloalkyl or fused C3-6 cycloalkyl taken together form a cyclopropyl group.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused ring selected from 1-methylpyrrolidine, 4- methyl-3-oxo-morpholine, 1-methylimidazole, 1-methylpiperidine, 1-methyl-2- oxopyrrolidine, and 1-methylpyrazole, each of which is optionally substituted with 1 or 2 R A substituents.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused ring selected from pyrrolidine, 3-oxo- morpholine, imidazole, piperidine, 2-oxopyrrolidine, and pyrazole, each of which is optionally substituted with 1 or 2 R A substituents.
  • R 3 is C1-6 alkyl, halo, C1-6 hydroxyalkyl, C1-6 haloalkyl, CN, OR a2 , 1-pyrrolidinyl, 2-oxo-1-pyrrolidinyl, NR c2 C(O)OR a2 , -( C 1-6 alkyl)-NR c2 C(O)OR a2 , C(O)NR c2 R d2 , NR c2 R d2 , piperazinylmethyl, 4-methylpiperazinylmethyl, piperidinyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl, morpholinylmethyl, or 3-cyano-1- pyrrolidinyl.
  • R 3 is C 1-6 alkyl, CN, OR a2 , 1-pyrrolidinyl, 2-oxo-1- pyrrolidinyl, C(O)NR c2 R d2 , NR c2 R d2 , piperazinylmethyl, 4-methylpiperazinylmethyl, piperidinyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl, morpholinylmethyl or 3- cyano-1-pyrrolidinyl.
  • R 3 is CN, F, hydroxymethyl, (CH 3 O)C(O)N(CH 3 )-,
  • R 3 is, at each occurrence, CN, F, hydroxymethyl
  • R 3 is CN, F, hydroxymethyl, (CH3O)C(O)N(CH3)-,
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form fused 5- or 6-membered heterocycloalkyl, fused C 3-6 cycloalkyl or fused 5- or 6-membered heteroaryl, each of which is optionally substituted with 1-2 independently selected R A substituents, wherein a ring carbon of the fused 5- or 6- membered heterocycloalkyl or fused C3-6 cycloalkyl is optionally replaced by a carbonyl group.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form fused 5- or 6-membered heterocycloalkyl, which is optionally substituted with 1-2 independently selected R A substituents, wherein a ring carbon of the fused 5- or 6-membered heterocycloalkyl is optionally replaced by a carbonyl group.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-1H-pyrrolyl; 2-oxo-2,3-dihydro- 1H-pyrrolyl; 2,3-dihydro-oxazolyl; 2-oxo-2,3-dihydro-oxazolyl; 3,4-dihydro-2H-1,4- oxazinyl; 3-oxo-3,4-dihydro-2H-1,4-oxazinyl; or 2,3-dihydro-furanyl group, each of which is optionally substituted with 1-2 independently selected R A substituents.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-1H-pyrrolyl group, which is optionally substituted with one R A substituent.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a 2-oxo-2,3-dihydro-1H-pyrrolyl group, which is optionally substituted with one R A substituent.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-oxazolyl group, which is optionally substituted with one R A substituent.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 2-oxo-2,3-dihydro-oxazolyl group, which is optionally substituted with one R A substituent.
  • two adjacent R 3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-furanyl group, which is optionally substituted with one R A substituent.
  • R A is C1-4 alkyl.
  • R A is methyl
  • R A is -C(O)NR c4 R d4 , wherein R c4 and R d4 are each, independently selected from H and C 1-4 alkyl.
  • R A is -C(O)N(CH3)2.
  • R 1 is -L 1 -R 6 or–L 2 -NR 7 R 8 .
  • R 1 is–L 2 -NR 7 R 8 , wherein L 2 is a bond, -C(O)-, C1-4 alkylene, - O-C1-4 alkylene, -C1-4 alkylene-O-, C1-4 alkylene-NH- or–NH-C1-4 alkylene.
  • L 2 is a -O-C 1-4 alkylene.
  • R 7 and R 8 together with the nitrogen atom to which they are attached form 4- to 6-membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R 7 and R 8 , wherein a ring- forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected R B substituents.
  • R 1 is -L 1 -R 6 .
  • L 1 is -O-.
  • R 6 is 5- to 10-membered heteroaryl-C1-4 alkyl or 4- to 10- membered heterocycloalkyl-C 1-4 alkyl, each of which is optionally substituted with 1, 2, 3 or 4 independently selected R A substituents.
  • R 6 is 4- to 10-membered heterocycloalkyl-C 1-4 alkyl which is optionally substituted with 1, 2, 3 or 4 independently selected R A substituents.
  • R 6 is pyrrolidinyl-C 1-4 alkyl- which is optionally substituted with 1, 2 or 3 independently selected R A substituents. In some embodiments, R 6 is pyrrolidinyl-methylene- which is optionally substituted with 1, 2 or 3 independently selected R A substituents.
  • R 6 is piperidinyl-C1-4 alkyl- which is optionally substituted with 1, 2 or 3 independently selected R A substituents. In some embodiments, R 6 is
  • piperidinyl- methylene- which is optionally substituted with 1, 2 or 3 independently selected R A substituents.
  • R 1 is OR a1 .
  • R 1 is OR a1 , wherein R a1 is C 1-6 alkyl substituted with Cy 4 . In some embodiments, R 1 is OR a1 , wherein R a1 is methylene substituted with Cy 4 . In some embodiments, R 1 is OR a1 , wherein R a1 is methylene substituted with 4-10 membered heterocycloalkyl optionally substituted with 1, 2, 3, or 4 substituents
  • R 1 is OR a1 , wherein R a1 is methylene substituted with 4-7 membered heterocycloalkyl optionally substituted with 1, 2, 3, or 4 substituents
  • Cy 4 is pyrrolidinyl or piperidinyl optionally substituted with 1 or 2 substituents independently selected from R Cy .
  • R 1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3- yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, (2-hydroxyethylpiperidin-3-yl)methoxy, (2-methoxyethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, 7-methyl-2,7-diazaspiro[4.4]non-2-yl, or (1-methylpyrrolidin- 3-yl)methoxy.
  • R 1 is (1-methylpiperidin-3-yl)methoxy or (1-methylpyrrolidin- 3-yl)methoxy.
  • R 1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3- yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, (2-hydroxypropylpiperidin-3-yl)methoxy, or 2-hydroxy-2- methylpropyl)piperidin-3-yl]methoxy.
  • R 1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3- yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, (2-hydroxyethylpiperidin-3-yl)methoxy, (2-methoxyethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, 7-methyl-2,7-diazaspiro[4.4]non-2-yl, (1-methylpyrrolidin-3- yl)methoxy, or 2-hydroxy-2-methylpropyl)piperidin-3-yl]methoxy.
  • R 2 is H.
  • R 4 is H.
  • R 5 is H.
  • R U is H.
  • R X is H.
  • m is 1.
  • n 1
  • the compounds of the invention have Formula IVa, IVb, IVc, IVd, IVe, or IVf:
  • the compounds provided herein have Formula IVg, IVh, or IVi:
  • the compounds of the invention have Formula IVa.
  • the compounds of the invention have Formula IVb.
  • the compounds of the invention have Formula IVc.
  • the compounds of the invention have Formula IVd.
  • the compounds of the invention have Formula IVe.
  • the compounds of the invention have Formula IVf.
  • the compounds of the invention have Formula IVg.
  • the compounds of the invention have Formula IVh.
  • the compounds of the invention have Formula IVi.
  • X 1 is CH or N.
  • R 3 substituents taken together with the carbon atoms to which they are attached form a fused 5-membered heterocycloalkyl ring or a fused 5-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected R A substituents, wherein a ring carbon of the fused 5-membered heterocycloalkyl ring is optionally replaced by a carbonyl group;
  • X 1 is N or CH
  • L 2 is a bond or O-C 1-4 alkylene
  • R 7 and R 8 together with the nitrogen atom to which they are attached form 4- to 7- membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R 7 and R 8 , wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected R B substituents.
  • X 1 is CH. In other aspects of these embodiments X 1 is N. In some aspects of these embodiments, L 2 is a bond, -C(O)-, C 1-4 alkylene, -O-C1-4 alkylene-, -C1-4 alkylene-O-, -C1-4 alkylene-NR 9 -, or–NR 9 -C1-4 alkylene-.
  • two R 3 substituents taken together with the carbon atoms to which they are attached form a fused 5-membered heterocycloalkyl ring or a fused 5- membered heteroaryl, each of which is optionally substituted with 1 or 2 independently selected R A substituents, wherein a ring carbon of the fused 5-membered heterocycloalkyl ring is optionally replaced by a carbonyl group.
  • R A is C 1-4 alkyl such as methyl.
  • the fused 5-membered heterocycloalkyl ring or fused 5-membered heteroaryl has 1 or 2 heteroatoms as ring members selected from O, N or S.
  • R 7 and R 8 together with the nitrogen atom to which they are attached form 4- to 7-membered heterocycloalkyl ring having 0, 1 or 2 additional heteroatoms selected from N and S as ring members, wherein a ring-forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and
  • heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected R B substituents.
  • R B is C 1-4 alkyl such as methyl.
  • L 2 is a bond. In another embodiment of compounds of Formula V, L 2 is -O-C 1-4 alkylene-. In yet another embodiment of compounds of Formula V, L 2 is -OCH2-.
  • R 3 substituents taken together with the carbon atoms to which they are attached form a fused pyrazole ring optionally substituted with 1 or 2 R A substituents.
  • R A is C1-4 alkyl such as methyl.
  • R 3 substituents taken together with the carbon atoms to which they are attached form a fused 2-oxo-oxazolidine ring, which is optionally substituted with 1 or 2 R B substitutents.
  • R B is C1-4 alkyl such as methyl.
  • moiety Formula V is 1-methyl-1H- pyrazolo[3,4-b]pyridin-5-yl, 1-methyl-1H-indazol-5-yl, 3-methyl-2-oxo-3,4-dihydro-2H-1,3- benzoxazin-7-yl; 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl; 3-methyl-2-oxo- 2,3-dihydro-1,3-benzoxazol-6-yl; 5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl; 4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl; 2-(difluoromethyl)-1-methyl-1H- benzimidazol-5-yl; 1,2-dimethyl-1H-benzimidazol-5-yl, 6-methoxypyri
  • the compounds of the invention have Formula VIa, VIb, or VIc:
  • the compounds of the invention have Formula VIa.
  • the compounds of the invention have Formula VIb.
  • the compounds of the invention have Formula VIc.
  • the phrase "optionally substituted” means unsubstituted or substituted.
  • substituted means that a hydrogen atom is removed and replaced by a monovalent substituent, or two hydrogen atoms are replaced with a divalent substituent like a terminal oxo group. It is to be understood that substitution at a given atom is limited by valency.
  • C i-j indicates a range which includes the endpoints, wherein i and j are integers and indicate the number of carbons. Examples include C 1-4 , C 1-6 , and the like.
  • z-membered typically describes the number of ring-forming atoms in a moiety where the number of ring-forming atoms is z.
  • piperidinyl is an example of a 6-membered heterocycloalkyl ring
  • pyrazolyl is an example of a 5-membered heteroaryl ring
  • pyridyl is an example of a 6-membered heteroaryl ring
  • 1, 2, 3, 4-tetrahydro-naphthalene is an example of a 10-membered cycloalkyl group.
  • C i-j alkyl refers to a saturated hydrocarbon group that may be straight-chain or branched, having i to j carbons.
  • the alkyl group contains from 1 to 6 carbon atoms or from 1 to 4 carbon atoms, or from 1 to 3 carbon atoms.
  • alkyl moieties include, but are not limited to, chemical groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, s- butyl, and t-butyl.
  • Ci-j alkylene employed alone or in combination with other terms, means a saturated divalent linking hydrocarbon group that may be straight-chain or
  • the alkylene group contains from 1 to 4 carbon atoms, from 1 to 3 carbon atoms, or from 1 to 2 carbon atoms.
  • alkylene moieties include, but are not limited to, chemical groups such as methylene, ethylene, 1,1- ethylene, 1,2-ethylene , 1,3-propylene, 1,2-propylene, 1,1-propylene, isopropylene, and the like.
  • C i-j alkoxy employed alone or in combination with other terms, refers to a group of formula -O-alkyl, wherein the alkyl group has i to j carbons.
  • Example alkoxy groups include methoxy, ethoxy, and propoxy (e.g., n-propoxy and isopropoxy).
  • the alkyl group has 1 to 3 carbon atoms.
  • C i-j alkenyl refers to an unsaturated hydrocarbon group having one or more double carbon-carbon bonds and having i to j carbons.
  • the alkenyl moiety contains 2 to 6 or 2 to 4 carbon atoms.
  • Example alkenyl groups include, but are not limited to, ethenyl, n-propenyl, isopropenyl, n-butenyl, sec-butenyl, and the like.
  • C i-j alkynyl refers to an unsaturated hydrocarbon group having one or more triple carbon-carbon bonds and having i to j carbons.
  • Example alkynyl groups include, but are not limited to, ethynyl, propyn-1-yl, propyn-2-yl, and the like.
  • the alkynyl moiety contains 2 to 6 or 2 to 4 carbon atoms.
  • Ci-j alkylamino employed alone or in combination with other terms, refers to a group of formula -NH(alkyl), wherein the alkyl group has i to j carbon atoms. In some embodiments, the alkyl group has 1 to 6 or 1 to 4 carbon atoms. In some embodiments, the alkylamino group is–NH(C 1-4 alkyl) such as, for example, methylamino, ethylamino, or propylamino.
  • di-C i-j -alkylamino refers to a group of formula -N(alkyl)2, wherein each of the two alkyl groups has, independently, i to j carbon atoms. In some embodiments, each alkyl group independently has 1 to 6 or 1 to 4 carbon atoms. In some embodiments, the dialkylamino group is–N(C1-4 alkyl) 2 such as, for example, dimethylamino or diethylamino.
  • Ci-j alkylthio employed alone or in combination with other terms, refers to a group of formula -S-alkyl, wherein the alkyl group has i to j carbon atoms. In some embodiments, the alkyl group has 1 to 6 or 1 to 4 carbon atoms. In some
  • the alkylthio group is C1-4 alkylthio such as, for example, methylthio or ethylthio.
  • amino employed alone or in combination with other terms, refers to a group of formula–NH 2 .
  • aryl refers to a monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic hydrocarbon, such as, but not limited to, phenyl, 1-naphthyl, 2-naphthyl, anthracenyl, phenanthrenyl, and the like.
  • aryl is C 6-10 aryl.
  • the aryl group is a naphthalene ring or phenyl ring.
  • the aryl group is phenyl.
  • aryl-C i-j alkyl employed alone or in combination with other terms, refers to an alkyl group substituted by an aryl group.
  • An example of an aryl-Ci-j alkyl group is benzyl.
  • carbonyl employed alone or in combination with other terms, refers to a -C(O)- group.
  • Cycloalkyl refers to a non-aromatic cyclic hydrocarbon moiety having i to j ring-forming carbon atoms, which may optionally contain one or more alkenylene groups as part of the ring structure.
  • Cycloalkyl groups can include mono- or polycyclic (e.g., having 2, 3 or 4 fused rings) ring systems.
  • cycloalkyl moieties that have one or more aromatic rings fused (i.e., having a bond in common with) to the cycloalkyl ring, for example, benzo derivatives of cyclopentane, cyclopentene, cyclohexane, and the like.
  • a cycloalkyl group that includes a fused aromatic ring can be attached to the core or scaffold via any ring-forming atom, including a ring-forming atom of the fused aromatic group.
  • One or more ring-forming carbon atoms of a cycloalkyl group can be oxidized to form carbonyl linkages.
  • cycloalkyl is C 3-10 cycloalkyl, C 3-7 cycloalkyl, or C 5-6 cycloalkyl.
  • exemplary cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclopentenyl, cyclohexenyl, cyclohexadienyl, cycloheptatrienyl, norbornyl, norpinyl, norcarnyl, and the like.
  • Further exemplary cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
  • Ci-j cycloalkyl-Ci-j alkyl refers to an alkyl group substituted by a cycloalkyl group.
  • An example of a Ci-j cycloalkyl-Ci-j alkyl group is cyclopropylmethyl.
  • Ci-j haloalkoxy employed alone or in combination with other terms, refers to a group of formula–O-haloalkyl having i to j carbon atoms.
  • An example haloalkoxy group is OCF3.
  • An additional example haloalkoxy group is OCHF2.
  • the haloalkoxy group is fluorinated only.
  • the alkyl group has 1 to 6 or 1 to 4 carbon atoms.
  • the haloalkoxy group is C 1-4 haloalkoxy.
  • halo refers to a halogen atom selected from F, Cl, I or Br. In some embodiments, "halo" refers to a halogen atom selected from F, Cl, or Br. In some embodiments, the halo substituent is F.
  • C i-j haloalkyl refers to an alkyl group having from one halogen atom to 2s+1 halogen atoms which may be the same or different, where "s" is the number of carbon atoms in the alkyl group, wherein the alkyl group has i to j carbon atoms.
  • the haloalkyl group is fluorinated only.
  • the haloalkyl group is fluoromethyl, difluoromethyl, or trifluoromethyl.
  • the haloalkyl group is trifluoromethyl.
  • the alkyl group has 1 to 6 or 1 to 4 carbon atoms.
  • heteroaryl refers to a monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic heterocylic moiety, having one or more heteroatom ring members selected from nitrogen, sulfur and oxygen.
  • the heteroaryl group has 1, 2, 3, or 4 heteroatom ring members.
  • the heteroaryl group has 1, 2, or 3 heteroatom ring members.
  • the heteroaryl group has 1 or 2 heteroatom ring members.
  • the heteroaryl group has 1 heteroatom ring member.
  • the heteroaryl group is 5- to 10-membered or 5- to 6-membered.
  • the heteroaryl group is 5-membered. In some embodiments, the heteroaryl group is 6-membered. When the heteroaryl group contains more than one heteroatom ring member, the heteroatoms may be the same or different. The nitrogen atoms in the ring(s) of the heteroaryl group can be oxidized to form N-oxides.
  • Examplary heteroaryl groups include, but are not limited to, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, pyrrolyl, pyrazolyl, azolyl, oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, imidazolyl, furanyl, thiophenyl, triazolyl, tetrazolyl, thiadiazolyl, quinolinyl, isoquinolinyl, indolyl,
  • the heteroaryl group is pyridyl, 1H-indazolyl, 1H- pyrrolo[2,3-b]pyridinyl, or 1H-benzo[d]imidazolyl.
  • a 5-membered heteroaryl is a heteroaryl group having five ring-forming atoms comprising wherein one or more of the ring-forming atoms are independently selected from N, O, and S.
  • the 5-membered heteroaryl group has 1, 2, 3, or 4 heteroatom ring members.
  • the 5-membered heteroaryl group has 1, 2,
  • the 5-membered heteroaryl group has 1 or 2 heteroatom ring members. In some embodiments, the 5-membered heteroaryl group has 1 heteroatom ring member.
  • Example ring-forming members include CH, N, NH, O, and S.
  • Example five-membered ring heteroaryls are thienyl, furyl, pyrrolyl, imidazolyl, thiazolyl, oxazolyl, pyrazolyl, isothiazolyl, isoxazolyl, 1, 2, 3-triazolyl, tetrazolyl, 1, 2, 3-thiadiazolyl, 1, 2, 3-oxadiazolyl, 1, 2, 4-triazolyl, 1, 2, 4-thiadiazolyl, 1, 2, 4-oxadiazolyl, 1, 3, 4-triazolyl, 1, 3, 4-thiadiazolyl, and 1, 3, 4-oxadiazolyl.
  • a 6-membered heteroaryl is a heteroaryl group having six ring-forming atoms wherein one or more of the ring-forming atoms is N. In some embodiments, the 6-membered heteroaryl group has 1, 2, or 3 heteroatom ring members. In some embodiments, the 6- membered heteroaryl group has 1 or 2 heteroatom ring members. In some embodiments, the 6-membered heteroaryl group has 1 heteroatom ring member.
  • Example ring-forming members include CH and N.
  • Example six-membered ring heteroaryls are pyridyl, pyrazinyl, pyrimidinyl, triazinyl, and pyridazinyl.
  • heteroaryl-C i-j alkyl refers to an alkyl group substituted by a heteroaryl group.
  • An example of a heteroaryl-C i-j alkyl group is pyridylmethyl.
  • heterocycloalkyl refers to non-aromatic heterocyclic ring system, which may optionally contain one or more unsaturations as part of the ring structure, and which has at least one heteroatom ring member independently selected from nitrogen, sulfur and oxygen.
  • the heterocycloalkyl group has 1, 2, 3, or 4 heteroatom ring members.
  • the heterocycloalkyl group has 1, 2, or 3 heteroatom ring members.
  • the heterocycloalkyl group has 1 or 2 heteroatom ring members.
  • the heterocycloalkyl group has 1 heteroatom ring member.
  • heterocycloalkyl group contains more than one heteroatom in the ring
  • the heteroatoms may be the same or different.
  • Example ring-forming members include CH, CH 2 , C(O), N, NH, O, S, S(O), and S(O) 2 .
  • Heterocycloalkyl groups can include mono- or polycyclic (e.g., having 2, 3 or 4 fused rings) ring systems, including spiro systems. Also included in the definition of heterocycloalkyl are moieties that have one or more aromatic rings fused to (i.e., having a bond in common with) the non-aromatic ring, for example, 1,2,3,4-tetrahydro-quinoline, dihydrobenzofuran, and the like.
  • a heterocycloalkyl group including a fused aromatic ring can be attached to the core or scaffold via any ring-forming atom, including a ring-forming atom of the fused aromatic group.
  • the S or N ring-forming atoms can be optionally“oxidized” to include one or two
  • oxo groups as valency permits e.g., sulfonyl or sulfinyl or N-oxide.
  • One or more ring- forming carbon atoms of the heterocycloalkyl group can include an oxo moiety to form a ring-forming carbonyl.
  • a ring-forming nitrogen atom can be quaternized.
  • the heterocycloalkyl is 5- to 10-membered, 4- to 10- membered, 4- to 7-membered, 5-membered, or 6-membered.
  • heterocycloalkyl groups include 1, 2, 3, 4-tetrahydro-quinolinyl, dihydrobenzofuranyl, azetidinyl, azepanyl, pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, thiomorpholinyl, dihydrofuranyl, tetrahydrofuranyl, 2-oxopyrrolidinyl, 3-oxomorpholinyl, 2-oxooxazolidinyl, and pyranyl.
  • heterocycloalkyl groups include 2,3-dihydro-1H-pyrrolyl; 2-oxo-2,3- dihydro-1H-pyrrolyl; 2,3-dihydro-oxazolyl; 2-oxo-2,3-dihydro-oxazolyl; 3,4-dihydro-2H-1,4- oxazinyl; 3-oxo-3,4-dihydro-2H-1,4-oxazinyl; or 2,3-dihydro-furanyl.
  • the heterocycloalkyl group is azetidinyl, piperidinyl, pyrrolidinyl, diazapanyl, or diazaspirononanyl.
  • the heterocycloalkyl group is 2,3-dihydro- 1H-indolyl; 2,3-dihydro-1,3-benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3,4- dihydro-2H-1,4-benzoxazinyl; or 2,3-dihydro-1-benzofuran.
  • heterocycloalkyl-Ci-j alkyl employed alone or in combination with other terms, refers to an alkyl group substituted by a heterocycloalkyl group.
  • An example of a heterocycloalkyl-Ci-j alkyl group is pyrrolidinylmethyl.
  • the compounds described herein can be asymmetric (e.g., having one or more stereocenters). All stereoisomers, such as enantiomers and diastereoisomers, are intended unless otherwise indicated.
  • the compounds of the invention can be any of the possible stereoisomers.
  • the compounds with a single chiral center the compounds with a single chiral center.
  • stereochemistry of the chiral center can be (R) or (S).
  • the stereochemistry of the chiral centers can each be independently (R) or (S) so the configuration of the chiral centers can be (R) and (R), (R) and (S); (S) and (R), or (S) and (S).
  • the stereochemistry each of the three chiral centers can be (R) or (S).
  • the configuration of the chiral centers can be (R), (R) and (R); (R), (R) and (S); (R), (S) and (R); (R), (S) and (S); (S), (R) and (R); (S), (R) and (S); (S), (S) and (R); or (S), (S) and (S).
  • An example method includes fractional recrystallization using a chiral resolving acid which is an optically active, salt-forming organic acid.
  • Suitable resolving agents for fractional recrystallization methods are, for example, optically active acids, such as the D and L forms of tartaric acid, diacetyltartaric acid, dibenzoyltartaric acid, mandelic acid, malic acid, lactic acid or the various optically active camphorsulfonic acids such as ⁇ -camphorsulfonic acid.
  • resolving agents suitable for fractional crystallization methods include stereoisomerically pure forms of ⁇ -methylbenzylamine (e.g., S and R forms, or diastereoisomerically pure forms), 2-phenylglycinol, norephedrine, ephedrine, N- methylephedrine, cyclohexylethylamine, 1, 2-diaminocyclohexane, and the like.
  • Resolution of racemic mixtures can also be carried out by elution on a column packed with an optically active resolving agent (e.g., dinitrobenzoylphenylglycine).
  • an optically active resolving agent e.g., dinitrobenzoylphenylglycine
  • Suitable elution solvent composition can be determined by one skilled in the art.
  • Tautomeric forms result from the swapping of a single bond with an adjacent double bond together with the concomitant migration of a proton.
  • Tautomeric forms include prototropic tautomers which are isomeric protonation states having the same empirical formula and total charge.
  • Example prototropic tautomers include ketone– enol pairs, amide - imidic acid pairs, lactam– lactim pairs, amide - imidic acid pairs, enamine– imine pairs, and annular forms where a proton can occupy two or more positions of a heterocyclic system, for example, 1H- and 3H-imidazole, 1H-, 2H- and 4H- 1, 2, 4-triazole, 1H- and 2H- isoindole, and 1H- and 2H-pyrazole.
  • Tautomeric forms can be in equilibrium or sterically locked into one form by appropriate substitution.
  • Compounds of the invention can also include all isotopes of atoms occurring in the intermediates or final compounds.
  • Isotopes include those atoms having the same atomic number but different mass numbers.
  • the present invention includes compounds which are prepared synthetically, formed through a biological process or transformation, or a combination thereof.
  • All compounds, and pharmaceutically acceptable salts thereof, can be found together with other substances such as water and solvents (e.g., hydrates and solvates) or can be isolated.
  • the compounds of the invention, or salts thereof are substantially isolated.
  • substantially isolated is meant that the compound is at least partially or substantially separated from the environment in which it was formed or detected.
  • Partial separation can include, for example, a composition enriched in a compound of the invention.
  • Substantial separation can include compositions containing at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% by weight of the compounds of the invention, or salt thereof. Methods for isolating compounds and their salts are routine in the art.
  • phrases "pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • ambient temperature and “room temperature,” as used herein, are understood in the art, and refer generally to a temperature, e.g., a reaction temperature, that is about the temperature of the room in which the reaction is carried out, for example, a temperature from about 20 oC to about 30 oC.
  • the present invention also includes pharmaceutically acceptable salts of the compounds described herein.
  • pharmaceutically acceptable salts refers to derivatives of the disclosed compounds wherein the parent compound is modified by converting an existing acid or base moiety to its salt form.
  • examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like.
  • the pharmaceutically acceptable salts of the present invention include the conventional non-toxic salts of the parent compound formed, for example, from non-toxic inorganic or organic acids.
  • the pharmaceutically acceptable salts of the present invention can be synthesized from the parent compound which contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free
  • Suitable solvents can be substantially non-reactive with the starting materials (reactants), the
  • reaction can be carried out in one solvent or a mixture of more than one solvent.
  • suitable solvents for a particular reaction step can be selected by the skilled artisan.
  • Reactions can be monitored according to any suitable method known in the art.
  • product formation can be monitored by spectroscopic means, such as nuclear magnetic resonance spectroscopy (e.g., 1 H or 13 C), infrared spectroscopy, spectrophotometry (e.g., UV-visible), mass spectrometry, or by chromatographic methods such as high performance liquid chromatography (HPLC), liquid chromatography-mass spectroscopy (LCMS), or thin layer chromatography (TLC).
  • HPLC high performance liquid chromatography
  • LCMS liquid chromatography-mass spectroscopy
  • TLC thin layer chromatography
  • Compounds can be purified by those skilled in the art by a variety of methods, including high performance liquid chromatography (HPLC) ("Preparative LC-MS Purification: Improved Compound Specific Method Optimization" Karl F. Blom, Brian Glass, Richard Sparks, Andrew P. Combs J. Combi. Chem.2004, 6(6), 874- 883, which is incorporated
  • the bromide in compound 6 can be coupled to a compound of formula 7, in which M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR) 2 , Sn(Alkyl) 4 , or Zn-Hal], under standard Suzuki coupling conditions (e.g., in the presence of a palladium catalyst and a suitable base) or standard Stille coupling conditions (e.g., in the presence of a palladium catalyst), or standard Negishi coupling conditions (e.g., in the presence of a palladium catalyst) to give the derivative of formula 8.
  • M is a boronic acid, boronic ester or an appropriately substituted metal
  • M is B(OR) 2 , Sn(Alkyl) 4 , or Zn-Hal
  • Suzuki coupling conditions e.g., in the presence of a palladium catalyst and a suitable base
  • Stille coupling conditions e.g., in the presence of a palla
  • compound 7 can be a cyclic amine (where M is H and attached to an amine nitrogen) and the coupling of arylbromide 6 with the cyclic amine 7 can be performed under Buchwald amination conditions (e.g., in the presence of a palladium catalyst and a base such
  • the coupling of compound 9 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl)4], or standard Negishi coupling conditions (when M is Zn-Hal) to give compound 11.
  • Scheme 2 starting from compound 4 which can be prepared as described in Scheme 1.
  • Compound 4 can be converted to a formamidoxime derivative of formula 12 by reacting with N,N-dimethylformamide dimethyl acetal, followed by treatment with hydroxylamine.
  • the formamidoxime derivative 12 can undergo cyclization upon treating with trifluoroacetic anhydride (TFAA) to afford the triazole compound of formula 13.
  • TFAA trifluoroacetic anhydride
  • the preparation of compound 14 from compound 13 can be achieved using similar conditions as described in Scheme 1 (i.e., conditions used for preparation of compound 11 from compound 8).
  • Acylation of the amine 18 using acetic formic anhydride can generate an amide intermediate 19, which can undergo cyclization upon treatment with POCl 3 to provide a bicyclic imidazole derivative of formula 20.
  • Introduction of the ring A can be achieved by selective coupling of compound 20 with compound 7 using similar conditions as described in Scheme 1 (i.e., conditions for preparation of compound 8 from compound 6) to give compound of formula 21.
  • Suzuki coupling of compound 21 with boronic ester/acid of formula 2 can give compound 22, which can be converted to the arylchloride 23 by reacting with POCl3.
  • Coupling of arylchloride 23 with compound 10 using similar conditions as described in Scheme 1 can generate compound of formula 24.
  • Scheme 4 starting from the commercially available compound 25.
  • Introduction of the hydrazine moiety can be achieved via SNAr displacement of the chloride in compound 25 with hydrazine to give compound 26.
  • a condensation reaction can be performed between compound 26 with compound of formula 27 at elevated temperature to produce compound 28.
  • Preparation of compound 29 from compound 28 can be achieved using similar procedures as described in Scheme 3 (i.e., conditions used for preparation of compound 24 from compound 20).
  • Ring A can be achieved using similar conditions as described in Scheme 1 (i.e., conditions used for preparation of compound 8 from compound 6) to give compound 36.
  • the phenol derivative 37 can be prepared by demethylation of compound 36 under a suitable condition [i.e., boron tribromide (BBr 3 ) or trimethylsilyl iodide (TMSI)].
  • BBr 3 boron tribromide
  • TMSI trimethylsilyl iodide
  • Compound 38 can be prepared from compound 37 via Mitsunobu reaction with an alcohol
  • R a1 -OH alkylation with R a1 -Lg
  • Lg is a leaving group such as halide or OMs
  • the phenol 37 can be converted to triflate 39 under suitable conditions (i.e., in the presence of triflic anhydride and a base such as pyridine).
  • suitable conditions i.e., in the presence of triflic anhydride and a base such as pyridine.
  • the coupling of triflate 39 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl)4], or standard Negishi coupling conditions (when M is Zn-Hal) to give compound 40.
  • Scheme 8 starting from the commercially available compound 47.
  • Selective introduction of cyano group can be achieved by oxidation of the pyridine 47 with meta-chloroperoxybenzoic acid (m-CPBA) to N-oxide, followed by treatment with trimethylsilyl cyanide (TMS-CN) to give the cyano-derivative 48.
  • TMS-CN trimethylsilyl cyanide
  • Reduction of the cyanide with a suitable reducing agent such as diisobutylaluminium hydride (DIBAL), lithium aluminium hydride (LAH) or borane (BH3) can afford the amine 49.
  • DIBAL diisobutylaluminium hydride
  • LAH lithium aluminium hydride
  • BH3 borane
  • the bromide in compound 60 can be coupled to a compound of formula 7, in which M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal], under standard Suzuki coupling conditions (e.g., in the presence of a palladium catalyst and a suitable base) or standard Stille coupling conditions (e.g., in the presence of a palladium catalyst), or standard Negishi coupling conditions (e.g., in the presence of a palladium catalyst) to give the derivative of formula 61.
  • M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal]
  • Suzuki coupling conditions e.g., in the presence of a palladium catalyst and a suitable base
  • Stille coupling conditions e.g., in the presence of a palladium
  • compound 7 can be a cyclic amine (where M is H and attached to an amine nitrogen) and the coupling of arylbromide 60 with the cyclic amine 7 can be performed under Buchwald amination conditions (e.g., in the presence of a palladium catalyst
  • the coupling of compound 62 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl) 4 ], or standard Negishi coupling conditions (when M is Zn- Hal) to give compound 59.
  • N-bromosuccinimide (e.g., in the presence of a palladium catalyst and a base such as potassium carbonate) to afford compound 3.
  • Bromination of compound 3 in the presence of N-bromosuccinimide (NBS) can give the compound of formula 4.
  • Condensation of compound 4 with the carbonyl derivatives of formula 55 (Hal is a halide such as Cl or Br) at elevated temperature can generate the bicyclic compound of formula 56.
  • the hydroxyl group in compound 56 can be replaced with a halide (such as e.g. Cl), by treating compound 56 with an acid halide (e.g. acid chloride, such as for example phosphorus trichloride or phosphoryl chloride (phosphorus oxychloride)) to yield a compound of formula 57.
  • an acid halide e.g. acid chloride, such as for example phosphorus trichloride or phosphoryl chloride (phosphorus oxychloride)
  • diisopropylethylamine at elevated temperature can give compound of formula 58.
  • the coupling of compound 57 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl) 4 ], or standard Negishi coupling conditions (when M is Zn- Hal) to give compound 58.
  • the bromide in compound 58 can be coupled to a compound of formula 7, in which M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal], under standard Suzuki coupling conditions (e.g., in the presence of a palladium catalyst and a suitable base) or standard Stille coupling conditions (e.g., in the presence of a palladium catalyst), or standard Negishi coupling conditions (e.g., in the presence of a palladium catalyst) to give the derivative of formula 59.
  • M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal]
  • Suzuki coupling conditions e.g., in the presence of a palladium catalyst and a suitable base
  • Stille coupling conditions e.g., in the presence of a palla
  • compound 7 can be a cyclic amine (where M is H and attached to an amine nitrogen) and the coupling of arylbromide 58 with the cyclic amine 7 can be performed under Buchwald amination conditions (e.g., in the presence of a palladium catalyst and a base such as sodium tert-butoxide) to yield a compound of formula 59.
  • Buchwald amination conditions e.g., in the presence of a palladium catalyst and a base such as sodium tert-butoxide
  • Compounds of the invention are LSD1 inhibitors and, thus, are useful in treating diseases and disorders associated with activity of LSD1.
  • any of the compounds of the invention including any of the embodiments thereof, may be used.
  • the present invention is directed to a method of modulating LSD1 comprising contacting the LSD1 with a compound of Formula I.
  • the present invention is further directed to a method of mediating LSD1 comprising contacting the LSD1 with a compound of
  • the present invention is further directed to a method of modulating LSD1 signaling comprising contacting the LSD1 with a compound of Formula I.
  • the compounds of the invention are selective for LSD1 over LSD2, meaning that the compounds bind to or inhibit LSD1 with greater affinity or potency, compared to LSD2.
  • selectivity can be at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 50-fold, at least about 100-fold, at least about 200-fold, at least about 500-fold or at least about 1000-fold.
  • LSD1-mediated disease or“LSD1-mediated disorder” refers to any disease or condition in which LSD1 plays a role, or where the disease or condition is associated with expression or activity of LSD1.
  • the compounds of the invention can therefore be used to treat or lessen the severity of diseases and conditions where LSD1 is known to play a role.
  • Diseases and conditions treatable using the compounds of the invention include, generally cancers, inflammation, autoimmune diseases, viral induced pathogenesis, beta- globinopathies, and other diseases linked to LSD1 activity.
  • Cancers treatable using compounds according to the present invention include, for example, hematological cancers, sarcomas, lung cancers, gastrointestinal cancers, genitourinary tract cancers, liver cancers, bone cancers, nervous system cancers,
  • Examplary hematological cancers includelymphomas and leukemias such as acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), acute promyelocytic leukemia (APL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), diffuse large B-cell lymphoma (DLBCL), mantle cell lymphoma, Non-Hodgkin lymphoma (including relapsed or refractory NHL and recurrent follicular), Hodgkin lymphoma, myeloproliferative diseases (e.g., primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocytosis (ET)), myelodysplasia syndrome (MDS), and multiple myeloma.
  • ALL acute lymphoblastic leukemia
  • AML acute myelogenous leukemia
  • APL acute promyelocytic le
  • Examplary sarcomas includechondrosarcoma, Ewing’s sarcoma, osteosarcoma, rhabdomyosarcoma, angiosarcoma, fibrosarcoma, liposarcoma, myxoma, rhabdomyoma, fibroma, lipoma, harmatoma, and teratoma.
  • Examplary lung cancers includenon-small cell lung cancer (NSCLC), bronchogenic carcinoma (squamous cell, undifferentiated small cell, undifferentiated large cell,
  • adenocarcinoma adenocarcinoma
  • alveolar (bronchiolar) carcinoma bronchial adenoma
  • chondromatous hamartoma chondromatous hamartoma
  • mesothelioma adenocarcinoma
  • Examplary gastrointestinal cancers includecancers of the esophagus (squamous cell carcinoma, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel (adenocarcinoma, lymphoma, carcinoid tumors, Kaposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma), and colorectal cancer.
  • Examplary genitourinary tract cancers includecancers of the kidney (adenocarcinoma, Wilm's tumor [nephroblastoma]), bladder and urethra (squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), and testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma).
  • adenocarcinoma Wilm's tumor [nephroblastoma]
  • bladder and urethra squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma
  • prostate adenocarcinoma, sarcoma
  • testis seminoma, teratoma, embryonal
  • liver cancers includehepatoma (hepatocellular carcinoma),
  • cholangiocarcinoma hepatoblastoma, angiosarcoma, hepatocellular adenoma, and hemangioma.
  • Examplary bone cancers include, for example, osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma, malignant giant cell tumor chordoma, osteochronfroma (osteocartilaginous exostoses), benign chondroma,
  • Examplary nervous system cancers includecancers of the skull (osteoma,
  • hemangioma hemangioma, granuloma, xanthoma, osteitis deformans), meninges (meningioma, meningiosarcoma, gliomatosis), brain (astrocytoma, meduoblastoma, glioma, ependymoma, germinoma (pinealoma), glioblastoma multiform, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), and spinal cord (neurofibroma, meningioma, glioma, sarcoma), as well as neuroblastoma and Lhermitte-Duclos disease.
  • Examplary gynecological cancers includecancers of the uterus (endometrial carcinoma), cervix (cervical carcinoma, pre -tumor cervical dysplasia), ovaries (ovarian carcinoma (serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma), granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma,
  • adenocarcinoma adenocarcinoma, fibrosarcoma, melanoma
  • vagina vagina (clear cell carcinoma, squamous cell
  • botryoid sarcoma embryonic rhabdomyosarcoma
  • fallopian tubes
  • Examplary skin cancers includemelanoma, basal cell carcinoma, squamous cell carcinoma, Kaposi's sarcoma, moles dysplastic nevi, lipoma, angioma, dermatofibroma, and keloids.
  • the compounds of the invention can further be used to treat cancer types where LSD1 may be overexpressed including, for example, breast, prostate, head and neck, laryngeal, oral, and thyroid cancers (e.g., papillary thyroid carcinoma).
  • cancer types where LSD1 may be overexpressed including, for example, breast, prostate, head and neck, laryngeal, oral, and thyroid cancers (e.g., papillary thyroid carcinoma).
  • the compounds of the invention can further be used to treat genetic disorders such as Cowden syndrome and Bannayan-Zonana syndrome.
  • the compounds of the invention can further be used to treat viral diseases such as herpes simplex virus (HSV), varicella zoster virus (VZV), human cytomegalovirus, hepatitis B virus (HBV), and adenovirus.
  • viral diseases such as herpes simplex virus (HSV), varicella zoster virus (VZV), human cytomegalovirus, hepatitis B virus (HBV), and adenovirus.
  • the compounds of the invention can further be used to treat beta-globinopathies including, for example, beta-thalassemia and sickle cell anemia.
  • contacting refers to the bringing together of indicated moieties in an in vitro system or an in vivo system.
  • "contacting" a LSD1 protein with a compound of the invention includes the administration of a compound of the present invention to an individual or patient, such as a human, having a LSD1 protein, as well as, for example, introducing a compound of the invention into a sample containing a cellular or purified preparation containing the LSD1 protein.
  • the phrase "therapeutically effective amount” refers to the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response that is being sought in a tissue, system, animal, individual or human by a researcher, veterinarian, medical doctor or other clinician.
  • treating refers to inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e.,, arresting further development of the pathology and/or symptomatology) or ameliorating the disease; for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or
  • preventing refers to preventing the onset and development of a disease; for example, preventing a disease, condition or disorder in an individual who may be predisposed to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease.
  • the compounds of the invention can be used in combination treatments where the compound of the invention is administered in conjunction with other treatments such as the administration of one or more additional therapeutic agents.
  • the additional therapeutic agents are typically those which are normally used to treat the particular condition to be treated.
  • the additional therapeutic agents can include, e.g., chemotherapeutics, anti-inflammatory agents, steroids, immunosuppressants, as well as Bcr-Abl, Flt-3, RAF, FAK, JAK, PIM, PI3K, PD-1, PD-L1, bromodomain, indoleamine 2,3-dioxygenase (IDO), TAM, FGFR inhibitors and other tumor directed therapies (small molecules or biologics in nature) for treatment of LSD1- mediated diseases, disorders or conditions.
  • chemotherapeutics include, e.g., chemotherapeutics, anti-inflammatory agents, steroids, immunosuppressants, as well as Bcr-Abl, Flt-3, RAF, FAK, JAK, P
  • the one or more additional pharmaceutical agents can be administered to a patient simultaneously or sequentially.
  • the compounds of the present disclosure can be used in combination with a vaccine, an immunotherapy, such as LADD immunotherapy, CRS-207 or DPX-Survivac for the treatement of cancer.
  • the compounds of the invention can be used in combination with a therapeutic agent that targets an epigenetic regulator.
  • epigenetic regulators include bromodomain inhibitors, the histone lysine methyltransferases, histone arginine methyl transferases, histone demethylases, histone deacetylases, histone acetylases, and DNA methyltransferases.
  • Histone deacetylase inhibitors include, e.g., vorinostat.
  • the compounds of the invention can be used in combination with chemotherapeutic agents, agonists or antagonists of nuclear receptors, or other anti-proliferative agents.
  • the compounds of the invention can also be used in combination with a medical therapy such as surgery or radiotherapy, e.g., gamma- radiation, neutron beam radiotherapy, electron beam radiotherapy, proton therapy, brachytherapy, and systemic radioactive isotopes.
  • chemotherapeutic agents include any of: abarelix, aldesleukin, alemtuzumab, alitretinoin, allopurinol, altretamine, anastrozole, arsenic trioxide, asparaginase, azacitidine, bendamustine,
  • bevacizumab bexarotene, bleomycin, bortezombi, bortezomib, busulfan intravenous, busulfan oral, calusterone, capecitabine, carboplatin, carmustine, cetuximab, chlorambucil, cisplatin, cladribine, clofarabine, cyclophosphamide, cytarabine, dacarbazine, dactinomycin, dalteparin sodium, dasatinib, daunorubicin, decitabine, denileukin, denileukin diftitox, dexrazoxane, docetaxel, doxorubicin, dromostanolone propionate, eculizumab, epirubicin, erlotinib, estramustine, etoposide phosphate, etoposide, exemestane, fentanyl citrate, filgra
  • meclorethamine megestrol acetate, melphalan, mercaptopurine, methotrexate, methoxsalen, mitomycin C, mitotane, mitoxantrone, nandrolone phenpropionate, nelarabine, nofetumomab, oxaliplatin, paclitaxel, pamidronate, panobinostat, panitumumab, pegaspargase,
  • pegfilgrastim pemetrexed disodium, pentostatin, pipobroman, plicamycin, procarbazine, quinacrine, rasburicase, rituximab, ruxolitinib, sorafenib, streptozocin, sunitinib, sunitinib maleate, tamoxifen, temozolomide, teniposide, testolactone, thalidomide, thioguanine, thiotepa, topotecan, toremifene, tositumomab, trastuzumab, tretinoin, uracil mustard, valrubicin, vinblastine, vincristine, vinorelbine, vorinostat, and zoledronate.
  • biological anticancer drugs such as antibodies and cytokines
  • drugs modulating microenvironment or immune responses can be combined with the compounds of the invention.
  • examples of such drugs include anti-Her2 antibodies, anti-CD20 antibodies, anti- CTLA1, anti-PD-1, anti-PDL1, and other immunotherapeutic drugs.
  • the compounds of the invention can be used in combination with targeted therapies, including JAK kinase inhibitors
  • PI3 kinase inhibitors including PI3K-delta selective (e.g., INCB50797), PI3K- gamma selective and broad spectrum PI3K inhibitors, MEK inhibitors, Cyclin Dependent kinase inhibitors, BRAF inhibitors, mTOR inhibitors, proteasome inhibitors (Bortezomib, Carfilzomib), HDAC-inhibitors (panobinostat, vorinostat), DNA methyl transferase inhibitors, dexamethasone, bromo and extra terminal family members inhibitors (for example, bromodomain inhibitors or BET inhibitors such as INCB54329 and INCB57643), FGFR inhibitors (e.g., INCB54828, INCB62079 and INCB63904) and indoleamine 2,3- di
  • the compound of the invention can be administered in combination with a corticosteroid such as triamcinolone,
  • dexamethasone fluocinolone, cortisone, prednisolone, or flumetholone.
  • the compound of the invention can be administered in combination with an immune suppressant such as fluocinolone acetonide (Retisert®), rimexolone (AL-2178, Vexol, Alcon), or cyclosporine (Restasis®).
  • an immune suppressant such as fluocinolone acetonide (Retisert®), rimexolone (AL-2178, Vexol, Alcon), or cyclosporine (Restasis®).
  • the compound of the invention can be administered in combination with one or more additional agents selected from
  • dehydroepiandrosterone anakinra, efalizumab, mycophenolate sodium, etanercept
  • the compound of the invention can be administered in combination with one or more additional agents such as Hydrea®
  • the compound of the invention can be administered in combination with one or more agents selected from an antibiotic, antiviral, antifungal, anesthetic, anti-inflammatory agents including steroidal and non-steroidal anti- inflammatories, and anti-allergic agents.
  • suitable medicaments include aminoglycosides such as amikacin, gentamycin, tobramycin, streptomycin, netilmycin, and kanamycin; fluoroquinolones such as ciprofloxacin, norfloxacin, ofloxacin, trovafloxacin, lomefloxacin, levofloxacin, and enoxacin; naphthyridine; sulfonamides; polymyxin;
  • chloramphenicol neomycin; paramomycin; colistimethate; bacitracin; vancomycin;
  • rifampins tetracyclines
  • rifampins tetracyclines
  • rifampins tetracyclines
  • cycloserine beta-lactams
  • cephalosporins cephalosporins; amphotericins; fluconazole; flucytosine; natamycin; miconazole;
  • ketoconazole corticosteroids; diclofenac; flurbiprofen; ketorolac; suprofen; cromolyn;
  • lodoxamide lodoxamide; levocabastin; naphazoline; antazoline; pheniramine; or azalide antibiotic.
  • agents one or more of which a provided LSD1 inhibitor compound may also be combined with include: a treatment for Alzheimer's Disease such as donepezil and rivastigmine; a treatment for Parkinson's Disease such as L-DOPA/carbidopa, entacapone, ropinirole, pramipexole, bromocriptine, pergolide, trihexyphenidyl, and amantadine; an agent for treating multiple sclerosis (MS) such as beta interferon (e.g., Avonex® and Rebif®), glatiramer acetate, and mitoxantrone; a treatment for asthma such as albuterol and montelukast; an agent for treating schizophrenia such as zyprexa, risperdal, seroquel, and haloperidol; an anti-inflammatory agent such as a corticosteroid, such as dexamethasone or prednisone, a TNF blocker, IL-1 RA
  • cholestyramine an interferon, and an anti-viral agent
  • an agent for treating blood disorders such as a corticosteroid, an anti-leukemic agent, or a growth factor
  • an agent for treating immunodeficiency disorders such as gamma globulin.
  • immune checkpoint inhibitors include inhibitors against immune checkpoint molecules such as CD27, CD28, CD40, CD122, CD96, CD73, CD47, OX40, GITR, CSF1R, JAK, PI3K delta, PI3K gamma, TAM, arginase, CD137 (also known as 4-1BB), ICOS, A2AR, B7-H3, B7-H4, BTLA, CTLA-4, LAG3, TIM3, VISTA, PD-1, PD-L1 and PD-L2.
  • immune checkpoint inhibitors include inhibitors against immune checkpoint molecules such as CD27, CD28, CD40, CD122, CD96, CD73, CD47, OX40, GITR, CSF1R, JAK, PI3K delta, PI3K gamma, TAM, arginase, CD137 (also known as 4-1BB), ICOS, A2AR, B7-H3, B7-H4, BTLA, CTLA-4, LAG3, TIM
  • the immune checkpoint molecule is a stimulatory checkpoint molecule selected from CD27, CD28, CD40, ICOS, OX40, GITR and CD137.
  • the immune checkpoint molecule is an inhibitory checkpoint molecule selected from A2AR, B7-H3, B7-H4, BTLA, CTLA-4, IDO, KIR, LAG3, PD-1, TIM3, and VISTA.
  • the compounds provided herein can be used in
  • KIR inhibitors selected from KIR inhibitors, TIGIT inhibitors, LAIR1 inhibitors, CD160 inhibitors, 2B4 inhibitors and TGFR beta inhibitors.
  • the inhibitor of an immune checkpoint molecule is anti-PD1 antibody, anti-PD-L1 antibody, or anti-CTLA-4 antibody.
  • the inhibitor of an immune checkpoint molecule is an inhibitor of PD-1, e.g., an anti-PD-1 monoclonal antibody.
  • the anti-PD-1 monoclonal antibody is nivolumab, pembrolizumab (also known as MK-3475), pidilizumab, SHR-1210, PDR001, or AMP-224.
  • the anti-PD-1 monoclonal antibody is nivolumab or pembrolizumab.
  • the anti-PD1 antibody is pembrolizumab.
  • the anti PD-1 antibody is SHR-1210.
  • the inhibitor of an immune checkpoint molecule is an inhibitor of PD-L1, e.g., an anti-PD-L1 monoclonal antibody.
  • the anti-PD-L1 monoclonal antibody is BMS-935559, MEDI4736, MPDL3280A (also known as RG7446), or MSB0010718C.
  • the anti-PD-L1 monoclonal antibody is BMS-935559, MEDI4736, MPDL3280A (also known as RG7446), or MSB0010718C.
  • the anti-PD-L1 monoclonal antibody is
  • the inhibitor of an immune checkpoint molecule is an inhibitor of CTLA-4, e.g., an anti-CTLA-4 antibody.
  • the anti-CTLA-4 antibody is ipilimumab.
  • the inhibitor of an immune checkpoint molecule is an inhibitor of LAG3, e.g., an anti-LAG3 antibody.
  • the anti-LAG3 antibody is BMS-986016 or LAG525.
  • the inhibitor of an immune checkpoint molecule is an inhibitor of GITR, e.g., an anti-GITR antibody.
  • the anti-GITR antibody is TRX518 or MK-4166.
  • the inhibitor of an immune checkpoint molecule is an inhibitor of OX40, e.g., an anti-OX40 antibody or OX40L fusion protein.
  • OX40 e.g., an anti-OX40 antibody or OX40L fusion protein.
  • the anti-OX40 antibody is MEDI0562.
  • the OX40L fusion protein is MEDI6383.
  • the agent is an alkylating agent, a proteasome inhibitor, a corticosteroid, or an immunomodulatory agent.
  • an alkylating agent include cyclophosphamide (CY), melphalan (MEL), and bendamustine.
  • the proteasome inhibitor is carfilzomib.
  • the corticosteroid is dexamethasone (DEX).
  • the immunomodulatory agent is lenalidomide (LEN) or pomalidomide (POM).
  • the compounds of the invention can be administered in the form of pharmaceutical compositions.
  • These compositions can be prepared in a manner well known in the pharmaceutical art, and can be administered by a variety of routes, depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including transdermal, epidermal, ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal or intranasal), oral or parenteral.
  • topical including transdermal, epidermal, ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery
  • pulmonary e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal or intranasal
  • oral or parenteral e.g., by inhal
  • Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal intramuscular or injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
  • Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump.
  • Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
  • compositions which contain, as the active ingredient, the compound of the invention or a pharmaceutically acceptable salt thereof, in combination with one or more pharmaceutically acceptable carriers (excipients).
  • the composition is suitable for topical administration.
  • the active ingredient is typically mixed with an excipient, diluted by an excipient or enclosed within such a carrier in the form of, for example, a capsule, sachet, paper, or other container.
  • the excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier or medium for the active ingredient.
  • compositions can be in the form of tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, suppositories, sterile injectable solutions, and sterile packaged powders.
  • the active compound can be milled to provide the appropriate particle size prior to combining with the other ingredients. If the active compound
  • the particle size can be adjusted by milling to provide a substantially uniform distribution in the formulation, e.g., about 40 mesh.
  • the compounds of the invention may be milled using known milling procedures such as wet milling to obtain a particle size appropriate for tablet formation and for other formulation types.
  • Finely divided (nanoparticulate) preparations of the compounds of the invention can be prepared by processes known in the art, e.g., see International App. No. WO 2002/000196.
  • excipients include lactose, dextrose, sucrose, sorbitol, mannitol, starches, gum acacia, calcium phosphate, alginates, tragacanth, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, and methyl cellulose.
  • the formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl- and propylhydroxy-benzoates; sweetening agents; and flavoring agents.
  • the compositions of the invention can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art.
  • compositions can be formulated in a unit dosage form, each dosage containing from about 5 to about 1,000 mg (1 g), more usually about 100 mg to about 500 mg, of the active ingredient.
  • unit dosage forms refers to physically discrete units suitable as unitary dosages for human subjects and other mammals, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient.
  • the active compound may be effective over a wide dosage range and is generally administered in a pharmaceutically effective amount. It will be understood, however, that the amount of the compound actually administered will usually be determined by a physician, according to the relevant circumstances, including the condition to be treated, the chosen route of administration, the actual compound administered, the age, weight, and response of the individual patient, the severity of the patient's symptoms, and the like.
  • the principal active ingredient is mixed with a pharmaceutical excipient to form a solid preformulation composition containing a homogeneous mixture of a compound of the present invention.
  • a pharmaceutical excipient for preparing solid compositions such as tablets, the principal active ingredient is mixed with a pharmaceutical excipient to form a solid preformulation composition containing a homogeneous mixture of a compound of the present invention.
  • the active ingredient is typically dispersed evenly throughout the composition so that the composition can be readily subdivided into
  • preformulation is then subdivided into unit dosage forms of the type described above containing from, for example, about 0.1 to about 1000 mg of the active ingredient of the present invention.
  • the tablets or pills of the present invention can be coated or otherwise compounded to provide a dosage form affording the advantage of prolonged action.
  • the tablet or pill can comprise an inner dosage and an outer dosage component, the latter being in the form of an envelope over the former.
  • the two components can be separated by an enteric layer which serves to resist disintegration in the stomach and permit the inner component to pass intact into the duodenum or to be delayed in release.
  • enteric layers or coatings such materials including a number of polymeric acids and mixtures of polymeric acids with such materials as shellac, cetyl alcohol, and cellulose acetate.
  • liquid forms in which the compounds and compositions of the present invention can be incorporated for administration orally or by injection include aqueous solutions, suitably flavored syrups, aqueous or oil suspensions, and flavored emulsions with edible oils such as cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as elixirs and similar pharmaceutical vehicles.
  • compositions for inhalation or insufflation include solutions and suspensions in pharmaceutically acceptable, aqueous or organic solvents, or mixtures thereof, and powders.
  • the liquid or solid compositions may contain suitable pharmaceutically acceptable excipients as described supra.
  • the compositions are administered by the oral or nasal respiratory route for local or systemic effect.
  • Compositions can be nebulized by use of inert gases. Nebulized solutions may be breathed directly from the nebulizing device or the nebulizing device can be attached to a face masks tent, or intermittent positive pressure breathing machine. Solution, suspension, or powder compositions can be administered orally or nasally from devices which deliver the formulation in an appropriate manner.
  • Topical formulations can contain one or more conventional carriers.
  • ointments can contain water and one or more hydrophobic carriers selected from, for example, liquid paraffin, polyoxyethylene alkyl ether, propylene glycol, white vaseline, and the like.
  • Carrier compositions of creams can be based on water in combination with glycerol and one or more other components, e.g., glycerinemonostearate, PEG- glycerinemonostearate and cetylstearyl alcohol.
  • Gels can be formulated using isopropyl alcohol and water, suitably in combination with other components such as, for example,
  • topical formulations contain at least about 0.1, at least about 0.25, at least about 0.5, at least about 1, at least about 2, or at least about 5 wt % of the compound of the invention.
  • the topical formulations can be suitably packaged in tubes of, for example, 100 g which are optionally associated with instructions for the treatment of the select indication, e.g., psoriasis or other skin condition.
  • compositions can be administered to a patient already suffering from a disease in an amount sufficient to cure or at least partially arrest the symptoms of the disease and its complications. Effective doses will depend on the disease condition being treated as well as by the judgment of the attending clinician depending upon factors such as the severity of the disease, the age, weight and general condition of the patient, and the like.
  • compositions administered to a patient can be in the form of pharmaceutical compositions described above. These compositions can be sterilized by conventional sterilization techniques, or may be sterile filtered. Aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile aqueous carrier prior to administration.
  • the pH of the compound preparations typically will be between 3 and 11, more preferably from 5 to 9 and most preferably from 7 to 8. It will be understood that use of certain of the foregoing excipients, carriers, or stabilizers will result in the formation of pharmaceutical salts.
  • the therapeutic dosage of a compound of the present invention can vary according to, for example, the particular use for which the treatment is made, the manner of administration of the compound, the health and condition of the patient, and the judgment of the prescribing physician.
  • the compounds of the invention can be provided in an aqueous physiological buffer solution containing about 0.1 to about 10% w/v of the compound for parenteral administration.
  • Some typical dose ranges are from about 1 ⁇ g/kg to about 1 g/kg of body weight per day. In some embodiments, the dose range is from about 0.01 mg/kg to about 100 mg/kg of body weight per day.
  • the dosage is likely to depend on such variables as the type and extent of progression of the disease or disorder, the overall health status of the particular patient, the
  • Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.
  • compositions of the invention can further include one or more additional pharmaceutical agents such as a chemotherapeutic, steroid, anti-inflammatory compound, or immunosuppressant, examples of which are listed hereinabove.
  • additional pharmaceutical agents such as a chemotherapeutic, steroid, anti-inflammatory compound, or immunosuppressant, examples of which are listed hereinabove.
  • the compounds of the invention can be provided with or used in combination with a companion diagnostic.
  • a companion diagnostic refers to a diagnostic device useful for determining the safe and effective use of a therapeutic agent.
  • a companion diagnostic may be used to customize dosage of a therapeutic agent for a given subject, identify appropriate subpopulations for treatment, or identify populations who should not receive a particular treatment because of an increased risk of a serious side effect.
  • the companion diagnostic is used to monitor treatment response in a patient. In some embodiments, the companion diagnostic is used to identify a subject that is likely to benefit from a given compound or therapeutic agent. In some embodiments, the companion diagnostic is used to identify a subject having an increased risk of adverse side effects from administration of a therapeutic agent, compared to a reference standard. In some embodiments, the companion diagnostic is an in vitro diagnostic or imaging tool selected from the list of FDA cleared or approved companion diagnostic devices. In some embodiments, the companion diagnostic is selected from the list of tests that have been cleared or approved by the Center for Devices and Radiological Health. Labeled Compounds and Assay Methods
  • Another aspect of the present invention relates to labeled compounds of the invention (radio-labeled, fluorescent-labeled, etc.) that would be useful not only in imaging techniques but also in assays, both in vitro and in vivo, for localizing and quantitating LSD1 in tissue samples, including human, and for identifying LSD1 ligands by inhibition binding of a labeled compound.
  • the present invention includes LSD1 assays that contain such labeled compounds.
  • the present invention further includes isotopically-labeled compounds of the invention.
  • An “isotopically” or “radio-labeled” compound is a compound of the invention where one or more atoms are replaced or substituted by an atom having an atomic mass or mass number different from the atomic mass or mass number typically found in nature (i.e.,
  • radionuclides that may be incorporated in compounds of the present invention include but are not limited to 3 H (also written as T for tritium), 11 C, 13 C, 14 C, 13 N, 15 N, 15 O, 17 O, 18 O, 18 F, 35 S, 36 Cl, 82 Br, 75 Br, 76 Br, 77 Br, 123 I, 124 I, 125 I and 131 I.
  • the radionuclide that is incorporated in the instant radio-labeled compounds will depend on the specific application of that radio-labeled compound.
  • a “radio-labeled " or “labeled compound” is a compound that has incorporated at least one radionuclide.
  • the radionuclide is selected from the group consisting of 3 H, 14 C, 125 I, 35 S and 82 Br.
  • the compound incorporates 1, 2, or 3 deuterium atoms.
  • the present invention can further include synthetic methods for incorporating radio- isotopes into compounds of the invention. Synthetic methods for incorporating radio-isotopes into organic compounds are well known in the art, and an ordinary skill in the art will readily recognize the methods applicable for the compounds of invention.
  • a newly synthesized or identified compound i.e., test compound
  • a test compound which is labeled
  • a test compound can be evaluated for its ability to reduce binding of another compound which is known to bind to LSD1 (i.e., standard compound). Accordingly, the ability of a test compound to compete with the standard compound for binding to LSD1directly correlates to its binding affinity.
  • the standard compound is labeled and test compounds are unlabeled. Accordingly, the concentration of the labeled standard compound is monitored in order to evaluate the competition between the standard compound and the test compound, and the relative binding affinity of the test compound is thus ascertained.
  • LCMS liquid chromatography mass spectrometry
  • Typical preparative reverse- phase high performance liquid chromatography (RP-HPLC) column conditions are as follows:
  • pH 2 purifications: Waters Sunfire TM C 18 5 ⁇ m particle size, 19 x 100 mm column, eluting with mobile phase A: 0.1% TFA (trifluoroacetic acid) in water and mobile phase B: acetonitrile; the flow rate was 30 mL/minute, the separating gradient was optimized for each compound using the Compound Specific Method Optimization protocol as described in the literature [see “Preparative LCMS Purification: Improved Compound Specific Method Optimization", K. Blom, B. Glass, R. Sparks, A. Combs, J. Comb. Chem., 6, 874-883 (2004)]. Typically, the flow rate used with the 30 x 100 mm column was 60 mL/minute.
  • N-Bromosuccinimide (1.3 g, 7.5 mmol) was added to a solution of 4-(6-amino-2- methoxypyrimidin-4-yl)benzonitrile (1.7 g, 7.5 mmol) in dimethyl sulfoxide (15
  • Phosphoryl chloride (12 mL, 130 mmol) was added to a mixture of 4-(8-bromo-5- hydroxyimidazo[1,2-c]pyrimidin-7-yl)benzonitrile (1.0 g, 3.2 mmol) in acetonitrile (12 mL). The resulting mixture was stirred at 110 °C overnight then cooled to room temperature and concentrated. The residue was dissolved in methylene chloride then washed with sat'd NaHCO3 solution, water and brine. The organic layer was dried over Na2SO4, filtered and concentrated.
  • Step 8 4-(8-(4-methylphenyl)-5- ⁇ [(3R)-1-methylpiperidin-3-yl]methoxy ⁇ imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
  • Step 1 4-(8-bromo-5- ⁇ [(3R)-1-methylpyrrolidin-3-yl]methoxy ⁇ imidazo[1,2-c]pyrimidin-7- yl)benzonitrile
  • Step 1 1-methyl-5-(4,4,5,5-tetrame -1 2- r -2-yl)-1,3-dihydro-2H-indol-2-one
  • This compound was prepared using similar procedures as described for Example 1 with 1-methyl-4-[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl]piperazine (Combi- Blocks, cat#PN-8801) replacing (4-methylphenyl)boronic acid in Step 8.
  • Step 1 4-(8-(4-formylphenyl)-5- ⁇ [(3R)-1-methylpiperidin-3-yl]methoxy ⁇ imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
  • Step 1 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-3,4-dihydro-2H-pyrido[3,2- b][1,4]oxazine
  • Step 2 4-(8-(4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-7-yl)-5- ⁇ [(3R)-1- methylpiperidin-3-yl]methoxy ⁇ imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
  • Step 1 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-1,4-benzoxazin-3(4H)- one
  • This compound was prepared using similar procedures as described for Example 2 with 2-pyrrolidin-1-yl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (Combi- Blocks, cat#PN-8695) replacing (4-methylphenyl)boronic acid in Step 2.
  • Step 1 tert-butyl (3R)-3-( ⁇ [7-(4-cyanophenyl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-5-yl]oxy ⁇ methyl)piperidine-1-carboxylate
  • reaction mixture was cooled to room temperature then diluted with methylene chloride, washed with saturated NaHCO3, water and brine. The organic layer was dried over Na 2 SO 4 , filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 10% MeOH in methylene chloride to give the desired product (119 mg, 86%).
  • Step 2 4-(8-[3-fluoro-4-(hydroxymethyl)-5-methylphenyl]-5- ⁇ [(3R)-1-methylpiperidin-3- yl]methoxy ⁇ imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
  • Step 1 4- ⁇ 8-bromo-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-7- yl ⁇ benzonitrile
  • N,N-diisopropylethylamine (0.63 mL, 3.6 mmol) and 4-(8-bromo-5- chloroimidazo[1,2-c]pyrimidin-7-yl)benzonitrile (prepared in Example 1, Step 4: 600. mg, 1.80 mmol) in acetonitrile (10 mL) was added N,N-dimethylpiperidin-4-amine (Alfa Aesar, cat#L20176: 0.51 mL, 3.6 mmol). The resulting reaction mixture was stirred at room temperature for 1 h then water (80 mL) was added.
  • Step 1 4- ⁇ 8-bromo-5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]imidazo[1,2-c]pyrimidin-7- yl ⁇ benzonitrile
  • Step 2 4-[5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
  • Step 1 tert-butyl 7-[8-bromo-7-(4-cyanophenyl)imidazo[1,2-c]pyrimidin-5-yl]-2,7- diazaspiro[4.4]nonane-2- r
  • Step 2 tert-butyl 7-[7-(4-cyanophenyl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-5-yl]-2,7-diazaspiro[4.4]nonane-2-carboxylate
  • Step 1 1-[2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]-N- methylmethanamine
  • Step 2 methyl [2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)benzyl]methylcarbamate
  • Step 3 methyl [4-(7-(4-cyanophenyl)-5- ⁇ [(3R)-1-methylpiperidin-3-yl]methoxy ⁇ imidazo[1,2- c]pyrimidin-8-yl)-2-fluorobenzyl]methylcarbamate
  • Step 1 5-bromo-2-[(methylamino)meth l henol
  • This compound was prepared using similar procedures as described for Example 6, Step 1 with 7-bromo-3-methyl-3,4-dihydro-2H-1,3-benzoxazin-2-one (crude product from Step 2) replacing 5-bromo-1-methyl-1,3-dihydro-2H-indol-2-one.
  • the reaction mixture was concentrated, diluted with methylene chloride, washed over saturated NaHCO3.
  • the aqueous phase was extracted with methylene chloride.
  • the organic layer was dried over Na 2 SO 4 , filtered and concentrated.
  • the residue was purified by flash chromatography on a silica gel column eluting with 0 to 25% AcOEt in hexanes to give the desired product.
  • Step 1 1,3-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-dihydro-2H- benzimidazol-2-one
  • Step 2 4-(8-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-5- ⁇ [(3R)-1- methylpiperidin-3-yl]methoxy ⁇ imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
  • Step 3 5-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one
  • This compound was prepared using similar procedures as described for Example 6, Step 1 with 6-bromo-5-fluoro-3-methyl-1,3-benzoxazol-2(3H)-one (product from Step 2) replacing 5-bromo-1-methyl-1,3-dihydro-2H-indol-2-one.
  • the reaction mixture was concentrated, diluted with methylene chloride, washed over saturated NaHCO 3 .
  • the aqueous phase was extracted with methylene chloride.
  • the combined organic layers were dried over Na2SO4, filtered and concentrated.
  • the residue was purified by flash chromatography on a silica gel column eluting with 0 to 4% methanol in methylene chloride to give the desired product.
  • This compound was prepared using similar procedures as described for Example 37 with 1-[5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2-yl]pyrrolidin-2-one (JPM2 Pharma, cat#JPM2-00-744) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)-1H-pyrazolo[3,4-b]pyridine in Step 2.
  • This compound was prepared using similar procedures as described for Example 37 with 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-1,4-benzoxazin-3(4H)- one (Prepared in Example 15, Step 1) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2- dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2.
  • Step 2 2-(difluoromethyl)-1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- benzimidazole
  • 5-bromo-2-(difluoromethyl)-1-methyl-1H-benzimidazole (0.59 g, 2.2 mmol)
  • 4,4,5,5,4',4',5',5'-Octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (860 mg, 3.4 mmol)
  • Step 8 4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
  • Step 2 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)[1,3]oxazolo[4,5-b]pyridin- 2(3H)-one
  • Step 1 2-methyl-5-(4,4,5,5-tetrameth l-132-dioxaborolan-2- l nicotinonitrile
  • Step 3 methyl (5- ⁇ 7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl ⁇ pyridin-2-yl)methylcarbamate
  • Step 1 methyl (4-bromo-2-fluorophen l meth lcarbamate
  • Step 3 methyl [4-(7-(4-cyanophenyl)-5- ⁇ [(3R)-1-methylpiperidin-3-yl]methoxy ⁇ imidazo[1,2- c]pyrimidin-8-yl)-2-fluorophenyl]methylcarbamate
  • Reactions were started by addition of 10 ⁇ L of assay buffer containing 0.4 ⁇ M Biotin-labeled Histone H3 peptide substrate: ART-K(Me1)- QTARKSTGGKAPRKQLA-GGK(Biotin) SEQ ID NO:1 (AnaSpec 64355) and incubated for 1 hour at 25 o C.
  • IC 50 data for the example compounds is provided in Table 1 (the symbol “+” refers to IC50 ⁇ 50 nM;“++” refers to IC50 > 50 nM and ⁇ 500 nM;“+++” refers to IC50 > 500 nM and ⁇ 1000 nM).

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Abstract

The present invention is directed to compounds of Formula I which are LSD1 inhibitors useful in the treatment of diseases such as cancer.

Description

HETEROCYCLIC COMPOUNDS AS LSD1 INHIBITORS
FIELD OF THE INVENTION
The present invention is directed to heterocyclic compounds and compostions thereof which are LSD1 inhibitors useful in the treatment of diseases such as cancer. BACKGROUND OF THE INVENTION
Epigenetic modifications can impact genetic variation but, when dysregulated, can also contribute to the development of various diseases (Portela, A. and M. Esteller,
Epigenetic modifications and human disease. Nat Biotechnol, 2010.28(10): p.1057-68; Lund, A.H. and M. van Lohuizen, Epigenetics and cancer. Genes Dev, 2004.18(19): p. 2315-35). Recently, in depth cancer genomics studies have discovered many epigenetic regulatory genes are often mutated or their own expression is abnormal in a variety of cancers (Dawson, M.A. and T. Kouzarides, Cancer epigenetics: from mechanism to therapy. Cell, 2012.150(1): p.12-27; Waldmann, T. and R. Schneider, Targeting histone modifications-- epigenetics in cancer. Curr Opin Cell Biol, 2013.25(2): p.184-9; Shen, H. and P.W. Laird, Interplay between the cancer genome and epigenome. Cell, 2013.153(1): p.38-55). This implies epigenetic regulators function as cancer drivers or are permissive for tumorigenesis or disease progression. Therefore, deregulated epigenetic regulators are attractive therapeutic targets.
One particular enzyme which is associated with human diseases is lysine specific demethylase-1 (LSD1), the first discovered histone demethylase (Shi, Y., et al., Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 2004.119(7): p. 941-53). It consists of three major domains: the N-terminal SWIRM which functions in nucleosome targeting, the tower domain which is involved in protein-protein interaction, such as transcriptional co-repressor, co-repressor of RE1-silencing transcription factor (CoREST), and lastly the C terminal catalytic domain whose sequence and structure share homology with  the flavin adenine dinucleotide (FAD)-dependent monoamine oxidases (i.e., MAO-A and MAO-B) (Forneris, F., et al., Structural basis of LSD1-CoREST selectivity in histone H3 recognition. J Biol Chem, 2007.282(28): p.20070-4; Anand, R. and R. Marmorstein, Structure and mechanism of lysine-specific demethylase enzymes. J Biol Chem, 2007.
282(49): p.35425-9; Stavropoulos, P., G. Blobel, and A. Hoelz, Crystal structure and   mechanism of human lysine-specific demethylase-1. Nat Struct Mol Biol, 2006.13(7): p.626- 32; Chen, Y., et al., Crystal structure of human histone lysine-specific demethylase 1 (LSD1). Proc Natl Acad Sci U S A, 2006.103(38): p.13956-61). LSD1 also shares a fair degree of homology with another lysine specific demethylase (LSD2) (Karytinos, A., et al., A novel  mammalian flavin-dependent histone demethylase. J Biol Chem, 2009.284(26): p.17775- 82). Although the biochemical mechanism of action is conserved in two isoforms, the substrate specificities are thought to be distinct with relatively small overlap. The enzymatic reactions of LSD1 and LSD2 are dependent on the redox process of FAD and the requirement of a protonated nitrogen in the methylated lysine is thought to limit the activity of LSD1/2 to  mono- and di-methylated lysines at the position of 4 or 9 of histone 3 (H3K4 or H3K9).
These mechanisms make LSD1/2 distinct from other histone demethylase families (i.e.
Jumonji domain containing family) that can demethylate mono-, di-, and tri-methylated lysines through alpha-ketoglutarate dependent reactions (Kooistra, S.M. and K. Helin, Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell  Biol, 2012.13(5): p.297-311; Mosammaparast, N. and Y. Shi, Reversal of histone
methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem, 2010.79: p.155-79).
Methylated histone marks on H3K4 and H3K9 are generally coupled with transcriptional activation and repression, respectively. As part of corepressor complexes (e.g., CoREST), LSD1 has been reported to demethylate H3K4 and repress transcription, whereas LSD1, in nuclear hormone receptor complex (e.g., androgen receptor), may demethylate H3K9 to activate gene expression (Metzger, E., et al., LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature, 2005.437(7057): p.436-9; Kahl, P., et al., Androgen receptor coactivators lysine-specific histone demethylase 1 and four and a half LIM domain protein 2 predict risk of prostate cancer recurrence. Cancer Res, 2006.66(23): p.11341-7). This suggests the substrate specificity of LSD1 can be determined by associated factors, thereby regulating alternative gene expressions in a context dependent manner. In addition to histone proteins, LSD1 may demethylate non-histone proteins. These include p53 (Huang, J., et al., p53 is regulated by the lysine demethylase LSD1. Nature, 2007.449(7158): p.105-8.), E2F (Kontaki, H. and I. Talianidis, Lysine methylation regulates E2F1-induced cell death. Mol Cell, 2010.39(1): p. 152-60), STAT3 (Yang, J., et al., Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes. Proc Natl Acad Sci U S A, 2010.107(50): p.21499-504), Tat (Sakane, N., et al., Activation of HIV transcription by the viral Tat protein requires a
  demethylation step mediated by lysine-specific demethylase 1 (LSD1/KDM1). PLoS Pathog, 2011.7(8): p. e1002184), and myosin phosphatase target subunit 1 (MYPT1) (Cho, H.S., et al., Demethylation of RB regulator MYPT1 by histone demethylase LSD1 promotes cell cycle progression in cancer cells. Cancer Res, 2011.71(3): p.655-60). The lists of non-histone substrates are growing with technical advances in functional proteomics studies. These suggest additional oncogenic roles of LSD1 beyond regulating chromatin remodeling. LSD1 also associates with other epigenetic regulators, such as DNA methyltransferase 1 (DNMT1) (Wang, J., et al., The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat Genet, 2009.41(1): p.125-9) and histone deacetylases (HDACs) complexes (Hakimi, M.A., et al., A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. Proc Natl Acad Sci U S A, 2002.99(11): p. 7420-5; Lee, M.G., et al., Functional interplay between histone demethylase and deacetylase enzymes. Mol Cell Biol, 2006.26(17): p.6395-402; You, A., et al., CoREST is an integral component of the CoREST- human histone deacetylase complex. Proc Natl Acad Sci U S A, 2001.98(4): p.1454-8). These associations augment the activities of DNMT or HDACs. LSD1 inhibitors may therefore potentiate the effects of HDAC or DNMT inhibitors. Indeed, preclinical studies have shown such potential already (Singh, M.M., et al., Inhibition of LSD1 sensitizes glioblastoma cells to histone deacetylase inhibitors. Neuro Oncol, 2011.13(8): p. 894-903; Han, H., et al., Synergistic re-activation of epigenetically silenced genes by combinatorial inhibition of DNMTs and LSD1 in cancer cells. PLoS One, 2013.8(9): p. e75136).
LSD1 has been reported to contribute to a variety of biological processes, including cell proliferation, epithelial-mesenchymal transition (EMT), and stem cell biology (both embryonic stem cells and cancer stem cells) or self-renewal and cellular transformation of somatic cells (Chen, Y., et al., Lysine-specific histone demethylase 1 (LSD1): A potential molecular target for tumor therapy. Crit Rev Eukaryot Gene Expr, 2012.22(1): p.53-9; Sun, G., et al., Histone demethylase LSD1 regulates neural stem cell proliferation. Mol Cell Biol, 2010.30(8): p.1997-2005; Adamo, A., M.J. Barrero, and J.C. Izpisua Belmonte, LSD1 and pluripotency: a new player in the network. Cell Cycle, 2011.10(19): p.3215-6; Adamo, A., et al., LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells. Nat Cell Biol, 2011.13(6): p.652-9). In particular, cancer stem cells or cancer initiating cells have some pluripotent stem cell properties that contribute to the heterogeneity of cancer cells. This feature may render cancer cells more resistant to conventional therapies, such as chemotherapy or radiotherapy, and then develop recurrence  
after treatment (Clevers, H., The cancer stem cell: premises, promises and challenges. Nat Med, 2011.17(3): p.313-9; Beck, B. and C. Blanpain, Unravelling cancer stem cell potential. Nat Rev Cancer, 2013.13(10): p.727-38). LSD1 was reported to maintain an undifferentiated tumor initiating or cancer stem cell phenotype in a spectrum of cancers (Zhang, X., et al., Pluripotent Stem Cell Protein Sox2 Confers Sensitivity to LSD1 Inhibition in Cancer Cells. Cell Rep, 2013.5(2): p.445-57; Wang, J., et al., Novel histone demethylase LSD1 inhibitors selectively target cancer cells with pluripotent stem cell properties. Cancer Res, 2011.71(23): p.7238-49). Acute myeloid leukemias (AMLs) are an example of neoplastic cells that retain some of their less differentiated stem cell like phenotype or leukemia stem cell (LSC) potential. Analysis of AML cells including gene expression arrays and chromatin immunoprecipitation with next generation sequencing (ChIP-Seq) revealed that LSD1 may regulate a subset of genes involved in multiple oncogenic programs to maintain LSC (Harris, W.J., et al., The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells. Cancer Cell, 2012.21(4): p.473-87; Schenk, T., et al., Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia. Nat Med, 2012.18(4): p.605-11). These findings suggest potential therapeutic benefit of LSD1 inhibitors targeting cancers having stem cell properties, such as AMLs.
Overexpression of LSD1 is frequently observed in many types of cancers, including bladder cancer, NSCLC, breast carcinomas, ovary cancer, glioma, colorectal cancer, sarcoma including chondrosarcoma, Ewing’s sarcoma, osteosarcoma, and rhabdomyosarcoma, neuroblastoma, prostate cancer, esophageal squamous cell carcinoma, and papillary thyroid carcinoma. Notably, studies found over-expression of LSD1 was significantly associated with clinically aggressive cancers, for example, recurrent prostate cancer, NSCLC, glioma, breast, colon cancer, ovary cancer, esophageal squamous cell carcinoma, and neuroblastoma. In these studies, either knockdown of LSD1expression or treatment with small molecular inhibitors of LSD1 resulted in decreased cancer cell proliferation and/or induction of apoptosis. See, e.g., Hayami, S., et al., Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers. Int J Cancer, 2011.128(3): p.574-86; Lv, T., et al., Over-expression of LSD1 promotes proliferation, migration and invasion in non-small cell lung cancer. PLoS One, 2012.7(4): p. e35065; Serce, N., et al., Elevated expression of LSD1 (Lysine-specific demethylase 1) during tumour progression from pre-invasive to invasive ductal carcinoma of the breast. BMC Clin Pathol, 2012.12: p. 13; Lim, S., et al., Lysine-specific demethylase 1 (LSD1) is highly expressed in ER-negative  
breast cancers and a biomarker predicting aggressive biology. Carcinogenesis, 2010.31(3): p.512-20; Konovalov, S. and I. Garcia-Bassets, Analysis of the levels of lysine-specific demethylase 1 (LSD1) mRNA in human ovarian tumors and the effects of chemical LSD1 inhibitors in ovarian cancer cell lines. J Ovarian Res, 2013.6(1): p.75; Sareddy, G.R., et al., KDM1 is a novel therapeutic target for the treatment of gliomas. Oncotarget, 2013.4(1): p. 18-28; Ding, J., et al., LSD1-mediated epigenetic modification contributes to proliferation and metastasis of colon cancer. Br J Cancer, 2013.109(4): p.994-1003; Bennani-Baiti, I.M., et al., Lysine-specific demethylase 1 (LSD1/KDM1A/AOF2/BHC110) is expressed and is an epigen5etic drug target in chondrosarcoma, Ewing's sarcoma, osteosarcoma, and rhabdomyosarcoma. Hum Pathol, 2012.43(8): p.1300-7; Schulte, J.H., et al., Lysine-specific demethylase 1 is strongly expressed in poorly differentiated neuroblastoma: implications for therapy. Cancer Res, 2009.69(5): p.2065-71; Crea, F., et al., The emerging role of histone lysine demethylases in prostate cancer. Mol Cancer, 2012.11: p.52; Suikki, H.E., et al., Genetic alterations and changes in expression of histone demethylases in prostate cancer. Prostate, 2010.70(8): p.889-98; Yu, Y., et al., High expression of lysine-specific demethylase 1 correlates with poor prognosis of patients with esophageal squamous cell carcinoma. Biochem Biophys Res Commun, 2013.437(2): p.192-8; Kong, L., et al., Immunohistochemical expression of RBP2 and LSD1 in papillary thyroid carcinoma. Rom J Morphol Embryol, 2013.54(3): p.499-503.
Recently, the induction of CD86 expression by inhibiting LSD1 activity was reported (Lynch, J.T., et al., CD86 expression as a surrogate cellular biomarker for pharmacological inhibition of the histone demethylase lysine-specific demethylase 1. Anal Biochem, 2013. 442(1): p.104-6). CD86 expression is a marker of maturation of dendritic cells (DCs) which are involved in antitumor immune response. Notably, CD86 functions as a co-stimulatory factor to activate T cell proliferation (Greaves, P. and J.G. Gribben, The role of B7 family molecules in hematologic malignancy. Blood, 2013.121(5): p.734-44; Chen, L. and D.B. Flies, Molecular mechanisms of T cell co-stimulation and co-inhibition. Nat Rev Immunol, 2013.13(4): p.227-42).
In addition to playing a role in cancer, LSD1 activity has also been associated with viral pathogenesis. Particularly, LSD1 activity appears to be linked with viral replications and expressions of viral genes. For example, LSD1 functions as a co-activator to induce gene expression from the viral immediate early genes of various type of herpes virus including herpes simplex virus (HSV), varicella zoster virus (VZV), and ^-herpesvirus human  
cytomegalovirus (Liang, Y., et al., Targeting the JMJD2 histone demethylases to
epigenetically control herpesvirus infection and reactivation from latency. Sci Transl Med, 2013.5(167): p.167ra5; Liang, Y., et al., Inhibition of the histone demethylase LSD1 blocks alpha-herpesvirus lytic replication and reactivation from latency. Nat Med, 2009.15(11): p. 1312-7). In this setting, a LSD1 inhibitor showed antiviral activity by blocking viral replication and altering virus associated gene expression.
Recent studies have also shown that the inhibition of LSD1 by either genetic depletion or pharmacological intervention increased fetal globin gene expression in erythroid cells (Shi, L., et al., Lysine-specific demethylase 1 is a therapeutic target for fetal hemoglobin induction. Nat Med, 2013.19(3): p.291-4; Xu, J., et al., Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A. Proc Natl Acad Sci U S A, 2013.110(16): p.6518- 23). Inducing fetal globin gene would be potentially therapeutically beneficial for the disease of ^-globinopathies, including ^-thalassemia and sickle cell disease where the production of normal β-globin, a component of adult hemoglobin, is impaired (Sankaran, V.G. and S.H. Orkin, The switch from fetal to adult hemoglobin. Cold Spring Harb Perspect Med, 2013. 3(1): p. a011643; Bauer, D.E., S.C. Kamran, and S.H. Orkin, Reawakening fetal hemoglobin: prospects for new therapies for the beta-globin disorders. Blood, 2012.120(15): p.2945-53). Moreover, LSD1 inhibition may potentiate other clinically used therapies, such as hydroxyurea or azacitidine. These agents may act, at least in part, by increasing ^-globin gene expression through different mechanisms.
In summary, LSD1 contributes to tumor development by altering epigenetic marks on histones and non-histone proteins. Accumulating data have validated that either genetic depletion or pharmacological intervention of LSD1 normalizes altered gene expressions, thereby inducing differentiation programs into mature cell types, decreasing cell proliferation, and promoting apoptosis in cancer cells. Therefore, LSD1 inhibitors alone or in combination with established therapeutic drugs would be effective to treat the diseases associated with LSD1 activity. SUMMARY OF THE INVENTION
The present invention is directed to, inter alia, a compound of Formula I:
 
Figure imgf000008_0001
I
or a pharmaceutically acceptable salt thereof, wherein constituent variables are defined herein.
The present invention is further directed to a pharmaceutical composition comprising a compound of Formula I and at least one pharmaceutically acceptable carrier.
The present invention is further directed to a method of inhibiting LSD1 comprising contacting the LSD1 with a compound of Formula I.
The present invention is further directed to a method of modulating LSD1 comprising contacting the LSD1 with a compound of Formula I. The present invention is further directed to a method of mediating LSD1 comprising contacting the LSD1 with a compound of Formula I. The present invention is further directed to a method of modulating LSD1 signaling comprising contacting the LSD1 with a compound of Formula I.
The present invention is further directed to a method of treating an LSD1-mediated disease in a patient comprising administering to the patient a therapeutically effective amount of a compound of Formula I. DETAILED DESCRIPTION
The present invention provides, inter alia, LSD1-inhibiting compounds such as a compound of Formula I:
Figure imgf000008_0002
I
or a pharmaceutically acceptable salt thereof, wherein:
 
ring A is C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, or 4-10 membered heterocycloalkyl, wherein the 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the C3-10 cycloalkyl or 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group;
X is N or CRX, wherein RX is H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C1-4 haloalkoxy, NHC1-4 alkyl, N(C1-4 alkyl)2 or C1-4 alkylthio;
U is N or CRU, wherein RU is H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C1-4 haloalkoxy, NHC1-4 alkyl, N(C1-4 alkyl)2 or C1-4 alkylthio;
Y is N or CR4;
Z is N or CR5;
with the proviso that at least one of U, Y, and Z is N;
R1 is H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, C1-6haloalkoxy, NHOH, NHOC1-6 alkyl, Cy1, CN, ORa1, SRa1, C(O)Rb1, C(O)NRc1Rd1, C(O)ORa1, OC(O)Rb1, OC(O)NRc1Rd1, NRc1Rd1, NRc1C(O)Rb1, NRc1C(O)ORa1, NRc1C(O)NRc1Rd1, C(=NRe1)Rb1, C(=NRe1)NRc1Rd1, NRc1C(=NRe1)NRc1Rd1, NRc1S(O)Rb1, NRc1S(O)2Rb1, NRc1S(O)2NRc1Rd1, S(O)Rb1, S(O)NRc1Rd1, S(O)2Rb1, S(O)2NRc1Rd1, -L1-R6, or–L2-NR7R8; wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from Cy1, halo, CN, OH, ORa1, SRa1, C(O)Rb1, C(O)NRc1Rd1, C(O)ORa1, OC(O)Rb1, OC(O)NRc1Rd1, NRc1Rd1, NRc1C(O)Rb1, NRc1C(O)ORa1,
NRc1C(O)NRc1Rd1, C(=NRe1)Rb1, C(=NRe1)NRc1Rd1, NRc1C(=NRe1)NRc1Rd1, NRc1S(O)Rb1, NRc1S(O)2Rb1, NRc1S(O)2NRc1Rd1, S(O)Rb1, S(O)NRc1Rd1, S(O)2Rb1, and S(O)2NRc1Rd1;
L1 is a bond, -O-, -NR9-, -C(O)NH-, -NHC(O)-, C1-4 alkylene; wherein R9 is H, C1-6 alkyl, -C(O)C1-6 alkyl or–C(O)OC1-6 alkyl;
L2 is a bond, -C(O)-, C1-4 alkylene, -O-C1-4 alkylene-, -C1-4 alkylene-O-, -C1-4 alkylene-NR9-, or–NR9-C1-4 alkylene-;
R2, at each occurrence, is independently selected from H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C1-4 haloalkoxy, NHC1-4 alkyl, N(C1-4 alkyl)2, and C1-4 alkylthio;
R3, at each occurrence, is independently selected from H, Cy2, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, CN, ORa2, SRa2, C(O)Rb2, C(O)NRc2Rd2, C(O)ORa2, OC(O)Rb2, OC(O)NRc2Rd2, NRc2Rd2, NRc2C(O)Rb2, NRc2C(O)ORa2, NRc2C(O)NRc2Rd2, C(=NRe2)Rb2, C(=NRe2)NRc2Rd2, NRc2C(=NRe2)NRc2Rd2, NRc2S(O)Rb2, NRc2S(O)2Rb2,  
NRc2S(O)2NRc2Rd2, S(O)Rb2, S(O)NRc2Rd2, S(O)2Rb2, and S(O)2NRc2Rd2; wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from Cy2, halo, CN, ORa2, SRa2, C(O)Rb2, C(O)NRc2Rd2, C(O)ORa2, OC(O)Rb2, OC(O)NRc2Rd2, NRc2Rd2, NRc2C(O)Rb2, NRc2C(O)ORa2, NRc2C(O)NRc2Rd2, C(=NRe2)Rb2, C(=NRe2)NRc2Rd2, NRc2C(=NRe2)NRc2Rd2, NRc2S(O)Rb2, NRc2S(O)2Rb2, NRc2S(O)2NRc2Rd2, S(O)Rb2, S(O)NRc2Rd2, S(O)2Rb2, and S(O)2NRc2Rd2;
or two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 5- or 6-membered heterocycloalkyl ring, a fused C3-6 cycloalkyl ring, or a fused 5- or 6-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected RA substituents, wherein a ring carbon of the fused 5- or 6- membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring is optionally replaced by a carbonyl group;
alternatively, two RA substituents attached to the same carbon of the fused 5- or 6- membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring taken together form a C3-6 cycloalkyl ring or 4- to 7-membered heterocycloalkyl ring;
R4 and R5 are each independently selected from H, Cy3, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, CN, ORa3, SRa3, C(O)Rb3, C(O)NRc3Rd3, C(O)ORa3, OC(O)Rb3, OC(O)NRc3Rd3, NRc3Rd3, NRc3C(O)Rb3, NRc3C(O)ORa3, NRc3C(O)NRc3Rd3, C(=NRe3)Rb3, C(=NRe3)NRc3Rd3, NRc3C(=NRe3)NRc3Rd3, NRc3S(O)Rb3, NRc3S(O)2Rb3, NRc3S(O)2NRc3Rd3, S(O)Rb3, S(O)NRc3Rd3, S(O)2Rb3, and S(O)2NRc3Rd3; wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from Cy3, halo, CN, ORa3, SRa3, C(O)Rb3, C(O)NRc3Rd3, C(O)ORa3, OC(O)Rb3, OC(O)NRc3Rd3, NRc3Rd3, NRc3C(O)Rb3, NRc3C(O)ORa3, NRc3C(O)NRc3Rd3, C(=NRe3)Rb3, C(=NRe3)NRc3Rd3, NRc3C(=NRe3)NRc3Rd3, NRc3S(O)Rb3, NRc3S(O)2Rb3, NRc3S(O)2NRc3Rd3, S(O)Rb3, S(O)NRc3Rd3, S(O)2Rb3, and S(O)2NRc3Rd3;
R6 is 5- to 10-membered heteroaryl, 5- to 10-membered heteroaryl-C1-4 alkyl, 4- to 10- membered heterocycloalkyl, or 4- to 10-membered heterocycloalkyl-C1-4 alkyl, each of which is optionally substituted with 1, 2, 3 or 4 independently selected RA substituents;
R7 and R8 together with the nitrogen atom to which they are attached form 4- to 10- membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R7 and R8, wherein a ring-forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected RB substituents;
 
each RA is independently selected from H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, C1-6 haloalkoxy, Cy2, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl- C1-4 alkyl, 4-10 membered heterocycloalkyl-C1-4 alkyl, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4,
NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, C(=NRe4)Rb4, C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, Cy3, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl-C1-4 alkyl, and 4-10 membered heterocycloalkyl-C1-4 alkyl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1- 6 haloalkyl, C1-6 haloalkoxy, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4, NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, C(=NRe4)Rb4, C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4;
each RB is independently selected from H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, C1-6 haloalkoxy, Cy3, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl- C1-4 alkyl, 4-10 membered heterocycloalkyl-C1-4 alkyl, CN, NO2, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, Cy4, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl-C1-4 alkyl and 4-10 membered heterocycloalkyl-C1-4 alkyl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1- 6 haloalkyl, CN, NO2, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5,
OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Cy1, Cy2, Cy3, and Cy4 is independently selected from C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, and 4-10 membered heterocycloalkyl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from RCy;
each RCy is independently selected from H, halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, C2-6 alkenyl, C2-6 alkynyl, phenyl, C3-7 cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl, phenyl-C1-4 alkyl-, C3-7 cycloalkyl-C1-4 alkyl-, (5-6 membered heteroaryl)-C1-4 alkyl-, and (4-7 membered heterocycloalkyl)-C1-4 alkyl-, oxo, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4,
 
C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4, NRc4C(O)ORa4,
NRc4C(O)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4, wherein said C1-4 alkyl, C2-6 alkenyl, C2-6 alkynyl, phenyl, C3-7 cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl, phenyl-C1-4 alkyl-, C3- 7 cycloalkyl-C1-4 alkyl-, (5-6 membered heteroaryl)-C1-4 alkyl-, and (4-7 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted by 1, 2, or 3 substituents independently selected from C1-6 alkyl, C1-4 haloalkyl, C1-6 cyanoalkyl, halo, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4, NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4;
each Ra1, Rb1, Rc1, and Rd1 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5; or any Rc1 and Rd1 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, C6-10 aryl, 5-6 membered heteroaryl, C1-6 haloalkyl, halo CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, C6-10 aryl, and 5-6 membered heteroaryl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
 
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra2, Rb2, Rc2, and Rd2 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5; or any Rc2 and Rd2 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, 5-6 membered heteroaryl, C1-6 haloalkyl, halo, CN, ORa5, SRa5, C(O)Rb5,
C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, and 5-6 membered heteroaryl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra3, Rb3, Rc3, and Rd3 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered
 
heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5; or any Rc3 and Rd3 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, 5-6 membered heteroaryl, C1-6 haloalkyl, halo, CN, ORa5, SRa5, C(O)Rb5,
C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, and 5-6 membered heteroaryl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra4, Rb4, Rc4, and Rd4 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, and C2-6 alkynyl, wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
or any Rc4 and Rd4 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C1-6 haloalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5,  
NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra5, Rb5, Rc5, and Rd5 is independently selected from H, C1-4 alkyl, C1-4 haloalkyl, C2-4 alkenyl, and C2-4 alkynyl, wherein said C1-4 alkyl, C2-4 alkenyl, and C2-4 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from OH, CN, amino, halo, C1-4 alkyl, C1-4 alkoxy, C1-4 alkylthio, C1-4 alkylamino, di(C1-4 alkyl)amino, C1-4 haloalkyl, and C1-4 haloalkoxy;
each Re1, Re2, Re3, Re4, and Re5 is independently selected from H, C1-4 alkyl, and CN; the subscript m is 1 or 2; and
the subscript n is 1, 2, 3 or 4. In some embodiments, the compounds of the invention have Formula II:
Figure imgf000015_0001
Figure imgf000015_0002
In some embodiments, U is CRU. In some embodiments, the compounds of the invention have Formula IIIb:
 
Figure imgf000016_0001
  IIIb.
In some embodiments, U is N.
In some embodiments, h m n f h in n i n h ve Formula IIIa:
Figure imgf000016_0002
In some embodiments, Y is N.
In some embodiments, Y is CR4.
In some embodiments, Z is N.
In some embodiments, Z is CR5.
In some embodiments, Y and Z are each CH.
In some embodiments, (i) U, Y and Z are each N; (ii) U and Z are N and Y is CR4; (iii) U and Y are N and Z is CR5; (iv) U is N, Y is CR4, and Z is CR5; (v) U is CRU and both Yand Z are N; (vi) U is CRU, Y is N, and Z is CR5; or (vii) U is CRU, Y is CR4, and Z is N.
In some embodiments, U, Y and Z are each N.
In some embodiments, U and Z are N and Y is CR4.
In some embodiments, U and Y are N and Z is CR5.
In some embodiments, U is N, Y is CR4, and Z is CR5.
In some embodiments, U is CRU and both Yand Z are N.
In some embodiments, U is CRU, Y is N, and Z is CR5.
In some embodiments, U is CRU, Y is CR4, and Z is N.
In some embodiments, two of U, Y, and Z are N.
In some embodiments, one of U, Y, and Z are N.
 
In some embodiments, ring A is C6-10 aryl, 5-10 membered heteroaryl, or 4-10 membered heterocycloalkyl, wherein the 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group.
In some embodiments, ring A is phenyl, 5-6 membered heteroaryl, or 4-7 membered heterocycloalkyl, wherein the 5-6 membered heteroaryl or 4-7 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group. In some embodiments, ring A is C6-10 aryl.
In some embodiments, ring A is phenyl.
In some embodiments, ring A is 5-10 membered heteroaryl. In some embodiments, ring A is 5-6 membered heteroaryl. In some embodiments, ring A is 6 membered heteroaryl. In some embodiments, ring A is 5 membered heteroaryl.
In some embodiments, ring A is pyridyl, 1H-indazolyl, 1H-pyrrolo[2,3-b]pyridinyl, or 1H-benzo[d]imidazolyl.
In some embodiments, ring A is pyridyl.
In some embodiments, ring A is 4-10 membered heterocycloalkyl having at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized, and wherein a ring-forming carbon atom is optionally substituted by oxo to form a carbonyl group.
In some embodiments, ring A is 4-7 membered heterocycloalkyl having at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S optionally oxidized, and wherein a ring-forming carbon atom is optionally substituted by oxo to form a carbonyl group.
In some embodiments, ring A is 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro- 1,3-benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; 1H-pyrazolo[3,4-b]pyridinyl; 3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin- 7-yl; 2-oxo-2,3-dihydro-1H-benzimidazolyl; 1H-benzimidazolyl; 2-oxo-2,3- dihydro[1,3]oxazolo[4,5-b]pyridinyl, or 2,3-dihydro-1-benzofuranyl.
 
In some embodiments, ring A is 2,3-dihydro-1H-indolyl; 2,3-dihydro-1,3- benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3,4-dihydro-2H-1,4-benzoxazinyl; or 2,3-dihydro-1-benzofuran.
In some embodiments, ring A is 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro- 1,3-benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; or 2,3-dihydro-1-benzofuran.
In some embodiments, ring A is phenyl; 2,3-dihydro-1,4-benzodioxine; 2,3-dihydro- 1H-pyrrolo[2,3-b]pyridin-5-yl; 5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl; 2-oxo-1,2,3,4- tetrahydroquinolin-7-yl; pyridyl; 2-oxo-2,3-dihydro-1,3-benzoxazolyl; 1,3-benzothiazol-5-yl; 2,3-dihydro-1H-inden-5-yl; 1H-pyrrolo[2,3-b]pyridinyl; 8-quinoxalin-6-yl; 2-oxo-1,2,3,4- tetrahydroquinolin-6-yl; or 1H-pyrazolo[3,4-b]pyridinyl.
In some embodiments, ring A is phenyl; pyridyl; 1H-indazolyl; 1H-pyrrolo[2,3- b]pyridinyl; 1H-benzo[d]imidazolyl; 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro-1,3- benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; 1H-pyrazolo[3,4-b]pyridinyl; 3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin- 7-yl; 2-oxo-2,3-dihydro-1H-benzimidazolyl; 1H-benzimidazolyl; 2-oxo-2,3- dihydro[1,3]oxazolo[4,5-b]pyridinyl; 2,3-dihydro-1-benzofuranyl; 2,3-dihydro-1H-indolyl; 2,3-dihydro-1,3-benzoxazolyl; 3,4-dihydro-2H-1,4-benzoxazinyl; 2,3-dihydro-1,4- benzodioxine; 2,3-dihydro-1H-pyrrolo[2,3-b]pyridin-5-yl; 5,6,7,8-tetrahydro-1,8- naphthyridin-3-yl; 2-oxo-1,2,3,4-tetrahydroquinolin-7-yl; 1,3-benzothiazol-5-yl; 2,3-dihydro- 1H-inden-5-yl; 8-quinoxalin-6-yl; or 2-oxo-1,2,3,4-tetrahydroquinolin-6-yl.
In some embodiments, R3, at each occurrence, is independently selected from Cy2, C1- 6 alkyl, CN, ORa2, C(O)NRc2Rd2, and NRc2Rd2; wherein said C1-6 alkyl is optionally substituted with 1, 2, or 3 substituents independently selected from Cy2, C(O)Rb2, and C(O)NRc2Rd2.
In some embodiments, R3 is, at each occurrence, CN, methyl, methoxy, 1- pyrrolidinyl, 2-oxo-1-pyrrolidinyl, -C(O)N(CH3)2, dimethylamino, 4- methylpiperazinylmethyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl,
morpholinylmethyl, morpholinoethyl, or 3-cyano-1-pyrrolidinylmethyl.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 5- or 6-membered heterocycloalkyl ring, a fused C3-6 cycloalkyl ring, or a fused 5- or 6-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected RA substituents; wherein a ring  
carbon of the fused 5- or 6-membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring is optionally replaced by a carbonyl group;
alternatively, two RA substituents attached to the same carbon of the fused 5- or 6- membered heterocycloalkyl or fused C3-6 cycloalkyl taken together form a C3-6 cycloalkyl or 4- to 7-membered heterocycloalkyl ring.
In some embodiments, two RA substituents attached to the same carbon of the fused 5- or 6-membered heterocycloalkyl or fused C3-6 cycloalkyl taken together form a cyclopropyl group.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused ring selected from 1-methylpyrrolidine, 4- methyl-3-oxo-morpholine, 1-methylimidazole, 1-methylpiperidine, 1-methyl-2- oxopyrrolidine, and 1-methylpyrazole, each of which is optionally substituted with 1 or 2 RA substituents.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused ring selected from pyrrolidine, 3-oxo- morpholine, imidazole, piperidine, 2-oxopyrrolidine, and pyrazole, each of which is optionally substituted with 1 or 2 RA substituents.
In some embodiments, R3 is C1-6 alkyl, halo, C1-6 hydroxyalkyl, C1-6 haloalkyl, CN, ORa2, 1-pyrrolidinyl, 2-oxo-1-pyrrolidinyl, NRc2C(O)ORa2, -( C1-6 alkyl)-NRc2C(O)ORa2, C(O)NRc2Rd2, NRc2Rd2, piperazinylmethyl, 4-methylpiperazinylmethyl, piperidinyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl, morpholinylmethyl, or 3-cyano-1- pyrrolidinyl.
In some embodiments, R3 is C1-6 alkyl, CN, ORa2, 1-pyrrolidinyl, 2-oxo-1- pyrrolidinyl, C(O)NRc2Rd2, NRc2Rd2, piperazinylmethyl, 4-methylpiperazinylmethyl, piperidinyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl, morpholinylmethyl or 3- cyano-1-pyrrolidinyl.
In some embodiments, R3 is CN, F, hydroxymethyl, (CH3O)C(O)N(CH3)-,
(CH3O)C(O)N(CH3)-methyl, difluoromethyl, amino, methyl, methoxy, 1-pyrrolidinyl, 2-oxo- 1-pyrrolidinyl, -C(O)N(CH3)2, dimethylamino, 4-methylpiperazinylmethyl, morpholinyl, 4- methylpiperazinylcarbonylmethyl, morpholinylmethyl, morpholinoethyl, or 3-cyano-1- pyrrolidinylmethyl.
In some embodiments, R3 is, at each occurrence, CN, F, hydroxymethyl,
(CH3O)C(O)N(CH3)-, (CH3O)C(O)N(CH3)-methyl, difluoromethyl, methyl, methoxy, - C(O)N(CH3)2, dimethylamino, morpholinylmethyl, (CH3)S(O2)N(CH3)-methyl,
 
(CH3)2NC(O)N(CH3)-methyl , Cl, 1-hydroxyethyl, methoxymethyl, isopropyl, ethyl, (CH3)S(O2)N(CH3)-, or ethoxy.
In some embodiments, R3 is CN, F, hydroxymethyl, (CH3O)C(O)N(CH3)-,
(CH3O)C(O)N(CH3)-methyl, difluoromethyl, amino, methyl, methoxy, 1-pyrrolidinyl, 2-oxo- 1-pyrrolidinyl, -C(O)N(CH3)2, dimethylamino, 4-methylpiperazinylmethyl, morpholinyl, 4- methylpiperazinylcarbonylmethyl, morpholinylmethyl, morpholinoethyl, or 3-cyano-1- pyrrolidinylmethyl, (CH3)S(O2)N(CH3)-methyl, (CH3)2NC(O)N(CH3)-methyl , Cl, 1- hydroxyethyl, methoxymethyl, isopropyl, ethyl, (CH3)S(O2)N(CH3)-, or ethoxy.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form fused 5- or 6-membered heterocycloalkyl, fused C3-6 cycloalkyl or fused 5- or 6-membered heteroaryl, each of which is optionally substituted with 1-2 independently selected RA substituents, wherein a ring carbon of the fused 5- or 6- membered heterocycloalkyl or fused C3-6 cycloalkyl is optionally replaced by a carbonyl group.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form fused 5- or 6-membered heterocycloalkyl, which is optionally substituted with 1-2 independently selected RA substituents, wherein a ring carbon of the fused 5- or 6-membered heterocycloalkyl is optionally replaced by a carbonyl group.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-1H-pyrrolyl; 2-oxo-2,3-dihydro- 1H-pyrrolyl; 2,3-dihydro-oxazolyl; 2-oxo-2,3-dihydro-oxazolyl; 3,4-dihydro-2H-1,4- oxazinyl; 3-oxo-3,4-dihydro-2H-1,4-oxazinyl; or 2,3-dihydro-furanyl group, each of which is optionally substituted with 1-2 independently selected RA substituents.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-1H-pyrrolyl group, which is optionally substituted with one RA substituent.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a 2-oxo-2,3-dihydro-1H-pyrrolyl group, which is optionally substituted with one RA substituent.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-oxazolyl group, which is optionally substituted with one RA substituent.
 
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 2-oxo-2,3-dihydro-oxazolyl group, which is optionally substituted with one RA substituent.
In some embodiments, two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 2,3-dihydro-furanyl group, which is optionally substituted with one RA substituent.
In some embodiments, RA is C1-4 alkyl.
In some embodiments, RA is methyl.
In some embodiments, RA is -C(O)NRc4Rd4, wherein Rc4 and Rd4 are each, independently selected from H and C1-4 alkyl.
In some embodiments, RA is -C(O)N(CH3)2.
In some embodiments, R1 is -L1-R6 or–L2-NR7R8.
In some embodiments, R1 is–L2-NR7R8, wherein L2 is a bond, -C(O)-, C1-4 alkylene, - O-C1-4 alkylene, -C1-4 alkylene-O-, C1-4 alkylene-NH- or–NH-C1-4 alkylene.
In some embodiments, L2 is a -O-C1-4 alkylene.
In some embodiments, R7 and R8 together with the nitrogen atom to which they are attached form 4- to 6-membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R7 and R8, wherein a ring- forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected RB substituents.
In some embodiments, R1 is -L1-R6.
In some embodiments, L1 is -O-.
In some embodiments, R6 is 5- to 10-membered heteroaryl-C1-4 alkyl or 4- to 10- membered heterocycloalkyl-C1-4 alkyl, each of which is optionally substituted with 1, 2, 3 or 4 independently selected RA substituents.
In some embodiments, R6 is 4- to 10-membered heterocycloalkyl-C1-4 alkyl which is optionally substituted with 1, 2, 3 or 4 independently selected RA substituents.
In some embodiments, R6 is pyrrolidinyl-C1-4 alkyl- which is optionally substituted with 1, 2 or 3 independently selected RA substituents. In some embodiments, R6 is pyrrolidinyl-methylene- which is optionally substituted with 1, 2 or 3 independently selected RA substituents.
In some embodiments, R6 is piperidinyl-C1-4 alkyl- which is optionally substituted with 1, 2 or 3 independently selected RA substituents. In some embodiments, R6 is
 
piperidinyl- methylene- which is optionally substituted with 1, 2 or 3 independently selected RA substituents.
In some embodiments, R1 is ORa1.
In some embodiments, R1 is ORa1, wherein Ra1 is C1-6 alkyl substituted with Cy4. In some embodiments, R1 is ORa1, wherein Ra1 is methylene substituted with Cy4. In some embodiments, R1 is ORa1, wherein Ra1 is methylene substituted with 4-10 membered heterocycloalkyl optionally substituted with 1, 2, 3, or 4 substituents
independently selected from RCy.
In some embodiments, R1 is ORa1, wherein Ra1 is methylene substituted with 4-7 membered heterocycloalkyl optionally substituted with 1, 2, 3, or 4 substituents
independently selected from RCy.
In some embodiments, Cy4 is pyrrolidinyl or piperidinyl optionally substituted with 1 or 2 substituents independently selected from RCy.
In some embodiments, R1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3- yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, (2-hydroxyethylpiperidin-3-yl)methoxy, (2-methoxyethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, 7-methyl-2,7-diazaspiro[4.4]non-2-yl, or (1-methylpyrrolidin- 3-yl)methoxy.
In some embodiments, R1 is (1-methylpiperidin-3-yl)methoxy or (1-methylpyrrolidin- 3-yl)methoxy.
In some embodiments, R1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3- yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, (2-hydroxypropylpiperidin-3-yl)methoxy, or 2-hydroxy-2- methylpropyl)piperidin-3-yl]methoxy.
In some embodiments, R1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3- yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, (2-hydroxyethylpiperidin-3-yl)methoxy, (2-methoxyethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, 7-methyl-2,7-diazaspiro[4.4]non-2-yl, (1-methylpyrrolidin-3- yl)methoxy, or 2-hydroxy-2-methylpropyl)piperidin-3-yl]methoxy.
In some embodiments, R2 is H.
In some embodiments, R4 is H.
In some embodiments, R5 is H.
In some embodiments, RU is H.
In some embodiments, RX is H.
 
In some embodiments, m is 1.
In some embodiments, n is 1.
In some embodiments, the compounds of the invention have Formula IVa, IVb, IVc, IVd, IVe, or IVf:
Figure imgf000023_0001
IVe            IVf or a pharmaceutically acceptable salt thereof.
In some embodiments, the compounds provided herein have Formula IVg, IVh, or IVi:
 
Figure imgf000024_0001
IVg IVh
Figure imgf000024_0002
IVi
or a pharmaceutically acceptable salt thereof.
In m m im n h m n f h in n i n h F rm l I r I
(
Figure imgf000024_0003
IVa IVb
or a pharmaceutically acceptable salt thereof.
In some embodiments, the compounds of the invention have Formula IVa.
In some embodiments, the compounds of the invention have Formula IVb.
In some embodiments, the compounds of the invention have Formula IVc.
In some embodiments, the compounds of the invention have Formula IVd.
In some embodiments, the compounds of the invention have Formula IVe.
In some embodiments, the compounds of the invention have Formula IVf.
In some embodiments, the compounds of the invention have Formula IVg.
In some embodiments, the compounds of the invention have Formula IVh.
In some embodiments, the compounds of the invention have Formula IVi.
In some embodiments of compounds of Formula I, the present disclosure provides compounds having Formula V:
 
Figure imgf000025_0001
wherein X1 is CH or N.
In some embodiments of the compounds of Formula V:
two R3 substituents taken together with the carbon atoms to which they are attached form a fused 5-membered heterocycloalkyl ring or a fused 5-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected RA substituents, wherein a ring carbon of the fused 5-membered heterocycloalkyl ring is optionally replaced by a carbonyl group;
X1 is N or CH;
L2 is a bond or O-C 1-4 alkylene; and
R7 and R8 together with the nitrogen atom to which they are attached form 4- to 7- membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R7 and R8, wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected RB substituents.
In some aspects of these embodiments, X1 is CH. In other aspects of these embodiments X1 is N. In some aspects of these embodiments, L2 is a bond, -C(O)-, C1-4 alkylene, -O-C1-4 alkylene-, -C1-4 alkylene-O-, -C1-4 alkylene-NR9-, or–NR9-C1-4 alkylene-. In some aspects of these embodiments, two R3 substituents taken together with the carbon atoms to which they are attached form a fused 5-membered heterocycloalkyl ring or a fused 5- membered heteroaryl, each of which is optionally substituted with 1 or 2 independently selected RA substituents, wherein a ring carbon of the fused 5-membered heterocycloalkyl ring is optionally replaced by a carbonyl group. In some instances, a ring carbon of the fused 5-membered heterocycloalkyl ring is replaced by a carbonyl group. In some instances, RA is C1-4 alkyl such as methyl. In some instances, the fused 5-membered heterocycloalkyl ring or fused 5-membered heteroaryl has 1 or 2 heteroatoms as ring members selected from O, N or S. In some aspects of these embodiments, R7 and R8 together with the nitrogen atom to which they are attached form 4- to 7-membered heterocycloalkyl ring having 0, 1 or 2 additional heteroatoms selected from N and S as ring members, wherein a ring-forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and
 
wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected RB substituents. In some instances, RB is C1-4 alkyl such as methyl.
In one embodiment of compounds of Formula V, L2 is a bond. In another embodiment of compounds of Formula V, L2 is -O-C1-4 alkylene-. In yet another embodiment of compounds of Formula V, L2 is -OCH2-.
In some embodiments of compounds of Formula V, two R3 substituents taken together with the carbon atoms to which they are attached form a fused pyrazole ring optionally substituted with 1 or 2 RA substituents. In some aspects of these embodiments, RA is C1-4 alkyl such as methyl.
In some embodiments of compounds of Formula V, two R3 substituents taken together with the carbon atoms to which they are attached form a fused 2-oxo-oxazolidine ring, which is optionally substituted with 1 or 2 RB substitutents. In some aspects of these embodiments, RB is C1-4 alkyl such as methyl.
In some embodiments, moiety
Figure imgf000026_0001
Formula V is 1-methyl-1H- pyrazolo[3,4-b]pyridin-5-yl, 1-methyl-1H-indazol-5-yl, 3-methyl-2-oxo-3,4-dihydro-2H-1,3- benzoxazin-7-yl; 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl; 3-methyl-2-oxo- 2,3-dihydro-1,3-benzoxazol-6-yl; 5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl; 4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl; 2-(difluoromethyl)-1-methyl-1H- benzimidazol-5-yl; 1,2-dimethyl-1H-benzimidazol-5-yl, 6-methoxypyridin-3-yl, 5-fluoro-6- methoxypyridin-3-yl, 6-(2-oxopyrrolidin-1-yl)pyridin-3-yl, 1-methyl-1H-benzimidazol-5-yl, 6-methoxy-5-methylpyridin-3-yl, 4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl, 3-methyl-2-oxo-2,3-dihydro[1,3]oxazolo[4,5-b]pyridin-6-yl, 1-methyl-2-oxo-2,3-dihydro- 1H-indol-5-yl, 2-methylnicotinonitrile, or 5,6-dimethylpyridin-3-yl.
In some embodiments, the compounds of the invention have Formula VIa, VIb, or VIc:
Figure imgf000026_0002
VIa VIb
 
Figure imgf000027_0001
 
VIc.
In some embodiments, the compounds of the invention have Formula VIa.
In some embodiments, the compounds of the invention have Formula VIb.
In some embodiments, the compounds of the invention have Formula VIc.
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, can also be provided in combination in a single embodiment. Conversely, various features of the invention which are, for brevity, described in the context of a single embodiment, can also be provided separately or in any suitable subcombination.
As used herein, the phrase "optionally substituted" means unsubstituted or substituted. As used herein, the term "substituted" means that a hydrogen atom is removed and replaced by a monovalent substituent, or two hydrogen atoms are replaced with a divalent substituent like a terminal oxo group. It is to be understood that substitution at a given atom is limited by valency. Throughout the definitions, the term "Ci-j" indicates a range which includes the endpoints, wherein i and j are integers and indicate the number of carbons. Examples include C1-4, C1-6, and the like.
The term "z-membered" (where z is an integer) typically describes the number of ring-forming atoms in a moiety where the number of ring-forming atoms is z. For example, piperidinyl is an example of a 6-membered heterocycloalkyl ring, pyrazolyl is an example of a 5-membered heteroaryl ring, pyridyl is an example of a 6-membered heteroaryl ring, and 1, 2, 3, 4-tetrahydro-naphthalene is an example of a 10-membered cycloalkyl group.
As used herein, the term "Ci-j alkyl," employed alone or in combination with other terms, refers to a saturated hydrocarbon group that may be straight-chain or branched, having i to j carbons. In some embodiments, the alkyl group contains from 1 to 6 carbon atoms or from 1 to 4 carbon atoms, or from 1 to 3 carbon atoms. Examples of alkyl moieties include, but are not limited to, chemical groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, s- butyl, and t-butyl.
As used herein, the term "Ci-j alkylene," employed alone or in combination with other terms, means a saturated divalent linking hydrocarbon group that may be straight-chain or  
branched, having i to j carbons. In some embodiments, the alkylene group contains from 1 to 4 carbon atoms, from 1 to 3 carbon atoms, or from 1 to 2 carbon atoms. Examples of alkylene moieties include, but are not limited to, chemical groups such as methylene, ethylene, 1,1- ethylene, 1,2-ethylene , 1,3-propylene, 1,2-propylene, 1,1-propylene, isopropylene, and the like.
As used herein, the term "Ci-j alkoxy," employed alone or in combination with other terms, refers to a group of formula -O-alkyl, wherein the alkyl group has i to j carbons.
Example alkoxy groups include methoxy, ethoxy, and propoxy (e.g., n-propoxy and isopropoxy). In some embodiments, the alkyl group has 1 to 3 carbon atoms.
As used herein, "Ci-j alkenyl," employed alone or in combination with other terms, refers to an unsaturated hydrocarbon group having one or more double carbon-carbon bonds and having i to j carbons. In some embodiments, the alkenyl moiety contains 2 to 6 or 2 to 4 carbon atoms. Example alkenyl groups include, but are not limited to, ethenyl, n-propenyl, isopropenyl, n-butenyl, sec-butenyl, and the like.
As used herein, "Ci-j alkynyl," employed alone or in combination with other terms, refers to an unsaturated hydrocarbon group having one or more triple carbon-carbon bonds and having i to j carbons. Example alkynyl groups include, but are not limited to, ethynyl, propyn-1-yl, propyn-2-yl, and the like. In some embodiments, the alkynyl moiety contains 2 to 6 or 2 to 4 carbon atoms.
As used herein, the term "Ci-j alkylamino," employed alone or in combination with other terms, refers to a group of formula -NH(alkyl), wherein the alkyl group has i to j carbon atoms. In some embodiments, the alkyl group has 1 to 6 or 1 to 4 carbon atoms. In some embodiments, the alkylamino group is–NH(C1-4 alkyl) such as, for example, methylamino, ethylamino, or propylamino.
As used herein, the term "di-Ci-j-alkylamino," employed alone or in combination with other terms, refers to a group of formula -N(alkyl)2, wherein each of the two alkyl groups has, independently, i to j carbon atoms. In some embodiments, each alkyl group independently has 1 to 6 or 1 to 4 carbon atoms. In some embodiments, the dialkylamino group is–N(C1-4 alkyl)2 such as, for example, dimethylamino or diethylamino.
As used herein, the term "Ci-j alkylthio," employed alone or in combination with other terms, refers to a group of formula -S-alkyl, wherein the alkyl group has i to j carbon atoms. In some embodiments, the alkyl group has 1 to 6 or 1 to 4 carbon atoms. In some
embodiments, the alkylthio group is C1-4 alkylthio such as, for example, methylthio or ethylthio.
 
As used herein, the term "amino," employed alone or in combination with other terms, refers to a group of formula–NH2.
As used herein, the term "aryl," employed alone or in combination with other terms, refers to a monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic hydrocarbon, such as, but not limited to, phenyl, 1-naphthyl, 2-naphthyl, anthracenyl, phenanthrenyl, and the like. In some embodiments, aryl is C6-10 aryl. In some embodiments, the aryl group is a naphthalene ring or phenyl ring. In some embodiments, the aryl group is phenyl.
As used herein, the term "aryl-Ci-j alkyl," employed alone or in combination with other terms, refers to an alkyl group substituted by an aryl group. An example of an aryl-Ci-j alkyl group is benzyl.
As used herein, the term "carbonyl", employed alone or in combination with other terms, refers to a -C(O)- group.
As used herein, the term "Ci-j cycloalkyl," employed alone or in combination with other terms, refers to a non-aromatic cyclic hydrocarbon moiety having i to j ring-forming carbon atoms, which may optionally contain one or more alkenylene groups as part of the ring structure. Cycloalkyl groups can include mono- or polycyclic (e.g., having 2, 3 or 4 fused rings) ring systems. Also included in the definition of cycloalkyl are moieties that have one or more aromatic rings fused (i.e., having a bond in common with) to the cycloalkyl ring, for example, benzo derivatives of cyclopentane, cyclopentene, cyclohexane, and the like. A cycloalkyl group that includes a fused aromatic ring can be attached to the core or scaffold via any ring-forming atom, including a ring-forming atom of the fused aromatic group. One or more ring-forming carbon atoms of a cycloalkyl group can be oxidized to form carbonyl linkages. In some embodiments, cycloalkyl is C3-10 cycloalkyl, C3-7 cycloalkyl, or C5-6 cycloalkyl. Exemplary cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclopentenyl, cyclohexenyl, cyclohexadienyl, cycloheptatrienyl, norbornyl, norpinyl, norcarnyl, and the like. Further exemplary cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
As used herein, the term "Ci-j cycloalkyl-Ci-j alkyl," employed alone or in combination with other terms, refers to an alkyl group substituted by a cycloalkyl group. An example of a Ci-j cycloalkyl-Ci-j alkyl group is cyclopropylmethyl.
As used herein, "Ci-j haloalkoxy," employed alone or in combination with other terms, refers to a group of formula–O-haloalkyl having i to j carbon atoms. An example haloalkoxy group is OCF3. An additional example haloalkoxy group is OCHF2. In some embodiments,  
the haloalkoxy group is fluorinated only. In some embodiments, the alkyl group has 1 to 6 or 1 to 4 carbon atoms. In some embodiments, the haloalkoxy group is C1-4 haloalkoxy.
As used herein, the term "halo," employed alone or in combination with other terms, refers to a halogen atom selected from F, Cl, I or Br. In some embodiments, "halo" refers to a halogen atom selected from F, Cl, or Br. In some embodiments, the halo substituent is F.
As used herein, the term "Ci-j haloalkyl," employed alone or in combination with other terms, refers to an alkyl group having from one halogen atom to 2s+1 halogen atoms which may be the same or different, where "s" is the number of carbon atoms in the alkyl group, wherein the alkyl group has i to j carbon atoms. In some embodiments, the haloalkyl group is fluorinated only. In some embodiments, the haloalkyl group is fluoromethyl, difluoromethyl, or trifluoromethyl. In some embodiments, the haloalkyl group is trifluoromethyl. In some embodiments, the alkyl group has 1 to 6 or 1 to 4 carbon atoms.
As used herein, the term "heteroaryl," employed alone or in combination with other terms, refers to a monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic heterocylic moiety, having one or more heteroatom ring members selected from nitrogen, sulfur and oxygen. In some embodiments, the heteroaryl group has 1, 2, 3, or 4 heteroatom ring members. In some embodiments, the heteroaryl group has 1, 2, or 3 heteroatom ring members. In some embodiments, the heteroaryl group has 1 or 2 heteroatom ring members. In some embodiments, the heteroaryl group has 1 heteroatom ring member. In some embodiments, the heteroaryl group is 5- to 10-membered or 5- to 6-membered. In some embodiments, the heteroaryl group is 5-membered. In some embodiments, the heteroaryl group is 6-membered. When the heteroaryl group contains more than one heteroatom ring member, the heteroatoms may be the same or different. The nitrogen atoms in the ring(s) of the heteroaryl group can be oxidized to form N-oxides. Examplary heteroaryl groups include, but are not limited to, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, pyrrolyl, pyrazolyl, azolyl, oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, imidazolyl, furanyl, thiophenyl, triazolyl, tetrazolyl, thiadiazolyl, quinolinyl, isoquinolinyl, indolyl,
benzothiophenyl, benzofuranyl, benzisoxazolyl, imidazo[1, 2-b]thiazolyl, purinyl, triazinyl, and the like. In some embodiments, the heteroaryl group is pyridyl, 1H-indazolyl, 1H- pyrrolo[2,3-b]pyridinyl, or 1H-benzo[d]imidazolyl.
A 5-membered heteroaryl is a heteroaryl group having five ring-forming atoms comprising wherein one or more of the ring-forming atoms are independently selected from N, O, and S. In some embodiments, the 5-membered heteroaryl group has 1, 2, 3, or 4 heteroatom ring members. In some embodiments, the 5-membered heteroaryl group has 1, 2,  
or 3 heteroatom ring members. In some embodiments, the 5-membered heteroaryl group has 1 or 2 heteroatom ring members. In some embodiments, the 5-membered heteroaryl group has 1 heteroatom ring member. Example ring-forming members include CH, N, NH, O, and S. Example five-membered ring heteroaryls are thienyl, furyl, pyrrolyl, imidazolyl, thiazolyl, oxazolyl, pyrazolyl, isothiazolyl, isoxazolyl, 1, 2, 3-triazolyl, tetrazolyl, 1, 2, 3-thiadiazolyl, 1, 2, 3-oxadiazolyl, 1, 2, 4-triazolyl, 1, 2, 4-thiadiazolyl, 1, 2, 4-oxadiazolyl, 1, 3, 4-triazolyl, 1, 3, 4-thiadiazolyl, and 1, 3, 4-oxadiazolyl.
A 6-membered heteroaryl is a heteroaryl group having six ring-forming atoms wherein one or more of the ring-forming atoms is N. In some embodiments, the 6-membered heteroaryl group has 1, 2, or 3 heteroatom ring members. In some embodiments, the 6- membered heteroaryl group has 1 or 2 heteroatom ring members. In some embodiments, the 6-membered heteroaryl group has 1 heteroatom ring member. Example ring-forming members include CH and N. Example six-membered ring heteroaryls are pyridyl, pyrazinyl, pyrimidinyl, triazinyl, and pyridazinyl.
As used herein, the term "heteroaryl-Ci-j alkyl," employed alone or in combination with other terms, refers to an alkyl group substituted by a heteroaryl group. An example of a heteroaryl-Ci-j alkyl group is pyridylmethyl.
As used herein, the term "heterocycloalkyl," employed alone or in combination with other terms, refers to non-aromatic heterocyclic ring system, which may optionally contain one or more unsaturations as part of the ring structure, and which has at least one heteroatom ring member independently selected from nitrogen, sulfur and oxygen. In some embodiments, the heterocycloalkyl group has 1, 2, 3, or 4 heteroatom ring members. In some embodiments, the heterocycloalkyl group has 1, 2, or 3 heteroatom ring members. In some embodiments, the heterocycloalkyl group has 1 or 2 heteroatom ring members. In some embodiments, the heterocycloalkyl group has 1 heteroatom ring member. When the heterocycloalkyl group contains more than one heteroatom in the ring, the heteroatoms may be the same or different. Example ring-forming members include CH, CH2, C(O), N, NH, O, S, S(O), and S(O)2. Heterocycloalkyl groups can include mono- or polycyclic (e.g., having 2, 3 or 4 fused rings) ring systems, including spiro systems. Also included in the definition of heterocycloalkyl are moieties that have one or more aromatic rings fused to (i.e., having a bond in common with) the non-aromatic ring, for example, 1,2,3,4-tetrahydro-quinoline, dihydrobenzofuran, and the like. A heterocycloalkyl group including a fused aromatic ring can be attached to the core or scaffold via any ring-forming atom, including a ring-forming atom of the fused aromatic group. The S or N ring-forming atoms can be optionally“oxidized” to include one or two  
oxo groups as valency permits (e.g., sulfonyl or sulfinyl or N-oxide). One or more ring- forming carbon atoms of the heterocycloalkyl group can include an oxo moiety to form a ring-forming carbonyl. In some embodiments, a ring-forming nitrogen atom can be quaternized. In some embodiments, the heterocycloalkyl is 5- to 10-membered, 4- to 10- membered, 4- to 7-membered, 5-membered, or 6-membered. Examples of heterocycloalkyl groups include 1, 2, 3, 4-tetrahydro-quinolinyl, dihydrobenzofuranyl, azetidinyl, azepanyl, pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, thiomorpholinyl, dihydrofuranyl, tetrahydrofuranyl, 2-oxopyrrolidinyl, 3-oxomorpholinyl, 2-oxooxazolidinyl, and pyranyl. Further examples of heterocycloalkyl groups include 2,3-dihydro-1H-pyrrolyl; 2-oxo-2,3- dihydro-1H-pyrrolyl; 2,3-dihydro-oxazolyl; 2-oxo-2,3-dihydro-oxazolyl; 3,4-dihydro-2H-1,4- oxazinyl; 3-oxo-3,4-dihydro-2H-1,4-oxazinyl; or 2,3-dihydro-furanyl. In further
embodiments, the heterocycloalkyl group is azetidinyl, piperidinyl, pyrrolidinyl, diazapanyl, or diazaspirononanyl. In yet further embodiments, the heterocycloalkyl group is 2,3-dihydro- 1H-indolyl; 2,3-dihydro-1,3-benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3,4- dihydro-2H-1,4-benzoxazinyl; or 2,3-dihydro-1-benzofuran.
As used herein, the term "heterocycloalkyl-Ci-j alkyl," employed alone or in combination with other terms, refers to an alkyl group substituted by a heterocycloalkyl group. An example of a heterocycloalkyl-Ci-j alkyl group is pyrrolidinylmethyl.
The compounds described herein can be asymmetric (e.g., having one or more stereocenters). All stereoisomers, such as enantiomers and diastereoisomers, are intended unless otherwise indicated. Compounds of the present invention that contain asymmetrically substituted carbon atoms can be isolated in optically active or racemic forms. Methods on how to prepare optically active forms from optically inactive starting materials are known in the art, such as by resolution of racemic mixtures or by stereoselective synthesis. Many geometric isomers of olefins, C=N double bonds, and the like can also be present in the compounds described herein, and all such stable isomers are contemplated in the present invention. Cis and trans geometric isomers of the compounds of the present invention are described and may be isolated as a mixture of isomers or as separated isomeric forms.
When the compounds of the invention contain a chiral center, the compounds can be any of the possible stereoisomers. In compounds with a single chiral center, the
stereochemistry of the chiral center can be (R) or (S). In compounds with two chiral centers, the stereochemistry of the chiral centers can each be independently (R) or (S) so the configuration of the chiral centers can be (R) and (R), (R) and (S); (S) and (R), or (S) and (S). In compounds with three chiral centers, the stereochemistry each of the three chiral centers  
can each be independently (R) or (S) so the configuration of the chiral centers can be (R), (R) and (R); (R), (R) and (S); (R), (S) and (R); (R), (S) and (S); (S), (R) and (R); (S), (R) and (S); (S), (S) and (R); or (S), (S) and (S).
Resolution of racemic mixtures of compounds can be carried out by any of numerous methods known in the art. An example method includes fractional recrystallization using a chiral resolving acid which is an optically active, salt-forming organic acid. Suitable resolving agents for fractional recrystallization methods are, for example, optically active acids, such as the D and L forms of tartaric acid, diacetyltartaric acid, dibenzoyltartaric acid, mandelic acid, malic acid, lactic acid or the various optically active camphorsulfonic acids such as ^-camphorsulfonic acid. Other resolving agents suitable for fractional crystallization methods include stereoisomerically pure forms of ^-methylbenzylamine (e.g., S and R forms, or diastereoisomerically pure forms), 2-phenylglycinol, norephedrine, ephedrine, N- methylephedrine, cyclohexylethylamine, 1, 2-diaminocyclohexane, and the like.
Resolution of racemic mixtures can also be carried out by elution on a column packed with an optically active resolving agent (e.g., dinitrobenzoylphenylglycine). Suitable elution solvent composition can be determined by one skilled in the art.
Compounds of the invention also include tautomeric forms. Tautomeric forms result from the swapping of a single bond with an adjacent double bond together with the concomitant migration of a proton. Tautomeric forms include prototropic tautomers which are isomeric protonation states having the same empirical formula and total charge. Example prototropic tautomers include ketone– enol pairs, amide - imidic acid pairs, lactam– lactim pairs, amide - imidic acid pairs, enamine– imine pairs, and annular forms where a proton can occupy two or more positions of a heterocyclic system, for example, 1H- and 3H-imidazole, 1H-, 2H- and 4H- 1, 2, 4-triazole, 1H- and 2H- isoindole, and 1H- and 2H-pyrazole.
Tautomeric forms can be in equilibrium or sterically locked into one form by appropriate substitution.
Compounds of the invention can also include all isotopes of atoms occurring in the intermediates or final compounds. Isotopes include those atoms having the same atomic number but different mass numbers.
The term "compound" as used herein is meant to include all stereoisomers, geometric isomers, tautomers, and isotopes of the structures depicted. Compounds herein identified by name or structure as one particular tautomeric form are intended to include other tautomeric forms unless otherwise specified. The compounds of the invention are not limited by the  
manner in which they are made or formed. For example, the present invention includes compounds which are prepared synthetically, formed through a biological process or transformation, or a combination thereof.
All compounds, and pharmaceutically acceptable salts thereof, can be found together with other substances such as water and solvents (e.g., hydrates and solvates) or can be isolated.
In some embodiments, the compounds of the invention, or salts thereof, are substantially isolated. By "substantially isolated" is meant that the compound is at least partially or substantially separated from the environment in which it was formed or detected. Partial separation can include, for example, a composition enriched in a compound of the invention. Substantial separation can include compositions containing at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% by weight of the compounds of the invention, or salt thereof. Methods for isolating compounds and their salts are routine in the art.
The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
The expressions, "ambient temperature" and "room temperature," as used herein, are understood in the art, and refer generally to a temperature, e.g., a reaction temperature, that is about the temperature of the room in which the reaction is carried out, for example, a temperature from about 20 ºC to about 30 ºC.
The present invention also includes pharmaceutically acceptable salts of the compounds described herein. As used herein, "pharmaceutically acceptable salts" refers to derivatives of the disclosed compounds wherein the parent compound is modified by converting an existing acid or base moiety to its salt form. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts of the present invention include the conventional non-toxic salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. The pharmaceutically acceptable salts of the present invention can be synthesized from the parent compound which contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free  
acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, non-aqueous media like ether, ethyl acetate, alcohols (e.g., methanol, ethanol, iso-propanol, or butanol) or acetonitrile (MeCN) are preferred. Lists of suitable salts are found in Remington's
Pharmaceutical Sciences, 17th Ed., (Mack Publishing Company, Easton, 1985), p.1418, Berge et al., J. Pharm. Sci., 1977, 66(1), 1-19, and in Stahl et al., Handbook of
Pharmaceutical Salts: Properties, Selection, and Use, (Wiley, 2002).
The following abbreviations may be used herein: AcOH (acetic acid); Ac2O (acetic anhydride); aq. (aqueous); atm. (atmosphere(s)); Boc (t-butoxycarbonyl); BOP
((benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate); br (broad); Cbz (carboxybenzyl); calc. (calculated); d (doublet); dd (doublet of doublets); DBU (1,8- diazabicyclo[5.4.0]undec-7-ene); DCM (dichloromethane); DIAD (N, N'-diisopropyl azidodicarboxylate); DIEA (N,N-diisopropylethylamine); DIPEA (N, N- diisopropylethylamine); DMF (N, N-dimethylformamide); Et (ethyl); EtOAc (ethyl acetate); g (gram(s)); h (hour(s)); HATU (N, N, N', N'-tetramethyl-O-(7-azabenzotriazol-1-yl)uronium hexafluorophosphate); HCl (hydrochloric acid); HPLC (high performance liquid
chromatography); Hz (hertz); IPA (isopropyl alcohol); J (coupling constant); LCMS (liquid chromatography– mass spectrometry); m (multiplet); M (molar); mCPBA (3- chloroperoxybenzoic acid); MS (Mass spectrometry); Me (methyl); MeCN (acetonitrile); MeOH (methanol); mg (milligram(s)); min. (minutes(s)); mL (milliliter(s)); mmol
(millimole(s)); N (normal); nM (nanomolar); NMP (N-methylpyrrolidinone); NMR (nuclear magnetic resonance spectroscopy); OTf (trifluoromethanesulfonate); Ph (phenyl); pM (picomolar); RP-HPLC (reverse phase high performance liquid chromatography); s (singlet); t (triplet or tertiary); TBS (tert-butyldimethylsilyl); tert (tertiary); tt (triplet of triplets); TFA (trifluoroacetic acid); THF (tetrahydrofuran); µg (microgram(s)); µL (microliter(s)); µM (micromolar); wt % (weight percent). Synthesis
Compounds of the invention, including salts thereof, can be prepared using known organic synthesis techniques and can be synthesized according to any of numerous possible synthetic routes.
The reactions for preparing compounds of the invention can be carried out in suitable solvents which can be readily selected by one of skill in the art of organic synthesis. Suitable solvents can be substantially non-reactive with the starting materials (reactants), the
 
intermediates, or products at the temperatures at which the reactions are carried out, e.g., temperatures which can range from the solvent's freezing temperature to the solvent's boiling temperature. A given reaction can be carried out in one solvent or a mixture of more than one solvent. Depending on the particular reaction step, suitable solvents for a particular reaction step can be selected by the skilled artisan.
Preparation of compounds of the invention can involve the protection and
deprotection of various chemical groups. The need for protection and deprotection, and the selection of appropriate protecting groups, can be readily determined by one skilled in the art. The chemistry of protecting groups can be found, for example, in P. G. M. Wuts and T. W. Greene, Protective Groups in Organic Synthesis, 4th Ed., Wiley & Sons, Inc., New York (2006), which is incorporated herein by reference in its entirety. Protecting groups in the synthetic schemes are typically represented by“PG.”
Reactions can be monitored according to any suitable method known in the art. For example, product formation can be monitored by spectroscopic means, such as nuclear magnetic resonance spectroscopy (e.g., 1H or 13C), infrared spectroscopy, spectrophotometry (e.g., UV-visible), mass spectrometry, or by chromatographic methods such as high performance liquid chromatography (HPLC), liquid chromatography-mass spectroscopy (LCMS), or thin layer chromatography (TLC). Compounds can be purified by those skilled in the art by a variety of methods, including high performance liquid chromatography (HPLC) ("Preparative LC-MS Purification: Improved Compound Specific Method Optimization" Karl F. Blom, Brian Glass, Richard Sparks, Andrew P. Combs J. Combi. Chem.2004, 6(6), 874- 883, which is incorporated herein by reference in its entirety) and normal phase silica chromatography.
 
Figure imgf000037_0001
Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 1. The commercially available starting material 1 can undergo Suzuki coupling with the boronic acid or ester of formula 2 (R=H or alkyl) under standard Suzuki conditions (e.g., in the presence of a palladium catalyst and a base such as potassium carbonate) to afford compound 3. Bromination of compound 3 in the presence of N-bromosuccinimide (NBS) can give the compound of formula 4. Condensation of compound 4 with the carbonyl derivatives of formula 5 (Hal is a halide such as Cl or Br) at elevated temperature can generate the bicyclic compound of formula 6. The bromide in compound 6 can be coupled to a compound of formula 7, in which M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal], under standard Suzuki coupling conditions (e.g., in the presence of a palladium catalyst and a suitable base) or standard Stille coupling conditions (e.g., in the presence of a palladium catalyst), or standard Negishi coupling conditions (e.g., in the presence of a palladium catalyst) to give the derivative of formula 8. Alternatively, compound 7 can be a cyclic amine (where M is H and attached to an amine nitrogen) and the coupling of arylbromide 6 with the cyclic amine 7 can be performed under Buchwald amination conditions (e.g., in the presence of a palladium catalyst and a base such  
as sodium tert-butoxide). Convertion of the methoxy group in compound 8 to chloride can be achieved in the presence of phosphoryl chloride (POCl3) at suitable temperature to give compound of formula 9. Displacement of the chloride in compound 9 with a nucleophile of formula 10 (wherein R1-M is an alcohol or an amine, e.g., M is H which is attached to an alcohol oxygen or an amine nitrogen) in the presence of a suitable base such as sodium hydride, sodium hydroxide, potassium carbonate or diisopropylethylamine at elevated temperature can give compound of formula 11. Alternatively, the coupling of compound 9 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl)4], or standard Negishi coupling conditions (when M is Zn-Hal) to give compound 11.
Figure imgf000038_0001
14 Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 2 starting from compound 4 which can be prepared as described in Scheme 1. Compound 4 can be converted to a formamidoxime derivative of formula 12 by reacting with N,N-dimethylformamide dimethyl acetal, followed by treatment with hydroxylamine. The formamidoxime derivative 12 can undergo cyclization upon treating with trifluoroacetic anhydride (TFAA) to afford the triazole compound of formula 13. The preparation of compound 14 from compound 13 can be achieved using similar conditions as described in Scheme 1 (i.e., conditions used for preparation of compound 11 from compound 8).
 
Figure imgf000039_0001
22 23 24 Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 3. Bromination of compound 1 with a suitable reagent such as NBS can give compound 15. The amino group in compound 15 can be converted to iodine in the presence of a suitable nitrite such as isoamyl nitrite and an iodine source such as copper iodide (CuI) to give compound 16. Selective cyanation of compound 16 using Zn(CN)2 in the presence of a catalyst can deliver the pyrimidyl cyanide of formula 17. Reduction of the cyanide with a suitable reducing agent such as diisobutylaluminium hydride (DIBAL), lithium aluminium hydride (LAH) or borane (BH3) can afford the amine 18. Acylation of the amine 18 using acetic formic anhydride can generate an amide intermediate 19, which can undergo cyclization upon treatment with POCl3 to provide a bicyclic imidazole derivative of formula 20. Introduction of the ring A can be achieved by selective coupling of compound 20 with compound 7 using similar conditions as described in Scheme 1 (i.e., conditions for preparation of compound 8 from compound 6) to give compound of formula 21. Suzuki coupling of compound 21 with boronic ester/acid of formula 2 can give compound 22, which can be converted to the arylchloride 23 by reacting with POCl3. Coupling of arylchloride 23 with compound 10 using similar conditions as described in Scheme 1 can generate compound of formula 24.
 
Scheme 4
Figure imgf000040_0001
Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 4 starting from the commercially available compound 25. Introduction of the hydrazine moiety can be achieved via SNAr displacement of the chloride in compound 25 with hydrazine to give compound 26. A condensation reaction can be performed between compound 26 with compound of formula 27 at elevated temperature to produce compound 28. Preparation of compound 29 from compound 28 can be achieved using similar procedures as described in Scheme 3 (i.e., conditions used for preparation of compound 24 from compound 20).
 
(
Figure imgf000041_0001
Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 5. Selective Suzuki coupling of iodo-derivative of formula 30 with boronic acid/ester 2 under standard Suzuki coupling conditions (i.e. in the presence of a palladium catalyst and a suitable base) can give dichloro-compound 31. Selective displacement of one of the chlorides in compound 31 with methoxy by reacting with sodium methoxide can give compound 32. Bromination of compound 32 under suitable conditions (i.e. in the presence of NBS) can give compound 33, which can react with ammonia to give the aminopyridine derivative 34. Condensation of compound 34 with compound 5 can give the bicyclic compound 35. Installation of Ring A can be achieved using similar conditions as described in Scheme 1 (i.e., conditions used for preparation of compound 8 from compound 6) to give compound 36. The phenol derivative 37 can be prepared by demethylation of compound 36 under a suitable condition [i.e., boron tribromide (BBr3) or trimethylsilyl iodide (TMSI)]. Compound 38 can be prepared from compound 37 via Mitsunobu reaction with an alcohol  
(Ra1-OH) or alkylation with Ra1-Lg (Lg is a leaving group such as halide or OMs).
Alternatively, the phenol 37 can be converted to triflate 39 under suitable conditions (i.e., in the presence of triflic anhydride and a base such as pyridine). The coupling of triflate 39 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl)4], or standard Negishi coupling conditions (when M is Zn-Hal) to give compound 40.
Figure imgf000042_0001
43
 
Compounds of the invention can be prepared using the synthetic route outlined in Scheme 6. Condensation of aminopyridine 34 with N,N-dimethylformamide dimethyl acetal, followed by treatment with hydroxylamine can give the formamidoxime derivative of formula 41, which can undergo cyclization upon treating with trifluoroacetic anhydride (TFAA) to afford the triazole compound of formula 42. The preparation of compound 43 from compound 42 can be achieved using similar synthetic conditions as described in
Scheme 5 (i.e. procedures used for preparation of compound 40 or 38 from compound 35).
 
Scheme 7
Figure imgf000043_0001
Compounds of the invention can be prepared using the synthetic route outlined in Scheme 7. Introduction of the hydrazine moiety can be achieved via SNAr displacement of the chloride in compound 33 with hydrazine to give compound 44. A condensation reaction can be performed between compound 44 with compound of formula 27 at elevated temperature to produce compound 45. Preparation of compound 46 from compound 45 can be achieved using similar procedures as described in Scheme 5 (i.e. procedures used for preparation of compound 40 or 38 from compound 35).
 
Figure imgf000044_0001
53 54 Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 8 starting from the commercially available compound 47. Selective introduction of cyano group can be achieved by oxidation of the pyridine 47 with meta-chloroperoxybenzoic acid (m-CPBA) to N-oxide, followed by treatment with trimethylsilyl cyanide (TMS-CN) to give the cyano-derivative 48. Reduction of the cyanide with a suitable reducing agent such as diisobutylaluminium hydride (DIBAL), lithium aluminium hydride (LAH) or borane (BH3) can afford the amine 49. Acylation of the amine 49 using acetic formic anhydride can generate an amide intermediate 50, which can undergo cyclization upon treatment with POCl3 to provide a bicyclic imidazole derivative of formula 51. Installation of ring A can be achieved under standard cross-coupling conditions (i.e. conditions used for preparation of compound 8 from compound 6 as described in Scheme 1) to give compound 52. Suzuki coupling of the imidazopyridine chloride 52 with boronic acid/ester 2 can give compound 53. Compound 54 can be prepared from compound 53 using similar conditions as described in Scheme 5 (i.e., conditions used for the preparation of compound 38 or 40 from compound 36).
 
Scheme 9
Figure imgf000045_0001
Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 9. The commercially available starting material 1 can undergo Suzuki coupling with the boronic acid or ester of formula 2 (R=H or alkyl) under standard Suzuki conditions (e.g., in the presence of a palladium catalyst and a base such as potassium carbonate) to afford compound 3. Bromination of compound 3 in the presence of N-bromosuccinimide (NBS) can give the compound of formula 4. Condensation of compound 4 with the carbonyl derivatives of formula 55 (Hal is a halide such as Cl or Br) at elevated temperature can generate the bicyclic compound of formula 60. The bromide in compound 60 can be coupled to a compound of formula 7, in which M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal], under standard Suzuki coupling conditions (e.g., in the presence of a palladium catalyst and a suitable base) or standard Stille coupling conditions (e.g., in the presence of a palladium catalyst), or standard Negishi coupling conditions (e.g., in the presence of a palladium catalyst) to give the derivative of formula 61. Alternatively, compound 7 can be a cyclic amine (where M is H and attached to an amine nitrogen) and the coupling of arylbromide 60 with the cyclic amine 7 can be performed under Buchwald amination conditions (e.g., in the presence of a palladium catalyst  
and a base such as sodium tert-butoxide) to yield a compound of formula 61. Convertion of the methoxy group in compound 61 to chloride can be achieved in the presence of phosphoryl chloride (POCl3) at suitable temperature to give compound of formula 62. Displacement of the chloride in compound 62 with a nucleophile of formula 10 (wherein R1-M’ is an alcohol or an amine, e.g., M’ is H which is attached to an alcohol oxygen or an amine nitrogen) in the presence of a suitable base such as sodium hydride, sodium hydroxide, potassium carbonate or diisopropylethylamine at elevated temperature can give compound of formula 59.
Alternatively, the coupling of compound 62 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl)4], or standard Negishi coupling conditions (when M is Zn- Hal) to give compound 59.
Scheme 10
Figure imgf000046_0001
Compounds of the invention can be prepared via the synthetic route outlined in
Scheme 10. The commercially available starting material 1 can undergo Suzuki coupling with the boronic acid or ester of formula 2 (R=H or alkyl) under standard Suzuki conditions  
(e.g., in the presence of a palladium catalyst and a base such as potassium carbonate) to afford compound 3. Bromination of compound 3 in the presence of N-bromosuccinimide (NBS) can give the compound of formula 4. Condensation of compound 4 with the carbonyl derivatives of formula 55 (Hal is a halide such as Cl or Br) at elevated temperature can generate the bicyclic compound of formula 56. The hydroxyl group in compound 56 can be replaced with a halide (such as e.g. Cl), by treating compound 56 with an acid halide (e.g. acid chloride, such as for example phosphorus trichloride or phosphoryl chloride (phosphorus oxychloride)) to yield a compound of formula 57. Displacement of the chloride in compound 57 with a nucleophile of formula 10 (wherein R1-M’ is an alcohol or an amine, e.g., M’ is H which is attached to an alcohol oxygen or an amine nitrogen) in the presence of a suitable base such as sodium hydride, sodium hydroxide, potassium carbonate or
diisopropylethylamine at elevated temperature can give compound of formula 58.
Alternatively, the coupling of compound 57 with compound 10 can be performed under standard Suzuki conditions (when M is boronic acid or ester), or standard Stille coupling conditions [when M is Sn(Alkyl)4], or standard Negishi coupling conditions (when M is Zn- Hal) to give compound 58. The bromide in compound 58 can be coupled to a compound of formula 7, in which M is a boronic acid, boronic ester or an appropriately substituted metal [e.g., M is B(OR)2, Sn(Alkyl)4, or Zn-Hal], under standard Suzuki coupling conditions (e.g., in the presence of a palladium catalyst and a suitable base) or standard Stille coupling conditions (e.g., in the presence of a palladium catalyst), or standard Negishi coupling conditions (e.g., in the presence of a palladium catalyst) to give the derivative of formula 59. Alternatively, compound 7 can be a cyclic amine (where M is H and attached to an amine nitrogen) and the coupling of arylbromide 58 with the cyclic amine 7 can be performed under Buchwald amination conditions (e.g., in the presence of a palladium catalyst and a base such as sodium tert-butoxide) to yield a compound of formula 59. Methods of Use
Compounds of the invention are LSD1 inhibitors and, thus, are useful in treating diseases and disorders associated with activity of LSD1. For the uses described herein, any of the compounds of the invention, including any of the embodiments thereof, may be used.
The present invention is directed to a method of modulating LSD1 comprising contacting the LSD1 with a compound of Formula I. The present invention is further directed to a method of mediating LSD1 comprising contacting the LSD1 with a compound of  
Formula I. The present invention is further directed to a method of modulating LSD1 signaling comprising contacting the LSD1 with a compound of Formula I.
In some embodiments, the compounds of the invention are selective for LSD1 over LSD2, meaning that the compounds bind to or inhibit LSD1 with greater affinity or potency, compared to LSD2. In general, selectivity can be at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 50-fold, at least about 100-fold, at least about 200-fold, at least about 500-fold or at least about 1000-fold.
As inhibitors of LSD1, the compounds of the invention are useful in treating LSD1- mediated diseases and disorders. The term "LSD1-mediated disease” or“LSD1-mediated disorder" refers to any disease or condition in which LSD1 plays a role, or where the disease or condition is associated with expression or activity of LSD1. The compounds of the invention can therefore be used to treat or lessen the severity of diseases and conditions where LSD1 is known to play a role.
Diseases and conditions treatable using the compounds of the invention include, generally cancers, inflammation, autoimmune diseases, viral induced pathogenesis, beta- globinopathies, and other diseases linked to LSD1 activity.
Cancers treatable using compounds according to the present invention include, for example, hematological cancers, sarcomas, lung cancers, gastrointestinal cancers, genitourinary tract cancers, liver cancers, bone cancers, nervous system cancers,
gynecological cancers, and skin cancers.
Examplary hematological cancers includelymphomas and leukemias such as acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), acute promyelocytic leukemia (APL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), diffuse large B-cell lymphoma (DLBCL), mantle cell lymphoma, Non-Hodgkin lymphoma (including relapsed or refractory NHL and recurrent follicular), Hodgkin lymphoma, myeloproliferative diseases (e.g., primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocytosis (ET)), myelodysplasia syndrome (MDS), and multiple myeloma.
Examplary sarcomas includechondrosarcoma, Ewing’s sarcoma, osteosarcoma, rhabdomyosarcoma, angiosarcoma, fibrosarcoma, liposarcoma, myxoma, rhabdomyoma, fibroma, lipoma, harmatoma, and teratoma.
Examplary lung cancers includenon-small cell lung cancer (NSCLC), bronchogenic carcinoma (squamous cell, undifferentiated small cell, undifferentiated large cell,  
adenocarcinoma), alveolar (bronchiolar) carcinoma, bronchial adenoma, chondromatous hamartoma, and mesothelioma.
Examplary gastrointestinal cancers includecancers of the esophagus (squamous cell carcinoma, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel (adenocarcinoma, lymphoma, carcinoid tumors, Kaposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma), and colorectal cancer.
Examplary genitourinary tract cancers includecancers of the kidney (adenocarcinoma, Wilm's tumor [nephroblastoma]), bladder and urethra (squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), and testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma).
Examplary liver cancers includehepatoma (hepatocellular carcinoma),
cholangiocarcinoma, hepatoblastoma, angiosarcoma, hepatocellular adenoma, and hemangioma.
Examplary bone cancers include, for example, osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma, malignant giant cell tumor chordoma, osteochronfroma (osteocartilaginous exostoses), benign chondroma,
chondroblastoma, chondromyxofibroma, osteoid osteoma, and giant cell tumors
Examplary nervous system cancers includecancers of the skull (osteoma,
hemangioma, granuloma, xanthoma, osteitis deformans), meninges (meningioma, meningiosarcoma, gliomatosis), brain (astrocytoma, meduoblastoma, glioma, ependymoma, germinoma (pinealoma), glioblastoma multiform, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), and spinal cord (neurofibroma, meningioma, glioma, sarcoma), as well as neuroblastoma and Lhermitte-Duclos disease.
Examplary gynecological cancers includecancers of the uterus (endometrial carcinoma), cervix (cervical carcinoma, pre -tumor cervical dysplasia), ovaries (ovarian carcinoma (serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma), granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma,
adenocarcinoma, fibrosarcoma, melanoma), vagina (clear cell carcinoma, squamous cell  
carcinoma, botryoid sarcoma (embryonal rhabdomyosarcoma), and fallopian tubes
(carcinoma).
Examplary skin cancers includemelanoma, basal cell carcinoma, squamous cell carcinoma, Kaposi's sarcoma, moles dysplastic nevi, lipoma, angioma, dermatofibroma, and keloids.
The compounds of the invention can further be used to treat cancer types where LSD1 may be overexpressed including, for example, breast, prostate, head and neck, laryngeal, oral, and thyroid cancers (e.g., papillary thyroid carcinoma).
The compounds of the invention can further be used to treat genetic disorders such as Cowden syndrome and Bannayan-Zonana syndrome.
The compounds of the invention can further be used to treat viral diseases such as herpes simplex virus (HSV), varicella zoster virus (VZV), human cytomegalovirus, hepatitis B virus (HBV), and adenovirus.
The compounds of the invention can further be used to treat beta-globinopathies including, for example, beta-thalassemia and sickle cell anemia.
As used herein, the term "contacting" refers to the bringing together of indicated moieties in an in vitro system or an in vivo system. For example, "contacting" a LSD1 protein with a compound of the invention includes the administration of a compound of the present invention to an individual or patient, such as a human, having a LSD1 protein, as well as, for example, introducing a compound of the invention into a sample containing a cellular or purified preparation containing the LSD1 protein.
As used herein, the term "individual" or "patient, " used interchangeably, refers to any animal, including mammals, preferably mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, and most preferably humans.
As used herein, the phrase "therapeutically effective amount" refers to the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response that is being sought in a tissue, system, animal, individual or human by a researcher, veterinarian, medical doctor or other clinician.
As used herein, the term "treating" or "treatment" refers to inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e.,, arresting further development of the pathology and/or symptomatology) or ameliorating the disease; for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or  
disorder (i.e.,, reversing the pathology and/or symptomatology) such as decreasing the severity of disease.
As used herein, the term "preventing" or "prevention" refers to preventing the onset and development of a disease; for example, preventing a disease, condition or disorder in an individual who may be predisposed to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease. Combination Therapies
The compounds of the invention can be used in combination treatments where the compound of the invention is administered in conjunction with other treatments such as the administration of one or more additional therapeutic agents. The additional therapeutic agents are typically those which are normally used to treat the particular condition to be treated. The additional therapeutic agents can include, e.g., chemotherapeutics, anti-inflammatory agents, steroids, immunosuppressants, as well as Bcr-Abl, Flt-3, RAF, FAK, JAK, PIM, PI3K, PD-1, PD-L1, bromodomain, indoleamine 2,3-dioxygenase (IDO), TAM, FGFR inhibitors and other tumor directed therapies (small molecules or biologics in nature) for treatment of LSD1- mediated diseases, disorders or conditions. The one or more additional pharmaceutical agents can be administered to a patient simultaneously or sequentially. In some embodiments, the compounds of the present disclosure can be used in combination with a vaccine, an immunotherapy, such as LADD immunotherapy, CRS-207 or DPX-Survivac for the treatement of cancer.
In some embodiments, the compounds of the invention can be used in combination with a therapeutic agent that targets an epigenetic regulator. Examples of epigenetic regulators include bromodomain inhibitors, the histone lysine methyltransferases, histone arginine methyl transferases, histone demethylases, histone deacetylases, histone acetylases, and DNA methyltransferases. Histone deacetylase inhibitors include, e.g., vorinostat.
For treating cancer and other proliferative diseases, the compounds of the invention can be used in combination with chemotherapeutic agents, agonists or antagonists of nuclear receptors, or other anti-proliferative agents. The compounds of the invention can also be used in combination with a medical therapy such as surgery or radiotherapy, e.g., gamma- radiation, neutron beam radiotherapy, electron beam radiotherapy, proton therapy, brachytherapy, and systemic radioactive isotopes. Examples of suitable chemotherapeutic agents include any of: abarelix, aldesleukin, alemtuzumab, alitretinoin, allopurinol, altretamine, anastrozole, arsenic trioxide, asparaginase, azacitidine, bendamustine,
 
bevacizumab, bexarotene, bleomycin, bortezombi, bortezomib, busulfan intravenous, busulfan oral, calusterone, capecitabine, carboplatin, carmustine, cetuximab, chlorambucil, cisplatin, cladribine, clofarabine, cyclophosphamide, cytarabine, dacarbazine, dactinomycin, dalteparin sodium, dasatinib, daunorubicin, decitabine, denileukin, denileukin diftitox, dexrazoxane, docetaxel, doxorubicin, dromostanolone propionate, eculizumab, epirubicin, erlotinib, estramustine, etoposide phosphate, etoposide, exemestane, fentanyl citrate, filgrastim, floxuridine, fludarabine, fluorouracil, fulvestrant, gefitinib, gemcitabine, gemtuzumab ozogamicin, goserelin acetate, histrelin acetate, ibritumomab tiuxetan, idarubicin, ifosfamide, imatinib mesylate, interferon alfa 2a, irinotecan, lapatinib ditosylate, lenalidomide, letrozole, leucovorin, leuprolide acetate, levamisole, lomustine,
meclorethamine, megestrol acetate, melphalan, mercaptopurine, methotrexate, methoxsalen, mitomycin C, mitotane, mitoxantrone, nandrolone phenpropionate, nelarabine, nofetumomab, oxaliplatin, paclitaxel, pamidronate, panobinostat, panitumumab, pegaspargase,
pegfilgrastim, pemetrexed disodium, pentostatin, pipobroman, plicamycin, procarbazine, quinacrine, rasburicase, rituximab, ruxolitinib, sorafenib, streptozocin, sunitinib, sunitinib maleate, tamoxifen, temozolomide, teniposide, testolactone, thalidomide, thioguanine, thiotepa, topotecan, toremifene, tositumomab, trastuzumab, tretinoin, uracil mustard, valrubicin, vinblastine, vincristine, vinorelbine, vorinostat, and zoledronate.
In some embodiments, biological anticancer drugs, such as antibodies and cytokines, can be combined with the compounds of the present invention. In addition, drugs modulating microenvironment or immune responses can be combined with the compounds of the invention. Examples of such drugs include anti-Her2 antibodies, anti-CD20 antibodies, anti- CTLA1, anti-PD-1, anti-PDL1, and other immunotherapeutic drugs.
For treating cancer and other proliferative diseases, the compounds of the invention can be used in combination with targeted therapies, including JAK kinase inhibitors
(Ruxolitinib, additional JAK1/2 and JAK1-selective), Pim kinase inhibitors, TAM kinase inhibitors, PI3 kinase inhibitors including PI3K-delta selective (e.g., INCB50797), PI3K- gamma selective and broad spectrum PI3K inhibitors, MEK inhibitors, Cyclin Dependent kinase inhibitors, BRAF inhibitors, mTOR inhibitors, proteasome inhibitors (Bortezomib, Carfilzomib), HDAC-inhibitors (panobinostat, vorinostat), DNA methyl transferase inhibitors, dexamethasone, bromo and extra terminal family members inhibitors (for example, bromodomain inhibitors or BET inhibitors such as INCB54329 and INCB57643), FGFR inhibitors (e.g., INCB54828, INCB62079 and INCB63904) and indoleamine 2,3- dioxygenase inhibitors (e.g., epacadostat and GDC0919).
 
For treating autoimmune or inflammatory conditions, the compound of the invention can be administered in combination with a corticosteroid such as triamcinolone,
dexamethasone, fluocinolone, cortisone, prednisolone, or flumetholone.
For treating autoimmune or inflammatory conditions, the compound of the invention can be administered in combination with an immune suppressant such as fluocinolone acetonide (Retisert®), rimexolone (AL-2178, Vexol, Alcon), or cyclosporine (Restasis®).
For treating autoimmune or inflammatory conditions, the compound of the invention can be administered in combination with one or more additional agents selected from
Dehydrex™ (Holles Labs), Civamide (Opko), sodium hyaluronate (Vismed, Lantibio/TRB Chemedia), cyclosporine (ST-603, Sirion Therapeutics), ARG101(T) (testosterone, Argentis), AGR1012(P) (Argentis), ecabet sodium (Senju-Ista), gefarnate (Santen), 15-(s)- hydroxyeicosatetraenoic acid (15(S)-HETE), cevilemine, doxycycline (ALTY-0501, Alacrity), minocycline, iDestrin™ (NP50301, Nascent Pharmaceuticals), cyclosporine A (Nova22007, Novagali), oxytetracycline (Duramycin, MOLI1901, Lantibio), CF101 (2S, 3S, 4R, 5R)-3, 4-dihydroxy-5-[6-[(3-iodophenyl)methylamino]purin-9-yl]-N-methyl-oxolane-2- carbamyl, Can-Fite Biopharma), voclosporin (LX212 or LX214, Lux Biosciences), ARG103 (Agentis), RX-10045 (synthetic resolvin analog, Resolvyx), DYN15 (Dyanmis Therapeutics), rivoglitazone (DE011, Daiichi Sanko), TB4 (RegeneRx), OPH-01 (Ophtalmis Monaco), PCS101 (Pericor Science), REV1-31 (Evolutec), Lacritin (Senju), rebamipide (Otsuka- Novartis), OT-551 (Othera), PAI-2 (University of Pennsylvania and Temple University), pilocarpine, tacrolimus, pimecrolimus (AMS981, Novartis), loteprednol etabonate, rituximab, diquafosol tetrasodium (INS365, Inspire), KLS-0611 (Kissei Pharmaceuticals),
dehydroepiandrosterone, anakinra, efalizumab, mycophenolate sodium, etanercept
(Embrel®), hydroxychloroquine, NGX267 (TorreyPines Therapeutics), or thalidomide.
For treating beta-thalassemia or sickle cell disease, the compound of the invention can be administered in combination with one or more additional agents such as Hydrea®
(hydroxyurea).
In some embodiments, the compound of the invention can be administered in combination with one or more agents selected from an antibiotic, antiviral, antifungal, anesthetic, anti-inflammatory agents including steroidal and non-steroidal anti- inflammatories, and anti-allergic agents. Examples of suitable medicaments include aminoglycosides such as amikacin, gentamycin, tobramycin, streptomycin, netilmycin, and kanamycin; fluoroquinolones such as ciprofloxacin, norfloxacin, ofloxacin, trovafloxacin, lomefloxacin, levofloxacin, and enoxacin; naphthyridine; sulfonamides; polymyxin;
 
chloramphenicol; neomycin; paramomycin; colistimethate; bacitracin; vancomycin;
tetracyclines; rifampin and its derivatives ("rifampins"); cycloserine; beta-lactams;
cephalosporins; amphotericins; fluconazole; flucytosine; natamycin; miconazole;
ketoconazole; corticosteroids; diclofenac; flurbiprofen; ketorolac; suprofen; cromolyn;
lodoxamide; levocabastin; naphazoline; antazoline; pheniramine; or azalide antibiotic.
Other examples of agents, one or more of which a provided LSD1 inhibitor compound may also be combined with include: a treatment for Alzheimer's Disease such as donepezil and rivastigmine; a treatment for Parkinson's Disease such as L-DOPA/carbidopa, entacapone, ropinirole, pramipexole, bromocriptine, pergolide, trihexyphenidyl, and amantadine; an agent for treating multiple sclerosis (MS) such as beta interferon (e.g., Avonex® and Rebif®), glatiramer acetate, and mitoxantrone; a treatment for asthma such as albuterol and montelukast; an agent for treating schizophrenia such as zyprexa, risperdal, seroquel, and haloperidol; an anti-inflammatory agent such as a corticosteroid, such as dexamethasone or prednisone, a TNF blocker, IL-1 RA, azathioprine, cyclophosphamide, and sulfasalazine; an immunomodulatory agent, including immunosuppressive agents, such as cyclosporin, tacrolimus, rapamycin, mycophenolate mofetil, an interferon, a corticosteroid, cyclophosphamide, azathioprine, and sulfasalazine; a neurotrophic factor such as an acetylcholinesterase inhibitor, an MAO inhibitor, an interferon, an anti-convulsant, an ion channel blocker, riluzole, or an anti-Parkinson's agent; an agent for treating cardiovascular disease such as a beta-blocker, an ACE inhibitor, a diuretic, a nitrate, a calcium channel blocker, or a statin; an agent for treating liver disease such as a corticosteroid,
cholestyramine, an interferon, and an anti-viral agent; an agent for treating blood disorders such as a corticosteroid, an anti-leukemic agent, or a growth factor; or an agent for treating immunodeficiency disorders such as gamma globulin.
Compounds of the present disclosure can be used in combination with one or more immune checkpoint inhibitors. Exemplary immune checkpoint inhibitors include inhibitors against immune checkpoint molecules such as CD27, CD28, CD40, CD122, CD96, CD73, CD47, OX40, GITR, CSF1R, JAK, PI3K delta, PI3K gamma, TAM, arginase, CD137 (also known as 4-1BB), ICOS, A2AR, B7-H3, B7-H4, BTLA, CTLA-4, LAG3, TIM3, VISTA, PD-1, PD-L1 and PD-L2. In some embodiments, the immune checkpoint molecule is a stimulatory checkpoint molecule selected from CD27, CD28, CD40, ICOS, OX40, GITR and CD137. In some embodiments, the immune checkpoint molecule is an inhibitory checkpoint molecule selected from A2AR, B7-H3, B7-H4, BTLA, CTLA-4, IDO, KIR, LAG3, PD-1, TIM3, and VISTA. In some embodiments, the compounds provided herein can be used in  
combination with one or more agents selected from KIR inhibitors, TIGIT inhibitors, LAIR1 inhibitors, CD160 inhibitors, 2B4 inhibitors and TGFR beta inhibitors.
In some embodiments, the inhibitor of an immune checkpoint molecule is anti-PD1 antibody, anti-PD-L1 antibody, or anti-CTLA-4 antibody.
In some embodiments, the inhibitor of an immune checkpoint molecule is an inhibitor of PD-1, e.g., an anti-PD-1 monoclonal antibody. In some embodiments, the anti-PD-1 monoclonal antibody is nivolumab, pembrolizumab (also known as MK-3475), pidilizumab, SHR-1210, PDR001, or AMP-224. In some embodiments, the anti-PD-1 monoclonal antibody is nivolumab or pembrolizumab. In some embodiments, the anti-PD1 antibody is pembrolizumab. In some embodiments, the anti PD-1 antibody is SHR-1210.
In some embodiments, the inhibitor of an immune checkpoint molecule is an inhibitor of PD-L1, e.g., an anti-PD-L1 monoclonal antibody. In some embodiments, the anti-PD-L1 monoclonal antibody is BMS-935559, MEDI4736, MPDL3280A (also known as RG7446), or MSB0010718C. In some embodiments, the anti-PD-L1 monoclonal antibody is
MPDL3280A or MEDI4736.
In some embodiments, the inhibitor of an immune checkpoint molecule is an inhibitor of CTLA-4, e.g., an anti-CTLA-4 antibody. In some embodiments, the anti-CTLA-4 antibody is ipilimumab.
In some embodiments, the inhibitor of an immune checkpoint molecule is an inhibitor of LAG3, e.g., an anti-LAG3 antibody. In some embodiments, the anti-LAG3 antibody is BMS-986016 or LAG525.
In some embodiments, the inhibitor of an immune checkpoint molecule is an inhibitor of GITR, e.g., an anti-GITR antibody. In some embodiments, the anti-GITR antibody is TRX518 or MK-4166.
In some embodiments, the inhibitor of an immune checkpoint molecule is an inhibitor of OX40, e.g., an anti-OX40 antibody or OX40L fusion protein. In some embodiments, the anti-OX40 antibody is MEDI0562. In some embodiments, the OX40L fusion protein is MEDI6383.
Compounds of the present disclosure can be used in combination with one or more agents for the treatment of diseases such as cancer. In some embodiments, the agent is an alkylating agent, a proteasome inhibitor, a corticosteroid, or an immunomodulatory agent. Examples of an alkylating agent include cyclophosphamide (CY), melphalan (MEL), and bendamustine. In some embodiments, the proteasome inhibitor is carfilzomib. In some  
embodiments, the corticosteroid is dexamethasone (DEX). In some embodiments, the immunomodulatory agent is lenalidomide (LEN) or pomalidomide (POM). Formulation, Dosage Forms and Administration
When employed as pharmaceuticals, the compounds of the invention can be administered in the form of pharmaceutical compositions. These compositions can be prepared in a manner well known in the pharmaceutical art, and can be administered by a variety of routes, depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including transdermal, epidermal, ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal or intranasal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal intramuscular or injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump. Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
This invention also includes pharmaceutical compositions which contain, as the active ingredient, the compound of the invention or a pharmaceutically acceptable salt thereof, in combination with one or more pharmaceutically acceptable carriers (excipients). In some embodiments, the composition is suitable for topical administration. In making the compositions of the invention, the active ingredient is typically mixed with an excipient, diluted by an excipient or enclosed within such a carrier in the form of, for example, a capsule, sachet, paper, or other container. When the excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier or medium for the active ingredient. Thus, the compositions can be in the form of tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, suppositories, sterile injectable solutions, and sterile packaged powders.
In preparing a formulation, the active compound can be milled to provide the appropriate particle size prior to combining with the other ingredients. If the active compound  
is substantially insoluble, it can be milled to a particle size of less than 200 mesh. If the active compound is substantially water soluble, the particle size can be adjusted by milling to provide a substantially uniform distribution in the formulation, e.g., about 40 mesh.
The compounds of the invention may be milled using known milling procedures such as wet milling to obtain a particle size appropriate for tablet formation and for other formulation types. Finely divided (nanoparticulate) preparations of the compounds of the invention can be prepared by processes known in the art, e.g., see International App. No. WO 2002/000196.
Some examples of suitable excipients include lactose, dextrose, sucrose, sorbitol, mannitol, starches, gum acacia, calcium phosphate, alginates, tragacanth, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, and methyl cellulose. The formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl- and propylhydroxy-benzoates; sweetening agents; and flavoring agents. The compositions of the invention can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art.
The compositions can be formulated in a unit dosage form, each dosage containing from about 5 to about 1,000 mg (1 g), more usually about 100 mg to about 500 mg, of the active ingredient. The term "unit dosage forms" refers to physically discrete units suitable as unitary dosages for human subjects and other mammals, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient.
The active compound may be effective over a wide dosage range and is generally administered in a pharmaceutically effective amount. It will be understood, however, that the amount of the compound actually administered will usually be determined by a physician, according to the relevant circumstances, including the condition to be treated, the chosen route of administration, the actual compound administered, the age, weight, and response of the individual patient, the severity of the patient's symptoms, and the like.
For preparing solid compositions such as tablets, the principal active ingredient is mixed with a pharmaceutical excipient to form a solid preformulation composition containing a homogeneous mixture of a compound of the present invention. When referring to these preformulation compositions as homogeneous, the active ingredient is typically dispersed evenly throughout the composition so that the composition can be readily subdivided into  
equally effective unit dosage forms such as tablets, pills and capsules. This solid
preformulation is then subdivided into unit dosage forms of the type described above containing from, for example, about 0.1 to about 1000 mg of the active ingredient of the present invention.
The tablets or pills of the present invention can be coated or otherwise compounded to provide a dosage form affording the advantage of prolonged action. For example, the tablet or pill can comprise an inner dosage and an outer dosage component, the latter being in the form of an envelope over the former. The two components can be separated by an enteric layer which serves to resist disintegration in the stomach and permit the inner component to pass intact into the duodenum or to be delayed in release. A variety of materials can be used for such enteric layers or coatings, such materials including a number of polymeric acids and mixtures of polymeric acids with such materials as shellac, cetyl alcohol, and cellulose acetate.
The liquid forms in which the compounds and compositions of the present invention can be incorporated for administration orally or by injection include aqueous solutions, suitably flavored syrups, aqueous or oil suspensions, and flavored emulsions with edible oils such as cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as elixirs and similar pharmaceutical vehicles.
Compositions for inhalation or insufflation include solutions and suspensions in pharmaceutically acceptable, aqueous or organic solvents, or mixtures thereof, and powders. The liquid or solid compositions may contain suitable pharmaceutically acceptable excipients as described supra. In some embodiments, the compositions are administered by the oral or nasal respiratory route for local or systemic effect. Compositions can be nebulized by use of inert gases. Nebulized solutions may be breathed directly from the nebulizing device or the nebulizing device can be attached to a face masks tent, or intermittent positive pressure breathing machine. Solution, suspension, or powder compositions can be administered orally or nasally from devices which deliver the formulation in an appropriate manner.
Topical formulations can contain one or more conventional carriers. In some embodiments, ointments can contain water and one or more hydrophobic carriers selected from, for example, liquid paraffin, polyoxyethylene alkyl ether, propylene glycol, white vaseline, and the like. Carrier compositions of creams can be based on water in combination with glycerol and one or more other components, e.g., glycerinemonostearate, PEG- glycerinemonostearate and cetylstearyl alcohol. Gels can be formulated using isopropyl alcohol and water, suitably in combination with other components such as, for example,  
glycerol, hydroxyethyl cellulose, and the like. In some embodiments, topical formulations contain at least about 0.1, at least about 0.25, at least about 0.5, at least about 1, at least about 2, or at least about 5 wt % of the compound of the invention. The topical formulations can be suitably packaged in tubes of, for example, 100 g which are optionally associated with instructions for the treatment of the select indication, e.g., psoriasis or other skin condition.
The amount of compound or composition administered to a patient will vary depending upon what is being administered, the purpose of the administration, such as prophylaxis or therapy, the state of the patient, the manner of administration, and the like. In therapeutic applications, compositions can be administered to a patient already suffering from a disease in an amount sufficient to cure or at least partially arrest the symptoms of the disease and its complications. Effective doses will depend on the disease condition being treated as well as by the judgment of the attending clinician depending upon factors such as the severity of the disease, the age, weight and general condition of the patient, and the like.
The compositions administered to a patient can be in the form of pharmaceutical compositions described above. These compositions can be sterilized by conventional sterilization techniques, or may be sterile filtered. Aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile aqueous carrier prior to administration. The pH of the compound preparations typically will be between 3 and 11, more preferably from 5 to 9 and most preferably from 7 to 8. It will be understood that use of certain of the foregoing excipients, carriers, or stabilizers will result in the formation of pharmaceutical salts.
The therapeutic dosage of a compound of the present invention can vary according to, for example, the particular use for which the treatment is made, the manner of administration of the compound, the health and condition of the patient, and the judgment of the prescribing physician. The proportion or concentration of a compound of the invention in a
pharmaceutical composition can vary depending upon a number of factors including dosage, chemical characteristics (e.g., hydrophobicity), and the route of administration. For example, the compounds of the invention can be provided in an aqueous physiological buffer solution containing about 0.1 to about 10% w/v of the compound for parenteral administration. Some typical dose ranges are from about 1 ^g/kg to about 1 g/kg of body weight per day. In some embodiments, the dose range is from about 0.01 mg/kg to about 100 mg/kg of body weight per day. The dosage is likely to depend on such variables as the type and extent of progression of the disease or disorder, the overall health status of the particular patient, the  
relative biological efficacy of the compound selected, formulation of the excipient, and its route of administration. Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.
The compositions of the invention can further include one or more additional pharmaceutical agents such as a chemotherapeutic, steroid, anti-inflammatory compound, or immunosuppressant, examples of which are listed hereinabove.
The compounds of the invention can be provided with or used in combination with a companion diagnostic. As used herein, the term“companion diagnostic” refers to a diagnostic device useful for determining the safe and effective use of a therapeutic agent. For example, a companion diagnostic may be used to customize dosage of a therapeutic agent for a given subject, identify appropriate subpopulations for treatment, or identify populations who should not receive a particular treatment because of an increased risk of a serious side effect.
In some embodiments, the companion diagnostic is used to monitor treatment response in a patient. In some embodiments, the companion diagnostic is used to identify a subject that is likely to benefit from a given compound or therapeutic agent. In some embodiments, the companion diagnostic is used to identify a subject having an increased risk of adverse side effects from administration of a therapeutic agent, compared to a reference standard. In some embodiments, the companion diagnostic is an in vitro diagnostic or imaging tool selected from the list of FDA cleared or approved companion diagnostic devices. In some embodiments, the companion diagnostic is selected from the list of tests that have been cleared or approved by the Center for Devices and Radiological Health. Labeled Compounds and Assay Methods
Another aspect of the present invention relates to labeled compounds of the invention (radio-labeled, fluorescent-labeled, etc.) that would be useful not only in imaging techniques but also in assays, both in vitro and in vivo, for localizing and quantitating LSD1 in tissue samples, including human, and for identifying LSD1 ligands by inhibition binding of a labeled compound. Accordingly, the present invention includes LSD1 assays that contain such labeled compounds.
The present invention further includes isotopically-labeled compounds of the invention. An "isotopically" or "radio-labeled" compound is a compound of the invention where one or more atoms are replaced or substituted by an atom having an atomic mass or mass number different from the atomic mass or mass number typically found in nature (i.e.,  
naturally occurring). Suitable radionuclides that may be incorporated in compounds of the present invention include but are not limited to 3H (also written as T for tritium), 11C, 13C, 14C, 13N, 15N, 15O, 17O, 18O, 18F, 35S, 36Cl, 82Br, 75Br, 76Br, 77Br, 123I, 124I, 125I and 131I. The radionuclide that is incorporated in the instant radio-labeled compounds will depend on the specific application of that radio-labeled compound.
It is to be understood that a "radio-labeled " or "labeled compound" is a compound that has incorporated at least one radionuclide. In some embodiments the radionuclide is selected from the group consisting of 3H, 14C, 125I, 35S and 82Br. In some embodiments, the compound incorporates 1, 2, or 3 deuterium atoms.
The present invention can further include synthetic methods for incorporating radio- isotopes into compounds of the invention. Synthetic methods for incorporating radio-isotopes into organic compounds are well known in the art, and an ordinary skill in the art will readily recognize the methods applicable for the compounds of invention.
A labeled compound of the invention can be used in a screening assay to
identify/evaluate compounds. For example, a newly synthesized or identified compound (i.e., test compound) which is labeled can be evaluated for its ability to bind LSD1 by monitoring its concentration variation when contacting with LSD1, through tracking of the labeling. For example, a test compound (labeled) can be evaluated for its ability to reduce binding of another compound which is known to bind to LSD1 (i.e., standard compound). Accordingly, the ability of a test compound to compete with the standard compound for binding to LSD1directly correlates to its binding affinity. Conversely, in some other screening assays, the standard compound is labeled and test compounds are unlabeled. Accordingly, the concentration of the labeled standard compound is monitored in order to evaluate the competition between the standard compound and the test compound, and the relative binding affinity of the test compound is thus ascertained.
The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of non- critical parameters which can be changed or modified to yield essentially the same results. The compounds of the Examples were found to be inhibitors of LSD1 as described below. EXAMPLES
Experimental procedures for compounds of the invention are provided below.
Preparatory LC-MS purifications of some of the compounds prepared were performed on  
Waters mass directed fractionation systems. The basic equipment setup, protocols, and control software for the operation of these systems have been described in detail in the literature. See e.g.“Two-Pump At Column Dilution Configuration for Preparative LC-MS”, K. Blom, J. Combi. Chem., 4, 295 (2002);“Optimizing Preparative LC-MS Configurations and Methods for Parallel Synthesis Purification”, K. Blom, R. Sparks, J. Doughty, G. Everlof, T. Haque, A. Combs, J. Combi. Chem., 5, 670 (2003); and "Preparative LC-MS Purification: Improved Compound Specific Method Optimization", K. Blom, B. Glass, R. Sparks, A. Combs, J. Combi. Chem., 6, 874-883 (2004). The compounds separated were typically subjected to analytical liquid chromatography mass spectrometry (LCMS) for purity check under the following conditions: Instrument; Agilent 1100 series, LC/MSD, Column: Waters SunfireTM C185µm particle size, 2.1 x 5.0 mm, Buffers: mobile phase A: 0.025% TFA in water and mobile phase B: acetonitrile; gradient 2% to 80% of B in 3 minutes with flow rate 2.0 mL/minute.
Some of the compounds prepared were also separated on a preparative scale by reverse-phase high performance liquid chromatography (RP-HPLC) with MS detector or flash chromatography (silica gel) as indicated in the Examples. Typical preparative reverse- phase high performance liquid chromatography (RP-HPLC) column conditions are as follows:
pH = 2 purifications: Waters SunfireTM C185 µm particle size, 19 x 100 mm column, eluting with mobile phase A: 0.1% TFA (trifluoroacetic acid) in water and mobile phase B: acetonitrile; the flow rate was 30 mL/minute, the separating gradient was optimized for each compound using the Compound Specific Method Optimization protocol as described in the literature [see "Preparative LCMS Purification: Improved Compound Specific Method Optimization", K. Blom, B. Glass, R. Sparks, A. Combs, J. Comb. Chem., 6, 874-883 (2004)]. Typically, the flow rate used with the 30 x 100 mm column was 60 mL/minute. pH = 10 purifications: Waters XBridge C185 µm particle size, 19 x 100 mm column, eluting with mobile phase A: 0.15% NH4OH in water and mobile phase B: acetonitrile; the flow rate was 30 mL/minute, the separating gradient was optimized for each compound using the Compound Specific Method Optimization protocol as described in the literature [See "Preparative LCMS Purification: Improved Compound Specific Method Optimization", K. Blom, B. Glass, R. Sparks, A. Combs, J. Comb. Chem., 6, 874-883 (2004)]. Typically, the flow rate used with 30 x 100 mm column was 60 mL/minute. EXAMPLES
 
Example 1
4-(8-(4-methylphenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000063_0001
Step 1: 4-(6-amino-2-methoxypyrimidin-4-yl)benzonitrile
Figure imgf000063_0002
To a mixture of 6-chloro-2-methoxypyrimidin-4-amine (Ark Pharm, cat#AK-25131: 1.3 g, 8.0 mmol), (4-cyanophenyl)boronic acid (1.41 g, 9.60 mmol) and sodium carbonate (1.7 g, 16 mmol) in 1,4-dioxane (15 mL) and water (5 mL) was added dichloro(bis{di-tert- butyl[4-(dimethylamino)phenyl]phosphoranyl})palladium (170 mg, 0.24 mmol). The reaction mixture was purged with nitrogen then stirred at 95 °C overnight. The reaction mixture was cooled to room temperature then water (20 mL) was added. The resulting precipitate was collected via filtration then dried to give the desired product (1.7 g, 94 %), which was used in the next step without further purification. LC-MS calculated for C12H11N4O (M+H)+: m/z = 227.1; found 227.1. Step 2: 4-(6-amino-5-bromo-2-methoxypyrimidin-4-yl)benzonitrile
Figure imgf000063_0003
N-Bromosuccinimide (1.3 g, 7.5 mmol) was added to a solution of 4-(6-amino-2- methoxypyrimidin-4-yl)benzonitrile (1.7 g, 7.5 mmol) in dimethyl sulfoxide (15
mL)/acetonitrile (8 mL)/water (0.5 mL) at 0 °C. The resulting mixture was stirred at 0 °C for 2 h then water (25 mL) was added. The resulting precipitate was collected via filtration then dried to give the desired product (2.1 g, 92 %), which was used in the next step without further purification. LC-MS calculated for C12H10BrN4O (M+H)+: m/z = 305.0; found 305.0.  
Step 3: 4-(8-bromo-5-hydroxyimidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000064_0001
Chloroacetaldehyde (7 M in water, 6 mL, 42 mmol) was added to a mixture of 4-(6- amino-5-bromo-2-methoxypyrimidin-4-yl)benzonitrile (1.5 g, 4.9 mmol) in isopropyl alcohol (15 mL). The resulting mixture was stirred at 110 °C for 4 h then cooled to room temperature and concentrated. The residue was titurated with ethyl acetate to give desired product as the HCl salt (1.3 g, 84 %), which was used in the next step without further purification. LC-MS calculated for C13H8BrN4O (M+H)+: m/z = 315.0; found 315.1. Step 4: 4-(8-bromo-5-chloroimidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000064_0002
Phosphoryl chloride (12 mL, 130 mmol) was added to a mixture of 4-(8-bromo-5- hydroxyimidazo[1,2-c]pyrimidin-7-yl)benzonitrile (1.0 g, 3.2 mmol) in acetonitrile (12 mL). The resulting mixture was stirred at 110 °C overnight then cooled to room temperature and concentrated. The residue was dissolved in methylene chloride then washed with sat'd NaHCO3 solution, water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 30 % EtOAc/DCM to give the desired product (0.68 g, 64 %). LC-MS calculated for C13H7BrClN4 (M+H)+: m/z = 333.0; found 333.0. Step 5: tert-butyl (3R)-3-({[8-bromo-7-(4-cyanophenyl)imidazo[1,2-c]pyrimidin-5- yl]oxy}methyl)piperidine-1-carboxylate
Figure imgf000064_0003
 
Sodium hydride (49 mg, 1.2 mmol) was added to a solution of tert-butyl (3R)-3- (hydroxymethyl)piperidine-1-carboxylate (D-L Chiral Chemicals, cat#LAC-B-393: 260 mg, 1.2 mmol) in N,N-dimethylformamide (3 mL) at 0 °C. The resulting mixture was stirred at room temperature for 20 min then added to a suspension of 4-(8-bromo-5- chloroimidazo[1,2-c]pyrimidin-7-yl)benzonitrile (370 mg, 1.1 mmol) in N,N- dimethylformamide (3 mL) at 0 °C. The resulting mixture was stirred at room temperature for 1 h then quenched with water and extracted with ethyl acetate. The combined extracts were washed with sat'd NaHCO3, water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 40 % EtOAc/DCM to give the desired product (0.52 g, 91 %). LC- MS calculated for C24H27BrN5O3 (M+H)+: m/z = 512.1; found 512.1. Step 6: 4-{8-bromo-5-[(3R)-piperidin-3-ylmethoxy]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile hydrochloride
Figure imgf000065_0001
4.0 M Hydrogen chloride in dioxane (3 mL, 12 mmol) was added to a solution of tert- butyl (3R)-3-({[8-bromo-7-(4-cyanophenyl)imidazo[1,2-c]pyrimidin-5- yl]oxy}methyl)piperidine-1-carboxylate (0.52 g, 1.0 mmol) in methylene chloride (2 mL). The resulting mixture was stirred at room temperature for 30 min then concentrated. The residue was used in the next step without further purification. LC-MS calculated for
C19H19BrN5O (M+H)+: m/z = 412.1; found 412.1. Step 7: 4-(8-bromo-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7- yl)benzonitrile
Figure imgf000065_0002
7.0 M Formaldehyde in water (2 mL, 14 mmol) was added to a mixture of 4-{8- bromo-5-[(3R)-piperidin-3-ylmethoxy]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile  
hydrochloride (400 mg, 0.89 mmol) and N,N-diisopropylethylamine (310 μL, 1.8 mmol) in methylene chloride (8 mL). The resulting mixture was stirred at room temperature for 30 min then sodium triacetoxyborohydride (380 mg, 1.8 mmol) was added. The reaction mixture was stirred at room temperature for 1 h then diluted with methylene chloride, washed with 1 N NaOH, water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 10 % MeOH/DCM to give the desired product (0.35 g, 92 %). LC-MS calculated for
C20H21BrN5O (M+H)+: m/z = 426.1; found 426.1. Step 8: 4-(8-(4-methylphenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
A mixture of (4-methylphenyl)boronic acid (6.4 mg, 0.047 mmol), 4-(8-bromo-5- {[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile (10. mg, 0.023 mmol), sodium carbonate (7.5 mg, 0.070 mmol), and dichloro[1,1'- bis(dicyclohexylphosphino)ferrocene]palladium(II) (1.8 mg, 0.0023 mmol) in tert-butyl alcohol (0.1 mL) and water (0.2 mL) was first purged with nitrogen, then heated to 105 °C and stirred for 4 h. The reaction mixture was cooled to room temperature then purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H28N5O (M+H)+: m/z = 438.2; found 438.2. Example 2
4-(8-(4-methylphenyl)-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000066_0001
Step 1: 4-(8-bromo-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7- yl)benzonitrile
Figure imgf000066_0002
 
This compound was prepared using similar procedures as described for Example 1, Step 1-7, with tert-butyl (3R)-3-(hydroxymethyl)pyrrolidine-1-carboxylate (Synnovator, cat#PB00887) replacing tert-butyl (3R)-3-(hydroxymethyl)piperidine-1-carboxylate in Step 5. The crude product was purified by flash chromatography on a silica gel column eluting with 0 to 10 % MeOH/DCM to give the desired product. LC-MS calculated for C19H19BrN5O (M+H)+: m/z = 412.1; found 412.1. Step 2: 4-(8-(4-methylphenyl)-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
A mixture of (4-methylphenyl)boronic acid (23 mg, 0.17 mmol), 4-(8-bromo-5- {[(3R)-1-methylpyrrolidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile (35 mg, 0.085 mmol), sodium carbonate (18 mg, 0.17 mmol), and dichloro[1,1'- bis(dicyclohexylphosphino)ferrocene]palladium(II) (6.4 mg, 0.0085 mmol) in tert-butyl alcohol (0.5 mL) and water (0.3 mL) was purged with nitrogen, then stirred at 105 °C for 4 h. The reaction mixture was cooled to room temperature then purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H26N5O (M+H)+: m/z = 424.2; found 424.2. Example 3
4-(8-(6-methoxypyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000067_0001
This compound was prepared using similar procedures as described for Example 1 with (6-methoxypyridin-3-yl)boronic acid (Aldrich, cat#637610) replacing (4- methylphenyl)boronic acid in Step 8. The product was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H27N6O2 (M+H)+: m/z = 455.2; found 455.2.1H NMR (500 MHz, DMSO) δ 8.09– 8.04 (m, 2H), 7.83– 7.78 (m, 2H), 7.73– 7.71 (m, 1H), 7.66 (dd, J = 8.6, 2.5 Hz, 1H), 7.60– 7.54 (m, 2H), 6.88– 6.83 (m, 1H), 4.68– 4.62 (m, 1H), 4.59– 4.52 (m, 1H), 3.86 (s, 3H), 3.71–
 
3.63 (m, 1H), 3.49– 3.41 (m, 1H), 3.00– 2.78 (m, 5H), 2.46– 2.36 (m, 1H), 1.97– 1.85 (m, 2H), 1.81– 1.65 (m, 1H), 1.46– 1.32 (m, 1H). Example 4
4-(8-[6-(dimethylamino)pyridin-3-yl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000068_0001
This compound was prepared using similar procedures as described for Example 1 with [6-(dimethylamino)pyridin-3-yl]boronic acid (Combi-Blocks, cat#FA-2296) replacing (4-methylphenyl)boronic acid in Step 8. The product was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H30N7O (M+H)+: m/z = 468.3; found 468.2. Example 5
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(6-pyrrolidin-1-ylpyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000068_0002
This compound was prepared using similar procedures as described for Example 1 with 2-pyrrolidin-1-yl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (Combi- Blocks, cat#PN-8695) replacing (4-methylphenyl)boronic acid in Step 8. The product was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H32N7O (M+H)+: m/z = 494.3; found 494.3. Example 6
4-(8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)-5-{[(3R)-1-methylpiperidin-3-  
yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000069_0001
Step 1: 1-methyl-5-(4,4,5,5-tetrame -1 2- r -2-yl)-1,3-dihydro-2H-indol-2-one
Figure imgf000069_0002
A mixture of 5-bromo-1-methyl-1,3-dihydro-2H-indol-2-one (Maybridge, cat #CC63010: 0.30 g, 1.3 mmol), 4,4,5,5,4',4',5',5'-octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (500 mg, 2.0 mmol), [1,1'-Bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with dichloromethane (1:1) (50 mg, 0.07 mmol) and potassium acetate (390 mg, 4.0 mmol) in 1,4-dioxane (10 mL) was purged with nitrogen then heated at 90 °C overnight. The reaction mixture was cooled to room temperature then concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 25 %
EtOAc/Hexanes to give the desired product. LC-MS calculated for C15H21BNO3 (M+H)+: m/z = 274.2; found 274.1. Step 2: 4-(8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-dihydro-2H-indol-2-one (prepared in Step 1) replacing (4-methylphenyl)boronic acid in Step 8. The product was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H29N6O2 (M+H)+: m/z = 493.2; found 493.2. Example 7
4-(8-(3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
 
Step 1: 6-bromo-3-methyl-1,
Figure imgf000070_0001
A mixture of 6-bromo-1,3-benzoxazol-2(3H)-one (Aldrich, cat#697036: 0.32 g, 1.5 mmol), methyl iodide (0.28 mL, 4.5 mmol) and potassium carbonate (210 mg, 1.5 mmol) in acetone (3 mL) was heated to 80 °C and stirred for 3 h. The reaction mixture was cooled to room temperature then diluted with water and extracted with EtOAc. The combined extracts were dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C8H7BrNO2 (M+H)+: m/z = 228.0; found 227.9. Step 2: 3-methyl-6-(4,4,5,5-tetrame -1 2- r -2-yl)-1,3-benzoxazol-2(3H)-one
A mixture of the crude product from Step 1, 4,4,5,5,4',4',5',5'-octamethyl- [2,2']bi[[1,3,2]dioxaborolanyl] (580 mg, 2.3 mmol), [1,1'- bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with dichloromethane (1:1) (60 mg, 0.08 mmol) and potassium acetate (440 mg, 4.5 mmol) in 1,4-dioxane (10 mL) was purged with nitrogen then heated at 90 °C overnight. The reaction mixture was cooled to room temperature then concentrated. The residue was purified by flash
chromatography on a silica gel column eluting with 0 to 25 % EtOAc/Hexanes to give the desired product. LC-MS calculated for C14H19BNO4 (M+H)+: m/z = 276.1; found 276.2. Step 3: 4-(8-(3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
This compound was prepared using similar procedures as described for Example 1 with 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol-2(3H)-one  
(prepared in Step 2) replacing (4-methylphenyl)boronic acid in Step 8. The product was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H27N6O3 (M+H)+: m/z = 495.2; found 495.2.1H NMR (500 MHz, DMSO) δ 8.07 (d, J = 1.4 Hz, 1H), 7.75 (d, J = 8.5 Hz, 2H), 7.71 (d, J = 1.4 Hz, 1H), 7.57– 7.52 (m, 2H), 7.36 (d, J = 1.4 Hz, 1H), 7.21 (d, J = 8.1 Hz, 1H), 7.06 (dd, J = 8.1, 1.5 Hz, 1H), 4.68– 4.62 (m, 1H), 4.59– 4.52 (m, 1H), 3.70– 3.62 (m, 1H), 3.47– 3.40 (m, 1H), 3.35 (s, 3H), 3.00– 2.77 (m, 5H), 2.46– 2.37 (m, 1H), 1.97– 1.85 (m, 2H), 1.82– 1.67 (m, 1H), 1.45– 1.32 (m, 1H). Example 8
4-(8-(1-methyl-1H-indazol-5-yl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000071_0001
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indazole (Adv
ChemBlocks, cat#C-2063) replacing (4-methylphenyl)boronic acid in Step 8. The product was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H28N7O (M+H)+: m/z = 478.2; found 478.2. Example 9
4-(8-{4-[(4-methylpiperazin-1-yl)methyl]phenyl}-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000071_0002
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-4-[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl]piperazine (Combi- Blocks, cat#PN-8801) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired  
product. LC-MS calculated for C32H38N7O (M+H)+: m/z = 536.3; found 536.3. Example 10
4-(8-{4-[2-(4-methylpiperazin-1-yl)-2-oxoethyl]phenyl}-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000072_0001
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-4-{[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]acetyl}piperazine (Combi-Blocks, cat#PN-6945) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C33H38N7O2 (M+H)+: m/z = 564.3; found 564.3. Example 11
4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[4-(2-morpholin-4- ylethyl)phenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile
Figure imgf000072_0002
This compound was prepared using similar procedures as described for Example 1 with [4-(2-morpholin-4-ylethyl)phenyl]boronic acid (Combi-Blocks, cat#BB-5640) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C32H37N6O2 (M+H)+: m/z = 537.3; found 537.3. Example 12
4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[4-(morpholin-4- ylmethyl)phenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile  
Figure imgf000073_0001
Step 1: 4-(8-(4-formylphenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000073_0002
This compound was prepared using similar procedures as described for Example 1 with (4-formylphenyl)boronic acid (Aldrich, cat#431966) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by flash chromatography on a silica gel column eluting with 0 to 10 % MeOH/DCM to give the desired product. LC-MS calculated for C27H26N5O2 (M+H)+: m/z = 452.2; found 452.2. Step 2: 4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[4-(morpholin-4- ylmethyl)phenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile
A mixture of 4-(8-(4-formylphenyl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile (9.0 mg, 0.020 mmol) and morpholine (20 μL, 0.2 mmol) in methylene chloride (1 mL) was stirred at room temperature for 15 min then sodium triacetoxyborohydride (9.0 mg, 0.043 mmol) was added. The resulting mixture was stirred at room temperature for 2 h then quenched with saturated NaHCO3 solution and extracted with DCM. The combined extracts were dried over Na2SO4 and concentrated. The residue was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C31H35N6O2 (M+H)+: m/z = 523.3; found 523.2. Example 13
(3S)-1-[4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)benzyl]pyrrolidine-3-carbonitrile
 
Figure imgf000074_0001
This compound was prepared using similar procedures as described for Example 12 with (3S)-pyrrolidine-3-carbonitrile hydrochloride (Tyger, cat#C90004) replacing morpholine in Step 2. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C32H34N7O (M+H)+: m/z = 532.3; found 532.3. Example 14
4-(8-(4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]meth enzonitrile
Figure imgf000074_0002
Step 1: 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-3,4-dihydro-2H-pyrido[3,2- b][1,4]oxazine
Figure imgf000074_0003
A mixture of 7-bromo-4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazine
(Maybridge, cat#CC62010: 300 mg, 1 mmol), 4,4,5,5,4',4',5',5'-octamethyl- [2,2']bi[[1,3,2]dioxaborolanyl] (660 mg, 2.6 mmol), potassium acetate (380 mg, 3.9 mmol), [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with
dichloromethane (1:1) (50 mg, 0.06 mmol) in 1,4-dioxane (10 mL, 100 mmol) was purged with nitrogen then heated to 90 ˚C and stirred overnight. The reaction mixture was cooled to room temperature then concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 40 % EtOAc/DCM to give the desired product. LC-MS calculated for C14H22BN2O3 (M+H)+: m/z = 277.2; found 277.1.  
Step 2: 4-(8-(4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
This compound was prepared using similar procedures as described for Example 1 with 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-3,4-dihydro-2H-pyrido[3,2- b][1,4]oxazine (prepared in Step 1) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H30N7O2 (M+H)+: m/z = 496.2; found 496.2. Example 15
4-(8-(4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-5-{[(3R)-1-methylpiperidin- 3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000075_0001
Step 1: 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-1,4-benzoxazin-3(4H)- one
Figure imgf000075_0002
A mixture of 7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-1,4-benzoxazin- 3(4H)-one (Combi-Blocks, cat#FM-4852: 0.54 g, 2.0 mmol), methyl iodide (0.18 mL, 2.9 mmol) and potassium carbonate (0.81 g, 5.9 mmol) in N,N-dimethylformamide (8 mL) was stirred at room temperature for 3 h then diluted with water and extracted with EtOAc. The combined extracts were dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C15H21BNO4 (M+H)+: m/z = 290.2; found 290.1. Step 2: 4-(8-(4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
 
This compound was prepared using similar procedures as described for Example 1 with 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-1,4-benzoxazin-3(4H)-one (prepared in Step 1) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H29N6O3 (M+H)+: m/z = 509.2; found 509.2. Example 16
4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[6-(2-oxopyrrolidin-1-yl)pyridin-3- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile
Figure imgf000076_0001
This compound was prepared using similar procedures as described for Example 1 with 1-[5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2-yl]pyrrolidin-2-one (JPM2 Pharma, cat#JPM2-00-744) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H30N7O2 (M+H)+: m/z = 508.2; found 508.2. Example 17
4-(8-(1-methyl-1H-benzimidazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000076_0002
This compound was prepared using similar procedures as described for Example 1 with (1-methyl-1H-benzimidazol-5-yl)boronic acid (Combi-Blocks, cat#FA-4841) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS  
calculated for C28H28N7O (M+H)+: m/z = 478.2; found 478.2. Example 18
4-(8-(1-methyl-1H-indazol-6-yl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000077_0001
This compound was prepared using similar procedures as described for Example 1 with (1-methyl-1H-indazol-6-yl)boronic acid (Aldrich, cat#720798) replacing (4- methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H28N7O (M+H)+: m/z = 478.2; found 478.1. Example 19
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrrolo[2,3-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000077_0002
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridine (AstaTech, cat#37406) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H28N7O (M+H)+: m/z = 478.2; found 478.4. Example 20
5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-N,N-dimethyl-2,3-dihydro-1-benzofuran-2-carboxamide  
Figure imgf000078_0001
Step 1: 5-bromo-N,N-dimethyl-2,3-dihydro-1-benzofuran-2-carboxamide
Figure imgf000078_0002
A mixture of 5-bromo-2,3-dihydro-1-benzofuran-2-carboxylic acid (0.50 g, 2.0 mmol), 2.0 M dimethylamine in THF (4 mL, 8 mmol), benzotriazol-1- yloxytris(dimethylamino)phosphonium hexafluorophosphate (1.2 g, 2.7 mmol) in methylene chloride (4 mL) was stirred at room temperature overnight then concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 40 %
EtOAc/Hexanes to give the desired product (0.49 g, 88 %). LC-MS calculated for
C11H13BrNO2 (M+H)+: m/z = 270.0; found 270.0. Step 2: N,N-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,3-dihydro-1- benzofuran-2-carboxamide
Figure imgf000078_0003
A mixture of 5-bromo-N,N-dimethyl-2,3-dihydro-1-benzofuran-2-carboxamide (0.49 g, 1.8 mmol), 4,4,5,5,4',4',5',5'-Octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (0.51 g, 2.0 mmol), potassium acetate (0.44 g, 4.5 mmol) and [1,1'- bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with dichloromethane (1:1) (70 mg, 0.09 mmol) and 1,1'-Bis(diphenylphosphino)ferrocene (50 mg, 0.09 mmol) in 1,4-dioxane (9.0 mL) was purged with nitrogen then stirred at 100 °C for 3 h. The reaction mixture was cooled to room temperature and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 50 % EtOAc/Hexanes to afford the desired product. LC-MS calculated for C17H25BNO4 (M+H)+: m/z = 318.2; found 318.1. Step 3: 5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-N,N-dimethyl-2,3-dihydro-1-benzofuran-2-carboxamide  
This compound was prepared using similar procedures as described for Example 1 with N,N-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,3-dihydro-1- benzofuran-2-carboxamide (prepared in Step 2) replacing (4-methylphenyl)boronic acid in Step 8. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C31H33N6O3 (M+H)+: m/z = 537.3; found 537.3. Example 21
4-(8-[6-(dimethylamino)pyridin-3-yl]-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000079_0001
This compound was prepared using similar procedures as described for Example 2 with [6-(dimethylamino)pyridin-3-yl]boronic acid (Combi-Blocks, cat#FA-2296) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C26H28N7O (M+H)+: m/z = 454.2; found 454.2. Example 22
4-[5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}-8-(6-pyrrolidin-1-ylpyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000079_0002
This compound was prepared using similar procedures as described for Example 2 with 2-pyrrolidin-1-yl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (Combi- Blocks, cat#PN-8695) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired  
product. LC-MS calculated for C28H30N7O (M+H)+: m/z = 480.3; found 480.3. Example 23
4-(8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000080_0001
This compound was prepared using similar procedures as described for Example 2 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-dihydro-2H-indol-2-one (Example 6, Step 1) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C28H27N6O2 (M+H)+: m/z = 479.2; found 479.2. Example 24
4-(8-(4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-7-yl)-5-{[(3R)-1- methylpyrrolidin-3-yl]meth )benzonitrile
Figure imgf000080_0002
This compound was prepared using similar procedures as described for Example 2 with 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-3,4-dihydro-2H-pyrido[3,2- b][1,4]oxazine (Example 14, Step 1) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H28N7O2 (M+H)+: m/z = 482.2; found 482.2. Example 25
4-(8-(1-methyl-1H-benzimidazol-5-yl)-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile  
Figure imgf000081_0001
This compound was prepared using similar procedures as described for Example 2 with (1-methyl-1H-benzimidazol-5-yl)boronic acid (Combi-Blocks, cat#FA-4841) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H26N7O (M+H)+: m/z = 464.2; found 464.2. Example 26
4-(8-(3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000081_0002
This compound was prepared using similar procedures as described for Example 2 with 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol-2(3H)-one (Example 7, Step 2) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C27H25N6O3 (M+H)+: m/z = 481.2; found 481.2. Example 27
4-(8-(1-methyl-1H-indazol-5-yl)-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000081_0003
This compound was prepared using similar procedures as described for Example 2  
with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indazole (Adv
ChemBlocks, cat#C-2063) replacing (4-methylphenyl)boronic acid in Step 2. The reaction mixture was purified by prep-HPLC (pH = 10, acetonitrile/water+NH4OH) to give the desired product. LC-MS calculated for C27H26N7O (M+H)+: m/z = 464.2; found 464.3. Example 28
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000082_0001
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine (PharmaBlock, cat#PB02930) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H27N8O (M+H)+: m/z = 479.2; found 479.2. 1H NMR (500 MHz, CD3OD) δ 8.38 (d, J = 2.1 Hz, 1H), 8.34 (d, J = 2.0 Hz, 1H), 8.21 (d, J = 1.9 Hz, 1H), 8.14 (s, 1H), 7.86 (d, J = 1.8 Hz, 1H), 7.65– 7.58 (m, 4H), 4.86– 4.83 (m, 1H), 4.77– 4.72 (m, 1H), 4.14 (s, 3H), 3.85– 3.79 (m, 1H), 3.61– 3.55 (m, 1H), 3.08– 2.97 (m, 2H), 2.95 (s, 3H), 2.64– 2.52 (m, 1H), 2.15– 2.05 (m, 2H), 1.96– 1.84 (m, 1H), 1.61– 1.50 (m, 1H). Example 29
4-[5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000082_0002
Step 1: tert-butyl (3R)-3-({[7-(4-cyanophenyl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-5-yl]oxy}methyl)piperidine-1-carboxylate  
Figure imgf000083_0001
A mixture of 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine (PharmaBlock, cat#PB02930: 127 mg, 0.492 mmol), tert-butyl (3R)- 3-({[8-bromo-7-(4-cyanophenyl)imidazo[1,2-c]pyrimidin-5-yl]oxy}methyl)piperidine-1- carboxylate (prepared in Example 1, Step 5: 126 mg, 0.246 mmol), sodium carbonate (52.1 mg, 0.492 mmol), and dichloro[1,1'-bis(dicyclohexylphosphino)ferrocene]palladium(II) (19 mg, 0.024 mmol) in tert-butyl alcohol (4 mL) and water (2 mL) was first purged with nitrogen, then stirred and heated at 105 °C for 2 h. The reaction mixture was cooled to room temperature then diluted with methylene chloride, washed with saturated NaHCO3, water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 10% MeOH in methylene chloride to give the desired product (119 mg, 86%). LCMS calculated for C31H33N8O3 (M+H)+: m/z = 565.3; found 565.2 Step 2: 4-{8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-5-[(3R)-piperidin-3- ylmethoxy]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile
Figure imgf000083_0002
To a solution of tert-butyl (3R)-3-({[7-(4-cyanophenyl)-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-5-yl]oxy}methyl)piperidine-1-carboxylate (29.5 mg, 0.0522 mmol) in methylene chloride (100 μL) was added trifluoroacetic acid (50 μL). The resulting reaction mixture was stirred at room temperature for 30 min then concentrated. The residue was used in the next step without further purification. LC-MS calculated for
C26H25N8O (M+H)+: m/z = 465.2; found 465.2. Step 3: 4-[5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin- 5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile  
The crude product from Step 2 was dissolved in methylene chloride (0.6 mL) then N,N-diisopropylethylamine (30 μL, 0.2 mmol) was added. The resulting mixture was stirred at room temperature for 10 min then acetaldehyde (17 μL, 0.5 mmol) was added. The resultant reaction mixture was stirred for 30 min then sodium triacetoxyborohydride (30 mg, 0.2 mmol) was added. The reaction mixture was stirred at room temperature for 2 h then diluted with MeOH and purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H29N8O (M+H)+: m/z = 493.2; found 493.3.1H NMR (500 MHz, CD3OD) δ 8.40– 8.35 (m, 3H), 8.15 (s, 1H), 8.01 (d, J = 2.1 Hz, 1H), 7.66– 7.60 (m, 4H), 4.93– 4.88 (m, 1H), 4.83– 4.77 (m, 1H), 4.14 (s, 3H), 3.91 – 3.83 (m, 1H), 3.69– 3.60 (m, 1H), 3.30– 3.22 (m, 2H), 3.06– 2.91 (m, 2H), 2.72– 2.59 (m, 1H), 2.17– 2.07 (m, 2H), 2.02– 1.88 (m, 1H), 1.67– 1.55 (m, 1H), 1.39 (t, J = 7.3 Hz, 3H). Example 30
4-(8-[3-fluoro-4-(hydroxymethyl)-5-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000084_0001
Step 1: [2-fluoro-6-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]methanol
Figure imgf000084_0002
This compound was prepared using similar procedures as described for Example 6 with (4-bromo-2-fluoro-6-methylphenyl)methanol (Oxchem, cat#AX8271172) replacing 5- bromo-1-methyl-1,3-dihydro-2H-indol-2-one in Step 1. The reaction mixture was filtered through celite, then concentrated. The crude product was used without further purification. LC-MS calculated for C14H19BFO2 (M+H-H2O)+: m/z = 249.1; found 249.1. Step 2: 4-(8-[3-fluoro-4-(hydroxymethyl)-5-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
 
This compound was prepared using similar procedures as described for Example 1 with [2-fluoro-6-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]methanol replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H29FN5O2 (M+H)+: m/z = 486.2; found 486.2.1H NMR (400 MHz, CD3OD) δ 8.29 (d, J = 2.1 Hz, 1H), 7.95 (d, J = 2.1 Hz, 1H), 7.71– 7.63 (m, 4H), 7.07 (s, 1H), 6.97 (d, J = 9.8 Hz, 1H), 4.86– 4.83 (m, 2H, overlapped with H2O peak), 4.76– 4.72 (m, 2H), 3.87– 3.78 (m, 1H), 3.62– 3.52 (m, 1H), 3.09– 2.96 (m, 2H), 2.94 (s, 3H), 2.67– 2.54 (m, 1H), 2.44 (s, 3H), 2.15– 2.03 (m, 2H), 2.02– 1.84 (m, 1H), 1.62– 1.47 (m, 1H). Example 31
4-(8-[3-fluoro-4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000085_0001
This compound was prepared using similar procedures as described for Example 1 with 3-fluoro-4-hydroxymethylbenzeneboronic acid (Combi-Blocks, cat# FA-4306) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H27FN5O2 (M+H)+: m/z = 472.2; found 472.2. Example 32
4-(8-[3,5-difluoro-4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000085_0002
This compound was prepared using similar procedures as described for Example 1 with 3,5-difluoro-4-(hydroxymethyl)phenylboronic acid (Combi-Blocks, cat# BB-8390) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by  
prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H26F2N5O2 (M+H)+: m/z = 490.2; found 490.2. Example 33
4-[5-{[(3R)-1-(2-cyanoethyl)piperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000086_0001
To a solution of 2-propenenitrile (2.0 μL, 0.030 mmol) and 4-{8-(1-methyl-1H- pyrazolo[3,4-b]pyridin-5-yl)-5-[(3R)-piperidin-3-ylmethoxy]imidazo[1,2-c]pyrimidin-7- yl}benzonitrile (prepared in Example 29, Step 2: 10 mg, 0.02 mmol) in acetonitrile (0.4 mL) was added 1,8-diazabicyclo[5.4.0]undec-7-ene (9 μL, 0.06 mmol). The reaction mixture was stirred at 80 °C for 3 h. The mixture was cooled to room temperature, diluted with methanol then purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H28N9O (M+H)+: m/z = 518.2; found 518.1. Example 34
4-[5-{[(3R)-1-(2-hydroxyethyl)piperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000086_0002
To a solution of 4-{8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-5-[(3R)-piperidin-3- ylmethoxy]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile (prepared in Example 29, Step 2: 10 mg, 0.02 mmol) and 2-bromoethanol (7 μL, 0.1 mmol) in N,N-dimethylformamide (0.4 mL) was added potassium carbonate (30 mg, 0.2 mmol). The reaction mixture was stirred at 45 °C for 2 h. The mixture was cooled to room temperature, filtered and purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H29N8O2 (M+H)+: m/z = 509.2; found 509.2.  
Example 35
4-(8-[4-(hydroxymethyl)-3-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000087_0001
This compound was prepared using similar procedures as described for Example 1 with 4-hydroxymethyl-3-methylphenylboronic acid (Aurum Pharmatech, cat#B-6677) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H30N5O2 (M+H)+: m/z = 468.2; found 468.2. Example 36
4-(8-[4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile
Figure imgf000087_0002
This compound was prepared using similar procedures as described for Example 1 with 4-hydroxymethylbenzeneboronic acid (Combi-Blocks, cat# BB-2317) replacing (4- methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H28N5O2 (M+H)+: m/z = 454.2; found 454.2. Example 37
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
 
Figure imgf000088_0001
Step 1: 4-{8-bromo-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-7- yl}benzonitrile
Figure imgf000088_0002
To a mixture of N,N-diisopropylethylamine (0.63 mL, 3.6 mmol) and 4-(8-bromo-5- chloroimidazo[1,2-c]pyrimidin-7-yl)benzonitrile (prepared in Example 1, Step 4: 600. mg, 1.80 mmol) in acetonitrile (10 mL) was added N,N-dimethylpiperidin-4-amine (Alfa Aesar, cat#L20176: 0.51 mL, 3.6 mmol). The resulting reaction mixture was stirred at room temperature for 1 h then water (80 mL) was added. The resulting precipitate was collected via filtration then washed with water and dried to give the desired product (660 mg, 86 %), which was used in the next step without further purification. LC-MS calculated for C20H22BrN6 (M+H)+: m/z = 425.1; found 425.1. Step 2: 4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
A mixture of 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine (PharmaBlock, cat#PB02930: 366 mg, 1.41 mmol), 4-{8-bromo-5- [4-(dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile (300 mg, 0.71 mmol), sodium carbonate (150 mg, 1.41 mmol), and dichloro[1,1'- bis(dicyclohexylphosphino)ferrocene]palladium(II) (53 mg, 0.07 mmol) in tert-butyl alcohol (10 mL) and water (6 mL) was first purged with nitrogen, then heated to 95 °C and stirred for 3 h. The reaction mixture was cooled to room temperature then purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H28N9 (M+H)+: m/z = 478.2; found 478.2.1H NMR (400 MHz, CD3OD) δ 8.38 (d, J = 2.0 Hz, 1H), 8.33 (d, J = 2.0 Hz, 1H), 8.18 (d, J = 2.1 Hz, 1H), 8.15 (s, 1H), 7.97 (d, J = 2.1 Hz, 1H), 7.67– 7.57 (m, 4H), 4.43– 4.33 (m, 2H), 4.14 (s, 3H), 3.69– 3.57 (m, 1H), 3.41– 3.32   (m, 2H), 2.96 (s, 6H), 2.36– 2.26 (m, 2H), 2.19– 2.05 (m, 2H). Example 38
4-[5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000089_0001
Step 1: 4-{8-bromo-5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]imidazo[1,2-c]pyrimidin-7- yl}benzonitrile
Figure imgf000089_0002
(3R)-N,N-dimethylpyrrolidin-3-amine (Aldrich, cat#656712: 6.8 mg, 0.060 mmol) was added to a solution of 4-(8-bromo-5-chloroimidazo[1,2-c]pyrimidin-7-yl)benzonitrile (prepared in Example 1, Step 4: 10 mg, 0.03 mmol) in N,N-dimethylformamide (0.2 mL). The reaction mixture was microwaved at 120 °C for 10 min. and then cooled to room temperature and concentrated to dryness. The crude reaction mixture was used in the next step without further purification. LC-MS calculated for C19H20BrN6 (M+H)+: m/z = 411.1; found 411.2. Step 2: 4-[5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
This compound was prepared using similar procedures as described for Example 37 with 4-{8-bromo-5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]imidazo[1,2-c]pyrimidin-7- yl}benzonitrile replacing 4-{8-bromo-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-7-yl}benzonitrile in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H26N9 (M+H)+: m/z = 464.2; found 464.2. Example 39
 
4-[5-(7-methyl-2,7-diazaspiro[4.4]non-2-yl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000090_0001
 
Step 1: tert-butyl 7-[8-bromo-7-(4-cyanophenyl)imidazo[1,2-c]pyrimidin-5-yl]-2,7- diazaspiro[4.4]nonane-2- r
Figure imgf000090_0002
 
This compound was prepared using similar procedures as described for Example 38 with tert-butyl 2,7-diazaspiro[4.4]nonane-2-carboxylate (Synthonix, cat#D5983) replacing (3R)-N,N-dimethylpyrrolidin-3-amine in Step 1. The reaction mixture was concentrated and the residue was used in the next step without further purification. LC-MS calculated for C25H28BrN6O2 (M+H)+: m/z = 523.1; found 523.2. Step 2: tert-butyl 7-[7-(4-cyanophenyl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-5-yl]-2,7-diazaspiro[4.4]nonane-2-carboxylate
Figure imgf000090_0003
 
This compound was prepared using similar procedures as described for Example 37, Step 2 with tert-butyl 7-[8-bromo-7-(4-cyanophenyl)imidazo[1,2-c]pyrimidin-5-yl]-2,7- diazaspiro[4.4]nonane-2-carboxylate replacing 4-{8-bromo-5-[4-(dimethylamino)piperidin-1- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile. The reaction mixture was diluted with methylene chloride, washed with saturated NaHCO3, water and brine. The organic layer was
  dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C32H34N9O2 (M+H)+: m/z = 576.3; found 576.2. Step 3: 4-[5-(7-methyl-2,7-diazaspiro[4.4]non-2-yl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin- 5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
To the solution of tert-butyl 7-[7-(4-cyanophenyl)-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-5-yl]-2,7-diazaspiro[4.4]nonane-2-carboxylate (20 mg) in methylene chloride (0.4 mL) was added trifluoroacetic acid (0.1 mL). The resulting mixture was stirred at room temperature for 1 h then concentrated. The residue was dissolved in acetonitrile (0.4 mL) then N,N-diisopropylethylamine (50 μL, 0.3 mmol) was added, followed by the addition of 7.0 M formaldehyde in water (0.08 mL, 0.6 mmol). The resulting mixture was stirred at room temperature for 30 min then sodium triacetoxyborohydride (60 mg, 0.3 mmol) was added. The reaction mixture was stirred at room temperature for 2 h then quenched with MeOH and purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H28N9 (M+H)+: m/z = 490.2; found 490.2. Example 40
methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-fluorobenzyl]methylcarbamate
Figure imgf000091_0001
Step 1: 1-[2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]-N- methylmethanamine
Figure imgf000091_0002
To a solution of 2.0 M methylamine in tetrahydrofuran (3 mL, 6 mmol) was added dropwise a solution of 2-[4-(bromomethyl)-3-fluorophenyl]-4,4,5,5-tetramethyl-1,3,2- dioxaborolane (Combi-Blocks, cat# PN-5654: 200 mg, 0.6 mmol) in tetrahydrofuran (10 mL).  
The reaction mixture was stirred at room temperature for 2 h, then concentrated. The crude product was used in the next step without further purification. Step 2: methyl [2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)benzyl]methylcarbamate
Figure imgf000092_0001
To a solution of 1-[2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]- N-methylmethanamine (40 mg, 0.2 mmol) and N,N-diisopropylethylamine (0.056 mL, 0.32 mmol) in methylene chloride (2 mL) was added methyl chloroformate (19 μL, 0.24 mmol). The reaction was stirred at room temperature for 2 h, then concentrated. The crude product was used in the next step without further purification. LC-MS calculated for C16H24BFNO4 (M+H)+: m/z = 324.2; found 324.2. Step 3: methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-fluorobenzyl]methylcarbamate
This compound was prepared using similar procedures as described for Example 1 with methyl [2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)benzyl]methylcarbamate replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C30H32FN6O3 (M+H)+: m/z = 543.2; found 543.3. Example 41
4-[5-{[(3R)-1-(2-methoxyethyl)piperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000092_0002
This compound was prepared using similar procedures as described for Example 34  
with 1-bromo-2-methoxyethane replacing 2-bromoethanol. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H32N8O2 (M+H)+: m/z = 523.3; found 523.3. Example 42
4-(8-(3-amino-1-methyl-1H-indazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000093_0001
This compound was prepared using similar procedures as described for Example 1 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indazol-3-amine (Combi- Blocks, cat#FF-5931) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H29N8O (M+H)+: m/z = 493.2; found 493.2. Example 43
4-(8-(3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin-7-yl)-5-{[(3R)-1-methylpiperidin- 3-yl]methoxy}imidazo[1,2-
Figure imgf000093_0002
Step 1: 5-bromo-2-[(methylamino)meth l henol
Figure imgf000093_0003
To a solution of 4-bromo-2-hydroxybenzaldehyde (Ark Pharm, cat#AK-24055: 800 mg, 4 mmol) and methylamine (4.0 mL, 30. mmol) in 1,2-dichloroethane (20 mL, 200 mmol) was added sodium triacetoxyborohydride (1.3 g, 6.0 mmol). The reaction mixture was stirred at rt for 2 h. The reaction mixture was then diluted with methylene chloride, washed with saturated NaHCO3. The aqueous phase was extracted with methylene chloride. The organic  
layer was dried over Na2SO4, filtered and concentrated. The residue was concentrated and used for next step without further purification. LC-MS calculated for C8H11BrNO4 (M+H)+: m/z = 216.1; found 216.1. Step 2: 7-bromo-3-methyl-3,4-dihydro-2H-1,3-benzoxazin-2-one
Figure imgf000094_0001
To a solution of 5-bromo-2-[(methylamino)methyl]phenol (crude product from Step 1) and triethylamine (3 mL, 20 mmol) in tetrahydrofuran (30 mL) was added triphosgene (1.4 g, 4.8 mmol) at 0 °C. The resulting mixture was stirred for 1 h before 1M NaOH (2 mL) was added. The reaction mixture was allowed to stir for another 1 h, then diluted with methylene chloride, washed with saturated NaHCO3. The aqueous phase was extracted with methylene chloride. The combined organic layers were dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C9H9BrNO2 (M+H)+: m/z = 242.1; found 242.1. Step 3: 3-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-3,4-dihydro-2H-1,3- benzoxazin-2-one
Figure imgf000094_0002
This compound was prepared using similar procedures as described for Example 6, Step 1 with 7-bromo-3-methyl-3,4-dihydro-2H-1,3-benzoxazin-2-one (crude product from Step 2) replacing 5-bromo-1-methyl-1,3-dihydro-2H-indol-2-one. After cooling to room temperature, the reaction mixture was concentrated, diluted with methylene chloride, washed over saturated NaHCO3. The aqueous phase was extracted with methylene chloride. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 25% AcOEt in hexanes to give the desired product. LC-MS calculated for C15H21BNO4 (M+H)+: m/z = 290.2; found 290.1. Step 4: 4-(8-(3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
This compound was prepared using similar procedures as described for Example 1   with 3-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-3,4-dihydro-2H-1,3- benzoxazin-2-one replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H29N6O3 (M+H)+: m/z = 509.2; found 509.3. Example 44
4-(8-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000095_0001
Step 1: 1,3-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-dihydro-2H- benzimidazol-2-one
Figure imgf000095_0002
This compound was prepared using similar procedures as described for Example 6, Step 1 with 5-bromo-1,3-dimethyl-1,3-dihydro-2H-benzimidazol-2-one (Aurum Pharmatech, cat# NE22745) replacing 5-bromo-1-methyl-1,3-dihydro-2H-indol-2-one. After cooling to room temperature, the reaction mixture was concentrated, diluted with methylene chloride then washed with saturated NaHCO3. The aqueous phase was extracted with methylene chloride. The combined organic layers were dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 4% methanol in methylene chloride to give the desired product. LC-MS calculated for
C15H22BN2O3 (M+H)+: m/z = 289.2; found 289.1. Step 2: 4-(8-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
This compound was prepared using similar procedures as described for Example 1 with 1,3-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-dihydro-2H- benzimidazol-2-one replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture   was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H30N7O2 (M+H)+: m/z = 508.2; found 508.3. Example 45
4-(8-(5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000096_0001
To a mixture of 2-amino-5-bromo-4-fluorophenol (0.3 g, 1 mmol) and triethylamine (1.0 mL, 7.3 mmol) in tetrahydrofuran (20 mL) was added triphosgene (0.52 g, 1.7 mmol) at 0 °C and the resulting reaction mixture was stirred for 1 h before 1M NaOH (2 mL) was added. The reaction mixture was allowed to stir for another 1 h, then diluted with methylene chloride, washed with saturated NaHCO3. The aqueous phase was extracted with methylene chloride. The combined organic layers were dried over Na2SO4, filtered and concentrated. The residue was used for next step without further purification. LC-MS calculated for C7H4BrFNO2 (M+H)+: m/z = 231.9; found 231.9. Step 2: 6-bromo-5-fluoro-3-methyl-1,3-benzoxazol-2(3H)-one
Figure imgf000096_0002
To a mixture of 6-bromo-5-fluoro-1,3-benzoxazol-2(3H)-one (crude product from Step 1) and potassium carbonate (0.4g, 3 mmol) in acetone (5 mL) was added methyl iodide (0.2 mL, 3 mmol). The reaction mixture was heated at 80 °C overnight then cooled to room temperature and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 4% methanol in methylene chloride to give the desired product. LC-MS calculated for C8H6BrFNO2 (M+H)+: m/z = 246.0; found 245.9.
 
Step 3: 5-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one
Figure imgf000097_0001
This compound was prepared using similar procedures as described for Example 6, Step 1 with 6-bromo-5-fluoro-3-methyl-1,3-benzoxazol-2(3H)-one (product from Step 2) replacing 5-bromo-1-methyl-1,3-dihydro-2H-indol-2-one. After cooling to room temperature, the reaction mixture was concentrated, diluted with methylene chloride, washed over saturated NaHCO3. The aqueous phase was extracted with methylene chloride. The combined organic layers were dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 4% methanol in methylene chloride to give the desired product. LC-MS calculated for C14H18BFNO4 (M+H)+: m/z = 294.1; found 294.1. Step 4: 4-(8-(5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
This compound was prepared using similar procedures as described for Example 1 with 5-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H26FN6O3 (M+H)+: m/z = 513.2; found 513.2.1H NMR (400 MHz, MeOD) δ 8.17 (d, J = 1.8 Hz, 1H), 7.84 (d, J = 1.6 Hz, 1H), 7.70– 7.62 (m, 4H), 7.30 (dd, J = 5.5, 2.1 Hz, 1H), 7.12 (d, J = 8.8 Hz, 1H), 4.84– 4.78 (m, 1H), 4.77– 4.68 (m, 1H), 3.86– 3.76 (m, 1H), 3.63– 3.53 (m, 1H), 3.42 (s, 3H), 3.08– 2.96 (m, 2H), 2.94 (s, 3H), 2.64– 2.50 (m, 1H), 2.15– 2.03 (m, 2H), 2.01– 1.82 (m, 1H), 1.63– 1.47 (m, 1H). Example 46
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-1H-indazol-5-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile
 
Figure imgf000098_0001
This compound was prepared using similar procedures as described for Example 37 with (1-methyl-1H-indazol-5-yl)boronic acid (Ark Pharm, cat#AK-39590) replacing 1- methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H29N8 (M+H)+: m/z = 477.2; found 477.3. Example 47
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6- yl)imidazo[1,2-c]pyrimidin-7- l nz ni ril
Figure imgf000098_0002
N This compound was prepared using similar procedures as described for Example 37 with 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol-2(3H)-one (prepared in Example 7, Step 2) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2- dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H28N7O2 (M+H)+: m/z = 494.2; found 494.2.1H NMR (500 MHz, CD3OD) δ 8.17 (d, J = 2.2 Hz, 1H), 7.98 (d, J = 2.2 Hz, 1H), 7.66– 7.61 (m, 4H), 7.34 (d, J = 1.3 Hz, 1H), 7.25 (d, J = 8.0 Hz, 1H), 7.16 (dd, J = 8.0, 1.6 Hz, 1H), 4.40– 4.31 (m, 2H), 3.67– 3.56 (m, 1H), 3.44 (s, 3H), 3.39– 3.34 (m, 2H), 2.95 (s, 6H), 2.35– 2.27 (m, 2H), 2.17 – 2.05 (m, 2H). Example 48
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-methoxypyridin-3-yl)imidazo[1,2-  
c]pyrimidin-7-yl]benzonitrile
Figure imgf000099_0001
This compound was prepared using similar procedures as described for Example 37 with (6-methoxypyridin-3-yl)boronic acid (Aldrich, cat#637610) replacing 1-methyl-5- (4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H28N7O (M+H)+: m/z = 454.2; found 454.2.1H NMR (500 MHz, CD3OD) δ 8.16 (d, J = 2.2 Hz, 1H), 8.11– 8.09 (m, 1H), 7.96 (d, J = 2.1 Hz, 1H), 7.71– 7.68 (m, 2H), 7.66– 7.61 (m, 3H), 6.94– 6.89 (m, 1H), 4.39 – 4.31 (m, 2H), 3.96 (s, 3H), 3.66– 3.55 (m, 1H), 3.38– 3.32 (m, 2H), 2.95 (s, 6H), 2.35– 2.25 (m, 2H), 2.17– 2.05 (m, 2H). Example 49
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5-fluoro-6-methoxypyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile
Figure imgf000099_0002
This compound was prepared using similar procedures as described for Example 37 with 3-Fluoro-2-methoxypyridine-5-boronic acid (Combi-Blocks, cat#BB-8460) replacing 1- methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H27FN7O (M+H)+: m/z = 472.2; found 472.2. Example 50
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[6-(2-oxopyrrolidin-1-yl)pyridin-3- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile  
Figure imgf000100_0001
This compound was prepared using similar procedures as described for Example 37 with 1-[5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2-yl]pyrrolidin-2-one (JPM2 Pharma, cat#JPM2-00-744) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H31N8O (M+H)+: m/z = 507.2; found 507.2.1H NMR (400 MHz, CD3OD) δ 8.46 (d, J = 8.7 Hz, 1H), 8.28 (d, J = 1.7 Hz, 1H), 8.14 (d, J = 2.1 Hz, 1H), 7.95 (d, J = 2.1 Hz, 1H), 7.80 (dd, J = 8.7, 2.4 Hz, 1H), 7.68 (d, J = 8.5 Hz, 2H), 7.62 (d, J = 8.6 Hz, 2H), 4.42– 4.29 (m, 2H), 4.12 (t, J = 7.1 Hz, 2H), 3.68– 3.54 (m, 1H), 3.38– 3.32 (m, 2H), 2.95 (s, 6H), 2.69 (t, J = 8.1 Hz, 2H), 2.34– 2.25 (m, 2H), 2.23– 2.03 (m, 4H). Example 51
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-methyl-3-oxo-3,4-dihydro-2H-1,4- benzoxazin-7-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000100_0002
This compound was prepared using similar procedures as described for Example 37 with 4-methyl-7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2H-1,4-benzoxazin-3(4H)- one (Prepared in Example 15, Step 1) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2- dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H30N7O2 (M+H)+: m/z = 508.2; found 508.2.1H NMR (500 MHz, CD3OD) δ 8.17 (d, J = 2.2 Hz, 1H), 7.99 (d, J = 2.2 Hz, 1H), 7.70– 7.64 (m, 4H), 7.24 (d, J = 8.3 Hz, 1H), 7.06 (d, J = 1.9 Hz, 1H), 7.01 (dd, J = 8.3, 2.0 Hz, 1H), 4.68 (s, 2H), 4.39– 4.30   (m, 2H), 3.66– 3.56 (m, 1H), 3.39 (s, 3H), 3.38– 3.32 (m, 2H), 2.95 (s, 6H), 2.34– 2.25 (m, 2H), 2.16– 2.04 (m, 2H). Example 52
4-{8-[2-(difluoromethyl)-1-methyl-1H-benzimidazol-5-yl]-5-[4- (dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile
Figure imgf000101_0001
Step 1: 5-bromo-2-(difluoromethyl)-1-methyl-1H-benzimidazole
Figure imgf000101_0002
A mixture of 4-bromo-N1-methylbenzene-1,2-diamine (Combi-Blocks, cat# AN-3666: 0.5 g, 2.5 mmol), difluoroacetic acid (0.79 mL) and a few drops of concentrated hydrochloric acid was stirred at 120 °C overnight. After cooling to room temperature, the reaction mixture was concentrated, diluted with EtOAc, washed with saturated NaHCO3. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C9H8BrF2N2 (M+H)+: m/z = 261.0; found 261.0. Step 2: 2-(difluoromethyl)-1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- benzimidazole
Figure imgf000101_0003
A mixture of 5-bromo-2-(difluoromethyl)-1-methyl-1H-benzimidazole (0.59 g, 2.2 mmol), 4,4,5,5,4',4',5',5'-Octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (860 mg, 3.4 mmol), [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with
dichloromethane (1:1) (90 mg, 0.1 mmol) and potassium acetate (660 mg, 6.8 mmol) in 1,4- dioxane (20 mL) was purged with nitrogen then heated at 90 °C overnight. After cooling to  
room temperature, the reaction mixture was concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 15% AcOEt in hexanes to give the desired product. LC-MS calculated for C15H20BF2N2O2 (M+H)+: m/z = 309.2; found 309.2. Step 3: 4-{8-[2-(difluoromethyl)-1-methyl-1H-benzimidazol-5-yl]-5-[4- (dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile
This compound was prepared using similar procedures as described for Example 37 with 2-(difluoromethyl)-1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- benzimidazole replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H29F2N8 (M+H)+: m/z = 527.2; found 527.2.1H NMR (500 MHz, CD3OD) δ 8.18 (d, J = 2.2 Hz, 1H), 7.96 (d, J = 2.2 Hz, 1H), 7.84– 7.80 (m, 1H), 7.76 (d, J = 8.5 Hz, 1H), 7.62– 7.57 (m, 4H), 7.36 (dd, J = 8.5, 1.5 Hz, 1H), 7.17 (t, J = 52.3 Hz, 1H), 4.41– 4.31 (m, 2H), 4.05 (s, 3H), 3.68– 3.56 (m, 1H), 3.40– 3.32 (m, 2H), 2.96 (s, 6H), 2.36– 2.26 (m, 2H), 2.19 – 2.06 (m, 2H). Example 53
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-methoxy-5-methylpyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile
Figure imgf000102_0001
This compound was prepared using similar procedures as described for Example 37 with (6-methoxy-5-methylpyridin-3-yl)boronic acid (Combi-Blocks, cat#BB-6068) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H30N7O (M+H)+: m/z = 468.2; found 468.2. Example 54
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-  
benzoxazol-6-yl)imidazo[1,2- rimi in- - l nz ni ril
Figure imgf000103_0001
N F
This compound was prepared using similar procedures as described for Example 37 with 5-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one (Prepared in Example 45, Step 3) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2- dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H27FN7O2 (M+H)+: m/z = 512.2; found 512.2.  Example 55
4-[5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-(3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000103_0002
This compound was prepared using similar procedures as described for Example 29 with 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol-2(3H)-one (prepared in Example 7, Step 2) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2- dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 1. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H29N6O3 (M+H)+: m/z = 509.2; found 509.3. Example 56
4-[5-{[(3R)-1-(2-hydroxyethyl)piperidin-3-yl]methoxy}-8-(6-methoxypyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
 
Figure imgf000104_0001
This compound was prepared using similar procedures as described for Example 34 with (6-methoxypyridin-3-yl)boronic acid (Aldrich, cat#637610)  replacing 1-methyl-5- (4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H29N6O3 (M+H)+: m/z = 485.2; found 485.2.  Example 57
4-(8-(5-fluoro-6-methoxypyridin-3-yl)-5-{[(3R)-1-(2-hydroxyethyl)piperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000104_0002
 
This compound was prepared using similar procedures as described for Example 34 with 3-fluoro-2-methoxypyridine-5-boronic acid (Combi-Blocks, cat#BB-8460) replacing 1- methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine. The reaction mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H28FN6O3 (M+H)+: m/z = 503.2; found 503.2.  Example 58
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
 
Figure imgf000105_0001
Step 1: 1-(benzyloxy)-3-fluoro-2-nitrobenzene
Figure imgf000105_0002
A mixture of 1,3-difluoro-2-nitrobenzene (1 g, 6 mmol), benzyl alcohol (0.81 mL, 7.8 mmol), potassium carbonate (1.79 g, 13.0 mmol) in N,N-dimethylformamide (5 mL) was heated at 60 °C for 18 h. The reaction mixture was cooled to room temperature then diluted with EtOAc and washed with water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 20% EtOAc in Hexanes to give the desired product. Step 2: 2-(benzyloxy)-6-fluoroaniline
Figure imgf000105_0003
A mixture of 1-(benzyloxy)-3-fluoro-2-nitrobenzene (2 g, 8 mmol), tin dichloride (4 g, 20 mmol), hydrogen chloride (1M in water, 4.8 mL, 4.8 mmol) in ethanol (25 mL) was refluxed for 18 h. The mixture was cooled to room temperature then concentrated. The residue was dissolved in EtOAc and water then adjusted to basic with NaOH. The precipitate was filtered and the organic phase was separated then dried over Na2SO4 and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 20% EtOAc in Hexanes to give the desired product. LC-MS calculated for C13H13FNO (M+H)+: m/z = 218.1; found 218.1. Step 3: 2-(benzyloxy)-4-bromo-6-fluor
Figure imgf000105_0004
Bromine (0.20 mL, 3.8 mmol) was added to a mixture of 2-(benzyloxy)-6-   fluoroaniline (650 mg, 3.0 mmol) in methanol (2.27 mL) and acetic acid (0.76 mL) at 0 °C. The mixture was stirred at 0 °C for 4 h then concentrated. The residue was dissolved in EtOAc then washed with 1N NaOH, water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C13H12BrFNO (M+H)+: m/z = 296.0; found 296.0. Step 4: 2-amino-5-bromo-3-fluorophenol
Figure imgf000106_0001
To a solution of 2-(benzyloxy)-4-bromo-6-fluoroaniline (900 mg, 3 mmol) in tetrahydrofuran (6.0 mL) was added platinum dioxide (55 mg, 0.24 mmol). The resulting mixture was purged with H2, then stirred at room temperature overnight under 1 atm of H2. The reaction mixture was filtered then concentrated. The residue was used in the next step without further purification. LC-MS calculated for C6H6BrFNO (M+H)+: m/z = 206.0; found 206.0. Step 5: 6-bromo-4-fluoro-1,3-benzoxazol-2(3H)-one
Figure imgf000106_0002
2-Amino-5-bromo-3-fluorophenol (0.2 g, 1 mmol) was dissolved in tetrahydrofuran (10 mL) at 0 °C then triethylamine (0.68 mL, 4.8 mmol) was added, followed by triphosgene (0.34 g, 1.2 mmol). The mixture was stirred at 0 °C for1 h, then 1.0 M sodium hydroxide in water (1.9 mL, 1.9 mmol) was added. The resulting mixture was stirred at room temperature for 1 h then diluted with EtOAc and washed with water and brine. The organic layer was dried over Na2SO4 and the solvents were removed under reduced pressure. The residue was used in the next step without further purification. Step 6: 6-bromo-4-fluoro-3-methyl-1,3-benzoxazol-2(3H)-one
r
Figure imgf000106_0003
A mixture of 6-bromo-4-fluoro-1,3-benzoxazol-2(3H)-one (crude product from Step 5), potassium carbonate (0.3 g, 2 mmol) and methyl iodide (0.1 mL, 2 mmol) in acetone (3  
mL) was heated at 80 °C for overnight. The reaction mixture was cooled to room temperature then concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 25% EtOAc in Hexanes to give the desired product. LC-MS calculated for C8H6BrFNO (M+H)+: m/z = 246.0; found 245.9. Step 7: 4-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one
Figure imgf000107_0001
A mixture of [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with dichloromethane (1:1) (10 mg, 0.02 mmol), 6-bromo-4-fluoro-3-methyl-1,3-benzoxazol- 2(3H)-one (90 mg, 0.4 mmol), 4,4,5,5,4',4',5',5'-octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (140 mg, 0.55 mmol) and potassium acetate (100 mg, 1 mmol) in 1,4-dioxane (3 mL) was purged with nitrogen then stirred at 90 °C for overnight. The reaction mixture was cooled to room temperature then diluted with EtOAc and washed with water and brine. The organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 25% EtOAc in Hexanes to give the desired product. LC-MS calculated for C14H18BFNO4 (M+H)+: m/z = 294.1; found 294.1. Step 8: 4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
This compound was prepared using similar procedures as described for Example 37 with 4-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H27FN7O2 (M+H)+: m/z = 512.2; found 512.2.  Example 59
4-(8-(4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile  
Figure imgf000108_0001
This compound was prepared using similar procedures as described for Example 1 with 4-fluoro-3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-benzoxazol- 2(3H)-one (prepared in Example 58, Step 7) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H26FN6O3 (M+H)+: m/z = 513.2; found 513.2. Example 60
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(3-methyl-2-oxo-2,3-dihydro[1,3]oxazolo[4,5- b]pyridin-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000108_0002
To a solution of 6-bromo[1,3]oxazolo[4,5-b]pyridin-2(3H)-one (Ark Pharm, cat#AK- 24539: 0.394 g, 1.83 mmol) in N,N-dimethylformamide (5 mL) at– 40 °C was added sodium hydride (60 wt % in mineral oil, 290 mg, 7.3 mmol). The resulting mixture was stirred at -40 °C for 1 hour then methyl iodide (1.14 mL, 18.3 mmol) was added dropwise. The reaction mixture was stirred at -40 °C for another 2 hours, then warmed to 0 °C and quenched by saturated NH4Cl aqueous solution. The mixture was extracted with EtOAc, then DCM/iPrOH (2:1). The combined extracts were dried over Na2SO4, filtered and concentrated. The residue was used in the next step without further purification. LC-MS calculated for C7H6BrN2O2 (M+H)+: m/z = 229.0; found 229.0.
  Step 2: 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)[1,3]oxazolo[4,5-b]pyridin- 2(3H)-one
Figure imgf000109_0001
A mixture of 6-bromo-3-methyl[1,3]oxazolo[4,5-b]pyridin-2(3H)-one (0.15 g, 0.66 mmol), 4,4,5,5,4',4',5',5'-octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (250 mg, 0.98 mmol), [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complex with dichloromethane (1:1) (30 mg, 0.03 mmol) and potassium acetate (190 mg, 2.0 mmol) in 1,4-dioxane (6 mL) was purged with nitrogen then heated at 90 °C overnight. After cooling to room temperature, the reaction mixture was concentrated. The crude material was purified by flash chromatography on a silica gel column eluting with 0 to 5 % MeOH in DCM to give the desired product. LC-MS calculated for C13H18BN2O4 (M+H)+: m/z = 277.1; found 277.1. Step 3: 4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(3-methyl-2-oxo-2,3- dihydro[1,3]oxazolo[4,5-b]pyridin-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
This compound was prepared using similar procedures as described for Example 37 with 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)[1,3]oxazolo[4,5-b]pyridin- 2(3H)-one replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H27N8O2 (M+H)+: m/z = 495.2; found 495.2.  Example 61
4-(8-(3-methyl-2-oxo-2,3-dihydro[1,3]oxazolo[4,5-b]pyridin-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000109_0002
This compound was prepared using similar procedures as described for Example 1   with 3-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)[1,3]oxazolo[4,5-b]pyridin- 2(3H)-one (prepared in Example 60, Step 2) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H26N7O3 (M+H)+: m/z = 496.2; found 496.2. Example 62
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000110_0001
This compound was prepared using similar procedures as described for Example 37 with 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3-dihydro-2H-indol-2-one (Example 6, Step 1) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H30N7O (M+H)+: m/z = 492.3; found 492.2.  Example 63
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1,2-dimethyl-1H-benzimidazol-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
Figure imgf000110_0002
  A mixture of [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with dichloromethane (1:1) (40 mg, 0.04 mmol), 5-bromo-1,2-dimethyl-1H-benzimidazole (200 mg, 0.9 mmol), 4,4,5,5,4',4',5',5'-octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (340 mg, 1.3 mmol) and potassium acetate (300 mg, 3 mmol) in 1,4-dioxane (7 mL) was purged with nitrogen then stirred at 90 °C overnight. The reaction mixture was cooled to room temperature then concentrated. The residue was purified by flash chromatography eluting with 0 to 30% MeOH in DCM to give the desired product. LC-MS calculated for
C15H22BN2O2 (M+H)+: m/z = 273.2; found 273.2. Step 2: 4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1,2-dimethyl-1H-benzimidazol-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile
This compound was prepared using similar procedures as described for Example 37 with 1,2-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-benzimidazole replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4- b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2,
acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H31N8 (M+H)+: m/z = 491.3; found 491.3.  Example 64
4-(8-[2-(difluoromethyl)-1-methyl-1H-benzimidazol-5-yl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000111_0001
This compound was prepared using similar procedures as described for Example 1 with 2-(difluoromethyl)-1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- benzimidazole (prepared in Example 52, Step 2) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H28F2N7O (M+H)+: m/z = 528.2; found 528.2. Example 65
 
4-(8-(1,2-dimethyl-1H-benzimidazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000112_0001
This compound was prepared using similar procedures as described for Example 1 with 1,2-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-benzimidazole (Prepared in Example 63, Step 1) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H30N7O (M+H)+: m/z = 492.3; found 492.2. Example 66
5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-8- yl}-2-methylnicotinonitrile
Figure imgf000112_0002
Step 1: 2-methyl-5-(4,4,5,5-tetrameth l-132-dioxaborolan-2- l nicotinonitrile
Figure imgf000112_0003
A mixture of 5-bromo-2-methylnicotinonitrile (Combi-Blocks, cat#PY-1861: 100 mg, 0.50 mmol), 4,4,5,5,4',4',5',5'-octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (140 mg, 0.55 mmol), [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with dichloromethane (1:1) (20 mg, 0.02 mmol) and potassium acetate (150 mg, 1.5 mmol) in 1,4- dioxane (5 mL) was purged with nitrogen then heated at 90 °C overnight. After cooling to room temperature, the reaction mixture was concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 15% AcOEt in hexanes to give the   desired product. LC-MS calculated for C13H18BN2O2 (M+H)+: m/z = 245.2; found 245.2. Step 2: 5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin- 8-yl}-2-methylnicotinonitrile
This compound was prepared using similar procedures as described for Example 37 with 2-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)nicotinonitrile replacing 1- methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H27N8 (M+H)+: m/z = 463.2; found 463.2. Example 67
Methyl (5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl}pyridin-2-yl)methylcarbamate
Figure imgf000113_0001
To a solution of 5-bromo-N-methylpyridin-2-amine (Combi-Blocks, cat# PY-1235: 138 mg, 0.738 mmol) in tetrahydrofuran (4 mL) was added cesium carbonate (288 mg, 0.885 mmol) and methyl chloroformate (285 μL, 3.69 mmol). The resulted mixture was heated for 12 h at 50 °C, then diluted with ethyl acetate, filtered, and concentrated. The crude product was used without further purification. LC-MS calculated for C8H10BrN2O2 (M+H)+: m/z = 245.0; found 245.0. Step 2: methyl methyl[5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2-yl]carbamate
 
Figure imgf000114_0001
This compound was prepared using similar procedures as described for Example 6, Step 1 with methyl (5-bromopyridin-2-yl)methylcarbamate replacing 5-bromo-1-methyl-1,3- dihydro-2H-indol-2-one. The reaction mixture was filtered through celite, and then concentrated. The crude product was used in the next step without further purification. Step 3: methyl (5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl}pyridin-2-yl)methylcarbamate
This compound was prepared using similar procedures as described for Example 37 with methyl methyl[5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2-yl]carbamate replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazolo[3,4- b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2,
acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H31N8O2 (M+H)+: m/z = 511.3; found 511.2. Example 68
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5,6-dimethylpyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile
Figure imgf000114_0002
This compound was prepared using similar procedures as described for Example 37 with 2,3-dimethyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (Combi-Blocks, cat#FM-6236) replacing 1-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H- pyrazolo[3,4-b]pyridine in Step 2. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H30N7 (M+H)+: m/z = 452.3; found 452.2. Example 69
 
4-(8-(6-methoxy-5-methylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000115_0001
This compound was prepared using similar procedures as described for Example 1 with (6-methoxy-5-methylpyridin-3-yl)boronic acid (Aurum Pharmatech, cat# A-3579) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H29N6O2 (M+H)+: m/z = 469.2; found 469.2. Example 70
5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-methy
Figure imgf000115_0002
This compound was prepared using similar procedures as described for Example 1 with 2-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)nicotinonitrile (Example 66, Step 1) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C27H26N7O (M+H)+: m/z = 464.2; found 464.2. Example 71
4-(8-[3-(hydroxymethyl)-4-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
 
Figure imgf000116_0001
This compound was prepared using similar procedures as described for Example 1 with [2-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]methanol (Combi- Blocks, cat# FM-2080) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H30N5O2 (M+H)+: m/z = 468.2; found 468.2. Example 72
4-(8-[2-(hydroxymethyl)-4-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000116_0002
This compound was prepared using similar procedures as described for Example 1 with [2-(hydroxymethyl)-4-methylphenyl]boronic acid (Combi-Blocks, cat# 21-2055) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C28H30N5O2 (M+H)+: m/z = 468.2; found 468.2. Example 73
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(6-methylpyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile
Figure imgf000116_0003
 
This compound was prepared using similar procedures as described for Example 1 with 2-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (Combi-Blocks, cat# PN-5068) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H27N6O (M+H)+: m/z = 439.2; found 439.2. Example 74
4-(8-(5-fluoro-6-methylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile
Figure imgf000117_0001
This compound was prepared using similar procedures as described for Example 1 with 3-fluoro-2-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine
(PharmaBlock Inc, cat# PBS07313) replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C26H26FN6O (M+H)+: m/z = 457.2; found 457.2. Example 75
Methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-fluor
Figure imgf000117_0002
Step 1: methyl (4-bromo-2-fluorophen l meth lcarbamate
Figure imgf000117_0003
To a solution of 4-bromo-2-fluoro-N-methylaniline hydrochloride (Combi-Blocks,  
cat#HC-3277: 100 mg, 0.4 mmol) and N,N-diisopropylethylamine (220 μL, 1.2 mmol) in methylene chloride (0.3 mL, 5 mmol) was added methyl chloroformate (38 μL, 0.50 mmol). The resultant mixture was stirred at room temperature overnight, then was quenched with saturated NaHCO3. The aqueous phase was extracted with methylene chloride, and the organic layer was dried over Na2SO4, filtered and concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 40% EtOAc in hexanes to give the desired product. Step 2: methyl [2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)phenyl]methylcarbamate
Figure imgf000118_0001
A mixture of methyl (4-bromo-2-fluorophenyl)methylcarbamate (58 mg, 0.22 mmol), 4,4,5,5,4',4',5',5'-octamethyl-[2,2']bi[[1,3,2]dioxaborolanyl] (62 mg, 0.24 mmol), [1,1'-bis(diphenylphosphino)ferrocene]dichloropalladium(II) complexed with
dichloromethane (1:1) (9 mg, 0.01 mmol) and potassium acetate (65 mg, 0.66 mmol) in 1,4- dioxane (2 mL) was purged with nitrogen then heated at 90 °C overnight. After cooling to room temperature, the reaction mixture was concentrated. The residue was purified by flash chromatography on a silica gel column eluting with 0 to 15% AcOEt in hexanes to give the desired product. LC-MS calculated for C15H22BFNO4 (M+H)+: m/z = 310.2; found 310.2. Step 3: methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-fluorophenyl]methylcarbamate
This compound was prepared using similar procedures as described for Example 1 with methyl [2-fluoro-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2- yl)phenyl]methylcarbamate replacing (4-methylphenyl)boronic acid in Step 8. The resulting mixture was purified by prep-HPLC (pH = 2, acetonitrile/water+TFA) to give the desired product as the TFA salt. LC-MS calculated for C29H30FN6O3 (M+H)+: m/z = 529.2; found 529.2.
  Table 2. The compounds in Table 2 were prepared using analogous procedures as in Example 75 using the appropriate Suzuki coupling partners.
Figure imgf000119_0001
 
Figure imgf000120_0001
 
Figure imgf000121_0001
 
Figure imgf000122_0001
cpyrm n--y enzon r e
F  
Figure imgf000123_0001
 
Figure imgf000124_0001
 
Figure imgf000125_0001
 
Figure imgf000126_0002
  Example A: LSD1 histone demethylase biochemical assay
LANCE LSD1/KDM1A demethylase assay- 10 ^L of 1 nM LSD-1 enzyme (ENZO BML-SE544-0050) in the assay buffer (50 mM Tris, pH 7.5, 0.01% Tween-20, 25 mM NaCl, 5 mM DTT) were preincubated for 1 hour at 25oC with 0.8 ^L compound/DMSO dotted in black 384 well polystyrene plates. Reactions were started by addition of 10 ^L of assay buffer containing 0.4 ^M Biotin-labeled Histone H3 peptide substrate: ART-K(Me1)- QTARKSTGGKAPRKQLA-GGK(Biotin) SEQ ID NO:1 (AnaSpec 64355) and incubated for 1 hour at 25oC. Reactions were stopped by addition of 10 ^L 1X LANCE Detection Buffer (PerkinElmer CR97-100) supplemented with 1.5 nM Eu-anti-unmodified H3K4 Antibody (PerkinElmer TRF0404), and 225 nM LANCE Ultra Streptavidin (PerkinElmer TRF102) along with 0.9 mM Tranylcypromine-HCl (Millipore 616431). After stopping the reactions plates were incubated for 30 minutes and read on a PHERAstar FS plate reader (BMG Labtech). IC50 data for the example compounds is provided in Table 1 (the symbol “+” refers to IC50≤ 50 nM;“++” refers to IC50 > 50 nM and≤ 500 nM;“+++” refers to IC50 > 500 nM and≤ 1000 nM).
Table 1
Figure imgf000126_0001
   
Figure imgf000127_0001
 
Figure imgf000128_0001
Figure imgf000129_0001
 
Various modifications of the invention, in addition to those described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. Each reference, including all patent, patent applications, and publications, cited in the present application is incorporated herein by reference in its entirety.
 

Claims

What is claimed is:
1. A compound of Formula I:
Figure imgf000131_0001
or a pharmaceutically acceptable salt thereof, wherein:
ring A is C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, or 4-10 membered heterocycloalkyl, wherein the 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the C3-10 cycloalkyl or 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group;
X is N or CRX, wherein RX is H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C1-4 haloalkoxy, NHC1-4 alkyl, N(C1-4 alkyl)2 or C1-4 alkylthio;
U is N or CRU, wherein RU is H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C1-4 haloalkoxy, NHC1-4 alkyl, N(C1-4 alkyl)2 or C1-4 alkylthio;
Y is N or CR4;
Z is N or CR5;
with the proviso that at least one of U, Y, and Z is N;
R1 is H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, C1-6haloalkoxy, NHOH, NHOC1-6 alkyl, Cy1, CN, ORa1, SRa1, C(O)Rb1, C(O)NRc1Rd1, C(O)ORa1, OC(O)Rb1, OC(O)NRc1Rd1, NRc1Rd1, NRc1C(O)Rb1, NRc1C(O)ORa1, NRc1C(O)NRc1Rd1, C(=NRe1)Rb1, C(=NRe1)NRc1Rd1, NRc1C(=NRe1)NRc1Rd1, NRc1S(O)Rb1, NRc1S(O)2Rb1, NRc1S(O)2NRc1Rd1, S(O)Rb1, S(O)NRc1Rd1, S(O)2Rb1, S(O)2NRc1Rd1, -L1-R6, or–L2-NR7R8; wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from Cy1, halo, CN, OH, ORa1, SRa1, C(O)Rb1, C(O)NRc1Rd1, C(O)ORa1, OC(O)Rb1, OC(O)NRc1Rd1, NRc1Rd1, NRc1C(O)Rb1, NRc1C(O)ORa1,
NRc1C(O)NRc1Rd1, C(=NRe1)Rb1, C(=NRe1)NRc1Rd1, NRc1C(=NRe1)NRc1Rd1, NRc1S(O)Rb1, NRc1S(O)2Rb1, NRc1S(O)2NRc1Rd1, S(O)Rb1, S(O)NRc1Rd1, S(O)2Rb1, and S(O)2NRc1Rd1;
 
L1 is a bond, -O-, -NR9-, -C(O)NH-, -NHC(O)-, C1-4 alkylene; wherein R9 is H, C1-6 alkyl, -C(O)C1-6 alkyl or–C(O)OC1-6 alkyl;
L2 is a bond, -C(O)-, C1-4 alkylene, -O-C1-4 alkylene-, -C1-4 alkylene-O-, -C1-4 alkylene-NR9-, or–NR9-C1-4 alkylene-;
R2, at each occurrence, is independently selected from H, OH, CN, halo, NH2, C1-4 alkyl, C1-4 alkoxy, C1-4 haloalkyl, C1-4 haloalkoxy, NHC1-4 alkyl, N(C1-4 alkyl)2, and C1-4 alkylthio;
R3, at each occurrence, is independently selected from H, Cy2, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, CN, ORa2, SRa2, C(O)Rb2, C(O)NRc2Rd2, C(O)ORa2, OC(O)Rb2, OC(O)NRc2Rd2, NRc2Rd2, NRc2C(O)Rb2, NRc2C(O)ORa2, NRc2C(O)NRc2Rd2, C(=NRe2)Rb2, C(=NRe2)NRc2Rd2, NRc2C(=NRe2)NRc2Rd2, NRc2S(O)Rb2, NRc2S(O)2Rb2, NRc2S(O)2NRc2Rd2, S(O)Rb2, S(O)NRc2Rd2, S(O)2Rb2, and S(O)2NRc2Rd2; wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from Cy2, halo, CN, ORa2, SRa2, C(O)Rb2, C(O)NRc2Rd2, C(O)ORa2, OC(O)Rb2, OC(O)NRc2Rd2, NRc2Rd2, NRc2C(O)Rb2, NRc2C(O)ORa2, NRc2C(O)NRc2Rd2, C(=NRe2)Rb2, C(=NRe2)NRc2Rd2, NRc2C(=NRe2)NRc2Rd2, NRc2S(O)Rb2, NRc2S(O)2Rb2, NRc2S(O)2NRc2Rd2, S(O)Rb2, S(O)NRc2Rd2, S(O)2Rb2, and S(O)2NRc2Rd2;
or two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 5- or 6-membered heterocycloalkyl ring, a fused C3-6 cycloalkyl ring, or a fused 5- or 6-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected RA substituents, wherein a ring carbon of the fused 5- or 6- membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring is optionally replaced by a carbonyl group;
alternatively, two RA substituents attached to the same carbon of the fused 5- or 6- membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring taken together form a C3-6 cycloalkyl ring or 4- to 7-membered heterocycloalkyl ring;
R4 and R5 are each independently selected from H, Cy3, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, CN, ORa3, SRa3, C(O)Rb3, C(O)NRc3Rd3, C(O)ORa3, OC(O)Rb3, OC(O)NRc3Rd3, NRc3Rd3, NRc3C(O)Rb3, NRc3C(O)ORa3, NRc3C(O)NRc3Rd3, C(=NRe3)Rb3, C(=NRe3)NRc3Rd3, NRc3C(=NRe3)NRc3Rd3, NRc3S(O)Rb3, NRc3S(O)2Rb3, NRc3S(O)2NRc3Rd3, S(O)Rb3, S(O)NRc3Rd3, S(O)2Rb3, and S(O)2NRc3Rd3; wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from Cy3, halo, CN, ORa3, SRa3, C(O)Rb3, C(O)NRc3Rd3, C(O)ORa3, OC(O)Rb3, OC(O)NRc3Rd3, NRc3Rd3, NRc3C(O)Rb3, NRc3C(O)ORa3, NRc3C(O)NRc3Rd3, C(=NRe3)Rb3,  
C(=NRe3)NRc3Rd3, NRc3C(=NRe3)NRc3Rd3, NRc3S(O)Rb3, NRc3S(O)2Rb3, NRc3S(O)2NRc3Rd3, S(O)Rb3, S(O)NRc3Rd3, S(O)2Rb3, and S(O)2NRc3Rd3;
R6 is 5- to 10-membered heteroaryl, 5- to 10-membered heteroaryl-C1-4 alkyl, 4- to 10- membered heterocycloalkyl, or 4- to 10-membered heterocycloalkyl-C1-4 alkyl, each of which is optionally substituted with 1, 2, 3 or 4 independently selected RA substituents;
R7 and R8 together with the nitrogen atom to which they are attached form 4- to 10- membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R7 and R8, wherein a ring-forming carbon atom of the heterocycloalkyl group is optionally substituted by an oxo group, and wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected RB substituents;
each RA is independently selected from H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, C1-6 haloalkoxy, Cy2, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl- C1-4 alkyl, 4-10 membered heterocycloalkyl-C1-4 alkyl, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4,
NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, C(=NRe4)Rb4, C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, Cy3, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl-C1-4 alkyl, and 4-10 membered heterocycloalkyl-C1-4 alkyl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1- 6 haloalkyl, C1-6 haloalkoxy, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4, NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, C(=NRe4)Rb4, C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4;
each RB is independently selected from H, halo, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C1-6 haloalkyl, C1-6 haloalkoxy, Cy3, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl- C1-4 alkyl, 4-10 membered heterocycloalkyl-C1-4 alkyl, CN, NO2, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, Cy4, C3-10 cycloalkyl-C1-4 alkyl, 5-10 membered heteroaryl-C1-4 alkyl and 4-10 membered heterocycloalkyl-C1-4 alkyl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1- 6 haloalkyl, CN, NO2, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5,
 
OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Cy1, Cy2, Cy3, and Cy4 is independently selected from C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, and 4-10 membered heterocycloalkyl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from RCy;
each RCy is independently selected from H, halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, C2-6 alkenyl, C2-6 alkynyl, phenyl, C3-7 cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl, phenyl-C1-4 alkyl-, C3-7 cycloalkyl-C1-4 alkyl-, (5-6 membered heteroaryl)-C1-4 alkyl-, (4-7 membered heterocycloalkyl)-C1-4 alkyl-, oxo, CN, NO2, ORa4, SRa4, C(O)Rb4, C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, C(=NRe4)NRc4Rd4, NRc4C(=NRe4)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4, NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4, wherein said C1-4 alkyl, C2-6 alkenyl, C2-6 alkynyl, phenyl, C3-7 cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl, phenyl-C1-4 alkyl-, C3-7 cycloalkyl-C1- 4 alkyl-, (5-6 membered heteroaryl)-C1-4 alkyl-, and (4-7 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted by 1, 2, or 3 substituents independently selected from C1-6 alkyl, C1-4 haloalkyl, C1-6 cyanoalkyl, halo, CN, NO2, ORa4, SRa4, C(O)Rb4,
C(O)NRc4Rd4, C(O)ORa4, OC(O)Rb4, OC(O)NRc4Rd4, C(=NRe4)NRc4Rd4,
NRc4C(=NRe4)NRc4Rd4, NRc4Rd4, NRc4C(O)Rb4, NRc4C(O)ORa4, NRc4C(O)NRc4Rd4, NRc4S(O)Rb4, NRc4S(O)2Rb4, NRc4S(O)2NRc4Rd4, S(O)Rb4, S(O)NRc4Rd4, S(O)2Rb4, and S(O)2NRc4Rd4;
each Ra1, Rb1, Rc1, and Rd1 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;  
or any Rc1 and Rd1 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, C6-10 aryl, 5-6 membered heteroaryl, C1-6 haloalkyl, halo CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, C6-10 aryl, and 5-6 membered heteroaryl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra2, Rb2, Rc2, and Rd2 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5; or any Rc2 and Rd2 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, 5-6 membered heteroaryl, C1-6 haloalkyl, halo, CN, ORa5, SRa5, C(O)Rb5,
C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl,  
phenyl, and 5-6 membered heteroaryl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra3, Rb3, Rc3, and Rd3 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4- 10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl-, (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl-, wherein said C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C6-10 aryl, C3-10 cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl, C6-10 aryl-C1-4 alkyl-, C3-10 cycloalkyl-C1-4 alkyl- , (5-10 membered heteroaryl)-C1-4 alkyl-, and (4-10 membered heterocycloalkyl)-C1-4 alkyl- are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5,
NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5; or any Rc3 and Rd3 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, 5-6 membered heteroaryl, C1-6 haloalkyl, halo, CN, ORa5, SRa5, C(O)Rb5,
C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5, wherein said C1-6 alkyl, C3-7 cycloalkyl, 4-7 membered heterocycloalkyl, phenyl, and 5-6 membered heteroaryl are each optionally substituted by 1, 2, or 3 substituents independently selected from halo, C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5, NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra4, Rb4, Rc4, and Rd4 is independently selected from H, C1-6 alkyl, C1-4 haloalkyl, C2-6 alkenyl, and C2-6 alkynyl, wherein said C1-6 alkyl, C2-6 alkenyl, and C2-6  
alkynyl are each optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from C1-4 alkyl, C1-4 haloalkyl, C1-4 cyanoalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
or any Rc4 and Rd4 together with the N atom to which they are attached form a 4-, 5-, 6-, or 7-membered heterocycloalkyl group optionally substituted with 1, 2, or 3 substituents independently selected from C1-6 alkyl, C1-6 haloalkyl, halo, CN, ORa5, SRa5, C(O)Rb5, C(O)NRc5Rd5, C(O)ORa5, OC(O)Rb5, OC(O)NRc5Rd5, NRc5Rd5, NRc5C(O)Rb5,
NRc5C(O)ORa5, NRc5C(O)NRc5Rd5, C(=NRe5)Rb5, C(=NRe5)NRc5Rd5, NRc5C(=NRe5)NRc5Rd5, NRc5S(O)Rb5, NRc5S(O)2Rb5, NRc5S(O)2NRc5Rd5, S(O)Rb5, S(O)NRc5Rd5, S(O)2Rb5, and S(O)2NRc5Rd5;
each Ra5, Rb5, Rc5, and Rd5 is independently selected from H, C1-4 alkyl, C1-4 haloalkyl, C2-4 alkenyl, and C2-4 alkynyl, wherein said C1-4 alkyl, C2-4 alkenyl, and C2-4 alkynyl are each optionally substituted with 1, 2, or 3 substituents independently selected from OH, CN, amino, halo, C1-4 alkyl, C1-4 alkoxy, C1-4 alkylthio, C1-4 alkylamino, di(C1-4 alkyl)amino, C1-4 haloalkyl, and C1-4 haloalkoxy;
each Re1, Re2, Re3, Re4, and Re5 is independently selected from H, C1-4 alkyl, and CN; the subscript m is 1 or 2; and
the subscript n is 1, 2, 3 or 4.
2. The compound of claim 1 havin Formula II:
Figure imgf000137_0001
or a pharmaceutically acceptable salt thereof.
3. The compound of claim 1, having Formula III:
 
Figure imgf000138_0001
or a pharmaceutically acceptable salt thereof.
4. The compound of any one of claims 1-3, or a pharmaceutically acceptable salt thereof, wherein U is CRU.
5. The compound of claim 1, having Formula IIIa:
Figure imgf000138_0002
or a pharmaceutically acceptable salt thereof.
6. The compound of any one of claims 1-5, or a pharmaceutically acceptable salt thereof, wherein Y is N.
7. The compound of any one of claims 1-5, or a pharmaceutically acceptable salt thereof, wherein Y is CR4.
8. The compound of any one of claims 1-7, or a pharmaceutically acceptable salt thereof, wherein Z is N.
9. The compound of any one of claims 1-7, or a pharmaceutically acceptable salt thereof, wherein Z is CR5.
10. The compound of any one of claims 1-5, or a pharmaceutically acceptable salt thereof, wherein Y and Z are each CH.  
11. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is C6-10 aryl, 5-10 membered heteroaryl, or 4-10 membered heterocycloalkyl, wherein the 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl of ring A each has at least one ring-forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized; and wherein a ring-forming carbon atom of the 4-10 membered heterocycloalkyl is optionally substituted by oxo to form a carbonyl group.
12. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is C6-10 aryl.
13. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is phenyl.
14. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is 5-10 membered heteroaryl.
15. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is pyridyl, 1H-indazolyl, 1H-pyrrolo[2,3-b]pyridinyl, or 1H- benzo[d]imidazolyl.
16. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is pyridyl.
17. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is 4-10 membered heterocycloalkyl having at least one ring- forming carbon atom and 1, 2, 3, or 4 ring-forming heteroatoms selected from N, O, and S, wherein N or S is optionally oxidized, and wherein a ring-forming carbon atom is optionally substituted by oxo to form a carbonyl group.
18. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro-1,3- benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4-   benzoxazinyl; 1H-pyrazolo[3,4-b]pyridinyl, 3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin- 7-yl; 2-oxo-2,3-dihydro-1H-benzimidazolyl; 1H-benzimidazolyl; 2-oxo-2,3- dihydro[1,3]oxazolo[4,5-b]pyridinyl, or 2,3-dihydro-1-benzofuranyl.
19. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is 2-oxo-2,3-dihydro-1H-indolyl; 2-oxo-2,3-dihydro-1,3- benzoxazolyl; 3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazinyl; 3-oxo-3,4-dihydro-2H-1,4- benzoxazinyl; or 2,3-dihydro-1-benzofuranyl.
20. The compound of any one of claims 1-10, or a pharmaceutically acceptable salt thereof, wherein ring A is phenyl; 2,3-dihydro-1,4-benzodioxine; 2,3-dihydro-1H- pyrrolo[2,3-b]pyridin-5-yl; 5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl; 2-oxo-1,2,3,4- tetrahydroquinolin-7-yl; pyridyl; 2-oxo-2,3-dihydro-1,3-benzoxazolyl; 1,3-benzothiazol-5-yl; 2,3-dihydro-1H-inden-5-yl; 1H-pyrrolo[2,3-b]pyridinyl; 8-quinoxalin-6-yl; 2-oxo-1,2,3,4- tetrahydroquinolin-6-yl; or 1H-pyrazolo[3,4-b]pyridinyl.
21. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein R3, at each occurrence, is independently selected from Cy2, C1-6 alkyl, CN, ORa2, C(O)NRc2Rd2, and NRc2Rd2; wherein the C1-6 alkyl is optionally substituted with 1, 2, or 3 substituents independently selected from Cy2, C(O)Rb2, and C(O)NRc2Rd2.
22. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein two adjacent R3 substituents on ring A taken together with the atoms to which they are attached form a fused 5- or 6-membered heterocycloalkyl ring, a fused C3-6 cycloalkyl ring, or a fused 5- or 6-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected RA substituents; wherein a ring carbon of the fused 5- or 6-membered heterocycloalkyl ring or fused C3-6 cycloalkyl ring is optionally replaced by a carbonyl group;
alternatively, two RA substituents attached to the same carbon of the fused 5- or 6- membered heterocycloalkyl or fused C3-6 cycloalkyl taken together form a C3-6 cycloalkyl or 4- to 7-membered heterocycloalkyl ring.
23. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein two adjacent R3 substituents on ring A taken together with the atoms to   which they are attached form a fused ring selected from 1-methylpyrrolidine, 4-methyl-3- oxo-morpholine, 1-methylimidazole, 1-methylpiperidine, 1-methyl-2-oxopyrrolidine, and 1- methylpyrazole, each of which is optionally substituted with 1 or 2 RA substituents.
24. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein R3 is C1-6 alkyl, halo, C1-6 hydroxyalkyl, C1-6 haloalkyl, CN, ORa2, 1- pyrrolidinyl, 2-oxo-1-pyrrolidinyl, NRc2C(O)ORa2, -( C1-6 alkyl)-NRc2C(O)ORa2,
C(O)NRc2Rd2, NRc2Rd2, piperazinylmethyl, 4-methylpiperazinylmethyl, piperidinyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl, morpholinylmethyl, or 3-cyano-1- pyrrolidinyl.
25. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein R3 is C1-6 alkyl, CN, ORa2, 1-pyrrolidinyl, 2-oxo-1-pyrrolidinyl, C(O)NRc2Rd2, NRc2Rd2, piperazinylmethyl, 4-methylpiperazinylmethyl, piperidinyl, morpholinyl, 4-methylpiperazinylcarbonylmethyl, morpholinylmethyl, or 3-cyano-1- pyrrolidinyl.
26. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein R3 is, at each occurrence, CN, F, hydroxymethyl, (CH3O)C(O)N(CH3)-, (CH3O)C(O)N(CH3)-methyl, difluoromethyl, amino, methyl, methoxy, 1-pyrrolidinyl, 2-oxo- 1-pyrrolidinyl, -C(O)N(CH3)2, dimethylamino, 4-methylpiperazinylmethyl, morpholinyl, 4- methylpiperazinylcarbonylmethyl, morpholinylmethyl, morpholinoethyl, or 3-cyano-1- pyrrolidinylmethyl.
27. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein R3 is, at each occurrence, CN, methyl, methoxy, 1-pyrrolidinyl, 2-oxo-1- pyrrolidinyl, -C(O)N(CH3)2, dimethylamino, 4-methylpiperazinylmethyl, morpholinyl, 4- methylpiperazinylcarbonylmethyl, morpholinylmethyl, morpholinoethyl, or 3-cyano-1- pyrrolidinylmethyl.
28. The compound of any one of claims 1-20, or a pharmaceutically acceptable salt thereof, wherein R3 is, at each occurrence, CN, F, hydroxymethyl, (CH3O)C(O)N(CH3)-, (CH3O)C(O)N(CH3)-methyl, difluoromethyl, methyl, methoxy, -C(O)N(CH3)2,
dimethylamino, morpholinylmethyl, (CH3)S(O2)N(CH3)-methyl, (CH3)2NC(O)N(CH3)-   methyl , Cl, 1-hydroxyethyl, methoxymethyl, isopropyl, ethyl, (CH3)S(O2)N(CH3)-, or ethoxy.
29. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is -L1-R6 or–L2-NR7R8.
30. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is–L2-NR7R8, wherein L2 is a bond, -C(O)-, -C1-4 alkylene-, -O-C1-4 alkylene,
-C1-4 alkylene-O-, -C1-4 alkylene-NH-, or -NH-C1-4 alkylene-.
31. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is ORa1.
32. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is ORa1, wherein Ra1 is C1-6 alkyl substituted with Cy4.
33. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is ORa1, wherein Ra1 is methylene substituted with Cy4.
34. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is ORa1, wherein Ra1 is methylene substituted with 4-10 membered heterocycloalkyl optionally substituted with 1, 2, 3, or 4 substituents independently selected from RCy.
35. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3-yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, (2-hydroxyethylpiperidin-3-yl)methoxy, (2- methoxyethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, 7-methyl-2,7-diazaspiro[4.4]non-2-yl, or (1-methylpyrrolidin- 3-yl)methoxy.
 
36. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is (1-methylpiperidin-3-yl)methoxy or (1-methylpyrrolidin-3- yl)methoxy.
37. The compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein R1 is (1-methylpiperidin-3-yl)methoxy, (1-ethylpiperidin-3-yl)methoxy, (2-cyanoethylpiperidin-3-yl)methoxy, 4-dimethylaminopiperidin-1-yl, 3- dimethylaminopyrrolidin-1-yl, (2-hydroxypropylpiperidin-3-yl)methoxy, or 2-hydroxy-2- methylpropyl)piperidin-3-yl]methoxy.
38. The compound of any one of claims 1-37, or a pharmaceutically acceptable salt thereof, wherein R2 is H.
39. The compound of any one of claims 1-5 and 7-38, or a pharmaceutically acceptable salt thereof, wherein R4 is H.
40. The compound of any one of claims 1-7, and 9-39, or a pharmaceutically acceptable salt thereof, wherein R5 is H.
41. The compound of any one of claims 1-40, or a pharmaceutically acceptable salt thereof, wherein m is 1.
42. The compound of any one of claims 1-41, or a pharmaceutically acceptable salt thereof, wherein n is 1.
43. The compound of any one of claims 1-5, 7, 9-28, and 42, having Formula IVa, IVb, IVc, IVd, IVe, or IVf:
Figure imgf000143_0001
 
Figure imgf000144_0001
or a pharmaceutically acceptable salt thereof.
44. The compound of any one of claims 1-5, 7, 9-28, and 42, having Formula IVg, IVh, or IVi:
Figure imgf000144_0002
or a pharmaceutically acceptable salt thereof.
45. The compound of any one of claims 1-5, 7, 9-28, and 42, having Formula IVa or IVb:
 
Figure imgf000145_0001
or a pharmaceutically acceptable salt thereof.
46. The compound of any one of claims 1-5, 7, 9-28, and 42, having Formula VIa, VIb, or VIc:
Figure imgf000145_0002
or a pharmaceutically acceptable salt thereof.
47. The compound of an one of claims 1-5 and 7, having Formula V:
Figure imgf000145_0003
or a pharmaceutically acceptable salt thereof, wherein:
two R3 substituents taken together with the carbon atoms to which they are attached form a fused 5-membered heterocycloalkyl ring or a fused 5-membered heteroaryl ring, each of which is optionally substituted with 1 or 2 independently selected RA substituents, wherein
  a ring carbon of the fused 5-membered heterocycloalkyl ring is optionally replaced by a carbonyl group;
X1 is N or CH;
L2 is a bond or O-C 1-4 alkylene; and
R7 and R8 together with the nitrogen atom to which they are attached form 4- to 7- membered heterocycloalkyl ring having 0, 1 or 2 heteroatoms selected from N and S in addition to the nitrogen atom connected to R7 and R8, wherein the heterocycloalkyl is optionally substituted with 1, 2, 3 or 4 independently selected RB substituents.
48. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound is selected from:
4-(8-(4-methylphenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile,
4-(8-(4-methylphenyl)-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile,
4-(8-(6-methoxypyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-7-yl)benzonitrile,
4-(8-[6-(dimethylamino)pyridin-3-yl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(6-pyrrolidin-1-ylpyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1-methylpiperidin- 3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(1-methyl-1H-indazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-{4-[(4-methylpiperazin-1-yl)methyl]phenyl}-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-{4-[2-(4-methylpiperazin-1-yl)-2-oxoethyl]phenyl}-5-{[(3R)-1-methylpiperidin- 3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[4-(2-morpholin-4- ylethyl)phenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[4-(morpholin-4-   ylmethyl)phenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
(3S)-1-[4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)benzyl]pyrrolidine-3-carbonitrile,
4-(8-(4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-{5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-[6-(2-oxopyrrolidin-1-yl)pyridin-3- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-(8-(1-methyl-1H-benzimidazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(1-methyl-1H-indazol-6-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrrolo[2,3-b]pyridin- 5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-N,N-dimethyl-2,3-dihydro-1-benzofuran-2-carboxamide,
4-(8-[6-(dimethylamino)pyridin-3-yl]-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}-8-(6-pyrrolidin-1-ylpyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(4-methyl-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-7-yl)-5-{[(3R)-1- methylpyrrolidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(1-methyl-1H-benzimidazol-5-yl)-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1-methylpyrrolidin- 3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile, and
4-(8-(1-methyl-1H-indazol-5-yl)-5-{[(3R)-1-methylpyrrolidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile.
49. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound is selected from:
 
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin- 5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-[3-fluoro-4-(hydroxymethyl)-5-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[3-fluoro-4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[3,5-difluoro-4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-(2-cyanoethyl)piperidin-3-yl]methoxy}-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-{[(3R)-1-(2-hydroxyethyl)piperidin-3-yl]methoxy}-8-(1-methyl-1H- pyrazolo[3,4-b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-[4-(hydroxymethyl)-3-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-8-(1-methyl-1H-pyrazolo[3,4- b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-(7-methyl-2,7-diazaspiro[4.4]non-2-yl)-8-(1-methyl-1H-pyrazolo[3,4-b]pyridin- 5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-8-yl)-2-fluorobenzyl]methylcarbamate,
4-[5-{[(3R)-1-(2-methoxyethyl)piperidin-3-yl]methoxy}-8-(1-methyl-1H- pyrazolo[3,4-b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(3-amino-1-methyl-1H-indazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(3-methyl-2-oxo-3,4-dihydro-2H-1,3-benzoxazin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
 
4-(8-(5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-1H-indazol-5-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-methoxypyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5-fluoro-6-methoxypyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[6-(2-oxopyrrolidin-1-yl)pyridin-3- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-methyl-3-oxo-3,4-dihydro-2H-1,4- benzoxazin-7-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-{8-[2-(difluoromethyl)-1-methyl-1H-benzimidazol-5-yl]-5-[4- (dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-methoxy-5-methylpyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-(3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-{[(3R)-1-(2-hydroxyethyl)piperidin-3-yl]methoxy}-8-(6-methoxypyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(5-fluoro-6-methoxypyridin-3-yl)-5-{[(3R)-1-(2-hydroxyethyl)piperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3- benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(4-fluoro-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(3-methyl-2-oxo-2,3- dihydro[1,3]oxazolo[4,5-b]pyridin-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(3-methyl-2-oxo-2,3-dihydro[1,3]oxazolo[4,5-b]pyridin-6-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
 
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-2-oxo-2,3-dihydro-1H-indol-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1,2-dimethyl-1H-benzimidazol-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-[2-(difluoromethyl)-1-methyl-1H-benzimidazol-5-yl]-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(1,2-dimethyl-1H-benzimidazol-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2-c]pyrimidin- 8-yl}-2-methylnicotinonitrile,
methyl (5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl}pyridin-2-yl)methylcarbamate,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5,6-dimethylpyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile,
4-(8-(6-methoxy-5-methylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-methylnicotinonitrile,
4-(8-[3-(hydroxymethyl)-4-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[2-(hydroxymethyl)-4-methylphenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(6-methylpyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile,
4-(8-(5-fluoro-6-methylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile, and
methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1, 2-c]pyrimidin-8-yl)-2-fluorophenyl]methylcarbamate.
50. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound is selected from:
7-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-N,N-dimethyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide,  
4-(8-(1-methyl-2,3-dihydro-1H-pyrrolo[2,3-b]pyridin-5-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-methylpiperidin-3-yl]methoxy}-8-(8-methyl-5,6,7,8-tetrahydro- 1,8-naphthyridin-3-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(1-methyl-2-oxo-1,2,3,4-tetrahydroquinolin-7-yl)-5-{[(3R)-1- methylpiperidin-3-yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[3-fluoro-4-(morpholin-4-ylmethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-{[(3R)-1-(2-cyanoethyl)piperidin-3-yl]methoxy}-8-(5-fluoro-6- methoxypyridin-3-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-{8-[6-(dimethylamino)-5-fluoropyridin-3-yl]-5-[4-(dimethylamino)piperidin- 1-yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-[5-{[(3R)-1-(2-cyanoethyl)piperidin-3-yl]methoxy}-8-(3-methyl-2-oxo-2,3- dihydro-1,3-benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
N-[4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1, 2-c]pyrimidin-8-yl)-2-fluorobenzyl]-N-methylmethanesulfonamide,
N-[4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1, 2-c]pyrimidin-8-yl)-2-fluorobenzyl]-N,N',N'-trimethylurea,
N-[4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1, 2-c]pyrimidin-8-yl)benzyl]-N,N',N'-trimethylurea,
methyl [4-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-8-yl)benzyl]methylcarbamate,
4-(8-(5-chloro-6-methoxypyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[3-fluoro-4-(hydroxymethyl)-5- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{8-[3,5-difluoro-4-(hydroxymethyl)phenyl]-5-[4-(dimethylamino)piperidin-1- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[4-(hydroxymethyl)-3- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-(8-(5-chloro-6-methylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[3-(1-hydroxyethyl)-4-methylphenyl]-5-{[(3R)-1-methylpiperidin-3-  
yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[4-(methoxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-[2-fluoro-4-(morpholin-4-ylmethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3-yl]methoxy}imidazo[1,2- c]pyrimidin-8-yl)-2-methylbenzonitrile,
N-(4-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl}-2-fluorobenzyl)-N,N',N'-trimethylurea,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[3-fluoro-4-(morpholin-4- ylmethyl)phenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-[3-(hydroxymethyl)-4- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-8-[3-(hydroxymethyl)-4- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-(8-[3-chloro-4-(hydroxymethyl)phenyl]-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[3-(hydroxymethyl)-4- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{8-(5-chloro-6-methylpyridin-3-yl)-5-[4-(dimethylamino)piperidin-1- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{8-(5-chloro-6-methoxypyridin-3-yl)-5-[4-(dimethylamino)piperidin-1- yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl}-2-methoxynicotinonitrile,
methyl [5-(7-(4-cyanophenyl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-8-yl)-2-methylphenyl]methylcarbamate,
4-(8-(6-ethylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(6-isopropylpyridin-3-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-{5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-[3-fluoro-4-(hydroxymethyl)-5- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,  
4-{5-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-8-[3-fluoro-4-(hydroxymethyl)- 5-methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-[2-(hydroxymethyl)-4- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-methylpyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(5-fluoro-6-methylpyridin-3- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
methyl (4-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1, 2-c]pyrimidin-8-yl}phenyl)methylcarbamate,
N-(5-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-8-yl}pyridin-2-yl)-N-methylmethanesulfonamide,
methyl (4-{7-(4-cyanophenyl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1, 2-c]pyrimidin-8-yl}-2-fluorophenyl)methylcarbamate,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-ethoxypyridin-3-yl)imidazo[1,2- c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-isopropylpyridin-3-yl)imidazo[1, 2-c]pyrimidin-7-yl]benzonitrile,
4-{5-{[(3R)-1-ethylpiperidin-3-yl]methoxy}-8-[2-(hydroxymethyl)-4- methylphenyl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-{8-(1,3-benzothiazol-5-yl)-5-[4-(dimethylamino)piperidin-1-yl]imidazo[1,2- c]pyrimidin-7-yl}benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(3-hydroxy-2,3-dihydro-1H-inden-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(2-hydroxy-2,3-dihydro-1H-inden-5- yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-(8-(3-hydroxy-2,3-dihydro-1H-inden-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-(8-(2-hydroxy-2,3-dihydro-1H-inden-5-yl)-5-{[(3R)-1-methylpiperidin-3- yl]methoxy}imidazo[1,2-c]pyrimidin-7-yl)benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-1H-pyrrolo[2,3-b]pyridin- 5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-{5-[4-(dimethylamino)piperidin-1-yl]-8-quinoxalin-6-ylimidazo[1,2-   c]pyrimidin-7-yl}benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(4-fluoro-1,3-dimethyl-2-oxo-2,3- dihydro-1H-benzimidazol-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(7-fluoro-1,3-dimethyl-2-oxo-2,3- dihydro-1H-benzimidazol-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(6-fluoro-1,3-dimethyl-2-oxo-2,3- dihydro-1H-benzimidazol-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-2-oxo-1,2,3,4- tetrahydroquinolin-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-[4-(dimethylamino)piperidin-1-yl]-8-(1-methyl-2-oxo-1,2,3,4- tetrahydroquinolin-7-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-{8-[5-(difluoromethyl)-6-methylpyridin-3-yl]-5-[4-(dimethylamino)piperidin- 1-yl]imidazo[1,2-c]pyrimidin-7-yl}benzonitrile,
4-[5-({(3R)-1-[(2R)-2-hydroxypropyl]piperidin-3-yl}methoxy)-8-(3-methyl-2- oxo-2,3-dihydro-1,3-benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-({(3R)-1-[(2S)-2-hydroxypropyl]piperidin-3-yl}methoxy)-8-(3-methyl-2- oxo-2,3-dihydro-1,3-benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-{[(3R)-1-(2-hydroxy-2-methylpropyl)piperidin-3-yl]methoxy}-8-(3- methyl-2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)imidazo[1,2-c]pyrimidin-7- yl]benzonitrile,
4-[5-({(3R)-1-[(2R)-2-hydroxypropyl]piperidin-3-yl}methoxy)-8-(1-methyl- 1H-pyrazolo[3,4-b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile,
4-[5-({(3R)-1-[(2S)-2-hydroxypropyl]piperidin-3-yl}methoxy)-8-(1-methyl- 1H-pyrazolo[3,4-b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile, and
4-[5-{[(3R)-1-(2-hydroxy-2-methylpropyl)piperidin-3-yl]methoxy}-8-(1- methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)imidazo[1,2-c]pyrimidin-7-yl]benzonitrile.
51. A pharmaceutical composition comprising a compound of any one of claims 1-50, or a pharmaceutically acceptable salt thereof, and at least one pharmaceutically acceptable carrier.
52. A method for inhibiting lysine specific demethylase-1 (LSD1), said method comprising contacting a compound of any one of claims 1-50, or a pharmaceutically acceptable salt thereof, with the LSD1.
 
53. A method for treating a disease comprising: administering to a patient in need thereof a therapeutically effective amount of a compound of any one of claims 1-50, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of claim 51, wherein said disease is cancer.
54. The method of claim 53, wherein the cancer is a hematological cancer.
55. The method of claim 54, wherein said hematological cancer is selected from acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), acute promyelocytic leukemia (APL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), diffuse large B-cell lymphoma (DLBCL), mantle cell lymphoma, non- Hodgkin lymphoma (including relapsed or refractory NHL and recurrent follicular), Hodgkin lymphoma, primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocytosis (ET), myelodysplasia syndrome (MDS), or multiple myeloma.
56. The method of claim 53, wherein the cancer is a sarcoma, lung cancer, gastrointestinal cancer, genitourinary tract cancer, liver cancer, bone cancer, nervous system cancer, gynecological cancer, or skin cancer.
57. A method of treating a disease comprising: administering to a patient in need thereof a therapeutically effective amount of a compound of any one of claims 1-50, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of claim 51, wherein the disease is a viral disease or a beta-globinopathy.
 
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