US20200172499A9 - Inhibitors of cyclin-dependent kinases - Google Patents

Inhibitors of cyclin-dependent kinases Download PDF

Info

Publication number
US20200172499A9
US20200172499A9 US15/758,982 US201615758982A US2020172499A9 US 20200172499 A9 US20200172499 A9 US 20200172499A9 US 201615758982 A US201615758982 A US 201615758982A US 2020172499 A9 US2020172499 A9 US 2020172499A9
Authority
US
United States
Prior art keywords
optionally substituted
certain embodiments
ring
alkyl
compound
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
US15/758,982
Other versions
US20180362483A1 (en
US11142507B2 (en
Inventor
Nathanael S. Gray
Tinghu Zhandg
Nicholas Paul Kwiatkowski
Mingfeng Hao
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Dana Farber Cancer Institute Inc
Original Assignee
Dana Farber Cancer Institute Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Dana Farber Cancer Institute Inc filed Critical Dana Farber Cancer Institute Inc
Priority to US15/758,982 priority Critical patent/US11142507B2/en
Publication of US20180362483A1 publication Critical patent/US20180362483A1/en
Publication of US20200172499A9 publication Critical patent/US20200172499A9/en
Assigned to NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT reassignment NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT CONFIRMATORY LICENSE (SEE DOCUMENT FOR DETAILS). Assignors: DANA-FARBER CANCER INST
Application granted granted Critical
Publication of US11142507B2 publication Critical patent/US11142507B2/en
Active legal-status Critical Current
Adjusted expiration legal-status Critical

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D277/00—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings
    • C07D277/02—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings
    • C07D277/20—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
    • C07D277/32—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D277/38—Nitrogen atoms
    • C07D277/44—Acylated amino or imino radicals
    • C07D277/46—Acylated amino or imino radicals by carboxylic acids, or sulfur or nitrogen analogues thereof
    • 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
    • A61K31/4965—Non-condensed pyrazines
    • A61K31/497—Non-condensed pyrazines containing further heterocyclic rings
    • 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
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
    • C07D417/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
    • C07D417/12—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/14—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing three or more hetero rings

Definitions

  • CDK cyclin-dependent kinase
  • CDK7 has consolidated kinase activities, regulating both the cell cycle and transcription.
  • CDK7 exists as a heterotrimeric complex and is believed to function as a CDK1/2-activating kinase (CAK), whereby phosphorylation of conserved residues in CDK1/2 by CDK7 is required for full catalytic CDK activity and cell cycle progression (Desai et al., “Effects of phosphorylation by CAK on cyclin binding by CDC2 and CDK2 .” Mol. Cell Biol. 15, 345-350 (1995); Kaldis et al., “Analysis of CAK activities from human cells.” Eur. J. Biochem.
  • CDK7 forms the kinase core of the RNA polymerase (RNAP) II general transcription factor complex and is charged with phosphorylating the C-terminal domain (CTD) of RNAP II, a requisite step in gene transcriptional initiation (Serizawa.
  • RNAP RNA polymerase
  • CTD C-terminal domain
  • CDK12 and CDK13 were identified in cDNA screens for cell cycle regulators. Because their cyclin partners were not yet known, they were initially named CRKRS and CDC2L5 (Ko et al., J. Cell Sci., 2001, 114, 2591-2603; Marqués et al., Biochem Biophys Res Commun., 2000, 279(3):832-837), respectively. They were found to be 1490- and 1512-amino acid proteins, respectively, with a conserved central CTD kinase domain and degenerate RS domains identified in their N- and C-terminal regions (Even et al., J Cell Biochem., 2006, 99(3), 890-904).
  • CDK12 and CDK13 play an important role in cancer development.
  • a comprehensive genomic approach identified CDK12 to be one of the most frequently somatically mutated genes in high-grade serous ovarian cancer, the most fatal form of the disease (Erratum, Nature, 2011, 474(7353), 609-615).
  • Several identified point mutations in the kinase domain point to the critical importance of the kinase activity of CDK12 for the development/progression of this disease.
  • CDK12 has also been found to contribute to the development of breast cancer.
  • CDK12 is located on chromosome 17, within the 17q21 locus that contains several candidate genes for breast cancer susceptibility (Kauraniemi et al., Cancer Res., 2001, 61(22), 8235-8240), and it is co-amplified with the tyrosine kinase receptor ERBB2, a protein amplified and overexpressed in about 20% of breast tumors. Gene fusion between CDK12 and ERBB2 was also detected in gastric cancer (Zang et al., Cancer Res., 2011, 71(1), 29-39).
  • CDK12 is also implicated in the modification of tamoxifen sensitivity in estrogen-positive breast cancer via the modulation of the mitogen-activated protein kinase pathway (Iorns et al., Carcinogenesis, 2009, 30(10):1696-1701).
  • kinases Due to the important regulatory functions of kinases, such as CDK7, CDK12, and CDK13, in cell cycle control, cell proliferation, differentiation, and apoptosis, it is important to develop modulators of the activities of these kinases, including selective modulators, for use as research tools as well as therapeutic agents in the treatment of diseases.
  • CDKs Cyclin dependent kinases
  • CDK7, CDK12, and CDK13 are key regulators of the cell cycle. Their successive activation and inactivation drives the cycle forward.
  • the activity of CDKs is regulated by multiple mechanisms such as positive and negative phosphorylation, binding of regulatory proteins like cyclins, and CDK inhibitors.
  • Most CDKs require the phosphorylation of a threonine residue located in the T-loop to achieve full kinase activity. This threonine residue is conserved in all CDKs that function in cell cycle regulation. The enzyme responsible for this phosphorylation is therefore termed CDK-activating-kinase or CAK.
  • CAK complexes have been found to be composed of CDK7, CDK12, CDK13, cyclin H, and MAT1. Besides its CAK function, CDK7, CDK12, and CDK13 also play a role in transcription and possibly in DNA repair. This suggests that the CDK7, CDK12, and CDK13 enzyme complexes are involved in multiple functions in the cell, e.g., cell cycle control, apoptosis, transcription regulation, and DNA repair.
  • the present invention provides compounds of Formulae (I′), (II′), (I), (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof.
  • the compounds of Formulae (I′), (II′), (I), (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof may inhibit the activity of a kinase.
  • the compounds described herein may in certain embodiments selectively inhibit specific CDK subtypes, for example, CDK7, CDK12, or CDK13.
  • the compounds of Formulae (I′), (II′), (I), and (II) are selective for CDK7 compared to other kinases.
  • the compounds of Formulae (I′), (II′), (I), and (II) are selective for CDK12 and/or CDK13 compared to other kinases.
  • the present invention also provides methods of using the inventive compounds, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, to study the inhibition of a kinase (e.g., CDK7, CDK12, and/or CDK13) and as therapeutics for the prevention and/or treatment of diseases associated with the overexpression and/or aberrant activity of a kinase (e.g., CDK7, CDK12, and/or CDK13).
  • a kinase e.g., CDK7, CDK12, and/or CDK13
  • the inventive compounds are used for the prevention and/or treatment of proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject.
  • cancers e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer
  • benign neoplasms e.g., diseases associated with angiogenesis,
  • CDK7, CDK12, and CDK13 Since the discovery of selective inhibitors of CDK7, CDK12, and CDK13 has been hampered by the high sequence and structural similarities of the kinase domain of CDK family members, the development of selective inhibitors of the transcriptional cyclin-dependent kinases (tCDKs) will allow dissection of their individual contributions to the regulation of transcription and evaluation of their therapeutic potential.
  • tCDKs transcriptional cyclin-dependent kinases
  • inventive compounds' selectivity for CDK7, CDK12, and/or CDK13 may be due to the compounds' ability to covalently modify a specific cysteine residue of these kinases (e.g., Cys312 of CDK7, Cys1039 of CDK12, Cys1017 of CDK13).
  • the present invention provides compounds of Formula (I′):
  • R 1 , R 2 , R A , R B , R C , Ring A, Ring B, Ring C, L 1 , L 2 , X, a1, b1, and c1 are as defined herein.
  • the present invention provides compounds of Formula (I):
  • R 1 , R 2 , R A , R B , R C , Ring A, Ring B, Ring C, L 1 , L 2 , X, a1, b1, and c1 are as defined herein.
  • the present invention provides compounds of Formula (II′):
  • R 1 , R 2 , R A , R B , Ring A, Ring B, L 2 , X, a1, and b1 are as defined herein.
  • the present invention provides compounds of Formula (II):
  • R 1 , R 2 , R A , R B , Ring A, Ring B, L 2 , X, a1, and b1 are as defined herein.
  • the present disclosure provides pharmaceutical compositions including a compound described herein, and optionally a pharmaceutically acceptable excipient.
  • the pharmaceutical compositions described herein include a therapeutically or prophylactically effective amount of a compound described herein.
  • the pharmaceutical composition may be useful for treating a proliferative disease in a subject in need thereof, preventing a proliferative disease in a subject in need thereof, inhibiting the activity of a protein kinase in a subject, biological sample, tissue, or cell, and/or inducing apoptosis in a cell.
  • the proliferative disease is an inflammatory disease.
  • the inflammatory disease is rheumatoid arthritis, Crohn's disease, or fibrosis.
  • the present invention provides methods for treating and/or preventing a proliferative disease.
  • proliferative diseases which may be treated include cancer, benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases.
  • the cancer is selected from the group consisting of pancreatic cancer, lung cancer (e.g., small cell lung cancer (SCLC), and non-small cell lung cancer), prostate cancer, breast cancer, ovarian cancer, kidney cancer, liver cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, and colorectal cancer.
  • Another aspect of the invention relates to methods of inhibiting the activity of a kinase (e.g., CDK (e.g., CDK7, CDK12, CDK13)) using a compound described herein in a biological sample or subject.
  • a kinase e.g., CDK (e.g., CDK7, CDK12, CDK13)
  • the method involves the selective inhibition of CDK7.
  • the method involves the selective inhibition of CDK12.
  • the method involves the selective inhibition of CDK13.
  • genes affected by the activity of CDK7 may be inhibited by a compound of the invention.
  • these genes are one or more selected from the group consisting of MYC, RUNX1, MYB, TAL1, GATA3, KLF2, HNRPDL, p21, ASCL1, MYCN, INSM1, NEUROD1, NEUROG1, FOXG1, FOXA1, SOX2, SOX4, BCL11A, OTX2, GAT2, PHOX2B, PLK2, TAF1, CTGF, WEE1, SDIM, JUN, PIM1, IL8, and FOS1.
  • genes affected by the activity of CDK12 may be inhibited by a compound of the invention.
  • these genes are one or more selected from the group consisting of BRCA1, FANCI, ATR, FANCD2, APEX1, NEK9, CHEK1, CHEK2, ATM, RAD51C, RAD51D, ORC3L, MDC1, TERF2, ERCC4, FANCF, PARP9, RUNX1, MYB, TAL1, MCL1, MYC, BCL2, ETS1, and EWS-FLI.
  • the transcription of genes affected by the activity of CDK13 may be inhibited by a compound of the invention.
  • the gene is SNORA38.
  • the present invention also provides methods of inhibiting cell growth in a biological sample or subject.
  • the present invention provides methods of inducing apoptosis of a cell in a biological sample or subject.
  • the present invention provides methods for administering to a subject in need thereof an effective amount of a compound, or pharmaceutical composition thereof, as described herein. Also described are methods for contacting a cell with an effective amount of a compound, or pharmaceutical composition thereof, as described herein. In certain embodiments, a method described herein further includes administering to the subject an additional pharmaceutical agent. In certain embodiments, a method described herein further includes contacting the cell with an additional pharmaceutical agent. The methods described herein may further include performing radiotherapy, immunotherapy, and/or transplantation on the subject.
  • the present invention provides compounds of Formulae (I′), (II′), (I), (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, for use in the treatment of a disease (e.g., a proliferative disease such as cancer) in a subject.
  • a disease e.g., a proliferative disease such as cancer
  • kits comprising a container with a compound, or pharmaceutical composition thereof, as described herein.
  • the kits described herein may include a single dose or multiple doses of the compound or pharmaceutical composition.
  • the kits may be useful in a method of the disclosure.
  • the kit further includes instructions for using the compound or pharmaceutical composition.
  • a kit described herein may also include information (e.g. prescribing information) as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA).
  • FDA U.S. Food and Drug Administration
  • FIG. 1 shows the chemical structures of exemplary compounds described herein and the IC 50 values of the exemplary compounds in inhibiting select cyclin-dependent kinases.
  • FIG. 2A shows that compound B12 exhibits binding of intracellular CDK12 and CDK13 at concentrations between 62.5 nM to 1 ⁇ M treatment.
  • Jurkat cells treated with compound B12 for 6 hours show decreased pulldown of CDK12 and CDK13-associated cyclin K by biotin-THZ1 relative to DMSO-treated cells.
  • B12 cellular treatment blocks biotin-THZ1 from binding CDK12 and CDK13-associated cyclin K complexes by successful binding of these complexes in cells at these concentrations.
  • Cyclin H (Cyc H) pulldown was not affected, indicating that CDK7 binding is not affected.
  • FIG. 2B shows the structure of compound B12.
  • FIG. 3 shows the binding of compounds B12, B15, and B16 (relative to DMSO control) to CDK12 and CDK13-associated cyclin K at concentrations of 100 nM, 50 nM, 25 nM, and 12.5 nM.
  • Jurkat cells were treated with each compound (or DMSO) for 6 hours, followed by lysis and pulldown with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H).
  • Compound B12 exhibits binding to CDK12 and CDK13-associated cyclin K, while compounds B15 and B16 do not.
  • Compound B12 is able to block pulldown of CDK12 and CDK13-associated cyclin K down to 25 nM treatment, while compounds B15 and B16 show very little effect on cyclin K pulldown. These results indicate that at concentrations as low as 25 nM B12 successfully targets intracellular CDK12 and CDK13-associated cyclin K complexes.
  • FIG. 4 shows binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds.
  • Jurkat cells were treated with each compound at a concentration of 500 nM for 6 hours, followed by lysing and pulldown with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H).
  • Compounds B1, B3, B4, B5, B6, B8, B9, and B12 show a loss in CDK12 and CDK13-associated cyclin K pulldown, indicating that these compounds successfully bind CDK12 and CDK13-associated cyclin K complexes in cells thus blocking biotin-THZ1 pull down, while compounds B5, B8, and B9 show a more pronounced loss of cyclin H pulldown, indicating that these compounds successfully target CDK7-cyclin H complexes in cells and interfere with biotin-THZ1 pull down.
  • FIG. 5 shows exemplary results of growth assays of select compounds described herein.
  • Jurkat cells were plated at 30,000 cells/well and treated with a titration of compounds indicated. Cells were allowed to grow for 72 hours. Cells were assayed using CELLTITER GLO (Promega) to determine cell viability by measuring the amount of ATP present, which is an indicator of cell metabolic activity.
  • Top panel luminescent values (y-axis); concentration in ⁇ M (uM) (x-axis); the curves are generated using PRISM.
  • Bottom panel IC 50 values in ⁇ M. Error bars indicate +/ ⁇ standard deviation. All compounds tested showed anti-proliferative effects to varying extents.
  • FIG. 6 shows exemplary mass spectrum labeling of CDK12 with compound B12.
  • Compound B12 is able to label CDK12 once treated with a 5-fold excess of compound B12 for 1 hour at 4° C.
  • FIG. 7 shows the binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds.
  • Jurkat cells were treated with each compound at a concentration of 500 nM for 6 hours, followed by lysing and pull down with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H).
  • Cyc K cyclin K
  • Cyc H cyclin H
  • compounds MFH 2-90-1 and MFH 2-102-1 show a loss in cyclin K pulldown by biotin-THZ1, indicating that these compounds were able to bind intracellular CDK12 and CDK13-associated cyclin K complexes and block pull down by biotin-THZ1.
  • compounds MFH 2-90-1, MFH 3-103-1, and MFH 3-151-1 show a loss in cyclin K pulldown by biotin-THZ1, indicating that these compounds were able to bind intracellular CDK12 and CDK13-associated cyclin K complexes and thus block pull down by biotin-THZ1.
  • FIG. 8 shows the binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds.
  • Jurkat cells were treated with each compound at a concentration of 500 nM for 6 hours, followed by lysing and pull down with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H).
  • Cyc K cyclin K
  • Cyc H cyclin H
  • compound THZ 5-31 and MFH 2-90-1 show a loss in cyclin K pulldown by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding.
  • compounds THZ 5-31, MFH 2-90-1, THZ-CE B-15, and THZ-CE B-16 show a loss in cyclin K pull down by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding.
  • FIG. 9 shows the binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds.
  • Jurkat cells were treated with each compound at a concentration of 500 nM for 4 hours, followed by lysing and pull down with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H).
  • Cyc K cyclin K
  • Cyc H cyclin H
  • compounds THZ 5-31, MFH 2-90-1, MFH 3-75-1, and MFH 3-81-1 show a loss in cyclin K pull down by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding.
  • compounds THZ 5-31, MFH 4-70-1, and MFH 4-70-1 show a loss in cyclin K pull down, by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding.
  • Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers.
  • the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer.
  • Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses.
  • HPLC high pressure liquid chromatography
  • C 1-6 is intended to encompass, C 1 , C 2 , C 3 , C 4 , C 5 , C 6 , C 1-6 , C 1-5 , C 1-4 , C 1-3 , C 1-2 , C 2-6 , C 2-5 , C 2-4 , C 2-3 , C 3-6 , C 3-5 , C 3-4 , C 4-6 , C 4-5 , and C 5-6 .
  • aliphatic includes both saturated and unsaturated, straight chain (i.e., unbranched), branched, acyclic, cyclic, or polycyclic aliphatic hydrocarbons, which are optionally substituted with one or more functional groups.
  • “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties.
  • alkyl includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl”, and the like.
  • alkyl encompass both substituted and unsubstituted groups.
  • lower alkyl is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.
  • the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-4 carbon atoms.
  • Illustrative aliphatic groups thus include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH 2 -cyclopropyl, vinyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, cyclobutyl, —CH 2 -cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl, cyclopentyl, —CH 2 -cyclopentyl, n-hexyl, sec-hexyl, cyclohexyl, —CH 2 -cyclohexyl moieties and the like, which again, may bear one or more substituents.
  • Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and the like.
  • Representative alkynyl groups include, but are not limited to, ethynyl, 2-propynyl (propargyl), 1-propynyl, and the like.
  • alkyl refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms (“C 1-10 alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C 1-9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C 1-8 alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C 1-7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C 1-6 alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“C 1-5 alkyl”).
  • an alkyl group has 1 to 4 carbon atoms (“C 1-4 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C 1-3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C 1-2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C 1 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C 2-6 alkyl”).
  • C 1-6 alkyl groups include methyl (C 1 ), ethyl (C 2 ), propyl (C 3 ) (e.g., n-propyl, isopropyl), butyl (C 4 ) (e.g., n-butyl, tert-butyl, sec-butyl, iso-butyl), pentyl (C 5 ) (e.g., n-pentyl, 3-pentanyl, amyl, neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C 6 ) (e.g., n-hexyl).
  • alkyl groups include n-heptyl (C 7 ), n-octyl (C 8 ), and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents (e.g., halogen, such as F).
  • substituents e.g., halogen, such as F
  • the alkyl group is an unsubstituted C 1-10 alkyl (such as unsubstituted C 1-6 alkyl, e.g., —CH 3 (Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstituted n-propyl (n-Pr), unsubstituted isopropyl (i-Pr)), unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (n-Bu), unsubstituted tert-butyl (tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu), unsubstituted isobutyl (i-Bu)).
  • the alkyl group is a substituted C 1-10 alkyl (such as substituted C 1-6 alkyl, e.g.,
  • Alkenyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon double bonds, and no triple bonds (“C 2-20 alkenyl”). In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C 2-10 alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C 2-9 alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C 2-8 alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C 2-7 alkenyl”).
  • an alkenyl group has 2 to 6 carbon atoms (“C 2-6 alkenyl”). In some embodiments, an alkenyl group has 2 to 5 carbon atoms (“C 2-5 alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (“C 2-4 alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C 2-3 alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C 2 alkenyl”). The one or more carbon-carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl).
  • Examples of C 2-4 alkenyl groups include ethenyl (C 2 ), 1-propenyl (C 3 ), 2-propenyl (C 3 ), 1-butenyl (C 4 ), 2-butenyl (C 4 ), butadienyl (C 4 ), and the like.
  • Examples of C 2-6 alkenyl groups include the aforementioned C 2-4 alkenyl groups as well as pentenyl (C 5 ), pentadienyl (C 5 ), hexenyl (C 6 ), and the like. Additional examples of alkenyl include heptenyl (C 7 ), octenyl (C 8 ), octatrienyl (C 8 ), and the like.
  • each instance of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more substituents.
  • the alkenyl group is unsubstituted C 2-10 alkenyl.
  • the alkenyl group is substituted C 2-10 alkenyl.
  • a C ⁇ C double bond for which the stereochemistry is not specified e.g., —CH ⁇ CHCH 3 or
  • Alkynyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon triple bonds, and optionally one or more double bonds (“C 2-20 alkynyl”).
  • an alkynyl group has 2 to 10 carbon atoms (“C 2-10 alkynyl”).
  • an alkynyl group has 2 to 9 carbon atoms (“C 2-9 alkynyl”).
  • an alkynyl group has 2 to 8 carbon atoms (“C 2-8 alkynyl”).
  • an alkynyl group has 2 to 7 carbon atoms (“C 2-7 alkynyl”).
  • an alkynyl group has 2 to 6 carbon atoms (“C 2-6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C 2-5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C 2-4 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C 2-3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C 2 alkynyl”). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl).
  • Examples of C 2-4 alkynyl groups include, without limitation, ethynyl (C 2 ), 1-propynyl (C 3 ), 2-propynyl (C 3 ), 1-butynyl (C 4 ), 2-butynyl (C 4 ), and the like.
  • Examples of C 2-6 alkenyl groups include the aforementioned C 2-4 alkynyl groups as well as pentynyl (C 5 ), hexynyl (C 6 ), and the like. Additional examples of alkynyl include heptynyl (C 7 ), octynyl (C 8 ), and the like.
  • each instance of an alkynyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents.
  • the alkynyl group is unsubstituted C 2-10 alkynyl.
  • the alkynyl group is substituted C 2-10 alkynyl.
  • Carbocyclyl or “carbocyclic” refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C 3-10 carbocyclyl”) and zero heteroatoms in the non-aromatic ring system.
  • a carbocyclyl group has 3 to 8 ring carbon atoms (“C 3-8 carbocyclyl”).
  • a carbocyclyl group has 3 to 6 ring carbon atoms (“C 3-6 carbocyclyl”).
  • a carbocyclyl group has 3 to 6 ring carbon atoms (“C 3-6 carbocyclyl”).
  • a carbocyclyl group has 5 to 10 ring carbon atoms (“C 5-10 carbocyclyl”).
  • Exemplary C 3-6 carbocyclyl groups include, without limitation, cyclopropyl (C 3 ), cyclopropenyl (C 3 ), cyclobutyl (C 4 ), cyclobutenyl (C 4 ), cyclopentyl (C 5 ), cyclopentenyl (C 5 ), cyclohexyl (C 6 ), cyclohexenyl (C 6 ), cyclohexadienyl (C 6 ), and the like.
  • Exemplary C 3-8 carbocyclyl groups include, without limitation, the aforementioned C 3-6 carbocyclyl groups as well as cycloheptyl (C 7 ), cycloheptenyl (C 7 ), cycloheptadienyl (C 7 ), cycloheptatrienyl (C 7 ), cyclooctyl (C 8 ), cyclooctenyl (C 8 ), bicyclo[2.2.1]heptanyl (C 7 ), bicyclo[2.2.2]octanyl (C 8 ), and the like.
  • Exemplary C 3-10 carbocyclyl groups include, without limitation, the aforementioned C 3-8 carbocyclyl groups as well as cyclononyl (C 9 ), cyclononenyl (C 9 ), cyclodecyl (C 10 ), cyclodecenyl (C 10 ), octahydro-1H-indenyl (C 9 ), decahydronaphthalenyl (C 10 ), spiro[4.5]decanyl (C 10 ), and the like.
  • the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) and can be saturated or can be partially unsaturated.
  • “Carbocyclyl” also includes ring systems wherein the carbocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclic ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system.
  • each instance of a carbocyclyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents.
  • the carbocyclyl group is unsubstituted C 3-10 carbocyclyl.
  • the carbocyclyl group is substituted C 3-10 carbocyclyl.
  • “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C 3-10 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C 3-8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C 3-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C 5-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C 5-10 cycloalkyl”).
  • C 5-6 cycloalkyl groups include cyclopentyl (C 5 ) and cyclohexyl (C 5 ).
  • Examples of C 3-6 cycloalkyl groups include the aforementioned C 5-6 cycloalkyl groups as well as cyclopropyl (C 3 ) and cyclobutyl (C 4 ).
  • Examples of C 3-8 cycloalkyl groups include the aforementioned C 3-6 cycloalkyl groups as well as cycloheptyl (C 7 ) and cyclooctyl (C 8 ).
  • each instance of a cycloalkyl group is independently unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents.
  • the cycloalkyl group is unsubstituted C 3-10 cycloalkyl.
  • the cycloalkyl group is substituted C 3-10 cycloalkyl.
  • Heterocyclyl or “heterocyclic” refers to a radical of a 3- to 10-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 membered heterocyclyl”).
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • a heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged, or spiro ring system, such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or can be partially unsaturated.
  • Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heterocyclyl also includes ring systems wherein the heterocyclic ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclic ring, or ring systems wherein the heterocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclic ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclic ring system.
  • each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents.
  • the heterocyclyl group is unsubstituted 3-10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3-10 membered heterocyclyl.
  • a heterocyclyl group is a 5-10 membered, non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5-10 membered heterocyclyl”).
  • a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”).
  • a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”).
  • the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • Exemplary 3-membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, thiiranyl.
  • Exemplary 4-membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl.
  • Exemplary 5-membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl, and pyrrolyl-2,5-dione.
  • Exemplary 5-membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one.
  • Exemplary 5-membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl.
  • Exemplary 6-membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl.
  • Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl. Exemplary 7-membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.
  • Exemplary 5-membered heterocyclyl groups fused to a C 6 aryl ring include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like.
  • Exemplary 6-membered heterocyclyl groups fused to an aryl ring include, without limitation, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.
  • Aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 pi electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C 6-14 aryl”).
  • an aryl group has six ring carbon atoms (“C 6 aryl”; e.g., phenyl).
  • an aryl group has ten ring carbon atoms (“C 10 aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl).
  • an aryl group has fourteen ring carbon atoms (“C 14 aryl”; e.g., anthracyl).
  • Aryl also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups, wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system.
  • each instance of an aryl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents.
  • the aryl group is unsubstituted C 6-14 aryl.
  • the aryl group is substituted C 6-14 aryl.
  • “Aralkyl” refers to an optionally substituted alkyl group substituted by an optionally substituted aryl group. In certain embodiments, the aralkyl is optionally substituted benzyl. In certain embodiments, the aralkyl is benzyl. In certain embodiments, the aralkyl is optionally substituted phenethyl. In certain embodiments, the aralkyl is phenethyl.
  • Heteroaryl refers to a radical of a 5-10 membered, monocyclic or bicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 pi electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5-10 membered heteroaryl”).
  • heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heteroaryl includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system.
  • Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom e.g., indolyl, quinolinyl, carbazolyl, and the like
  • the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).
  • a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”).
  • a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”).
  • a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”).
  • the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • each instance of a heteroaryl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”) with one or more substituents.
  • the heteroaryl group is unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5-14 membered heteroaryl.
  • Exemplary 5-membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl, and thiophenyl.
  • Exemplary 5-membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl.
  • Exemplary 5-membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl.
  • Exemplary 5-membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl.
  • Exemplary 6-membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl.
  • Exemplary 6-membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.
  • Exemplary 6-membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively.
  • Exemplary 7-membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl.
  • Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl.
  • Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • Heteroaralkyl is a subset of alkyl and heteroaryl and refers to an optionally substituted alkyl group substituted by an optionally substituted heteroaryl group.
  • “Unsaturated” or “partially unsaturated” refers to a group that includes at least one double or triple bond.
  • a “partially unsaturated” ring system is further intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl groups).
  • “saturated” refers to a group that does not contain a double or triple bond, i.e., contains all single bonds.
  • Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, which are divalent linking groups, are further referred to using the suffix-ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.
  • An atom, moiety, or group described herein may be unsubstituted or substituted, as valency permits, unless otherwise provided expressly.
  • the term “optionally substituted” refers to substituted or unsubstituted.
  • alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups are optionally substituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or “unsubstituted” heteroaryl group).
  • substituted means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
  • a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position.
  • substituted is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound.
  • the present disclosure contemplates any and all such combinations in order to arrive at a stable compound.
  • heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
  • the substituent is a carbon atom substituent.
  • the substituent is a nitrogen atom substituent.
  • the substituent is an oxygen atom substituent.
  • the substituent is a sulfur atom substituent.
  • Exemplary carbon atom substituents include, but are not limited to, halogen, —CN, —NO 2 , —N 3 , —SO 2 H, —SO 3 H, —OH, —OR aa , —ON(R bb ) 2 , —N(R bb ) 2 , —N(R bb ) 3 + X ⁇ , —N(OR cc )R bb , —SH, —SR aa , —SSR cc , —C( ⁇ O)R aa , —CO 2 H, —CHO, —C(OR cc ) 2 , —CO 2 R aa , —OC( ⁇ O)R aa , —OCO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —OC( ⁇ O)N(R bb ) 2 , —NR bb C
  • each instance of R aa is, independently, selected from C 1-10 alkyl, C 1-10 perhaloalkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 carbocyclyl, 3-14 membered heterocyclyl, C 6-14 aryl, and 5-14 membered heteroaryl, or two R aa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups;
  • each instance of R bb is, independently, selected from hydrogen, —OH, —OR aa , —N(R cc ) 2 , —CN, —C( ⁇ O)R aa , —C( ⁇ O)N(R cc ) 2 , —CO 2 R aa , —SO 2 R aa , —C( ⁇ NR cc )OR aa , —C( ⁇ NR cc )N(R cc ) 2 , —SO 2 N(R cc ) 2 , —SO 2 R cc , —SO 2 OR cc , —SOR aa , —C( ⁇ S)N(R cc ) 2 , —C( ⁇ O)SR cc , —C( ⁇ S)SR cc , —P( ⁇ O)(R aa ) 2 , —P( ⁇ O)(OR cc ) 2
  • each instance of R cc is, independently, selected from hydrogen, C 1-10 alkyl, C 1-10 perhaloalkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 carbocyclyl, 3-14 membered heterocyclyl, C 6-14 aryl, and 5-14 membered heteroaryl, or two R cc groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups;
  • each instance of R dd is, independently, selected from halogen, —CN, —NO 2 , —N 3 , —SO 2 H, —SO 3 H, —OH, —OR ee , —ON(R ff ) 2 , —N(R ff ) 2 , —N(R ff ) 3 + X ⁇ , —N(OR ee )R ff , —SH, —SR ee , —SSR ee , —C( ⁇ O)R ee , —CO 2 H, —CO 2 R ee , —OC( ⁇ O)R ee , —OCO 2 R ee , —C( ⁇ O)N(R ff ) 2 , —OC( ⁇ O)N(R ff ) 2 , —NR ff C( ⁇ O)R ee , —NR ff CO 2 R
  • each instance of R ee is, independently, selected from C 1-6 alkyl, C 1-6 perhaloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 carbocyclyl, C 6-10 aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups;
  • each instance of R ff is, independently, selected from hydrogen, C 1-6 alkyl, C 1-6 perhaloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-10 carbocyclyl, 3-10 membered heterocyclyl, C 6-10 aryl and 5-10 membered heteroaryl, or two R ff groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups; and
  • each instance of R gg is, independently, halogen, —CN, —NO 2 , —N 3 , —SO 2 H, —SO 3 H, —OH, —OC 1-6 alkyl, —ON(C 1-6 alkyl) 2 , —N(C 1-6 alkyl) 2 , —N(C 1-6 alkyl) 3 + X ⁇ , —NH(C 1-6 alkyl) 2 + X ⁇ , —NH 2 (C 1-6 alkyl) + X ⁇ , —NH 3 + X ⁇ , —N(OC 1-6 alkyl)(C 1-6 alkyl), —N(OH)(C 1-6 alkyl), —NH(OH), —SH, —SC 1-6 alkyl, —SS(C 1-6 alkyl), —C( ⁇ O)(C 1-6 alkyl), —CO 2 H, —CO 2 (C 1-6 alkyl), —OC( ⁇ O)
  • a “counterion” or “anionic counterion” is a negatively charged group associated with a positively charged group in order to maintain electronic neutrality.
  • An anionic counterion may be monovalent (i.e., including one formal negative charge).
  • An anionic counterion may also be multivalent (i.e., including more than one formal negative charge), such as divalent or trivalent.
  • Exemplary counterions include halide ions (e.g., F ⁇ , Cl ⁇ , Br ⁇ , I ⁇ ), NO 3 ⁇ , ClO 4 ⁇ , OH ⁇ , H 2 PO 4 ⁇ , HCO 3 ⁇ , HSO 4 ⁇ , sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic acid-2-sulfonate, and the like), carboxylate ions (e.g., acetate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, gluconate, and the like), BF 4
  • Exemplary counterions which may be multivalent include CO 3 2 ⁇ , HPO 4 2 ⁇ , PO 4 3 ⁇ , B 4 O 7 2 ⁇ , SO 4 2 ⁇ , S 2 O 3 2 ⁇ , carboxylate anions (e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like), and carboranes.
  • carboxylate anions e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like
  • carboranes e.g., tartrate, citrate, fumarate, maleate, mal
  • Halo or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro, —Cl), bromine (bromo, —Br), or iodine (iodo, —I).
  • hydroxyl refers to the group —OH.
  • substituted hydroxyl or “substituted hydroxyl,” by extension, refers to a hydroxyl group wherein the oxygen atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from —OR aa , —ON(R bb ) 2 , —OC( ⁇ O)SR aa , —OC( ⁇ O)R aa , —OCO 2 R aa , —OC( ⁇ O)N(R bb ) 2 , —OC( ⁇ NR bb )R aa , —OC( ⁇ NR bb )OR aa , —OC( ⁇ NR bb )N(R bb ) 2 , —OS( ⁇ O)R aa , —OSO 2 R aa , —OSi(R aa ) 3 , —
  • “Acyl” refers to a moiety selected from the group consisting of —C( ⁇ O)R aa , —CHO, —CO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —C( ⁇ NR bb )R aa , —C( ⁇ NR bb )OR aa , —C( ⁇ NR bb )N(R bb ) 2 , —C( ⁇ O)NR bb SO 2 R aa , —C( ⁇ S)N(R bb ) 2 , —C( ⁇ O)SR aa , or —C( ⁇ S)SR aa , wherein R aa and R bb are as defined herein.
  • amino refers to the group —NH 2 .
  • substituted amino by extension, refers to a monosubstituted amino, a disubstituted amino, or a trisubstituted amino. In certain embodiments, the “substituted amino” is a monosubstituted amino or a disubstituted amino group.
  • Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quaternary nitrogen atoms.
  • Exemplary nitrogen atom substituents include, but are not limited to, hydrogen, —OH, —OR aa , —N(R cc ) 2 , —CN, —C( ⁇ O)R aa , —C( ⁇ O)N(R cc ) 2 , —CO 2 R aa , —SO 2 R aa , —C( ⁇ NR bb )R aa , —C( ⁇ NR cc )OR aa , —C( ⁇ NR cc )N(R cc ) 2 , —SO 2 N(R cc ) 2 , —SO 2 R cc , —SO 2 OR cc , —SOR aa , —C( ⁇ S)N(R
  • the substituent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group).
  • Nitrogen protecting groups include, but are not limited to, —OH, —OR aa , —N(R cc ) 2 , —C( ⁇ O)R aa , —C( ⁇ O)N(R cc ) 2 , —CO 2 R aa , —SO 2 R aa , —C( ⁇ NR cc )R aa , —C( ⁇ NR cc )OR aa , —C( ⁇ NR cc )N(R cc ) 2 , —SO 2 N(R cc ) 2 , —SO 2 R cc , —SO 2 OR cc , —SOR aa , —C( ⁇ S)N(R cc ) 2 , —C( ⁇ O)SR cc , —C(C(
  • Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis , T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • nitrogen protecting groups such as amide groups (e.g., —C( ⁇ O)R aa ) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitrophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocin
  • Nitrogen protecting groups such as carbamate groups include, but are not limited to, methyl carbamate, ethyl carbamate, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluorenylmethyl carbamate, 2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethyl carbamate
  • Nitrogen protecting groups such as sulfonamide groups include, but are not limited to, p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide
  • Ts p-toluenesulfonamide
  • nitrogen protecting groups include, but are not limited to, phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacyl derivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4
  • oxygen atom substituents include, but are not limited to, —R aa , —N(R bb ) 2 , —C( ⁇ O)SR aa , —C( ⁇ O)R aa , —CO 2 R aa , —C( ⁇ O)N(R bb ) 22 , —C( ⁇ NR bb )R aa , —C( ⁇ NR bb )OR aa , —C( ⁇ NR bb )N(R bb ), —S( ⁇ O)R aa , —SO 2 R aa , —Si(R aa ) 3 , —P(R cc ) 2 , —P(R cc ) 3 + X ⁇ , —P(OR cc ) 2 , —P(OR cc ) 3 + X ⁇ , —P(OR cc ) 3 +
  • the oxygen atom substituent present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl protecting group).
  • Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis , T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • oxygen protecting groups include, but are not limited to, methyl, t-butyloxycarbonyl (BOC or Boc), methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-me
  • Exemplary sulfur atom substituents include, but are not limited to, —R aa , —N(R bb ) 2 , —C( ⁇ O)SR aa , —C( ⁇ O)R aa , —CO 2 R aa , —C( ⁇ O)N(R bb ) 2 , —C( ⁇ NR bb )R aa , —C( ⁇ NR bb )OR aa , —C( ⁇ NR bb )N(R bb ) 2 , —S( ⁇ O)R aa , —SO 2 R aa , —Si(R aa ) 3 , —P(R cc ) 2 , —P(R cc ) 3 + X ⁇ , —P(OR cc ) 2 , —P(OR cc ) 3 + X ⁇ , —P(OR cc
  • the sulfur atom substituent present on a sulfur atom is a sulfur protecting group (also referred to as a thiol protecting group).
  • Sulfur protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis , T. W. Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • a “hydrocarbon chain” refers to a substituted or unsubstituted divalent alkyl, alkenyl, or alkynyl group.
  • a hydrocarbon chain includes (1) one or more chains of carbon atoms immediately between the two radicals of the hydrocarbon chain; (2) optionally one or more hydrogen atoms on the chain(s) of carbon atoms; and (3) optionally one or more substituents (“non-chain substituents,” which are not hydrogen) on the chain(s) of carbon atoms.
  • a chain of carbon atoms consists of consecutively connected carbon atoms (“chain atoms” or “carbon units”) and does not include hydrogen atoms or heteroatoms.
  • a non-chain substituent of a hydrocarbon chain may include any atoms, including hydrogen atoms, carbon atoms, and heteroatoms.
  • hydrocarbon chain —C A H(C B H 2 C C H 3 )— includes one chain atom C A , one hydrogen atom on C A , and non-chain substituent —(C B H 2 C C H 3 ).
  • C x hydrocarbon chain wherein x is a positive integer, refers to a hydrocarbon chain that includes x number of chain atom(s) between the two radicals of the hydrocarbon chain. If there is more than one possible value of x, the smallest possible value of x is used for the definition of the hydrocarbon chain.
  • —CH(C 2 H 5 )— is a C 1 hydrocarbon chain
  • a C 3-10 hydrocarbon chain refers to a hydrocarbon chain where the number of chain atoms of the shortest chain of carbon atoms immediately between the two radicals of the hydrocarbon chain is 3, 4, 5, 6, 7, 8, 9, or 10.
  • a hydrocarbon chain may be saturated (e.g., —(CH 2 ) 4 —).
  • a hydrocarbon chain may also be unsaturated and include one or more C ⁇ C and/or C ⁇ C bonds anywhere in the hydrocarbon chain.
  • —CH ⁇ CH—(CH 2 ) 2 —, —CH 2 —C ⁇ C—CH 2 —, and —C ⁇ C—CH ⁇ CH— are all examples of a unsubstituted and unsaturated hydrocarbon chain.
  • the hydrocarbon chain is unsubstituted (e.g., —C ⁇ C— or —(CH 2 ) 4 —).
  • the hydrocarbon chain is substituted (e.g., —CH(C 2 H 5 )— and —CF 2 —). Any two substituents on the hydrocarbon chain may be joined to form an optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl ring.
  • any two substituents on the hydrocarbon chain may be joined to form an optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl ring.
  • leaving group is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile.
  • suitable leaving groups include, but are not limited to, halogen (such as F, Cl, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixel, and haloformates.
  • halogen such as F, Cl, Br, or I (iodine
  • the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate, —OTs), methanesulfonate (mesylate, —OMs), p-bromobenzenesulfonyloxy (brosylate, —OBs), —OS( ⁇ O) 2 (CF 2 ) 3 CF 3 (nonaflate, —ONf), or trifluoromethanesulfonate (triflate, -OTf).
  • the leaving group is a brosylate, such as p-bromobenzenesulfonyloxy.
  • the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy.
  • the leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate.
  • phosphineoxide e.g., formed during a Mitsunobu reaction
  • an internal leaving group such as an epoxide or cyclic sulfate.
  • Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties.
  • Exemplary leaving groups include, but are not limited to, halo (e.g., chloro, bromo, iodo) and activated substituted hydroxyl groups (e.g., —OC( ⁇ O)SR aa , —OC( ⁇ O)R aa , —OCO 2 R aa , —OC( ⁇ O)N(R bb ) 2 , —OC( ⁇ NR bb )R aa , —OC( ⁇ NR bb )OR aa , —OC( ⁇ NR bb )N(R bb ) 2 , —OS( ⁇ O)R aa , —OSO 2 R aa , —OP(R cc ) 2 , —OP(R cc ) 3 , —OP( ⁇ O) 2 R aa , —OP( ⁇ O)(R aa ) 2 , —OP( ⁇ O)(OR cc
  • pharmaceutically acceptable salt refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio.
  • Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference.
  • Pharmaceutically acceptable salts of the compounds described herein include those derived from suitable inorganic and organic acids and bases.
  • Examples of pharmaceutically acceptable, non-toxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid
  • organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange.
  • salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate,
  • Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N + (C 1-4 alkyl) 4 ⁇ salts.
  • Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
  • solvate refers to forms of the compound that are associated with a solvent, usually by a solvolysis reaction. This physical association may include hydrogen bonding.
  • Conventional solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and the like.
  • the compounds described herein may be prepared, e.g., in crystalline form, and may be solvated.
  • Suitable solvates include pharmaceutically acceptable solvates and further include both stoichiometric solvates and non-stoichiometric solvates. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid.
  • “Solvate” encompasses both solution-phase and isolatable solvates. Representative solvates include hydrates, ethanolates, and methanolates.
  • hydrate refers to a compound that is associated with water.
  • the number of the water molecules contained in a hydrate of a compound is in a definite ratio to the number of the compound molecules in the hydrate. Therefore, a hydrate of a compound may be represented, for example, by the general formula R.x H 2 O, wherein R is the compound, and x is a number greater than 0.
  • a given compound may form more than one type of hydrate, including, e.g., monohydrates (x is 1), lower hydrates (x is a number greater than 0 and smaller than 1, e.g., hemihydrates (R.0.5H 2 O)), and polyhydrates (x is a number greater than 1, e.g., dihydrates (R.2H 2 O) and hexahydrates (R.6H 2 O)).
  • monohydrates x is 1
  • lower hydrates x is a number greater than 0 and smaller than 1, e.g., hemihydrates (R.0.5H 2 O)
  • polyhydrates x is a number greater than 1, e.g., dihydrates (R.2H 2 O) and hexahydrates (R.6H 2 O)
  • tautomers or “tautomeric” refers to two or more interconvertible compounds resulting from at least one formal migration of a hydrogen atom and at least one change in valency (e.g., a single bond to a double bond, a triple bond to a single bond, or vice versa).
  • the exact ratio of the tautomers depends on several factors, including temperature, solvent, and pH. Tautomerizations (i.e., the reaction providing a tautomeric pair) may catalyzed by acid or base.
  • Exemplary tautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim, enamine-to-imine, and enamine-to-(a different enamine) tautomerizations.
  • stereoisomers that are not mirror images of one another are termed “diastereomers” and those that are non-superimposable mirror images of each other are termed “enantiomers.”
  • enantiomers When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible.
  • An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (i.e., as (+) or ( ⁇ )-isomers respectively).
  • a chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a “racemic mixture.”
  • polymorphs refers to a crystalline form of a compound (or a salt, hydrate, or solvate thereof) in a particular crystal packing arrangement. All polymorphs have the same elemental composition. Different crystalline forms usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Various polymorphs of a compound can be prepared by crystallization under different conditions.
  • co-crystal refers to a crystalline structure composed of at least two components.
  • a co-crystal may contain a compound of the present invention and one or more other component, including but not limited to, atoms, ions, molecules, or solvent molecules.
  • a co-crystal may contain a compound of the present invention and one or more components related to said compound, including not limited to, an isomer, tautomer, salt, solvate, hydrate, synthetic precursor, synthetic derivative, fragment or impurity of said compound.
  • isotopically labeled derivative or “isotopically labeled” refers to a compound wherein one or more atoms in the compound (or in an associated ion or molecule of a salt, hydrate, or solvate) has been replaced with an isotope of the same element.
  • the isotope will be enriched, or present in a higher percentage of all atoms of the element or of all atoms at the position in the molecule in a sample, relative to an unlabeled variant.
  • the enriched isotope will be a stable isotope.
  • the enriched isotope will be an unstable or radioactive isotope (e.g., a radionuclide).
  • the enriched isotope may be detected by a measurement technique, including but not limited to nuclear magnetic resonance, mass spectrometry, infrared spectroscopy, or a technique that measures radioactive decay.
  • prodrugs refers to compounds that have cleavable groups and become by solvolysis or under physiological conditions the compounds described herein, which are pharmaceutically active in vivo. Such examples include, but are not limited to, choline ester derivatives and the like, N-alkylmorpholine esters and the like. Other derivatives of the compounds described herein have activity in both their acid and acid derivative forms, but in the acid sensitive form often offer advantages of solubility, tissue compatibility, or delayed release in the mammalian organism (see, Bundgard, H., Design of Prodrugs , pp. 7-9, 21-24, Elsevier, Amsterdam 1985).
  • Prodrugs include acid derivatives well known to practitioners of the art, such as, for example, esters prepared by reaction of the parent acid with a suitable alcohol, or amides prepared by reaction of the parent acid compound with a substituted or unsubstituted amine, or acid anhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters, amides, and anhydrides derived from acidic groups pendant on the compounds described herein are particular prodrugs. In some cases it is desirable to prepare double ester type prodrugs such as (acyloxy)alkyl esters or ((alkoxycarbonyl)oxy)alkylesters.
  • C 1 -C 8 alkyl, C 2 -C 8 alkenyl, C 2 -C 8 alkynyl, aryl, C 7 -C 12 substituted aryl, and C 7 -C 12 arylalkyl esters of the compounds described herein may be preferred.
  • inhibitor refers to the ability of a compound to reduce, slow, halt or prevent activity of a particular biological process (e.g., CDK kinase activity)) in a cell relative to vehicle.
  • the compound, pharmaceutical composition, method, use, or kit When a compound, pharmaceutical composition, method, use, or kit is referred to as “selectively,” “specifically,” or “competitively” binding a first protein kinase, the compound, pharmaceutical composition, method, use, or kit binds the first protein kinase (e.g., CDK) with a higher binding affinity (e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold) than binding a second protein or second chromatin that is different from the first protein and the first chromatin.
  • a higher binding affinity e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold
  • a compound, pharmaceutical composition, method, use, or kit When a compound, pharmaceutical composition, method, use, or kit is referred to as “selectively,” “specifically,” or “competitively” modulating (e.g., increasing or inhibiting) the activity of a first protein kinase, the compound, pharmaceutical composition, method, use, or kit modulates the activity of the first protein kinase (e.g., CDK) to a greater extent (e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold) than the activity of a second protein kinase that is different from the first protein kinase.
  • the first protein kinase e.g., CDK
  • abnormal activity refers to activity deviating from normal activity, that is, abnormal activity.
  • increased activity refers to activity higher than normal activity.
  • composition and “formulation” are used interchangeably.
  • a “subject” to which administration is contemplated refers to a human (i.e., male or female of any age group, e.g., pediatric subject (e.g., infant, child, or adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) or non-human animal.
  • the non-human animal is a mammal (e.g., primate (e.g., cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g., cattle, pig, horse, sheep, goat, cat, or dog), or bird (e.g., commercially relevant bird, such as chicken, duck, goose, or turkey)).
  • primate e.g., cynomolgus monkey or rhesus monkey
  • commercially relevant mammal e.g., cattle, pig, horse, sheep, goat, cat, or dog
  • bird e.g., commercially relevant bird, such as
  • the non-human animal is a fish, reptile, or amphibian.
  • the non-human animal may be a male or female at any stage of development.
  • the non-human animal may be a transgenic animal or genetically engineered animal.
  • a “patient” refers to a human subject in need of treatment of a disease.
  • tissue sample refers to any sample including tissue samples (such as tissue sections and needle biopsies of a tissue); cell samples (e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection); samples of whole organisms (such as samples of yeasts or bacteria); or cell fractions, fragments or organelles (such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise).
  • tissue samples such as tissue sections and needle biopsies of a tissue
  • cell samples e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection) or samples of cells obtained by microdissection
  • samples of whole organisms such as samples of yeasts or bacteria
  • cell fractions, fragments or organelles such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise.
  • biological samples include blood, serum, urine, semen, fecal matter, cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from another biological sample.
  • biopsied tissue e.g., obtained by a surgical biopsy or needle biopsy
  • nipple aspirates milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from another biological sample.
  • administer refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing a compound described herein, or a composition thereof, into, in, or on a subject.
  • treatment refers to reversing, alleviating, delaying the onset of or inhibiting the progress of a disease described herein.
  • treatment may be administered after one or more signs or symptoms of the disease have developed or have been observed.
  • treatment may be administered in the absence of signs or symptoms of the disease.
  • treatment may be administered to a susceptible subject prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of exposure to a pathogen). Treatment may also be continued after symptoms have resolved, for example, to delay or prevent recurrence.
  • an “effective amount” of a compound described herein refers to an amount sufficient to elicit the desired biological response, i.e., treating the condition.
  • the effective amount of a compound described herein may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject.
  • an effective amount is a therapeutically effective amount.
  • an effective amount is a prophylactic treatment.
  • an effective amount is the amount of a compound described herein in a single dose.
  • an effective amount is the combined amounts of a compound described herein in multiple doses.
  • a “therapeutically effective amount” of a compound described herein is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition.
  • a therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the condition.
  • the term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms, signs, or causes of the condition, and/or enhances the therapeutic efficacy of another therapeutic agent.
  • a “prophylactically effective amount” of a compound described herein is an amount sufficient to prevent a condition, or one or more symptoms associated with the condition or prevent its recurrence.
  • a prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the condition.
  • the term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.
  • proliferative disease refers to a disease that occurs due to abnormal growth or extension by the multiplication of cells (Walker, Cambridge Dictionary of Biology ; Cambridge University Press: Cambridge, UK, 1990).
  • a proliferative disease may be associated with: 1) the pathological proliferation of normally quiescent cells; 2) the pathological migration of cells from their normal location (e.g., metastasis of neoplastic cells); 3) the pathological expression of proteolytic enzymes such as the matrix metalloproteinases (e.g., collagenases, gelatinases, and elastases); or 4) the pathological angiogenesis as in proliferative retinopathy and tumor metastasis.
  • Exemplary proliferative diseases include cancers (i.e., “malignant neoplasms”), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, and autoimmune diseases.
  • angiogenesis refers to the physiological process through which new blood vessels form from pre-existing vessels.
  • Angiogenesis is distinct from vasculogenesis, which is the de novo formation of endothelial cells from mesoderm cell precursors. The first vessels in a developing embryo form through vasculogenesis, after which angiogenesis is responsible for most blood vessel growth during normal or abnormal development.
  • Angiogenesis is a vital process in growth and development, as well as in wound healing and in the formation of granulation tissue.
  • angiogenesis is also a fundamental step in the transition of tumors from a benign state to a malignant one, leading to the use of angiogenesis inhibitors in the treatment of cancer.
  • Angiogenesis may be chemically stimulated by angiogenic proteins, such as growth factors (e.g., VEGF).
  • angiogenic proteins such as growth factors (e.g., VEGF).
  • VEGF growth factors
  • “Pathological angiogenesis” refers to abnormal (e.g., excessive or insufficient) angiogenesis that amounts to and/or is associated with a disease.
  • neoplasm and “tumor” are used herein interchangeably and refer to an abnormal mass of tissue wherein the growth of the mass surpasses and is not coordinated as in the growth of normal tissue.
  • a neoplasm or tumor may be “benign” or “malignant,” depending on the following characteristics: degree of cellular differentiation (including morphology and functionality), rate of growth, local invasion, and metastasis.
  • a “benign neoplasm” is generally well differentiated, has characteristically slower growth than a malignant neoplasm, and remains localized to the site of origin.
  • a benign neoplasm does not have the capacity to infiltrate, invade, or metastasize to distant sites.
  • Exemplary benign neoplasms include, but are not limited to, lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheic keratoses, lentigos, and sebaceous hyperplasias.
  • certain “benign” tumors may later give rise to malignant neoplasms, which may result from additional genetic changes in a subpopulation of the tumor's neoplastic cells, and these tumors are referred to as “pre-malignant neoplasms.”
  • An exemplary pre-malignant neoplasm is a teratoma.
  • a “malignant neoplasm” is generally poorly differentiated (anaplasia) and has characteristically rapid growth accompanied by progressive infiltration, invasion, and destruction of the surrounding tissue. Furthermore, a malignant neoplasm generally has the capacity to metastasize to distant sites.
  • the term “metastasis,” “metastatic,” or “metastasize” refers to the spread or migration of cancerous cells from a primary or original tumor to another organ or tissue and is typically identifiable by the presence of a “secondary tumor” or “secondary cell mass” of the tissue type of the primary or original tumor and not of that of the organ or tissue in which the secondary (metastatic) tumor is located.
  • a prostate cancer that has migrated to bone is said to be metastasized prostate cancer and includes cancerous prostate cancer cells growing in bone tissue.
  • cancer refers to a class of diseases characterized by the development of abnormal cells that proliferate uncontrollably and have the ability to infiltrate and destroy normal body tissues. See, e.g., Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia, 1990.
  • Exemplary cancers include, but are not limited to, hematological malignancies.
  • Additional exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer, anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast, triple negative breast cancer (TNBC)); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adeno
  • liver cancer e.g., hepatocellular cancer (HCC), malignant hepatoma
  • lung cancer e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung
  • leiomyosarcoma LMS
  • mastocytosis e.g., systemic mastocytosis
  • muscle cancer myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a.
  • myelofibrosis MF
  • chronic idiopathic myelofibrosis chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)
  • neuroblastoma e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis
  • neuroendocrine cancer e.g., gastroenteropancreatic neuroendocrine tumor (GEP-NET), carcinoid tumor
  • osteosarcoma e.g., bone cancer
  • ovarian cancer e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma
  • papillary adenocarcinoma pancreatic cancer
  • pancreatic cancer e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors
  • penile cancer
  • hematological malignancy refers to tumors that affect blood, bone marrow, and/or lymph nodes.
  • exemplary hematological malignancies include, but are not limited to, leukemia, such as acute lymphoblastic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphoma, such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL, such as diffuse large cell lymphoma (DLCL) (e.g
  • inflammatory disease refers to a disease caused by, resulting from, or resulting in inflammation.
  • inflammatory disease may also refer to a dysregulated inflammatory reaction that causes an exaggerated response by macrophages, granulocytes, and/or T-lymphocytes leading to abnormal tissue damage and/or cell death.
  • An inflammatory disease can be either an acute or chronic inflammatory condition and can result from infections or non-infectious causes.
  • Inflammatory diseases include, without limitation, atherosclerosis, arteriosclerosis, autoimmune disorders, multiple sclerosis, systemic lupus erythematosus, polymyalgia rheumatica (PMR), gouty arthritis, degenerative arthritis, tendonitis, bursitis, psoriasis, cystic fibrosis, arthrosteitis, rheumatoid arthritis, inflammatory arthritis, Sjogren's syndrome, giant cell arteritis, progressive systemic sclerosis (scleroderma), ankylosing spondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid, diabetes (e.g., Type I), myasthenia gravis, Hashimoto's thyroiditis, Graves' disease, Goodpasture's disease, mixed connective tissue disease, sclerosing cholangitis, inflammatory bowel disease, Crohn's disease, ulcerative colitis, per
  • autoimmune disease refers to a disease arising from an inappropriate immune response of the body of a subject against substances and tissues normally present in the body. In other words, the immune system mistakes some part of the body as a pathogen and attacks its own cells. This may be restricted to certain organs (e.g., in autoimmune thyroiditis) or involve a particular tissue in different places (e.g., Goodpasture's disease which may affect the basement membrane in both the lung and kidney).
  • the treatment of autoimmune diseases is typically with immunosuppression, e.g., medications which decrease the immune response.
  • Exemplary autoimmune diseases include, but are not limited to, glomerulonephritis, Goodpasture's syndrome, necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemic lupus erythematosis, rheumatoid arthritis, psoriatic arthritis, systemic lupus erythematosis, psoriasis, ulcerative colitis, systemic sclerosis, dermatomyositis/polymyositis, anti-phospholipid antibody syndrome, scleroderma, pemphigus vulgaris, ANCA-associated vasculitis (e.g., Wegener's granulomatosis, microscopic polyangiitis), uveitis, Sjogren's syndrome, Crohn's disease, Reiter's syndrome, ankylosing spondylitis, Lyme disease, Guillain-Barré syndrome, Hashimoto's thyroiditis, and cardio
  • kinase is a class of enzyme that transfers a phosphate group from a high energy donor molecules, such as ATP, to a specific substrate, referred to as phosphorylation.
  • Kinases are part of the larger family of phosphotransferases.
  • One of the largest groups of kinases are protein kinases, which act on and modify the activity of specific proteins.
  • Kinases are used extensively to transmit signals and control complex processes in cells.
  • Various other kinases act on small molecules such as lipids, carbohydrates, amino acids, and nucleotides, either for signaling or to prime them for metabolic pathways.
  • Kinases are often named after their substrates. More than 500 different protein kinases have been identified in humans.
  • Exemplary human protein kinases include, but are not limited to, AAK1, ABL, ACK, ACTR2, ACTR2B, AKT1, AKT2, AKT3, ALK, ALK1, ALK2, ALK4, ALK7, AMPKa1, AMPKa2, ANKRD3, ANPa, ANPb, ARAF, ARAFps, ARG, AurA, AurAps1, AurAps2, AurB, AurBps1, AurC, AXL, BARK1, BARK2, BIKE, BLK, BMPR1A, BMPR1Aps1, BMPR1Aps2, BMPR1B, BMPR2, BMX, BRAF, BRAFps, BRK, BRSK1, BRSK2, BTK, BUB1, BUBR1, CaMK1a, CaMK1b, CaMK1d, CaMK1g, CaMK2a, CaMK2b, CaMK2d, CaMK2g,
  • SRC family kinase refers to a family of non-receptor tyrosine protein kinases that includes nine members: SRCA subfamily that includes c-SRC (proto-oncogene tyrosine-protein kinase SRC), YES (proto-oncogene tyrosine-protein kinase Yes), FYN (proto-oncogene tyrosine-protein kinase FYN), and FGR (Gardner-Rasheed feline sarcoma viral (v-FGR) oncogene homolog); SRCB subfamily that includes LCK (lymphocyte-specific protein tyrosine kinase), HCK (tyrosine-protein kinase HCK, hemopoietic cell kinase), BLK (tyrosine-protein kinase BLK), and LYN (tyrosine-protein kinase LYN); and FRK (F
  • CDK refers to a cyclin-dependent kinase.
  • a CDK binds a cyclin (e.g., Cyclin H), which is a regulatory protein.
  • CDKs phosphorylate their substrates at serines and threonines.
  • the consensus sequence for the phosphorylation site in the amino acid sequence of a CDK substrate is [S/T*]PX[K/R], where S/T* is the phosphorylated serine or threonine, P is proline, X is any amino acid, K is lysine, and R is arginine.
  • CDKs include CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19. and CDK20.
  • CDK7 cyclin-dependent kinase 7, is a CDK, wherein the substrate is Cyclin H, MAT1 (e.g., MNAT1), or Cyclin H and MAT1.
  • CDK7 is alternatively referred to as CAK1, HCAK, MO15, STK1, CDKN7, and p39MO15.
  • Non-limiting examples of the nucleotide and protein sequences for human CDK7 are described in GenBank Accession Number: NP_001790, incorporated herein by reference. The amino acid sequence of this CDK7 is as follows:
  • CDK12 cyclin-dependent kinase 12 is a CDK, wherein the substrate is Cyclin K or flavopiridol.
  • CDK12 is alternatively referred to as Cdc2-related kinase, CDC2-related protein kinase 7, Cell division cycle 2-related protein kinase 7, Cell division protein kinase 12, CRK7, CRKR, CRKRS, cyclin-dependent kinase 12, or KIAA0904.
  • Non-limiting examples of the nucleotide and protein sequences for human CDK12 are described in Uniprot Number: Q9NYV4, which is incorporated herein by reference.
  • the amino acid sequence of this CDK12 is as follows:
  • CDK13 cyclin-dependent kinase 13
  • CDK13 is a CDK, wherein the relevant cyclin is cyclin K and a reference inhibitor is the pan-CDK inhibitor flavopiridol and the c-terminal domain (CTD) of RNA-polymerase II is a physiological substrate.
  • CDK13 is alternatively referred to as CHED; CDC2L; CDC2L5; or hCDK13.
  • Non-limiting examples of the nucleotide and protein sequences for human CDK12 are described in GenBank Accession Number M80629, which is incorporated herein by reference. The amino acid sequence of this CDK13 is as follows:
  • CDKs Cyclin dependent kinases
  • Their successive activation and inactivation drives the cycle forward.
  • the activity of CDKs is regulated by multiple mechanisms such as positive and negative phosphorylation, binding of regulatory proteins like cyclins, and CDK inhibitors.
  • CDK7 plays a critical role in the regulation of RNA polymerase II-mediated transcription of protein-encoding genes. Disruption of CDK7, CDK12, and/or CDK13 signaling causes defects in transcription. However, a complete understanding of how these disruptions affect global transcription is lacking.
  • the present invention provides selective CDK7, CDK12, and/or CDK13 inhibitors, which covalently modify a cysteine residue located outside of the canonical kinase domain (i.e., Cys312 of CDK7, Cys1039 of CDK12, and Cys1017 of CDK13).
  • Selective covalent inhibitors of these kinases may be useful in the treatment of various proliferative diseases including cancer.
  • the present invention provides compounds, which inhibit the activity of a kinase, for the prevention and/or treatment of a subject with a proliferative disease.
  • the inventive compounds inhibit the activity of a cyclin-dependent kinase (CDK).
  • the inventive compounds inhibit the activity of a cyclin-dependent kinase 7 (CDK7).
  • the inventive compounds inhibit the activity of a cyclin-dependent kinase 12 (CDK12).
  • the inventive compounds inhibit the activity of a cyclin-dependent kinase 13 (CDK13).
  • the present invention also provides methods of using the compounds described herein, e.g., as biological probes to study the inhibition of the activity of a kinase (e.g., CDK (e.g. CDK7, CDK12, and/or CDK13)), and as therapeutics, e.g., in the prevention and/or treatment of diseases associated with the overexpression and/or aberrant activity of a kinase (e.g., CDK (e.g. CDK7, CDK12, and/or CDK13)).
  • a kinase e.g., CDK (e.g. CDK7, CDK12, and/or CDK13)
  • CDK e.g. CDK7, CDK12, and/or CDK13
  • the diseases are proliferative diseases.
  • the proliferative diseases that may be treated and/or prevented include, but are not limited to, cancers (e.g., breast cancer, leukemia, melanoma, multiple myeloma), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases.
  • cancers e.g., breast cancer, leukemia, melanoma, multiple my
  • a compound described herein may be useful in treating and/or preventing proliferative diseases in a subject, inhibiting the activity of a protein kinase (e.g., CDK) in a subject or biological sample, and inducing apoptosis of a cell.
  • a compound described herein is a compound of any one of Formulae (I′), (II′), (I), (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • a compound described herein is a compound of Formula (I′), or a pharmaceutically acceptable salt thereof. In certain embodiments, a compound described herein is a compound of Formula (I), or a pharmaceutically acceptable salt thereof. In certain embodiments, a compound described herein is a compound of Formula (II′), or a pharmaceutically acceptable salt thereof. In certain embodiments, a compound described herein is a compound of Formula (II), or a pharmaceutically acceptable salt thereof.
  • a compound described herein is of Formula (I′):
  • R 1 is hydrogen, halogen, or optionally substituted alkyl
  • M is O, S, or NR M ;
  • R M is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring C is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted monocyclic or bicyclic aryl, or optionally substituted monocyclic or bicyclic heteroaryl;
  • each instance of R A , R B , and R C is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —NO 2 , —N 3 , or optionally substituted acyl;
  • each instance of R a is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of R a are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1, b1, and c1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L 1 is —CH 2 —, lc —S( ⁇ O) 2 — lb , —O—, —S—, —NR L1 —, —C( ⁇ O)—, lc —NR L1 C( ⁇ O)— lb , lc —C( ⁇ O)NR L1 — lb , lc —OC( ⁇ O)— lb , or lc —C( ⁇ O)O— lb ; wherein lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C;
  • L 2 is —O—, —S—, —NR L2 —, lb —NR L2 C( ⁇ O)— lm , lb —C( ⁇ O)NR L2 — lm ; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is xm —CH 2 CH 2 — xa , xm —CH ⁇ CH— xa , xm —CH 2 —NR LXxa , xm —CH 2 —O—CH 2 — xa , xm —CH 2 —NR LX —CH 2 — xa , —O—, —S—, —NR LX —, xm —O—CH 2 — xa , xm —S—CH 2 — xa , xm —S—C( ⁇ O)CH 2 — xa , or xm —NR LX —CH 2 — xa ; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of R L1 , R L2 , and R LX is independently hydrogen, optionally substituted C 1-6 alkyl, or a nitrogen protecting group;
  • R 2 is any of Formulae (i-1)-(i-41):
  • a compound described herein is of Formula (I):
  • R 1 is hydrogen, halogen, or optionally substituted alkyl
  • M is O, S, or NR M ;
  • R M is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring C is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • each instance of R A , R B , and R C is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —NO 2 , —N 3 , or optionally substituted acyl;
  • each instance of R a is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of R a are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1, b1, and c1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L 1 is —O—, —S—, —NR L1 —, —C( ⁇ O)—, lc —NR L1 C( ⁇ O)— lb , lc —C( ⁇ O)NR L1 — lb , lc —OC( ⁇ O)— lb , or lc —C( ⁇ O)O— lb ; wherein lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C;
  • L 2 is —O—, —S—, —NR L2 —, lb —NR L2 C( ⁇ O)— lm , lb —C( ⁇ O)NR L2 — lm ; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is —O—, —S—, —NR LX —, xm —O—CH 2 — xa , xm —S—CH 2 — xa , or xm —NR LX —CH 2 — xa ; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of R L1 , R L2 , and R LX is independently hydrogen, optionally substituted C 1-6 alkyl, or a nitrogen protecting group;
  • R 2 is any of Formulae (i-1)-(i-46):
  • L 3 is a bond or an optionally substituted C 1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C ⁇ O—, —O—, —S—, —NR L3a —, —NR L3a C( ⁇ O)—, —C( ⁇ O)NR L3a —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L3a C( ⁇ S)—, —C( ⁇ S)NR L3a —, trans-CR L3b ⁇ CR L3b —, cis-CR L3b ⁇ CR L3b , —C ⁇ C—, —S( ⁇ O)—, —S( ⁇ O)O—, —OS( ⁇ O)—, —S( ⁇ O)NR L3a —, —NR L3a S( ⁇ O)—, —S( ⁇ O
  • L 4 is a bond or an optionally substituted, branched or unbranched C 1 hydrocarbon chain
  • each of R E1 , R E2 , and R E3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH 2 OR EE , —CH 2 N(R EE ) 2 , —CH 2 SR EE , —OR EE , —N(R EE ) 2 , —Si(R EE ) 3 , and —SR EE , wherein each occurrence of R EE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two R EE groups are
  • R E4 is a leaving group
  • R E5 is halogen
  • R E6 is hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group
  • each instance of Y is independently O, S, or NR E7 , wherein R E7 is hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group;
  • a is 1 or 2;
  • each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
  • a compound described herein is of Formula (II′):
  • R 1 is hydrogen, halogen, or optionally substituted alkyl
  • M is O, S, or NR M ;
  • R M is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • each instance of R A and R B is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C( ⁇ NR a )R a , —C( ⁇ NR a )OR a , —C( ⁇ NR a )N(R a ) 2 , —C( ⁇ O)R a , —C( ⁇ O)OR a , —C( ⁇ O)N(R a ) 2 , —NO 2 , —NR a C( ⁇ O)R a , —NR a C( ⁇ O)OR a , —NR a C( ⁇ O)N(R
  • each instance of R a is independently hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of R a are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1 and b1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L 2 is —O—, —S—, —NR L2 —, lb —NR L2 C( ⁇ O)— lm , lb —C( ⁇ O)NR L2 — lm ; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is a bond, —O—, —S—, —NR LX —, xm —O—CH 2 — xa , xm —S—CH 2 — xa , or xm —NR LX —CH 2 — xa ; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of R L2 and R LX is independently hydrogen, optionally substituted C 1-6 alkyl, or a nitrogen protecting group;
  • R 2 is any of Formulae (i-1)-(i-41):
  • a compound described herein is of Formula (I):
  • R 1 is hydrogen, halogen, or optionally substituted alkyl
  • M is O, S, or NR M ;
  • R M is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • each instance of R A and R B is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C( ⁇ NR a )R a , —C( ⁇ NR a )OR a , —C( ⁇ NR a )N(R a ) 2 , —C( ⁇ O)R a , —C( ⁇ O)OR a , —C( ⁇ O)N(R a ) 2 , —NO 2 , —NR a C( ⁇ O)R a , —NR a C( ⁇ O)OR a , —NR a C( ⁇ O)N(R
  • each instance of R a is independently hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of R a are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1 and b1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L 2 is —O—, —S—, —NR L2 —, lb —NR L2 C( ⁇ O)— lm , lb —C( ⁇ O)NR L2 — lm ; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is —O—, —S—, —NR LX —, xm —O—CH 2 — xa , xm —S—CH 2 — xa , or xm —NR LX —CH 2 — xa ; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of R L2 and R LX is independently hydrogen, optionally substituted C 1-6 alkyl, or a nitrogen protecting group;
  • R 2 is any of Formulae (i-1)-(i-46):
  • L 3 is a bond or an optionally substituted C 1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C ⁇ O—, —O—, —S—, —NR L3a —, —NR L3a C( ⁇ O)—, —C( ⁇ O)NR L3a —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L3a C( ⁇ S)—, —C( ⁇ S)NR L3a , trans-CR L3b ⁇ CR L3b —, cis-CR L3b ⁇ CR L3b —, —C ⁇ C—, —S( ⁇ O)—, —S( ⁇ O)O—, —OS( ⁇ O)—, —S( ⁇ O)NR L3a —, —NR L3a S( ⁇ O)—, —S( ⁇ O
  • L 4 is a bond or an optionally substituted, branched or unbranched C 1-6 hydrocarbon chain
  • each of R E1 , R E2 , and R E3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH 2 OR EE , —CH 2 N(R EE ) 2 , —CH 2 SR EE , —OR EE , —N(R EE ) 2 , —Si(R EE ) 3 , and —SR EE , wherein each occurrence of R EE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two R EE groups are
  • R E1 and R E3 , or R E2 and R E3 , or R E1 and R E2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
  • R E4 is a leaving group
  • R E5 is halogen
  • R E6 is hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group
  • each instance of Y is independently O, S, or NR E7 , wherein R E7 is hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group;
  • a is 1 or 2;
  • each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
  • R 1 is hydrogen, halogen, or optionally substituted alkyl.
  • R 1 is hydrogen, halogen, or optionally substituted alkyl.
  • R 1 is hydrogen.
  • R 1 is halogen.
  • R 1 is F.
  • R 1 is Cl.
  • R 1 is Br.
  • R 1 is I.
  • R 1 is optionally substituted alkyl.
  • R 1 is unsubstituted alkyl.
  • R 1 is unsubstituted C 1-6 alkyl.
  • R 1 is methyl.
  • R 1 is substituted alkyl.
  • R 1 is substituted C 1-6 alkyl.
  • M is O. In certain embodiments, M is S. In certain embodiments, M is NR M , wherein R M is as defined herein. In certain embodiments, M is NH. In certain embodiments, M is NR M , wherein R M is optionally substituted alkyl. In certain embodiments, M is NR M , wherein R M is unsubstituted alkyl. In certain embodiments, M is NCH 3 . In certain embodiments, M is NAc.
  • Ring A may be optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl. In certain embodiments, Ring A is optionally substituted monocyclic carbocyclyl. In certain embodiments, Ring A is optionally substituted cyclohexyl. In certain embodiments, Ring A is optionally substituted monocyclic heterocyclyl. In certain embodiments, Ring A is optionally substituted piperidinyl.
  • Ring A is optionally substituted piperizinyl. In certain embodiments, Ring A is optionally substituted tetrahydropyranyl. In certain embodiments, Ring A is optionally substituted phenyl. In certain embodiments, Ring A is phenyl substituted with only X. In certain embodiments, Ring A is optionally substituted monocyclic heteroaryl. In certain embodiments, Ring A is optionally substituted 5-membered heteroaryl. In certain embodiments, Ring A is optionally substituted 6-membered heteroaryl. In certain embodiments, Ring A is optionally substituted pyridine. In certain embodiments, Ring A is optionally substituted pyrimidine.
  • Ring A is of Formula (x-i):
  • each of V 10 , V 11 , V 12 , V 13 , and V 14 is independently O, S, N, NR A1 , C, or CR A2 , as valency permits;
  • each instance of R A1 is independently selected from the group consisting of hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and a nitrogen protecting group;
  • each instance of R A2 is independently selected from the group consisting of hydrogen, halogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —CN, —OR A2a , —N(R A2a ) 2 , and —SR A2a ; and
  • each occurrence of R A2a is independently selected from the group consisting of hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or two R A2a groups are joined to form a substituted or unsubstituted heterocyclic ring.
  • V 10 , V 11 , V 12 , V 13 , and V 14 is selected from the group consisting of O, S, N, and NR A1 .
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • V 10 , V 11 , V 12 , V 13 , and V 14 are each independently selected from the group consisting of O, S, N, and NR A1 .
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of Formula (x-ii):
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • V 10 , V 11 , V 12 , V 13 , and V 14 are each independently selected from the group consisting of O, S, N, and NR A1 .
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A may also be a substituted or unsubstituted 6-membered heteroaryl ring. In certain embodiments, Ring A is of the formula:
  • each of V 10 , V 11 , V 12 , V 13 , V 14 , and V 15 is independently N, C, or CR A2 , as valency permits, wherein R A2 is as defined herein.
  • R A2 is as defined herein.
  • only one of V 10 , V 11 , V 12 , V 13 , V 14 , and V 15 is N.
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • R A and a1 are as defined herein.
  • a1 is 1; and Ring A is one of the formulae:
  • a1 is 2; and Ring A is one of the formulae:
  • a2 is 3; and R 61 is one of the formulae:
  • a2 is 4; and R 61 is one of the formulae:
  • a2 is 5; and R 61 is of the formula
  • Ring A is of the formula:
  • R A and a1 are as defined herein.
  • a1 is 1; and Ring A is one of the formulae:
  • a1 is 2; and Ring A is one of the formulae:
  • a2 is 3; and R 61 is one of the formulae:
  • a2 is 4; and R 61 is one of the formulae:
  • a2 is 5; and R 61 is of the formula
  • Ring A is optionally substituted monocyclic heterocyclyl. In certain embodiments, Ring A is optionally substituted 5-membered heterocyclyl. In certain embodiments, Ring A is optionally substituted 6-membered heterocyclyl. In certain embodiments, Ring A is optionally substituted 6-membered heterocyclyl with one heteroatom selected from the group of S, O, and N.
  • Ring A is of the formula:
  • H A is S, O, or NR HA ;
  • R HA is hydrogen, optionally substituted alkyl, or a nitrogen protecting group; and
  • R A and a1 are as defined herein.
  • Ring A is of the formula:
  • H A , R A and a1 are as defined herein.
  • Ring A is of the formula:
  • H A , R A and a1 are as defined herein.
  • H A is S. In certain embodiments, H A is O. In certain embodiments, H A is NR HA .
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • R A is hydrogen. In certain embodiments, R A is halogen. In certain embodiments, R A is F. In certain embodiments, R A is Cl. In certain embodiments, R A is Br. In certain embodiments, R A is I. In certain embodiments, R A is optionally substituted alkyl. In certain embodiments, R A is unsubstituted alkyl.
  • R A is methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, t-pentyl, neo-pentyl, i-pentyl, s-pentyl, or 3-pentyl.
  • R A is t-butyl.
  • R A is substituted alkyl.
  • R A is haloalkyl.
  • R A is —CF 3 , —CHF 2 , or —CH 2 F.
  • R A is optionally substituted alkenyl.
  • R A is optionally substituted alkynyl. In certain embodiments, R A is optionally carbocyclyl. In certain embodiments, R A is optionally substituted heterocyclyl. In certain embodiments, R A is optionally substituted aryl. In certain embodiments, R A is optionally substituted heteroaryl. In certain embodiments, R A is —OR a , wherein R a is as defined herein. In certain embodiments, R A is —OH. In certain embodiments, R A is —OR a , wherein R a is optionally substituted alkyl or an oxygen protecting group. In certain embodiments, R A is —OR a , wherein R a is unsubstituted alkyl.
  • R A is —OCH 3 .
  • R A is —N(R a ) 2 , wherein R a is as defined herein.
  • R A is —NH 2 .
  • R A is —N(R a ) 2 , wherein each instance of R a is optionally substituted alkyl or a nitrogen protecting group.
  • R A is —N(CH 3 ) 2 .
  • R A is —NHR a , wherein R a is optionally substituted alkyl or a nitrogen protecting group.
  • R A is —NHCH 3 .
  • At least one instance of R A1 is H (hydrogen). In certain embodiments, at least one instance of R A1 is halogen. In certain embodiments, at least one instance of R A1 is F (fluorine). In certain embodiments, at least one instance of R A1 is Cl (chlorine). In certain embodiments, at least one instance of R A1 is Br (bromine). In certain embodiments, at least one instance of R A1 is I (iodine). In certain embodiments, at least one instance of R A1 is substituted acyl. In certain embodiments, at least one instance of R A1 is unsubstituted acyl. In certain embodiments, at least one instance of R A1 is acetyl.
  • At least one instance of R A1 is substituted acetyl. In certain embodiments, at least one instance of R A1 is substituted alkyl. In certain embodiments, at least one instance of R A1 is unsubstituted alkyl. In certain embodiments, at least one instance of R A1 is C 1-6 alkyl. In certain embodiments, at least one instance of R A1 is methyl. In certain embodiments, at least one instance of R A1 is ethyl. In certain embodiments, at least one instance of R A1 is propyl. In certain embodiments, at least one instance of R A1 is butyl. In certain embodiments, at least one instance of R A1 is substituted alkenyl.
  • At least one instance of R A1 is unsubstituted alkenyl. In certain embodiments, at least one instance of R A1 is vinyl. In certain embodiments, at least one instance of R A1 is substituted alkynyl. In certain embodiments, at least one instance of R A1 is unsubstituted alkynyl. In certain embodiments, at least one instance of R A1 is ethynyl. In certain embodiments, at least one instance of R A1 is substituted carbocyclyl. In certain embodiments, at least one instance of R A1 is unsubstituted carbocyclyl. In certain embodiments, at least one instance of R A1 is substituted heterocyclyl.
  • At least one instance of R A1 is unsubstituted heterocyclyl. In certain embodiments, at least one instance of R A1 is substituted aryl. In certain embodiments, at least one instance of R A1 is unsubstituted aryl. In certain embodiments, at least one instance of R A1 is substituted phenyl. In certain embodiments, at least one instance of R A1 is unsubstituted phenyl. In certain embodiments, at least one instance of R A1 is substituted heteroaryl. In certain embodiments, at least one instance of R A1 is unsubstituted heteroaryl. In certain embodiments, at least one instance of R A1 is substituted pyridyl.
  • At least one instance of R A1 is unsubstituted pyridyl. In certain embodiments, at least one instance of R A1 is a nitrogen protecting group. In certain embodiments, at least one instance of R A1 is BOC.
  • At least one R A1 is hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group. In certain embodiments, all instances of R A1 are each independently hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group. In certain embodiments, all instances of R A1 are hydrogen.
  • At least one R A2 is H. In certain embodiments, at least one R A2 is halogen. In certain embodiments, at least one R A2 is F. In certain embodiments, at least one R A2 is Cl. In certain embodiments, at least one R A2 is Br. In certain embodiments, at least one R A2 is I (iodine). In certain embodiments, at least one R A2 is substituted acyl. In certain embodiments, at least one R A2 is unsubstituted acyl. In certain embodiments, at least one R A2 is acetyl. In certain embodiments, at least one R A2 is substituted acetyl. In certain embodiments, at least one R A2 is substituted alkyl.
  • At least one R A2 is unsubstituted alkyl. In certain embodiments, at least one R A2 is C 1-6 alkyl. In certain embodiments, at least one R A2 is methyl. In certain embodiments, at least one R A2 is ethyl. In certain embodiments, at least one R A2 is propyl. In certain embodiments, at least one R A2 is butyl. In certain embodiments, at least one R A2 is substituted alkenyl. In certain embodiments, at least one R A2 is unsubstituted alkenyl. In certain embodiments, at least one R A2 is vinyl. In certain embodiments, at least one R A2 is substituted alkynyl.
  • At least one R A2 is unsubstituted alkynyl. In certain embodiments, at least one R A2 is ethynyl. In certain embodiments, at least one R A2 is substituted carbocyclyl. In certain embodiments, at least one R A2 is unsubstituted carbocyclyl. In certain embodiments, at least one R A2 is substituted heterocyclyl. In certain embodiments, at least one R A2 is unsubstituted heterocyclyl. In certain embodiments, at least one R A2 is substituted aryl. In certain embodiments, at least one R A2 is unsubstituted aryl. In certain embodiments, at least one R A2 is substituted phenyl.
  • At least one R A2 is unsubstituted phenyl. In certain embodiments, at least one R A2 is substituted heteroaryl. In certain embodiments, at least one R A2 is unsubstituted heteroaryl. In certain embodiments, at least one R A2 is substituted pyridyl. In certain embodiments, at least one R A2 is unsubstituted pyridyl. In certain embodiments, at least one R A2 is —OR A2 , wherein R A2a is as defined herein. In certain embodiments, at least one R A2 is —OR A2a , wherein R A2a is hydrogen.
  • At least one R A2 is —OR A2a , wherein R A2a is substituted or unsubstituted C 1-6 alkyl. In certain embodiments, at least one R A2 is —OR A2a , wherein R A2a is unsubstituted C 1-6 alkyl. In certain embodiments, at least one R A2 is —OCH 3 . In certain embodiments, at least one R A2 is —N(R A2a ) 2 . In certain embodiments, at least one R A2 is —SR A2a . In certain embodiments, all instances of R A2 are hydrogen.
  • R A1 and R A2 are hydrogen.
  • R A1 is hydrogen; and at least one R A2 is substituted or unsubstituted alkyl.
  • R A1 is hydrogen; and at least one R A2 is unsubstituted alkyl.
  • R A1 is hydrogen; and at least one R A2 is methyl, ethyl, or n-propyl.
  • R A1 is hydrogen; and at least one R A2 is —OR A2a , wherein R A2a is as defined herein.
  • R A1 is hydrogen; and at least one R A2 is —OR A2a , wherein R A2a is substituted or unsubstituted C 1-6 alkyl.
  • R A1 is hydrogen; and at least one R A2 is —OR A2a , wherein R A2a is unsubstituted C 1-6 alkyl.
  • R A1 is hydrogen; and at least one R A2 is —OCH 3 .
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of the formula:
  • Ring A is of one of the formula:
  • Ring A is of the formula:
  • Ring B between linker L 1 and linker L 2 .
  • Compounds of any one of Formulae (I)-(II) include Ring B between linker L 1 and linker L 2 .
  • Ring B may be optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl.
  • Ring B is optionally substituted monocyclic carbocyclyl.
  • Ring B is optionally substituted monocyclic heterocyclyl.
  • Ring B is optionally substituted pyrrolidinyl.
  • Ring B is optionally substituted phenyl. In certain embodiments, Ring B is optionally substituted monocyclic heteroaryl. In certain embodiments, Ring B is phenyl substituted with only L 1 and L 2 . In certain embodiments, Ring B is optionally substituted cyclohexyl. In certain embodiments, Ring B is optionally substituted piperidinyl. In certain embodiments, Ring B is optionally substituted piperizinyl. In certain embodiments, Ring B is optionally substituted pyridinyl. In certain embodiments, Ring B is optionally substituted pyrimidinyl.
  • Ring B is
  • Ring B is
  • Ring B is
  • Ring B is
  • Ring B is
  • Ring B is
  • Ring B is
  • Ring B is
  • each ring atom is optionally substituted, and L 1 and L 2 may attach to Ring B at either indicated position.
  • Ring C between linker L 1 and R 2 .
  • Ring C may be optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl.
  • Ring C is optionally substituted monocyclic carbocyclyl.
  • Ring C is optionally substituted monocyclic heterocyclyl.
  • Ring C is optionally substituted monocyclic aryl.
  • Ring C is optionally substituted phenyl.
  • Ring C is optionally substituted bicyclic aryl.
  • Ring C is optionally substituted 2,3-dihydro-1H-indene.
  • Ring C is optionally substituted naphthalene.
  • Ring C is:
  • Ring C is:
  • Ring C is optionally substituted monocyclic heteroaryl. In certain embodiments, Ring C is phenyl substituted with only L 1 and R 2 . In certain embodiments, Ring C is optionally substituted cyclohexyl. In certain embodiments, Ring C is optionally substituted pyridinone. In certain embodiments, Ring C is:
  • Ring C is:
  • Ring C is optionally substituted piperidinyl. In certain embodiments, Ring C is optionally substituted piperizinyl. In certain embodiments, Ring C is optionally substituted pyridinyl. In certain embodiments, Ring C is optionally substituted pyrimidinyl. In certain embodiments, Ring C is optionally substituted bicyclic heteroaryl. In certain embodiments, Ring C is optionally substituted indolyl. In certain embodiments, Ring C is optionally substituted indolinyl. In certain embodiments, Ring C is:
  • Ring C is:
  • L 1 is —CH 2 —. In certain embodiments, for Formula (I′), L 1 is lc —S( ⁇ O) 2 — lb . In certain embodiments, L 1 is —O—. In certain embodiments, L 1 is —S—. In certain embodiments, L 1 is —NR L1 —. In certain embodiments, L 1 is —C( ⁇ O)—. In certain embodiments, L 1 is —NR L1 —. In certain embodiments, L 1 is lc —OC( ⁇ O)— lb . In certain embodiments, L 1 is lc —C( ⁇ O)O— lb .
  • L 1 is lc —NR L1 C( ⁇ O)— lb . In certain embodiments, L 1 is lc —C(O)NR L1 — lb . As used herein, lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C.
  • R L1 is hydrogen. In certain embodiments, R L1 is optionally substituted C 1-6 alkyl. In certain embodiments, R L1 is unsubstituted C 1-6 alkyl. In certain embodiments, R L1 is methyl. In certain embodiments, R L1 is substituted C 1-6 alkyl. In certain embodiments, R L1 is a nitrogen protecting group.
  • L 2 is —O—. In certain embodiments, L 2 is —S—. In certain embodiments, L 2 is —NR L2 —. In certain embodiments, L 2 is lb —NR L2 C( ⁇ O)— lm . In certain embodiments, L 2 is lb —C( ⁇ O)NR L2 — lm . As used herein, lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M.
  • R L2 is hydrogen. In certain embodiments, R L2 is optionally substituted C 1-6 alkyl. In certain embodiments, R L2 is unsubstituted C 1-6 alkyl. In certain embodiments, R L2 is methyl. In certain embodiments, R L2 is substituted C 1-6 alkyl. In certain embodiments, R L2 is a nitrogen protecting group.
  • X is a bond. In certain embodiments, for Formula (I′), X is xm —CH 2 CH 2 — xa . In certain embodiments, for Formula (I′), X is xm —CH ⁇ CH— xa . In certain embodiments, for Formula (I′), X is xm —CH 2 —NR LX — xa . In certain embodiments, for Formula (I′), X is xm —CH 2 —NH— xa . In certain embodiments, for Formula (I′), X is xm —CH 2 —O—CH 2 — xa .
  • X is xa —CH 2 —NH—CH 2 — xa .
  • X is —O—.
  • X is —S—.
  • X is xm —S—C( ⁇ O)CH 2 — xa .
  • X is —NR LX —.
  • X is —O—CH 2 —.
  • X is —S—CH 2 —.
  • X is —NR LX —CH 2 —.
  • X is —NH—CH 2 —.
  • a1 is 1. In certain embodiments, a1 is 2. In certain embodiments, a1 is 3.
  • b1 is 1. In certain embodiments, b1 is 2. In certain embodiments, b1 is 3.
  • c1 is 1. In certain embodiments, c1 is 2. In certain embodiments, c1 is 3.
  • R B is optionally substituted alkyl. In certain embodiments, R B is optionally substituted C 1 -C 6 alkyl. In certain embodiments, R B is unsubstituted C 1 -C 6 alkyl. In certain embodiments, R B is methyl or ethyl. In certain embodiments, R B is substituted C 1 -C 6 alkyl. In certain embodiments, R B is hydroxy C 1 -C 6 alkyl. In certain embodiments, R B is —CH 2 OH. In certain embodiments, R B is —CH 2 CH 2 OH. In certain embodiments, R B is —N(R a ) 2 , wherein R a is as defined herein.
  • R B is —NHR a , wherein R a is as defined herein. In certain embodiments, R B is —NHR a , wherein R a is hydrogen or optionally substituted C 1 -C 6 alkyl. In certain embodiments, R B is —NH 2 . In certain embodiments, R B is —NHR a , wherein R a is optionally substituted C 1 -C 6 alkyl. In certain embodiments, R B is —NHR a , wherein R a is unsubstituted C 1 -C 6 alkyl. In certain embodiments, R B is —NHR a , wherein R a is methyl or ethyl.
  • R B is —NHCH 3 . In certain embodiments, R B is —NHR a , wherein R a is a nitrogen protecting group. In certain embodiments, R B is —N(CH 3 )R a , wherein R a is optionally substituted C 1 -C 6 alkyl. In certain embodiments, R B is —N(CH 3 )R a , wherein R a is unsubstituted C 1 -C 6 alkyl. In certain embodiments, R B is —N(CH 3 )R a , wherein R a is methyl or ethyl. In certain embodiments, R B is —N(CH 3 ) 2 . In certain embodiments, R B is —N(CH 3 )R a , wherein R a is a nitrogen protecting group.
  • R C is optionally substituted alkyl. In certain embodiments, R C is optionally substituted C 1 -C 6 alkyl. In certain embodiments, R C is unsubstituted C 1 -C 6 alkyl. In certain embodiments, R C is methyl or ethyl. In certain embodiments, R C is substituted C 1 -C 6 alkyl. In certain embodiments, R C is hydroxy C 1 -C 6 alkyl. In certain embodiments, R C is —CH 2 OH. In certain embodiments, R C is —CH 2 CH 2 OH. In certain embodiments, R C is —N(R a ) 2 , wherein R a is as defined herein.
  • R C is —NHR a , wherein R a is as defined herein. In certain embodiments, R C is —NHR a , wherein R a is hydrogen or optionally substituted C 1 -C 6 alkyl. In certain embodiments, R C is —NH 2 . In certain embodiments, R C is —NHR a , wherein R a is optionally substituted C 1 -C 6 alkyl. In certain embodiments, R C is —NHR a , wherein R a is unsubstituted C 1 -C 6 alkyl. In certain embodiments, R C is —NHR a , wherein R a is methyl or ethyl.
  • R C is —NHCH 3 . In certain embodiments, R C is —NHR a , wherein R a is a nitrogen protecting group. In certain embodiments, R C is —N(CH 3 )R a , wherein R a is optionally substituted C 1 -C 6 alkyl. In certain embodiments, R C is —N(CH 3 )R a , wherein R a is unsubstituted C 1 -C 6 alkyl. In certain embodiments, R C is —N(CH 3 )R a , wherein R a is methyl or ethyl. In certain embodiments, R C is —N(CH 3 ) 2 . In certain embodiments, R C is —N(CH 3 )R a , wherein R a is a nitrogen protecting group.
  • Compounds of Formula (I′) include R 2 attached to Ring C.
  • Compounds of Formula (I) include R 2 attached to Ring C.
  • Compounds of Formula (I) include R 2 attached to Ring B.
  • Compounds of Formula (I′) include R 2 attached to Ring B.
  • R 2 comprises an electrophilic moiety.
  • R 2 comprises a Michael acceptor moiety.
  • the electrophilic moiety may react with a cysteine residue of a kinase (e.g., CDK (e.g., CDK7)) to allow for covalent attachment of the compound to the kinase.
  • a kinase e.g., CDK (e.g., CDK7)
  • the electrophilic moiety may react with a cysteine residue of a kinase (e.g., CDK (e.g., CDK7)). In certain embodiments, the electrophilic moiety (e.g., Michael acceptor moiety) may react with the Cys312 residue of CDK7.
  • the covalent attachment is irreversible. In certain embodiments, the covalent attachment is reversible.
  • R 2 may be any one of Formulae (i-1)-(i-41). In certain embodiments, R 2 is of Formula (i-1):
  • R 2 is of Formula (i-2):
  • R 2 is of Formula (i-3):
  • R 2 is of Formula (i-4):
  • R 2 is of Formula (i-5):
  • R 2 is of Formula (i-6):
  • R 2 is of Formula (i-7):
  • R 2 is of Formula (i-8):
  • R 2 is of Formula (i-9):
  • R 2 is of Formula (i-10):
  • R 2 is of Formula (i-11):
  • R 2 is of Formula (i-12):
  • R 2 is of Formula (i-13):
  • R 2 is of Formula (i-14):
  • R 2 is of Formula (i-15):
  • R 2 is of Formula (i-16):
  • R 2 is of Formula (i-17):
  • R 2 is of Formula (i-18):
  • R 2 is of Formula (i-19):
  • R 2 is of Formula (i-20):
  • R 2 is of Formula (i-21):
  • R 2 is of Formula (i-22):
  • R 2 is of Formula (i-23):
  • R 2 is of Formula (i-24):
  • R 2 is of Formula (i-25):
  • R 2 is of Formula (i-26):
  • R 2 is of Formula (i-27):
  • R 2 is of Formula (i-28):
  • R 2 is of Formula (i-29):
  • R 2 is of Formula (i-30):
  • R 2 is of Formula (i-31):
  • R 2 is of Formula (i-32):
  • R 2 is of Formula (i-33):
  • R 2 is of Formula (i-34):
  • R 2 is of Formula (i-35):
  • R 2 is of Formula (i-36):
  • R 2 is of Formula (i-37):
  • R 2 is of Formula (i-38):
  • R 2 is of Formula (i-39)
  • R 2 is of Formula (i-40):
  • R 2 is of Formula (i-41):
  • R 2 is of Formula (i-1a):
  • R 2 is of Formula (i-1b):
  • R 2 is of Formula (i-1c):
  • R 2 is of Formula (i-1d):
  • R 2 is of Formula (i-1e):
  • R 2 is of Formula (i-1f):
  • R 2 is of Formula (i-1g)
  • R 2 is
  • R 2 is
  • R 2 is
  • R 2 is of Formula (i-1h):
  • R 2 is
  • R 2 is of Formula (i-1a):
  • R 2 is of Formula (i-1b):
  • R 2 is of Formula (i-1c):
  • R 2 is of Formula (i-18a):
  • R 2 is of Formula (i-18b):
  • R 2 is of Formula (i-18c):
  • R 2 is of Formula (i-15a):
  • R 2 is of Formula (i-15b):
  • R 2 is of Formula (i-15c):
  • R 2 may contain linker L 3 or L 4 .
  • L 3 is a bond.
  • L 3 is an optionally substituted C 1-4 hydrocarbon chain.
  • L 3 is an optionally substituted C 1-4 hydrocarbon chain, wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C( ⁇ O)—, —O—, —S—, —NR L3a —, —NR L3a C( ⁇ O)—, —C( ⁇ O)NR L3a —, —SC( ⁇ O)—, —C( ⁇ O)S—, —OC( ⁇ O)—, —C( ⁇ O)O—, —NR L3a C( ⁇ S)—, —C(—S)NR L3a —, trans-CR L3b ⁇ CR L3b —, cis-CR L3b ⁇ CR L3b —, —C ⁇ C—, —S( ⁇ O)—, —S( ⁇ O)O—,
  • L 3 is an optionally substituted C 1-4 hydrocarbon chain, wherein one carbon unit of the hydrocarbon chain is replaced with —NR L3a — (e.g., —NH—).
  • L 3 is of the formula: —(CH 2 ) 1-4 —NR L3a — (e.g., —(CH 2 ) 1-4 —NH—) or —NR L3a —CH 2 ) 1-4 —(e.g., —NH—CH 2 ) 1-4 —).
  • L 3 is —NR L3a .
  • L 3 is —NR L3a (C ⁇ O)—.
  • L 3 is —(C ⁇ O)NR L3a —. In certain embodiments, L 3 is —NH—. In certain embodiments, L 3 is —(C ⁇ O)—. In certain embodiments, L 3 is —NH(C ⁇ O)—. In certain embodiments, L 3 is —(C ⁇ O)NH—. In certain embodiments, L 3 is —O—. In certain embodiments, L 3 is —S—. In certain embodiments, L 4 is a bond. In certain embodiments, L 4 is an optionally substituted C 1-4 hydrocarbon chain.
  • Linker L 3 may contain groups R L3a or R L3b .
  • R L3a is hydrogen.
  • at least one instance of R L3b is hydrogen.
  • each instance of R L3b is hydrogen.
  • at least one instance of R L3b is —Cl, —Br, or —I.
  • each instance of R L3b is —Cl, —Br, or —I.
  • at least one instance of R L3b is —F.
  • each instance of R L3b is —F.
  • R L3b is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.
  • two R L3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring.
  • R 2 may contain groups R E1 , R E2 , and/or R E3 .
  • R E1 is hydrogen.
  • R E2 is hydrogen.
  • R E3 is hydrogen.
  • R E1 is —Cl, —Br, or —I.
  • R E2 is —Cl, —Br, or —I.
  • R E3 is —Cl, —Br, or —I.
  • R E1 is —F.
  • R E2 is —F.
  • R E3 is —F.
  • R E1 is optionally substituted alkyl (e.g., substituted or unsubstituted C 1-6 alkyl).
  • R E2 is optionally substituted alkyl (e.g., substituted or unsubstituted C 1-6 alkyl).
  • R E3 is optionally substituted alkyl (e.g., substituted or unsubstituted C 1-6 alkyl).
  • R E1 is optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH 2 OR EE , —CH 2 N(R EE ) 2 , —CH 2 SR EE , —OR EE , —N(R EE ) 2 , —Si(R EE ) 3 , or —SR EE .
  • R E2 is optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH 2 OR EE , —CH 2 N(R EE ) 2 , —CH 2 SR EE , —OR EE , —N(R EE ) 2 , —Si(R EE ) 3 , or —SR EE .
  • R E3 is optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH 2 OR EE , —CH 2 N(R EE ) 2 , —CH 2 SR EE , —OR EE , —N(R EE ) 2 , —Si(R EE ) 3 , or —SR EE .
  • R E1 is —N(R EE ) 2 .
  • R E2 is —N(R EE ) 2 .
  • R E3 is —N(R EE ) 2 . In certain embodiments, R E1 is —N(CH 3 ) 2 . In certain embodiments, R E2 is —N(CH 3 ) 2 . In certain embodiments, R E3 is —N(CH 3 ) 2 . In certain embodiments, R E1 is —CH 2 N(R EE ) 2 . In certain embodiments, R E2 is —CH 2 N(R EE ) 2 . In certain embodiments, R E3 is —CH 2 N(R EE ) 2 . In certain embodiments, R E1 is —CH 2 N(CH 3 ) 2 .
  • R E2 is —CH 2 N(CH 3 ) 2 . In certain embodiments, R E3 is —CH 2 N(CH 3 ) 2 . In certain embodiments, R E1 is —CN. In certain embodiments, R E2 is —CN. In certain embodiments, R E3 is —CN.
  • R E1 and R E3 are joined to form an optionally substituted carbocyclic ring. In certain embodiments, R E1 and R E3 are joined to form an optionally substituted heterocyclic ring. In certain embodiments, R E2 and R E3 are joined to form an optionally substituted carbocyclic ring. In certain embodiments, R E2 and R E3 are joined to form an optionally substituted heterocyclic ring. In certain embodiments, R E1 and R E2 are joined to form an optionally substituted carbocyclic ring. In certain embodiments, R E1 and R E2 are joined to form an optionally substituted heterocyclic ring.
  • R 2 may contain group R E4 , where R E4 is a leaving group.
  • R E4 is —Cl, —Br, or —I.
  • R E4 is —F.
  • R E4 is —OS( ⁇ O)R E4a or —OS( ⁇ O) 2 R E4a , wherein R E4a is substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R E4 is —OR E4a .
  • R E4 is —OMs, —OTf —OTs, —OBs, or 2-nitrobenzenesulfonyloxy.
  • R E4 is —OR E4a .
  • R E4 is —OMe, —OCF 3 , or —OPh.
  • R E4 is —OC( ⁇ O)R E4a .
  • R E4 is —OC( ⁇ O)Me, —OC( ⁇ O)CF 3 , —OC( ⁇ O)Ph, or —OC( ⁇ O)Cl.
  • R E4 is —OC(O)OR E4a .
  • R E4 is —OC( ⁇ O)OMe or —OC( ⁇ O)O(t-Bu).
  • R 2 may contain group R E5 , where R E5 is a halogen.
  • R E5 is —Cl, —Br, or —I.
  • R E5 is —F.
  • R 2 may contain group R E6 .
  • R E6 is hydrogen.
  • R E6 is substituted or unsubstituted C 1 -C 6 alkyl.
  • R E6 is a nitrogen protecting group.
  • a is 1. In certain embodiments, a is 2.
  • z is 0. In certain embodiments, z is 1. In certain embodiments, z is 2. In certain embodiments, z is 3, 4, 5, or 6.
  • R 2 may contain group Y.
  • Y is O.
  • Y is S.
  • Y is NR E7 .
  • Y is NH.
  • a compound of Formula (I′) is of Formula (I).
  • the compound of Formula (I) is the formula:
  • the compound of Formula (I) is the formula:
  • the compound of Formula (I) is the formula:
  • a compound of Formula (I) is of Formula (I-i):
  • L 1 , L 2 , X, Ring A, Ring C, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-ii):
  • L 1 , L 2 , X, Ring A, Ring C, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-ii-a):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-ii-b):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-ii-c):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-ii-A):
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-ii):
  • L 1 , L 2 , X, Ring A, Ring C, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-iv):
  • L 1 , L 2 , X, Ring A, Ring C, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-iv-a):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-iv-b):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-v):
  • L 1 , L 2 , X, Ring A, Ring C, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-v-a):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of Formula (I-v-b):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I′) is of Formula (I′-A):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I′) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , b1, and c1 are as defined herein.
  • a compound of Formula (I′) is of Formula (I′-i):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I′) is of Formula (I′-ii):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I′) is of Formula (I′-iii):
  • L 1 , L 2 , X, Ring A, R 1 , R 2 , R A , R B , R C , a1, b1, and c1 are as defined herein.
  • a compound of Formula (I′) is of the formula:
  • L 1 , L 2 , X, R 1 , R 2 , R A , R B , R C , b1, and c1 are as defined herein.
  • a compound of Formula (II′) is of Formula (II).
  • the compound of Formula (II) is the formula:
  • the compound of Formula (II) is the formula:
  • the compound of Formula (II) is the formula:
  • a compound of Formula (II) is of Formula (II-i):
  • a compound of Formula (II) is of the formula:
  • a compound of Formula (II) is of the formula:
  • a compound of Formula (II′) is of Formula (II′-i):
  • the compound of Formula (II′) is of the formula:
  • a compound of Formula (II) is of Formula (II-ii):
  • a compound of Formula (II) is of the formula:
  • a compound of Formula (II) is of the formula:
  • a compound of Formula (II) is of Formula (II-iii):
  • a compound of Formula (II) is of the formula:
  • a compound of Formula (II) is of the formula:
  • a compound of Formula (I′) is of the formula:
  • a compound of Formula (I) is of the formula:
  • a compound of Formula (I) is of the formula:
  • a compound of Formula (II′) is of the formula:
  • a compound of Formula (II) is of the formula:
  • compositions described herein may be useful in treating and/or preventing proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject.
  • cancers e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer
  • benign neoplasms e.g., diseases associated with angio
  • compositions described herein may also be useful for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject, biological sample, tissue, or cell.
  • a protein kinase e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)
  • the compositions described herein may also be useful for inducing apoptosis in a cell.
  • compositions comprising a compound described herein (e.g., a compound of any one of Formulae (I′), (II′), (I), (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, and optionally a pharmaceutically acceptable excipient.
  • the pharmaceutical composition of the invention comprises a compound described herein, or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.
  • a pharmaceutical composition described herein comprises a compound described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • the compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof is provided in an effective amount in the pharmaceutical composition.
  • the effective amount is a therapeutically effective amount (e.g., amount effective for treating a proliferative disease in a subject in need thereof). In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject in need thereof. In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a cell. In certain embodiments, the effective amount is an amount effective for inducing apoptosis in a cell.
  • a therapeutically effective amount e.g., amount effective for treating a proliferative disease in a subject in need thereof.
  • the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.
  • the effective amount is a prophylactically effective amount (e.g., amount effective for preventing a proliferative disease in a subject in need thereof and/or for keeping a subject in need thereof in remission of a proliferative disease).
  • the protein kinase being inhibited is a CDK. In certain embodiments, the protein kinase being inhibited is CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19, or CDK20. In certain embodiments, the protein kinase being inhibited is CDK7. In certain embodiments, the protein kinase being inhibited is CDK12. In certain embodiments, the protein kinase being inhibited is CDK13.
  • the protein kinase being inhibited is a Src family kinase. In certain embodiments, the protein kinase being inhibited is SRC. In certain embodiments, the protein kinase being inhibited is FGR. In certain embodiments, the protein kinase being inhibited is BUB1B. In certain embodiments, the protein kinase being inhibited is CHEK2. In certain embodiments, the protein kinase being inhibited is HIPK4. In certain embodiments, the protein kinase being inhibited is PRKCQ. In certain embodiments, the protein kinase being inhibited is R EE T.
  • the protein kinase being inhibited is MELK. In certain embodiments, the protein kinase being inhibited is IRAK1, IRAK4, BMX, or PI3K. In certain embodiments, the protein kinase being inhibited is ABL, ARG, BLK, CSK, EphB1, EphB2, FGR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, or TEC.
  • the protein kinase being inhibited is ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FGR, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated, ABL1 (Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR1, EPHB1, ERBB4, p38-alpha, ABL2, ABL1(Q252H)-phosphorylated, SIK, EPHA8, MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK, EPHA2, ABL1(M351T)
  • the protein kinase being inhibited is ABL1(F317L)-nonphosphorylated, ABL1 (H396P)-nonphosphorylated, ABL1 (H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3, FGR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR1, EPHA2, ABL1 (Q252H)-phosphorylated, MEK5, ABL1 (Q252H)-nonphosphorylated, ABL2, FYN, EPHB1, ABL1(E255K)-phosphorylated, ABL
  • the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or at least about 98%.
  • a protein kinase e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)
  • CDK protein kinase
  • the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by not more than 10%, not more than 20%, not more than 30%, not more than 40%, not more than 50%, not more than 60%, not more than 70%, not more than 80%, not more than 90%, not more than 95%, or not more than 98%.
  • a protein kinase e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)
  • CDK protein kinase
  • the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by a range between a percentage described in this paragraph and another percentage described in this paragraph, inclusive.
  • a protein kinase e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)
  • compositions described herein can be prepared by any method known in the art of pharmacology.
  • preparatory methods include bringing the compound described herein (i.e., the “active ingredient”) into association with a carrier or excipient, and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping, and/or packaging the product into a desired single- or multi-dose unit.
  • compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses.
  • a “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient.
  • the amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage, such as one-half or one-third of such a dosage.
  • Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition described herein will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered.
  • the composition may comprise between about 0.1% and about 100% (w/w) of the active ingredient.
  • compositions used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.
  • Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.
  • Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose, and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, and mixtures thereof.
  • crospovidone cross-linked poly(vinyl-pyrrolidone)
  • sodium carboxymethyl starch sodium starch glycolate
  • Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g., acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminum silicate)), long chain amino acid derivatives, high molecular weight alcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g., carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulos
  • Exemplary binding agents include starch (e.g., cornstarch and starch paste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g., acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum®), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, and/or mixtures
  • Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, antiprotozoan preservatives, alcohol preservatives, acidic preservatives, and other preservatives.
  • the preservative is an antioxidant.
  • the preservative is a chelating agent.
  • antioxidants include alpha tocopherol, ascorbic acid, ascorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.
  • Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof.
  • EDTA ethylenediaminetetraacetic acid
  • salts and hydrates thereof e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like
  • citric acid and salts and hydrates thereof e.g., citric acid mono
  • antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.
  • antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.
  • Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.
  • Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.
  • preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant® Plus, Phenonip®, methylparaben, Germall® 115, Germaben® II, Neolone®, Kathon®, and Euxyl®.
  • Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D-gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer
  • Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, and mixtures thereof.
  • Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus , evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba , macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea
  • Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixtures thereof.
  • Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
  • inert diluents commonly used in the art such as, for example, water or other solvents, so
  • the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
  • adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
  • the conjugates described herein are mixed with solubilizing agents such as Cremophor®, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and mixtures thereof.
  • sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation can be a sterile injectable solution, suspension, or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S.P., and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil can be employed including synthetic mono- or di-glycerides.
  • fatty acids such as oleic acid are used in the preparation of injectables.
  • the injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
  • compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates described herein with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol, or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
  • suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol, or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
  • the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or (a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, (b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, (c) humectants such as glycerol, (d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, (e) solution retarding agents such as paraffin, (f) absorption accelerators such as quaternary ammonium compounds, (g) wetting agents such as, for example, cetyl alcohol and glycerol mono
  • Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the art of pharmacology. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
  • encapsulating compositions which can be used include polymeric substances and waxes.
  • Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • the active ingredient can be in a micro-encapsulated form with one or more excipients as noted above.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings, and other coatings well known in the pharmaceutical formulating art.
  • the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose, or starch.
  • Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose.
  • the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
  • encapsulating agents which can be used include polymeric substances and waxes.
  • Dosage forms for topical and/or transdermal administration of a compound described herein may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants, and/or patches.
  • the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable carrier or excipient and/or any needed preservatives and/or buffers as can be required.
  • the present disclosure contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body.
  • Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium.
  • the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.
  • Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices.
  • Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin.
  • conventional syringes can be used in the classical mantoux method of intradermal administration.
  • Jet injection devices which deliver liquid formulations to the dermis via a liquid jet injector and/or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable.
  • Ballistic powder/particle delivery devices which use compressed gas to accelerate the compound in powder form through the outer layers of the skin to the dermis are suitable.
  • Formulations suitable for topical administration include, but are not limited to, liquid and/or semi-liquid preparations such as liniments, lotions, oil-in-water and/or water-in-oil emulsions such as creams, ointments, and/or pastes, and/or solutions and/or suspensions.
  • Topically administrable formulations may, for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of the active ingredient can be as high as the solubility limit of the active ingredient in the solvent.
  • Formulations for topical administration may further comprise one or more of the additional ingredients described herein.
  • a pharmaceutical composition described herein can be prepared, packaged, and/or sold in a formulation suitable for pulmonary administration via the buccal cavity.
  • a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers, or from about 1 to about 6 nanometers.
  • Such compositions are conveniently in the form of dry powders for administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and/or using a self-propelling solvent/powder dispensing container such as a device comprising the active ingredient dissolved and/or suspended in a low-boiling propellant in a sealed container.
  • Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers.
  • Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.
  • Low boiling propellants generally include liquid propellants having a boiling point of below 65° F. at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w/w) of the composition, and the active ingredient may constitute 0.1 to 20% (w/w) of the composition.
  • the propellant may further comprise additional ingredients such as a liquid non-ionic and/or solid anionic surfactant and/or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).
  • compositions described herein formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and/or suspension.
  • Such formulations can be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and/or atomization device.
  • Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methylhydroxybenzoate.
  • the droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.
  • Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition described herein.
  • Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered by rapid inhalation through the nasal passage from a container of the powder held close to the nares.
  • Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w/w) to as much as 100% (w/w) of the active ingredient, and may comprise one or more of the additional ingredients described herein.
  • a pharmaceutical composition described herein can be prepared, packaged, and/or sold in a formulation for buccal administration.
  • Such formulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may contain, for example, 0.1 to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein.
  • formulations for buccal administration may comprise a powder and/or an aerosolized and/or atomized solution and/or suspension comprising the active ingredient.
  • Such powdered, aerosolized, and/or aerosolized formulations when dispersed, may have an average particle and/or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.
  • a pharmaceutical composition described herein can be prepared, packaged, and/or sold in a formulation for ophthalmic administration.
  • Such formulations may, for example, be in the form of eye drops including, for example, a 0.1-1.0% (w/w) solution and/or suspension of the active ingredient in an aqueous or oily liquid carrier or excipient.
  • Such drops may further comprise buffering agents, salts, and/or one or more other of the additional ingredients described herein.
  • Other opthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and/or in a liposomal preparation. Ear drops and/or eye drops are also contemplated as being within the scope of this disclosure.
  • compositions are principally directed to pharmaceutical compositions which are suitable for administration to humans, such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.
  • the compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions described herein will be decided by a physician within the scope of sound medical judgment.
  • the specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex, and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.
  • the compounds and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol.
  • enteral e.g., oral
  • parenteral intravenous, intramuscular, intra-arterial, intramedullary
  • intrathecal subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal
  • topical as by powders, ointments, creams, and/or drops
  • mucosal nasal,
  • Specifically contemplated routes are oral administration, intravenous administration (e.g., systemic intravenous injection), regional administration via blood and/or lymph supply, and/or direct administration to an affected site.
  • intravenous administration e.g., systemic intravenous injection
  • regional administration via blood and/or lymph supply e.g., via blood and/or lymph supply
  • direct administration e.g., direct administration to an affected site.
  • the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), and/or the condition of the subject (e.g., whether the subject is able to tolerate oral administration).
  • the compound or pharmaceutical composition described herein is suitable for topical administration to the eye of a subject.
  • any two doses of the multiple doses include different or substantially the same amounts of a compound described herein.
  • the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses a day, two doses a day, one dose a day, one dose every other day, one dose every third day, one dose every week, one dose every two weeks, one dose every three weeks, or one dose every four weeks.
  • the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is one dose per day. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is two doses per day.
  • the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses per day.
  • the duration between the first dose and last dose of the multiple doses is one day, two days, four days, one week, two weeks, three weeks, one month, two months, three months, four months, six months, nine months, one year, two years, three years, four years, five years, seven years, ten years, fifteen years, twenty years, or the lifetime of the subject, biological sample, tissue, or cell.
  • the duration between the first dose and last dose of the multiple doses is three months, six months, or one year.
  • the duration between the first dose and last dose of the multiple doses is the lifetime of the subject, biological sample, tissue, or cell.
  • a dose (e.g., a single dose, or any dose of multiple doses) described herein includes independently between 0.1 ⁇ g and 1 ⁇ g, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg, between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg, between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and 300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive, of a compound described herein.
  • a dose described herein includes independently between 1 mg and 3 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 3 mg and 10 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 10 mg and 30 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 30 mg and 100 mg, inclusive, of a compound described herein.
  • Dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult.
  • the amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.
  • a dose described herein is a dose for an adult human whose body weight is approximately 70 kg.
  • a compound or composition, as described herein, may be administered in combination with one or more additional pharmaceutical agents (e.g., therapeutically and/or prophylactically active agents) useful in treating and/or preventing a proliferative disease.
  • additional pharmaceutical agents e.g., therapeutically and/or prophylactically active agents
  • the compounds or compositions can be administered in combination with additional pharmaceutical agents that improve their activity (e.g., activity (e.g., potency and/or efficacy) in treating a proliferative disease in a subject in need thereof, in preventing a proliferative disease in a subject in need thereof, and/or in inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject, biological sample, tissue, or cell), improve bioavailability, improve safety, reduce drug resistance, reduce and/or modify metabolism, inhibit excretion, and/or modify distribution in a subject, biological sample, tissue
  • a pharmaceutical composition described herein including a compound described herein and an additional pharmaceutical agent shows a synergistic effect that is absent in a pharmaceutical composition including one of the compound and the additional pharmaceutical agent, but not both.
  • the compound or composition can be administered concurrently with, prior to, or subsequent to one or more additional pharmaceutical agents, which are different from the compound or composition and may be useful as, e.g., combination therapies in treating and/or preventing a proliferative disease.
  • Pharmaceutical agents include therapeutically active agents.
  • Pharmaceutical agents also include prophylactically active agents.
  • Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved for human or veterinary use by the U.S.
  • the additional pharmaceutical agent is a pharmaceutical agent useful in treating a proliferative disease. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful in preventing a proliferative disease.
  • the additional pharmaceutical agent is a pharmaceutical agent useful in inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject, biological sample, tissue, or cell.
  • a protein kinase e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)
  • the additional pharmaceutical agent is a pharmaceutical agent useful in inducing apoptosis in a cell.
  • the additional pharmaceutical agent is a pharmaceutical agent approved by a regulatory agency (e.g., the US FDA) for treating and/or preventing a proliferative disease.
  • Each additional pharmaceutical agent may be administered at a dose and/or on a time schedule determined for that pharmaceutical agent.
  • the additional pharmaceutical agent(s) may also be administered together with each other and/or with the compound or composition described herein in a single dose or administered separately in different doses.
  • the particular combination to employ in a regimen will take into account compatibility of the compound described herein with the additional pharmaceutical agent(s) and/or the desired therapeutic and/or prophylactic effect to be achieved.
  • the additional pharmaceutical agent(s) in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
  • the additional pharmaceutical agent is a cytotoxic agent. In certain embodiments, the additional pharmaceutical agent is an anti-proliferative agent (e.g., anti-cancer agent). In certain embodiments, the additional pharmaceutical agent is an anti-leukemia agent.
  • the additional pharmaceutical agent is ABITREXATE (methotrexate), ADE, Adriamycin RDF (doxorubicin hydrochloride), Ambochlorin (chlorambucil), ARRANON (nelarabine), ARZERRA (ofatumumab), BOSULIF (bosutinib), BUSULFEX (busulfan), CAMPATH (alemtuzumab), CERUBIDINE (daunorubicin hydrochloride), CLAFEN (cyclophosphamide), CLOFAREX (clofarabine), CLOLAR (clofarabine), CVP, CYTOSAR-U (cytarabine), CYTOXAN (cyclophosphamide), ERWINAZE (Asparaginase Erwinia Chrysanthemi ), FLUDARA (fludarabine phosphate), FOLEX (methotrexate), FOLEX PFS (methotrexate), GAZY
  • the additional pharmaceutical agent is an anti-lymphoma agent.
  • the additional pharmaceutical agent is ABITREXATE (methotrexate), ABVD, ABVE, ABVE-PC, ADCETRIS (brentuximab vedotin), ADRIAMYCIN PFS (doxorubicin hydrochloride), ADRIAMYCIN RDF (doxorubicin hydrochloride), AMBOCHLORIN (chlorambucil), AMBOCLORIN (chlorambucil), ARRANON (nelarabine), BEACOPP, BECENUM (carmustine), BELEODAQ (belinostat), BEXXAR (tositumomab and iodine I 131 tositumomab), BICNU (carmustine), BLENOXANE (bleomycin), CARMUBRIS (carmustine), CHOP, CLAFEN (cyclophosphamide), COPP, COPP-ABV,
  • the additional pharmaceutical agent is ABITREXATE (methotrexate), ABRAXANE (paclitaxel albumin-stabilized nanoparticle formulation), AC, AC-T, ADE, ADRIAMYCIN PFS (doxorubicin hydrochloride), ADRUCIL (fluorouracil), AFINITOR (everolimus), AFINITOR DISPERZ (everolimus), ALDARA (imiquimod), ALIMTA (pemetrexed disodium), AREDIA (pamidronate disodium), ARIMIDEX (anastrozole), AROMASIN (exemestane), AVASTIN (bevacizumab), BECENUM (carmustine), BEP, BICNU (carmustine), BLENOXANE (bleomycin), CAF, CAMPTOSAR (irinotecan hydrochloride), CAPOX, CAPRELSA (vandetanib), CARBOPLATIN-TAXOL, CARMUBRIS (carmustine), CASODE
  • the additional pharmaceutical agent is a kinase inhibitor.
  • the additional pharmaceutical agent is a protein kinase inhibitor (e.g., tyrosine protein kinase inhibitor).
  • the additional pharmaceutical agent is an inhibitor of a Src family kinase.
  • the additional pharmaceutical agent is a CDK inhibitor.
  • the additional pharmaceutical agent is a CDK7 inhibitor.
  • the additional pharmaceutical agent is a CDK12 inhibitor.
  • the additional pharmaceutical agent is a CDK13 inhibitor.
  • the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of IRAK1, IRAK4, BMX, and PI3K. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of BUB1B, CDK2, CDK9, CHEK2, FGR, HIPK4, PRKCQ, RET, SRC, and MELK.
  • the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL, ARG, BLK, CSK, EphB1, EphB2, FOR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, and TEC.
  • the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FOR, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated, ABL1(Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR1, EPHB1, ERBB4, p38-alpha, ABL2, ABL1(Q252H)-phosphorylated, SIK, EPHA8, MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK, EPHA
  • the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL1 (F317L)-nonphosphorylated, ABL1 (H396P)-nonphosphorylated, ABL1 (H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3, FOR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR1, EPHA2, ABL1(Q252H)-phosphorylated, MEK5, ABL1(Q252H)-nonphosphorylated, ABL2, FYN, EPHB1, ABL1 (E) protein kin
  • the additional pharmaceutical agent is an anti-angiogenesis agent, anti-inflammatory agent, immunosuppressant, anti-bacterial agent, anti-viral agent, cardiovascular agent, cholesterol-lowering agent, anti-diabetic agent, anti-allergic agent, pain-relieving agent, or a combination thereof.
  • the compounds described herein or pharmaceutical compositions can be administered or used in combination with an anti-cancer therapy including, but not limited to, transplantation (e.g., bone marrow transplantation, stem cell transplantation), surgery, radiation therapy, immunotherapy, and chemotherapy.
  • kits e.g., pharmaceutical packs.
  • the kits provided may comprise a pharmaceutical composition or compound described herein and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container).
  • a container e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container.
  • provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of a pharmaceutical composition or compound described herein.
  • the pharmaceutical composition or compound described herein provided in the first container and the second container are combined to form one unit dosage form.
  • the present invention also provides methods for the treatment or prevention of a proliferative disease (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases).
  • a proliferative disease e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with
  • the compounds described herein may exhibit kinase inhibitory activity; the ability to inhibit cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinase 7 (CDK7); the ability to inhibit cyclin-dependent kinase 7 (CDK7), without inhibiting another cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinase 12 (CDK12); the ability to inhibit cyclin-dependent kinase 12 (CDK12), without inhibiting another cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinase 13 (CDK13); the ability to inhibit cyclin-dependent kinase 13 (CDK13), without inhibiting another cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinases 12 and 13 (CDK12 and CDK13); the ability to inhibit cyclin-dependent kinases 12 and 13 (CDK12 and
  • the compounds described herein are able to bind (e.g., covalently modify) the protein kinase being inhibited.
  • the R 2 group of a compound described herein is able to bind (e.g., covalently modify) to the protein kinase.
  • the R 2 group of a compound described herein is able to covalently bind a cysteine residue of the protein kinase.
  • the compound is capable of covalently modifying CDK7 (e.g., Cys312 of CDK7).
  • the R 2 group of a compound described herein is able to covalently modify residue Cys312 of CDK7.
  • the compound is capable of covalently modifying CDK12 (e.g., Cys1039 of CDK12).
  • the R 2 group of a compound described herein is able to covalently modify residue Cys1039 of CDK12.
  • the compound is capable of covalently modifying CDK13 (e.g., Cys1017 of CDK13).
  • the R 2 group of a compound described herein is able to covalently modify residue Cys1017 of CDK13.
  • the present disclosure provides methods of inhibiting the activity of a protein kinase in a subject, the methods comprising administering to the subject an effective amount (e.g., therapeutically effective amount) of a compound, or pharmaceutical composition thereof, as described herein.
  • an effective amount e.g., therapeutically effective amount
  • the present disclosure provides methods of inhibiting the activity of a protein kinase in a biological sample, the methods comprising contacting the biological sample with an effective amount of a compound, or pharmaceutical composition thereof, as described herein.
  • the present disclosure provides methods of inhibiting the activity of a protein kinase in a tissue, the methods comprising contacting the tissue with an effective amount of a compound, or pharmaceutical composition thereof, as described herein.
  • the present disclosure provides methods of inhibiting the activity of a protein kinase in a cell, the methods comprising contacting the cell with an effective amount of a compound, or pharmaceutical composition thereof, as described herein.
  • the subject being treated is a mammal.
  • the subject is a human.
  • the subject is a domesticated animal, such as a dog, cat, cow, pig, horse, sheep, or goat.
  • the subject is a companion animal such as a dog or cat.
  • the subject is a livestock animal such as a cow, pig, horse, sheep, or goat.
  • the subject is a zoo animal.
  • the subject is a research animal such as a rodent, dog, or non-human primate.
  • the subject is a non-human transgenic animal such as a transgenic mouse or transgenic pig.
  • the biological sample being contacted with the compound or composition is breast tissue, bone marrow, lymph node, lymph tissue, spleen, or blood.
  • the cell being contacted with the compound or composition is in vitro. In certain embodiments, the cell being contacted with the compound or composition is in vivo. In certain embodiments, the cell being contacted with the compound or composition is ex vivo. In certain embodiments, the cell being contacted with the compound or composition is a malignant cell (e.g., malignant blood cell). In certain embodiments, the cell being contacted with the compound or composition is a malignant hematopoietic stem cell (e.g., malignant myeloid cell or malignant lymphoid cell). In certain embodiments, the cell being contacted with the compound or composition is a malignant lymphocyte (e.g., malignant T-cell or malignant B-cell).
  • a malignant lymphocyte e.g., malignant T-cell or malignant B-cell.
  • the cell being contacted with the compound or composition is a malignant red blood cell, malignant white blood cell, or malignant platelet. In certain embodiments, the cell being contacted with the compound or composition is a malignant neutrophil, malignant macrophage, or malignant plasma cell. In certain embodiments, the cell being contacted with the compound or composition is a carcinoma cell. In certain embodiments, the cell being contacted with the compound or composition is a carcinoma breast cell. In certain embodiments, the cell being contacted with the compound or composition is a sarcoma cell. In certain embodiments, the cell being contacted with the compound or composition is a sarcoma cell from breast tissue.
  • the proliferative disease to be treated or prevented using the compounds described herein may be associated with overexpression of a kinase, such as cyclin-dependent kinase (CDK).
  • a kinase such as cyclin-dependent kinase (CDK).
  • CDK cyclin-dependent kinase
  • G1, S, G2, and M The process of eukaryotic cell division may be broadly divided into a series of sequential phases termed G1, S, G2, and M. Correct progression through the various phases of the cell cycle has been shown to be critically dependent upon the spatial and temporal regulation of a family of proteins known as cyclin dependent kinases (CDKs) and a diverse set of their cognate protein partners termed cyclins.
  • CDKs cyclin dependent kinases
  • CDKs are CDC2 (also known as CDK1) homologous serine-threonine kinase proteins that are able to utilize ATP as a substrate in the phosphorylation of diverse polypeptides in a sequence-dependent context.
  • Cyclins are a family of proteins characterized by a homology region, containing approximately 100 amino acids, termed the “cyclin box” which is used in binding to, and defining selectivity for, specific CDK partner proteins.
  • Modulation of the expression levels, degradation rates, protein levels, and activity levels of various CDKs and cyclins throughout the cell cycle leads to the cyclical formation of a series of CDK/cyclin complexes, in which the CDKs are enzymatically active.
  • the formation of these complexes controls passage through discrete cell cycle checkpoints and thereby enables the process of cell division to continue.
  • Failure to satisfy the prerequisite biochemical criteria at a given cell cycle checkpoint, i.e., failure to form a required CDK/cyclin complex can lead to cell cycle arrest and/or cellular apoptosis. Aberrant cellular proliferation can often be attributed to loss of correct cell cycle control.
  • CDK enzymatic activity therefore provides a means by which abnormally dividing cells can have their division arrested and/or be killed.
  • the diversity of CDKs, and CDK complexes, and their critical roles in mediating the cell cycle, provides a broad spectrum of potential therapeutic targets selected on the basis of a defined biochemical rationale.
  • CDK7 a member of the CDK family, was originally isolated as the catalytic subunit of the trimeric CDK-activating kinase (CAK) complex.
  • This complex consisting of CDK7, cyclin H, and MAT1, is responsible for activation of the mitotic promoting factor in vitro.
  • TFIIH basal transcription repair factor IIH
  • TFIIH is a multi-subunit protein complex identified as a factor required for RNA polymerase II (RNAP 1)-catalyzed transcription, and subsequently this complex was found to play a key role in nucleotide excision repair.
  • CDK7 is a component of at least three complexes, i.e., the trimeric CAK complex, the quaternary complex with the XPD (or ERCC2, a protein involved in transcription-coupled nucleotide excision repair), and the nine-subunit TFIIH complex.
  • the two functions of CDK7 in CAK and CTD phosphorylation support critical facets of cellular proliferation, cell cycling, and transcription.
  • Overexpression of CDK7 may inhibit apoptosis, promote transcription and cell proliferation, and/or disrupt DNA repair, and therefore, cause proliferative diseases.
  • the proliferative disease to be treated or prevented using the compounds described herein may be associated with overexpression of a CDK (e.g., CDK7).
  • Cdk12 and Cdk13 are Cdc2-related proteins that share 92% identity in their kinase domains (Chen et al., Exp. Neurol., 2014, 261, 10-21).
  • CDK12 plays a critical role in cell processes, for example, regulating transcription and splicing machinery by stabilizing the RNAPII and DNA interaction, and regulating DNA damage response (DDR) and maintenance of genomic stability by modulating the expression of DDR genes.
  • DDR DNA damage response
  • Overexpression of CDK12 has been found to correlate, both at the transcriptional and protein level, with pathological parameters of breast cancer disease.
  • a proliferative disease may be associated with aberrant activity of a CDK (e.g., CDK7, CDK12, and/or CDK13).
  • Aberrant activity of a CDK e.g., CDK7, CDK12, and/or CDK13
  • CDK7, CDK12, and/or CDK13 may be an elevated and/or an inappropriate activity of the CDK.
  • Deregulation of cell cycle progression is a characteristic of a proliferative disease, and a majority of proliferative diseases have abnormalities in some component of CDK (e.g., CDK7, CDK12, and/or CDK13) activity, frequently through elevated and/or inappropriate CDK activation.
  • CDK7 is not overexpressed, and the activity of CDK7 is elevated and/or inappropriate. In certain other embodiments, CDK7 is overexpressed, and the activity of CDK7 is elevated and/or inappropriate. In certain embodiments, CDK12 is not overexpressed, and the activity of CDK12 is elevated and/or inappropriate. In certain embodiments, CDK12 is overexpressed, and the activity of CDK12 is elevated and/or inappropriate.
  • CDK13 is not overexpressed, and the activity of CDK13 is elevated and/or inappropriate. In certain other embodiments, CDK13 is overexpressed, and the activity of CDK13 is elevated and/or inappropriate.
  • the compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may inhibit the activity of CDK7 and be useful in treating and/or preventing proliferative diseases.
  • the compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may inhibit the activity of CDK12 and/or CDK13 and be useful in treating and/or preventing proliferative diseases.
  • a proliferative disease may also be associated with inhibition of apoptosis of a cell in a biological sample or subject. All types of biological samples described herein or known in the art are contemplated as being within the scope of the invention.
  • Apoptosis is the process of programmed cell death. Inhibition of apoptosis may result in uncontrolled cell proliferation and, therefore, may cause proliferative diseases.
  • the cell cycle CDKs (CDK1, 2, 4, and 6) are activated by phosphorylation by CDK7/cyclin H (also called CAK). Inhibition of CDK7 would therefore result in cell-cycle arrest at multiple points in the cell cycle due to failure to activate the cell cycle CDKs.
  • CDK7 activates transcription by phosphorylating the CTD of RNAP II.
  • CTD phosphorylation has been shown to inhibit transcription and reduce expression of short lived proteins, including those involved in apoptosis regulation. It is appreciated in the art that stalling of RNA polymerase may activate p53 (also known as protein 53 or tumor protein 53, a tumor suppressor protein that is encoded in humans by the TP53 gene), leading to apoptosis. Thus, inhibition of the activity of CDK7 are expected to cause cytotoxicity by inducing apoptosis.
  • p53 also known as protein 53 or tumor protein 53, a tumor suppressor protein that is encoded in humans by the TP53 gene
  • the compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may induce apoptosis, and therefore, be useful in treating and/or preventing proliferative diseases.
  • the CycK/Cdk12 complex regulates phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and expression of a small subset of human genes, as revealed in expression microarrays.
  • DNA damage response genes i.e. oncogenes
  • CycK/Cdk12 protects cells from genomic instability.
  • the DNA damage response genes are BRCA1, BRCA2, HER1, HER2, ATR, FANCI, or FANCD2.
  • the DNA damage response genes are BRCA1, HER2, ATR, FANCI, and FANCD2.
  • the DNA damage response genes are BRCA1.
  • the DNA damage response genes are HER2.
  • the proliferative disease to be treated or prevented using the compounds described herein is cancer. All types of cancers disclosed herein or known in the art are contemplated as being within the scope of the invention.
  • the proliferative disease is a cancer associated with BCL-2 anti-apoptotic proteins (e.g., MCL-1 and/or XIAP) (e.g., cancer associated with dependence on BCL-2 anti-apoptotic proteins).
  • the proliferative disease is a cancer associated with overexpression of MYC (a gene that codes for a transcription factor).
  • the cancer is a MYC-dependent cancer.
  • the proliferative disease is a cancer associated with amplification of BRCA1.
  • the proliferative disease is a cancer associated with amplification of HER2. In certain embodiments, the proliferative disease is a hematological malignancy. In certain embodiments, the proliferative disease is a blood cancer. In certain embodiments, the proliferative disease is a hematological malignancy. In certain embodiments, the proliferative disease is leukemia. In certain embodiments, the proliferative disease is chronic lymphocytic leukemia (CLL). In certain embodiments, the proliferative disease is acute lymphoblastic leukemia (ALL). In certain embodiments, the proliferative disease is T-cell acute lymphoblastic leukemia (T-ALL).
  • ALL acute lymphoblastic leukemia
  • T-ALL T-cell acute lymphoblastic leukemia
  • the proliferative disease is chronic myelogenous leukemia (CML). In certain embodiments, the proliferative disease is acute myelogenous leukemia (AML). In certain embodiments, the proliferative disease is acute monocytic leukemia (AMoL). In certain embodiments, the proliferative disease is lymphoma. In some embodiments, the proliferative disease is Burkitt's lymphoma. In certain embodiments, the proliferative disease is a Hodgkin's lymphoma. In certain embodiments, the proliferative disease is a non-Hodgkin's lymphoma. In certain embodiments, the proliferative disease is multiple myeloma.
  • the proliferative disease is melanoma. In certain embodiments, the proliferative disease is colorectal cancer. In certain embodiments, the proliferative disease is breast cancer. In certain embodiments, the proliferative disease is recurring breast cancer. In certain embodiments, the proliferative disease is mutant breast cancer. In certain embodiments, the proliferative disease is HER2+ breast cancer. In certain embodiments, the proliferative disease is HER2-breast cancer. In certain embodiments, the proliferative disease is triple-negative breast cancer (TNBC). In certain embodiments, the proliferative disease is a bone cancer. In certain embodiments, the proliferative disease is osteosarcoma.
  • the proliferative disease is Ewing's sarcoma. In some embodiments, the proliferative disease is a brain cancer. In some embodiments, the proliferative disease is neuroblastoma. In some embodiments, the proliferative disease is a lung cancer. In some embodiments, the proliferative disease is small cell lung cancer (SCLC). In some embodiments, the proliferative disease is non-small cell lung cancer. In some embodiments, the proliferative disease is a benign neoplasm. All types of benign neoplasms disclosed herein or known in the art are contemplated as being within the scope of the invention. In some embodiments, the proliferative disease is associated with angiogenesis.
  • the proliferative disease is an inflammatory disease. All types of inflammatory diseases disclosed herein or known in the art are contemplated as being within the scope of the invention. In certain embodiments, the inflammatory disease is rheumatoid arthritis.
  • the proliferative disease is an acute inflammatory disease.
  • the acute inflammatory disease is rheumatoid arthritis, chron's disease, or fibrosis.
  • the proliferative disease is an autoinflammatory disease. All types of autoinflammatory diseases disclosed herein or known in the art are contemplated as being within the scope of the invention.
  • the proliferative disease is an autoimmune disease. All types of autoimmune diseases disclosed herein or known in the art are contemplated as being within the scope of the invention.
  • the kinase is a CDK. In certain embodiments, the kinase is CDK7. In certain embodiments, the kinase is CDK12. In certain embodiments, the kinase is CDK13. In certain embodiments, the activity of the kinase is aberrant activity of the kinase. In certain embodiments, the activity of the kinase is increased activity of the kinase. In certain embodiments, the inhibition of the activity of the kinase is irreversible. In other embodiments, the inhibition of the activity of the kinase is reversible. In certain embodiments, the methods of inhibiting the activity of the kinase include attaching a compound described herein to the kinase.
  • genes affected by the activity of CDK7 may be inhibited by a compound of the invention.
  • the genes which may have their transcription inhibited by the activity of CDK7 are one or more selected from the group consisting of MYC, RUNX1, MYB, TAL1, GATA3, KLF2, HNRPDL, p21, ASCL1, MYCN, INSM1, NEUROD1, NEUROG1, FOXG1, FOXA1, SOX2, SOX4, BCL11A, OTX2, GAT2, PHOX2B, PLK2, TAF1, CTGF, WEE1, SDIM, JUN, PIM1, IL8, and FOS1.
  • the genes which may have their transcription inhibited by the activity of CDK7 include MYC, KLF2, E2F2, CDK6, CCND3, E2F3, HNRPDL, TET1, IL7R, BRCA1, BRCA2, HER1, and HER2.
  • the transcription of genes affected by the activity of CDK12 may be inhibited by a compound of the invention.
  • the genes which may have their transcription inhibited by the activity of CDK12 are one or more selected from the group consisting of BRCA1, FANCI, ATR, FANCD2, APEX1, NEK9, CHEK1, CHEK2, ATM, RAD51C, RAD51D, ORC3L, MDC1, TERF2, ERCC4, FANCF, PARP9, RUNX1, MYB, TAL1, MCL1, MYC, BCL2, ETS1, and EWS-FLI.
  • the transcription of genes affected by the activity of CDK13 may be inhibited by a compound of the invention.
  • the gene is SNORA38.
  • the present invention also provides methods of inhibiting cell growth in a biological sample, tissue, cell, or subject.
  • the present invention provides methods of inducing apoptosis of a cell in a biological sample, tissue, cell, or subject.
  • the methods described herein include administering to a subject or contacting a biological sample with an effective amount of a compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, or a pharmaceutical composition thereof.
  • the methods described herein include administering to a subject or contacting a biological sample with an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof.
  • the compound is contacted with a biological sample.
  • the compound is administered to a subject.
  • the compound is administered in combination with one or more additional pharmaceutical agents described herein.
  • the additional pharmaceutical agent may be an anti-proliferative agent. In certain embodiments, the additional pharmaceutical agent is an anti-cancer agent.
  • the additional pharmaceutical agent may also be a kinase inhibitor. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a CDK. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK7. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of CDK7. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of CDK7. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK12. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of CDK12.
  • the additional pharmaceutical agent is a nonselective inhibitor of CDK12. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK13. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of CDK13. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of CDK13. In certain embodiments, the additional pharmaceutical agent is an inhibitor of another CDK. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of another CDK. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of another CDK.
  • the additional pharmaceutical agent is flavopiridol, triptolide, SNS-032 (BMS-387032), PHA-767491, PHA-793887, BS-181, (S)—CR8, (R)—CR8, or NU6140.
  • the additional pharmaceutical agent is an inhibitor of a mitogen-activated protein kinase (MAPK).
  • the additional pharmaceutical agent is an inhibitor of a glycogen synthase kinase 3 (GSK3).
  • the additional pharmaceutical agent is an inhibitor of an AGC kinase.
  • the additional pharmaceutical agent is an inhibitor of a calmodulin-dependent kinase (CaM Kinase).
  • the additional pharmaceutical agent is an inhibitor of a casein kinase 1. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a STE kinase. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a tyrosine kinase.
  • the additional pharmaceutical agent is a topoisomerase inhibitor, a MCL1 inhibitor, a BCL-2 inhibitor, a BCL-xL inhibitor, a BRD4 inhibitor, a BRCA1 inhibitor, BRCA2 inhibitor, HER1 inhibitor, HER2 inhibitor, a CDK9 inhibitor, a Jumonji histone demethylase inhibitor, or a DNA damage inducer.
  • the additional pharmaceutical agent is etoposide, obatoclax, navitoclax, JQ1, 4-(((5′-chloro-2′-(((1R,4R)-4-(((R)-1-methoxypropan-2-yl)amino)cyclohexyl)amino)-[2,4′-bipyridin]-6-yl)amino)methyl)tetrahydro-2H-pyran-4-carbonitrile, JIB04, or cisplatin.
  • the additional pharmaceutical agent is etoposide, obatoclax, or navitoclax
  • the disease to be treated is breast cancer, e.g., triple-negative breast cancer, HER2 positive breast cancer, HER2 negative breast cancer, ER-positive breast cancer, ER-negative breast cancer, or ER/PR-positive breast cancer.
  • the additional pharmaceutical agent is etoposide, JIB04, or cisplatin, and the disease to be treated is Ewing's sarcoma.
  • the additional pharmaceutical agent is JQ1 or NVP2
  • the disease to be treated is leukemia, e.g., acute myelogenous leukemia, myeloblastic leukemia, promyelocytic leukemia, myelomonocytic leukemia, monocytic leukemia, monoblastic leukemia, or megakaryoblastic leukemia.
  • a pharmaceutical composition described herein further comprises a combination of the additional pharmaceutical agents described herein.
  • inventive compounds or compositions may synergistically augment inhibition of CDK7 induced by the additional pharmaceutical agent(s) in the biological sample or subject.
  • inventive compounds or compositions may synergistically augment inhibition of CDK12 induced by the additional pharmaceutical agent(s) in the biological sample or subject.
  • inventive compounds or compositions may synergistically augment inhibition of CDK12 and/or CDK13 induced by the additional pharmaceutical agent(s) in the biological sample or subject.
  • the combination of the inventive compounds or compositions and the additional pharmaceutical agent(s) may be useful in treating proliferative diseases resistant to a treatment using the additional pharmaceutical agent(s) without the inventive compounds or compositions.
  • the activity of a protein kinase is non-selectively inhibited by the compounds or pharmaceutical compositions described herein.
  • the activity of the protein kinase being inhibited is selectively inhibited by the compounds or pharmaceutical compositions described herein, compared to the activity of a different protein (e.g., a different protein kinase).
  • the activity of CDK e.g., CDK7, CDK12, or CDK13
  • CDK is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of a different protein.
  • the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of a different CDK protein. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK12. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK13. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK12 and the activity of CDK13.
  • the activity of CDK12 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK7.
  • the activity of CDK13 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK7.
  • the activity of CDK12 and the activity of CDK13 are selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK7.
  • the selectivity of a compound or pharmaceutical composition described herein in inhibiting the activity of a protein kinase over a different protein may be measured by the quotient of the IC 50 value of the compound or pharmaceutical composition in inhibiting the activity of the different protein over the IC 50 value of the compound or pharmaceutical composition in inhibiting the activity of the protein kinase.
  • the selectivity of a compound or pharmaceutical composition described herein for a protein kinase over a different protein may also be measured by the quotient of the K d value of an adduct of the compound or pharmaceutical composition and the different protein over the K d value of an adduct of the compound or pharmaceutical composition and the protein kinase.
  • the selectivity is at least 2-fold, at least 3-fold, at least 5-fold, at least 10-fold, at least 30-fold, at least 100-fold, at least 300-fold, at least 1,000-fold, at least 3,000-fold, at least 10,000-fold, at least 30,000-fold, or at least 100,000-fold. In certain embodiments, the selectivity is not more than 100,000-fold, not more than 10,000-fold, not more than 1,000-fold, not more than 100-fold, not more than 10-fold, or not more than 2-fold. Combinations of the above-referenced ranges (e.g., at least 2-fold and not more than 10,000-fold) are also within the scope of the disclosure.
  • a kit described herein includes a first container comprising a compound or pharmaceutical composition described herein.
  • a kit described herein is useful in treating a proliferative disease (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject in need thereof, preventing a proliferative disease in a subject in need thereof, inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, or CDK13)) in a subject, biological sample, tissue, or cell, and/or induc
  • kits described herein further includes instructions for using the compound or pharmaceutical composition included in the kit.
  • a kit described herein may also include information as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA).
  • the information included in the kits is prescribing information.
  • the kits and instructions provide for treating a proliferative disease in a subject in need thereof, preventing a proliferative disease in a subject in need thereof, inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, or CDK13)) in a subject, biological sample, tissue, or cell, and/or inducing apoptosis in a cell.
  • a kit described herein may include one or more additional pharmaceutical agents described herein as a separate composition.
  • Jurkat cells were treated with DMSO or concentration of compound indicated. 6 hours after treatment, cells were washed and harvested by resuspending in lysis buffer (50 mM Hepes pH 7.4, 150 mM NaCl, 1% NP-40, 5 mM EDTA, protease and phosphatase inhibitors) and lysing on ice 30 minutes. Lysates were cleared by centrifugation at 15,000 rpm 30 minutes. Biotin-labeled THZ1 was added to 1 ⁇ M to lysates and rotated at 4° C. overnight. Streptavidin-agarose beads were washed and 30 ⁇ L slurry was added to each lysate and rotated for 1 hour at 4° C.
  • lysis buffer 50 mM Hepes pH 7.4, 150 mM NaCl, 1% NP-40, 5 mM EDTA, protease and phosphatase inhibitors
  • Jurkat cells were plated at 30,000 cells/well and treated with a titration of compounds indicated. Cells were allowed to grow for 72 hours. Cells were assayed using CELLTITER GLO (Promega) to determine cell viability by measuring the amount of ATP present, which is an indicator of cell metabolic activity. Results are graphed as luminescent values. Curves were generated using PRISM and an IC 50 value was determined.
  • TLC thin layer chromatography
  • E. Merck pre-coated silica gel plates 60 F 2 4
  • Waters LCMS system Waters 2489 UV/Visible Detector, Waters 3100 Mass, Waters 515 HPLC pump, Waters 2545 Binary Gradient
  • MFH-2-91-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH 3 CN (2 mL) was added acryloyl chloride (8 mg, 0.08 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H 2 O, 0.05% TFA) to provide MFH-2-92-1 (11 mg, yield 33%). LCMS (m/z): 526 [M+H]+.
  • MFH-2-94-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH 3 CN (2 mL) was added acryloyl chloride (8 mg, 0.08 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H 2 O, 0.05% TFA) to provide MFH-2-95-1 (15.9 mg, yield 48%). LCMS (m/z): 532 [M+H]+.
  • MFH-2-103-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH 3 CN (2 mL) was added acryloyl chloride (8 mg, 0.08 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H 2 O, 0.05% TFA) to provide MFH-2-104-1 (10.2 mg, yield 30%). LCMS (m/z): 533 [M+H]+.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Animal Behavior & Ethology (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Epidemiology (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Neurology (AREA)
  • Neurosurgery (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Plural Heterocyclic Compounds (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Enzymes And Modification Thereof (AREA)

Abstract

The present invention provides novel compounds of Formulae (I′), (I), (II′), and (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. Also provided are methods and kits involving the inventive compounds or compositions for treating and/or preventing proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, ovarian cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject. Treatment of a subject with a proliferative disease using a compound or composition of the invention may inhibit the aberrant activity of a kinase, such as a cyclin-dependent kinase (CDK) (e.g., CDK7, CDK12, or CDK13), and therefore, induce cellular apoptosis and/or inhibit transcription in the subject.

Description

    RELATED APPLICATIONS
  • This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional application, U.S. Ser. No. 62/216,271, filed Sep. 9, 2015, which is incorporated herein by reference.
    • GOVERNMENT SUPPORT
  • This invention was made with government support under grant number 1 R01 CA179483-01A1 awarded by the National Institutes of Health. The government has certain rights in the invention.
    • BACKGROUND OF THE INVENTION
  • The members of the cyclin-dependent kinase (CDK) family play critical regulatory roles in cell proliferation. There are currently twenty known mammalian CDKs. While CDK7 to CDK13 have been linked to transcription, CDK1, 2, 4, and 6 show demonstrable association with the cell cycle.
  • Unique among the mammalian CDKs, CDK7 has consolidated kinase activities, regulating both the cell cycle and transcription. In the cytosol, CDK7 exists as a heterotrimeric complex and is believed to function as a CDK1/2-activating kinase (CAK), whereby phosphorylation of conserved residues in CDK1/2 by CDK7 is required for full catalytic CDK activity and cell cycle progression (Desai et al., “Effects of phosphorylation by CAK on cyclin binding by CDC2 and CDK2.” Mol. Cell Biol. 15, 345-350 (1995); Kaldis et al., “Analysis of CAK activities from human cells.” Eur. J. Biochem. 267, 4213-4221 (2000); Larochelle et al., “Requirements for CDK7 in the assembly of CDK1/cyclin B and activation of CDK2 revealed by chemical genetics in human cells.” Mol. Cell 25, 839-850 (2007)). In the nucleus, CDK7 forms the kinase core of the RNA polymerase (RNAP) II general transcription factor complex and is charged with phosphorylating the C-terminal domain (CTD) of RNAP II, a requisite step in gene transcriptional initiation (Serizawa. et al., “Association of CDK-activating kinase subunits with transcription factor TFIIH.” Nature 374, 280-282 (1995); Shiekhattar et al., “CDK-activating kinase complex is a component of human transcription factor TFIIH.” Nature 374, 283-287 (1995); Drapkin et al., “Human cyclin-dependent kinase-activating kinase exists in three distinct complexes.” Proc. Natl. Acad. Sci. U.S.A. 93, 6488-6493 (1996); Liu. et al., “Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex.” Mol. Cell Biol. 24, 1721-1735 (2004); Akhtar et al., “TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II.” Mol. Cell 34, 387-393 (2009); Glover-Cutter et al., “TFIIH-associated CDK7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II.” Mol. Cell Biol. 29, 5455-5464 (2009)). Together, the two functions of CDK7, i.e., CAK and CTD phosphorylation, support critical facets of cellular proliferation, cell cycling, and transcription.
  • CDK12 and CDK13 were identified in cDNA screens for cell cycle regulators. Because their cyclin partners were not yet known, they were initially named CRKRS and CDC2L5 (Ko et al., J. Cell Sci., 2001, 114, 2591-2603; Marqués et al., Biochem Biophys Res Commun., 2000, 279(3):832-837), respectively. They were found to be 1490- and 1512-amino acid proteins, respectively, with a conserved central CTD kinase domain and degenerate RS domains identified in their N- and C-terminal regions (Even et al., J Cell Biochem., 2006, 99(3), 890-904).
  • Evidence has shown CDK12 and CDK13 play an important role in cancer development. A comprehensive genomic approach identified CDK12 to be one of the most frequently somatically mutated genes in high-grade serous ovarian cancer, the most fatal form of the disease (Erratum, Nature, 2011, 474(7353), 609-615). Several identified point mutations in the kinase domain point to the critical importance of the kinase activity of CDK12 for the development/progression of this disease. CDK12 has also been found to contribute to the development of breast cancer. Notably, CDK12 is located on chromosome 17, within the 17q21 locus that contains several candidate genes for breast cancer susceptibility (Kauraniemi et al., Cancer Res., 2001, 61(22), 8235-8240), and it is co-amplified with the tyrosine kinase receptor ERBB2, a protein amplified and overexpressed in about 20% of breast tumors. Gene fusion between CDK12 and ERBB2 was also detected in gastric cancer (Zang et al., Cancer Res., 2011, 71(1), 29-39). CDK12 is also implicated in the modification of tamoxifen sensitivity in estrogen-positive breast cancer via the modulation of the mitogen-activated protein kinase pathway (Iorns et al., Carcinogenesis, 2009, 30(10):1696-1701).
  • Due to the important regulatory functions of kinases, such as CDK7, CDK12, and CDK13, in cell cycle control, cell proliferation, differentiation, and apoptosis, it is important to develop modulators of the activities of these kinases, including selective modulators, for use as research tools as well as therapeutic agents in the treatment of diseases.
    • SUMMARY OF THE INVENTION
  • Cyclin dependent kinases (CDKs), e.g., CDK7, CDK12, and CDK13, are key regulators of the cell cycle. Their successive activation and inactivation drives the cycle forward. The activity of CDKs is regulated by multiple mechanisms such as positive and negative phosphorylation, binding of regulatory proteins like cyclins, and CDK inhibitors. Most CDKs require the phosphorylation of a threonine residue located in the T-loop to achieve full kinase activity. This threonine residue is conserved in all CDKs that function in cell cycle regulation. The enzyme responsible for this phosphorylation is therefore termed CDK-activating-kinase or CAK. CAK complexes have been found to be composed of CDK7, CDK12, CDK13, cyclin H, and MAT1. Besides its CAK function, CDK7, CDK12, and CDK13 also play a role in transcription and possibly in DNA repair. This suggests that the CDK7, CDK12, and CDK13 enzyme complexes are involved in multiple functions in the cell, e.g., cell cycle control, apoptosis, transcription regulation, and DNA repair.
  • The present invention provides compounds of Formulae (I′), (II′), (I), (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. The compounds of Formulae (I′), (II′), (I), (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may inhibit the activity of a kinase. The compounds described herein may in certain embodiments selectively inhibit specific CDK subtypes, for example, CDK7, CDK12, or CDK13. In certain embodiments, the compounds of Formulae (I′), (II′), (I), and (II) are selective for CDK7 compared to other kinases. In certain embodiments, the compounds of Formulae (I′), (II′), (I), and (II) are selective for CDK12 and/or CDK13 compared to other kinases. The present invention also provides methods of using the inventive compounds, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, to study the inhibition of a kinase (e.g., CDK7, CDK12, and/or CDK13) and as therapeutics for the prevention and/or treatment of diseases associated with the overexpression and/or aberrant activity of a kinase (e.g., CDK7, CDK12, and/or CDK13). In certain embodiments, the inventive compounds are used for the prevention and/or treatment of proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject.
  • Since the discovery of selective inhibitors of CDK7, CDK12, and CDK13 has been hampered by the high sequence and structural similarities of the kinase domain of CDK family members, the development of selective inhibitors of the transcriptional cyclin-dependent kinases (tCDKs) will allow dissection of their individual contributions to the regulation of transcription and evaluation of their therapeutic potential. Without wishing to be bound by any particular theory, the inventive compounds' selectivity for CDK7, CDK12, and/or CDK13 may be due to the compounds' ability to covalently modify a specific cysteine residue of these kinases (e.g., Cys312 of CDK7, Cys1039 of CDK12, Cys1017 of CDK13).
  • In one aspect, the present invention provides compounds of Formula (I′):
  • Figure US20200172499A9-20200604-C00001
  • and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, wherein R1, R2, RA, RB, RC, Ring A, Ring B, Ring C, L1, L2, X, a1, b1, and c1 are as defined herein.
  • In one aspect, the present invention provides compounds of Formula (I):
  • Figure US20200172499A9-20200604-C00002
  • and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, wherein R1, R2, RA, RB, RC, Ring A, Ring B, Ring C, L1, L2, X, a1, b1, and c1 are as defined herein.
  • In one aspect, the present invention provides compounds of Formula (II′):
  • Figure US20200172499A9-20200604-C00003
  • and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, wherein R1, R2, RA, RB, Ring A, Ring B, L2, X, a1, and b1 are as defined herein.
  • In one aspect, the present invention provides compounds of Formula (II):
  • Figure US20200172499A9-20200604-C00004
  • and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, wherein R1, R2, RA, RB, Ring A, Ring B, L2, X, a1, and b1 are as defined herein.
  • In another aspect, the present disclosure provides pharmaceutical compositions including a compound described herein, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical compositions described herein include a therapeutically or prophylactically effective amount of a compound described herein. The pharmaceutical composition may be useful for treating a proliferative disease in a subject in need thereof, preventing a proliferative disease in a subject in need thereof, inhibiting the activity of a protein kinase in a subject, biological sample, tissue, or cell, and/or inducing apoptosis in a cell. In certain embodiments, the proliferative disease is an inflammatory disease. In certain embodiments, the inflammatory disease is rheumatoid arthritis, Crohn's disease, or fibrosis.
  • In another aspect, the present invention provides methods for treating and/or preventing a proliferative disease. Exemplary proliferative diseases which may be treated include cancer, benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases. In certain embodiments, the cancer is selected from the group consisting of pancreatic cancer, lung cancer (e.g., small cell lung cancer (SCLC), and non-small cell lung cancer), prostate cancer, breast cancer, ovarian cancer, kidney cancer, liver cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, and colorectal cancer.
  • Another aspect of the invention relates to methods of inhibiting the activity of a kinase (e.g., CDK (e.g., CDK7, CDK12, CDK13)) using a compound described herein in a biological sample or subject. In certain embodiments, the method involves the selective inhibition of CDK7. In certain embodiments, the method involves the selective inhibition of CDK12. In certain embodiments, the method involves the selective inhibition of CDK13.
  • Also provided by the present invention are methods of inhibiting the transcription of one or more genes in the cell of a biological sample or subject using a compound described herein. The transcription of genes affected by the activity of CDK7 may be inhibited by a compound of the invention. In certain embodiments, these genes are one or more selected from the group consisting of MYC, RUNX1, MYB, TAL1, GATA3, KLF2, HNRPDL, p21, ASCL1, MYCN, INSM1, NEUROD1, NEUROG1, FOXG1, FOXA1, SOX2, SOX4, BCL11A, OTX2, GAT2, PHOX2B, PLK2, TAF1, CTGF, WEE1, SDIM, JUN, PIM1, IL8, and FOS1. The transcription of genes affected by the activity of CDK12 may be inhibited by a compound of the invention. In certain embodiments, these genes are one or more selected from the group consisting of BRCA1, FANCI, ATR, FANCD2, APEX1, NEK9, CHEK1, CHEK2, ATM, RAD51C, RAD51D, ORC3L, MDC1, TERF2, ERCC4, FANCF, PARP9, RUNX1, MYB, TAL1, MCL1, MYC, BCL2, ETS1, and EWS-FLI. The transcription of genes affected by the activity of CDK13 may be inhibited by a compound of the invention. In certain embodiments, the gene is SNORA38.
  • The present invention also provides methods of inhibiting cell growth in a biological sample or subject. In still another aspect, the present invention provides methods of inducing apoptosis of a cell in a biological sample or subject.
  • The present invention provides methods for administering to a subject in need thereof an effective amount of a compound, or pharmaceutical composition thereof, as described herein. Also described are methods for contacting a cell with an effective amount of a compound, or pharmaceutical composition thereof, as described herein. In certain embodiments, a method described herein further includes administering to the subject an additional pharmaceutical agent. In certain embodiments, a method described herein further includes contacting the cell with an additional pharmaceutical agent. The methods described herein may further include performing radiotherapy, immunotherapy, and/or transplantation on the subject.
  • In yet another aspect, the present invention provides compounds of Formulae (I′), (II′), (I), (II), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, for use in the treatment of a disease (e.g., a proliferative disease such as cancer) in a subject.
  • Another aspect of the present disclosure relates to kits comprising a container with a compound, or pharmaceutical composition thereof, as described herein. The kits described herein may include a single dose or multiple doses of the compound or pharmaceutical composition. The kits may be useful in a method of the disclosure. In certain embodiments, the kit further includes instructions for using the compound or pharmaceutical composition. A kit described herein may also include information (e.g. prescribing information) as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA).
  • The details of one or more embodiments of the invention are set forth herein. Other features, objects, and advantages of the invention will be apparent from the Detailed Description, Examples, Figures, and Claims.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • The accompanying drawing, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the invention and together with the description, serve to explain the principles of the invention.
  • FIG. 1 shows the chemical structures of exemplary compounds described herein and the IC50 values of the exemplary compounds in inhibiting select cyclin-dependent kinases.
  • FIG. 2A shows that compound B12 exhibits binding of intracellular CDK12 and CDK13 at concentrations between 62.5 nM to 1 μM treatment. Jurkat cells treated with compound B12 for 6 hours show decreased pulldown of CDK12 and CDK13-associated cyclin K by biotin-THZ1 relative to DMSO-treated cells. These data indicate that B12 cellular treatment blocks biotin-THZ1 from binding CDK12 and CDK13-associated cyclin K complexes by successful binding of these complexes in cells at these concentrations. Cyclin H (Cyc H) pulldown was not affected, indicating that CDK7 binding is not affected. FIG. 2B shows the structure of compound B12.
  • FIG. 3 shows the binding of compounds B12, B15, and B16 (relative to DMSO control) to CDK12 and CDK13-associated cyclin K at concentrations of 100 nM, 50 nM, 25 nM, and 12.5 nM. Jurkat cells were treated with each compound (or DMSO) for 6 hours, followed by lysis and pulldown with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H). Compound B12 exhibits binding to CDK12 and CDK13-associated cyclin K, while compounds B15 and B16 do not. Compound B12 is able to block pulldown of CDK12 and CDK13-associated cyclin K down to 25 nM treatment, while compounds B15 and B16 show very little effect on cyclin K pulldown. These results indicate that at concentrations as low as 25 nM B12 successfully targets intracellular CDK12 and CDK13-associated cyclin K complexes.
  • FIG. 4 shows binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds. Jurkat cells were treated with each compound at a concentration of 500 nM for 6 hours, followed by lysing and pulldown with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H). Compounds B1, B3, B4, B5, B6, B8, B9, and B12 show a loss in CDK12 and CDK13-associated cyclin K pulldown, indicating that these compounds successfully bind CDK12 and CDK13-associated cyclin K complexes in cells thus blocking biotin-THZ1 pull down, while compounds B5, B8, and B9 show a more pronounced loss of cyclin H pulldown, indicating that these compounds successfully target CDK7-cyclin H complexes in cells and interfere with biotin-THZ1 pull down.
  • FIG. 5 shows exemplary results of growth assays of select compounds described herein. Jurkat cells were plated at 30,000 cells/well and treated with a titration of compounds indicated. Cells were allowed to grow for 72 hours. Cells were assayed using CELLTITER GLO (Promega) to determine cell viability by measuring the amount of ATP present, which is an indicator of cell metabolic activity. Top panel: luminescent values (y-axis); concentration in μM (uM) (x-axis); the curves are generated using PRISM. Bottom panel: IC50 values in μM. Error bars indicate +/− standard deviation. All compounds tested showed anti-proliferative effects to varying extents.
  • FIG. 6 shows exemplary mass spectrum labeling of CDK12 with compound B12. Compound B12 is able to label CDK12 once treated with a 5-fold excess of compound B12 for 1 hour at 4° C.
  • FIG. 7 shows the binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds. Jurkat cells were treated with each compound at a concentration of 500 nM for 6 hours, followed by lysing and pull down with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H). Compounds that decrease the pull down efficiency of CDK12 and CDK13-associated cyclin K complexes indicate those compounds successfully targeted intracellular CDK12 and CDK13-associated cyclin K complexes and therefore were able to block biotin-THZ1 pull down of these complexes. In FIG. 7A, compounds MFH 2-90-1 and MFH 2-102-1, show a loss in cyclin K pulldown by biotin-THZ1, indicating that these compounds were able to bind intracellular CDK12 and CDK13-associated cyclin K complexes and block pull down by biotin-THZ1. In FIG. 7B, compounds MFH 2-90-1, MFH 3-103-1, and MFH 3-151-1, show a loss in cyclin K pulldown by biotin-THZ1, indicating that these compounds were able to bind intracellular CDK12 and CDK13-associated cyclin K complexes and thus block pull down by biotin-THZ1.
  • FIG. 8 shows the binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds. Jurkat cells were treated with each compound at a concentration of 500 nM for 6 hours, followed by lysing and pull down with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H). Compounds that decrease the pull down efficiency of CDK12 and CDK13-associated cyclin K complexes indicate those compounds successfully targeted intracellular CDK12 and CDK13-associated cyclin K complexes and therefore were able to block biotin-THZ1 pull down of these complexes. In FIG. 8A, compound THZ 5-31 and MFH 2-90-1 show a loss in cyclin K pulldown by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding. In FIG. 8B, compounds THZ 5-31, MFH 2-90-1, THZ-CE B-15, and THZ-CE B-16, show a loss in cyclin K pull down by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding.
  • FIG. 9 shows the binding of intracellular CDK12 and CDK13-associated cyclin K complexes by exemplified compounds. Jurkat cells were treated with each compound at a concentration of 500 nM for 4 hours, followed by lysing and pull down with biotin-THZ1, and subsequent western blotting for cyclin K (Cyc K) and cyclin H (Cyc H). Compounds that decrease the pull down efficiency of CDK12 and CDK13-associated cyclin K complexes indicate those compounds successfully targeted intracellular CDK12 and CDK13-associated cyclin K complexes and therefore were able to block biotin-THZ1 pull down of these complexes. In FIG. 9A, compounds THZ 5-31, MFH 2-90-1, MFH 3-75-1, and MFH 3-81-1 show a loss in cyclin K pull down by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding. In FIG. 9B, compounds THZ 5-31, MFH 4-70-1, and MFH 4-70-1 show a loss in cyclin K pull down, by biotin-THZ1, indicating that these compounds successfully targeted CDK12 and CDK13-associated complexes in cells and block biotin-THZ1 binding.
    •  DEFINITIONS
  • Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., inside cover, and specific functional groups are generally defined as described therein.
  • Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Thomas Sorrell, Organic Chemistry, University Science Books, Sausalito, 1999; Smith and March, March's Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern Methods of Organic Synthesis, 3rd Edition, Cambridge University Press, Cambridge, 1987. The disclosure is not intended to be limited in any manner by the exemplary listing of substituents described herein.
  • Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistry of Carbon Compounds (McGraw-Hill, N Y, 1962); and Wilen, Tables of Resolving Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, Ind. 1972). The disclosure additionally encompasses compounds described herein as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.
  • When a range of values is listed, it is intended to encompass each value and sub-range within the range. For example “C1-6” is intended to encompass, C1, C2, C3, C4, C5, C6, C1-6, C1-5, C1-4, C1-3, C1-2, C2-6, C2-5, C2-4, C2-3, C3-6, C3-5, C3-4, C4-6, C4-5, and C5-6.
  • The term “aliphatic” includes both saturated and unsaturated, straight chain (i.e., unbranched), branched, acyclic, cyclic, or polycyclic aliphatic hydrocarbons, which are optionally substituted with one or more functional groups. As will be appreciated by one of ordinary skill in the art, “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. Thus, the term “alkyl” includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl”, and the like. Furthermore, the terms “alkyl”, “alkenyl”, “alkynyl”, and the like encompass both substituted and unsubstituted groups. In certain embodiments, “lower alkyl” is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.
  • In certain embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-4 carbon atoms. Illustrative aliphatic groups thus include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH2-cyclopropyl, vinyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, cyclobutyl, —CH2-cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl, cyclopentyl, —CH2-cyclopentyl, n-hexyl, sec-hexyl, cyclohexyl, —CH2-cyclohexyl moieties and the like, which again, may bear one or more substituents. Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and the like. Representative alkynyl groups include, but are not limited to, ethynyl, 2-propynyl (propargyl), 1-propynyl, and the like.
  • The term “alkyl” refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms (“C1-10 alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C1-9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C1-8 alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C1-7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C1-6 alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“C1-5 alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C1-4 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C1-3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C1-2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C1 alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C2-6 alkyl”). Examples of C1-6 alkyl groups include methyl (C1), ethyl (C2), propyl (C3) (e.g., n-propyl, isopropyl), butyl (C4) (e.g., n-butyl, tert-butyl, sec-butyl, iso-butyl), pentyl (C5) (e.g., n-pentyl, 3-pentanyl, amyl, neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C6) (e.g., n-hexyl). Additional examples of alkyl groups include n-heptyl (C7), n-octyl (C8), and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents (e.g., halogen, such as F). In certain embodiments, the alkyl group is an unsubstituted C1-10 alkyl (such as unsubstituted C1-6 alkyl, e.g., —CH3 (Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstituted n-propyl (n-Pr), unsubstituted isopropyl (i-Pr)), unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (n-Bu), unsubstituted tert-butyl (tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu), unsubstituted isobutyl (i-Bu)). In certain embodiments, the alkyl group is a substituted C1-10 alkyl (such as substituted C1-6 alkyl, e.g., —CF3, Bn).
  • “Alkenyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon double bonds, and no triple bonds (“C2-20 alkenyl”). In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C2-10 alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C2-9 alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C2-8 alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C2-7 alkenyl”). In some embodiments, an alkenyl group has 2 to 6 carbon atoms (“C2-6 alkenyl”). In some embodiments, an alkenyl group has 2 to 5 carbon atoms (“C2-5 alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (“C2-4 alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C2-3 alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C2 alkenyl”). The one or more carbon-carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples of C2-4 alkenyl groups include ethenyl (C2), 1-propenyl (C3), 2-propenyl (C3), 1-butenyl (C4), 2-butenyl (C4), butadienyl (C4), and the like. Examples of C2-6 alkenyl groups include the aforementioned C2-4 alkenyl groups as well as pentenyl (C5), pentadienyl (C5), hexenyl (C6), and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (C8), octatrienyl (C8), and the like. Unless otherwise specified, each instance of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more substituents. In certain embodiments, the alkenyl group is unsubstituted C2-10 alkenyl. In certain embodiments, the alkenyl group is substituted C2-10 alkenyl. In an alkenyl group, a C═C double bond for which the stereochemistry is not specified (e.g., —CH═CHCH3 or
  • Figure US20200172499A9-20200604-C00005
  • may be an (E)- or (Z)-double bond.
  • “Alkynyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon triple bonds, and optionally one or more double bonds (“C2-20 alkynyl”). In some embodiments, an alkynyl group has 2 to 10 carbon atoms (“C2-10 alkynyl”). In some embodiments, an alkynyl group has 2 to 9 carbon atoms (“C2-9 alkynyl”). In some embodiments, an alkynyl group has 2 to 8 carbon atoms (“C2-8 alkynyl”). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (“C2-7 alkynyl”). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C2-6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C2-5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C2-4 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C2-3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C2 alkynyl”). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples of C2-4 alkynyl groups include, without limitation, ethynyl (C2), 1-propynyl (C3), 2-propynyl (C3), 1-butynyl (C4), 2-butynyl (C4), and the like. Examples of C2-6 alkenyl groups include the aforementioned C2-4 alkynyl groups as well as pentynyl (C5), hexynyl (C6), and the like. Additional examples of alkynyl include heptynyl (C7), octynyl (C8), and the like. Unless otherwise specified, each instance of an alkynyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents. In certain embodiments, the alkynyl group is unsubstituted C2-10 alkynyl. In certain embodiments, the alkynyl group is substituted C2-10 alkynyl.
  • “Carbocyclyl” or “carbocyclic” refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C3-10 carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms (“C3-8 carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C3-6 carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C3-6 carbocyclyl”). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms (“C5-10 carbocyclyl”). Exemplary C3-6 carbocyclyl groups include, without limitation, cyclopropyl (C3), cyclopropenyl (C3), cyclobutyl (C4), cyclobutenyl (C4), cyclopentyl (C5), cyclopentenyl (C5), cyclohexyl (C6), cyclohexenyl (C6), cyclohexadienyl (C6), and the like. Exemplary C3-8 carbocyclyl groups include, without limitation, the aforementioned C3-6 carbocyclyl groups as well as cycloheptyl (C7), cycloheptenyl (C7), cycloheptadienyl (C7), cycloheptatrienyl (C7), cyclooctyl (C8), cyclooctenyl (C8), bicyclo[2.2.1]heptanyl (C7), bicyclo[2.2.2]octanyl (C8), and the like. Exemplary C3-10 carbocyclyl groups include, without limitation, the aforementioned C3-8 carbocyclyl groups as well as cyclononyl (C9), cyclononenyl (C9), cyclodecyl (C10), cyclodecenyl (C10), octahydro-1H-indenyl (C9), decahydronaphthalenyl (C10), spiro[4.5]decanyl (C10), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) and can be saturated or can be partially unsaturated. “Carbocyclyl” also includes ring systems wherein the carbocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclic ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents. In certain embodiments, the carbocyclyl group is unsubstituted C3-10 carbocyclyl. In certain embodiments, the carbocyclyl group is substituted C3-10 carbocyclyl.
  • In some embodiments, “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C3-10 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C3-8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C3-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C5-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C5-10 cycloalkyl”). Examples of C5-6 cycloalkyl groups include cyclopentyl (C5) and cyclohexyl (C5). Examples of C3-6 cycloalkyl groups include the aforementioned C5-6 cycloalkyl groups as well as cyclopropyl (C3) and cyclobutyl (C4). Examples of C3-8 cycloalkyl groups include the aforementioned C3-6 cycloalkyl groups as well as cycloheptyl (C7) and cyclooctyl (C8). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents. In certain embodiments, the cycloalkyl group is unsubstituted C3-10 cycloalkyl. In certain embodiments, the cycloalkyl group is substituted C3-10 cycloalkyl.
  • “Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to 10-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 membered heterocyclyl”). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged, or spiro ring system, such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or can be partially unsaturated. Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings. “Heterocyclyl” also includes ring systems wherein the heterocyclic ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclic ring, or ring systems wherein the heterocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclic ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclic ring system. Unless otherwise specified, each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents. In certain embodiments, the heterocyclyl group is unsubstituted 3-10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3-10 membered heterocyclyl.
  • In some embodiments, a heterocyclyl group is a 5-10 membered, non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5-10 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • Exemplary 3-membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, thiiranyl. Exemplary 4-membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5-membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl, and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl. Exemplary 7-membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl. Exemplary 5-membered heterocyclyl groups fused to a C6 aryl ring (also referred to herein as a 5,6-bicyclic heterocyclic ring) include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groups fused to an aryl ring (also referred to herein as a 6,6-bicyclic heterocyclic ring) include, without limitation, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.
  • “Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 pi electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C6-14 aryl”). In some embodiments, an aryl group has six ring carbon atoms (“C6 aryl”; e.g., phenyl). In some embodiments, an aryl group has ten ring carbon atoms (“C10 aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has fourteen ring carbon atoms (“C14 aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups, wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents. In certain embodiments, the aryl group is unsubstituted C6-14 aryl. In certain embodiments, the aryl group is substituted C6-14 aryl.
  • “Aralkyl” refers to an optionally substituted alkyl group substituted by an optionally substituted aryl group. In certain embodiments, the aralkyl is optionally substituted benzyl. In certain embodiments, the aralkyl is benzyl. In certain embodiments, the aralkyl is optionally substituted phenethyl. In certain embodiments, the aralkyl is phenethyl.
  • “Heteroaryl” refers to a radical of a 5-10 membered, monocyclic or bicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 pi electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5-10 membered heteroaryl”). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings. “Heteroaryl” includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system. Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).
  • In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”) with one or more substituents. In certain embodiments, the heteroaryl group is unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5-14 membered heteroaryl.
  • Exemplary 5-membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl, and thiophenyl. Exemplary 5-membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl. Exemplary 6-membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl. Exemplary 6-membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively. Exemplary 7-membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • “Heteroaralkyl” is a subset of alkyl and heteroaryl and refers to an optionally substituted alkyl group substituted by an optionally substituted heteroaryl group.
  • “Unsaturated” or “partially unsaturated” refers to a group that includes at least one double or triple bond. A “partially unsaturated” ring system is further intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl groups). Likewise, “saturated” refers to a group that does not contain a double or triple bond, i.e., contains all single bonds.
  • Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, which are divalent linking groups, are further referred to using the suffix-ene, e.g., alkylene, alkenylene, alkynylene, carbocyclylene, heterocyclylene, arylene, and heteroarylene.
  • An atom, moiety, or group described herein may be unsubstituted or substituted, as valency permits, unless otherwise provided expressly. The term “optionally substituted” refers to substituted or unsubstituted.
  • A group is optionally substituted unless expressly provided otherwise. The term “optionally substituted” refers to being substituted or unsubstituted. In certain embodiments, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups are optionally substituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or “unsubstituted” heteroaryl group). In general, the term “substituted”, whether preceded by the term “optionally” or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term “substituted” is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound. The present disclosure contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this disclosure, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety. In certain embodiments, the substituent is a carbon atom substituent. In certain embodiments, the substituent is a nitrogen atom substituent. In certain embodiments, the substituent is an oxygen atom substituent. In certain embodiments, the substituent is a sulfur atom substituent.
  • Exemplary carbon atom substituents include, but are not limited to, halogen, —CN, —NO2, —N3, —SO2H, —SO3H, —OH, —ORaa, —ON(Rbb)2, —N(Rbb)2, —N(Rbb)3 +X−, —N(ORcc)Rbb, —SH, —SRaa, —SSRcc, —C(═O)Raa, —CO2H, —CHO, —C(ORcc)2, —CO2Raa, —OC(═O)Raa, —OCO2Raa, —C(═O)N(Rbb)2, —OC(═O)N(Rbb)2, —NRbbC(═O)Raa, —NRbbCO2Raa, —NRbbC(═O)N(Rbb)2, —C(═NRbb)Raa, —C(═NRbb)ORaa, —OC(═NRbb)Raa, —OC(═NRbb)ORaa, —C(═NRbb)N(Rbb)2, —OC(═NRbb)N(Rbb)2, —NRbbC(═NRbb)N(Rbb)2, —C(═O)NRbbSO2Raa, —NRbbSO2Raa, —SO2N(Rbb)2, —SO2Raa, —SO2ORaa, —OSO2Raa, —S(═O)Raa, —OS(═O)Raa, —Si(Raa)3, —OSi(Raa)3—C(═S)N(Rbb)2, —C(═O)SRaa, —C(═S)SRaa, —SC(═S)SRaa, —SC(═O)SRaa, —OC(═O)SRaa, —SC(═O)ORaa, —SC(═O)Raa, —P(═O)(Raa)2, —P(═O)(ORcc)2, —OP(═O)(Raa)2, —OP(═O)(ORcc)2, —P(═O)(N(Rbb)2)2, —OP(═O)(N(Rbb)2)2, —NRbbP(═O)(Raa)2, —NRbbP(═O)(ORcc)2, —NRbbP(═O)(N(Rbb)2)2, —P(Rcc)2, —P(ORcc)2, —P(Rcc)3 +X−, —P(ORcc)3 +X−, —P(Rcc)4, —P(ORcc)4, —OP(Rcc)2, —OP(Rcc)3 +X−, —OP(ORcc)2, —OP(ORcc)3 +X−, —OP(Rcc)4, —OP(ORcc)4, —B(Raa)2, —B(ORcc)2, —BRaa(ORcc), C1-10 alkyl, C1-10 perhaloalkyl, C2-10 alkenyl, C2-10 alkynyl, heteroC1-10 alkyl, heteroC2-10 alkenyl, heteroC2-10 alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; wherein X− is a counterion;
  • or two geminal hydrogens on a carbon atom are replaced with the group ═O, ═S, ═NN(Rbb)2, ═NNRbbC(═O)Raa, ═NNRbbC(═O)ORaa, ═NNRbbS(═O)2Raa, ═NRbb, or ═NORcc;
  • each instance of Raa is, independently, selected from C1-10 alkyl, C1-10 perhaloalkyl, C2-10 alkenyl, C2-10 alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl, or two Raa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
  • each instance of Rbb is, independently, selected from hydrogen, —OH, —ORaa, —N(Rcc)2, —CN, —C(═O)Raa, —C(═O)N(Rcc)2, —CO2Raa, —SO2Raa, —C(═NRcc)ORaa, —C(═NRcc)N(Rcc)2, —SO2N(Rcc)2, —SO2Rcc, —SO2ORcc, —SORaa, —C(═S)N(Rcc)2, —C(═O)SRcc, —C(═S)SRcc, —P(═O)(Raa)2, —P(═O)(ORcc)2, —P(═O)(N(Rcc)2)2, C1-10 alkyl, C1-10 perhaloalkyl, C2-10 alkenyl, C2-10 alkynyl, heteroC1-10alkyl, heteroC2-10alkenyl, heteroC2-10alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl, or two Rbb groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; wherein X− is a counterion;
  • each instance of Rcc is, independently, selected from hydrogen, C1-10 alkyl, C1-10 perhaloalkyl, C2-10 alkenyl, C2-10 alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl, or two Rcc groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
  • each instance of Rdd is, independently, selected from halogen, —CN, —NO2, —N3, —SO2H, —SO3H, —OH, —ORee, —ON(Rff)2, —N(Rff)2, —N(Rff)3 +X−, —N(ORee)Rff, —SH, —SRee, —SSRee, —C(═O)Ree, —CO2H, —CO2Ree, —OC(═O)Ree, —OCO2Ree, —C(═O)N(Rff)2, —OC(═O)N(Rff)2, —NRffC(═O)Ree, —NRffCO2Ree, —NRffC(═O)N(Rff)2, —C(═NRff)ORee, —OC(═NRff)Ree, —OC(═NRff)ORee, —C(═NRff)N(Rff)2, —OC(═NRff)N(Rff)2, —NRffC(═NRff)N(Rff)2, —NRffSO2Ree, —SO2N(Rff)2, —SO2Ree, —SO2ORee, —OSO2Ree, —S(═O)Ree, —Si(Ree)3, —OSi(Ree)3, —C(═S)N(Rff)2, —C(═O)SRee, —C(═S)SRee, —SC(═S)SRee, —P(═O)(ORee)2, —P(═O)(Ree)2, —OP(═O)(Ree)2, —OP(═O)(ORee)2, C1-6 alkyl, C1-6 perhaloalkyl, C2-6 alkenyl, C2-6 alkynyl, heteroC1-6alkyl, heteroC2-6alkenyl, heteroC2-6alkynyl, C3-10 carbocyclyl, 3-10 membered heterocyclyl, C6-10 aryl, 5-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups, or two geminal Rdd substituents can be joined to form ═O or ═S; wherein X− is a counterion;
  • each instance of Ree is, independently, selected from C1-6 alkyl, C1-6 perhaloalkyl, C2-6 alkenyl, C2-6 alkynyl, C3-10 carbocyclyl, C6-10 aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups;
  • each instance of Rff is, independently, selected from hydrogen, C1-6 alkyl, C1-6 perhaloalkyl, C2-6 alkenyl, C2-6 alkynyl, C3-10 carbocyclyl, 3-10 membered heterocyclyl, C6-10 aryl and 5-10 membered heteroaryl, or two Rff groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups; and
  • each instance of Rgg is, independently, halogen, —CN, —NO2, —N3, —SO2H, —SO3H, —OH, —OC1-6 alkyl, —ON(C1-6 alkyl)2, —N(C1-6 alkyl)2, —N(C1-6 alkyl)3 +X−, —NH(C1-6 alkyl)2 +X−, —NH2(C1-6 alkyl)+X−, —NH3 +X−, —N(OC1-6 alkyl)(C1-6 alkyl), —N(OH)(C1-6 alkyl), —NH(OH), —SH, —SC1-6 alkyl, —SS(C1-6 alkyl), —C(═O)(C1-6 alkyl), —CO2H, —CO2(C1-6 alkyl), —OC(═O)(C1-6 alkyl), —OCO2(C1-6 alkyl), —C(═O)NH2, —C(═O)N(C1-6 alkyl)2, —OC(═O)NH(C1-6 alkyl), —NHC(═O)(C1-6 alkyl), —N(C1-6 alkyl)C(═O)(C1-6 alkyl), —NHCO2(C1-6 alkyl), —NHC(═O)N(C1-6 alkyl)2, —NHC(═O)NH(C1-6 alkyl), —NHC(═O)NH2, —C(═NH)O(C1-6 alkyl), —OC(═NH)(C1-6 alkyl), —OC(═NH)OC1-6 alkyl, —C(═NH)N(C1-6 alkyl)2, —C(═NH)NH(C1-6 alkyl), —C(═NH)NH2, —OC(═NH)N(C1-6 alkyl)2, —OC(NH)NH(C1-6 alkyl), —OC(NH)NH2, —NHC(NH)N(C1-6 alkyl)2, —NHC(═NH)NH2, —NHSO2(C1-6 alkyl), —SO2N(C1-6 alkyl)2, —SO2NH(C1-6 alkyl), —SO2NH2, —SO2C1-6 alkyl, —SO2OC1-6 alkyl, —OSO2C1-6 alkyl, —SOC1-6 alkyl, —Si(C1-6 alkyl)3, —OSi(C1-6 alkyl)3-C(═S)N(C1-6 alkyl)2, C(═S)NH(C1-6 alkyl), C(═S)NH2, —C(═O)S(C1-6 alkyl), —C(═S)SC1-6 alkyl, —SC(═S)SC1-6 alkyl, —P(═O)(OC1-6 alkyl)2, —P(═O)(C1-6 alkyl)2, —OP(═O)(C1-6 alkyl)2, —OP(═O)(OC1-6 alkyl)2, C1-6 alkyl, C1-6 perhaloalkyl, C2-6 alkenyl, C2-6 alkynyl, heteroC1-6alkyl, heteroC2-6alkenyl, heteroC2-6alkynyl, C3-10 carbocyclyl, C6-10 aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or two geminal Rgg substituents can be joined to form ═O or ═S; wherein X is a counterion.
  • A “counterion” or “anionic counterion” is a negatively charged group associated with a positively charged group in order to maintain electronic neutrality. An anionic counterion may be monovalent (i.e., including one formal negative charge). An anionic counterion may also be multivalent (i.e., including more than one formal negative charge), such as divalent or trivalent. Exemplary counterions include halide ions (e.g., F−, Cl−, Br−, I−), NO3 −, ClO4 −, OH−, H2PO4 −, HCO3 −, HSO4 −, sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic acid-2-sulfonate, and the like), carboxylate ions (e.g., acetate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, gluconate, and the like), BF4 −, PF4 −, PF6 −, AsF6 −, SbF6 −, B[3,5-(CF3)2C6H3]4]−, B(C6F5)4 −, BPh4 −, Al(OC(CF3)3)4 −, and carborane anions (e.g., CB11H12 − or (HCB11Me5Br6)−). Exemplary counterions which may be multivalent include CO3 2−, HPO4 2−, PO4 3−, B4O7 2−, SO4 2−, S2O3 2−, carboxylate anions (e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like), and carboranes.
  • “Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro, —Cl), bromine (bromo, —Br), or iodine (iodo, —I).
  • The term “hydroxyl” or “hydroxy” refers to the group —OH. The term “substituted hydroxyl” or “substituted hydroxyl,” by extension, refers to a hydroxyl group wherein the oxygen atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from —ORaa, —ON(Rbb)2, —OC(═O)SRaa, —OC(═O)Raa, —OCO2Raa, —OC(═O)N(Rbb)2, —OC(═NRbb)Raa, —OC(═NRbb)ORaa, —OC(═NRbb)N(Rbb)2, —OS(═O)Raa, —OSO2Raa, —OSi(Raa)3, —OP(Rcc)2, —OP(Rcc)3 +X−, —OP(ORcc)2, —OP(ORcc)3 +X−, —OP(═O)(Raa)2, —OP(═O)(ORcc)2, and —OP(═O)(N(Rbb))2, wherein X−, Raa, Rbb, and Rcc are as defined herein.
  • “Acyl” refers to a moiety selected from the group consisting of —C(═O)Raa, —CHO, —CO2Raa, —C(═O)N(Rbb)2, —C(═NRbb)Raa, —C(═NRbb)ORaa, —C(═NRbb)N(Rbb)2, —C(═O)NRbbSO2Raa, —C(═S)N(Rbb)2, —C(═O)SRaa, or —C(═S)SRaa, wherein Raa and Rbb are as defined herein.
  • The term “amino” refers to the group —NH2. The term “substituted amino,” by extension, refers to a monosubstituted amino, a disubstituted amino, or a trisubstituted amino. In certain embodiments, the “substituted amino” is a monosubstituted amino or a disubstituted amino group.
  • Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quaternary nitrogen atoms. Exemplary nitrogen atom substituents include, but are not limited to, hydrogen, —OH, —ORaa, —N(Rcc)2, —CN, —C(═O)Raa, —C(═O)N(Rcc)2, —CO2Raa, —SO2Raa, —C(═NRbb)Raa, —C(═NRcc)ORaa, —C(═NRcc)N(Rcc)2, —SO2N(Rcc)2, —SO2Rcc, —SO2ORcc, —SORaa, —C(═S)N(Rcc)2, —C(═O)SRcc, —C(═S)SRcc, —P(═O)(ORcc)2, —P(═O)(Raa)2, —P(═O)(N(Rcc)2)2, C1-10 alkyl, C1-10 perhaloalkyl, C2-10 alkenyl, C2-10 alkynyl, heteroC1-10alkyl, heteroC2-10alkenyl, heteroC2-10alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl, or two Rcc groups attached to an N atom are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein Raa, Rbb, Rcc and Rdd are as defined above.
  • In certain embodiments, the substituent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group). Nitrogen protecting groups include, but are not limited to, —OH, —ORaa, —N(Rcc)2, —C(═O)Raa, —C(═O)N(Rcc)2, —CO2Raa, —SO2Raa, —C(═NRcc)Raa, —C(═NRcc)ORaa, —C(═NRcc)N(Rcc)2, —SO2N(Rcc)2, —SO2Rcc, —SO2ORcc, —SORaa, —C(═S)N(Rcc)2, —C(═O)SRcc, —C(═S)SRcc, C1-10 alkyl (e.g., aralkyl, heteroaralkyl), C2-10 alkenyl, C2-10 alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein Raa, Rbb, Rcc and Rdd are as defined herein. Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • For example, nitrogen protecting groups such as amide groups (e.g., —C(═O)Raa) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitrophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine derivative, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.
  • Nitrogen protecting groups such as carbamate groups (e.g., —C(═O)ORaa) include, but are not limited to, methyl carbamate, ethyl carbamate, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluorenylmethyl carbamate, 2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethyl carbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate, 1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC), 1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), 1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc), 1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and 4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethyl carbamate, t-butyl carbamate (BOC or Boc), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz), p-nitrobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc), 1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate, p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methyl carbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate, 2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate, 1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate, 2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate, 1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate, i-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethyl carbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate, p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzyl carbamate.
  • Nitrogen protecting groups such as sulfonamide groups (e.g., —S(═O)2Raa) include, but are not limited to, p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.
  • Other nitrogen protecting groups include, but are not limited to, phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacyl derivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine, N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N-benzylamine, N-di(4-methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), N-2-picolylamino N-oxide, N-1,1-dimethylthiomethyleneamine, N-benzylideneamine, N-p-methoxybenzylideneamine, N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine, N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine, N-p-nitrobenzylideneamine, N-salicylideneamine, N-5-chlorosalicylideneamine, N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine, N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine, N-borane derivative, N-diphenylborinic acid derivative, N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate, N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).
  • Exemplary oxygen atom substituents include, but are not limited to, —Raa, —N(Rbb)2, —C(═O)SRaa, —C(═O)Raa, —CO2Raa, —C(═O)N(Rbb)22, —C(═NRbb)Raa, —C(═NRbb)ORaa, —C(═NRbb)N(Rbb), —S(═O)Raa, —SO2Raa, —Si(Raa)3, —P(Rcc)2, —P(Rcc)3 +X−, —P(ORcc)2, —P(ORcc)3 +X−, —P(═O)(Raa)2, —P(═O)(ORcc)2, and —P(═O)(N(Rbb)2)2, wherein X−, Raa, Rbb, and Rcc are as defined herein. In certain embodiments, the oxygen atom substituent present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl protecting group). Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference. Exemplary oxygen protecting groups include, but are not limited to, methyl, t-butyloxycarbonyl (BOC or Boc), methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranyl S,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl, 1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl, t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido, diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, α-naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl, tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl, 4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl, 4,4′,4″-tris(levulinoyloxyphenyl)methyl, 4,4′,4″-tris(benzoyloxyphenyl)methyl, 3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl, 1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl, 9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl, 1,3-benzodisulfuran-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, I-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec), 2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate, 4-ethoxy-1-naphthyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl, 4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate, o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkyl N,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).
  • Exemplary sulfur atom substituents include, but are not limited to, —Raa, —N(Rbb)2, —C(═O)SRaa, —C(═O)Raa, —CO2Raa, —C(═O)N(Rbb)2, —C(═NRbb)Raa, —C(═NRbb)ORaa, —C(═NRbb)N(Rbb)2, —S(═O)Raa, —SO2Raa, —Si(Raa)3, —P(Rcc)2, —P(Rcc)3 +X−, —P(ORcc)2, —P(ORcc)3 +X−, —P(═O)(Raa)2, —P(═O)(ORcc)2, and —P(═O)(N(Rbb)2)2, wherein Raa, Rbb, and Rcc are as defined herein. In certain embodiments, the sulfur atom substituent present on a sulfur atom is a sulfur protecting group (also referred to as a thiol protecting group). Sulfur protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • A “hydrocarbon chain” refers to a substituted or unsubstituted divalent alkyl, alkenyl, or alkynyl group. A hydrocarbon chain includes (1) one or more chains of carbon atoms immediately between the two radicals of the hydrocarbon chain; (2) optionally one or more hydrogen atoms on the chain(s) of carbon atoms; and (3) optionally one or more substituents (“non-chain substituents,” which are not hydrogen) on the chain(s) of carbon atoms. A chain of carbon atoms consists of consecutively connected carbon atoms (“chain atoms” or “carbon units”) and does not include hydrogen atoms or heteroatoms. However, a non-chain substituent of a hydrocarbon chain may include any atoms, including hydrogen atoms, carbon atoms, and heteroatoms. For example, hydrocarbon chain —CAH(CBH2CCH3)— includes one chain atom CA, one hydrogen atom on CA, and non-chain substituent —(CBH2CCH3). The term “Cx hydrocarbon chain,” wherein x is a positive integer, refers to a hydrocarbon chain that includes x number of chain atom(s) between the two radicals of the hydrocarbon chain. If there is more than one possible value of x, the smallest possible value of x is used for the definition of the hydrocarbon chain. For example, —CH(C2H5)— is a C1 hydrocarbon chain, and
  • Figure US20200172499A9-20200604-C00006
  • is a C3 hydrocarbon chain. When a range of values is used, the meaning of the range is as described herein. For example, a C3-10 hydrocarbon chain refers to a hydrocarbon chain where the number of chain atoms of the shortest chain of carbon atoms immediately between the two radicals of the hydrocarbon chain is 3, 4, 5, 6, 7, 8, 9, or 10. A hydrocarbon chain may be saturated (e.g., —(CH2)4—). A hydrocarbon chain may also be unsaturated and include one or more C═C and/or C≡C bonds anywhere in the hydrocarbon chain. For instance, —CH═CH—(CH2)2—, —CH2—C≡C—CH2—, and —C≡C—CH═CH— are all examples of a unsubstituted and unsaturated hydrocarbon chain. In certain embodiments, the hydrocarbon chain is unsubstituted (e.g., —C≡C— or —(CH2)4—). In certain embodiments, the hydrocarbon chain is substituted (e.g., —CH(C2H5)— and —CF2—). Any two substituents on the hydrocarbon chain may be joined to form an optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl ring. For instance,
  • Figure US20200172499A9-20200604-C00007
  • are all examples of a hydrocarbon chain. In contrast, in certain embodiments,
  • Figure US20200172499A9-20200604-C00008
  • are not within the scope of the hydrocarbon chains described herein. When a chain atom of a Cx hydrocarbon chain is replaced with a heteroatom, the resulting group is referred to as a Cx hydrocarbon chain wherein a chain atom is replaced with a heteroatom, as opposed to a Cx-1 hydrocarbon chain. For example,
  • Figure US20200172499A9-20200604-C00009
  • is a C3 hydrocarbon chain wherein one chain atom is replaced with an oxygen atom.
  • The term “leaving group” is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile. Examples of suitable leaving groups include, but are not limited to, halogen (such as F, Cl, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, pixel, and haloformates. In some cases, the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate, —OTs), methanesulfonate (mesylate, —OMs), p-bromobenzenesulfonyloxy (brosylate, —OBs), —OS(═O)2(CF2)3CF3 (nonaflate, —ONf), or trifluoromethanesulfonate (triflate, -OTf). In some cases, the leaving group is a brosylate, such as p-bromobenzenesulfonyloxy. In some cases, the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy. The leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate. Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties. Exemplary leaving groups include, but are not limited to, halo (e.g., chloro, bromo, iodo) and activated substituted hydroxyl groups (e.g., —OC(═O)SRaa, —OC(═O)Raa, —OCO2Raa, —OC(═O)N(Rbb)2, —OC(═NRbb)Raa, —OC(═NRbb)ORaa, —OC(═NRbb)N(Rbb)2, —OS(═O)Raa, —OSO2Raa, —OP(Rcc)2, —OP(Rcc)3, —OP(═O)2Raa, —OP(═O)(Raa)2, —OP(═O)(ORcc)2, —OP(═O)2N(Rbb)2, and —OP(═O)(NRbb)2, wherein Raa, Rbb, and Rcc are as defined herein).
  • The term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds described herein include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, non-toxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(C1-4 alkyl)4 − salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
  • The term “solvate” refers to forms of the compound that are associated with a solvent, usually by a solvolysis reaction. This physical association may include hydrogen bonding. Conventional solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and the like. The compounds described herein may be prepared, e.g., in crystalline form, and may be solvated. Suitable solvates include pharmaceutically acceptable solvates and further include both stoichiometric solvates and non-stoichiometric solvates. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid. “Solvate” encompasses both solution-phase and isolatable solvates. Representative solvates include hydrates, ethanolates, and methanolates.
  • The term “hydrate” refers to a compound that is associated with water. Typically, the number of the water molecules contained in a hydrate of a compound is in a definite ratio to the number of the compound molecules in the hydrate. Therefore, a hydrate of a compound may be represented, for example, by the general formula R.x H2O, wherein R is the compound, and x is a number greater than 0. A given compound may form more than one type of hydrate, including, e.g., monohydrates (x is 1), lower hydrates (x is a number greater than 0 and smaller than 1, e.g., hemihydrates (R.0.5H2O)), and polyhydrates (x is a number greater than 1, e.g., dihydrates (R.2H2O) and hexahydrates (R.6H2O)).
  • The term “tautomers” or “tautomeric” refers to two or more interconvertible compounds resulting from at least one formal migration of a hydrogen atom and at least one change in valency (e.g., a single bond to a double bond, a triple bond to a single bond, or vice versa). The exact ratio of the tautomers depends on several factors, including temperature, solvent, and pH. Tautomerizations (i.e., the reaction providing a tautomeric pair) may catalyzed by acid or base. Exemplary tautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim, enamine-to-imine, and enamine-to-(a different enamine) tautomerizations.
  • It is also to be understood that compounds that have the same molecular formula but differ in the nature or sequence of bonding of their atoms or the arrangement of their atoms in space are termed “isomers”. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.”
  • Stereoisomers that are not mirror images of one another are termed “diastereomers” and those that are non-superimposable mirror images of each other are termed “enantiomers.” When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible. An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (i.e., as (+) or (−)-isomers respectively). A chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a “racemic mixture.”
  • The term “polymorphs” refers to a crystalline form of a compound (or a salt, hydrate, or solvate thereof) in a particular crystal packing arrangement. All polymorphs have the same elemental composition. Different crystalline forms usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Various polymorphs of a compound can be prepared by crystallization under different conditions.
  • The term “co-crystal” refers to a crystalline structure composed of at least two components. In certain embodiments, a co-crystal may contain a compound of the present invention and one or more other component, including but not limited to, atoms, ions, molecules, or solvent molecules. In certain embodiments, a co-crystal may contain a compound of the present invention and one or more components related to said compound, including not limited to, an isomer, tautomer, salt, solvate, hydrate, synthetic precursor, synthetic derivative, fragment or impurity of said compound.
  • The term “isotopically labeled derivative” or “isotopically labeled” refers to a compound wherein one or more atoms in the compound (or in an associated ion or molecule of a salt, hydrate, or solvate) has been replaced with an isotope of the same element. For the given element or position in the molecule the isotope will be enriched, or present in a higher percentage of all atoms of the element or of all atoms at the position in the molecule in a sample, relative to an unlabeled variant. In certain embodiments, the enriched isotope will be a stable isotope. In certain embodiments, the enriched isotope will be an unstable or radioactive isotope (e.g., a radionuclide). In certain embodiments, the enriched isotope may be detected by a measurement technique, including but not limited to nuclear magnetic resonance, mass spectrometry, infrared spectroscopy, or a technique that measures radioactive decay.
  • The term “prodrugs” refers to compounds that have cleavable groups and become by solvolysis or under physiological conditions the compounds described herein, which are pharmaceutically active in vivo. Such examples include, but are not limited to, choline ester derivatives and the like, N-alkylmorpholine esters and the like. Other derivatives of the compounds described herein have activity in both their acid and acid derivative forms, but in the acid sensitive form often offer advantages of solubility, tissue compatibility, or delayed release in the mammalian organism (see, Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well known to practitioners of the art, such as, for example, esters prepared by reaction of the parent acid with a suitable alcohol, or amides prepared by reaction of the parent acid compound with a substituted or unsubstituted amine, or acid anhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters, amides, and anhydrides derived from acidic groups pendant on the compounds described herein are particular prodrugs. In some cases it is desirable to prepare double ester type prodrugs such as (acyloxy)alkyl esters or ((alkoxycarbonyl)oxy)alkylesters. C1-C8 alkyl, C2-C8 alkenyl, C2-C8 alkynyl, aryl, C7-C12 substituted aryl, and C7-C12 arylalkyl esters of the compounds described herein may be preferred.
  • The term “inhibition”, “inhibiting”, “inhibit,” or “inhibitor” refer to the ability of a compound to reduce, slow, halt or prevent activity of a particular biological process (e.g., CDK kinase activity)) in a cell relative to vehicle.
  • When a compound, pharmaceutical composition, method, use, or kit is referred to as “selectively,” “specifically,” or “competitively” binding a first protein kinase, the compound, pharmaceutical composition, method, use, or kit binds the first protein kinase (e.g., CDK) with a higher binding affinity (e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold) than binding a second protein or second chromatin that is different from the first protein and the first chromatin.
  • When a compound, pharmaceutical composition, method, use, or kit is referred to as “selectively,” “specifically,” or “competitively” modulating (e.g., increasing or inhibiting) the activity of a first protein kinase, the compound, pharmaceutical composition, method, use, or kit modulates the activity of the first protein kinase (e.g., CDK) to a greater extent (e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold) than the activity of a second protein kinase that is different from the first protein kinase.
  • The term “aberrant activity” refers to activity deviating from normal activity, that is, abnormal activity. The term “increased activity” refers to activity higher than normal activity.
  • The terms “composition” and “formulation” are used interchangeably.
  • A “subject” to which administration is contemplated refers to a human (i.e., male or female of any age group, e.g., pediatric subject (e.g., infant, child, or adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) or non-human animal. In certain embodiments, the non-human animal is a mammal (e.g., primate (e.g., cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g., cattle, pig, horse, sheep, goat, cat, or dog), or bird (e.g., commercially relevant bird, such as chicken, duck, goose, or turkey)). In certain embodiments, the non-human animal is a fish, reptile, or amphibian. The non-human animal may be a male or female at any stage of development. The non-human animal may be a transgenic animal or genetically engineered animal. A “patient” refers to a human subject in need of treatment of a disease.
  • The term “biological sample” refers to any sample including tissue samples (such as tissue sections and needle biopsies of a tissue); cell samples (e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection); samples of whole organisms (such as samples of yeasts or bacteria); or cell fractions, fragments or organelles (such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise). Other examples of biological samples include blood, serum, urine, semen, fecal matter, cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from another biological sample.
  • The terms “administer,” “administering,” or “administration” refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing a compound described herein, or a composition thereof, into, in, or on a subject.
  • The terms “treatment,” “treat,” and “treating” refer to reversing, alleviating, delaying the onset of or inhibiting the progress of a disease described herein. In some embodiments, treatment may be administered after one or more signs or symptoms of the disease have developed or have been observed. In other embodiments, treatment may be administered in the absence of signs or symptoms of the disease. For example, treatment may be administered to a susceptible subject prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of exposure to a pathogen). Treatment may also be continued after symptoms have resolved, for example, to delay or prevent recurrence.
  • The terms “condition,” “disease,” and “disorder” are used interchangeably.
  • An “effective amount” of a compound described herein refers to an amount sufficient to elicit the desired biological response, i.e., treating the condition. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound described herein may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject. In certain embodiments, an effective amount is a therapeutically effective amount. In certain embodiments, an effective amount is a prophylactic treatment. In certain embodiments, an effective amount is the amount of a compound described herein in a single dose. In certain embodiments, an effective amount is the combined amounts of a compound described herein in multiple doses.
  • A “therapeutically effective amount” of a compound described herein is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the condition. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms, signs, or causes of the condition, and/or enhances the therapeutic efficacy of another therapeutic agent.
  • A “prophylactically effective amount” of a compound described herein is an amount sufficient to prevent a condition, or one or more symptoms associated with the condition or prevent its recurrence. A prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the condition. The term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.
  • A “proliferative disease” refers to a disease that occurs due to abnormal growth or extension by the multiplication of cells (Walker, Cambridge Dictionary of Biology; Cambridge University Press: Cambridge, UK, 1990). A proliferative disease may be associated with: 1) the pathological proliferation of normally quiescent cells; 2) the pathological migration of cells from their normal location (e.g., metastasis of neoplastic cells); 3) the pathological expression of proteolytic enzymes such as the matrix metalloproteinases (e.g., collagenases, gelatinases, and elastases); or 4) the pathological angiogenesis as in proliferative retinopathy and tumor metastasis. Exemplary proliferative diseases include cancers (i.e., “malignant neoplasms”), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, and autoimmune diseases.
  • The term “angiogenesis” refers to the physiological process through which new blood vessels form from pre-existing vessels. Angiogenesis is distinct from vasculogenesis, which is the de novo formation of endothelial cells from mesoderm cell precursors. The first vessels in a developing embryo form through vasculogenesis, after which angiogenesis is responsible for most blood vessel growth during normal or abnormal development. Angiogenesis is a vital process in growth and development, as well as in wound healing and in the formation of granulation tissue. However, angiogenesis is also a fundamental step in the transition of tumors from a benign state to a malignant one, leading to the use of angiogenesis inhibitors in the treatment of cancer. Angiogenesis may be chemically stimulated by angiogenic proteins, such as growth factors (e.g., VEGF). “Pathological angiogenesis” refers to abnormal (e.g., excessive or insufficient) angiogenesis that amounts to and/or is associated with a disease.
  • The terms “neoplasm” and “tumor” are used herein interchangeably and refer to an abnormal mass of tissue wherein the growth of the mass surpasses and is not coordinated as in the growth of normal tissue. A neoplasm or tumor may be “benign” or “malignant,” depending on the following characteristics: degree of cellular differentiation (including morphology and functionality), rate of growth, local invasion, and metastasis. A “benign neoplasm” is generally well differentiated, has characteristically slower growth than a malignant neoplasm, and remains localized to the site of origin. In addition, a benign neoplasm does not have the capacity to infiltrate, invade, or metastasize to distant sites. Exemplary benign neoplasms include, but are not limited to, lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheic keratoses, lentigos, and sebaceous hyperplasias. In some cases, certain “benign” tumors may later give rise to malignant neoplasms, which may result from additional genetic changes in a subpopulation of the tumor's neoplastic cells, and these tumors are referred to as “pre-malignant neoplasms.” An exemplary pre-malignant neoplasm is a teratoma. In contrast, a “malignant neoplasm” is generally poorly differentiated (anaplasia) and has characteristically rapid growth accompanied by progressive infiltration, invasion, and destruction of the surrounding tissue. Furthermore, a malignant neoplasm generally has the capacity to metastasize to distant sites. The term “metastasis,” “metastatic,” or “metastasize” refers to the spread or migration of cancerous cells from a primary or original tumor to another organ or tissue and is typically identifiable by the presence of a “secondary tumor” or “secondary cell mass” of the tissue type of the primary or original tumor and not of that of the organ or tissue in which the secondary (metastatic) tumor is located. For example, a prostate cancer that has migrated to bone is said to be metastasized prostate cancer and includes cancerous prostate cancer cells growing in bone tissue.
  • The term “cancer” refers to a class of diseases characterized by the development of abnormal cells that proliferate uncontrollably and have the ability to infiltrate and destroy normal body tissues. See, e.g., Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia, 1990. Exemplary cancers include, but are not limited to, hematological malignancies. Additional exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer, anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast, triple negative breast cancer (TNBC)); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma; chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma); connective tissue cancer; epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi's sarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett's adenocarcinoma); Ewing's sarcoma; ocular cancer (e.g., intraocular melanoma, retinoblastoma); familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g., stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germ cell cancer; head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)); heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease; hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastic tumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreatic neuroendocrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of the penis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplastic syndromes; intraepithelial neoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g., appendix cancer); soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestine cancer; sweat gland carcinoma; synovioma; testicular cancer (e.g., seminoma, testicular embryonal carcinoma); thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).
  • The term “hematological malignancy” refers to tumors that affect blood, bone marrow, and/or lymph nodes. Exemplary hematological malignancies include, but are not limited to, leukemia, such as acute lymphoblastic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphoma, such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL, such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B-cell lymphoma (DLBCL, e.g., activated B-cell (ABC) DLBCL (ABC-DLBCL))), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphoma (e.g., mucosa-associated lymphoid tissue (MALT) lymphoma, nodal marginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt's lymphoma, Waldenström's macroglobulinemia (WM, lymphoplasmacytic lymphoma), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, central nervous system (CNS) lymphoma (e.g., primary CNS lymphoma and secondary CNS lymphoma); and T-cell NHL, such as precursor T-lymphoblastic lymphoma/leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g., mycosis fungoides, Sezary syndrome), angioimmunoblastic T-cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathy type T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplastic large cell lymphoma); lymphoma of an immune privileged site (e.g., cerebral lymphoma, ocular lymphoma, lymphoma of the placenta, lymphoma of the fetus, testicular lymphoma); a mixture of one or more leukemia/lymphoma as described above; myelodysplasia; and multiple myeloma (MM).
  • The term “inflammatory disease” refers to a disease caused by, resulting from, or resulting in inflammation. The term “inflammatory disease” may also refer to a dysregulated inflammatory reaction that causes an exaggerated response by macrophages, granulocytes, and/or T-lymphocytes leading to abnormal tissue damage and/or cell death. An inflammatory disease can be either an acute or chronic inflammatory condition and can result from infections or non-infectious causes. Inflammatory diseases include, without limitation, atherosclerosis, arteriosclerosis, autoimmune disorders, multiple sclerosis, systemic lupus erythematosus, polymyalgia rheumatica (PMR), gouty arthritis, degenerative arthritis, tendonitis, bursitis, psoriasis, cystic fibrosis, arthrosteitis, rheumatoid arthritis, inflammatory arthritis, Sjogren's syndrome, giant cell arteritis, progressive systemic sclerosis (scleroderma), ankylosing spondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid, diabetes (e.g., Type I), myasthenia gravis, Hashimoto's thyroiditis, Graves' disease, Goodpasture's disease, mixed connective tissue disease, sclerosing cholangitis, inflammatory bowel disease, Crohn's disease, ulcerative colitis, pernicious anemia, inflammatory dermatoses, usual interstitial pneumonitis (UIP), asbestosis, silicosis, bronchiectasis, berylliosis, talcosis, pneumoconiosis, sarcoidosis, desquamative interstitial pneumonia, lymphoid interstitial pneumonia, giant cell interstitial pneumonia, cellular interstitial pneumonia, extrinsic allergic alveolitis, Wegener's granulomatosis and related forms of angiitis (temporal arteritis and polyarteritis nodosa), inflammatory dermatoses, hepatitis, delayed-type hypersensitivity reactions (e.g., poison ivy dermatitis), pneumonia, respiratory tract inflammation, Adult Respiratory Distress Syndrome (ARDS), encephalitis, immediate hypersensitivity reactions, asthma, hay fever, allergies, acute anaphylaxis, rheumatic fever, glomerulonephritis, pyelonephritis, cellulitis, cystitis, chronic cholecystitis, ischemia (ischemic injury), reperfusion injury, allograft rejection, host-versus-graft rejection, appendicitis, arteritis, blepharitis, bronchiolitis, bronchitis, cervicitis, cholangitis, chorioamnionitis, conjunctivitis, dacryoadenitis, dermatomyositis, endocarditis, endometritis, enteritis, enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis, gingivitis, ileitis, iritis, laryngitis, myelitis, myocarditis, nephritis, omphalitis, oophoritis, orchitis, osteitis, otitis, pancreatitis, parotitis, pericarditis, pharyngitis, pleuritis, phlebitis, pneumonitis, proctitis, prostatitis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis, testitis, tonsillitis, urethritis, urocystitis, uveitis, vaginitis, vasculitis, vulvitis, vulvovaginitis, angitis, chronic bronchitis, osteomyelitis, optic neuritis, temporal arteritis, transverse myelitis, necrotizing fasciitis, and necrotizing enterocolitis.
  • An “autoimmune disease” refers to a disease arising from an inappropriate immune response of the body of a subject against substances and tissues normally present in the body. In other words, the immune system mistakes some part of the body as a pathogen and attacks its own cells. This may be restricted to certain organs (e.g., in autoimmune thyroiditis) or involve a particular tissue in different places (e.g., Goodpasture's disease which may affect the basement membrane in both the lung and kidney). The treatment of autoimmune diseases is typically with immunosuppression, e.g., medications which decrease the immune response. Exemplary autoimmune diseases include, but are not limited to, glomerulonephritis, Goodpasture's syndrome, necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemic lupus erythematosis, rheumatoid arthritis, psoriatic arthritis, systemic lupus erythematosis, psoriasis, ulcerative colitis, systemic sclerosis, dermatomyositis/polymyositis, anti-phospholipid antibody syndrome, scleroderma, pemphigus vulgaris, ANCA-associated vasculitis (e.g., Wegener's granulomatosis, microscopic polyangiitis), uveitis, Sjogren's syndrome, Crohn's disease, Reiter's syndrome, ankylosing spondylitis, Lyme disease, Guillain-Barré syndrome, Hashimoto's thyroiditis, and cardiomyopathy.
  • The term “kinase” is a class of enzyme that transfers a phosphate group from a high energy donor molecules, such as ATP, to a specific substrate, referred to as phosphorylation. Kinases are part of the larger family of phosphotransferases. One of the largest groups of kinases are protein kinases, which act on and modify the activity of specific proteins. Kinases are used extensively to transmit signals and control complex processes in cells. Various other kinases act on small molecules such as lipids, carbohydrates, amino acids, and nucleotides, either for signaling or to prime them for metabolic pathways. Kinases are often named after their substrates. More than 500 different protein kinases have been identified in humans. Exemplary human protein kinases include, but are not limited to, AAK1, ABL, ACK, ACTR2, ACTR2B, AKT1, AKT2, AKT3, ALK, ALK1, ALK2, ALK4, ALK7, AMPKa1, AMPKa2, ANKRD3, ANPa, ANPb, ARAF, ARAFps, ARG, AurA, AurAps1, AurAps2, AurB, AurBps1, AurC, AXL, BARK1, BARK2, BIKE, BLK, BMPR1A, BMPR1Aps1, BMPR1Aps2, BMPR1B, BMPR2, BMX, BRAF, BRAFps, BRK, BRSK1, BRSK2, BTK, BUB1, BUBR1, CaMK1a, CaMK1b, CaMK1d, CaMK1g, CaMK2a, CaMK2b, CaMK2d, CaMK2g, CaMK4, CaMKK1, CaMKK2, caMLCK, CASK, CCK4, CCRK, CDC2, CDC7, CDK10, CDK11, CDK2, CDK3, CDK4, CDK4ps, CDK5, CDK5ps, CDK6, CDK7, CDK7ps, CDK8, CDK8ps, CDK9, CDKL1, CDKL2, CDKL3, CDKL4, CDKL5, CGDps, CHED, CHK1, CHK2, CHK2ps1, CHK2ps2, CK1a, CK1a2, CK1aps1, CK1aps2, CK1aps3, CK1d, CK1e, CK1g1, CK1g2, CK1g2ps, CK1g3, CK2a1, CK2a1-rs, CK2a2, CLIK1, CLIK1L, CLK1, CLK2, CLK2ps, CLK3, CLK3ps, CLK4, COT, CRIK, CRK7, CSK, CTK, CYGD, CYGF, DAPK1, DAPK2, DAPK3, DCAMKL1, DCAMKL2, DCAMKL3, DDR1, DDR2, DLK, DMPK1, DMPK2, DRAK1, DRAK2, DYRK1A, DYRK1B, DYRK2, DYRK3, DYRK4, EGFR, EphA1, EphA10, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphB1, EphB2, EphB3, EphB4, EphB6, Erk1, Erk2, Erk3, Erk3ps1, Erk3ps2, Erk3ps3, Erk3ps4, Erk4, Erk5, Erk7, FAK, FER, FERps, FES, FGFR1, FGFR2, FGFR3, FGFR4, FGR, FLT1, FLT1ps, FLT3, FLT4, FMS, FRK, Fused, FYN, GAK, GCK, GCN2, GCN22, GPRK4, GPRK5, GPRK6, GPRK6ps, GPRK7, GSK3A, GSK3B, Haspin, HCK, HER2/ErbB2, HER3/ErbB3, HER4/ErbB4, HH498, HIPK1, HIPK2, HIPK3, HIPK4, HPK1, HRI, HRIps, HSER, HUNK, ICK, IGF1R, IKKa, IKKb, IKKe, ILK, INSR, IRAK1, IRAK2, IRAK3, IRAK4, IRE1, IRE2, IRR, ITK, JAK1, JAK2, JAK3, JNK1, JNK2, JNK3, KDR, KHS1, KHS2, KIS, KIT, KSGCps, KSR1, KSR2, LATS1, LATS2, LCK, LIMK1, LIMK2, LIMK2ps, LKB1, LMR1, LMR2, LMR3, LOK, LRRK1, LRRK2, LTK, LYN, LZK, MAK, MAP2K1, MAP2K1ps, MAP2K2, MAP2K2ps, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K8, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPKAPKps1, MARK1, MARK2, MARK3, MARK4, MARKps01, MARKps02, MARKps03, MARKps04, MARKps05, MARKps07, MARKps08, MARKps09, MARKps10, MARKps11, MARKps12, MARKps13, MARKps15, MARKps16, MARKps17, MARKps18, MARKps19, MARKps20, MARKps21, MARKps22, MARKps23, MARKps24, MARKps25, MARKps26, MARKps27, MARKps28, MARKps29, MARKps30, MAST1, MAST2, MAST3, MAST4, MASTL, MELK, MER, MET, MISR2, MLK1, MLK2, MLK3, MLK4, MLKL, MNK1, MNK1ps, MNK2, MOK, MOS, MPSK1, MPSK1ps, MRCKa, MRCKb, MRCKps, MSK1, MSK12, MSK2, MSK22, MSSK1, MST1, MST2, MST3, MST3ps, MST4, MUSK, MYO3A, MYO3B, MYT1, NDR1, NDR2, NEK1, NEK10, NEK11, NEK2, NEK2ps1, NEK2ps2, NEK2ps3, NEK3, NEK4, NEK4ps, NEK5, NEK6, NEK7, NEK8, NEK9, NIK, NIM1, NLK, NRBP1, NRBP2, NuaK1, NuaK2, Obscn, Obscn2, OSR1, p38a, p38b, p38d, p38g, p70S6K, p70S6Kb, p70S6Kps1, p70S6Kps2, PAK1, PAK2, PAK2ps, PAK3, PAK4, PAK5, PAK6, PASK, PBK, PCTAIRE1, PCTAIRE2, PCTAIRE3, PDGFRa, PDGFRb, PDK1, PEK, PFTAIRE1, PFTAIRE2, PHKg1, PHKg1ps1, PHKg1ps2, PHKg1ps3, PHKg2, PIK3R4, PIM1, PIM2, PIM3, PINK1, PITSLRE, PKACa, PKACb, PKACg, PKCa, PKCb, PKCd, PKCe, PKCg, PKCh, PKCi, PKCips, PKCt, PKCz, PKD1, PKD2, PKD3, PKG1, PKG2, PKN1, PKN2, PKN3, PKR, PLK1, PLK1ps1, PLK1ps2, PLK2, PLK3, PLK4, PRKX, PRKXps, PRKY, PRP4, PRP4ps, PRPK, PSKH1, PSKH1ps, PSKH2, PYK2, QIK, QSK, RAF1, RAF1ps, RET, RHOK, RIPK1, RIPK2, RIPK3, RNAseL, ROCK1, ROCK2, RON, ROR1, ROR2, ROS, RSK1, RSK12, RSK2, RSK22, RSK3, RSK32, RSK4, RSK42, RSKL1, RSKL2, RYK, RYKps, SAKps, SBK, SCYL1, SCYL2, SCYL2ps, SCYL3, SGK, SgK050ps, SgK069, SgK071, SgK085, SgK110, SgK196, SGK2, SgK223, SgK269, SgK288, SGK3, SgK307, SgK384ps, SgK396, SgK424, SgK493, SgK494, SgK495, SgK496, SIK (e.g., SIK1, SIK2), skMLCK, SLK, Slob, smMLCK, SNRK, SPEG, SPEG2, SRC, SRM, SRPK1, SRPK2, SRPK2ps, SSTK, STK33, STK33ps, STLK3, STLK5, STLK6, STLK6ps1, STLK6-rs, SuRTK106, SYK, TAK1, TAO1, TAO2, TAO3, TBCK, TBK1, TEC, TESK1, TESK2, TGFbR1, TGFbR2, TIE1, TIE2, TLK1, TLK1ps, TLK2, TLK2ps1, TLK2ps2, TNK1, Trad, Trb1, Trb2, Trb3, Trio, TRKA, TRKB, TRKC, TSSK1, TSSK2, TSSK3, TSSK4, TSSKps1, TSSKps2, TTBK1, TTBK2, TTK, TTN, TXK, TYK2, TYK22, TYRO3, TYRO3ps, ULK1, ULK2, ULK3, ULK4, VACAMKL, VRK1, VRK2, VRK3, VRK3ps, Wee1, Wee1B, Wee1Bps, Wee1ps1, Wee1ps2, Wnk1, Wnk2, Wnk3, Wnk4, YANK1, YANK2, YANK3, YES, YESps, YSK1, ZAK, ZAP70, ZC1/HGK, ZC2/TNIK, ZC3/MINK, and ZC4/NRK.
  • The term “SRC family kinase” refers to a family of non-receptor tyrosine protein kinases that includes nine members: SRCA subfamily that includes c-SRC (proto-oncogene tyrosine-protein kinase SRC), YES (proto-oncogene tyrosine-protein kinase Yes), FYN (proto-oncogene tyrosine-protein kinase FYN), and FGR (Gardner-Rasheed feline sarcoma viral (v-FGR) oncogene homolog); SRCB subfamily that includes LCK (lymphocyte-specific protein tyrosine kinase), HCK (tyrosine-protein kinase HCK, hemopoietic cell kinase), BLK (tyrosine-protein kinase BLK), and LYN (tyrosine-protein kinase LYN); and FRK (Fyn-related kinase).
  • The term “CDK” refers to a cyclin-dependent kinase. A CDK binds a cyclin (e.g., Cyclin H), which is a regulatory protein. CDKs phosphorylate their substrates at serines and threonines. The consensus sequence for the phosphorylation site in the amino acid sequence of a CDK substrate is [S/T*]PX[K/R], where S/T* is the phosphorylated serine or threonine, P is proline, X is any amino acid, K is lysine, and R is arginine. CDKs include CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19. and CDK20.
  • CDK7, cyclin-dependent kinase 7, is a CDK, wherein the substrate is Cyclin H, MAT1 (e.g., MNAT1), or Cyclin H and MAT1. CDK7 is alternatively referred to as CAK1, HCAK, MO15, STK1, CDKN7, and p39MO15. Non-limiting examples of the nucleotide and protein sequences for human CDK7 are described in GenBank Accession Number: NP_001790, incorporated herein by reference. The amino acid sequence of this CDK7 is as follows:
  • (SEQ ID NO: 1)
    MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSE
    AKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVEDFMETDLEV
    IIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGV
    LKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVG
    CILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFK
    SFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPG
    PTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF
  • CDK12, cyclin-dependent kinase 12, is a CDK, wherein the substrate is Cyclin K or flavopiridol. CDK12 is alternatively referred to as Cdc2-related kinase, CDC2-related protein kinase 7, Cell division cycle 2-related protein kinase 7, Cell division protein kinase 12, CRK7, CRKR, CRKRS, cyclin-dependent kinase 12, or KIAA0904. Non-limiting examples of the nucleotide and protein sequences for human CDK12 are described in Uniprot Number: Q9NYV4, which is incorporated herein by reference. The amino acid sequence of this CDK12 is as follows:
  • (SEQ ID NO 2)
    MPNSERHGGKKDGSGGASGTLQPSSGGGSSNSRERHRLVSKHKRHKSKHS
    KDMGLVTPEAASLGTVIKPLVEYDDISSDSDTFSDDMAFKLDRRENDERR
    GSDRSDRLHKHRHHQHRRSRDLLKAKQTEKEKSQEVSSKSGSMKDRISGS
    SKRSNEETDDYGKAQVAKSSSKESRSSKLHKEKTRKERELKSGHKDRSKS
    HRKRETPKSYKTVDSPKRRSRSPHRKWSDSSKQDDSPSGASYGQDYDLSP
    SRSHTSSNYDSYKKSPGSTSRRQSVSPPYKEPSAYQSSTRSPSPYSKRQR
    SVSPYSRRRSSSYERSGSYSGRSPSPYGRRRSSSPFLSKRSLSRSPLPSR
    KSMKSRSRSPAYSRHSSSHSKKKRSSSRSRHSSISPVRLPLNSSLGAELS
    RKKKERAAAAAAAKMDGKESKGSPVFLPRKENSSVEAKDSGLESKKLPRS
    VKLEKSAPDTELVNVTHLNTEVKNSSDTGKVKLDENSEKHLVKDLKAQGT
    RDSKPIALKEEIVTPKETETSEKETPPPLPTIASPPPPLPTTTPPPQTPP
    LPPLPPIPALPQQPPLPPSQPAFSQVPASSTSTLPPSTHSKTSAVSSQAN
    SQPPVQVSVKTQVSVTAAIPHLKTSTLPPLPLPPLLPGDDDMDSPKETLP
    SKPVKKEKEQRTRHLLTDLPLPPELPGGDLSPPDSPEPKAITPPQQPYKK
    RPKICCPRYGERRQTESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTG
    ELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDAL
    DFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYC
    HKKNFLHRDIKCSNILLNNSGQIKLADEGLARLYNSEESRPYTNKVITLW
    YRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISR
    LCGSPCPAVWPDVIKLPYFNTMKPKKQTRRRLREEFSFIPSAALDLLDHM
    LTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQ
    RQSGVVVEEPPPSKTSPKETTSGTSTEPVKNSSPAPPQPAPGKVESGAGD
    AIGLADITQQLNQSELAVLLNLLQSQTDLSIPQMAQLLNIHSNPEMQQQL
    EALNQSISALTEATSQQQDSETMAPEESLKEAPSAPVILPSAEQTTLEAS
    STPADMQNILAVLLSQLMKTQEPAGSLEENNSDKNSGPQGPRRTPTMPQE
    EAAACPPHILPPEKRPPEPPGPPPPPPPPPLVEGDLSSAPQELNPAVTAA
    LLQLLSQPEAEPPGHLPHEHQALRPMEYSTRPRPNRTYGNTDGPETGESA
    IDTDERNSGPALTESLVQTLVKNRTFSGSLSHLGESSSYQGTGSVQFPGD
    QDLRFARVPLALHPVVGQPFLKAEGSSNSVVHAETKLQNYGELGPGTTGA
    SSSGAGLHWGGPTQSSAYGKLYRGPTRVPPRGGRGRGVPY
  • CDK13, cyclin-dependent kinase 13, is a CDK, wherein the relevant cyclin is cyclin K and a reference inhibitor is the pan-CDK inhibitor flavopiridol and the c-terminal domain (CTD) of RNA-polymerase II is a physiological substrate. CDK13 is alternatively referred to as CHED; CDC2L; CDC2L5; or hCDK13. Non-limiting examples of the nucleotide and protein sequences for human CDK12 are described in GenBank Accession Number M80629, which is incorporated herein by reference. The amino acid sequence of this CDK13 is as follows:
  • (SEQ ID NO: 3)
    MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQ
    PPPPPPPLLFLAAPGTAAAAAAAAAASSSCFSPGPPLEVKRLARGKRRAG
    GRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVS
    SQSEQGLLLGGASAATAATAAGGTGGSGGSPASSSGTQRRGEGSERRPRR
    DRRSSSGRSKERHREHRRRDGQRGGSEASKSRSRESHSGEERAEVAKSGS
    SSSSGGRRKSASATSSSSSSRKDRDSKAHRSRTKSSKEPPSAYKEPPKAY
    REDKTEPKAYRRRRSLSPLGGRDDSPVSHRASQSLRSRKSPSPAGGGSSP
    YSRRLPRSPSPYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPYS
    PVLRRSGKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSLA
    AELNKNKKARAAEAARAAEAAKAAEATKAAEAAAKAAKASNTSTPTKGNT
    ETSASASQTNHVKDVKKIKIEHAPSPSSGGTLKNDKAKTKPPLQVTKVEN
    NLIVDKATKYAVIVGKESKSAATKEESVSLKEKTKPLTPSIGAKEKEQHV
    ALVTSTLPPLPLPPMLPEDKEADSLRGNISVKAVKKEVEKKLRCLLADLP
    LPPELPGGDDLSKSPEEKKTATQLHSKRRPKICGPPYGETKEKDIDWGKR
    CVDKFDISGIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAI
    REIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDLMG
    LLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQ
    IKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSC
    GCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTM
    KPKKQYRRKLREEFVFIPAAALDLFDYMLALDPSKRCTAEQALQCEFLRD
    VEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDVSTIKAPRKDLSLG
    LDDSRTNTPQGVLPSSQLKSQGSSNVAPVKTGPGQHLNHSELAILLNLLQ
    SKTSVNMADFVQVLNIKVNSETQQQLNKINLPAGILATGEKQTDPSTPQQ
    ESSKPLGGIQPSSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKD
    VLLEERENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMRILELTPEPD
    RPRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKA
    ALLQLLAQHQPQDDPKREGGIDYQAGDTYVSTSDYKDNFGSSSFSSAPYV
    SNDGLGSSSAPPLERRSFIGNSDIQSLDNYSTASSHSGGPPQPSAFSESF
    PSSVAGYGDIYLNAGPMLFSGDKDHRFEYSHGPIAVLANSSDPSTGPEST
    HPLPAKMHNYNYGGNLQENPSGPSLMHGQTWTSPAQGPGYSQGYRGHIST
    STGRGRGRGLPY
    • DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION
  • Cyclin dependent kinases (CDKs) are key regulators of the cell cycle. Their successive activation and inactivation drives the cycle forward. The activity of CDKs is regulated by multiple mechanisms such as positive and negative phosphorylation, binding of regulatory proteins like cyclins, and CDK inhibitors. CDK7 plays a critical role in the regulation of RNA polymerase II-mediated transcription of protein-encoding genes. Disruption of CDK7, CDK12, and/or CDK13 signaling causes defects in transcription. However, a complete understanding of how these disruptions affect global transcription is lacking. Furthermore, the absence of selective inhibitors of CDK7, CDK12, and CDK13 has hindered investigation of the transcriptional and functional consequences of acute and long-term inhibition of these kinases under normal and pathological conditions. The present invention provides selective CDK7, CDK12, and/or CDK13 inhibitors, which covalently modify a cysteine residue located outside of the canonical kinase domain (i.e., Cys312 of CDK7, Cys1039 of CDK12, and Cys1017 of CDK13). Selective covalent inhibitors of these kinases may be useful in the treatment of various proliferative diseases including cancer.
  • The present invention provides compounds, which inhibit the activity of a kinase, for the prevention and/or treatment of a subject with a proliferative disease. In certain embodiments, the inventive compounds inhibit the activity of a cyclin-dependent kinase (CDK). In certain embodiments, the inventive compounds inhibit the activity of a cyclin-dependent kinase 7 (CDK7). In certain embodiments, the inventive compounds inhibit the activity of a cyclin-dependent kinase 12 (CDK12). In certain embodiments, the inventive compounds inhibit the activity of a cyclin-dependent kinase 13 (CDK13). The present invention also provides methods of using the compounds described herein, e.g., as biological probes to study the inhibition of the activity of a kinase (e.g., CDK (e.g. CDK7, CDK12, and/or CDK13)), and as therapeutics, e.g., in the prevention and/or treatment of diseases associated with the overexpression and/or aberrant activity of a kinase (e.g., CDK (e.g. CDK7, CDK12, and/or CDK13)). In certain embodiments, the diseases are proliferative diseases. The proliferative diseases that may be treated and/or prevented include, but are not limited to, cancers (e.g., breast cancer, leukemia, melanoma, multiple myeloma), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases. Also provided by the present disclosure are pharmaceutical compositions, kits, methods, and uses including a compound of Formulae (I′), (II′), (I), and (II) as described herein.
    • Compounds
  • Aspects of the present disclosure relate to the compounds described herein. The compounds described herein may be useful in treating and/or preventing proliferative diseases in a subject, inhibiting the activity of a protein kinase (e.g., CDK) in a subject or biological sample, and inducing apoptosis of a cell. In certain embodiments, a compound described herein is a compound of any one of Formulae (I′), (II′), (I), (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof. In certain embodiments, a compound described herein is a compound of Formula (I′), or a pharmaceutically acceptable salt thereof. In certain embodiments, a compound described herein is a compound of Formula (I), or a pharmaceutically acceptable salt thereof. In certain embodiments, a compound described herein is a compound of Formula (II′), or a pharmaceutically acceptable salt thereof. In certain embodiments, a compound described herein is a compound of Formula (II), or a pharmaceutically acceptable salt thereof.
  • In certain embodiments, a compound described herein is of Formula (I′):
  • Figure US20200172499A9-20200604-C00010
  • or a pharmaceutically acceptable salt thereof, wherein:
  • R1 is hydrogen, halogen, or optionally substituted alkyl;
  • M is O, S, or NRM;
  • RM is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring C is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted monocyclic or bicyclic aryl, or optionally substituted monocyclic or bicyclic heteroaryl;
  • each instance of RA, RB, and RC is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —ORa, —N(Ra)2, —SRa, —CN, —SCN, —NO2, —N3, or optionally substituted acyl;
  • each instance of Ra is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Ra are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1, b1, and c1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L1 is —CH2—, lc—S(═O)2—lb, —O—, —S—, —NRL1—, —C(═O)—, lc—NRL1C(═O)—lb, lc—C(═O)NRL1—lb, lc—OC(═O)—lb, or lc—C(═O)O—lb; wherein lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C;
  • L2 is —O—, —S—, —NRL2—, lb—NRL2C(═O)—lm, lb—C(═O)NRL2—lm; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is xm—CH2CH2—xa, xm—CH═CH—xa, xm—CH2—NRLXxa, xm—CH2—O—CH2—xa, xm—CH2—NRLX—CH2—xa, —O—, —S—, —NRLX—, xm—O—CH2—xa, xm—S—CH2—xa, xm—S—C(═O)CH2—xa, or xm—NRLX—CH2—xa; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of RL1, RL2, and RLX is independently hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
  • R2 is any of Formulae (i-1)-(i-41):
  • Figure US20200172499A9-20200604-C00011
    Figure US20200172499A9-20200604-C00012
    Figure US20200172499A9-20200604-C00013
    Figure US20200172499A9-20200604-C00014
    Figure US20200172499A9-20200604-C00015
  • wherein:
      • L3 is a bond or an optionally substituted C14 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C═O—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(═S)NRL3a—, trans-CRL3b═CRL3b—, cis-CRL3b═CRL3b—, —C═C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NRL3a—, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a—, or —NRL3aS(═O)2—, wherein RL3a is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group, and wherein each occurrence of RL3b is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
      • L4 is a bond or an optionally substituted, branched or unbranched C1-6 hydrocarbon chain;
      • each of RE1, RE2, and RE3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, and —SREE, wherein each occurrence of REE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two REE groups are joined to form an optionally substituted heterocyclic ring;
      • or RE1 and RE3, or RE2 and RE3, or RE1 and RE2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
      • RE4 is a leaving group;
      • RE5 is halogen;
      • RE6 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
      • each instance of Y is independently O, S, or NRE7, wherein RE7 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
      • a is 1 or 2; and
      • each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
  • In certain embodiments, a compound described herein is of Formula (I):
  • Figure US20200172499A9-20200604-C00016
  • or a pharmaceutically acceptable salt thereof, wherein:
  • R1 is hydrogen, halogen, or optionally substituted alkyl;
  • M is O, S, or NRM;
  • RM is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring C is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • each instance of RA, RB, and RC is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —ORa, —N(Ra)2, —SRa, —CN, —SCN, —NO2, —N3, or optionally substituted acyl;
  • each instance of Ra is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Ra are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1, b1, and c1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L1 is —O—, —S—, —NRL1—, —C(═O)—, lc—NRL1C(═O)—lb, lc—C(═O)NRL1—lb, lc—OC(═O)—lb, or lc—C(═O)O—lb; wherein lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C;
  • L2 is —O—, —S—, —NRL2—, lb—NRL2C(═O)—lm, lb—C(═O)NRL2—lm; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is —O—, —S—, —NRLX—, xm—O—CH2—xa, xm—S—CH2—xa, or xm—NRLX—CH2—xa; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of RL1, RL2, and RLX is independently hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
  • R2 is any of Formulae (i-1)-(i-46):
  • Figure US20200172499A9-20200604-C00017
    Figure US20200172499A9-20200604-C00018
    Figure US20200172499A9-20200604-C00019
    Figure US20200172499A9-20200604-C00020
    Figure US20200172499A9-20200604-C00021
  • L3 is a bond or an optionally substituted C1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C═O—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(═S)NRL3a—, trans-CRL3b═CRL3b—, cis-CRL3b═CRL3b, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NRL3a—, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a, or —NRL3aS(═O)2—, wherein RL3a is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group, and wherein each occurrence of RL3b is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
  • L4 is a bond or an optionally substituted, branched or unbranched C1 hydrocarbon chain;
  • each of RE1, RE2, and RE3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, and —SREE, wherein each occurrence of REE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two REE groups are joined to form an optionally substituted heterocyclic ring; or RE1 and RE3, or RE2 and RE3, or RE1 and RE2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
  • RE4 is a leaving group;
  • RE5 is halogen;
  • RE6 is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group;
  • each instance of Y is independently O, S, or NRE7, wherein RE7 is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group;
  • a is 1 or 2; and
  • each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
  • In certain embodiments, a compound described herein is of Formula (II′):
  • Figure US20200172499A9-20200604-C00022
  • R1 is hydrogen, halogen, or optionally substituted alkyl;
  • M is O, S, or NRM;
  • RM is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • each instance of RA and RB is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —ORa, —N(Ra)2, —SRa, —CN, —SCN, —C(═NRa)Ra, —C(═NRa)ORa, —C(═NRa)N(Ra)2, —C(═O)Ra, —C(═O)ORa, —C(═O)N(Ra)2, —NO2, —NRaC(═O)Ra, —NRaC(═O)ORa, —NRaC(═O)N(Ra)2, —OC(═O)Ra, —OC(═O)ORa, or —OC(═O)N(Ra)2;
  • each instance of Ra is independently hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Ra are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1 and b1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L2 is —O—, —S—, —NRL2—, lb—NRL2C(═O)—lm, lb—C(═O)NRL2—lm; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is a bond, —O—, —S—, —NRLX—, xm—O—CH2—xa, xm—S—CH2—xa, or xm—NRLX—CH2—xa; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of RL2 and RLX is independently hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
  • R2 is any of Formulae (i-1)-(i-41):
  • Figure US20200172499A9-20200604-C00023
    Figure US20200172499A9-20200604-C00024
    Figure US20200172499A9-20200604-C00025
    Figure US20200172499A9-20200604-C00026
    Figure US20200172499A9-20200604-C00027
  • wherein:
      • L3 is a bond or an optionally substituted C1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C═O—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(═S)NRL3a—, trans-CRL3b═CRL3b—, cis-CRL3bCRL3b—, —C═C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NRL3a, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a—, or —NRL3aS(═O)2—, wherein RL3a is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group, and wherein each occurrence of RL3b is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
      • L4 is a bond or an optionally substituted, branched or unbranched C1-6 hydrocarbon chain;
      • each of RE1, RE2, and RE3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, and —SREE, wherein each occurrence of REE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two REE groups are joined to form an optionally substituted heterocyclic ring;
      • or RE1 and RE3, or RE2 and RE3, or RE1 and RE2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
      • RE4 is a leaving group;
      • RE5 is halogen;
      • RE6 is hydrogen, optionally substituted C14 alkyl, or a nitrogen protecting group; each instance of Y is independently O, S, or NRE7, wherein RE7 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
      • a is 1 or 2; and
      • each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
  • In certain embodiments, a compound described herein is of Formula (I):
  • Figure US20200172499A9-20200604-C00028
  • or a pharmaceutically acceptable salt thereof, wherein:
  • R1 is hydrogen, halogen, or optionally substituted alkyl;
  • M is O, S, or NRM;
  • RM is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
  • Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
  • each instance of RA and RB is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —ORa, —N(Ra)2, —SRa, —CN, —SCN, —C(═NRa)Ra, —C(═NRa)ORa, —C(═NRa)N(Ra)2, —C(═O)Ra, —C(═O)ORa, —C(═O)N(Ra)2, —NO2, —NRaC(═O)Ra, —NRaC(═O)ORa, —NRaC(═O)N(Ra)2, —OC(═O)Ra, —OC(═O)ORa, or —OC(═O)N(Ra)2;
  • each instance of Ra is independently hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Ra are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
  • each of a1 and b1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
  • L2 is —O—, —S—, —NRL2—, lb—NRL2C(═O)—lm, lb—C(═O)NRL2—lm; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
  • X is —O—, —S—, —NRLX—, xm—O—CH2—xa, xm—S—CH2—xa, or xm—NRLX—CH2—xa; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
  • each of RL2 and RLX is independently hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
  • R2 is any of Formulae (i-1)-(i-46):
  • Figure US20200172499A9-20200604-C00029
    Figure US20200172499A9-20200604-C00030
    Figure US20200172499A9-20200604-C00031
    Figure US20200172499A9-20200604-C00032
    Figure US20200172499A9-20200604-C00033
  • wherein:
  • L3 is a bond or an optionally substituted C1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C═O—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(═S)NRL3a, trans-CRL3b═CRL3b—, cis-CRL3b═CRL3b—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NRL3a—, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a—, or —NRL3aS(═O)2—, wherein RL3a is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group, and wherein each occurrence of RL3b is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
  • L4 is a bond or an optionally substituted, branched or unbranched C1-6 hydrocarbon chain;
  • each of RE1, RE2, and RE3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, and —SREE, wherein each occurrence of REE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two REE groups are joined to form an optionally substituted heterocyclic ring;
  • or RE1 and RE3, or RE2 and RE3, or RE1 and RE2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
  • RE4 is a leaving group;
  • RE5 is halogen;
  • RE6 is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group;
  • each instance of Y is independently O, S, or NRE7, wherein RE7 is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group;
  • a is 1 or 2; and
  • each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
  • As generally defined herein in Formulae (I′), (II′), (I), and (II), R1 is hydrogen, halogen, or optionally substituted alkyl. As generally defined herein in Formulae (I)-(II), R1 is hydrogen, halogen, or optionally substituted alkyl. In certain embodiments, R1 is hydrogen. In certain embodiments, R1 is halogen. In certain embodiments, R1 is F. In certain embodiments, R1 is Cl. In certain embodiments, R1 is Br. In certain embodiments, R1 is I. In certain embodiments, R1 is optionally substituted alkyl. In certain embodiments, R1 is unsubstituted alkyl. In certain embodiments, R1 is unsubstituted C1-6 alkyl. In certain embodiments, R1 is methyl. In certain embodiments, R1 is substituted alkyl. In certain embodiments, R1 is substituted C1-6alkyl.
  • In certain embodiments, M is O. In certain embodiments, M is S. In certain embodiments, M is NRM, wherein RM is as defined herein. In certain embodiments, M is NH. In certain embodiments, M is NRM, wherein RM is optionally substituted alkyl. In certain embodiments, M is NRM, wherein RM is unsubstituted alkyl. In certain embodiments, M is NCH3. In certain embodiments, M is NAc.
  • Compounds of any one of Formulae (I′), (II′), (I), and (II) include Ring A attached to linker X. Compounds of any one of Formulae (I)-(II) include Ring A attached to linker X. Ring A may be optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl. In certain embodiments, Ring A is optionally substituted monocyclic carbocyclyl. In certain embodiments, Ring A is optionally substituted cyclohexyl. In certain embodiments, Ring A is optionally substituted monocyclic heterocyclyl. In certain embodiments, Ring A is optionally substituted piperidinyl. In certain embodiments, Ring A is optionally substituted piperizinyl. In certain embodiments, Ring A is optionally substituted tetrahydropyranyl. In certain embodiments, Ring A is optionally substituted phenyl. In certain embodiments, Ring A is phenyl substituted with only X. In certain embodiments, Ring A is optionally substituted monocyclic heteroaryl. In certain embodiments, Ring A is optionally substituted 5-membered heteroaryl. In certain embodiments, Ring A is optionally substituted 6-membered heteroaryl. In certain embodiments, Ring A is optionally substituted pyridine. In certain embodiments, Ring A is optionally substituted pyrimidine.
  • In certain embodiments, Ring A is of Formula (x-i):
  • Figure US20200172499A9-20200604-C00034
  • wherein:
  • each of V10, V11, V12, V13, and V14 is independently O, S, N, NRA1, C, or CRA2, as valency permits;
  • each instance of RA1 is independently selected from the group consisting of hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and a nitrogen protecting group;
  • each instance of RA2 is independently selected from the group consisting of hydrogen, halogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —CN, —ORA2a, —N(RA2a)2, and —SRA2a; and
  • each occurrence of RA2a is independently selected from the group consisting of hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom, or two RA2a groups are joined to form a substituted or unsubstituted heterocyclic ring.
  • In certain embodiments, only one of V10, V11, V12, V13, and V14 is selected from the group consisting of O, S, N, and NRA1. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00035
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00036
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00037
  • In certain embodiments, only two of V10, V11, V12, V13, and V14 are each independently selected from the group consisting of O, S, N, and NRA1. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00038
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00039
  • In certain embodiments, Ring A is of Formula (x-ii):
  • Figure US20200172499A9-20200604-C00040
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00041
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00042
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00043
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00044
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00045
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00046
  • In certain embodiments, only three of V10, V11, V12, V13, and V14 are each independently selected from the group consisting of O, S, N, and NRA1. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00047
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00048
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00049
  • In certain embodiments, only four of V10, V11, V12, V13, and V14 are each independently selected from the group consisting of N and NRA1. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00050
  • In certain embodiments, Ring A may also be a substituted or unsubstituted 6-membered heteroaryl ring. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00051
  • wherein each of V10, V11, V12, V13, V14, and V15 is independently N, C, or CRA2, as valency permits, wherein RA2 is as defined herein. In certain embodiments, only one of V10, V11, V12, V13, V14, and V15 is N. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00052
  • wherein k is 0, 1, 2, 3, or 4, and RA2 is as defined herein. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00053
  • In certain embodiments, only two of V10, V11, V12, V13, V14, and V15 are N. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00054
  • In certain embodiments, only three of V10, V11, V12, V13, V14, and V15 are N. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00055
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00056
  • wherein RA and a1 are as defined herein.
  • In certain embodiments, a1 is 1; and Ring A is one of the formulae:
  • Figure US20200172499A9-20200604-C00057
  • In certain embodiments, a1 is 2; and Ring A is one of the formulae:
  • Figure US20200172499A9-20200604-C00058
  • In certain embodiments, a2 is 3; and R61 is one of the formulae:
  • Figure US20200172499A9-20200604-C00059
  • In certain embodiments, a2 is 4; and R61 is one of the formulae:
  • Figure US20200172499A9-20200604-C00060
  • In certain embodiments, a2 is 5; and R61 is of the formula
  • Figure US20200172499A9-20200604-C00061
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00062
  • wherein RA and a1 are as defined herein.
  • In certain embodiments, a1 is 1; and Ring A is one of the formulae:
  • Figure US20200172499A9-20200604-C00063
  • In certain embodiments, a1 is 2; and Ring A is one of the formulae:
  • Figure US20200172499A9-20200604-C00064
  • In certain embodiments, a2 is 3; and R61 is one of the formulae:
  • Figure US20200172499A9-20200604-C00065
  • In certain embodiments, a2 is 4; and R61 is one of the formulae:
  • Figure US20200172499A9-20200604-C00066
  • In certain embodiments, a2 is 5; and R61 is of the formula
  • Figure US20200172499A9-20200604-C00067
  • In certain embodiments, Ring A is optionally substituted monocyclic heterocyclyl. In certain embodiments, Ring A is optionally substituted 5-membered heterocyclyl. In certain embodiments, Ring A is optionally substituted 6-membered heterocyclyl. In certain embodiments, Ring A is optionally substituted 6-membered heterocyclyl with one heteroatom selected from the group of S, O, and N.
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00068
  • wherein HA is S, O, or NRHA; RHA is hydrogen, optionally substituted alkyl, or a nitrogen protecting group; and RA and a1 are as defined herein.
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00069
  • wherein HA, RA and a1 are as defined herein.
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00070
  • wherein HA, RA and a1 are as defined herein.
  • In certain embodiments, HA is S. In certain embodiments, HA is O. In certain embodiments, HA is NRHA.
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00071
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00072
  • wherein RHA is hydrogen, optionally substituted alkyl, or a nitrogen protecting group; and RA and a1 are as defined herein. In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00073
  • In certain embodiments, RA is hydrogen. In certain embodiments, RA is halogen. In certain embodiments, RA is F. In certain embodiments, RA is Cl. In certain embodiments, RA is Br. In certain embodiments, RA is I. In certain embodiments, RA is optionally substituted alkyl. In certain embodiments, RA is unsubstituted alkyl. In certain embodiments, RA is methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, t-pentyl, neo-pentyl, i-pentyl, s-pentyl, or 3-pentyl. In certain embodiments, RA is t-butyl. In certain embodiments, RA is substituted alkyl. In certain embodiments, RA is haloalkyl. In certain embodiments, RA is —CF3, —CHF2, or —CH2F. In certain embodiments, RA is optionally substituted alkenyl. In certain embodiments, RA is optionally substituted alkynyl. In certain embodiments, RA is optionally carbocyclyl. In certain embodiments, RA is optionally substituted heterocyclyl. In certain embodiments, RA is optionally substituted aryl. In certain embodiments, RA is optionally substituted heteroaryl. In certain embodiments, RA is —ORa, wherein Ra is as defined herein. In certain embodiments, RA is —OH. In certain embodiments, RA is —ORa, wherein Ra is optionally substituted alkyl or an oxygen protecting group. In certain embodiments, RA is —ORa, wherein Ra is unsubstituted alkyl. In certain embodiments, RA is —OCH3. In certain embodiments, RA is —N(Ra)2, wherein Ra is as defined herein. In certain embodiments, RA is —NH2. In certain embodiments, RA is —N(Ra)2, wherein each instance of Ra is optionally substituted alkyl or a nitrogen protecting group. In certain embodiments, RA is —N(CH3)2. In certain embodiments, RA is —NHRa, wherein Ra is optionally substituted alkyl or a nitrogen protecting group. In certain embodiments, RA is —NHCH3.
  • In certain embodiments, at least one instance of RA1 is H (hydrogen). In certain embodiments, at least one instance of RA1 is halogen. In certain embodiments, at least one instance of RA1 is F (fluorine). In certain embodiments, at least one instance of RA1 is Cl (chlorine). In certain embodiments, at least one instance of RA1 is Br (bromine). In certain embodiments, at least one instance of RA1 is I (iodine). In certain embodiments, at least one instance of RA1 is substituted acyl. In certain embodiments, at least one instance of RA1 is unsubstituted acyl. In certain embodiments, at least one instance of RA1 is acetyl. In certain embodiments, at least one instance of RA1 is substituted acetyl. In certain embodiments, at least one instance of RA1 is substituted alkyl. In certain embodiments, at least one instance of RA1 is unsubstituted alkyl. In certain embodiments, at least one instance of RA1 is C1-6 alkyl. In certain embodiments, at least one instance of RA1 is methyl. In certain embodiments, at least one instance of RA1 is ethyl. In certain embodiments, at least one instance of RA1 is propyl. In certain embodiments, at least one instance of RA1 is butyl. In certain embodiments, at least one instance of RA1 is substituted alkenyl. In certain embodiments, at least one instance of RA1 is unsubstituted alkenyl. In certain embodiments, at least one instance of RA1 is vinyl. In certain embodiments, at least one instance of RA1 is substituted alkynyl. In certain embodiments, at least one instance of RA1 is unsubstituted alkynyl. In certain embodiments, at least one instance of RA1 is ethynyl. In certain embodiments, at least one instance of RA1 is substituted carbocyclyl. In certain embodiments, at least one instance of RA1 is unsubstituted carbocyclyl. In certain embodiments, at least one instance of RA1 is substituted heterocyclyl. In certain embodiments, at least one instance of RA1 is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RA1 is substituted aryl. In certain embodiments, at least one instance of RA1 is unsubstituted aryl. In certain embodiments, at least one instance of RA1 is substituted phenyl. In certain embodiments, at least one instance of RA1 is unsubstituted phenyl. In certain embodiments, at least one instance of RA1 is substituted heteroaryl. In certain embodiments, at least one instance of RA1 is unsubstituted heteroaryl. In certain embodiments, at least one instance of RA1 is substituted pyridyl. In certain embodiments, at least one instance of RA1 is unsubstituted pyridyl. In certain embodiments, at least one instance of RA1 is a nitrogen protecting group. In certain embodiments, at least one instance of RA1 is BOC.
  • In certain embodiments, at least one RA1 is hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group. In certain embodiments, all instances of RA1 are each independently hydrogen, substituted or unsubstituted C1-6 alkyl, or a nitrogen protecting group. In certain embodiments, all instances of RA1 are hydrogen.
  • In certain embodiments, at least one RA2 is H. In certain embodiments, at least one RA2 is halogen. In certain embodiments, at least one RA2 is F. In certain embodiments, at least one RA2 is Cl. In certain embodiments, at least one RA2 is Br. In certain embodiments, at least one RA2 is I (iodine). In certain embodiments, at least one RA2 is substituted acyl. In certain embodiments, at least one RA2 is unsubstituted acyl. In certain embodiments, at least one RA2 is acetyl. In certain embodiments, at least one RA2 is substituted acetyl. In certain embodiments, at least one RA2 is substituted alkyl. In certain embodiments, at least one RA2 is unsubstituted alkyl. In certain embodiments, at least one RA2 is C1-6 alkyl. In certain embodiments, at least one RA2 is methyl. In certain embodiments, at least one RA2 is ethyl. In certain embodiments, at least one RA2 is propyl. In certain embodiments, at least one RA2 is butyl. In certain embodiments, at least one RA2 is substituted alkenyl. In certain embodiments, at least one RA2 is unsubstituted alkenyl. In certain embodiments, at least one RA2 is vinyl. In certain embodiments, at least one RA2 is substituted alkynyl. In certain embodiments, at least one RA2 is unsubstituted alkynyl. In certain embodiments, at least one RA2 is ethynyl. In certain embodiments, at least one RA2 is substituted carbocyclyl. In certain embodiments, at least one RA2 is unsubstituted carbocyclyl. In certain embodiments, at least one RA2 is substituted heterocyclyl. In certain embodiments, at least one RA2 is unsubstituted heterocyclyl. In certain embodiments, at least one RA2 is substituted aryl. In certain embodiments, at least one RA2 is unsubstituted aryl. In certain embodiments, at least one RA2 is substituted phenyl. In certain embodiments, at least one RA2 is unsubstituted phenyl. In certain embodiments, at least one RA2 is substituted heteroaryl. In certain embodiments, at least one RA2 is unsubstituted heteroaryl. In certain embodiments, at least one RA2 is substituted pyridyl. In certain embodiments, at least one RA2 is unsubstituted pyridyl. In certain embodiments, at least one RA2 is —ORA2, wherein RA2a is as defined herein. In certain embodiments, at least one RA2 is —ORA2a, wherein RA2a is hydrogen. In certain embodiments, at least one RA2 is —ORA2a, wherein RA2a is substituted or unsubstituted C1-6 alkyl. In certain embodiments, at least one RA2 is —ORA2a, wherein RA2a is unsubstituted C1-6 alkyl. In certain embodiments, at least one RA2 is —OCH3. In certain embodiments, at least one RA2 is —N(RA2a)2. In certain embodiments, at least one RA2 is —SRA2a. In certain embodiments, all instances of RA2 are hydrogen.
  • In certain embodiments, all RA1 and RA2 are hydrogen. In certain embodiments, RA1 is hydrogen; and at least one RA2 is substituted or unsubstituted alkyl. In certain embodiments, RA1 is hydrogen; and at least one RA2 is unsubstituted alkyl. In certain embodiments, RA1 is hydrogen; and at least one RA2 is methyl, ethyl, or n-propyl. In certain embodiments, RA1 is hydrogen; and at least one RA2 is —ORA2a, wherein RA2a is as defined herein. In certain embodiments, RA1 is hydrogen; and at least one RA2 is —ORA2a, wherein RA2a is substituted or unsubstituted C1-6 alkyl. In certain embodiments, RA1 is hydrogen; and at least one RA2 is —ORA2a, wherein RA2a is unsubstituted C1-6 alkyl. In certain embodiments, RA1 is hydrogen; and at least one RA2 is —OCH3.
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00074
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00075
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00076
  • In certain embodiments, Ring A is of one of the formula:
  • Figure US20200172499A9-20200604-C00077
  • In certain embodiments, Ring A is of the formula:
  • Figure US20200172499A9-20200604-C00078
  • Compounds of any one of Formulae (I′), (II′), (I), and (II) include Ring B between linker L1 and linker L2. Compounds of any one of Formulae (I)-(II) include Ring B between linker L1 and linker L2. Ring B may be optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl. In certain embodiments, Ring B is optionally substituted monocyclic carbocyclyl. In certain embodiments, Ring B is optionally substituted monocyclic heterocyclyl. In certain embodiments, Ring B is optionally substituted pyrrolidinyl. In certain embodiments, Ring B is optionally substituted phenyl. In certain embodiments, Ring B is optionally substituted monocyclic heteroaryl. In certain embodiments, Ring B is phenyl substituted with only L1 and L2. In certain embodiments, Ring B is optionally substituted cyclohexyl. In certain embodiments, Ring B is optionally substituted piperidinyl. In certain embodiments, Ring B is optionally substituted piperizinyl. In certain embodiments, Ring B is optionally substituted pyridinyl. In certain embodiments, Ring B is optionally substituted pyrimidinyl.
  • In certain embodiments of Formulae (I′), (II′), (I), and (II), Ring B is
  • Figure US20200172499A9-20200604-C00079
  • wherein each ring atom is optionally substituted. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00080
  • wherein each ring atom is optionally substituted. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00081
  • wherein each ring atom is optionally substituted. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00082
  • wherein each ring atom is optionally substituted, and L1 and L2 may attach to Ring B at either indicated position. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00083
  • wherein each ring atom is optionally substituted, and L2 and R2 may attach to Ring B at either indicated position. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00084
  • wherein each ring atom is optionally substituted, and L2 and R2 is attached to Ring B at either position indicated. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00085
  • wherein each ring atom is optionally substituted, and L1 and L2 may attach to Ring B at either indicated position. In certain embodiments, Ring B is
  • Figure US20200172499A9-20200604-C00086
  • wherein each ring atom is optionally substituted, and L1 and L2 may attach to Ring B at either indicated position.
  • Compounds of Formula (I′) and (I) include Ring C between linker L1 and R2. Ring C may be optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl. In certain embodiments, Ring C is optionally substituted monocyclic carbocyclyl. In certain embodiments, Ring C is optionally substituted monocyclic heterocyclyl. In certain embodiments, Ring C is optionally substituted monocyclic aryl. In certain embodiments, Ring C is optionally substituted phenyl. In certain embodiments, Ring C is optionally substituted bicyclic aryl. In certain embodiments, Ring C is optionally substituted 2,3-dihydro-1H-indene. In certain embodiments, Ring C is optionally substituted naphthalene. In certain embodiments, Ring C is:
  • Figure US20200172499A9-20200604-C00087
  • In certain embodiments, Ring C is:
  • Figure US20200172499A9-20200604-C00088
  • In certain embodiments, Ring C is optionally substituted monocyclic heteroaryl. In certain embodiments, Ring C is phenyl substituted with only L1 and R2. In certain embodiments, Ring C is optionally substituted cyclohexyl. In certain embodiments, Ring C is optionally substituted pyridinone. In certain embodiments, Ring C is:
  • Figure US20200172499A9-20200604-C00089
  • In certain embodiments, Ring C is:
  • Figure US20200172499A9-20200604-C00090
  • In certain embodiments, Ring C is optionally substituted piperidinyl. In certain embodiments, Ring C is optionally substituted piperizinyl. In certain embodiments, Ring C is optionally substituted pyridinyl. In certain embodiments, Ring C is optionally substituted pyrimidinyl. In certain embodiments, Ring C is optionally substituted bicyclic heteroaryl. In certain embodiments, Ring C is optionally substituted indolyl. In certain embodiments, Ring C is optionally substituted indolinyl. In certain embodiments, Ring C is:
  • Figure US20200172499A9-20200604-C00091
  • In certain embodiments, Ring C is:
  • Figure US20200172499A9-20200604-C00092
  • In certain embodiments, for Formula (I′), L1 is —CH2—. In certain embodiments, for Formula (I′), L1 is lc—S(═O)2—lb. In certain embodiments, L1 is —O—. In certain embodiments, L1 is —S—. In certain embodiments, L1 is —NRL1—. In certain embodiments, L1 is —C(═O)—. In certain embodiments, L1 is —NRL1—. In certain embodiments, L1 is lc—OC(═O)—lb. In certain embodiments, L1 is lc—C(═O)O—lb. In certain embodiments, L1 is lc—NRL1C(═O)—lb. In certain embodiments, L1 is lc—C(O)NRL1—lb. As used herein, lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C.
  • In certain embodiments, RL1 is hydrogen. In certain embodiments, RL1 is optionally substituted C1-6 alkyl. In certain embodiments, RL1 is unsubstituted C1-6 alkyl. In certain embodiments, RL1 is methyl. In certain embodiments, RL1 is substituted C1-6 alkyl. In certain embodiments, RL1 is a nitrogen protecting group.
  • In certain embodiments, L2 is —O—. In certain embodiments, L2 is —S—. In certain embodiments, L2 is —NRL2—. In certain embodiments, L2 is lb—NRL2C(═O)—lm. In certain embodiments, L2 is lb—C(═O)NRL2—lm. As used herein, lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M.
  • In certain embodiments, RL2 is hydrogen. In certain embodiments, RL2 is optionally substituted C1-6 alkyl. In certain embodiments, RL2 is unsubstituted C1-6 alkyl. In certain embodiments, RL2 is methyl. In certain embodiments, RL2 is substituted C1-6 alkyl. In certain embodiments, RL2 is a nitrogen protecting group.
  • In certain embodiments, for Formula (II′), X is a bond. In certain embodiments, for Formula (I′), X is xm—CH2CH2—xa. In certain embodiments, for Formula (I′), X is xm—CH═CH—xa. In certain embodiments, for Formula (I′), X is xm—CH2—NRLX—xa. In certain embodiments, for Formula (I′), X is xm—CH2—NH—xa. In certain embodiments, for Formula (I′), X is xm—CH2—O—CH2—xa. In certain embodiments, for Formula (I′), X is xa—CH2—NH—CH2—xa. In certain embodiments, X is —O—. In certain embodiments, X is —S—. In certain embodiments, X is xm—S—C(═O)CH2—xa. In certain embodiments, X is —NRLX—. In certain embodiments, X is —O—CH2—. In certain embodiments, X is —S—CH2—. In certain embodiments, X is —NRLX—CH2—. In certain embodiments, X is —NH—CH2—.
  • In certain embodiments, a1 is 1. In certain embodiments, a1 is 2. In certain embodiments, a1 is 3.
  • In certain embodiments, b1 is 1. In certain embodiments, b1 is 2. In certain embodiments, b1 is 3.
  • In certain embodiments, c1 is 1. In certain embodiments, c1 is 2. In certain embodiments, c1 is 3.
  • In certain embodiments, RB is optionally substituted alkyl. In certain embodiments, RB is optionally substituted C1-C6 alkyl. In certain embodiments, RB is unsubstituted C1-C6 alkyl. In certain embodiments, RB is methyl or ethyl. In certain embodiments, RB is substituted C1-C6 alkyl. In certain embodiments, RB is hydroxy C1-C6 alkyl. In certain embodiments, RB is —CH2OH. In certain embodiments, RB is —CH2CH2OH. In certain embodiments, RB is —N(Ra)2, wherein Ra is as defined herein. In certain embodiments, RB is —NHRa, wherein Ra is as defined herein. In certain embodiments, RB is —NHRa, wherein Ra is hydrogen or optionally substituted C1-C6 alkyl. In certain embodiments, RB is —NH2. In certain embodiments, RB is —NHRa, wherein Ra is optionally substituted C1-C6 alkyl. In certain embodiments, RB is —NHRa, wherein Ra is unsubstituted C1-C6 alkyl. In certain embodiments, RB is —NHRa, wherein Ra is methyl or ethyl. In certain embodiments, RB is —NHCH3. In certain embodiments, RB is —NHRa, wherein Ra is a nitrogen protecting group. In certain embodiments, RB is —N(CH3)Ra, wherein Ra is optionally substituted C1-C6 alkyl. In certain embodiments, RB is —N(CH3)Ra, wherein Ra is unsubstituted C1-C6 alkyl. In certain embodiments, RB is —N(CH3)Ra, wherein Ra is methyl or ethyl. In certain embodiments, RB is —N(CH3)2. In certain embodiments, RB is —N(CH3)Ra, wherein Ra is a nitrogen protecting group.
  • In certain embodiments, RC is optionally substituted alkyl. In certain embodiments, RC is optionally substituted C1-C6 alkyl. In certain embodiments, RC is unsubstituted C1-C6 alkyl. In certain embodiments, RC is methyl or ethyl. In certain embodiments, RC is substituted C1-C6 alkyl. In certain embodiments, RC is hydroxy C1-C6 alkyl. In certain embodiments, RC is —CH2OH. In certain embodiments, RC is —CH2CH2OH. In certain embodiments, RC is —N(Ra)2, wherein Ra is as defined herein. In certain embodiments, RC is —NHRa, wherein Ra is as defined herein. In certain embodiments, RC is —NHRa, wherein Ra is hydrogen or optionally substituted C1-C6 alkyl. In certain embodiments, RC is —NH2. In certain embodiments, RC is —NHRa, wherein Ra is optionally substituted C1-C6 alkyl. In certain embodiments, RC is —NHRa, wherein Ra is unsubstituted C1-C6 alkyl. In certain embodiments, RC is —NHRa, wherein Ra is methyl or ethyl. In certain embodiments, RC is —NHCH3. In certain embodiments, RC is —NHRa, wherein Ra is a nitrogen protecting group. In certain embodiments, RC is —N(CH3)Ra, wherein Ra is optionally substituted C1-C6 alkyl. In certain embodiments, RC is —N(CH3)Ra, wherein Ra is unsubstituted C1-C6 alkyl. In certain embodiments, RC is —N(CH3)Ra, wherein Ra is methyl or ethyl. In certain embodiments, RC is —N(CH3)2. In certain embodiments, RC is —N(CH3)Ra, wherein Ra is a nitrogen protecting group.
  • Compounds of Formula (I′) include R2 attached to Ring C. Compounds of Formula (I) include R2 attached to Ring C. Compounds of Formula (I) include R2 attached to Ring B. Compounds of Formula (I′) include R2 attached to Ring B. In certain embodiments, R2 comprises an electrophilic moiety. In certain embodiments, R2 comprises a Michael acceptor moiety. The electrophilic moiety (e.g., Michael acceptor moiety) may react with a cysteine residue of a kinase (e.g., CDK (e.g., CDK7)) to allow for covalent attachment of the compound to the kinase. In certain embodiments, the electrophilic moiety (e.g., Michael acceptor moiety) may react with a cysteine residue of a kinase (e.g., CDK (e.g., CDK7)). In certain embodiments, the electrophilic moiety (e.g., Michael acceptor moiety) may react with the Cys312 residue of CDK7. In certain embodiments, the covalent attachment is irreversible. In certain embodiments, the covalent attachment is reversible.
  • As generally defined herein in Formulae (I′), (II′), (I), and (II), R2 may be any one of Formulae (i-1)-(i-41). In certain embodiments, R2 is of Formula (i-1):
  • Figure US20200172499A9-20200604-C00093
  • In certain embodiments, R2 is of Formula (i-2):
  • Figure US20200172499A9-20200604-C00094
  • In certain embodiments, R2 is of Formula (i-3):
  • Figure US20200172499A9-20200604-C00095
  • In certain embodiments, R2 is of Formula (i-4):
  • Figure US20200172499A9-20200604-C00096
  • In certain embodiments, R2 is of Formula (i-5):
  • Figure US20200172499A9-20200604-C00097
  • In certain embodiments, R2 is of Formula (i-6):
  • Figure US20200172499A9-20200604-C00098
  • In certain embodiments, R2 is of Formula (i-7):
  • Figure US20200172499A9-20200604-C00099
  • In certain embodiments, R2 is of Formula (i-8):
  • Figure US20200172499A9-20200604-C00100
  • In certain embodiments, R2 is of Formula (i-9):
  • Figure US20200172499A9-20200604-C00101
  • In certain embodiments, R2 is of Formula (i-10):
  • Figure US20200172499A9-20200604-C00102
  • In certain embodiments, R2 is of Formula (i-11):
  • Figure US20200172499A9-20200604-C00103
  • In certain embodiments, R2 is of Formula (i-12):
  • Figure US20200172499A9-20200604-C00104
  • In certain embodiments, R2 is of Formula (i-13):
  • Figure US20200172499A9-20200604-C00105
  • In certain embodiments, R2 is of Formula (i-14):
  • Figure US20200172499A9-20200604-C00106
  • In certain embodiments, R2 is of Formula (i-15):
  • Figure US20200172499A9-20200604-C00107
  • In certain embodiments, R2 is of Formula (i-16):
  • Figure US20200172499A9-20200604-C00108
  • In certain embodiments, R2 is of Formula (i-17):
  • Figure US20200172499A9-20200604-C00109
  • In certain embodiments, R2 is of Formula (i-18):
  • Figure US20200172499A9-20200604-C00110
  • In certain embodiments, R2 is of Formula (i-19):
  • Figure US20200172499A9-20200604-C00111
  • In certain embodiments, R2 is of Formula (i-20):
  • Figure US20200172499A9-20200604-C00112
  • In certain embodiments, R2 is of Formula (i-21):
  • Figure US20200172499A9-20200604-C00113
  • In certain embodiments, R2 is of Formula (i-22):
  • Figure US20200172499A9-20200604-C00114
  • In certain embodiments, R2 is of Formula (i-23):
  • Figure US20200172499A9-20200604-C00115
  • In certain embodiments, R2 is of Formula (i-24):
  • Figure US20200172499A9-20200604-C00116
  • In certain embodiments, R2 is of Formula (i-25):
  • Figure US20200172499A9-20200604-C00117
  • In certain embodiments, R2 is of Formula (i-26):
  • Figure US20200172499A9-20200604-C00118
  • In certain embodiments, R2 is of Formula (i-27):
  • Figure US20200172499A9-20200604-C00119
  • In certain embodiments, R2 is of Formula (i-28):
  • Figure US20200172499A9-20200604-C00120
  • In certain embodiments, R2 is of Formula (i-29):
  • Figure US20200172499A9-20200604-C00121
  • In certain embodiments, R2 is of Formula (i-30):
  • Figure US20200172499A9-20200604-C00122
  • In certain embodiments, R2 is of Formula (i-31):
  • Figure US20200172499A9-20200604-C00123
  • In certain embodiments, R2 is of Formula (i-32):
  • Figure US20200172499A9-20200604-C00124
  • In certain embodiments, R2 is of Formula (i-33):
  • Figure US20200172499A9-20200604-C00125
  • In certain embodiments, R2 is of Formula (i-34):
  • Figure US20200172499A9-20200604-C00126
  • In certain embodiments, R2 is of Formula (i-35):
  • Figure US20200172499A9-20200604-C00127
  • In certain embodiments, R2 is of Formula (i-36):
  • Figure US20200172499A9-20200604-C00128
  • In certain embodiments, R2 is of Formula (i-37):
  • Figure US20200172499A9-20200604-C00129
  • In certain embodiments, R2 is of Formula (i-38):
  • Figure US20200172499A9-20200604-C00130
  • In certain embodiments, R2 is of Formula (i-39)
  • Figure US20200172499A9-20200604-C00131
  • In certain embodiments, R2 is of Formula (i-40):
  • Figure US20200172499A9-20200604-C00132
  • In certain embodiments, R2 is of Formula (i-41):
  • Figure US20200172499A9-20200604-C00133
  • In certain embodiments, R2 is of Formula (i-1a):
  • Figure US20200172499A9-20200604-C00134
  • In certain embodiments, R2 is of Formula (i-1b):
  • Figure US20200172499A9-20200604-C00135
  • In certain embodiments, R2 is of Formula (i-1c):
  • Figure US20200172499A9-20200604-C00136
  • In certain embodiments, R2 is of Formula (i-1d):
  • Figure US20200172499A9-20200604-C00137
  • In certain embodiments, R2 is of Formula (i-1e):
  • Figure US20200172499A9-20200604-C00138
  • In certain embodiments, R2 is of Formula (i-1f):
  • Figure US20200172499A9-20200604-C00139
  • In certain embodiments, R2 is of Formula (i-1g)
  • Figure US20200172499A9-20200604-C00140
  • In certain embodiments, R2 is
  • Figure US20200172499A9-20200604-C00141
  • In certain embodiments, R2 is
  • Figure US20200172499A9-20200604-C00142
  • In certain embodiments, R2 is
  • Figure US20200172499A9-20200604-C00143
  • In certain embodiments, R2 is of Formula (i-1h):
  • Figure US20200172499A9-20200604-C00144
  • In certain embodiments, R2 is
  • Figure US20200172499A9-20200604-C00145
  • In certain embodiments, R2 is of Formula (i-1a):
  • Figure US20200172499A9-20200604-C00146
  • In certain embodiments, R2 is of Formula (i-1b):
  • Figure US20200172499A9-20200604-C00147
  • In certain embodiments, R2 is of Formula (i-1c):
  • Figure US20200172499A9-20200604-C00148
  • In certain embodiments, R2 is of Formula (i-18a):
  • Figure US20200172499A9-20200604-C00149
  • In certain embodiments, R2 is of Formula (i-18b):
  • Figure US20200172499A9-20200604-C00150
  • In certain embodiments, R2 is of Formula (i-18c):
  • Figure US20200172499A9-20200604-C00151
  • In certain embodiments, R2 is of Formula (i-15a):
  • Figure US20200172499A9-20200604-C00152
  • In certain embodiments, R2 is of Formula (i-15b):
  • Figure US20200172499A9-20200604-C00153
  • In certain embodiments, R2 is of Formula (i-15c):
  • Figure US20200172499A9-20200604-C00154
  • R2 may contain linker L3 or L4. In certain embodiments, L3 is a bond. L3 is an optionally substituted C1-4 hydrocarbon chain. In certain embodiments, L3 is an optionally substituted C1-4 hydrocarbon chain, wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C(═O)—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(—S)NRL3a—, trans-CRL3b═CRL3b—, cis-CRL3b═CRL3b—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NRL3a—, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a—, or —NRL3aS(═O)2—. In certain embodiments, L3 is an optionally substituted C1-4 hydrocarbon chain, wherein one carbon unit of the hydrocarbon chain is replaced with —NRL3a— (e.g., —NH—). In certain embodiments, L3 is of the formula: —(CH2)1-4—NRL3a— (e.g., —(CH2)1-4—NH—) or —NRL3a—CH2)1-4—(e.g., —NH—CH2)1-4—). In certain embodiments, L3 is —NRL3a. In certain embodiments, L3 is —NRL3a(C═O)—. In certain embodiments, L3 is —(C═O)NRL3a—. In certain embodiments, L3 is —NH—. In certain embodiments, L3 is —(C═O)—. In certain embodiments, L3 is —NH(C═O)—. In certain embodiments, L3 is —(C═O)NH—. In certain embodiments, L3 is —O—. In certain embodiments, L3 is —S—. In certain embodiments, L4 is a bond. In certain embodiments, L4 is an optionally substituted C1-4 hydrocarbon chain.
  • Linker L3 may contain groups RL3a or RL3b. In certain embodiments, RL3a is hydrogen. In certain embodiments, at least one instance of RL3b is hydrogen. In certain embodiments, each instance of RL3b is hydrogen. In certain embodiments, at least one instance of RL3b is —Cl, —Br, or —I. In certain embodiments, each instance of RL3b is —Cl, —Br, or —I. In certain embodiments, at least one instance of RL3b is —F. In certain embodiments, each instance of RL3b is —F. In certain embodiments, at least one instance of RL3b is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl. In certain embodiments, two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring.
  • R2 may contain groups RE1, RE2, and/or RE3. In certain embodiments, RE1 is hydrogen. In certain embodiments, RE2 is hydrogen. In certain embodiments, RE3 is hydrogen. In certain embodiments, RE1 is —Cl, —Br, or —I. In certain embodiments, RE2 is —Cl, —Br, or —I. In certain embodiments, RE3 is —Cl, —Br, or —I. In certain embodiments, RE1 is —F. In certain embodiments, RE2 is —F. In certain embodiments, RE3 is —F. In certain embodiments, RE1 is optionally substituted alkyl (e.g., substituted or unsubstituted C1-6 alkyl). In certain embodiments, RE2 is optionally substituted alkyl (e.g., substituted or unsubstituted C1-6 alkyl). In certain embodiments, RE3 is optionally substituted alkyl (e.g., substituted or unsubstituted C1-6 alkyl). In certain embodiments, RE1 is optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, or —SREE. In certain embodiments, RE2 is optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, or —SREE. In certain embodiments, RE3 is optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, or —SREE. In certain embodiments, RE1 is —N(REE)2. In certain embodiments, RE2 is —N(REE)2. In certain embodiments, RE3 is —N(REE)2. In certain embodiments, RE1 is —N(CH3)2. In certain embodiments, RE2 is —N(CH3)2. In certain embodiments, RE3 is —N(CH3)2. In certain embodiments, RE1 is —CH2N(REE)2. In certain embodiments, RE2 is —CH2N(REE)2. In certain embodiments, RE3 is —CH2N(REE)2. In certain embodiments, RE1 is —CH2N(CH3)2. In certain embodiments, RE2 is —CH2N(CH3)2. In certain embodiments, RE3 is —CH2N(CH3)2. In certain embodiments, RE1 is —CN. In certain embodiments, RE2 is —CN. In certain embodiments, RE3 is —CN.
  • In certain embodiments, RE1 and RE3 are joined to form an optionally substituted carbocyclic ring. In certain embodiments, RE1 and RE3 are joined to form an optionally substituted heterocyclic ring. In certain embodiments, RE2 and RE3 are joined to form an optionally substituted carbocyclic ring. In certain embodiments, RE2 and RE3 are joined to form an optionally substituted heterocyclic ring. In certain embodiments, RE1 and RE2 are joined to form an optionally substituted carbocyclic ring. In certain embodiments, RE1 and RE2 are joined to form an optionally substituted heterocyclic ring.
  • R2 may contain group RE4, where RE4 is a leaving group. In certain embodiments, RE4 is —Cl, —Br, or —I. In certain embodiments, RE4 is —F. In certain embodiments, RE4 is —OS(═O)RE4a or —OS(═O)2RE4a, wherein RE4a is substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In certain embodiments, RE4 is —ORE4a. In certain embodiments, RE4 is —OMs, —OTf —OTs, —OBs, or 2-nitrobenzenesulfonyloxy. In certain embodiments, RE4 is —ORE4a. In certain embodiments, RE4 is —OMe, —OCF3, or —OPh. In certain embodiments, RE4 is —OC(═O)RE4a. In certain embodiments, RE4 is —OC(═O)Me, —OC(═O)CF3, —OC(═O)Ph, or —OC(═O)Cl. In certain embodiments, RE4 is —OC(O)ORE4a. In certain embodiments, RE4 is —OC(═O)OMe or —OC(═O)O(t-Bu).
  • R2 may contain group RE5, where RE5 is a halogen. In certain embodiments, RE5 is —Cl, —Br, or —I. In certain embodiments, RE5 is —F.
  • R2 may contain group RE6. In certain embodiments, RE6 is hydrogen. In certain embodiments, RE6 is substituted or unsubstituted C1-C6 alkyl. In certain embodiments, RE6 is a nitrogen protecting group.
  • In certain embodiments, a is 1. In certain embodiments, a is 2.
  • In certain embodiments, z is 0. In certain embodiments, z is 1. In certain embodiments, z is 2. In certain embodiments, z is 3, 4, 5, or 6.
  • R2 may contain group Y. In certain embodiments, Y is O. In certain embodiments, Y is S. In certain embodiments, Y is NRE7. In certain embodiments, Y is NH. In certain embodiments, a compound of Formula (I′) is of Formula (I).
  • In certain embodiments, the compound of Formula (I) is the formula:
  • Figure US20200172499A9-20200604-C00155
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, the compound of Formula (I) is the formula:
  • Figure US20200172499A9-20200604-C00156
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, the compound of Formula (I) is the formula:
  • Figure US20200172499A9-20200604-C00157
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-i):
  • Figure US20200172499A9-20200604-C00158
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, Ring C, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-ii):
  • Figure US20200172499A9-20200604-C00159
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L1, L2, X, Ring A, Ring C, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-ii-a):
  • Figure US20200172499A9-20200604-C00160
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00161
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00162
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00163
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00164
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00165
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00166
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-ii-b):
  • Figure US20200172499A9-20200604-C00167
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00168
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-ii-c):
  • Figure US20200172499A9-20200604-C00169
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00170
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-ii-A):
  • Figure US20200172499A9-20200604-C00171
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-ii):
  • Figure US20200172499A9-20200604-C00172
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof; wherein L1, L2, X, Ring A, Ring C, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-iv):
  • Figure US20200172499A9-20200604-C00173
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, Ring C, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-iv-a):
  • Figure US20200172499A9-20200604-C00174
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00175
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-iv-b):
  • Figure US20200172499A9-20200604-C00176
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00177
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-v):
  • Figure US20200172499A9-20200604-C00178
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L1, L2, X, Ring A, Ring C, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-v-a):
  • Figure US20200172499A9-20200604-C00179
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00180
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of Formula (I-v-b):
  • Figure US20200172499A9-20200604-C00181
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00182
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I′) is of Formula (I′-A):
  • Figure US20200172499A9-20200604-C00183
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I′) is of the formula:
  • Figure US20200172499A9-20200604-C00184
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I′) is of Formula (I′-i):
  • Figure US20200172499A9-20200604-C00185
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof; wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I′) is of Formula (I′-ii):
  • Figure US20200172499A9-20200604-C00186
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof; wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I′) is of Formula (I′-iii):
  • Figure US20200172499A9-20200604-C00187
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof; wherein L1, L2, X, Ring A, R1, R2, RA, RB, RC, a1, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (I′) is of the formula:
  • Figure US20200172499A9-20200604-C00188
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L1, L2, X, R1, R2, RA, RB, RC, b1, and c1 are as defined herein.
  • In certain embodiments, a compound of Formula (II′) is of Formula (II).
  • In certain embodiments, the compound of Formula (II) is the formula:
  • Figure US20200172499A9-20200604-C00189
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, the compound of Formula (II) is the formula:
  • Figure US20200172499A9-20200604-C00190
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, the compound of Formula (II) is the formula:
  • Figure US20200172499A9-20200604-C00191
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of Formula (II-i):
  • Figure US20200172499A9-20200604-C00192
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L2, X, Ring A, R1, R2, RA, RB, a1, and b1 are as defined herein.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00193
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00194
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II′) is of Formula (II′-i):
  • Figure US20200172499A9-20200604-C00195
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, wherein L2, X, Ring A, R1, R2, RA, RB, and b1 are as defined herein.
  • In certain embodiments, the compound of Formula (II′) is of the formula:
  • Figure US20200172499A9-20200604-C00196
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of Formula (II-ii):
  • Figure US20200172499A9-20200604-C00197
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof; wherein L2, X, Ring A, R1, R2, RA, RB, a1, and b1 are as defined herein.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00198
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00199
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of Formula (II-iii):
  • Figure US20200172499A9-20200604-C00200
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof wherein L2, X, Ring A, R1, R2, RA, RB, a1, and b1 are as defined herein.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00201
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00202
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (I′) is of the formula:
  • Figure US20200172499A9-20200604-C00203
    Figure US20200172499A9-20200604-C00204
    Figure US20200172499A9-20200604-C00205
    Figure US20200172499A9-20200604-C00206
    Figure US20200172499A9-20200604-C00207
    Figure US20200172499A9-20200604-C00208
    Figure US20200172499A9-20200604-C00209
    Figure US20200172499A9-20200604-C00210
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00211
    Figure US20200172499A9-20200604-C00212
    Figure US20200172499A9-20200604-C00213
    Figure US20200172499A9-20200604-C00214
    Figure US20200172499A9-20200604-C00215
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (I) is of the formula:
  • Figure US20200172499A9-20200604-C00216
    Figure US20200172499A9-20200604-C00217
    Figure US20200172499A9-20200604-C00218
    Figure US20200172499A9-20200604-C00219
    Figure US20200172499A9-20200604-C00220
    Figure US20200172499A9-20200604-C00221
    Figure US20200172499A9-20200604-C00222
    Figure US20200172499A9-20200604-C00223
    Figure US20200172499A9-20200604-C00224
    Figure US20200172499A9-20200604-C00225
    Figure US20200172499A9-20200604-C00226
    Figure US20200172499A9-20200604-C00227
    Figure US20200172499A9-20200604-C00228
    Figure US20200172499A9-20200604-C00229
    Figure US20200172499A9-20200604-C00230
    Figure US20200172499A9-20200604-C00231
    Figure US20200172499A9-20200604-C00232
    Figure US20200172499A9-20200604-C00233
    Figure US20200172499A9-20200604-C00234
    Figure US20200172499A9-20200604-C00235
    Figure US20200172499A9-20200604-C00236
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II′) is of the formula:
  • Figure US20200172499A9-20200604-C00237
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
  • In certain embodiments, a compound of Formula (II) is of the formula:
  • Figure US20200172499A9-20200604-C00238
    Figure US20200172499A9-20200604-C00239
  • or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof.
    • Pharmaceutical Compositions and Administration
  • The pharmaceutical compositions described herein may be useful in treating and/or preventing proliferative diseases (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject. The compositions described herein may also be useful for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject, biological sample, tissue, or cell. The compositions described herein may also be useful for inducing apoptosis in a cell.
  • The present disclosure provides pharmaceutical compositions comprising a compound described herein (e.g., a compound of any one of Formulae (I′), (II′), (I), (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises a compound described herein, or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient. In certain embodiments, a pharmaceutical composition described herein comprises a compound described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. In certain embodiments, the compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, is provided in an effective amount in the pharmaceutical composition.
  • In certain embodiments, the effective amount is a therapeutically effective amount (e.g., amount effective for treating a proliferative disease in a subject in need thereof). In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject in need thereof. In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a cell. In certain embodiments, the effective amount is an amount effective for inducing apoptosis in a cell. In certain embodiments, the effective amount is a prophylactically effective amount (e.g., amount effective for preventing a proliferative disease in a subject in need thereof and/or for keeping a subject in need thereof in remission of a proliferative disease).
  • In certain embodiments, the protein kinase being inhibited is a CDK. In certain embodiments, the protein kinase being inhibited is CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19, or CDK20. In certain embodiments, the protein kinase being inhibited is CDK7. In certain embodiments, the protein kinase being inhibited is CDK12. In certain embodiments, the protein kinase being inhibited is CDK13. In certain embodiments, the protein kinase being inhibited is a Src family kinase. In certain embodiments, the protein kinase being inhibited is SRC. In certain embodiments, the protein kinase being inhibited is FGR. In certain embodiments, the protein kinase being inhibited is BUB1B. In certain embodiments, the protein kinase being inhibited is CHEK2. In certain embodiments, the protein kinase being inhibited is HIPK4. In certain embodiments, the protein kinase being inhibited is PRKCQ. In certain embodiments, the protein kinase being inhibited is REET. In certain embodiments, the protein kinase being inhibited is MELK. In certain embodiments, the protein kinase being inhibited is IRAK1, IRAK4, BMX, or PI3K. In certain embodiments, the protein kinase being inhibited is ABL, ARG, BLK, CSK, EphB1, EphB2, FGR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, or TEC. In certain embodiments, the protein kinase being inhibited is ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FGR, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated, ABL1 (Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR1, EPHB1, ERBB4, p38-alpha, ABL2, ABL1(Q252H)-phosphorylated, SIK, EPHA8, MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK, EPHA2, ABL1(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q), ERBB2, ERBB3, EPHA5, ABL1(F317I)-nonphosphorylated, EGFR(L747-E749del, A750P), CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR, KIT-autoinhibited, or EGFR(E746-A750del). In certain embodiments, the protein kinase being inhibited is ABL1(F317L)-nonphosphorylated, ABL1 (H396P)-nonphosphorylated, ABL1 (H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3, FGR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR1, EPHA2, ABL1 (Q252H)-phosphorylated, MEK5, ABL1 (Q252H)-nonphosphorylated, ABL2, FYN, EPHB1, ABL1(E255K)-phosphorylated, ABL1 (F317L)-phosphorylated, EPHA1, ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5, EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V), KIT-autoinhibited, EGFR(L747-T751del,Sins), EGFR(L858R), EGFR(L747-E749del, A750P), or CSF1R.
  • In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or at least about 98%. In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by not more than 10%, not more than 20%, not more than 30%, not more than 40%, not more than 50%, not more than 60%, not more than 70%, not more than 80%, not more than 90%, not more than 95%, or not more than 98%. In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) by a range between a percentage described in this paragraph and another percentage described in this paragraph, inclusive.
  • Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include bringing the compound described herein (i.e., the “active ingredient”) into association with a carrier or excipient, and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping, and/or packaging the product into a desired single- or multi-dose unit.
  • Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses. A “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage, such as one-half or one-third of such a dosage.
  • Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition described herein will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered. The composition may comprise between about 0.1% and about 100% (w/w) of the active ingredient.
  • Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.
  • Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.
  • Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose, and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, and mixtures thereof.
  • Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g., acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminum silicate)), long chain amino acid derivatives, high molecular weight alcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g., carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g., carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g., polyoxyethylene sorbitan monolaurate (Tween® 20), polyoxyethylene sorbitan (Tween® 60), polyoxyethylene sorbitan monooleate (Tween® 80), sorbitan monopalmitate (Span® 40), sorbitan monostearate (Span® 60), sorbitan tristearate (Span®65), glyceryl monooleate, sorbitan monooleate (Spana 80), polyoxyethylene esters (e.g., polyoxyethylene monostearate (Myrj®45), polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol®), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g., Cremophor®), polyoxyethylene ethers, (e.g., polyoxyethylene lauryl ether (Brij® 30)), poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic® F-68, poloxamer P-188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, and/or mixtures thereof.
  • Exemplary binding agents include starch (e.g., cornstarch and starch paste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g., acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum®), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.
  • Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, antiprotozoan preservatives, alcohol preservatives, acidic preservatives, and other preservatives. In certain embodiments, the preservative is an antioxidant. In other embodiments, the preservative is a chelating agent.
  • Exemplary antioxidants include alpha tocopherol, ascorbic acid, ascorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.
  • Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.
  • Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.
  • Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.
  • Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.
  • Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant® Plus, Phenonip®, methylparaben, Germall® 115, Germaben® II, Neolone®, Kathon®, and Euxyl®.
  • Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D-gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer's solution, ethyl alcohol, and mixtures thereof.
  • Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, and mixtures thereof.
  • Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils. Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixtures thereof.
  • Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredients, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the conjugates described herein are mixed with solubilizing agents such as Cremophor®, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and mixtures thereof.
  • Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension, or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S.P., and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or di-glycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.
  • The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
  • In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This can be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution, which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form may be accomplished by dissolving or suspending the drug in an oil vehicle.
  • Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates described herein with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol, or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or (a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, (b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, (c) humectants such as glycerol, (d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, (e) solution retarding agents such as paraffin, (f) absorption accelerators such as quaternary ammonium compounds, (g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolin and bentonite clay, and (i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets, and pills, the dosage form may include a buffering agent.
  • Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the art of pharmacology. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of encapsulating compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • The active ingredient can be in a micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings, and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose, or starch. Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of encapsulating agents which can be used include polymeric substances and waxes.
  • Dosage forms for topical and/or transdermal administration of a compound described herein may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants, and/or patches. Generally, the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable carrier or excipient and/or any needed preservatives and/or buffers as can be required. Additionally, the present disclosure contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body. Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium. Alternatively or additionally, the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.
  • Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin. Alternatively or additionally, conventional syringes can be used in the classical mantoux method of intradermal administration. Jet injection devices which deliver liquid formulations to the dermis via a liquid jet injector and/or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable. Ballistic powder/particle delivery devices which use compressed gas to accelerate the compound in powder form through the outer layers of the skin to the dermis are suitable.
  • Formulations suitable for topical administration include, but are not limited to, liquid and/or semi-liquid preparations such as liniments, lotions, oil-in-water and/or water-in-oil emulsions such as creams, ointments, and/or pastes, and/or solutions and/or suspensions. Topically administrable formulations may, for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of the active ingredient can be as high as the solubility limit of the active ingredient in the solvent. Formulations for topical administration may further comprise one or more of the additional ingredients described herein.
  • A pharmaceutical composition described herein can be prepared, packaged, and/or sold in a formulation suitable for pulmonary administration via the buccal cavity. Such a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers, or from about 1 to about 6 nanometers. Such compositions are conveniently in the form of dry powders for administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and/or using a self-propelling solvent/powder dispensing container such as a device comprising the active ingredient dissolved and/or suspended in a low-boiling propellant in a sealed container. Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers. Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.
  • Low boiling propellants generally include liquid propellants having a boiling point of below 65° F. at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w/w) of the composition, and the active ingredient may constitute 0.1 to 20% (w/w) of the composition. The propellant may further comprise additional ingredients such as a liquid non-ionic and/or solid anionic surfactant and/or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).
  • Pharmaceutical compositions described herein formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and/or suspension. Such formulations can be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and/or atomization device. Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methylhydroxybenzoate. The droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.
  • Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition described herein. Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered by rapid inhalation through the nasal passage from a container of the powder held close to the nares.
  • Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w/w) to as much as 100% (w/w) of the active ingredient, and may comprise one or more of the additional ingredients described herein. A pharmaceutical composition described herein can be prepared, packaged, and/or sold in a formulation for buccal administration. Such formulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may contain, for example, 0.1 to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein. Alternately, formulations for buccal administration may comprise a powder and/or an aerosolized and/or atomized solution and/or suspension comprising the active ingredient. Such powdered, aerosolized, and/or aerosolized formulations, when dispersed, may have an average particle and/or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.
  • A pharmaceutical composition described herein can be prepared, packaged, and/or sold in a formulation for ophthalmic administration. Such formulations may, for example, be in the form of eye drops including, for example, a 0.1-1.0% (w/w) solution and/or suspension of the active ingredient in an aqueous or oily liquid carrier or excipient. Such drops may further comprise buffering agents, salts, and/or one or more other of the additional ingredients described herein. Other opthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and/or in a liposomal preparation. Ear drops and/or eye drops are also contemplated as being within the scope of this disclosure.
  • Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.
  • The compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions described herein will be decided by a physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex, and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.
  • The compounds and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol. Specifically contemplated routes are oral administration, intravenous administration (e.g., systemic intravenous injection), regional administration via blood and/or lymph supply, and/or direct administration to an affected site. In general, the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), and/or the condition of the subject (e.g., whether the subject is able to tolerate oral administration). In certain embodiments, the compound or pharmaceutical composition described herein is suitable for topical administration to the eye of a subject.
  • The exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound, mode of administration, and the like. An effective amount may be included in a single dose (e.g., single oral dose) or multiple doses (e.g., multiple oral doses). In certain embodiments, when multiple doses are administered to a subject or applied to a biological sample, tissue, or cell, any two doses of the multiple doses include different or substantially the same amounts of a compound described herein. In certain embodiments, when multiple doses are administered to a subject or applied to a biological sample, tissue, or cell, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses a day, two doses a day, one dose a day, one dose every other day, one dose every third day, one dose every week, one dose every two weeks, one dose every three weeks, or one dose every four weeks. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is one dose per day. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is two doses per day. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses per day. In certain embodiments, when multiple doses are administered to a subject or applied to a biological sample, tissue, or cell, the duration between the first dose and last dose of the multiple doses is one day, two days, four days, one week, two weeks, three weeks, one month, two months, three months, four months, six months, nine months, one year, two years, three years, four years, five years, seven years, ten years, fifteen years, twenty years, or the lifetime of the subject, biological sample, tissue, or cell. In certain embodiments, the duration between the first dose and last dose of the multiple doses is three months, six months, or one year. In certain embodiments, the duration between the first dose and last dose of the multiple doses is the lifetime of the subject, biological sample, tissue, or cell. In certain embodiments, a dose (e.g., a single dose, or any dose of multiple doses) described herein includes independently between 0.1 μg and 1 μg, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg, between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg, between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and 300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 1 mg and 3 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 3 mg and 10 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 10 mg and 30 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 30 mg and 100 mg, inclusive, of a compound described herein.
  • Dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult. In certain embodiments, a dose described herein is a dose for an adult human whose body weight is approximately 70 kg.
  • A compound or composition, as described herein, may be administered in combination with one or more additional pharmaceutical agents (e.g., therapeutically and/or prophylactically active agents) useful in treating and/or preventing a proliferative disease. The compounds or compositions can be administered in combination with additional pharmaceutical agents that improve their activity (e.g., activity (e.g., potency and/or efficacy) in treating a proliferative disease in a subject in need thereof, in preventing a proliferative disease in a subject in need thereof, and/or in inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject, biological sample, tissue, or cell), improve bioavailability, improve safety, reduce drug resistance, reduce and/or modify metabolism, inhibit excretion, and/or modify distribution in a subject, biological sample, tissue, or cell. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects. In certain embodiments, a pharmaceutical composition described herein including a compound described herein and an additional pharmaceutical agent shows a synergistic effect that is absent in a pharmaceutical composition including one of the compound and the additional pharmaceutical agent, but not both.
  • The compound or composition can be administered concurrently with, prior to, or subsequent to one or more additional pharmaceutical agents, which are different from the compound or composition and may be useful as, e.g., combination therapies in treating and/or preventing a proliferative disease. Pharmaceutical agents include therapeutically active agents. Pharmaceutical agents also include prophylactically active agents. Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved for human or veterinary use by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful in treating a proliferative disease. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful in preventing a proliferative disease. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful in inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, and/or CDK13)) in a subject, biological sample, tissue, or cell. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful in inducing apoptosis in a cell. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent approved by a regulatory agency (e.g., the US FDA) for treating and/or preventing a proliferative disease. Each additional pharmaceutical agent may be administered at a dose and/or on a time schedule determined for that pharmaceutical agent. The additional pharmaceutical agent(s) may also be administered together with each other and/or with the compound or composition described herein in a single dose or administered separately in different doses. The particular combination to employ in a regimen will take into account compatibility of the compound described herein with the additional pharmaceutical agent(s) and/or the desired therapeutic and/or prophylactic effect to be achieved. In general, it is expected that the additional pharmaceutical agent(s) in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
  • In certain embodiments, the additional pharmaceutical agent is a cytotoxic agent. In certain embodiments, the additional pharmaceutical agent is an anti-proliferative agent (e.g., anti-cancer agent). In certain embodiments, the additional pharmaceutical agent is an anti-leukemia agent. In certain embodiments, the additional pharmaceutical agent is ABITREXATE (methotrexate), ADE, Adriamycin RDF (doxorubicin hydrochloride), Ambochlorin (chlorambucil), ARRANON (nelarabine), ARZERRA (ofatumumab), BOSULIF (bosutinib), BUSULFEX (busulfan), CAMPATH (alemtuzumab), CERUBIDINE (daunorubicin hydrochloride), CLAFEN (cyclophosphamide), CLOFAREX (clofarabine), CLOLAR (clofarabine), CVP, CYTOSAR-U (cytarabine), CYTOXAN (cyclophosphamide), ERWINAZE (Asparaginase Erwinia Chrysanthemi), FLUDARA (fludarabine phosphate), FOLEX (methotrexate), FOLEX PFS (methotrexate), GAZYVA (obinutuzumab), GLEEVEC (imatinib mesylate), Hyper-CVAD, ICLUSIG (ponatinib hydrochloride), IMBRUVICA (ibrutinib), LEUKERAN (chlorambucil), LINFOLIZIN (chlorambucil), MARQIBO (vincristine sulfate liposome), METHOTREXATE LPF (methorexate), MEXATE (methotrexate), MEXATE-AQ (methotrexate), mitoxantrone hydrochloride, MUSTARGEN (mechlorethamine hydrochloride), MYLERAN (busulfan), NEOSAR (cyclophosphamide), ONCASPAR (Pegaspargase), PURINETHOL (mercaptopurine), PURIXAN (mercaptopurine), Rubidomycin (daunorubicin hydrochloride), SPRYCEL (dasatinib), SYNRIBO (omacetaxine mepesuccinate), TARABINE PFS (cytarabine), TASIGNA (nilotinib), TREANDA (bendamustine hydrochloride), TRISENOX (arsenic trioxide), VINCASAR PFS (vincristine sulfate), ZYDELIG (idelalisib), or a combination thereof. In certain embodiments, the additional pharmaceutical agent is an anti-lymphoma agent. In certain embodiments, the additional pharmaceutical agent is ABITREXATE (methotrexate), ABVD, ABVE, ABVE-PC, ADCETRIS (brentuximab vedotin), ADRIAMYCIN PFS (doxorubicin hydrochloride), ADRIAMYCIN RDF (doxorubicin hydrochloride), AMBOCHLORIN (chlorambucil), AMBOCLORIN (chlorambucil), ARRANON (nelarabine), BEACOPP, BECENUM (carmustine), BELEODAQ (belinostat), BEXXAR (tositumomab and iodine I 131 tositumomab), BICNU (carmustine), BLENOXANE (bleomycin), CARMUBRIS (carmustine), CHOP, CLAFEN (cyclophosphamide), COPP, COPP-ABV, CVP, CYTOXAN (cyclophosphamide), DEPOCYT (liposomal cytarabine), DTIC-DOME (dacarbazine), EPOCH, FOLEX (methotrexate), FOLEX PFS (methotrexate), FOLOTYN (pralatrexate), HYPER-CVAD, ICE, IMBRUVICA (ibrutinib), INTRON A (recombinant interferon alfa-2b), ISTODAX (romidepsin), LEUKERAN (chlorambucil), LINFOLIZIN (chlorambucil), Lomustine, MATULANE (procarbazine hydrochloride), METHOTREXATE LPF (methotrexate), MEXATE (methotrexate), MEXATE-AQ (methotrexate), MOPP, MOZOBIL (plerixafor), MUSTARGEN (mechlorethamine hydrochloride), NEOSAR (cyclophosphamide), OEPA, ONTAK (denileukin diftitox), OPPA, R-CHOP, REVLIMID (lenalidomide), RITUXAN (rituximab), STANFORD V, TREANDA (bendamustine hydrochloride), VAMP, VELBAN (vinblastine sulfate), VELCADE (bortezomib), VELSAR (vinblastine sulfate), VINCASAR PFS (vincristine sulfate), ZEVALIN (ibritumomab tiuxetan), ZOLINZA (vorinostat), ZYDELIG (idelalisib), or a combination thereof. In certain embodiments, the additional pharmaceutical agent is ABITREXATE (methotrexate), ABRAXANE (paclitaxel albumin-stabilized nanoparticle formulation), AC, AC-T, ADE, ADRIAMYCIN PFS (doxorubicin hydrochloride), ADRUCIL (fluorouracil), AFINITOR (everolimus), AFINITOR DISPERZ (everolimus), ALDARA (imiquimod), ALIMTA (pemetrexed disodium), AREDIA (pamidronate disodium), ARIMIDEX (anastrozole), AROMASIN (exemestane), AVASTIN (bevacizumab), BECENUM (carmustine), BEP, BICNU (carmustine), BLENOXANE (bleomycin), CAF, CAMPTOSAR (irinotecan hydrochloride), CAPOX, CAPRELSA (vandetanib), CARBOPLATIN-TAXOL, CARMUBRIS (carmustine), CASODEX (bicalutamide), CEENU (lomustine), CERUBIDINE (daunorubicin hydrochloride), CERVARIX (recombinant HPV bivalent vaccine), CLAFEN (cyclophosphamide), CMF, COMETRIQ (cabozantinib-s-malate), COSMEGEN (dactinomycin), CYFOS (ifosfamide), CYRAMZA (ramucirumab), CYTOSAR-U (cytarabine), CYTOXAN (cyclophosphamide), DACOGEN (decitabine), DEGARELIX, DOXIL (doxorubicin hydrochloride liposome), DOXORUBICIN HYDROCHLORIDE, DOX-SL (doxorubicin hydrochloride liposome), DTIC-DOME (dacarbazine), EFUDEX (fluorouracil), ELLENCE (epirubicin hydrochloride), ELOXATIN (oxaliplatin), ERBITUX (cetuximab), ERIVEDGE (vismodegib), ETOPOPHOS (etoposide phosphate), EVACET (doxorubicin hydrochloride liposome), FARESTON (toremifene), FASLODEX (fulvestrant), FEC, FEMARA (letrozole), FLUOROPLEX (fluorouracil), FOLEX (methotrexate), FOLEX PFS (methotrexate), FOLFIRI, FOLFIRI-BEVACIZUMAB, FOLFIRI-CETUXIMAB, FOLFIRINOX, FOLFOX, FU-LV, GARDASIL (recombinant human papillomavirus (HPV) quadrivalent vaccine), GEMCITABINE-CISPLATIN, GEMCITABINE-OXALIPLATIN, GEMZAR (gemcitabine hydrochloride), GILOTRIF (afatinib dimaleate), GLEEVEC (imatinib mesylate), GLIADEL (carmustine implant), GLIADEL WAFER (carmustine implant), HERCEPTIN (trastuzumab), HYCAMTIN (topotecan hydrochloride), IFEX (ifosfamide), IFOSFAMIDUM (ifosfamide), INLYTA (axitinib), INTRON A (recombinant interferon alfa-2b), IRESSA (gefitinib), IXEMPRA (ixabepilone), JAKAFI (ruxolitinib phosphate), JEVTANA (cabazitaxel), KADCYLA (ado-trastuzumab emtansine), KEYTRUDA (pembrolizumab), KYPROLIS (carfilzomib), LIPODOX (doxorubicin hydrochloride liposome), LUPRON (leuprolide acetate), LUPRON DEPOT (leuprolide acetate), LUPRON DEPOT-3 MONTH (leuprolide acetate), LUPRON DEPOT-4 MONTH (leuprolide acetate), LUPRON DEPOT-PED (leuprolide acetate), MEGACE (megestrol acetate), MEKINIST (trametinib), METHAZOLASTONE (temozolomide), METHOTREXATE LPF (methotrexate), MEXATE (methotrexate), MEXATE-AQ (methotrexate), MITOXANTRONE HYDROCHLORIDE, MITOZYTREX (mitomycin c), MOZOBIL (plerixafor), MUSTARGEN (mechlorethamine hydrochloride), MUTAMYCIN (mitomycin c), MYLOSAR (azacitidine), NAVELBINE (vinorelbine tartrate), NEOSAR (cyclophosphamide), NEXAVAR (sorafenib tosylate), NOLVADEX (tamoxifen citrate), NOVALDEX (tamoxifen citrate), OFF, PAD, PARAPLAT (carboplatin), PARAPLATIN (carboplatin), PEG-INTRON (peginterferon alfa-2b), PEMETREXED DISODIUM, PERJETA (pertuzumab), PLATINOL (cisplatin), PLATINOL-AQ (cisplatin), POMALYST (pomalidomide), prednisone, PROLEUKIN (aldesleukin), PROLIA (denosumab), PROVENGE (sipuleucel-t), REVLIMID (lenalidomide), RUBIDOMYCIN (daunorubicin hydrochloride), SPRYCEL (dasatinib), STIVARGA (regorafenib), SUTENT (sunitinib malate), SYLATRON (peginterferon alfa-2b), SYLVANT (siltuximab), SYNOVIR (thalidomide), TAC, TAFINLAR (dabrafenib), TARABINE PFS (cytarabine), TARCEVA (erlotinib hydrochloride), TASIGNA (nilotinib), TAXOL (paclitaxel), TAXOTERE (docetaxel), TEMODAR (temozolomide), THALOMID (thalidomide), TOPOSAR (etoposide), TORISEL (temsirolimus), TPF, TRISENOX (arsenic trioxide), TYKERB (lapatinib ditosylate), VECTIBIX (panitumumab), VEIP, VELBAN (vinblastine sulfate), VELCADE (bortezomib), VELSAR (vinblastine sulfate), VEPESID (etoposide), VIADUR (leuprolide acetate), VIDAZA (azacitidine), VINCASAR PFS (vincristine sulfate), VOTRIENT (pazopanib hydrochloride), WELLCOVORIN (leucovorin calcium), XALKORI (crizotinib), XELODA (capecitabine), XELOX, XGEVA (denosumab), XOFIGO (radium 223 dichloride), XTANDI (enzalutamide), YERVOY (ipilimumab), ZALTRAP (ziv-aflibercept), ZELBORAF (vemurafenib), ZOLADEX (goserelin acetate), ZOMETA (zoledronic acid), ZYKADIA (ceritinib), ZYTIGA (abiraterone acetate), or a combination thereof. In certain embodiments, the additional pharmaceutical agent is a kinase inhibitor. In certain embodiments, the additional pharmaceutical agent is a protein kinase inhibitor (e.g., tyrosine protein kinase inhibitor). In certain embodiments, the additional pharmaceutical agent is an inhibitor of a Src family kinase. In certain embodiments, the additional pharmaceutical agent is a CDK inhibitor. In certain embodiments, the additional pharmaceutical agent is a CDK7 inhibitor. In certain embodiments, the additional pharmaceutical agent is a CDK12 inhibitor. In certain embodiments, the additional pharmaceutical agent is a CDK13 inhibitor. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of IRAK1, IRAK4, BMX, and PI3K. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of BUB1B, CDK2, CDK9, CHEK2, FGR, HIPK4, PRKCQ, RET, SRC, and MELK. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL, ARG, BLK, CSK, EphB1, EphB2, FOR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, and TEC. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FOR, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated, ABL1(Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR1, EPHB1, ERBB4, p38-alpha, ABL2, ABL1(Q252H)-phosphorylated, SIK, EPHA8, MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK, EPHA2, ABL1(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q), ERBB2, ERBB3, EPHA5, ABL1(F317I)-nonphosphorylated, EGFR(L747-E749del, A750P), CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR, KIT-autoinhibited, and EGFR(E746-A750del). In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL1 (F317L)-nonphosphorylated, ABL1 (H396P)-nonphosphorylated, ABL1 (H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3, FOR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR1, EPHA2, ABL1(Q252H)-phosphorylated, MEK5, ABL1(Q252H)-nonphosphorylated, ABL2, FYN, EPHB1, ABL1 (E255K)-phosphorylated, ABL1(F317L)-phosphorylated, EPHA1, ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5, EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V), KIT-autoinhibited, EGFR(L747-T751del,Sins), EGFR(L858R), EGFR(L747-E749del, A750P), and CSF1R. In certain embodiments, the additional pharmaceutical agent is an anti-angiogenesis agent, anti-inflammatory agent, immunosuppressant, anti-bacterial agent, anti-viral agent, cardiovascular agent, cholesterol-lowering agent, anti-diabetic agent, anti-allergic agent, pain-relieving agent, or a combination thereof. In certain embodiments, the compounds described herein or pharmaceutical compositions can be administered or used in combination with an anti-cancer therapy including, but not limited to, transplantation (e.g., bone marrow transplantation, stem cell transplantation), surgery, radiation therapy, immunotherapy, and chemotherapy.
  • Also encompassed by the disclosure are kits (e.g., pharmaceutical packs). The kits provided may comprise a pharmaceutical composition or compound described herein and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of a pharmaceutical composition or compound described herein. In some embodiments, the pharmaceutical composition or compound described herein provided in the first container and the second container are combined to form one unit dosage form.
    • Methods of Treatment and Uses
  • The present invention also provides methods for the treatment or prevention of a proliferative disease (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases).
  • The compounds described herein may exhibit kinase inhibitory activity; the ability to inhibit cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinase 7 (CDK7); the ability to inhibit cyclin-dependent kinase 7 (CDK7), without inhibiting another cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinase 12 (CDK12); the ability to inhibit cyclin-dependent kinase 12 (CDK12), without inhibiting another cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinase 13 (CDK13); the ability to inhibit cyclin-dependent kinase 13 (CDK13), without inhibiting another cyclin-dependent kinase (CDK); the ability to inhibit cyclin-dependent kinases 12 and 13 (CDK12 and CDK13); the ability to inhibit cyclin-dependent kinases 12 and 13 (CDK12 and CDK13), without inhibiting another cyclin-dependent kinase (CDK); a therapeutic effect and/or preventative effect in the treatment of cancers; a therapeutic effect and/or preventative effect in the treatment of Myc-dependent cancers; and/or a therapeutic profile (e.g., optimum safety and curative effect) that is superior to existing chemotherapeutic agents.
  • Without wishing to be bound by any particular theory, the compounds described herein are able to bind (e.g., covalently modify) the protein kinase being inhibited. In certain embodiments, the R2 group of a compound described herein is able to bind (e.g., covalently modify) to the protein kinase. In certain embodiments, the R2 group of a compound described herein is able to covalently bind a cysteine residue of the protein kinase. In certain embodiments, the compound is capable of covalently modifying CDK7 (e.g., Cys312 of CDK7). In certain embodiments, the R2 group of a compound described herein is able to covalently modify residue Cys312 of CDK7. In certain embodiments, the compound is capable of covalently modifying CDK12 (e.g., Cys1039 of CDK12). In certain embodiments, the R2 group of a compound described herein is able to covalently modify residue Cys1039 of CDK12. In certain embodiments, the compound is capable of covalently modifying CDK13 (e.g., Cys1017 of CDK13). In certain embodiments, the R2 group of a compound described herein is able to covalently modify residue Cys1017 of CDK13.
  • In another aspect, the present disclosure provides methods of inhibiting the activity of a protein kinase in a subject, the methods comprising administering to the subject an effective amount (e.g., therapeutically effective amount) of a compound, or pharmaceutical composition thereof, as described herein.
  • In another aspect, the present disclosure provides methods of inhibiting the activity of a protein kinase in a biological sample, the methods comprising contacting the biological sample with an effective amount of a compound, or pharmaceutical composition thereof, as described herein.
  • In another aspect, the present disclosure provides methods of inhibiting the activity of a protein kinase in a tissue, the methods comprising contacting the tissue with an effective amount of a compound, or pharmaceutical composition thereof, as described herein.
  • In another aspect, the present disclosure provides methods of inhibiting the activity of a protein kinase in a cell, the methods comprising contacting the cell with an effective amount of a compound, or pharmaceutical composition thereof, as described herein.
  • In certain embodiments, the subject being treated is a mammal. In certain embodiments, the subject is a human. In certain embodiments, the subject is a domesticated animal, such as a dog, cat, cow, pig, horse, sheep, or goat. In certain embodiments, the subject is a companion animal such as a dog or cat. In certain embodiments, the subject is a livestock animal such as a cow, pig, horse, sheep, or goat. In certain embodiments, the subject is a zoo animal. In another embodiment, the subject is a research animal such as a rodent, dog, or non-human primate. In certain embodiments, the subject is a non-human transgenic animal such as a transgenic mouse or transgenic pig.
  • In certain embodiments, the biological sample being contacted with the compound or composition is breast tissue, bone marrow, lymph node, lymph tissue, spleen, or blood.
  • In certain embodiments, the cell being contacted with the compound or composition is in vitro. In certain embodiments, the cell being contacted with the compound or composition is in vivo. In certain embodiments, the cell being contacted with the compound or composition is ex vivo. In certain embodiments, the cell being contacted with the compound or composition is a malignant cell (e.g., malignant blood cell). In certain embodiments, the cell being contacted with the compound or composition is a malignant hematopoietic stem cell (e.g., malignant myeloid cell or malignant lymphoid cell). In certain embodiments, the cell being contacted with the compound or composition is a malignant lymphocyte (e.g., malignant T-cell or malignant B-cell). In certain embodiments, the cell being contacted with the compound or composition is a malignant red blood cell, malignant white blood cell, or malignant platelet. In certain embodiments, the cell being contacted with the compound or composition is a malignant neutrophil, malignant macrophage, or malignant plasma cell. In certain embodiments, the cell being contacted with the compound or composition is a carcinoma cell. In certain embodiments, the cell being contacted with the compound or composition is a carcinoma breast cell. In certain embodiments, the cell being contacted with the compound or composition is a sarcoma cell. In certain embodiments, the cell being contacted with the compound or composition is a sarcoma cell from breast tissue.
  • The proliferative disease to be treated or prevented using the compounds described herein may be associated with overexpression of a kinase, such as cyclin-dependent kinase (CDK). The process of eukaryotic cell division may be broadly divided into a series of sequential phases termed G1, S, G2, and M. Correct progression through the various phases of the cell cycle has been shown to be critically dependent upon the spatial and temporal regulation of a family of proteins known as cyclin dependent kinases (CDKs) and a diverse set of their cognate protein partners termed cyclins. CDKs are CDC2 (also known as CDK1) homologous serine-threonine kinase proteins that are able to utilize ATP as a substrate in the phosphorylation of diverse polypeptides in a sequence-dependent context. Cyclins are a family of proteins characterized by a homology region, containing approximately 100 amino acids, termed the “cyclin box” which is used in binding to, and defining selectivity for, specific CDK partner proteins.
  • Modulation of the expression levels, degradation rates, protein levels, and activity levels of various CDKs and cyclins throughout the cell cycle leads to the cyclical formation of a series of CDK/cyclin complexes, in which the CDKs are enzymatically active. The formation of these complexes controls passage through discrete cell cycle checkpoints and thereby enables the process of cell division to continue. Failure to satisfy the prerequisite biochemical criteria at a given cell cycle checkpoint, i.e., failure to form a required CDK/cyclin complex, can lead to cell cycle arrest and/or cellular apoptosis. Aberrant cellular proliferation can often be attributed to loss of correct cell cycle control. Inhibition of CDK enzymatic activity therefore provides a means by which abnormally dividing cells can have their division arrested and/or be killed. The diversity of CDKs, and CDK complexes, and their critical roles in mediating the cell cycle, provides a broad spectrum of potential therapeutic targets selected on the basis of a defined biochemical rationale.
  • CDK7, a member of the CDK family, was originally isolated as the catalytic subunit of the trimeric CDK-activating kinase (CAK) complex. This complex, consisting of CDK7, cyclin H, and MAT1, is responsible for activation of the mitotic promoting factor in vitro. The discovery that CDK7 was also a component of the basal transcription repair factor IIH (TFIIH) implicated a dual role for CDK7 in transcription as part of TFIIH and in the control of the cell cycle as the trimeric CAK complex. TFIIH is a multi-subunit protein complex identified as a factor required for RNA polymerase II (RNAP 1)-catalyzed transcription, and subsequently this complex was found to play a key role in nucleotide excision repair. CDK7 is a component of at least three complexes, i.e., the trimeric CAK complex, the quaternary complex with the XPD (or ERCC2, a protein involved in transcription-coupled nucleotide excision repair), and the nine-subunit TFIIH complex. The two functions of CDK7 in CAK and CTD phosphorylation support critical facets of cellular proliferation, cell cycling, and transcription. Overexpression of CDK7 may inhibit apoptosis, promote transcription and cell proliferation, and/or disrupt DNA repair, and therefore, cause proliferative diseases. In certain embodiments, the proliferative disease to be treated or prevented using the compounds described herein may be associated with overexpression of a CDK (e.g., CDK7).
  • Cdk12 and Cdk13 are Cdc2-related proteins that share 92% identity in their kinase domains (Chen et al., Exp. Neurol., 2014, 261, 10-21). CDK12 plays a critical role in cell processes, for example, regulating transcription and splicing machinery by stabilizing the RNAPII and DNA interaction, and regulating DNA damage response (DDR) and maintenance of genomic stability by modulating the expression of DDR genes. Overexpression of CDK12 has been found to correlate, both at the transcriptional and protein level, with pathological parameters of breast cancer disease.
  • A proliferative disease may be associated with aberrant activity of a CDK (e.g., CDK7, CDK12, and/or CDK13). Aberrant activity of a CDK (e.g., CDK7, CDK12, and/or CDK13) may be an elevated and/or an inappropriate activity of the CDK. Deregulation of cell cycle progression is a characteristic of a proliferative disease, and a majority of proliferative diseases have abnormalities in some component of CDK (e.g., CDK7, CDK12, and/or CDK13) activity, frequently through elevated and/or inappropriate CDK activation. Inhibition of the catalytic activity of CDK7, CDK12, and/or CDK13 would be expected to inhibit cell cycle progression by blocking the phosphorylation of cell cycle CDKs, and would additionally inhibit transcription of effectors of cell division. In certain embodiments, CDK7 is not overexpressed, and the activity of CDK7 is elevated and/or inappropriate. In certain other embodiments, CDK7 is overexpressed, and the activity of CDK7 is elevated and/or inappropriate. In certain embodiments, CDK12 is not overexpressed, and the activity of CDK12 is elevated and/or inappropriate. In certain embodiments, CDK12 is overexpressed, and the activity of CDK12 is elevated and/or inappropriate. In certain other embodiments, CDK13 is not overexpressed, and the activity of CDK13 is elevated and/or inappropriate. In certain other embodiments, CDK13 is overexpressed, and the activity of CDK13 is elevated and/or inappropriate. The compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may inhibit the activity of CDK7 and be useful in treating and/or preventing proliferative diseases. The compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may inhibit the activity of CDK12 and/or CDK13 and be useful in treating and/or preventing proliferative diseases.
  • A proliferative disease may also be associated with inhibition of apoptosis of a cell in a biological sample or subject. All types of biological samples described herein or known in the art are contemplated as being within the scope of the invention. Apoptosis is the process of programmed cell death. Inhibition of apoptosis may result in uncontrolled cell proliferation and, therefore, may cause proliferative diseases. The cell cycle CDKs (CDK1, 2, 4, and 6) are activated by phosphorylation by CDK7/cyclin H (also called CAK). Inhibition of CDK7 would therefore result in cell-cycle arrest at multiple points in the cell cycle due to failure to activate the cell cycle CDKs. CDK7 activates transcription by phosphorylating the CTD of RNAP II. Inhibition of CTD phosphorylation has been shown to inhibit transcription and reduce expression of short lived proteins, including those involved in apoptosis regulation. It is appreciated in the art that stalling of RNA polymerase may activate p53 (also known as protein 53 or tumor protein 53, a tumor suppressor protein that is encoded in humans by the TP53 gene), leading to apoptosis. Thus, inhibition of the activity of CDK7 are expected to cause cytotoxicity by inducing apoptosis. The compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, may induce apoptosis, and therefore, be useful in treating and/or preventing proliferative diseases.
  • The CycK/Cdk12 complex regulates phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and expression of a small subset of human genes, as revealed in expression microarrays. Through regulation of expression of DNA damage response genes (i.e. oncogenes), CycK/Cdk12 protects cells from genomic instability. In certain embodiments, the DNA damage response genes are BRCA1, BRCA2, HER1, HER2, ATR, FANCI, or FANCD2. In certain embodiments, the DNA damage response genes are BRCA1, HER2, ATR, FANCI, and FANCD2. In certain embodiments, the DNA damage response genes are BRCA1. In certain embodiments, the DNA damage response genes are HER2.
  • In certain embodiments, the proliferative disease to be treated or prevented using the compounds described herein is cancer. All types of cancers disclosed herein or known in the art are contemplated as being within the scope of the invention. In certain embodiments, the proliferative disease is a cancer associated with BCL-2 anti-apoptotic proteins (e.g., MCL-1 and/or XIAP) (e.g., cancer associated with dependence on BCL-2 anti-apoptotic proteins). In certain embodiments, the proliferative disease is a cancer associated with overexpression of MYC (a gene that codes for a transcription factor). In certain embodiments, the cancer is a MYC-dependent cancer. In certain embodiments, the proliferative disease is a cancer associated with amplification of BRCA1. In certain embodiments, the proliferative disease is a cancer associated with amplification of HER2. In certain embodiments, the proliferative disease is a hematological malignancy. In certain embodiments, the proliferative disease is a blood cancer. In certain embodiments, the proliferative disease is a hematological malignancy. In certain embodiments, the proliferative disease is leukemia. In certain embodiments, the proliferative disease is chronic lymphocytic leukemia (CLL). In certain embodiments, the proliferative disease is acute lymphoblastic leukemia (ALL). In certain embodiments, the proliferative disease is T-cell acute lymphoblastic leukemia (T-ALL). In certain embodiments, the proliferative disease is chronic myelogenous leukemia (CML). In certain embodiments, the proliferative disease is acute myelogenous leukemia (AML). In certain embodiments, the proliferative disease is acute monocytic leukemia (AMoL). In certain embodiments, the proliferative disease is lymphoma. In some embodiments, the proliferative disease is Burkitt's lymphoma. In certain embodiments, the proliferative disease is a Hodgkin's lymphoma. In certain embodiments, the proliferative disease is a non-Hodgkin's lymphoma. In certain embodiments, the proliferative disease is multiple myeloma. In certain embodiments, the proliferative disease is melanoma. In certain embodiments, the proliferative disease is colorectal cancer. In certain embodiments, the proliferative disease is breast cancer. In certain embodiments, the proliferative disease is recurring breast cancer. In certain embodiments, the proliferative disease is mutant breast cancer. In certain embodiments, the proliferative disease is HER2+ breast cancer. In certain embodiments, the proliferative disease is HER2-breast cancer. In certain embodiments, the proliferative disease is triple-negative breast cancer (TNBC). In certain embodiments, the proliferative disease is a bone cancer. In certain embodiments, the proliferative disease is osteosarcoma. In certain embodiments, the proliferative disease is Ewing's sarcoma. In some embodiments, the proliferative disease is a brain cancer. In some embodiments, the proliferative disease is neuroblastoma. In some embodiments, the proliferative disease is a lung cancer. In some embodiments, the proliferative disease is small cell lung cancer (SCLC). In some embodiments, the proliferative disease is non-small cell lung cancer. In some embodiments, the proliferative disease is a benign neoplasm. All types of benign neoplasms disclosed herein or known in the art are contemplated as being within the scope of the invention. In some embodiments, the proliferative disease is associated with angiogenesis. All types of angiogenesis disclosed herein or known in the art are contemplated as being within the scope of the invention. In certain embodiments, the proliferative disease is an inflammatory disease. All types of inflammatory diseases disclosed herein or known in the art are contemplated as being within the scope of the invention. In certain embodiments, the inflammatory disease is rheumatoid arthritis.
  • In certain embodiments, the proliferative disease is an acute inflammatory disease. In certain embodiments, the acute inflammatory disease is rheumatoid arthritis, chron's disease, or fibrosis. In some embodiments, the proliferative disease is an autoinflammatory disease. All types of autoinflammatory diseases disclosed herein or known in the art are contemplated as being within the scope of the invention. In some embodiments, the proliferative disease is an autoimmune disease. All types of autoimmune diseases disclosed herein or known in the art are contemplated as being within the scope of the invention.
  • Another aspect of the invention relates to methods of inhibiting the activity of a kinase in a biological sample, tissue, cell, or subject. In certain embodiments, the kinase is a CDK. In certain embodiments, the kinase is CDK7. In certain embodiments, the kinase is CDK12. In certain embodiments, the kinase is CDK13. In certain embodiments, the activity of the kinase is aberrant activity of the kinase. In certain embodiments, the activity of the kinase is increased activity of the kinase. In certain embodiments, the inhibition of the activity of the kinase is irreversible. In other embodiments, the inhibition of the activity of the kinase is reversible. In certain embodiments, the methods of inhibiting the activity of the kinase include attaching a compound described herein to the kinase.
  • Also provided in the present invention are methods of inhibiting transcription of genes in a biological sample or subject. In certain embodiments, the transcription of genes affected by the activity of CDK7 may be inhibited by a compound of the invention. In certain embodiments, the genes which may have their transcription inhibited by the activity of CDK7 are one or more selected from the group consisting of MYC, RUNX1, MYB, TAL1, GATA3, KLF2, HNRPDL, p21, ASCL1, MYCN, INSM1, NEUROD1, NEUROG1, FOXG1, FOXA1, SOX2, SOX4, BCL11A, OTX2, GAT2, PHOX2B, PLK2, TAF1, CTGF, WEE1, SDIM, JUN, PIM1, IL8, and FOS1. In certain embodiments, the genes which may have their transcription inhibited by the activity of CDK7 include MYC, KLF2, E2F2, CDK6, CCND3, E2F3, HNRPDL, TET1, IL7R, BRCA1, BRCA2, HER1, and HER2. In certain embodiments, the transcription of genes affected by the activity of CDK12 may be inhibited by a compound of the invention. In certain embodiments, the genes which may have their transcription inhibited by the activity of CDK12 are one or more selected from the group consisting of BRCA1, FANCI, ATR, FANCD2, APEX1, NEK9, CHEK1, CHEK2, ATM, RAD51C, RAD51D, ORC3L, MDC1, TERF2, ERCC4, FANCF, PARP9, RUNX1, MYB, TAL1, MCL1, MYC, BCL2, ETS1, and EWS-FLI. In certain embodiments, the transcription of genes affected by the activity of CDK13 may be inhibited by a compound of the invention. In certain embodiments, the gene is SNORA38.
  • The present invention also provides methods of inhibiting cell growth in a biological sample, tissue, cell, or subject.
  • In still another aspect, the present invention provides methods of inducing apoptosis of a cell in a biological sample, tissue, cell, or subject.
  • In certain embodiments, the methods described herein include administering to a subject or contacting a biological sample with an effective amount of a compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, or a pharmaceutical composition thereof. In certain embodiments, the methods described herein include administering to a subject or contacting a biological sample with an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In certain embodiments, the compound is contacted with a biological sample. In certain embodiments, the compound is administered to a subject. In certain embodiments, the compound is administered in combination with one or more additional pharmaceutical agents described herein. The additional pharmaceutical agent may be an anti-proliferative agent. In certain embodiments, the additional pharmaceutical agent is an anti-cancer agent. The additional pharmaceutical agent may also be a kinase inhibitor. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a CDK. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK7. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of CDK7. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of CDK7. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK12. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of CDK12. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of CDK12. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK13. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of CDK13. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of CDK13. In certain embodiments, the additional pharmaceutical agent is an inhibitor of another CDK. In certain embodiments, the additional pharmaceutical agent is a selective inhibitor of another CDK. In certain embodiments, the additional pharmaceutical agent is a nonselective inhibitor of another CDK. In certain embodiments, the additional pharmaceutical agent is flavopiridol, triptolide, SNS-032 (BMS-387032), PHA-767491, PHA-793887, BS-181, (S)—CR8, (R)—CR8, or NU6140. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a mitogen-activated protein kinase (MAPK). In certain embodiments, the additional pharmaceutical agent is an inhibitor of a glycogen synthase kinase 3 (GSK3). In certain embodiments, the additional pharmaceutical agent is an inhibitor of an AGC kinase. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a calmodulin-dependent kinase (CaM Kinase). In certain embodiments, the additional pharmaceutical agent is an inhibitor of a casein kinase 1. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a STE kinase. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a tyrosine kinase.
  • In some embodiments, the additional pharmaceutical agent is a topoisomerase inhibitor, a MCL1 inhibitor, a BCL-2 inhibitor, a BCL-xL inhibitor, a BRD4 inhibitor, a BRCA1 inhibitor, BRCA2 inhibitor, HER1 inhibitor, HER2 inhibitor, a CDK9 inhibitor, a Jumonji histone demethylase inhibitor, or a DNA damage inducer. In some embodiments, the additional pharmaceutical agent is etoposide, obatoclax, navitoclax, JQ1, 4-(((5′-chloro-2′-(((1R,4R)-4-(((R)-1-methoxypropan-2-yl)amino)cyclohexyl)amino)-[2,4′-bipyridin]-6-yl)amino)methyl)tetrahydro-2H-pyran-4-carbonitrile, JIB04, or cisplatin. In some embodiments, the additional pharmaceutical agent is etoposide, obatoclax, or navitoclax, and the disease to be treated is breast cancer, e.g., triple-negative breast cancer, HER2 positive breast cancer, HER2 negative breast cancer, ER-positive breast cancer, ER-negative breast cancer, or ER/PR-positive breast cancer. In some embodiments, the additional pharmaceutical agent is etoposide, JIB04, or cisplatin, and the disease to be treated is Ewing's sarcoma. In some embodiments, the additional pharmaceutical agent is JQ1 or NVP2, and the disease to be treated is leukemia, e.g., acute myelogenous leukemia, myeloblastic leukemia, promyelocytic leukemia, myelomonocytic leukemia, monocytic leukemia, monoblastic leukemia, or megakaryoblastic leukemia. In certain embodiments, a pharmaceutical composition described herein further comprises a combination of the additional pharmaceutical agents described herein.
  • The inventive compounds or compositions may synergistically augment inhibition of CDK7 induced by the additional pharmaceutical agent(s) in the biological sample or subject. The inventive compounds or compositions may synergistically augment inhibition of CDK12 induced by the additional pharmaceutical agent(s) in the biological sample or subject. The inventive compounds or compositions may synergistically augment inhibition of CDK12 and/or CDK13 induced by the additional pharmaceutical agent(s) in the biological sample or subject. Thus, the combination of the inventive compounds or compositions and the additional pharmaceutical agent(s) may be useful in treating proliferative diseases resistant to a treatment using the additional pharmaceutical agent(s) without the inventive compounds or compositions.
  • In some embodiments, the activity of a protein kinase is non-selectively inhibited by the compounds or pharmaceutical compositions described herein. In some embodiments, the activity of the protein kinase being inhibited is selectively inhibited by the compounds or pharmaceutical compositions described herein, compared to the activity of a different protein (e.g., a different protein kinase). In certain embodiments, the activity of CDK (e.g., CDK7, CDK12, or CDK13) is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of a different protein. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of a different CDK protein. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK12. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK13. In certain embodiments, the activity of CDK7 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK12 and the activity of CDK13. In certain embodiments, the activity of CDK12 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK7. In certain embodiments, the activity of CDK13 is selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK7. In certain embodiments, the activity of CDK12 and the activity of CDK13 are selectively inhibited by a compound or pharmaceutical composition described herein, compared to the activity of CDK7.
  • The selectivity of a compound or pharmaceutical composition described herein in inhibiting the activity of a protein kinase over a different protein (e.g., a different protein kinase) may be measured by the quotient of the IC50value of the compound or pharmaceutical composition in inhibiting the activity of the different protein over the IC50 value of the compound or pharmaceutical composition in inhibiting the activity of the protein kinase. The selectivity of a compound or pharmaceutical composition described herein for a protein kinase over a different protein may also be measured by the quotient of the Kd value of an adduct of the compound or pharmaceutical composition and the different protein over the Kd value of an adduct of the compound or pharmaceutical composition and the protein kinase. In certain embodiments, the selectivity is at least 2-fold, at least 3-fold, at least 5-fold, at least 10-fold, at least 30-fold, at least 100-fold, at least 300-fold, at least 1,000-fold, at least 3,000-fold, at least 10,000-fold, at least 30,000-fold, or at least 100,000-fold. In certain embodiments, the selectivity is not more than 100,000-fold, not more than 10,000-fold, not more than 1,000-fold, not more than 100-fold, not more than 10-fold, or not more than 2-fold. Combinations of the above-referenced ranges (e.g., at least 2-fold and not more than 10,000-fold) are also within the scope of the disclosure.
  • In certain embodiments, a kit described herein includes a first container comprising a compound or pharmaceutical composition described herein. In certain embodiments, a kit described herein is useful in treating a proliferative disease (e.g., cancers (e.g., leukemia, acute lymphoblastic leukemia, lymphoma, Burkitt's lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer, colorectal cancer), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject in need thereof, preventing a proliferative disease in a subject in need thereof, inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, or CDK13)) in a subject, biological sample, tissue, or cell, and/or inducing apoptosis in a cell.
  • In certain embodiments, a kit described herein further includes instructions for using the compound or pharmaceutical composition included in the kit. A kit described herein may also include information as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA). In certain embodiments, the information included in the kits is prescribing information. In certain embodiments, the kits and instructions provide for treating a proliferative disease in a subject in need thereof, preventing a proliferative disease in a subject in need thereof, inhibiting the activity of a protein kinase (e.g., CDK (e.g., CDK7, CDK12, or CDK13)) in a subject, biological sample, tissue, or cell, and/or inducing apoptosis in a cell. A kit described herein may include one or more additional pharmaceutical agents described herein as a separate composition.
    • EXAMPLES
  • In order that the invention described herein may be more fully understood, the following examples are set forth. The synthetic and biological examples described in this application are offered to illustrate the compounds, pharmaceutical compositions, and methods provided herein and are not to be construed in any way as limiting their scope.
    • Pulldown Assay (FIGS. 2-4 and 7-9)
  • Jurkat cells were treated with DMSO or concentration of compound indicated. 6 hours after treatment, cells were washed and harvested by resuspending in lysis buffer (50 mM Hepes pH 7.4, 150 mM NaCl, 1% NP-40, 5 mM EDTA, protease and phosphatase inhibitors) and lysing on ice 30 minutes. Lysates were cleared by centrifugation at 15,000 rpm 30 minutes. Biotin-labeled THZ1 was added to 1 μM to lysates and rotated at 4° C. overnight. Streptavidin-agarose beads were washed and 30 μL slurry was added to each lysate and rotated for 1 hour at 4° C. Beads were washed 5 times with lysis buffer and 50 μL 2×LDS buffer was added to each sample. Samples were boiled and equal volume of protein was loaded onto gel. Gel was transferred to nitrocellulose and blotted for Cyclin K and Cyclin H.
    • Interpretation of Results
  • We conclude that pre-treatment of cells with several of the compounds, but not DMSO, blocks biotin-THZ1 from being able to bind to CDK12, which blocks the pulldown of CDK12 and CDK13-associated Cyclin K. This indicates that active compounds are able to engage CDK12 and CDK13-associated cyclin K complexes in cells and block binding of these complexes by bio-THZ1. We do not see a similar loss of pulldown of Cyclin H, indicating that these compounds are not able to bind to CDK7-associated cyclin H complexes and block its association with biotin-THZ1.
    • Growth Assay (FIG. 5)
  • Jurkat cells were plated at 30,000 cells/well and treated with a titration of compounds indicated. Cells were allowed to grow for 72 hours. Cells were assayed using CELLTITER GLO (Promega) to determine cell viability by measuring the amount of ATP present, which is an indicator of cell metabolic activity. Results are graphed as luminescent values. Curves were generated using PRISM and an IC50 value was determined.
    • Interpretation of Results
  • We can conclude that several of the compounds generated and tested are more potent against cell growth than the parent SNS-032 compound in Jurkat cells.
    • Synthesis of the Compounds
  • The compounds provided herein can be prepared from readily available starting materials using the following general methods and procedures. Reactions were monitored by thin layer chromatography (TLC) with 0.25 mm E. Merck pre-coated silica gel plates (60 F2 4) and Waters LCMS system (Waters 2489 UV/Visible Detector, Waters 3100 Mass, Waters 515 HPLC pump, Waters 2545 Binary Gradient Module, Waters Reagent Manager, Waters 2767 Sample Manager) using SunFire™ C18 column (4.6×50 mm, 5 m particle size): solvent gradient=95% A at 0 min, 0% A at 5 min; solvent A=0.5% TFA in Water; solvent B=Methanol; flow rate: 1.5 mL/min. Purification of reaction products was carried out by flash chromatography using CombiFlash® Rf with Teledyne Isco RediSep® Rf High Performance Gold or Silicycle SiliaSep™ High Performance columns (4 g, 12 g, 24 g, 40 g, 80 g or 120 g) or by Waters preparative HPLC system with a C18 column: solvent gradient=100% A at 0 min, 0% A at 15 min; solvent A=0.5% TFA in Water; solvent B=Methanol; flow rate: 20 mL/min. The purity of all compounds was over 95% and was analyzed with Waters LCMS system. 1H NMR and 13C NMR spectra were obtained using a Varian Inova-600 or 400 MHz spectrometer. Chemical shifts are reported relative to chloroform (δ=7.24) for 1H NMR or dimethyl sulfoxide (δ=2.50) for 1H NMR and dimethyl sulfoxide (δ=39.51) for 13C NMR. Data are reported as (br=broad, s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet).
  • Figure US20200172499A9-20200604-C00240
    Figure US20200172499A9-20200604-C00241
    • 5-Thiocyanatothiazol-2-amine (MFH-2-76-1)
  • A mixture of 2-amino-5-bromothiazole hydrobromide (6.0 g, 23.08 mmol) and potassium thiocyanate (9.0 g, 92.32 mmol) in methanol (150 mL) was stirred at room temperature for 20 h. Methanol was evaporated and water (20 ml) was added. The pH of the aqueous solution was adjusted to pH=12 with 10% NaOH and then a precipitate was formed. The solid was collected by filtration to yield compound MFH-2-76-1 (1.5 g, 41%) as a solid. LCMS (m/z): 158 [M+H]+.
    • 5-((5-tert-Butyloxazol-2-yl)methylthio)thiazol-2-amine (MFH-2-80-1)
  • To a solution of compound MFH-2-76-1 (315 mg, 2 mmol) in EtOH (5 ml) was added NaBH4 (151 mg, 4 mmol) at room temperature. The mixture was stirred for 1 h, and then acetone (3 ml) was slowly added. After 1 h, a solution of 5-tert-Butyl-2-chloromethyloxazole (348 mg, 2 mmol) in EtOH (3 ml) was added. The resulting dark reaction mixture was heated to reflux for 1 h, and was then cooled and concentrated in reduced pressure. The residue was then dissolved in ethyl acetate and washed with water. The organic phase was separated, dried (MgSO4) and concentrated in reduced pressure to give a crude product MFH-2-80-1 (310 mg, 57%) LCMS (m/z): 270 [M+H]+.
    • 5-[[(5-t-buty2-oxazolyl)methyl]thio]-2-bromo (MFH-2-83-1)
  • To a solution of CuBr2 (1.8 g, 8 mmol) in acetonitrile (48 mL) at 0° C. was added t-BuONO (827 mg, 8 mmol) followed by compound MFH-2-80-1 (1.8 g, 6.68 mmol). The mixture was stirred at 0° C. for 1 h and then was warmed up to room temperature. Ethyl acetate was added and the organic mixture washed with hydrochloric acid (50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in reduced pressure. The residue was purified by chromatographed on silica gel to give product. MFH-2-83-1 (1.5g, 67%). LCMS (m/z): 334 [M+H]+.
    • (R)-tert-butyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)triazol-2-ylamino)piperidine-1-carboxylate (MFH-2-84-1)
  • The mixture of MFH-2-83-1 (1.5g, 4.5 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (1.6 g, 8.1 mmol) and DIEA (1.5 g, 11.25 mmol) in NMP (5 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-2-84-1 (1.36 g, yield 66.8%). LCMS (m/z): 453 [M+H]+.
    • (R)-5-((5-tert-butyloxazol-2-yl)methylthio)-N-(piperidin-3-yl)thiazol-2-amine (MFH-2-85-1)
  • To a solution of MFH-2-85-1 (1.36 g, 3 mmol) in methanol (18 mL) was added 4N HCl/dioxane (18 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 353 [M+H]+.
  • (R)-(3-(5-((5-tert-butyloxazol-2-yl)methylthi)triazol-2-ylamino)piperidin-1-yl)(4-nitrophenyl)methanone (MFH-2-86-1)
  • The mixture of MFH-2-85-1 (250 mg, 0.643 mmol), 4-nitrobenzoyl chloride (132 mg, 0.71 mmol) in pyridine (3 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 502 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-2-89-1)
  • To a solution of MFH-2-86-1 (270 mg, 0.54 mmol) in ethyl acetate and methanol (1:1) were added Tin (11) chloride dehydrate (1.2 g, 5.4 mmol) and conc. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-2-89-1 (140 mg, yield 55%). LCMS (m/z): 472 [M+H]+.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)triazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-2-90-1)
  • To a solution of MFH-2-89-1 (140 mg, 0.30 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (35 mg, 0.39 mmol) in DCM (0.8 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-2-90-1 (24.7 mg, yield 16%). LCMS (m/z): 526 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.27 (s, 1H), 7.97 (s, 1H), 7.67 (s, 2H), 7.35 (d, J=6.7 Hz, 2H), 6.87 (d, J=26.3 Hz, 1H), 6.70 (s, 1H), 6.43 (dd, J=17.0, 10.1 Hz, 1H), 6.27 (dd, J=17.0, 1.8 Hz, 1H), 5.77 (dd, J=10.1, 1.8 Hz, 1H), 3.94 (s, 2H), 3.79 (s, 1H), 3.63 (d, J=23.9 Hz, 2H), 3.14 (d, J=65.1 Hz, 2H), 1.95 (s, 1H), 1.76 (s, 1H), 1.52 (d, J=7.8 Hz, 2H), 1.17 (s, 9H).
  • Figure US20200172499A9-20200604-C00242
    Figure US20200172499A9-20200604-C00243
    • (S)-tert-butyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperline-1-carboxylate (MFH-2-82-1)
  • The mixture of MFH-2-83-1 (150 mg, 0.45 mmol), (S)-tert-butyl 3-aminopiperidine-1-carboxylate (160 mg, 0.81 mmol) and DIEA (150 mg, 1.13 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-2-82-1 (136 mg, yield 67%). LCMS (m/z): 453 [M+H]+.
    • (S)-5-((5-tert-butyloxazol-2-yl)methylthio)-N-(piperidin-3-yl)thiazol-2-amine (MFH-2-87-1)
  • To a solution of MFH-2-82-1 (136 mg, 0.3 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 353 [M+H]+.
    • (S)-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)(4-nitrophenyl)methanone (MFH-2-88-1)
  • The mixture of MFH-2-87-1 (250 mg, 0.643 mmol), 4-nitrobenzoyl chloride (132 mg, 0.71 mmol) in pyridine (3 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 502 [M+H]+.
    • (S)-(4-aminophenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-2-91-1)
  • To a solution of MFH-2-88-1 (270 mg, 0.54 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (1.2 g, 5.4 mmol) and cone. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol(4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-2-91-1 (140 mg, yield 55%). LCMS (m/z): 472 [M+H]+.
    • (S)—N-(4-(35-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-2-92-1)
  • To a solution of MFH-2-91-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (8 mg, 0.08 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-2-92-1 (11 mg, yield 33%). LCMS (m/z): 526 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.30 (s, 1H), 8.07 (s, 1H), 7.65 (s, 2H), 7.35 (d, J=6.7 Hz, 2H), 6.88 (d, J=37.7 Hz, 1H), 6.70 (s, 1H), 6.43 (dd, J=16.9, 10.1 Hz, 1H), 6.27 (dd, J=17.0, 1.6 Hz, 1H), 5.77 (dd, J=10.2, 1.7 Hz, 1H), 3.95 (s, 2H), 3.79 (s, 1H), 3.63 (d, J=23.9 Hz, 2H), 3.14 (d, J=65.1 Hz, 2H), 1.92 (s, J=18.7 Hz, 1H), 1.76 (s, 1H), 1.52 (d, J=6.6 Hz, 2H), 1.17 (s, 9H).
  • Figure US20200172499A9-20200604-C00244
    • (R)-tert-butyl4-3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)cyclohexylcarbamate (MFH-2-93-1)
  • The mixture of MFH-2-85-1 (116 mg, 0.33 mmol), 4-(tert-butoxycarbonylamino)cyclohexanecarboxylic acid (120 mg, 0.5 mmol), HOBT (68 mg, 0.5 mmol) and EDCI (96 mg, 0.5 mmol) in DCM (10 ml) was stirred for overnight. The reaction mixture was diluted with DCM (25 ml). The organic phase was washed with saturated Na2CO3 and brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-2-93-1 (80 mg, yield 42%). LCMS (m/z): 578 [M+H]+.
    • (R)-(4-aminocyclohexyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-2-94-1)
  • To a solution of MFH-2-93-1 (80 mg, 0.14 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 478 [M+H]+.
    • (R)—N-(4-(3-(5-(5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)cyclohexyl)acrylamide (MFH-2-95-1)
  • To a solution of MFH-2-94-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (8 mg, 0.08 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-2-95-1 (15.9 mg, yield 48%). LCMS (m/z): 532 [M+H]+.
  • Figure US20200172499A9-20200604-C00245
    • (R)-tert-butyl4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)triazol-2-ylamino)piperidine-1-carbonyl)benzylcarbamate (MFH-2-96-1)
  • The mixture of MFH-2-85-1 (88 mg, 0.25 mmol), 4-((tert-butoxycarbonylamino)methyl)benzoic acid (94 mg, 0.38 mmol), HOBT (51 mg, 0.38 mmol) and EDCI (72 mg, 0.38 mmol) in DCM (8 ml) was stirred for overnight. The reaction mixture was diluted with DCM (25 ml). The organic phase was washed with saturated Na2CO3 and brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-2-96-1 (125 mg, yield 85%). LCMS (m/z): 586 [M+H]+.
    • (R)-(4-(aminomethyl)phenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-2-97-1)
  • To a solution of MFH-2-96-1 (125 mg, 0.21 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 486 [M+H]+.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)benzyl)acrylamide (MFH-2-98-1)
  • To a solution of MFH-2-97-1 (50 mg, 0.1 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (12 mg, 0.13 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-2-98-1 (16.4 mg, yield 30%). LCMS (m/z): 540 [M+H]+. 1H NMR (500 MHz, DMSO) δ 8.62 (s, 1H), 8.08 (d, J=54.5 Hz, 1H), 7.28 (d, J=31.4 Hz, 4H), 6.91 (d, J=65.2 Hz, 1H), 6.72 (s, 1H), 6.28 (dd, J=17.1, 10.2 Hz, 1H), 6.13 (dd, J=17.1, 2.2 Hz, 1H), 5.62 (dd, J=10.2, 1.9 Hz, 1H), 4.36 (s, 2H), 3.95 (s, 2H), 3.67-3.62 (m, 2H), 3.33 (s, 1H), 3.14-2.83 (m, 2H), 1.94 (s, 1H), 1.74 (d, J=65.1 Hz, 1H), 1.53 (s, 2H), 1.20 (s, 9H).
  • Figure US20200172499A9-20200604-C00246
    • (R)-4-nitrophenyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-2-99-1)
  • To a solution of MFH-2-85-1 (210 mg, 0.6 mmol) and DIPEA (116 mg, 0.9 mmol) in DCM (8 mL) was added 4-nitrophenyl chloroformate (133 mg, 0.66 mmol) in DCM (1 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-2-99-1 (283 mg, yield 91%). LCMS (m/z): 518 [M+H]+.
    • (R)-4-aminophenyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-2-100-1)
  • To a solution of MFH-2-99-1 (106 mg, 0.21 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (462 mg, 2.1 mmol) and conc. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-2-100-1 (60 mg, yield 60%). LCMS (m/z): 488 [M+H]+.
    • (R)-4-acrylamidophenyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-2-102-1)
  • To a solution of MFH-2-100-1 (60 mg, 0.12 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (15 mg, 0.16 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-2-102-1 (18.1 mg, yield 27%). LCMS (m/z): 542 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.17 (s, 1H), 8.13 (d, J=14.2 Hz, 1H), 7.64 (s, 2H), 7.08 (s, 1H), 7.01 (d, J=9.0 Hz, 1H), 6.95 (s, 1H), 6.72 (dd, J=11.3, 7.1 Hz, 1H), 6.42 (dd, J=16.9, 10.1 Hz, 1H), 6.25 (dd, J=17.0, 1.7 Hz, 1H), 5.82-5.68 (m, 1H), 3.94 (s, 2H), 3.84 (s, 1H), 3.74 (s, 1H), 3.26 (d, J=44.4 Hz, 2H), 2.93 (s, 1H), 1.92 (d, J=13.1 Hz, 1H), 1.79 (d, J=6.3 Hz, 1H), 1.52 (s, 2H), 1.21 (s, 9H).
  • Figure US20200172499A9-20200604-C00247
    • (R)-tert-butyl1-(3-(5-(5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)piperidin-4-ylcarbamate (MFH-2-101-1)
  • The mixture of MFH-2-99-1 (177 mg, 0.34 mmol) and tert-butyl piperidin-4-ylcarbamate (89 mg, 0.44 mmol) in DMSO (3 mL) was stirred at 60° C. overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-2-101-1 (150 mg, yield 76%). LCMS (m/z): 579 [M+H]+.
    • (R)-(4-aminopiperidin-1-yl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-2-103-1)
  • To a solution of MFH-2-101-1 (150 mg, 0.26 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 479 [M+H]+.
    • (R)—N-(1-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)piperidin-4-yl)acrylamide (MFH-2-104-1)
  • To a solution of MFH-2-103-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (8 mg, 0.08 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-2-104-1 (10.2 mg, yield 30%). LCMS (m/z): 533 [M+H]+. 1H NMR (500 MHz, DMSO) δ 8.13 (s, 1H), 8.07 (d, J=7.7 Hz, 1H), 6.97 (s, 1H), 6.70 (d, J=5.5 Hz, 1H), 6.18 (dd, J=17.1, 10.1 Hz, 1H), 6.07 (dd, J=17.1, 2.2 Hz, 1H), 5.57 (dd, J=10.1, 2.2 Hz, 1H), 3.94 (s, 2H), 3.81-3.71 (m, 2H), 3.48 (s, 2H), 3.34-3.24 (m, 2H), 2.79 (t, J=11.6 Hz, 3H), 2.70 (dd, J=13.2, 9.5 Hz, 1H), 1.89 (d, J=10.4 Hz, 1H), 1.71 (d, J=13.1 Hz, 3H), 1.43 (dd, J=16.4, 8.5 Hz, 2H), 1.32 (m, 2H), 1.18 (s, 9H).
  • Figure US20200172499A9-20200604-C00248
    Figure US20200172499A9-20200604-C00249
    • 5-thiocyanato-1,3,4-thiadiazol-2-amine (MFH-2-202-1)
  • A mixture of 5-bromo-1,3,4-thiadiazol-2-amine (1.5 g, 8.3 mmol) and potassium thiocyanate (3.2 g, 33.3 mmol) in methanol (30 mL) was stirred at room temperature for 20 h. Methanol was evaporated and water (10 ml) was added. The pH of the aqueous solution was adjusted to pH=12 with 10% NaOH and precipitate formed. The solid was collected by filtration to yield compound MFH-2-202-1 (600 mg, 46%) as solid. LCMS (m/z): 159 [M+H]+.
    • 5-((5-tert-butyloxazol-2-yl)methylthio)-1,3,4-thiadiazol-2-amine (MFH-2-204-1)
  • To a solution of compound MFH-2-202-1 (315 mg, 2 mmol) in EtOH (5 ml) was added NaBH4 (151 mg, 4 mmol) at room temperature. The mixture was stirred for 1h, and then acetone (3 ml) was slowly added. After 1 h, a solution of 5-tert-Butyl-2-chloromethyloxazole (348 mg, 2 mmol) in EtOH (3 ml) was added. The resulting reaction mixture was heated to reflux for 1h and then was cooled followed by concentration in reduced pressure. The residue was dissolved in ethyl acetate. The organic phase was washed with brine (30 mL) and then the solvent was removed after drying with MgSO4. The crude product was then obtained MFH-2-204-1 (310 mg, 57%) as solid LCMS (m/z): 271 [M+H]+.
    • 2-((5-bromo-1,3,4-thiadiazol-2-ylthio)methyl)-5-tert-butyloxazole (MFH-2-208-1)
  • To a solution of CuBr2 (594 mg, 2.66 mmol) in acetonitrile (8 mL) at 0° C. was added t-BuONO (275 mg, 2.66 mmol) followed by compound MFH-2-204-1 (600 mg, 2.22 mmol). The mixture was stirred at 0° C. for 1h and then was warmed up to room temperature. After stirring for 1 h, ethyl acetate was added and the organic mixture washed with hydrochloric acid (50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in reduced pressure. The residue was chromatographed on silica gel to give the MFH-2-208-1 (700 mg, 94%). LCMS (m/z): 335 [M+H]+.
    • (R)-tert-butyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)-1,3,4-thiadiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-2-1)
  • The mixture of MFH-2-208-1 (250 mg, 0.75 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (225 mg, 1.12 mmol) and DIEA (242 mg, 1.87 mmol) in NMP (1 mL) was stirred at 140° C. overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-2-1 (180 mg, yield 53%). LCMS (m/z): 454 [M+H]+.
    • (R)-5-((5-tert-butyloxazol-2-yl)methylthio)-N-(piperidin-3-yl)-1,3,4-thiadiazol-2-amine (MFH-3-11-1)
  • To a solution of MFH-3-2-1 (250 mg, 0.55 mmol) in methanol (5 mL) was added 4N HCl/dioxane (5 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 354 [M+H]+.
    • (R)-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)-1,3,4-thiadiazol-2-ylamino)piperidin-1-yl)(4-nitrophenyl)methanone (MFH-3-14-1)
  • The mixture of MFH-3-11-1 (140 mg, 0.4 mmol), 4-nitrobenzoyl chloride (88 mg, 0.48 mmol) in pyridine (3 mL) was stirred overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 503 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)-1,3,4-thiadiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-18-1)
  • To a solution of MFH-3-14-1 (200 mg, 0.4 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (904 mg, 4 mmol) and conc. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-18-1 (45 mg, yield 24%). LCMS (m/z): 473 [M+H]+.
    • (R)—N-(4-(3-((5-tert-butyloxazol-2-yl)methylthio)-1,3,4-thiadiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-25-1)
  • To a solution of MFH-3-18-1 (22 mg, 0.05 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (6 mg, 0.06 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-25-1 (8.8 mg, yield 36%). LCMS (m/z): 527 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.29 (s, 1H), 8.02 (d, J=5.0 Hz, 1H), 7.68 (s, 2H), 7.35 (s, 2H), 6.75 (s, 1H), 6.44 (dd, J=17.0, 10.1 Hz, 1H), 6.28 (d, J=16.9 Hz, 1H), 5.86-5.70 (m, 1H), 4.33 (s, 2H), 3.74 (s, 1H), 3.60 (s, 2H), 3.21 (d, J=32.1 Hz, 2H), 1.99 (s, 1H), 1.77 (s, 1H), 1.58 (dd, J=22.4, 11.7 Hz, 2H), 1.29 (s, 9H).
  • Figure US20200172499A9-20200604-C00250
    Figure US20200172499A9-20200604-C00251
    • N1-(4-nitrophenyl)cyclohexane-1,3-diamine (MFH-3-26-1)
  • The mixture of 1-fluoro-4-nitrobenzene (200 mg, 1.42 mmol), cyclohexane-1,3-diamine (485 mg, 4.25 mmol) and K2CO3 (587 mg, 4.25 mmol) in DMF (3 mL) was stirred at 90° C. for 6h. The solution was then diluted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-26-1 (230 mg, yield 69%). LCMS (m/z): 236 [M+H]+.
    • (5-((5-tert-butyloxaxzol-2-yl)methylthio)thiazol-2-yl)-N3-(4-nitrophenyl)cyclohexane-1,3-diamine (MFH-3-29-1)
  • The mixture of MFH-2-83-1 (272 mg, 0.82 mmol), MFH-3-26-1 (230 mg, 0.98 mmol) and DIEA (316 mg, 2.46 mmol) in NMP (2 mL) was stirred at 140° C. overnight. The solution was diluted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-29-1 (80 mg, yield 20%). LCMS (m/z): 458 [M+H]+.
    • N1-(3 ((5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexyl)benzene-1,4-diamine (MFH-3-33-1)
  • To a solution of MFH-3-29-1 (80 mg, 0.16 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (370 mg, 1.6 mmol) and conc. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-33-1 (20 mg, yield 27%). LCMS (m/z): 458 [M+H]+.
    • N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexylamino)phenyl)acrylamide (MFH-3-35-1)
  • To a solution of MFH-3-33-1 (20 mg, 0.04 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (4 mg, 0.04 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at −40° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-35-1 (9.3 mg, yield 41%). LCMS (m/z): 512 [M+H]+.
  • Figure US20200172499A9-20200604-C00252
    • (R)-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)(2-methyl-4-nitrophenyl)methanone (MFH-3-64-1)
  • The mixture of MFH-2-85-1 (44 mg, 0.13 mmol), 4-((tert-butoxycarbonylamino)methyl)benzoic acid (47 mg, 0.19 mmol), HOBT (25 mg, 0.19 mmol) and EDCI (36 mg, 0.19 mmol) in DCM (3 ml) was stirred for overnight. The reaction mixture was diluted with DCM (25 ml). The organic phase was washed with saturated Na2CO3 and brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-64-1 (63 mg, yield 94%). LCMS (m/z): 516 [M+H]+.
    • (R)-(4-amino-2-methylphenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-66-1)
  • To a solution of MFH-3-64-1 (63 mg, 0.12 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (138 mg, 0.61 mmol) and conc. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-66-1 (20 mg, yield 34%). LCMS (m/z): 486 [M+H]+.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)-3-methylphenyl)acrylamide (MFH-3-75-1)
  • To a solution of MFH-3-66-1 (20 mg, 0.04 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (4 mg, 0.04 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-75-1 (9.4 mg, yield 41%). LCMS (m/z): 540 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.16 (d, J=35.4 Hz, 1H), 8.03 (d, J=59.1 Hz, 1H), 7.54 (d, J=9.3 Hz, 1H), 7.24-7.08 (m, 1H), 7.00 (d, J=9.0 Hz, 1H), 6.75 (d, J=10.5 Hz, 1H), 6.69 (s, 1H), 6.43 (dt, J=17.0, 10.5 Hz, 1H), 6.32-6.20 (m, 1H), 5.76 (t, J=11.0 Hz, 1H), 3.96 (s, J=11.8 Hz, 2H), 3.59 (d, J=52.3 Hz, 4H), 3.00 (s, 1H), 2.19 (s, 3H), 1.92 (dd, J=59.5, 33.2 Hz, 2H), 1.57 (d, J=57.5 Hz, 2H), 1.20 (s, 9H).
  • Figure US20200172499A9-20200604-C00253
    • (R)-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)(2-methoxy-4-nitrophenyl)methanone (MFH-3-65-1)
  • The mixture of MFH-2-85-1 (44 mg, 0.13 mmol), 4-((tert-butoxycarbonylamino)methyl)benzoic acid (47 mg, 0.19 mmol), HOBT (25 mg, 0.19 mmol) and EDCI (36 mg, 0.19 mmol) in DCM (3 ml) was stirred overnight. The reaction mixture was diluted with DCM (25 ml). The organic phase was washed with saturated Na2CO3 and brine (20 mL) and dried over Na2SO3. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-64-1 (71 mg, yield 100%). LCMS (m/z): 532 [M+H]+.
    • (R)-4-amino-2-methoxyphenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-67-1)
  • To a solution of MFH-3-64-1 (71 mg, 0.13 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (151 mg, 0.67 mmol) and conc. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-67-1 (30 mg, yield 45%). LCMS (m/z): 502 [M+H]+.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)-3-methoxyphenyl)acrylamide (MFH-3-81-1)
  • To a solution of MFH-3-67-1 (30 mg, 0.06 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (7 mg, 0.08 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-81-1 (11.8 mg, yield 35%). LCMS (m/z): 556 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.36-10.15 (m, 1H), 8.16-7.83 (m, 1H), 7.49 (d, J=14.3 Hz, 1H), 7.15 (dd, J=19.9, 7.7 Hz, 1H), 7.04-6.94 (m, 1H), 6.74 (dd, J=28.4, 22.6 Hz, 2H), 6.43 (dt, J=18.7, 9.3 Hz, 1H), 6.27 (ddd, J=17.0, 9.5, 1.8 Hz, 1H), 5.83-5.72 (m, 1H), 3.91 (s, 2H), 3.78 (s, 3H), 3.73 (s, 1H), 3.45 (d, J=13.3 Hz, 1H), 3.24 (t, J=32.2 Hz, 1H), 2.88 (dd, J=34.4, 22.2 Hz, 2H), 1.97 (d, J=18.3 Hz, 1H), 1.78 (s, 1H), 1.46 (s, 2H), 1.20 (s, 9H).
  • Figure US20200172499A9-20200604-C00254
    Figure US20200172499A9-20200604-C00255
    • (1R,3S)—3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexanecarboxylic acid (MFH-3-79-1)
  • The mixture of MFH-2-83-1 (200 mg, 0.6 mmol), 3-aminocyclohexanecarboxylic acid (138 mg, 0.96 mmol) and DIEA (233 mg, 1.8 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-79-1 (60 mg, yield 26%). LCMS (m/z): 396 [M+H]+.
    • tert-butyl1-((1R,3S)—3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexanecarbonyl)piperidin-4-ylcarbamate (MFH-3-83-1)
  • The mixture of MFH-3-79-1 (60 mg, 0.15 mmol), tert-butyl piperidin-4-ylcarbamate (46 mg, 0.23 mmol), HOBT (31 mg, 0.23 mmol) and EDCI (44 mg, 0.23 mmol) in DCM (6 ml) was stirred for overnight. The reaction mixture was diluted with DCM (25 ml). The organic phase was washed with saturated Na2CO3 and brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-83-1 (80 mg, yield 91%). LCMS (m/z): 578 [M+H]+.
    • (4-aminopiperidin-1-yl)((1R,3S)—3-(5-((5-tert-butyloxazol-2-yl)methylthio)triazol-2-ylamino)cyclohexyl)methanone (MFH-3-85-1)
  • To a solution of MFH-3-83-1 (80 mg, 0.14 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 478 [M+H]+.
    • N-(1-((1R,3S)—3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexanecarbonyl)piperidin-4-yl)acrylamide (MFH-3-88-1)
  • To a solution of MFH-3-85-1 (20 mg, 0.04 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (5 mg, 0.05 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-88-1 (3.7 mg, yield 17%). LCMS (m/z): 532 [M+H]+.
  • Figure US20200172499A9-20200604-C00256
    • 5-((5-tert-butyloxazol-2-yl)methylthio)-N-((1R,3R)-3-(4-nitrophenoxy)cyclohexyl)thiazol-2-amine (MFH-3-97-1)
  • The mixture of MFH-2-83-1 (180 mg, 0.54 mmol), (1R,3R)-3-(4-nitrophenoxy)cyclohexanamine (204 mg, 0.86 mmol) and DIEA (140 mg, 1.1 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-97-1 (80 mg, yield 30%). LCMS (m/z): 489 [M+H]+.
    • N-((1R,3R)-3-(4-aminophenoxy)cyclohexyl)-5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-amine (MFH-3-102-1)
  • To a solution of MFH-3-97-1 (80 mg, 0.16 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (300 mg, 1.3 mmol) and cone. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol(4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-102-1 (40 mg, yield 54%). LCMS (m/z): 459 [M+H]+.
    • N-(4-((1R,3R)-3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexyloxy)phenyl)acrylamide (MFH-3-103-1)
  • To a solution of MFH-3-102-1 (40 mg, 0.09 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (10 mg, 0.11 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-103-1 (9.6 mg, yield 21%). LCMS (m/z): 513 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.00 (s, 1H), 8.04 (d, J=7.3 Hz, 1H), 7.56 (d, J=9.0 Hz, 2H), 6.94 (s, 1H), 6.93-6.89 (m, 2H), 6.71 (s, 1H), 6.39 (dd, J=17.0, 10.1 Hz, 1H), 6.21 (dd, J=17.0, 2.0 Hz, 1H), 5.71 (dd, J=10.1, 2.0 Hz, 1H), 4.66 (s, 1H), 3.94 (s, 2H), 3.83 (s, 1H), 2.01 (d, J=13.3 Hz, 1H), 1.85 (s, 1H), 1.74-1.54 (m, 5H), 1.34 (dd, J=21.1, 11.1 Hz, 1H), 1.18 (s, 9H).
  • Figure US20200172499A9-20200604-C00257
    Figure US20200172499A9-20200604-C00258
    • (R)-tert-butyl3-(5-cyanothiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-72-1)
  • The mixture of 2-bromothiazole-5-carbonitrile (800 mg, 4.23 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (1.1 g, 5.5 mmol) and DIEA (820 mg, 6.35 mmol) in THF (15 mL) was stirred at 80° C. for 6h. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-72-1 (1.3 g, yield 100%). LCMS (m/z): 309 [M+H]+.
    • (R)-tert-butyl 3-(5-(aminomethyl)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-82-1)
  • To a solution of MFH-3-72-1 (300 mg, 1 mmol) and CoCl2 6H2O (232 mg, 1 mmol) in ethanol (8 mL) was added NaBH4 (110 mg, 3 mmol) at room temperature. The vial was sealed and stirred at room temperature for 3h and then was quenched with water. The obtained mixture was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-82-1 (89 g, yield 28%). LCMS (m/z): 313 [M+H]+.
    • (R)-tert-butyl3-((5-chloro-4-trifluoromethyl)pyridin-2-ylamino)methyl)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-99-1)
  • The mixture of MFH-2-82-1 (175 mg, 0.56 mmol), 2-bromo-5-chloro-4-(trifluoromethyl)pyridine (146 mg, 0.56 mmol) and DIEA (108 mg, 0.84 mmol) in NMP (1 mL) was stirred at 80° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-99-1 (90 mg, yield 58%). LCMS (m/z): 492 [M+H]+.
    • (R)-5-((5-chloro-4-(trifluoromethyl)pyridin-2-ylamino)methyl)-N-(piperidin-3-yl)thiazol-2-amine (MFH-3-106-1)
  • To a solution of MFH-3-99-1 (90 mg, 0.18 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 392 [M+H]+.
    • (R)—N-(4-(3-(5-((5-chloro-4-trifluoromethyl)pyridin-2-ylamino)methyl)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-107-1)
  • The mixture of MFH-3-106-1 (20 mg, 0.05 mmol), 4-acrylamidobenzoic acid (10 mg, 0.05 mmol), HOBT (8 mg, 0.06 mmol) and EDCI (11 mg, 0.06 mmol) in DMF (0.5 ml). Then the reaction mixture was stirred for overnight. The reaction mixture was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-107-1 (3.8 mg, yield 13%). LCMS (m/z): 565 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.31 (s, 1H), 8.28 (s, 1H), 7.68 (s, 3H), 7.36 (d, J=7.2 Hz, 2H), 7.25-6.81 (m, 3H), 6.45 (dd, J=17.0, 10.2 Hz, 1H), 6.28 (dd, J=17.0, 1.9 Hz, 1H), 5.78 (dd, J=10.1, 1.9 Hz, 1H), 4.46 (s, 2H), 3.69 (s, 3H), 3.18 (d, J=11.7 Hz, 2H), 1.96 (s, 1H), 1.75 (s, 1H), 1.55 (m, 2H).
  • Figure US20200172499A9-20200604-C00259
    Figure US20200172499A9-20200604-C00260
    • diethyl (5-tert-butyloxazol-2-yl)methylphosphonate (MFH-3-91-1)
  • A solution of 5-tert-butyl-2-(chloromethyl)oxazole (800 mg, 4.61 mmol) in triethyl phosphite (3.83 g, 23.04 mmol) was heated at 120° C. for overnight. The solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 276 [M+H]+.
    • (E)-tert-butyl5-(2-(5-tert-butyloxazol-2-yl)vinyl)thiazol-2-ylcarbamate (MFH-3-94-1)
  • To a solution of MFH-3-91-1 (500 mg, 1.82 mmol) in THF (5 mL) was added t-BuOK (370 mg, 3.3 mmol) at room temperature. The vial was sealed and stirred at room temperature for 10 min. Then, a solution of tert-butyl 5-formylthiazol-2-ylcarbamate (345 mg, 1.5 mmol) in THF (3 mL) was added. After completion, the reaction mixture was quenched with water. The obtained mixture was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-94-1 (440 mg, yield 84%). LCMS (m/z): 350 [M+H]+.
    • (E)-5-(2-(5-tert-butyloxzol-2-yl)vinyl)thiazol-2-amine (MFH-3-98-1)
  • To a solution of MFH-3-94-1 (220 mg, 0.63 mmol) in methanol (5 mL) was added 4N HCl/dioxane (5 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 250 [M+H]+.
    • (E)-2-(2-(2-bromothiazol-5-yl)vinyl)-5-tert-butyloxazole (MFH-3-105-1)
  • To a solution of CuBr2 (172 mg, 0.77 mmol) in acetonitrile (15 mL) at 0° C. was added t-BuONO (79 mg, 0.77 mmol) followed by compound MFH-3-98-1 (160 mg, 0.64 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour, ethyl acetate was added and the organic mixture washed with hydrochloric acid (20 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated under reduced pressure. The residue was chromatographed on silica gel to give the MFH-3-105-1 (50 mg, 25%). LCMS (m/z): 314 [M+H]+.
    • (R,E)-tert-butyl3-(5-(2-(5-tert-butyloxazol-2-yl))vinyl)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-108-1)
  • The mixture of MFH-3-105-1 (50 mg, 0.16 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (51 mg, 0.26 mmol) and DIEA (41 mg, 0.32 mmol) in NMP (0.5 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (10 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-108-1 (40 mg, yield 58%). LCMS (m/z): 433 [M+H]+.
    • (R,E)-5-(2-(5-tert-butyloxazol-2-yl)vinyl)-N-(piperidin-3-yl)thiazol-2-amine (MFH-3-109-1)
  • To a solution of MFH-3-108-1 (40 g, 0.09 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 333 [M+H]+.
    • (R,E)-N-(4-(3-(5-(2-(5-tert-butyloxazol-2-yl)vinyl)triazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-110-1)
  • The mixture of MFH-3-109-1 (35 mg, 0.1 mmol), 4-acrylamidobenzoic acid (30 mg, 0.16 mmol), HOBT (21 mg, 0.16 mmol) and EDCI (30 mg, 0.16 mmol) in DMF (0.5 ml). Then the reaction mixture was stirred for overnight. The reaction mixture was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-110-1 (5 mg, yield 10%). LCMS (m/z): 506 [M+H]+.
  • Figure US20200172499A9-20200604-C00261
    Figure US20200172499A9-20200604-C00262
    • 5-(2-(5-tert-butyloxazol-2-yl)ethyl)thiazol-2-amine (MFH-3-104-1)
  • A mixture of compound MFH-3-94-1 (250 mg, 1 mmol) and 10% Pd/C (20 mg) in MeOH (10 mL) was stirred for 5h at room temperature under H2 balloon. The mixture was filtered through celite. The filtrate was added 4N HCl/dioxane (5 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 252 [M+H]+.
    • 2-(2-(2-bromothiazol-5-yl)ethyl)-5-tert-butyloxazole (MFH-3-114-1)
  • To a solution of CuBr2 (53 mg, 0.24 mmol) in acetonitrile (2 mL) at 0° C. was added t-BuONO (25 mg, 0.24 mmol) followed by compound MFH-3-104-1 (60 mg, 0.24 mmol). The mixture was stirred at 0° C. for one hour, and then was warmed up to room temperature. Ethyl acetate was added and the organic mixture was washed with hydrochloric acid (20 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-3-114-1 (40 mg, 53%). LCMS (m/z): 316 [M+H]+.
    • (R)-tert-butyl3-(5-(2-(5-tert-butyloxazol-2-yl)ethyl)thiazol-2-ylamino)piperidin-1-carboxylate (MFH-3-115-1)
  • The mixture of MFH-3-114-1 (40 mg, 0.13 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (41 mg, 0.2 mmol) and DIEA (33 mg, 0.25 mmol) in NMP (0.5 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (10 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-115-1 (35 mg, yield 63%). LCMS (m/z): 435 [M+H]+.
    • (R)-5-(2-(5-tert-butyloxazol-2-yl)ethyl)-N-(piperidin-3-yl)thiazol-2-amine
  • To a solution of MFH-3-115-1 (35 mg, 0.08 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 335 [M+H]+.
    • (R)—N-(4-(3-(5-(2-(5-tert-butyloxazol-2-yl)ethyl)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-116-1)
  • The mixture of (R)-5-(2-(5-tert-butyloxazol-2-yl)ethyl)-N-(piperidin-3-yl)thiazol-2-amine (23 mg, 0.07 mmol), 4-acrylamidobenzoic acid (15 mg, 0.08 mmol), HOBT (12 mg, 0.09 mmol) and EDCI (17 mg, 0.09 mmol) in DMF (0.5 ml) was stirred for overnight. The reaction mixture was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-116-1 (5.5 mg, yield 16%). LCMS (m/z): 508 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.38 (s, 1H), 8.29 (d, J=7.5 Hz, 1H), 7.82 (d, J=8.8 Hz, 2H), 7.74 (d, J=8.8 Hz, 2H), 6.96 (s, 1H), 6.68 (s, 1H), 6.45 (dd, J=17.0, 10.2 Hz, 1H), 6.29 (dd, J=17.0, 1.9 Hz, 1H), 5.79 (dd, J=10.1, 1.9 Hz, 1H), 3.87 (dd, J=12.3, 4.0 Hz, 1H), 3.75-3.63 (m, 2H), 3.13-2.99 (m, 4H), 2.96 (t, J=6.8 Hz, 2H), 1.88 (m, 2H), 1.63 (m, 2H), 1.22 (s, 9H).
  • Figure US20200172499A9-20200604-C00263
    Figure US20200172499A9-20200604-C00264
    • 2-bromo-5-((3-(trifluoromethyl)benzyloxy)methyl)thiazole (MFH-3-111-1)
  • The mixture of (2-bromothiazol-5-yl)methanol (180 mg, 0.93 mmol), 1-(bromomethyl)-3-(trifluoromethyl)benzene (288 mg, 1.2 mmol) and NaOH (67 mg, 1.67 mmol) in DMF (2 mL) was stirred at 120° C. for 3h. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (PE/EA=0-50%) to obtain MFH-3-111-1 (160 mg, yield 49%). LCMS (m/z): 353 [M+H]+.
    • (R)-tert-butyl35-((3-(trifluoromethyl)benzyloxy)methyl)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-112-1)
  • The mixture of MFH-3-111-1 (160 mg, 0.34 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (109 mg, 0.55 mmol) and DIEA (88 mg, 0.68 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-112-1 (35 mg, yield 22%). LCMS (m/z): 472 [M+H]+.
    • (R)—N-(piperidin-3-yl)-5-((3-(trifluoromethyl)benzyloxy)methyl)thiazol-2-amine (MFH-3-119-1)
  • To a solution of MFH-3-112-1 (35 mg, 0.08 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 372 [M+H]+.
    • (R)—N-(4-(3-(5-((3-(trifluoromethyl)benzyloxy)methyl)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-120-1)
  • The mixture of MFH-3-119-1 (23 mg, 0.06 mmol), 4-acrylamidobenzoic acid (15 mg, 0.08 mmol), HOBT (12 mg, 0.09 mmol) and EDCI (17 mg, 0.09 mmol) in DMF (0.5 ml). Then the reaction mixture was stirred for overnight. The reaction mixture was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-120-1 (8.7 mg, yield 26%). LCMS (m/z): 545 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.32 (s, 1H), 7.72-7.57 (m, 7H), 7.37 (d, J=5.1 Hz, 3H), 6.47-6.40 (m, 1H), 6.27 (dd, J=16.6, 6.9 Hz, 1H), 5.77 (t, J=8.3 Hz, 1H), 4.58 (d, J=8.2 Hz, 2H), 4.56 (s, 2H), 3.78 (s, 3H), 3.20 (d, J=6.7 Hz, 2H), 1.98 (s, 1H), 1.76 (s, 1H), 1.55 (m, 2H).
  • Figure US20200172499A9-20200604-C00265
    Figure US20200172499A9-20200604-C00266
    • 2-(((2-bromothiazol-5-yl)methoxy)methyl)-5-tert-butyloxazole (MFH-3-121-1)
  • The mixture of (2-bromothiazol-5-yl)methanol (220 mg, 1.1 mmol), 5-tert-butyl-2-(chloromethyl)oxazole (256 mg, 1.5 mmol) and NaOH (82 mg, 2.04 mmol) in DMF (2 mL) was stirred at 120° C. for 3h. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (PE/EA=0-50%) to obtain MFH-3-111-1 (170 mg, yield 45%). LCMS (m/z): 332 [M+H]+.
    • (R)-tert-butyl3-(5-(((5-tert-butyloxazol-2-yl)methoxy)methyl)triazol-2-ylamino)piperidine-1-carboxylate (MFH-3-123-1)
  • The mixture of MFH-3-121-1 (170 mg, 0.51 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (164 mg, 0.82 mmol) and DIEA (133 mg, 1 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-123-1 (50 mg, yield 22%). LCMS (m/z): 451 [M+H]+.
    • (R)-5-(((5-tert-butyloxazol-2-yl)methoxy)methyl)-N-(piperidin-3-yl)thiazol-2-amine (MFH-3-126-1)
  • To a solution of MFH-3-123-1 (50 mg, 0.11 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 372 [M+H]+.
    • (R)—N-(4-(3-(((5-tert-butyloxazol-2-yl)methoxy)methyl)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-128-1)
  • The mixture of MFH-3-126-1 (23 mg, 0.06 mmol), 4-acrylamidobenzoic acid (15 mg, 0.08 mmol), HOBT (12 mg, 0.09 mmol) and EDCI (17 mg, 0.09 mmol) in DMF (0.5 ml) was stirred for overnight. The reaction mixture was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-128-1 (7 mg, yield 22%). LCMS (m/z): 524 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.37 (s, 1H), 8.33 (d, J=38.9 Hz, 1H), 7.84 (d, J=8.5 Hz, 2H), 7.75 (d, J=8.4 Hz, 2H), 7.37 (d, J=8.3 Hz, 1H), 6.89-6.71 (m, 1H), 6.46 (dd, J=16.9, 10.1 Hz, 1H), 6.29 (d, J=17.0 Hz, 1H), 5.80 (d, J=10.0 Hz, 1H), 4.59-4.40 (m, 2H), 4.05 (s, 1H), 3.99-3.85 (m, 2H), 3.33 (dd, J=31.2, 10.4 Hz, 2H), 3.00 (m, 2H), 1.93 (d, J=15.1 Hz, 1H), 1.84 (s, 1H), 1.62 (s, 2H), 1.23 (s, 9H).
  • Figure US20200172499A9-20200604-C00267
    Figure US20200172499A9-20200604-C00268
    • (R)-tert-butyl3-(5-(((5-tert-butyloxazol-2-yl)methylamino)methyl)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-90-1)
  • The mixture of MFH-2-82-1 (160 mg, 0.51 mmol), 5-tert-butyl-2-(chloromethyl)oxazole (89 mg, 0.51 mmol) and DIEA (132 mg, 1 mmol) in NMP (1 mL) was stirred at 80° C. for overnight. The solution was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-90-1 (133 mg, yield 58%). LCMS (m/z): 450 [M+H]+.
    • (R)-5-(((5-tert-butyloxazol-2-yl)methylamino)methyl)-N-(piperidin-3-yl)thiazol-2-amine (MFH-3-136-1)
  • To a solution of MFH-3-90-1 (60 mg, 0.13 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 350 [M+H]++.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylamino)methyl)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-137-1)
  • The mixture of MFH-3-136-1 (30 mg, 0.09 mmol), 4-acrylamidobenzoic acid (17 mg, 0.09 mmol) and TEA (9 mg, 0.09 mmol) in DMF (1 ml). The reaction mixture was cooled to −60° C., and HATU (33 mg, 0.09 mmol) was added in the reaction mixture. The reaction mixture was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-137-1 (18 mg, yield 38%). LCMS (m/z): 523 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.31 (s, 1H), 8.79-8.59 (m, 2H), 8.10-7.97 (m, 1H), 7.69 (s, 1H), 7.37 (s, 1H), 7.13 (d, J=6.5 Hz, 1H), 6.96 (dd, J=9.8, 4.5 Hz, 1H), 6.78 (s, 1H), 6.43 (d, J=6.7 Hz, 1H), 6.28 (s, 1H), 5.79 (dd, J=12.2, 4.2 Hz, 1H), 4.31 (s, 2H), 3.86 (s, 2H), 3.72 (s, 2H), 3.43 (d, J=10.6 Hz, 1H), 2.93-2.75 (m, 2H), 2.00 (d, J=8.6 Hz, 1H), 1.89 (d, J=22.0 Hz, 1H), 1.59 (m, 2H), 1.23 (s, 9H).
  • Figure US20200172499A9-20200604-C00269
    • (R)-tert-butyl4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)triazol-2-ylamino)piperidin-1-ylsulfonyl)phenylcarbamate (MFH-3-147-1)
  • The mixture of MFH-2-85-1 (60 mg, 0.17 mmol) and TEA (26 mg, 0.26 mmol) in DCM (1 ml) was cooled to 0° C. and then a solution of tert-butyl 4-(chlorosulfonyl)phenylcarbamate (50 mg, 0.17 mmol) in DCM (1 mL) was added. The reaction mixture was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-147-1 (80 mg, yield 78%). LCMS (m/z): 608 [M+H]+.
    • (R)—N-(1-(4-aminophenylsulfonyl)piperidin-3-yl)-5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-amine (MFH-3-148-1)
  • To a solution of MFH-3-147-1 (80 mg, 0.13 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 507 [M+H]+.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-ylsulfonyl)phenyl)acrylamide (MFH-3-151-1)
  • To a solution of MFH-3-148-1 (30 mg, 0.06 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (7 mg, 0.08 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-151-1 (8.5 mg, yield 25%). LCMS (m/z): 561 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.56 (d, J=22.3 Hz, 1H), 8.00 (d, J=7.3 Hz, 1H), 7.93-7.89 (m, 1H), 7.87 (dd, J=11.3, 4.4 Hz, 1H), 7.83-7.75 (m, 1H), 7.72-7.68 (m, 1H), 6.98 (d, J=2.7 Hz, 1H), 6.75-6.70 (m, 1H), 6.51-6.42 (m, 1H), 6.32 (ddd, J=17.0, 3.9, 1.9 Hz, 1H), 5.83 (ddd, J=10.1, 6.1, 1.9 Hz, 1H), 3.96 (d, J=3.8 Hz, 2H), 3.43-3.34 (m, 1H), 3.25 (d, J=11.8 Hz, 1H), 3.07-2.93 (m, 1H), 2.86 (dd, J=12.6, 9.7 Hz, 1H), 2.32-2.22 (m, 1H), 1.77 (d, J=6.7 Hz, 1H), 1.67 (d, J=3.5 Hz, 1H), 1.52 (d, J=10.2 Hz, 1H), 1.34 (dd, J=18.1, 10.1 Hz, 1H), 1.24-1.16 (m, 9H).
  • Figure US20200172499A9-20200604-C00270
    Figure US20200172499A9-20200604-C00271
    • tert-butyl 5-(benzylthio)indoline-1-carboxylate (MFH-3-158-1)
  • A mixture of tert-butyl 5-bromoindoline-1-carboxylate (600 mg, 2.02 mmol), phenylmethanethiol (276 mg, 2.22 mmol), Pd2(dba)3 (185 mg, 0.2 mmol), Xantphos (117 mg, 0.2 mmmol), and DIEA (783 mg, 6.06 mmol) in toluene (25 mL) was refluxed under N2 atmosphere for 5h. After cooling to room temperature, ethyl acetate (50 mL) and H2O (50 mL) were added to the mixture, and insoluble materials were removed by filtration. The filtrate was diluted with ethyl acetate (50 mL) and was washed with water, 0.2 M hydrochloric acid, aqueous NaHCO3 solution, and brine. The organic layer was dried over Na2SO4 and concentrated under reduced pressure. The residue was crystallized from AcOEt-i-Pr2O to give the title compound as a yellow solid (660 mg, 96%). LCMS (m/z): 342 [M+H]+.
    • tert-butyl 5-(chlorosulfonyl)indoline-1-carboxylate (MFH-3-159-1)
  • To a mixture of compound MFH-3-158-1 (660 g, 1.94 mmol), acetic acid (6 mL) in water (3 mL) was added N-chlorosuccinimide (1.1 g, 7.74 mol) at 0° C. The mixture was stirred at room temperature for 4 h. Precipitated solid was collected by filtration, washed with water and dried to give the title compound as a pale yellow solid (400 mg, 65%). This compound was used for the next step without further purification.
    • (R)-tert-butyl5-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-ylsulfonyl)indoline-1-carboxylate (MFH-3-162-1)
  • The mixture of MFH-2-85-1 (60 mg, 0.17 mmol) and TEA (26 mg, 0.26 mmol) in DCM (1 ml) was cooled to 0° C. and a solution of MFH-3-159-1 (54 mg, 0.17 mmol) in DCM (1 mL) was added. And reaction completed, the reaction mixture was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-162-1 (82 mg, yield 76%). LCMS (m/z): 634 [M+H]+.
    • (R)-5-((5-tert-butyloxazol-2-yl)methylthio)-N-(1-(indolin-5-ylsulfonyl)piperidin-3-yl)thiazol-2-amine (MFH-3-164-1)
  • To a solution of MFH-3-162-1 (82 mg, 0.13 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 534 [M+H]+.
    • (R)-1-(5-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-ylsulfonyl)indolin-1-yl)prop-2-en-1-one (MFH-3-168-1)
  • To a solution of MFH-3-164-1 (20 mg, 0.04 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (5 mg, 0.05 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-168-1 (5 mg, yield 23%). LCMS (m/z): 588 [M+H]+. 1H NMR (500 MHz, DMSO) δ 8.29 (s, 1H), 7.94 (d, J=7.4 Hz, 1H), 7.57 (dd, J=12.2, 3.8 Hz, 2H), 6.96 (s, 1H), 6.81-6.74 (m, 1H), 6.74 (s, 1H), 6.35 (dd, J=16.7, 2.0 Hz, 1H), 5.89 (dd, J=10.3, 2.0 Hz, 1H), 4.29 (t, J=8.7 Hz, 2H), 3.96 (s, 2H), 3.69 (s, 1H), 3.55 (d, J=8.0 Hz, 1H), 3.25 (t, J=8.4 Hz, 3H), 2.31-2.24 (m, 1H), 2.18 (t, J=7.4 Hz, 1H), 1.77 (d, J=6.6 Hz, 2H), 1.49 (dd, J=17.4, 10.0 Hz, 2H), 1.24 (s, 9H).
  • Figure US20200172499A9-20200604-C00272
    Figure US20200172499A9-20200604-C00273
    • 5-(pyridin-4-ylmethylthio)thiazol-2-amine (MFH-3-146-1)
  • To a solution of compound MFH-2-76-1 (300 mg, 1.91 mmol) in EtOH (5 ml) was added NaBH4 (144 mg, 3.82 mmol) room temperature. The mixture was stirred for 1h, and then acetone (3 ml) was slowly introduced. After 1 h, a solution of 4-(bromomethyl)pyridine hydrobromide (483 mg, 1.91 mmol) in EtOH (3 ml) was added. The resulting dark reaction mixture was heated to reflux for 1h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), and concentrated in vacuo to give a crude solid which was triturated with diethyl ether/hexane to provide compound MFH-3-146-1 (240 mg, 56%) as solid LCMS (m/z): 224 [M+H]+.
    • 2-bromo-5-(pyridin-4-ylmethylthio)thiazole (MFH-3-153-1)
  • To a solution of CuBr2 (288 mg, 1.29 mmol) in acetonitrile (8 mL) at 0° C. was added t-BuONO (133 mg, 1.29 mmol) followed by compound MFH-3-146-1 (240 g, 1.08 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour. Ethyl acetate was added and the organic mixture washed with hydrochloric acid (20 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-3-153-1 (130 mg, 42%). LCMS (m/z): 288 [M+H]+.
    • (R)-tert-butyl3-(5-(pyridin-4-ylmethylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-156-1)
  • The mixture of MFH-3-153-1 (130 mg, 0.45 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (145 mg, 0.72 mmol) and DIEA (117 mg, 0.91 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-156-1 (90 mg, yield 49%). LCMS (m/z): 407 [M+H]+.
    • (R)—N-(piperidin-3-yl)-5-(pyridin-4-ylmethylthio)thiazol-2-amine (MFH-3-157-1)
  • To a solution of MFH-3-156-1 (90 mg, 0.22 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 307 [M+H]+.
    • (R)-tert-butyl4-(3-(5-(pyridin-4-ylmethylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenylcarbamate (MFH-3-177-1)
  • The mixture of MFH-3-157-1 (60 mg, 0.2 mmol), 4-(tert-butoxycarbonylamino)benzoic acid (15 mg, 0.08 mmol), HOBT (12 mg, 0.09 mmol) and EDCI (60 mg, 0.26 mmol) in DMF (1 ml) was stirred for overnight. The reaction mixture was diluted with chloroform and iso-propanol (4:1). The saturated Na2CO3 was added and the reaction mixture was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-177-1 (90 mg, yield 86%). LCMS (m/z): 526 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-(pyridin-4-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-178-1)
  • To a solution of MFH-3-177-1 (90 mg, 0.17 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 426 [M+H]+.
    • (R)—N-(4-(3-(5-(pyridin-4-ylmethylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-179-1)
  • To a solution of MFH-3-178-1 (40 mg, 0.09 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (11 mg, 0.12 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-179-1 (4.4 mg, yield 10%). LCMS (m/z): 480 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.30 (s, 1H), 8.06 (s, 1H), 7.85 (s, 2H), 7.68 (s, 2H), 7.36 (s, 2H), 7.25-7.02 (m, 2H), 6.80 (s, 1H), 6.49-6.37 (m, 1H), 6.27 (d, J=16.9 Hz, 1H), 5.77 (d, J=10.1 Hz, 1H), 4.12 (s, 1H), 3.99 (s, 2H), 3.43-3.31 (m, 2H), 3.14 (d, J=28.5 Hz, 2H), 1.95 (s, 1H), 1.76 (s, 1H), 1.55 (s, 2H).
  • Figure US20200172499A9-20200604-C00274
    Figure US20200172499A9-20200604-C00275
    • 5-(pyridin-3-ylmethylthio)thiazol-2-amine (MFH-3-171-1)
  • To a solution of compound MFH-2-76-1 (300 mg, 1.91 mmol) in EtOH (5 ml) was added NaBH4 (144 mg, 3.82 mmol) portionwise at room temperature. The mixture was stirred for 1h, and then acetone (3 ml) was slowly introduced. After 1 h, a solution of 3-(bromomethyl)pyridine hydrobromide (483 mg, 1.91 mmol) in EtOH (3 mL) was added. The resulting dark reaction mixture was heated to reflux for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), and concentrated in vacuo to give a crude solid which was triturated with diethyl ether/hexane to provide compound MFH-3-171-1 (310 mg, 73%) LCMS (m/z): 224 [M+H]+.
    • 2-bromo-5-(pyridin-3-ylmethylthio)thiazole (MFH-3-180-1)
  • To a solution of CuBr2 (370 mg, 1.66 mmol) in acetonitrile (20 mL) at 0° C. was added t-BuONO (172 mg, 1.66 mmol) followed by compound MFH-3-171-1 (310 mg, 1.39 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour, ethyl acetate was added and the organic mixture washed with hydrochloric acid (2×50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-3-180-1 (288 mg, 72%). LCMS (m/z): 288 [M+H]+.
    • (R)-tert-butyl3-(5-(pyridin-3-ylmethylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-182-1)
  • The mixture of MFH-3-180-1 (288 mg, 1 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (320 mg, 1.6 mmol) and DIEA (194 mg, 1.5 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-182-1 (180 mg, yield 44%). LCMS (m/z): 407 [M+H]+.
    • (R)—N-(piperidin-3-yl-5-(pyridin-3-ylmethylthio)thiazol-2-amine (MFH-3-185-1)
  • To a solution of MFH-3-182-1 (180 mg, 0.44 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 307 [M+H]+.
    • (R)-(4-nitrophenyl)(3-(5-(pyridin-3-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-186-1)
  • The mixture of MFH-3-185-1 (120 mg, 0.39 mmol), 4-nitrobenzoyl chloride (72 mg, 0.39 mmol) in pyridine (2 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 456 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-(pyridin-3-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-187-1)
  • To a solution of MFH-3-186-1 (178 mg, 0.39 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (881 mg, 3.9 mmol) and cone. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-187-1 (20 mg, yield 12%). LCMS (m/z): 426 [M+H]+.
    • (R)—N-(4-(3-(5-(pyridin-3-ylmethylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-191-1)
  • To a solution of MFH-3-187-1 (20 mg, 0.05 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (6 mg, 0.06 mmol) in DCM (0.5 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-191-1 (6 mg, yield 26%). LCMS (m/z): 480 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.30 (s, 1H), 8.58 (d, J=53.1 Hz, 2H), 8.00 (d, J=44.0 Hz, 2H), 7.78-7.62 (m, 2H), 7.40 (d, J=29.7 Hz, 2H), 7.14 (dd, J=67.0, 35.1 Hz, 1H), 6.82 (s, 1H), 6.43 (dd, J=17.4, 10.0 Hz, 1H), 6.28 (t, J=12.8 Hz, 1H), 5.84-5.74 (m, 1H), 4.04 (s, 1H), 3.98 (s, 2H), 3.31 (s, 2H), 3.17 (s, 2H), 1.96 (s, 1H), 1.75 (s, 1H), 1.54 (s, 2H).
  • Figure US20200172499A9-20200604-C00276
    Figure US20200172499A9-20200604-C00277
    • (1R,3R)-3-(4-nitro-2-(trifluoromethyl)phenoxy)cyclohexanamine (MFH-3-166-1)
  • To a solution of compound (1R,3R)-3-aminocyclohexanol hydrochloride (120 mg, 0.8 mmol) in absolute DMF (1 ml) was added NaH (130 mg, 3.3 mmol) portionwise at 0° C. The mixture was stirred for 1 h, and then 1-fluoro-4-nitro-2-(trifluoromethyl)benzene (170 mg, 0.8 mmol) was slowly introduced. After 3h, the water was added slowly. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-166-1 (50 mg, yield 20%). LCMS (m/z): 305 [M+H]+.
    • 5-((5-tert-butyloxazol-2-yl)methylthio)-N-((1R,3R)-3-(4-nitro-2-(trifluoromethyl)phenoxy)cyclohexyl)thiazol-2-amine (MFH-3-183-1)
  • The mixture of MFH-2-83-1 (55 mg, 0.16 mmol), MFH-3-166-1 (50 mg, 0.16 mmol) and DIEA (32 mg, 0.25 mmol) in NMP (0.5 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-183-1 (28 mg, yield 31%). LCMS (m/z): 557 [M+H]+.
    • N-((1R,3R)-3-(4-amino-2-(trifluoromethyl)phenoxy)cyclohexyl)-5-((5-(tert-butyloxazol-2-yl)methylthio)thiazol-2-amine (MFH-3-188-1)
  • To a solution of MFH-3-183-1 (28 mg, 0.05 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (113 mg, 0.5 mmol) and conc. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-188-1 (20 mg, yield 75%). LCMS (m/z): 527 [M+H]+.
    • N-(4-((1R,3R)-3-(5-(((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)cyclohexyloxy)-3-(trifluoromethyl)phenyl)acrylamide (MFH-3-192-1)
  • To a solution of MFH-3-188-1 (20 mg, 0.04 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (5 mg, 0.05 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-192-1 (5.4 mg, yield 24%). LCMS (m/z): 581 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.27 (s, 1H), 8.04 (t, J=5.4 Hz, 2H), 7.82 (dd, J=9.0, 2.5 Hz, 1H), 7.25 (t, J=8.1 Hz, 1H), 6.95 (d, J=5.6 Hz, 1H), 6.70 (d, J=7.3 Hz, 1H), 6.39 (dd, J=17.0, 10.1 Hz, 1H), 6.26 (dd, J=17.0, 2.0 Hz, 1H), 5.77 (dd, J=10.1, 2.0 Hz, 1H), 4.92 (s, 1H), 3.93 (d, J=0.8 Hz, 2H), 2.10 (d, J=14.5 Hz, 1H), 1.93 (d, J=14.3 Hz, 1H), 1.79 (s, 1H), 1.65 (dd, J=22.7, 11.5 Hz, 2H), 1.59 (s, 2H), 1.32 (m, 1H), 1.23 (dd, J=11.2, 6.2 Hz, 1H), 1.17 (s, 9H).
  • Figure US20200172499A9-20200604-C00278
    Figure US20200172499A9-20200604-C00279
    • 5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)thiazol-2-amine (MFH-3-184-1)
  • To a solution of compound MFH-2-76-1 (300 mg, 1.91 mmol) in absolute EtOH (5 ml) was added NaBH4 (144 mg, 3.82 mol) at room temperature. The mixture was stirred for 1 h, and then acetone (3 ml) was slowly introduced. After 1 h, a solution of 5-(chloromethyl)-2-(trifluoromethyl)pyrimidine (375 mg, 1.91 mmol) in EtOH (3 ml) was added. The resulting dark reaction mixture was heated to reflux for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), and concentrated in vacuo to give a crude solid which was triturated with diethyl ether/hexane to provide compound MFH-3-184-1 (500 mg, 90%) LCMS (m/z): 293 [M+H]+.
    • 2-bromo-5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)thiazole (MFH-3-189-1)
  • To a solution of CuBr2 (458 mg, 2.05 mmol) in acetonitrile (15 mL) at 0° C. was added t-BuONO (211 mg, 2.05 mmol) followed by compound MFH-3-184-1 (500 mg, 1.71 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour. Ethyl acetate was added and the organic mixture was washed with hydrochloric acid (50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-3-189-1 (430 mg, 70%). LCMS (m/z): 357 [M+H]+.
    • (R)-tert-butyl3-(5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-190-1)
  • The mixture of MFH-3-189-1 (430 mg, 1.21 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (362 mg, 1.81 mmol) and DIEA (312 mg, 2.4 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-190-1 (380 mg, yield 66%). LCMS (m/z): 476 [M+H]+.
    • (R)—N-(piperidin-3-yl)-5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)thiazol-2-amine (MFH-3-194-1)
  • To a solution of MFH-3-190-1 (380 mg, 0.8 mmol) in methanol (5 mL) was added 4N HCl/dioxane (5 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 376 [M+H]+.
    • (R)-(4-nitrophenyl)(3-(5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)triazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-195-1)
  • The mixture of MFH-3-194-1 (230 mg, 0.61 mmol), 4-nitrobenzoyl chloride (113 mg, 0.61 mmol) in pyridine (2 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 525 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-198-1)
  • To a solution of MFH-3-195-1 (280 mg, 0.53 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (965 mg, 4.27 mmol) and cone. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-198-1 (200 mg, yield 76%). LCMS (m/z): 495 [M+H]+.
    • (R)—N-(4-(3-(5-((2-(trifluoromethyl)pyrimidin-5-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-201-1)
  • To a solution of MFH-3-198-1 (40 mg, 0.08 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (10 mg, 0.1 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-201-1 (9.8 mg, yield 22%). LCMS (m/z): 549 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.26 (s, 1H), 8.81 (s, 2H), 8.11 (s, 1H), 7.79-7.59 (m, 2H), 7.38 (t, J=13.1 Hz, 2H), 6.99-6.73 (m, 1H), 6.50-6.35 (m, 1H), 6.34-6.17 (m, 1H), 5.80 (m, 1H), 4.01 (s, 2H), 3.81-3.73 (m, 3H), 3.45-3.20 (m, 2H), 1.94 (d, J=18.7 Hz, 1H), 1.78 (m, 1H), 1.54 (s, 2H).
  • Figure US20200172499A9-20200604-C00280
    Figure US20200172499A9-20200604-C00281
    • 5-(pyridin-2-ylmethylthio)thiazol-2-amine (MFH-3-170-1)
  • To a solution of compound MFH-2-7-1 (300 mg, 1.91 mmol) in absolute EtOH (5 ml) was added NaBH4 (144 mg, 3.82 mmol) portionwise at room temperature. The mixture was stirred for 1h, and then acetone (3 ml) was slowly introduced. After 1 h, a solution of 2-(chloromethyl)pyridine hydrochloride (313 mg, 1.91 mmol) in EtOH (3 ml) was added. The resulting dark reaction mixture was heated to reflux for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), and concentrated in vacuo to give a crude solid which was triturated with diethyl ether/hexane to provide compound MFH-3-170-1 (260 mg, 61%) LCMS (m/z): 224 [M+H]+.
    • 2-bromo-5-(pyridin-2-ylmethylthio)thiazole (MFH-3-176-1)
  • To a solution of CuBr2 (313 mg, 1.4 mmol) in acetonitrile (20 mL) at 0° C. was added t-BuONO (144 mg, 1.4 mmol) followed by compound MFH-3-170-1 (260 mg, 1.16 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour. Ethyl acetate was added and the organic mixture washed with hydrochloric acid (2×50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-3-176-1 (90 mg, 27%). LCMS (m/z): 288 [M+H]+.
    • (R)-tert-butyl3-(5-(pyridin-2-ylmethylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-196-1)
  • The mixture of MFH-3-176-1 (180 mg, 0.63 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (200 mg, 1 mmol) and DIEA (162 mg, 1.3 mmol) in NMP (I mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-196-1 (120 mg, yield 47%). LCMS (m/z): 407 [M+H]+.
    • (R)—N-(piperidin-3-yl)-5-(pyridin-2-ylmethylthio)thiazol-2-amine (MFH-3-197-1)
  • To a solution of MFH-3-196-1 (120 mg, 0.3 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 307 [M+H]+.
    • (R)-(4-nitrophenyl)(3-(5-(pyridin-2-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-199-1)
  • The mixture of MFH-3-197-1 (80 mg, 0.26 mmol), 4-nitrobenzoyl chloride (48 mg, 0.26 mmol) in pyridine (2 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 456 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-(pyridin-2-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-200-1)
  • To a solution of MFH-3-199-1 (118 mg, 0.261 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (472 mg, 2.1 mmol) and conc. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-3-200-1 (60 mg, yield 54%). LCMS (m/z): 426 [M+H]+.
    • (R)—N-(4-(3-(5-(pyridin-3-ylmethylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-3-191-1)
  • To a solution of MFH-3-187-1 (40 mg, 0.1 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (12 mg, 0.12 mmol) in DCM (0.2 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-3-203-1 (8.4 mg, yield 19%). LCMS (m/z): 480 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.30 (s, 1H), 8.62 (s, 1H), 8.06 (d, J=50.5 Hz, 2H), 7.72 (d, J=21.6 Hz, 2H), 7.51 (s, 2H), 7.37 (s, 2H), 6.86 (s, 1H), 6.44 (dd, J=17.1, 10.2 Hz, 1H), 6.27 (d, J=16.9 Hz, 1H), 5.85-5.74 (m, 1H). 4.04 (s, 1H), 3.98 (s, 2H), 3.31 (s, 2H), 3.17 (s, 2H), 1.96 (s, 1H), 1.75 (s, 1H), 1.54 (s, 2H).
  • Figure US20200172499A9-20200604-C00282
    Figure US20200172499A9-20200604-C00283
    • 5-((tetrahydro-2H-pyran-4-yl)methylthio)thiazol-2-amine (MFH-3-202-1)
  • To a solution of compound MFH-2-76-1 (194 mg, 1.23 mmol) in absolute EtOH (4 ml) was added NaBH4 (93 mg, 2.47 mmol) at room temperature. The mixture was stirred for 1h, and then acetone (2 ml) was slowly introduced. After 1h, a solution of 4-(bromomethyl)-tetrahydro-2H-pyran (221 mg, 1.23 mmol) in EtOH (2 ml) was added. The resulting dark reaction mixture was heated to reflux for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), and concentrated in vacuo to give a crude solid which was triturated with diethyl ether/hexane to provide compound MFH-3-202-1 (250 mg, 88%) LCMS (m/z): 231 [M+H]+.
    • 2-bromo-5-((tetrahydro-2H-pyran-4-yl)methylthio)thiazole (MFH-3-204-1)
  • To a solution of CuBr2 (290 mg, 1.3 mmol) in acetonitrile (15 mL) at 0° C. was added t-BuONO (175 mg, 1.3 mmol) followed by compound MFH-3-202-1 (250 mg, 1.1 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour, ethyl acetate was added and the organic mixture washed with hydrochloric acid (2×30 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-3-204-1 (160 mg, 50%). LCMS (m/z): 295 [M+H]+.
    • (R)-tert-butyl3-(5-((tetrahydro-2H-pyran-4-yl)methylthio)thiazol-2-ylamino)piperidine-1-carboxylate (MFH-3-205-1)
  • The mixture of MFH-3-204-1 (160 mg, 0.54 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (174 mg, 0.87 mmol) and DIEA (112 mg, 0.87 mmol) in NMP (0.5 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-3-205-1 (120 mg, yield 53%). LCMS (m/z): 414 [M+H]+.
    • (R)—N-(piperidin-3-yl)-5-((tetrahydro-2H-pyran-4-yl)methylthio)thiazol-2-amine (MFH-3-206-1)
  • To a solution of MFH-3-205-1 (120 mg, 0.3 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 314 [M+H]+.
    • (R)-(4-nitrophenyl)3-(5-((tetrahydro-2H-pyran-4-yl)methylthio)triazol-2-ylamino)piperidin-1-yl)methanone (MFH-3-207-1)
  • The mixture of MFH-3-206-1 (80 mg, 0.26 mmol), 4-nitrobenzoyl chloride (48 mg, 0.26 mmol) in pyridine (2 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 463 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-((tetrahydro-2H-pyran-4-yl)methylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-4-2-1)
  • To a solution of MFH-3-207-1 (120 mg, 0.26 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (472 mg, 2.1 mmol) and conc. HCl (0.2 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-4-2-1 (60 mg, yield 54%). LCMS (m/z): 433 [M+H]+.
    • (R)—N-(4-(3-(5-((tetrahydro-2H-pyran-4-yl)methylthio)triazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-4-4-1)
  • To a solution of MFH-4-2-1 (30 mg, 0.07 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (8 mg, 0.09 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-4-4-1 (4.6 mg, yield 13%). LCMS (m/z): 487 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.32 (d, J=28.3 Hz, 1H), 8.07 (s, 1H), 7.77-7.62 (m, 2H), 7.40 (dd, J=32.0, 7.9 Hz, 2H), 7.15-6.93 (m, 1H), 6.45 (dd, J=17.0, 10.1 Hz, 1H), 6.28 (dd, J=17.0, 1.9 Hz, 1H), 5.79 (dd, J=10.1, 1.9 Hz, 1H), 3.83 (d, J=9.4 Hz, 2H), 3.62 (s, 4H), 3.24 (t, J=11.1 Hz, 2H), 3.11 (s, 1H), 2.58 (d, J=6.4 Hz, 1H), 1.98 (d, J=12.6 Hz, 1H), 1.77 (s, 1H), 1.70 (d, J=11.6 Hz, 2H), 1.57 (m, 3H), 1.21 (m, 3H).
  • Figure US20200172499A9-20200604-C00284
    Figure US20200172499A9-20200604-C00285
    • 5-(pyrimidin-5-ylmethylthio)thiazol-2-amine (MFH-3-208-1)
  • To a solution of compound MFH-2-76-1 (230 mg, 1.46 mmol) in absolute EtOH (5 ml) was added NaBH4 (166 mg, 4.38 mmol) at room temperature. The mixture was stirred for 1h, and then acetone (3 ml) was slowly introduced. After 1 h, a solution of 5-(chloromethyl)pyrimidine (241 mg, 1.46 mmol) in EtOH (3 ml) was added. The resulting dark reaction mixture was heated to reflux for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), and concentrated in vacuo to give a crude solid which was triturated with diethyl ether/hexane to provide compound MFH-3-208-1 (180 mg, 55%) LCMS (m/z): 225 [M+H]+.
    • 2-bromo-5-(pyrimidin-5-ylmethylthio)thiazole (MFH-4-1-1)
  • To a solution of CuBr2 (215 mg, 0.96 mmol) in acetonitrile (15 mL) at 0° C. was added t-BuONO (99 mg, 0.96 mmol) followed by compound MFH-3-208-1 (180 mg, 0.8 mmol). The mixture was stirred at 0° C. for one hour, then at room temperature for one hour, ethyl acetate was added and the organic mixture washed with hydrochloric acid (2×50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was chromatographed on silica gel to give the MFH-4-1-1 (90 mg, 39%). LCMS (m/z): 289 [M+H]+.
    • (R)-tert-butyl3-(5-(pyrimidin-5-ylmethylthio)triazol-2-ylamino)piperidine-1-carboxylate (MFH-4-3-1)
  • The mixture of MFH-4-1-1 (90 mg, 0.31 mmol), (R)-tert-butyl 3-aminopiperidine-1-carboxylate (100 mg, 0.5 mmol) and DIEA (65 mg, 0.5 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (20 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-4-3-1 (66 mg, yield 52%). LCMS (m/z): 408 [M+H]+.
    • (R)—N-(piperidin-3-yl)-5-(pyrimidin-5-ylmethylthio)thiazol-2-amine (MFH-4-5-1)
  • To a solution of MFH-4-3-1 (66 mg, 0.16 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 308 [M+H]+.
    • (R)-(4-nitrophenyl)(3-(5-(pyrimidin-5-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-4-6-1)
  • The mixture of MFH-4-5-1 (50 mg, 0.16 mmol), 4-nitrobenzoyl chloride (30 mg, 0.16 mmol) in pyridine (2 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 457 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-(pyrimidin-5-ylmethylthio)thiazol-2-ylamino)piperidin-1-yl)methanone (MFH-4-7-1)
  • To a solution of MFH-4-6-1 (74 mg, 0.16 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (292 mg, 1.3 mmol) and cone. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-4-7-1 (15 mg, yield 22%). LCMS (m/z): 427 [M+H]+.
    • (R)—N-(4-(3-(5-(pyrimidin-5-ylmethylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)acrylamide (MFH-4-10-1)
  • To a solution of MFH-4-7-1 (15 mg, 0.04 mmol) and DIPEA (0.1 mL) in CH3CN (2 mL) was added acryloyl chloride (4 mg, 0.05 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-4-10-1 (2.2 mg, yield 13%). LCMS (m/z): 481 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.26 (s, 1H), 9.07 (s, 1H) 8.81 (s, 2H), 8.11 (s, 1H), 7.79-7.59 (m, 2H), 7.38 (t, J=13.1 Hz, 2H), 6.99-6.73 (m, 1H), 6.50-6.35 (m, 1H), 6.34-6.17 (m, 1H), 5.80 (ddd, J=23.3, 10.0, 2.6 Hz, 1H), 4.01 (s, 2H), 3.81-3.73 (m, 3H), 3.45-3.20 (m, 2H), 1.94 (d, J=18.7 Hz, 1H), 1.78 (m, 1H), 1.54 (s, 2H).
  • Figure US20200172499A9-20200604-C00286
    • (R,E)-N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidine-1-carbonyl)phenyl)-4-(dimethylamino)but-2-enamide (MFH-4-13-1)
  • To a solution of (E)-4-bromobut-2-enoic acid (17 mg, 0.1 mmol) in SOCl2 (0.2 mL). The mixture was stirred at 70° C. for 1h under N2 atmosphere. The mixture was cooled to room temperature and then was concentrated under reduced pressure. The residue was diluted with dichloromethane and the resulted solution was added dropwise to a solution of MFH-2-20-1 (37 mg, 0.08 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) at 0° C. After stirring for 1 h at 0° C., a solution of dimethylamine in THF (2 mol/L, 0.1 ml, 0.2 mmol) was added and the reaction mixture was stirred at room temperature for 1h. The removal of the solvent under reduced pressure provided the residue which was purified by HPLC (MeOH/H2O, 0.05% TFA) to obtain MFH-4-13-1 (18 mg, yield 39%). LCMS (m/z): 583 [M+H]+; 1H NMR (500 MHz, DMSO) δ 10.18 (s, 1H), 7.96 (s, 1H), 7.66 (s, 2H), 7.34 (d, J=6.9 Hz, 2H), 6.84 (s, 1H), 6.80-6.65 (m, 2H), 6.27 (d, J=15.4 Hz, 1H), 3.94 (s, 2H), 3.79 (s, 1H), 3.65 (s, 2H), 3.14 (m, 2H), 3.06 (d, J=5.8, 2H), 2.18 (s, 6H), 1.95 (s, 1H), 1.75 (s, 1H), 1.51 (d, J=9.0 Hz, 2H), 1.17 (s, 9H).
  • Figure US20200172499A9-20200604-C00287
    • (R,E)-N-(4-(3-(5-((5-tert butyloxazol-2-yl)methylthio)thiazol-2-ylamino)piperidin-1-ylsulfonyl)phenyl)-4-(dimethylamino)but-2-enamide (MFH-4-40-1)
  • To a solution of (E)-4-bromobut-2-enoic acid (12 mg, 0.07 mmol) in SOCl2 (0.2 mL). The mixture was stirred at 70° C. for 1h under N2 atmosphere. The mixture was cooled to room temperature and then was concentrated under reduced pressure. The residue was diluted with dichloromethane and the resulted solution was added dropwise to a solution of MFH-4-40-1 (25 mg, 0.05 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) at 0° C. After stirring for 1 h at 0° C., a solution of dimethylamine in THF (2 mol/L, 0.05 ml, 0.1 mmol) was added and the reaction mixture was stirred at room temperature for 1h. The removal of the solvent under reduced pressure provided the residue which was purified by HPLC (MeOH/H2O, 0.05% TFA) to obtain MFH-4-40-1 (20 mg, yield 66%). LCMS (m/z): 619 [M+H]+; 1H NMR (500 MHz, DMSO) δ 10.76 (s, 1H), 7.98 (d, J=7.2 Hz, 1H), 7.90 (dd, J=6.5, 4.7 Hz, 2H), 7.70 (dd, J=6.6, 4.8 Hz, 2H), 6.97 (d, J=2.7 Hz, 1H), 6.83-6.75 (m, 1H), 6.72 (d, J=8.8 Hz, 1H), 6.48 (d, J=15.3 Hz, 1H), 3.96 (s, 2H), 3.71 (s, 2H), 3.53 (d, J=9.9 Hz, 2H), 3.24 (d, J=11.2 Hz, 1H), 3.17 (s, 2H), 2.81 (s, 6H), 2.34-2.22 (m, 1H), 1.84-1.70 (m, 2H), 1.52 (dd, J=10.1, 4.0 Hz, 1H), 1.22 (s, 9H).
  • Figure US20200172499A9-20200604-C00288
    Figure US20200172499A9-20200604-C00289
    • (R)-tert-butyl3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)pyrrolidine-1-carboxylate (MFH-4-30-1)
  • The mixture of MFH-2-83-1 (150 mg, 0.45 mmol), (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate (134 mg, 0.72 mmol) and DIEA (116 mg, 0.9 mmol) in NMP (1 mL) was stirred at 140° C. for overnight. The residue was extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (30 mL×2) and dried over Na2SO4. After removal of the solvent, the residue was purified by silica gel (MeOH/DCM=0-20%) to obtain MFH-4-30-1 (110 mg, yield 56%). LCMS (m/z): 439 [M+H]+.
    • (R)-5-((5-tert-butyloxazol-2-yl)methylthio)-N-(pyrrolidin-3-yl)thiazol-2-amine (MFH-4-39-1)
  • To a solution of MFH-4-30-1 (110 mg, 0.25 mmol) in methanol (3 mL) was added 4N HCl/dioxane (3 mL). The solution was then stirred for 3h at room temperature and the solvent was removed under reduced pressure to provide a crude which was directly used in the next step. LCMS (m/z): 339 [M+H]+.
    • (R)-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)pyrrolidin-1-yl)(4-nitrophenyl)methanone (MFH-4-41-1)
  • The mixture of MFH-4-39-1 (80 mg, 0.24 mmol), 4-nitrobenzoyl chloride (53 mg, 0.28 mmol) in pyridine (2 mL) was stirred for overnight at room temperature. Then the reaction mixture was concentrated under reduced pressure and the residue was directly used in the next step. LCMS (m/z): 488 [M+H]+.
    • (R)-(4-aminophenyl)(3-(5-((5-tert-butyloxazol-2-yl)methylthio)triazol-2-ylamino)pyrrolidin-1-yl)methanone (MFH-4-44-1)
  • To a solution of MFH-4-41-1 (117 mg, 0.24 mmol) in ethyl acetate and methanol (1:1) were added Tin(II) chloride dehydrate (427 mg, 1.9 mmol) and conc. HCl (0.1 mL). After stirring for 3 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1), concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give MFH-4-44-1 (90 mg, yield 83%). LCMS (m/z): 458 [M+H]+.
    • (R)—N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)pyrrolidine-1-carbonyl)phenyl)acrylamide (MFH-4-70-1)
  • To a solution of MFH-4-44-1 (22 mg, 0.05 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) was added acryloyl chloride (5 mg, 0.06 mmol) in DCM (0.1 mL) dropwise. The mixture was then stirred at 0° C. for 1 h. The solution was then concentrated under reduced pressure and the residue was purified by prep-HPLC (MeOH/H2O, 0.05% TFA) to provide MFH-4-70-1 (13.4 mg, yield 54%). LCMS (m/z): 512 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.33 (s, 1H), 8.38-8.21 (m, 1H), 7.73 (d, J=8.3 Hz, 2H), 7.52 (t, J=8.6 Hz, 2H), 7.04-6.85 (m, 1H), 6.77-6.65 (m, 1H), 6.45 (dd, J=17.0, 10.1 Hz, 1H), 6.29 (d, J=16.9 Hz, 1H), 5.84-5.75 (m, 1H), 3.96 (d, J=24.0 Hz, 2H), 3.82-3.72 (m, 1H), 3.57 (ddd, J=25.0, 12.1, 7.0 Hz, 3H), 3.33 (d, J=7.5 Hz, 1H), 2.15 (dt, J=30.0, 14.1 Hz, 1H), 1.92 (m, 1H), 1.23-1.12 (m, 9H).
  • Figure US20200172499A9-20200604-C00290
    • (R,E)-N-(4-(3-(5-((5-tert-butyloxazol-2-yl)methylthio)thiazol-2-ylamino)pyrrolidine-1-carbonyl)phenyl)-4-dimethylamino)but-2-enamide (MFH-4-73-1)
  • To a solution of (E)-4-bromobut-2-enoic acid (15 mg, 0.09 mmol) in SOCl2 (0.2 mL). The mixture was stirred at 70° C. for 1h under N2 atmosphere. The mixture was cooled to room temperature and then was concentrated under reduced pressure. The residue was diluted with dichloromethane and the resulted solution was added dropwise to a solution of MFH-4-40-1 (30 mg, 0.07 mmol) and DIPEA (0.2 mL) in CH3CN (2 mL) at 0° C. After stirring for 1 h at 0° C., a solution of dimethylamine in THF (2 mol/L, 0.1 ml, 0.2 mmol) was added and the reaction mixture was stirred at room temperature for 1h. The removal of the solvent under reduced pressure provided the residue which was purified by HPLC (MeOH/H2O, 0.05% TFA) to obtain MFH-4-73-1 (23 mg, yield 61%). LCMS (m/z): 569 [M+H]+; 1H NMR (500 MHz, DMSO) δ 10.52 (s, 1H), 8.30-8.19 (m, 1H), 7.73 (d, J=8.3 Hz, 2H), 7.53 (t, J=8.4 Hz, 2H), 7.03-6.85 (m, 1H), 6.78 (dd, J=15.1, 7.4 Hz, 1H), 6.75-6.65 (m, 1H), 6.48 (d, J=15.3 Hz, 1H), 3.97 (s, 2H), 3.93 (s, 2H), 3.81-3.71 (m, 1H), 3.65-3.42 (m, 3H), 3.32 (dd, J=10.0, 2.5 Hz, 1H), 2.81 (d, J=2.5 Hz, 6H), 2.21-2.10 (m, 1H), 1.99-1.85 (m, 1H), 1.23-1.12 (m, 9H).
  • Figure US20200172499A9-20200604-C00291
    • (4-aminophenyl)((3R)-3-((5-((5-(tert-butyl)oxazol-2-yl)methyl)sulfinyl)thiazol-2-yl)amino)piperidin-1-yl)methanone (YLIU-01-006-1)
  • To a solution of MFH-2-89-1 (30 mg, 0.064 mmol) in DCM (2 mL) was added m-CPBA (12 mg, 0.07 mmol), the reaction mixture was stirred at rt overnight. Then diluted with DCM, washed with NaHCO3 aq.(sat.), concentrated and purified with silica gel column (eluted with MeOH in DCM 0% to 15%) to give the title compound (20 mg, 64%) as a brown oil. LCMS (m/z): 488 [M+H]+.
    • N-(4-((3R)-3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)sulfinyl)thiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)acrylamide (YLIU-01-007-1)
  • To a solution of YLIU-01-006-1 (20 mg, 0.04 mmol) in MeCN (2 mL) was added DIPEA (25 mg, 0.2 mmol). At 0° C., acryloyl chloride (4 mg, 0.044 mmol) was added dropwise. Monitored with LCMS, when the reaction was completed, Na2CO3 aq.(sat.) was added, the resulting mixture was extracted with DCM/i-PrOH (4/1) (20 mL). The combined organic layer was concentrated and purified with Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (8 mg, 36.9%) as white solid. LCMS (m/z): 542 [M+H]+.
  • 1H NMR (500 MHz, DMSO) δ 10.18 (s, 1H), 8.45 (s, 1H), 7.71-7.48 (m, 2H), 7.39-7.10 (m, 3H), 6.68 (s, 1H), 6.42-6.24 (m, 1H), 6.23-6.06 (m, 1H), 5.77-5.57 (m, 1H), 4.62-4.44 (m, 2H), 4.42-4.20 (m, 2H), 3.56 (m, 3H), 2.02-1.68 (m, 2H), 1.57-1.32 (m, 2H), 0.99 (s, 9H).
  • Figure US20200172499A9-20200604-C00292
    Figure US20200172499A9-20200604-C00293
    • 5-Thiocyanatothiazol-2-amine (YLIU-01-004-1)
  • A mixture of 2-amino-5-bromothiazole hydrobromide (7.8 g, 30 mmol) and potassium thiocyanate (20.46 g, 210.93 mmol) in methanol (230 mL) was stirred at room temperature for 48 h. Methanol was evaporated and water (30 ml) was added. The pH of the aqueous solution was adjusted to pH=12 with 10% NaOH aq and precipitate formed. The solid was collected by filtration to yield compound YLIU-01-004-1 (3.3 g, 70%) as a brownish solid. LCMS (m/z): 158 [M+H]+.
    • 5-((5-tert-Butyloxazol-2-yl)methylthio)thiazol-2-amine (YLIU-01-005-1)
  • To a solution of compound YLIU-01-004-1 (156 mg, 1 mmol) in absolute EtOH (3 ml) was added NaBH4 (76 mg, 2 mmol) portionwise at 0° C. The mixture was stirred at rt for 1 h, and then acetone (2 ml) was slowly introduced. After 1 h, a solution of 2-(bromomethyl)-5-(tert-butyl)oxazole (240 mg, 1.1 mmol) in EtOH (2 ml) was added. The resulting dark reaction mixture was heated to 65° C. for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), concentrated and purified with silica gel column (eluted with MeOH in DCM 0% to 10%) to provide the title compound (120 mg, 44%) as a brown solid. LCMS (m/z): 270 [M+H]+.
    • 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (YLIU-01-017-1)
  • To a solution of CuBr2 (2.32 g, 10 mmol) in acetonitrile (50 mL) at 0° C. was added t-BuONO (1.1 g, 10 mmol) followed by compound YLIU-01-004-1 (1.66 g, 6.13 mmol). The mixture was stirred at 0° C. for 1 h, then at room temperature for 1 h. Ethyl acetate was added and the organic layer was washed with hydrochloric acid (2×50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was purified on silica gel column to give the YLIU-01-017-1 (690 mg, 33%) as orange oil. LCMS (m/z): 333 [M+H]+.
    • tert-butyl (R)-3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino) piperidine-1-carboxylate (YLIU-01-038-1)
  • A mixture of YLIU-01-017-1 (150 mg, 0.45 mmol), tert-butyl (R)-3-aminopiperidine-1-carboxylate (180 mg, 0.9 mmol), DIPEA (0.24 mL, 1.35 mmol) in NMP (3 mL) was heated to 140° C. overnight. The solution was diluted with water (20 mL) and extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-038-1 (150 mg, 73%). LCMS (m/z): 453 [M+H]+.
    • (R)-5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)thiazol-22-amine (YLIU-01-047-1)
  • To a mixture of compound YLIU-01-038-1 (150 mg, 0.33 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL) and the resulted solution was stirred at rt for 3 h. The mixture was concentrated under reduced pressure to give the title compound as HCl salt, which was directly used in the next step. LCMS (m/z): 353 [M+H]+.
    • (R)-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidin-1-yl)(5-nitropyridin-2-yl)methanone (YLIU-01-048-1)
  • To a mixture of YLIU-01-047-1 (50 mg, 0.12 mmol), 5-nitropicolinic acid (23 mg, 0.14 mmol) and DIPEA (78 mg, 0.6 mmol) in DCM (2 mL) was added T3P (50% solution in EA, 230 mg, 0.36 mmol) dropwise at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give the title compound (46 mg, 76%) as yellow solid. LCMS (m/z): 503 [M+H]+.
    • (R)-(5-aminopyridin-2-yl)(3-((5-((5-(tertbutyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidin-1-yl)methanone (YLIU-01-064-1)
  • To a solution of YLIU-01-048-1 (46 mg, 0.091 mmol) in ethyl acetate and methanol (2 mL, 1:1) was added Tin(II) chloride (138 mg, 0.73 mmol) at rt. After stirring for 2 h at 80° C., the reaction mixture was diluted with chloroform and iso-propanol (4:1), neutralized with saturated NaHCO3 aq. and filtered. The filtrate was extracted with chloroform and iso-propanol (4:1). The combined organic layer was concentrated under reduced pressure and the resulting residue was purified by silica gel column chromatography (MeOH/DCM=0-20%) to give YLIU-01-064-1 (16 mg, 37%) as yellow solid. LCMS (m/z): 473 [M+H]+.
    • (R)—N-(6-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)pyridin-3-yl)acrylamide (YLIU-01-067-1)
  • To a solution of YLIU-01-064-1 (16 mg, 0.034 mmol) and DIPEA (13 mg, 0.1 mmol) in MeCN (2 mL) was added acryloyl chloride (4 mg, 0.044 mmol) dropwise at 0° C. Monitored with LCMS, when the reaction was completed, Na2CO3 aq.(sat.) was added, the resulting mixture was extracted with DCM/i-PrOH (4/1) (20 mL×2). The combined organic layer was concentrated and purified with Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (1.3 mg, 7.27%) as white solid. LCMS (m/z): 527 [M+H]+.
  • Figure US20200172499A9-20200604-C00294
    Figure US20200172499A9-20200604-C00295
    • tert-butyl 4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (YLIU-01-062-1)
  • A mixture of YLIU-01-017-1 (150 mg, 0.45 mmol), tert-butyl 4-aminopiperidine-1-carboxylate (180 mg, 0.9 mmol), DIPEA (0.24 mL, 1.35 mmol) in NMP (3 mL) was heated to 140° C. overnight. The solution was diluted with water (20 mL) and extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-062-1 (150 mg, 73%). LCMS (m/z): 453 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-4-yl)thiazol-2-amine (YLIU-01-062A-1)
  • To a mixture of compound YLIU-01-062-1 (150 mg, 0.33 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL) and the resulted solution was stirred at rt for 3 h. The mixture was concentrated under reduced pressure to give the title compound as HCl salt, which was directly used in the next step. LCMS (m/z): 353 [M+H]+.
    • (4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidin-1-yl)(3-nitrophenyl)methanone (YLIU-01-068-1)
  • The mixture of YLIU-01-062A-1 (330 mg, 0.89 mmol), 3-nitrobenzoyl chloride (330 mg, 1.78 mmol) in pyridine (2 mL) was stirred at rt overnight. Then the reaction mixture was concentrated under reduced pressure and the residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-068-1 (320 mg, 72%) as yellow solid. LCMS (m/z): 502 [M+H]+.
    • (3-aminophenyl)(4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidin-1-yl)methanone (YLIU-01-076-1)
  • To a solution of YLIU-01-068-1 (100 mg, 0.2 mmol) in MeOH (3 mL) was added Pd/C (10%, 20 mg) and N2H4-H2O (0.1 mL). The reaction mixture was stirred at 80° C. overnight, then filtered through Celite. The filtrate was concentrated and purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (27 mg, 29%) as yellow oil. LCMS (m/z): 472 [M+H]+.
    • N-(3-(4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)acrylamide (YLIU-01-078-1)
  • To a solution of YLIU-01-076-1 (20 mg, 0.042 mmol) and DIPEA (17 mg, 0.13 mmol) in MeCN (2 mL) was added acryloyl chloride (4.2 mg, 0.046 mmol) dropwise at 0° C. Monitored with LCMS, when the reaction was completed, Na2CO3 aq.(sat.) was added, the resulting mixture was extracted with DCM/i-PrOH (4/1) (20 mL×2). The combined organic layer was concentrated and purified with Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (1.4 mg, 6.3%) as white solid. LCMS (m/z): 526 [M+H]+.
  • Figure US20200172499A9-20200604-C00296
    Figure US20200172499A9-20200604-C00297
    • 4-methyl-5-thiocyanatothiazol-2-amine (YLIU-01-056-1)
  • A mixture of 2-amino-5-bromothiazole hydrobromide (580 mg, 3 mmol) and potassium thiocyanate (2.9 g, 30 mmol) in methanol (20 mL) was stirred at room temperature for 48 h. Methanol was evaporated and water (3 ml) was added. The pH of the aqueous solution was adjusted to pH=12 with 10% NaOH aq and precipitate formed. The solid was collected by filtration to yield compound YLIU-01-056-1 (480 mg, 93%) as a brownish solid. LCMS (m/z): 172 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-4-methylthiazol-2-amine (YLIU-01-073-1)
  • To a solution of compound YLIU-01-056-1 (171 mg, 1 mmol) in absolute EtOH (3 ml) was added NaBH4 (76 mg, 2 mmol) portionwise at 0° C. The mixture was stirred at rt for 1 h, and then acetone (2 ml) was slowly introduced. After 1 h, a solution of 2-(bromomethyl)-5-(tert-butyl)oxazole (240 mg, 1.1 mmol) in EtOH (2 ml) was added. The resulting dark reaction mixture was heated to 65° C. for 1 h, and was then cooled and concentrated in vacuo. The residue was partitioned between EtOAc and brine. The organic phase was separated, dried (MgSO4), concentrated and purified with silica gel column (eluted with MeOH in DCM 0% to 10%) to provide the title compound (314 mg, >100%) as a brown oil. LCMS (m/z): 284 [M+H]+.
    • 2-(((2-bromo-4-methylthiazol-5-yl)thio)methyl)-5-(tert-butyl)-4-methyloxazole (YLIU-01-089-1)
  • To a solution of CuBr2 (423 mg, 1.9 mmol) in acetonitrile (10 mL) at 0° C. was added t-BuONO (200 mg, 1.9 mmol) followed by compound YLIU-01-073-1 (314 mg, 1.1 mmol). The mixture was stirred at 0° C. for 1 h, then at room temperature for 1 h. Ethyl acetate was added and the organic layer was washed with hydrochloric acid (2×50 mL), dried over magnesium sulfate, filtered through a pad of silica gel, and concentrated in vacuo. The residue was purified on silica gel column to give the YLIU-01-089-1 (140 mg, 37%) as orange oil. LCMS (m/z): 347 [M+H]+.
    • tert-butyl (R)-3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-4-methylthiazol-2-yl) amino)piperidine-1-carboxylate (YLIU-01-092-1)
  • A mixture of YLIU-01-089-1 (140 mg, 0.4 mmol), tert-butyl (R)-3-aminopiperidine-1-carboxylate (160 mg, 0.8 mmol), DIPEA (0.22 mL, 1.2 mmol) in NMP (3 mL) was heated to 140° C. overnight. The solution was diluted with water (20 mL) and extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-092-1 (220 mg, >100%). LCMS (m/z): 467 [M+H]+.
    • (R)-5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-4-methyl-N-(piperidin-3-yl)thiazol-2-amine (YLIU-01-096-1)
  • To a mixture of compound YLIU-01-092-1 (220 mg, 0.47 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL) and the resulted solution was stirred at rt for 3 h. The mixture was concentrated and the residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (88 mg, 51%) as yellow solid. LCMS (m/z): 367 [M+H]+.
    • (R)—N-(4-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-4-methylthiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)acrylamide (YLIU-01-099-1)
  • To a mixture of YLIU-01-096-1 (22 mg, 0.06 mmol), 4-acrylamidobenzoic acid (14 mg, 0.072 mmol) and DIPEA (39 mg, 0.3 mmol) in DCM (2 mL) was added T3P (50% solution in EA, 57 mg, 0.18 mmol) dropwise at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (17.1 mg, 53%) as yellow solid. LCMS (m/z): 540 [M+H]+.
  • 1H NMR (500 MHz, DMSO) δ 10.28 (s, 1H), 8.44-7.89 (m, 1H), 7.81-7.57 (m, 2H), 7.36 (m, 2H), 6.81-6.60 (m, 1H), 6.51-6.36 (m, 1H), 6.32-6.20 (m, 1H), 5.88-5.67 (m, 1H), 3.87 (m, 3H), 3.63 (s, 2H), 3.12 (m, 2H), 1.90 (m, 2H), 1.63-1.39 (m, 5H), 1.19 (s, 9H).
  • Figure US20200172499A9-20200604-C00298
    • tert-butyl 5-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)-3,3-difluoropiperidine-1-carboxylate (YLIU-01-101-1)
  • A mixture of YLIU-01-017-1 (130 mg, 0.4 mmol), tert-butyl 5-amino-3,3-difluoropiperidine-1-carboxylate (350 mg, 1.5 mmol), DIPEA (0.36 mL, 1.8 mmol) in NMP (3 mL) was heated to 140° C. overnight. The solution was diluted with water (20 mL) and extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-101-1 (12 mg, 6%). LCMS (m/z): 489 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(5,5-difluoropiperidin-3-yl)triazol-2-amine (YLIU-01-111-1)
  • To a mixture of compound YLIU-01-101-1 (12 mg, 0.024 mmol) in methanol (2 mL) was added 4N HCl/dioxane (2 mL) and the resulted solution was stirred at rt for 3 h. The mixture was concentrated and the crude product was used into next step directly as HCl salt. LCMS (m/z): 389 [M+H]+.
    • N-(4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)-3,3-difluoropiperidine-1-carbonyl)phenyl)acrylamide (YLIU-01-114-1)
  • To a mixture of YLIU-01-111-1 (10 mg, crude HCl salt), 4-acrylamidobenzoic acid (6 mg, 0.03 mmol) and DIPEA (16 mg, 0.12 mmol) in DCM (2 mL) was added T3P (50% solution in EA, 46 mg, 0.07 mmol) dropwise at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (2.5 mg, 19%) as yellow solid. LCMS (m/z): 562 [M+H]+.
  • 1H NMR (500 MHz, DMSO) δ 10.35 (s, 1H), 8.10 (s, 1H), 7.74 (d, J=8.3 Hz, 2H), 7.42 (d, J=8.6 Hz, 2H), 7.08-6.83 (m, 1H), 6.72 (m, 1H), 6.45 (m, 1H), 6.29 (m, 1H), 5.80 (m, 1H), 3.97 (s, 2H), 3.65-3.44 (m, 3H), 3.22-2.90 (m, 2H), 2.08 (m, 2H), 1.21 (s, 9H).
  • Figure US20200172499A9-20200604-C00299
    • Methyl 4-(N-acryloylacrylamido)-3-(trifluoromethyl)benzoate (YLIU-01-100-1)
  • To a solution of methyl 4-amino-3-(trifluoromethyl)benzoate (220 mg, 1 mmol) and DIPEA (390 mg, 3 mmol) in MeCN (5 mL) was added acryloyl chloride (108 mg, 1.2 mmol) dropwise at 0° C. The reaction was stirred at rt for 1 h, then Na2CO3 aq.(sat.) was added, the resulting mixture was extracted with DCM (20 mL×2). The combined organic layer was concentrated and purified with SGC (Hexane/EA-4/1) to give YLIU-01-100-1 (114 mg, 35%) as white solid. LCMS (m/z): 328 [M+H]+.
    • 4-acrylamido-3-(trifluoromethyl)benzoic acid (YLIU-01-115-1)
  • To a solution of YLIU-01-100-1 (114 mg, 0.35 mmol) in THF (4 mL) was added 1N LiOH aq. (4 mL). The reaction mixture was stirred at rt for 1h, then adjusted PH<7 with 4N HCl aq. The resulting mixture was extracted with EA (20 mL×3), washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated to give the desire product (110 mg, >100%) as a white solid. LCMS (m/z): 260 [M+H]+.
    • (R)—N-(4-(3-((4-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)-2-(trifluoromethyl)phenyl)acrylamide (YLIU-01-121-1)
  • To a mixture of YLIU-01-047-1 (20 mg, 0.057 mmol), YLIU-01-115-1 (18 mg, 0.068 mmol) and DIPEA (37 mg, 0.285 mmol) in DCM (2 mL) was added T3P (50% solution in EA, 108 mg, 0.17 mmol) dropwise at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (17.8 mg, 53%) as yellow solid. LCMS (m/z): 594 [M+H]+. 1H NMR (500 MHz, DMSO) δ 9.87 (m, 1H), 8.15 (m, 1H), 7.72 (m, 3H), 7.08-6.66 (m, 2H), 6.64-6.50 (m, 1H), 6.29 (m, 1H), 5.93-5.70 (m, 1H), 3.94 (m, 2H), 3.72 (m, 2H), 3.40 (m, 1H), 3.15 (m, 2H), 2.07-1.66 (m, 2H), 1.64-1.35 (m, 2H), 1.14 (s, 9H).
  • Figure US20200172499A9-20200604-C00300
    • methyl 4-acrylamido-3-fluorobenzoate (YLIU-01-116-1)
  • To a solution of methyl 4-amino-3-fluorobenzoate (500 mg, 3 mmol) and DIPEA (1.65 mL, 9 mmol) in MeCN (5 mL) was added acryloyl chloride (320 mg, 3.6 mmol) dropwise at 0° C. The reaction was stirred at rt for 1 h, then Na2CO3 aq.(sat.) was added, the resulting mixture was extracted with DCM (20 mL×2). The combined organic layer was concentrated and recrystallized from EA to give YLIU-01-116-1 (190 mg, 28%) as white solid. LCMS (m/z): 224 [M+H]+.
    • 4-acrylamido-3-fluorobenzoic acid (YLIU-01-119-1)
  • To a solution of YLIU-01-116-1 (190 mg, 0.85 mmol) in THF/water (4 mL/4 mL) was added LiOH (204 mg, 8.5 mmol). The reaction mixture was stirred at rt for 1h, then adjusted PH<7 with 4N HCl aq. The resulting mixture was extracted with EA (20 mL×3), washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated to give the desire product (110 mg, 61%) as a white solid. LCMS (m/z): 210 [M+H]+.
    • (R)—N-(4-(3-((4-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)-2-fluorophenyl)acrylamide (YLIU-01-123-1)
  • To a mixture of YLIU-01-047-1 (20 mg, 0.057 mmol), YLIU-01-115-1 (15 mg, 0.068 mmol) and DIPEA (37 mg, 0.285 mmol) in DCM (2 mL) was added T3P (50% solution in EA, 108 mg, 0.17 mmol) dropwise at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (23.8 mg, 77%) as yellow solid. LCMS (m/z): 544 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.06 (s, 1H), 8.05 (m, 2H), 7.44-6.97 (m, 2H), 6.74-6.53 (m, 3H), 6.36-6.21 (m, 1H), 5.80 (m, 1H), 3.69 (s, 2H), 3.53 (m, 3H), 3.31-3.01 (m, 2H), 1.86 (m, 2H), 1.51 (m, 2H), 1.16 (s, 9H).
  • Figure US20200172499A9-20200604-C00301
    • benzyl (2R,3R)-3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)triazol-2-yl)amino)-2-methylpiperidine-1-carboxylate (YLIU-01-142-1)
  • A mixture of YLIU-01-017-1 (80 mg, 0.24 mmol), benzyl (2R,3R)-3-amino-2-methyl piperidine-1-carboxylate (300 mg, 1.2 mmol), DIPEA (0.42 mL, 2.4 mmol) in NMP (3 mL) was heated to 140° C. overnight. The solution was diluted with water (20 mL) and extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-142-1 (70 mg, 58%) as yellow solid. LCMS (m/z): 501 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-((2R,3R)-2-methylpiperidin-3-yl)triazol-2-amine (YLIU-01-150-1)
  • To a mixture of compound YLIU-01-142-1 (70 mg, 0.14 mmol) in MeCN (4 mL) was added TMSI (280 mg, 1.4 mmol) and the resulted solution was stirred at 0° C. for 30 min. The reaction was quenched with water and the resulting solution was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (34 mg, 66%) as yellow solid. LCMS (m/z): 367 [M+H]+.
    • N-(4-((2R,3R)-3-((5-((5-tert-butyl)oxazol-2-yl)methyl)thio)triazol-2-yl)amino)-2-methylpiperidine-1-carbonyl)phenyl)acrylamide (YLIU-01-155-1)
  • To a mixture of YLIU-01-150-1 (17 mg, 0.046 mmol), 4-acrylamidobenzoic acid (10 mg, 0.055 mmol) and DIPEA (0.04 mL, 0.23 mmol) in DMF (2 mL) was added HATU (35 mg, 0.093 mmol) at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (8.2 mg, 33%) as yellow solid. LCMS (m/z): 540 [M+H]+.
  • 1H NMR (500 MHz, DMSO) δ 10.30 (s, 1H), 8.02 (s, 1H), 7.72 (d, J=8.6 Hz, 2H), 7.38 (d, J=8.3 Hz, 2H), 6.79 (m, 2H), 6.45 (dd, J=17.0, 10.2 Hz, 1H), 6.28 (dd, J=17.0, 1.9 Hz, 1H), 5.79 (dd, J=10.1, 1.9 Hz, 1H), 3.79 (m, 4H), 3.08 (m, 2H), 1.84-1.38 (m, 4H), 1.19 (s, 9H), 1.04 (s, 3H).
  • Figure US20200172499A9-20200604-C00302
    • benzyl (2S,5R)-5-((5-((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)-2-methylpiperidine-1-carboxylate (YLIU-01-143-1)
  • A mixture of YLIU-01-017-1 (80 mg, 0.24 mmol), benzyl (2S,5R)-5-amino-2-methyl piperidine-1-carboxylate (300 mg, 1.2 mmol), DIPEA (0.42 mL, 2.4 mmol) in NMP (3 mL) was heated to 140° C. overnight. The solution was diluted with water (20 mL) and extracted with chloroform and iso-propanol (4:1). The organic phase was washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column (MeOH/DCM, 0-20%) to give YLIU-01-143-1 (50 mg, 42%) as yellow solid. LCMS (m/z): 501 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-((3R,6S)—6-methylpiperidin-3-yl)triazol-2-amine (YLIU-01-151-1)
  • To a mixture of compound YLIU-01-143-1 (50 mg, 0.1 mmol) in MeCN (4 mL) was added TMSI (200 mg, 1 mmol) and the resulted solution was stirred at 0° C. for 30 min. The reaction was quenched with water and the resulting solution was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (20 mg, 54%) as yellow solid. LCMS (m/z): 367 [M+H]+.
    • N-(4-((2,5R)-5-((((5-(tertbutyl)oxazol-2-yl)methyl)thio)triazol-2-yl)amino)-2-methylpiperidine-1-carbonyl)phenyl)acrylamide (YLIU-01-156-1)
  • To a mixture of YLIU-01-151-1 (20 mg, 0.054 mmol), 4-acrylamidobenzoic acid (12.5 mg, 0.065 mmol) and DIPEA (0.05 mL, 0.27 mmol) in DMF (2 mL) was added HATU (41 mg, 0.108 mmol) at rt. The reaction mixture was stirred at rt overnight. The solution was diluted with DCM (20 mL) and washed with brine (50 mL×2) and dried over Na2SO4, filtered and concentrated. The residue was purified by Prep-HPLC (MeOH/H2O, 0.05% TFA) to give the title compound (11 mg, 38%) as yellow solid. LCMS (m/z): 540 [M+H]+. 1H NMR (500 MHz, DMSO) δ 10.30 (s, 1H), 8.03 (s, 1H), 7.73 (d, J=8.6 Hz, 2H), 7.39 (d, J=8.6 Hz, 2H), 6.97 (m, 1H), 6.71 (s, 1H), 6.45 (dd, J=17.0, 10.1 Hz, 1H), 6.28 (dd, J=17.0, 1.9 Hz, 1H), 5.79 (dd, J=10.1, 1.9 Hz, 1H), 3.95 (m, 2H), 3.57 (m, 2H), 3.34-3.02 (m, 1H), 2.68 (m, 1H), 1.71 (m, 4H), 1.35-0.88 (m, 12H).
    • Synthesis of B1
  • Figure US20200172499A9-20200604-C00303
    Figure US20200172499A9-20200604-C00304
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 ml) was slowly introduced. After 1 hours, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl 4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (186 mg, 0.69 mmol), 1-(tert-butoxycarbonyl)piperidine-4-carboxylic acid (229 mg, 0.94 mmol), DMAP (42.8 mg, 0.35 mmol), and triethylamine (0.2 ml, 1.4 mmol) in DMF (1 mL) and DCM (2 ml) was added EDAC (267 mg, 1.4 mmol) at room temperature. The reaction mixture was stirred for 1.5 hours, diluted with EtOAc, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (226 mg, 83%) of the title compound (3) as a white solid. MS m/z 481.18[M+H]+.
    • N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-4-carboxamide hydrochloride (4)
  • To a solution of tert-butyl 4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (117 mg, 0.24 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (100 mg, 100%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 381.14 [M+H]+.
    • (E)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)-1-(4-(dimethylamino)but-2-enoyl)piperidine-4-carboxamide (B1)
  • To a solution of N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-4-carboxamide hydrochloride (100 mg, 0.24 mmol) in DMF (1 mL) was added HATU (110 mg, 0.29 mmol), (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (45 mg, 0.27 mmol) and DIPEA (125 mg, 0.96 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (6 mg, 5.1%) of the title compound as a yellow solid. MS m/z 492.21 [M+H]+. 1H NMR (400 MHz, DMSO-d6) 12.42 (s, 1H), 10.66 (s, 2H), 7.77 (s, 2H), 7.40 (s, 3H), 6.83 (s, 1H), 6.72 (s, 1H), 6.51 (d, J=15.1 Hz, 1H), 4.52-4.17 (m, 1H), 4.07 (s, 2H), 3.63 (s, 1H), 3.08 (s, 2H), 2.77 (s, 6H), 2.02 (s, 2H), 1.72 (s, 3H), 1.46 (s, 2H), 1.19 (s, 9H).
    • Synthesis of B2
  • Figure US20200172499A9-20200604-C00305
    Figure US20200172499A9-20200604-C00306
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in Methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 ml) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl 4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (186 mg, 0.69 mmol), 1-(tert-butoxycarbonyl)piperidine-4-carboxylic acid (229 mg, 0.94 mmol), DMAP (42.8 mg, 0.35 mmol), and triethylamine (0.2 ml, 1.4 mmol) in DMF (1 mL) and DCM (2 ml) was added EDAC (267 mg, 1.4 mmol) at room temperature. The reaction mixture was stirred for 1.5 hours, diluted with EtOAc, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (226 mg, 83%) of the title compound (3) as a white solid. MS m/z 481.18[M+H]+.
    • N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-4-carboxamide hydrochloride (4)
  • To a solution of tert-butyl 4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (20 mg, 0.047 mmol) in 4 M HCl EtOAc (3 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (100 mg, 100%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 381.14 [M+H]+.
    • 1-acryloyl-N-(5-(((5-(tert-butyl)oxazol-2-yl)methylthio)thiazol-2-yl)piperidine-4-carboxamide (B2)
  • To a solution of N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-4-carboxamide hydrochloride (20 mg, 0.05 mmol) in THF (5 mL) was added DIPEA (17 mg, 0.15 mmol) and acryloyl chloride (43 mg, 0.05 mmol) at 0° C. for 1 hour. The resulting mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by an silica gel column to afford (11 mg, 50.7%) of the title compound as a slightly white solid. MS m/z 435.15 [M+H]+. 1H NMR (400 MHz, CDCl3) δ 11.64 (s, 1H), 7.29 (s, 1H), 6.58 (q, J=11.0 Hz, 2H), 6.28 (d, J=16.7 Hz, 1H), 5.71 (d, J=10.6 Hz, 1H), 4.58 (d, J=12.1 Hz, 1H), 4.09 (dd, J=17.6, 10.2 Hz, 1H), 3.96 (s, 2H), 3.21 (s, 1H), 2.90 (s, 1H), 2.68 (t, J=10.4 Hz, 1H), 1.95 (d, J=12.0 Hz, 2H), 1.82 (s, 2H), 1.24 (s, 9H).
    • Synthesis of B3
  • Figure US20200172499A9-20200604-C00307
    Figure US20200172499A9-20200604-C00308
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 m) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl (3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)triazol-2-yl)carbamoyl)cyclohexyl)carbamate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (160 mg, 0.6 mmol) in DMF (2 mL) was added HATU (456 mg, 1.2 mmol), 3-((tert-butoxycarbonyl)amino)cyclohexane-1-carboxylic acid (292 mg, 1.2 mmol), and DIPEA (143 mg, 2.4 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (150 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (210 mg, 70%) of the title compound (3) as a white solid. MS m/z 495.20[M+H]+.
    • 3-amino-N-(5-(((5-tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)cyclohexane-1-carboxamide hydrochloride (4)
  • To a solution of tert-butyl (3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)cyclohexyl)carbamate (210 mg, 0.424 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (182 mg, 99%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 395.15 [M+H]+.
    • (E)-N-(5-((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)-3-(4-(dimethylamino)but-2-enamido)cyclohexane-1-carboxamide (B3)
  • To a solution of 3-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)cyclohexane-1-carboxamide hydrochloride (130 mg, 0.3 mmol) in DMF (1 mL) was added HATU (228 mg, 0.6 mmol), (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (100 mg, 0.6 mmol), and DIPEA (0.214 ml, 1.2 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (48 mg, 33%) of the title compound as a white solid. MS m/z 506.26[M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.27 (s, 1H), 8.00 (d, J=8.0 Hz, 1H), 7.39 (s, 1H), 6.73 (s, 1H), 6.54 (d, J=16.2 Hz, 1H), 6.01 (d, J=15.7 Hz, 1H), 4.06 (s, 2H), 3.63 (d, J=26.0 Hz, 2H), 3.03 (s, 2H), 2.60 (s, 1H), 2.17 (s, 6H), 1.91 (d, J=11.2 Hz, 1H), 1.79 (s, 3H), 1.30 (s, 4H), 1.18 (s, 9H).
    • Synthesis of B4
  • Figure US20200172499A9-20200604-C00309
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 ml) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (200 mg, 0.74 mmol) in DMF (2 mL) was added HATU (562 mg, 1.5 mmol), 1-(tert-butoxycarbonyl)piperidine-3-carboxylic acid (343 mg, 1.5 mmol), and DIPEA (0.54 ml, 3 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (150 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (260 mg, 73%) of the title compound (3) as a white solid. MS m/z 481.19[M+H]+.
    • N-(5-(((5-tert-butyl)oxazol-2-yl)methyl)thio)triazol-2-yl)piperidine-3-carboxamide hydrochloride (4)
  • To a solution of tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (260 mg, 0.54 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (180 mg, 80%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 381.14 [M+H]+.
    • tert-butyl (4-(3-((5-((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carbonyl)phenyl)carbamate (5)
  • To a solution of N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-3-carboxamide hydrochloride (180 mg, 0.43 mmol) in DMF (2 mL) was added HATU (329 mg, 0.86 mmol), 4-((tert-butoxycarbonyl)amino)benzoic acid (205 mg, 0.86 mmol), and DIPEA (0.38 ml, 2.15 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (80 mg, 31%) of the title compound (5) as a white solid. MS m/z 600.23[M+H]+.
    • 1-(4-aminobenzoyl)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-3-carboxamide hydrochloride (6)
  • To a solution of tert-butyl (4-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carbonyl)phenyl)carbamate (80 mg, 0.133 mmol) in 4 M HCl EtOAc (3 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (65 mg, 91%) of the title compound (6) as a white solid, which was used without further purification. MS m/z 381.14 [M+H]+.
    • (E)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)-1-(4-(4-(dimethylamino)but-2-enamido)benzoyl)piperidine-3-carboxamide (B4)
  • To a solution of 1-(4-aminobenzoyl)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-3-carboxamide hydrochloride (0.60 g, 0.112 mmol) in DCM (5 mL) was added DIPEA (0.2 ml, 1.34 mmol) and (E)-4-bromobut-2-enoyl chloride (22.5 mg, 0.134 mmol) at 0° C. for 3 min. Then it was added 4.0 M dimethylamine in THF (2 mL). The resulting mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by an silica gel column to afford (8 mg, 11.7%) of the title compound as a slightly white solid. MS m/z 611.24 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.42 (s, 1H), 10.66 (s, 2H), 7.77 (s, 2H), 7.40 (s, 3H), 6.83 (s, 1H), 6.72 (s, 1H), 6.51 (d, J=15.1 Hz, 1H), 4.52-4.17 (m, 1H), 4.07 (s, 2H), 3.63 (s, 1H), 3.08 (s, 2H), 2.77 (s, 6H), 2.02 (s, 2H), 1.72 (s, 3H), 1.46 (s, 2H), 1.19 (s, 9H).
    • Synthesis of B5
  • Figure US20200172499A9-20200604-C00310
    Figure US20200172499A9-20200604-C00311
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 ml) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (65 mg, 0.24 mmol) in DMF (2 mL) was added HATU (183 mg, 0.48 mmol), 1-(tert-butoxycarbonyl)piperidine-3-carboxylic acid (83 mg, 0.36 mmol) and DIPEA (126 mg, 0.96 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (23 mg, 20%) of the title compound (3) as a white solid. MS m/z 481.19[M+H]+.
    • N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-3-carboxamide hydrochloride (4)
  • To a solution of tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)piperidine-1-carboxylate (23 mg, 0.048 mmol) in 4 M HCl EtOAc (2 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (16 mg, 80%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 381.14 [M+H]+.
    • 1-(4-acrylamidobenzoyl)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-3-carboxamide (B5)
  • To a solution of N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)piperidine-3-carboxamide hydrochloride (50 mg, 0.12 mmol) in DMF (1 mL) was added HATU (92 mg, 0.24 mmol), 4-acrylamidobenzoic acid (46 mg, 0.24 mmol), and DIPEA (0.22 ml, 1.2 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (8 mg, 12%) of the title compound as a white solid. MS m/z 554.21 [M+H]+. 1H NMR (400 MHz, DMSO-ds) δ 12.37 (s, 1H), 7.73 (d, J=7.8 Hz, 2H), 7.55-7.22 (m, 3H), 6.71 (s, 1H), 6.44 (dd, J=16.9, 10.3 Hz, 1H), 6.28 (d, J=16.8 Hz, 1H), 5.78 (d, J=9.9 Hz, 1H), 4.05 (s, 2H), 3.67 (s, 1H), 3.05 (s, 2H), 2.69 (s, 1H), 1.97 (s, 1H), 1.70 (d, J=12.1 Hz, 2H), 1.44 (s, 1H), 1.23 (s, 2H), 1.12 (s, 9H).
    • Synthesis of B6
  • Figure US20200172499A9-20200604-C00312
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 ml) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • 3-acrylamido-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide (B6)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (54 mg, 0.2 mmol) in DMF (1 mL) was added HATU (160 mg, 0.42 mmol), 3-acrylamidobenzoic acid (60 mg, 0.31 mmol), and DIPEA (52 mg, 0.4 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (7 mg, 8%) of the title compound as a white solid. MS m/z 443.12[M+H]+. 1H NMR (400 MHz, CDCl3) δ 12.36 (s, 1H), 9.08 (s, 1H), 8.24-7.99 (m, 2H), 7.90 (s, 1H), 7.63 (d, J=7.6 Hz, 1H), 7.41 (t, J=7.9 Hz, 1H), 6.95 (s, 1H), 6.55 (s, 1H), 6.44 (d, J=16.8 Hz, 1H), 6.32 (dd, J=16.8, 10.0 Hz, 1H), 5.76 (d, J=10.0 Hz, 1H), 3.95 (s, 2H), 1.23 (s, 9H).
    • Synthesis of B7
  • Figure US20200172499A9-20200604-C00313
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 ml) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 ml) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl (3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)phenyl)carbamate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (404 mg, 1.5 mmol) in DMF (2 mL) was added HATU (1.14 g, 3 mmol), 3-((tert-butoxycarbonyl)amino)benzoic acid (573 mg, 3 mmol), and DIPEA (1.05 ml, 6 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (200 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (490 mg, 67%) of the title compound (3) as a white solid. MS m/z 489.15[M+H]+.
    • 3-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide hydrochloride (4)
  • To a solution of tert-butyl (3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)phenyl)carbamate (245 mg, 0.5 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (212 mg, 100%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 389.11 [M+H]+.
    • (E)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)-3-(4-(dimethylamino)but-2-enamido)benzamide (B7)
  • To a solution of 3-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide hydrochloride (83 mg, 0.195 mmol) in MeCN (5 mL) was added DIPEA (77.6 mg, 0.6 mmol), and (E)-4-bromobut-2-enoyl chloride (40.26 mg, 0.22 mmol) at 0° C. for 3 min. Then it was added 4.0 M dimethylamine in THF (1 mL). The resulting mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by an silica gel column to afford (7 mg, 7.2%) of the title compound as a slightly yellow solid. MS m/z 500.18 [M+H]+. 1H NMR (400 MHz, CDCl3) δ 8.82 (s, 1H), 8.01 (d, J=16.7 Hz, 2H), 7.64 (s, 1H), 7.42 (s, 1H), 7.10 (s, 1H), 7.00 (s, 1H), 6.58 (s, 1H), 6.24 (d, J=13.7 Hz, 1H), 3.96 (s, 2H), 3.16 (s, 2H), 2.31 (s, 6H), 1.26 (s, 9H).
    • Synthesis of B8
  • Figure US20200172499A9-20200604-C00314
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 h and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]*.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 mL) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 mL) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl (4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)phenyl)carbamate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (220 mg, 0.82 mmol) in DMF (1 mL) was added HATU (623 mg, 1.64 mmol), 4-((tert-butoxycarbonyl)amino)benzoic acid (390 mg, 1.64 mmol) and DIPEA (0.6 ml, 3.28 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (150 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (200 mg, 50%) of the title compound (3) as a white solid. MS m/z 489.15[M+H]+.
    • 4-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide hydrochloride (4)
  • To a solution of tert-butyl (4-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)phenyl)carbamate (200 mg, 0.41 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (174 mg, 100%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 389.11 [M+H]+.
    • (E)-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)-44-(dimethylamino)but-2-enamido)benzamide (B8)
  • To a solution of 4-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide hydrochloride (75 mg, 0.177 mmol) in MeCN (5 mL) was added DIPEA (0.3 ml, 2.6 mmol) and (E)-4-bromobut-2-enoyl chloride (46.85 mg, 0.256 mmol) at 0° C. for 3 min. Then it was added 4.0 M dimethylamine in THF (1 mL). The resulting mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by an silica gel column to afford (7 mg, 8%) of the title compound as a slightly yellow solid. MS m/z 500.18 [M+H]+. 1H NMR (400 MHz, CDCl3) δ 8.57 (s, 1H), 7.90 (d, J=7.3 Hz, 2H), 7.76 (s, 2H), 7.19 (s, 1H), 7.05 (s, 1H), 6.61 (s, 1H), 6.23 (d, J=15.5 Hz, 1H), 3.98 (s, 2H), 3.18 (s, 2H), 2.34 (s, 6H), 1.27 (s, 9H).
    • Synthesis of B9
  • Figure US20200172499A9-20200604-C00315
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (5.2 g, 20 mmol) in methanol (100 mL) was added KSCN (19.5 g, 200 mmol) at room temperature. The resulting mixture was stirred for 20 h and then concentrated under vacuum. The residue was diluted with H2O (150 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (1.8 g, 58%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (1.8 g, 11.46 mmol) in absolute EtOH (50 mL) was added NaBH4 (0.87 g, 2.3 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 mL) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.19 g, 12.6 mmol) in EtOH (10 mL) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.1 g, 68%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • tert-butyl (3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl))thio)thiazol-2-yl)carbamoyl)phenyl)carbamate (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (404 mg, 1.5 mmol) in DMF (2 mL) was added HATU (1.14 g, 3 mmol), 3-((tert-butoxycarbonyl)amino)benzoic acid (573 mg, 3 mmol), and DIPEA (1.05 ml, 6 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (200 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (490 mg, 67%) of the title compound (3) as a white solid. MS m/z 489.15 [M+H]+.
    • 3-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide hydrochloride (4)
  • To a solution of tert-butyl (3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)carbamoyl)phenyl)carbamate (245 mg, 0.5 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (212 mg, 100%) of the title compound (4) as a white solid, which was used without further purification. MS m/z 389.11 [M+H]+.
    • 3-(4-acrylamidobenzamido)-N-(5-(((5-tert-butyl)oxazol-2-yl)methyl)thio)triazol-2-yl)benzamide (B9)
  • To a solution of 3-amino-N-(5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)benzamide hydrochloride (212 mg, 0.5 mmol) in DMF (2 mL) was added HATU (380 mg, 1 mmol), 4-acrylamidobenzoic acid (191 mg, 1 mmol), and DIPEA (0.5 ml, 3 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (200 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (93 mg, 34%) of the title compound as a white solid. MS m/z 562.18[M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.83 (s, 1H), 10.47 (s, 1H), 10.40 (s, 1H), 8.46 (s, 1H), 8.00 (dd, J=15, 5.0 Hz, 3H), 7.83 (d, J=15.0 Hz, 3H), 7.52 (d, J=5.0 Hz, 2H), 6.75 (s, 1H), 6.46 (d, J=6.3 Hz, 1H), 6.31 (d, J=6.5 Hz, 1H), 5.82 (d, J=15.0 Hz, 1H), 4.12 (s, 2H), 1.22 (s, 9H).
    • Synthesis of B12
  • Figure US20200172499A9-20200604-C00316
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (26 g, 100 mmol) in methanol (500 mL) was added KSCN (50 g, 500 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (300 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (8 g, 51%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (2 g, 13 mmol) in absolute EtOH (50 mL) was added NaBH4 (1 g, 26 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 mL) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.71 g, 15.6 mmol) in EtOH (10 mL) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.8 g, 80%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (404 mg, 1.5 mmol) in MeCN (10 mL) was added tert-butyl nitrite (239 mg, 2.25 mmol) at 0° C. The resulting mixture was stirred for 10 min, and then CuBr2 (402 mg, 1.8 mmol) was introduced. The resulting mixture was stirred at room temperature for 3 hours, the resulting mixture was concentrated in vacuo. The residue was purified by an silica gel column to afford (143 mg, 29%) of the title compound (3) as a pale yellow oil. MS m/z 333.96 [M+H]+.
    • tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (4)
  • To a solution of 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (80 mg, 0.22 mmol) in NMP (0.1 mL) was added tert-butyl 3-aminopiperidine-1-carboxylate (80 mg, 0.4 mmol) and DIPEA (0.084 ml, 0.48 mmol). The resulting mixture was heated at 140° C. for 8 hours. Then it was diluted with EtOAc (150 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (30 mg, 28%) of the title compound (4) as a slightly yellow solid. MS m/z 453.20 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)thiazol-2-amine hydrochloride (5)
  • To a solution of tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (38 mg, 0.084 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (35 mg, 98%) of the title compound (5) as a white solid, which was used without further purification. MS m/z 353.14 [M+H]+.
    • N-(4-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)acrylamide (B12)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)thiazol-2-amine hydrochloride (35 mg, 0.082 mmol) in DMF (0.5 mL) was added HATU (62.4 mg, 0.164 mmol), 4-acrylamidobenzoic acid (31.5 mg, 0.164 mmol), and DIPEA (42.6 mg, 0.33 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (70 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (5 mg, 12%) of the title compound as a white solid. MS m/z 526.21[M+H]+. 1H NMR (400 MHz, CDCl3) δ 9.83 (s, 1H), 7.59 (d, J=7.2 Hz, 2H), 7.29 (s, 2H), 6.86 (s, 1H), 6.66 (s, 1H), 6.56 (s, 1H), 6.44 (d, J=16.9 Hz, 1H), 6.26 (s, 1H), 5.72 (s, 1H), 4.03 (s, 1H), 3.84 (s, 2H), 3.55 (s, 1H), 3.46 (d, J=31.2 Hz, 2H), 2.03 (s, 3H), 1.84 (s, 2H), 1.32 (s, 9H).
    • Synthesis of B15
  • Figure US20200172499A9-20200604-C00317
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (26 g, 100 mmol) in methanol (500 mL) was added KSCN (50 g, 500 mmol) at room temperature. The resulting mixture was stirred for 20 h and then concentrated under vacuum. The residue was diluted with H2O (300 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (8 g, 51%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (2 g, 13 mmol) in absolute EtOH (50 mL) was added NaBH4 (1 g, 26 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 mL) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.71 g, 15.6 mmol) in EtOH (10 mL) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.8 g, 80%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2.02 g, 7.5 mmol) in MeCN (50 mL) was added tert-butyl nitrite (1.2 g, 11.7 mmol) at 0° C. The resulting mixture was stirred for 10 min, and then CuBr2 (2.01 mg, 9 mmol) was introduced. The resulting mixture was stirred at room temperature for 3 hours. the resulting mixture was concentrated in vacuo. The residue was purified by an silica gel column to afford (0.6 g, 24%) of the title compound (3) as a pale yellow oil. MS m/z 333.96 [M+H]+.
    • tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (4)
  • To a solution of 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (0.6 g, 1.8 mmol) in NMP (0.6 mL) was added tert-butyl 3-aminopiperidine-1-carboxylate (0.72 mg, 3.6 mmol) and DIPEA (0.65 ml, 3.6 mmol). The resulting mixture was heated at 140° C. for 8 hours. Then it was diluted with EtOAc (200 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (150 mg, 18.5%) of the title compound (4) as a slightly yellow solid. MS m/z 453.20 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)triazol-2-amine hydrochloride (5)
  • To a solution of tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (150 mg, 0.33 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (130 mg, 93%) of the title compound (5) as a white solid, which was used without further purification. MS m/z 353.14 [M+H]+.
    • N-(3-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)triazol-2-yl)amino)piperidine-1-carbonyl)phenyl)acrylamide (B12)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)thiazol-2-amine hydrochloride (55 mg, 0.13 mmol) in DMF (0.5 mL) was added HATU (99 mg, 0.26 mmol), 3-acrylamidobenzoic acid (49.7 mg, 0.26 mmol), and DIPEA (67 mg, 0.52 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (70 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (12 mg, 18%) of the title compound as a white solid. MS m/z 526.21 [M+H]+. 1H NMR (400 MHz, CDCl3) δ 9.41 (s, 1H), 7.85 (s, 1H), 7.57 (s, 1H), 7.07 (s, 1H), 6.86 (s, 1H), 6.64 (s, 1H), 6.45 (d, J=17.1 Hz, 1H), 6.41-6.20 (m, 1H), 5.73 (s, 1H), 5.55 (s, 1H), 4.03-3.80 (m, 2H), 3.71 (s, 1H), 3.56 (s, 2H), 2.04 (s, 2H), 1.85 (s, 4H), 1.29 (s, 9H).
    • Synthesis of B16
  • Figure US20200172499A9-20200604-C00318
    • 5-thiocyanatothiazol-2-amine (1)
  • To a solution of 5-bromothiazol-2-amine hydrobromide (26 g, 100 mmol) in methanol (500 mL) was added KSCN (50 g, 500 mmol) at room temperature. The resulting mixture was stirred for 20 hours and then concentrated under vacuum. The residue was diluted with H2O (300 mL). The pH of the solution was adjusted to 10 with 10% Na2CO3. The precipitate was filtered and washed with water to obtain (8 g, 51%) of the title compound (1) as a brown solid. MS m/z 158.95 [M+H]+.
    • 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2)
  • To a solution of 5-thiocyanatothiazol-2-amine (2 g, 13 mmol) in absolute EtOH (50 mL) was added NaBH4 (1 g, 26 mmol) portionwise at room temperature. The resulting mixture was stirred for 1 hour, and then acetone (20 mL) was slowly introduced. After 1 hour, a solution of 5-(tert-butyl)-2-(chloromethyl)oxazole (2.71 g, 15.6 mmol) in EtOH (10 mL) was added, and the resulting mixture was cooled, concentrated in vacuo, and then partitioned between EtOAc and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (2.8 g, 80%) of the title compound (2) as a pale red-brown solid. MS m/z 270.06 [M+H]+.
    • 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (3)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-amine (2.02 g, 7.5 mmol) in MeCN (50 mL) was added tert-butyl nitrite (1.2 g, 11.7 mmol) at 0° C. The resulting mixture was stirred for 10 min, and then CuBr2 (2.01 mg, 9 mmol) was introduced. The resulting mixture was stirred at room temperature for 3 hours. the resulting mixture was concentrated in vacuo. The residue was purified by an silica gel column to afford (0.6 g, 24%) of the title compound (3) as a pale yellow oil. MS m/z 333.96 [M+H]+.
    • tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (4)
  • To a solution of 2-(((2-bromothiazol-5-yl)thio)methyl)-5-(tert-butyl)oxazole (0.6 g, 1.8 mmol) in NMP (0.6 mL) was added tert-butyl 3-aminopiperidine-1-carboxylate (0.72 mg, 3.6 mmol) and DIPEA (0.65 ml, 3.6 mmol). The resulting mixture was heated at 140° C. for 8 hours. Then it was diluted with EtOAc (200 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (150 mg, 18.5%) of the title compound (4) as a slightly yellow solid. MS m/z 453.20 [M+H]+.
    • 5-((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)thiazol-2-amine hydrochloride (5)
  • To a solution of tert-butyl 3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carboxylate (150 mg, 0.33 mmol) in 4 M HCl EtOAc (5 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (130 mg, 93%) of the title compound (5) as a white solid, which was used without further purification. MS m/z 353.14 [M+H]+.
    • tert-butyl (4-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)carbamate (6)
  • To a solution of 5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)-N-(piperidin-3-yl)thiazol-2-amine hydrochloride (65 mg, 0.153 mmol) in DMF (0.5 mL) was added HATU (118 mg, 0.31 mmol), 4-((tert-butoxycarbonyl)amino)benzoic acid (72 mg, 0.31 mmol), and DIPEA (79 mg, 0.612 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (70 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (40 mg, 43%) of the title compound (6) as a white solid. MS m/z 572.22[M+H]+.
    • (4-aminophenyl)(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidin-1-yl)methanone hydrochloride (7)
  • To a solution of tert-butyl (4-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)carbamate (40 mg, 0.07 mmol) in 4 M HCl EtOAc (1 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was concentrated under vacuum to afford (35 mg, 93%) of the title compound (7) as a white solid, which was used without further purification. MS m/z 472.18 [M+H]+.
    • (E)-N-(4-(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidine-1-carbonyl)phenyl)-4-dimethylamino)but-2-enamide (B16)
  • To a solution of (4-aminophenyl)(3-((5-(((5-(tert-butyl)oxazol-2-yl)methyl)thio)thiazol-2-yl)amino)piperidin-1-yl)methanone hydrochloride (50 mg, 0.1 mmol) in MeCN (5 mL) was added DIPEA (65 mg, 0.5 mmol) and (E)-4-bromobut-2-enoyl chloride (22 mg, 0.12 mmol) at 0° C. for 3 min. Then it was added 4.0 M dimethylamine in THF (1 mL). The resulting mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by an silica gel column to afford (10 mg, 17%) of the title compound as a white solid. MS m/z 500.18 [M+H]+. 1H NMR (400 MHz, MeOD) δ 7.72 (s, 2H), 7.41 (s, 2H), 7.01-6.88 (m, 1H), 6.74 (d, J=22.4 Hz, 2H), 3.94 (s, 2H), 3.86-3.68 (m, 4H), 3.50 (s, 1H), 3.27 (d, J=6.6 Hz, 2H), 2.44 (s, 6H), 2.23 (d, J=21.3 Hz, 1H), 2.13 (d, J=20.0 Hz, 1H), 1.98 (s, 2H), 1.72 (s, 2H), 1.45-1.40 (m, 9H).
    • Synthesis of B17
  • Figure US20200172499A9-20200604-C00319
    • 5-morpholinothiazol-2-amine (1)
  • To a mixture of 5-bromothiazol-2-amine hydrobromide (2.6 g, 10 mmol) and powdered potassium carbonate (2.77 g, 20 mmol) in NMP (5 mL) was added morpholine (1.73 mL, 20 mmol) under argon atmosphere and heated at 60° C. for 3 hours. Reaction mixture was cooled to room temperature and poured over ice cold water (100 mL), extracted with EtOAc (3×100 mL), washed with brine, dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure. The residue was purified by an silica gel column to afford (420 mg, 45.4%) of the title compound (1) as a brown solid. MS m/z 186.07[M+H]+.
    • 3-acrylamido-N-(5-morpholinothiazol-2-yl)benzamide (B17)
  • To a solution of 5-morpholinothiazol-2-amine (90 mg, 0.5 mmol) in DMF (0.5 mL) was added HATU (380 mg, 1 mmol), 3-acrylamidobenzoic acid (191 mg, 1 mmol), and DIPEA (129 mg, 1 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (36 mg, 21%) of the title compound as a yellow solid. MS m/z 359.14 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.30 (s, 1H), 10.37 (s, 1H), 8.29 (s, 1H), 7.91 (d, J=7.2 Hz, 1H), 7.78 (d, J=7.0 Hz, 1H), 7.49 (d, J=6.9 Hz, 1H), 6.78 (s, 1H), 6.47 (dd, J=15.8, 10.4 Hz, 1H), 6.31 (d, J=16.8 Hz, 1H), 5.81 (d, J=9.8 Hz, 1H), 3.75 (s, 4H), 3.05 (s, 4H).
    • Synthesis of B18
  • Figure US20200172499A9-20200604-C00320
    • 5-(4-methylpiperazin-1-yl)thiazol-2-amine (1)
  • To a mixture of 5-bromothiazol-2-amine hydrobromide (2.6 g, 10 mmol) and powdered potassium carbonate (2.77 g, 20 mmol) in NMP (5 mL) was added 1-methylpiperazine (2.25 mL, 20 mmol) under argon atmosphere and heated at 60° C. for 3 hours. Reaction mixture was filtered and concentrated under reduced pressure. The residue was purified by an silica gel column to afford (340 mg, 34.3%) of the title compound (1) as a brown solid. MS m/z 199.10 [M+H]+.
    • 3-acrylamido-N-(5-(4-methylpiperazin-1-yl)thiazol-2-yl)benzamide (B18)
  • To a solution of 5-(4-methylpiperazin-1-yl)thiazol-2-amine (99 mg, 0.5 mmol) in DMF (0.5 mL) was added HATU (380 mg, 1 mmol), 3-acrylamidobenzoic acid (191 mg, 1 mmol), and DIPEA (129 mg, 1 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was purified by an silica gel column to afford (41 mg, 22%) of the title compound as a yellow solid. MS m/z 372.17 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.22 (s, 1H), 10.35 (s, 1H), 8.28 (s, 1H), 7.91 (d, J=6.9 Hz, 1H), 7.78 (d, J=6.7 Hz, 1H), 7.47 (t, J=7.7 Hz, 1H), 6.71 (s, 1H), 6.47 (dd, J=16.8, 10.1 Hz, 1H), 6.31 (d, J=17.0 Hz, 1H), 5.88-5.68 (m, 1H), 3.06 (s, 4H), 2.47 (s, 4H), 2.22 (s, 3H).
    • Synthesis of B19
  • Figure US20200172499A9-20200604-C00321
    • 5-(4-ethylpiperazin-1-yl)thiazol-2-amine (1)
  • To a mixture of 5-bromothiazol-2-amine hydrobromide (2.6 g, 10 mmol) and powdered potassium carbonate (2.77 g, 20 mmol) in NMP (5 mL) was added 1-ethylpiperazine (2.28 mL, 20 mmol) under argon atmosphere and heated at 60° C. for 3 hours. Reaction mixture was filtered and concentrated under reduced pressure. The residue was purified by an silica gel column to afford (382 mg, 36%) of the title compound (1) as a brown solid. MS m/z 213.11 [M+H]+.
    • 3-acrylamido-N-(5-(4-methylpiperazin-1-yl)thiazol-2-yl)benzamide (B19)
  • To a solution of 5-(4-ethylpiperazin-1-yl)thiazol-2-amine (106 mg, 0.5 mmol) in DMF (0.5 mL) was added HATU (380 mg, 1 mmol), 3-acrylamidobenzoic acid (191 mg, 1 mmol) and DIPEA (129 mg, 1 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was purified by an silica gel column to afford (20 mg, 10.3%) of the title compound as a yellow solid. MS m/z 386.20 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.23 (s, 1H), 10.35 (s, 1H), 8.29 (s, 1H), 7.91 (d, J=7.0 Hz, 1H), 7.79 (d, J=6.8 Hz, 1H), 7.49 (d, J=7.3 Hz, 1H), 6.72 (s, 1H), 6.58-6.43 (m, 1H), 6.31 (d, J=17.2 Hz, 1H), 5.81 (d, J=10.0 Hz, 1H), 3.07 (s, 4H), 2.52 (s, 4H), 2.38 (d, J=6.3 Hz, 2H), 1.03 (s, 3H).
    • Synthesis of B20
  • Figure US20200172499A9-20200604-C00322
    • tert-butyl 4-(2-aminothiazol-5-yl)piperazine-1-carboxylate (1)
  • To a mixture of 5-bromothiazol-2-amine hydrobromide (2.6 g, 10 mmol) and powdered potassium carbonate (2.77 g, 20 mmol) in NMP (5 mL) was added tert-butyl piperazine-1-carboxylate (3.72 g, 20 mmol) under argon atmosphere and heated at 60° C. for 3 hours. Reaction mixture was cooled to room temperature and poured over ice cold water (100 mL), extracted with EtOAc (3×100 mL), washed with brine, dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure. The residue was purified by an silica gel column to afford (600 mg, 42.3%) of the title compound (1) as a brown solid. MS m/z 285.13[M+H]+.
    • tert-butyl 4-(2-(3-acrylamidobenzamido)triazol-5-yl)piperazine-1-carboxylate (B20)
  • To a solution of tert-butyl 4-(2-aminothiazol-5-yl)piperazine-1-carboxylate (142 mg, 0.5 mmol) in DMF (0.5 mL) was added HATU (380 mg, 1 mmol), 3-acrylamidobenzoic acid (191 mg, 1 mmol), and DIPEA (129 mg, 1 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was diluted with EtOAc (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by an silica gel column to afford (31 mg, 13%) of the title compound as a yellow solid. MS m/z 458.25 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.29 (s, 1H), 10.35 (s, 1H), 8.29 (s, 1H), 7.91 (d, J=7.5 Hz, 1H), 7.79 (d, J=7.4 Hz, 1H), 7.48 (t, J=7.9 Hz, 1H), 6.79 (s, 1H), 6.57-6.40 (m, 1H), 6.31 (d, J=16.6 Hz, 1H), 5.85-5.68 (m, 2H), 3.49 (s, 4H), 3.03 (s, 4H), 1.43 (s, 9H).
    • Synthesis of B22
  • Figure US20200172499A9-20200604-C00323
    • tert-butyl 1-(2-aminothiazol-5-yl)piperidin-4-ylcarbamate (1)
  • To a mixture of 5-bromothiazol-2-amine hydrobromide (2.6 g, 10 mmol) and powdered potassium carbonate (2.77 g, 20 mmol) in NMP (5 mL) was added tert-butyl piperidin-4-ylcarbamate (4.0 g, 20 mmol) under argon atmosphere and heated at 60° C. for 3 hours. Reaction mixture was cooled to room temperature and poured over ice cold water (100 mL), extracted with EtOAc (3×100 mL), washed with brine, dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure. The residue was purified by an silica gel column to afford (400 mg, 13.4%) of the title compound (1) as a brown solid. MS m/z 299.15[M+H]+.
    • 5-(4-aminopiperidin-1-yl)thiazol-2-amine (2)
  • To a solution of tert-butyl 1-(2-aminothiazol-5-yl)piperidin-4-ylcarbamate (200 mg, 0.67 mmol) in 4 M HCl EtOAc (4 mL). The resulting mixture was stirred at room temperature for 30 min. Then it was diluted with EtOAc (100 mL). The pH of the solution was adjusted to 7 with 1 M NaOH. The organics washed with water and brine, dried (Na2SO4), and concentrated to afford (120 mg, 90%) of the title compound (2) as a slightly brown solid. MS m/z 199.10 [M+H]+.
    • 5-(4-(dimethylamino)piperidin-1-yl)thiazol-2-amine (3)
  • To a solution of 5-(4-aminopiperidin-1-yl)thiazol-2-amine (120 mg, 0.61 mmol) in MeOH (5 mL) was added paraformaldehyde (90 mg, 3 mmol), AcOH (1 drop), and NaBH3CN (251 mg, 4 mmol). The resulting mixture was stirred at room temperature for 15 hours. Then it was concentrated under reduced pressure. The residue was purified by an silica gel column to afford (9 mg, 5.8%) of the title compound (3) as a brown solid. MS m/z 227.15[M+H]+.
    • 3-acrylamido-N-(5-(4-(dimethylamino)piperidin-1-yl)triazol-2-yl)benzamide (B22)
  • To a solution of 5-(4-(dimethylamino)piperidin-1-yl)thiazol-2-amine (100 mg, 0.442 mmol) in DMF (0.5 mL) was added HATU (335 mg, 0.884 mmol), 3-acrylamidobenzoic acid (169 mg, 0.884 mmol), and DIPEA (228 mg, 1.768 mmol). The resulting mixture was stirred at room temperature for 1 hour. Then it was purified by an silica gel column to afford (35 mg, 17.5%) of the title compound as a yellow solid. MS m/z 400.20 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 12.21 (s, 1H), 10.36 (s, 1H), 8.27 (s, 1H), 7.89 (s, 1H), 7.76 (s, 1H), 7.46 (s, 1H), 6.69 (s, 1H), 6.52-6.40 (m, 1H), 6.30 (d, J=17.1 Hz, 1H), 5.79 (d, J=9.6 Hz, 1H), 3.42 (d, J=9.5 Hz, 2H), 2.74 (t, J=11.1 Hz, 2H), 2.19 (s, 7H), 1.82 (d, J=11.2 Hz, 2H), 1.54 (d, J=10.9 Hz, 2H).
    • Structure-Activity Analyses for Selected Compounds
  • Select compounds described herein were evaluated for structure-activity analyses. Exemplary results are shown in Table 1.
  • TABLE 1
    IC50 values of exemplary compounds described herein.
    WT CDK12/
    HAP1 CDK13
    CDK2 CDK7 CDK9 IC50 CS HAP1
    Compound (nM) (nM) (nM) (nM) IC50 (nM)
    Figure US20200172499A9-20200604-C00324
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00325
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00326
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00327
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00328
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00329
         		120 6020 114 8 308
    Figure US20200172499A9-20200604-C00330
         		185 5550 22
    Figure US20200172499A9-20200604-C00331
         		174 6170 182
    Figure US20200172499A9-20200604-C00332
         		>10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00333
         		24.6 362 20A
    Figure US20200172499A9-20200604-C00334
         		267 9230 212
    Figure US20200172499A9-20200604-C00335
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00336
         		15.7 557 30.9
    Figure US20200172499A9-20200604-C00337
    Figure US20200172499A9-20200604-C00338
         		126 >10,000 164
    Figure US20200172499A9-20200604-C00339
         		93.5 4400 199
    Figure US20200172499A9-20200604-C00340
         		334 1280 66.5 119 591
    Figure US20200172499A9-20200604-C00341
         		>1,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00342
         		22.9 3400 15.1
    Figure US20200172499A9-20200604-C00343
         		>10,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00344
         		>1,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00345
         		>1,000 >10,000 >10,000 >10,000 >10,000
    Figure US20200172499A9-20200604-C00346
         		3170 8870 7140 >10,000 >10,000
    Figure US20200172499A9-20200604-C00347
         		264 224 197 197 1096
    Figure US20200172499A9-20200604-C00348
         		>1,000 >1,000 >1,000
    Figure US20200172499A9-20200604-C00349
         		>1,000 >1,000 >1,000
    Figure US20200172499A9-20200604-C00350
         		>370 2870 1000
    Figure US20200172499A9-20200604-C00351
         		>1,000 >1,000 >1,000
    Figure US20200172499A9-20200604-C00352
         		124 447 1570
    Figure US20200172499A9-20200604-C00353
         		251 498 298
    Figure US20200172499A9-20200604-C00354
         		>1,000 >1,000 >1,000
    Figure US20200172499A9-20200604-C00355
         		>1,000 >1,000 7280
    Figure US20200172499A9-20200604-C00356
         		92.3 5000 65
    Figure US20200172499A9-20200604-C00357
         		689 158 474
    Figure US20200172499A9-20200604-C00358
         		9.86 242 33
    Figure US20200172499A9-20200604-C00359
         		11.9 230 54.5
    Figure US20200172499A9-20200604-C00360
         		10,000 10,000
    Figure US20200172499A9-20200604-C00361
         		122 2111
    Figure US20200172499A9-20200604-C00362
         		1539 3331
    Figure US20200172499A9-20200604-C00363
         		7480 10,000
    Figure US20200172499A9-20200604-C00364
         		1180 4960
    Figure US20200172499A9-20200604-C00365
         		412 944
    Figure US20200172499A9-20200604-C00366
         		61 618
    Figure US20200172499A9-20200604-C00367
    Figure US20200172499A9-20200604-C00368
    Figure US20200172499A9-20200604-C00369
    • Genome Editing:
  • With regard to the exemplary results for cellular assays shown in Table 1 above, genome editing was performed as follows. The CRISPR/Cas9 system was used to mutate the endogenous CDK12 and CDK13 loci to encode for CDK12 C1039S and CDK13 C1017S, both are putative CDK12/13 inhibitor-refractory mutants. Target-specific oligonucleotides were cloned into pX330, which carries a codon-optimized version of Cas9 and was further modified to express GFP for identifying transfectants. Cells were co-transfected (X-tremeGENE 9 (Roche)) with 1) pX330 expressing Cas9 and CDK12-targeting guide RNAs and 2) a pUC57-AMP construct bearing 1500 bp of modified CDK12 reference genome that is centered around the CRISPR targeting site in CDK12. Two days after transfection, cells were sorted using GFP as a marker of transfected cells and cells were re-plated for five days. Cells were then re-plated at low density to facilitate the isolation of individual clones. Individual clones were isolated, expanded, and PCR genotyped using mutant specific PCR primers. Following initial PCR screening, individual clones were Sanger sequenced to confirm the presence of the desired mutation. Western blot confirmed the presence of intact CDK12 kinase. The process was sequentially repeated this time with Cas9/sgRNA constructs to target and replace the CDK13 genetic loci. Subsequent experiments were conducted using a CDK12 C1039S/CDK13 C1017S clone and a WT control clone that was carried through the entirety of the CRISPR protocol but that was verified by Sanger sequencing to be WT for CDK12 and CDK13. The genomic sequence complementary to the CDK12-directed guide RNA that was cloned into pX330 and used in the genome editing experiments is: GGCAGGATTGCCATGAGTTG. The genomic sequence complementary to the CDK13-directed guide RNA that was cloned into pX330 and used in the genome editing experiments is: GGCAAGATTGTCATGAGTTA. The reference genome sequence used as a repair template for CDK12 and CDK13 CRISPR was edited to 1) introduce DNA coding for serine, 2) introduce mutations to either remove the PAM site (NGG) targeted by CRISPR/Cas9 or introduce sufficient wobble mutations such that the guide RNA could not recognize the repair template and thus could not be cut by CRISPR/Cas9, and 3) introduce mutations that could allow for mutant and WT-specific PCR amplification.
    • HAP1 Cell Proliferation Assay:
  • With regard to the exemplary results shown in Table 1 above, the HAP1 cell proliferation assay was performed as follows. HAP1 WT and double mutants cells were seeded at a density of 12,000 cells/well in 96-well plates. Twenty-four hours cells were then treated with the indicated compounds in a 10-pt dose escalation format from 1 nM to 10 μM or DMSO control for 72 hrs. After 72 hrs, cells were assayed using CellTiter-Glo Luminescent Cell Viability Assay (Promega) to determine cell viability by measuring the amount of ATP present in each sample cell population, which is an indicator of cell metabolic activity. Results are graphed as fraction of the DMSO control at 72 hrs. All data points were performed in biological triplicate.
  • HAP1 cells expressing putative inhibitor-refractory mutations in CDK12 (C1039S) and CDK13 (C1017S) show up to 20-fold less sensitivity to exemplary compounds as compared to control WT HAP1 cells. This result indicates that a substantial portion of intracellular compound activity comes from covalent inhibition of CDK12 and/or CDK13 and mutation of the targeted cysteine (C1039 in CDK12 and C1017 in CDK13) to less nucleophilic serines is sufficient to rescue a substantial portion of anti-proliferative activity.
    • EQUIVALENTS AND SCOPE
  • In the claims articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.
  • Furthermore, the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. It is also noted that the terms “comprising” and “containing” are intended to be open and permits the inclusion of additional elements or steps. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.
  • This application refers to various issued patents, published patent applications, journal articles, and other publications, all of which are incorporated herein by reference. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Because such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the invention can be excluded from any claim, for any reason, whether or not related to the existence of prior art.
  • Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. The scope of the present embodiments described herein is not intended to be limited to the above Description, but rather is as set forth in the appended claims. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims.

Claims (39)

1. A compound of Formula (I′):
Figure US20200172499A9-20200604-C00370
or a pharmaceutically acceptable salt thereof, wherein:
R1 is hydrogen, halogen, or optionally substituted alkyl;
M is O, S, or NRM;
RM is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
Ring C is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted monocyclic or bicyclic aryl, or optionally substituted monocyclic or bicyclic heteroaryl;
each instance of RA, RB, and RC is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —ORa, —N(Ra)2, —SRa, —CN, —SCN, —NO2, —N3, or optionally substituted acyl;
each instance of Ra is independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Ra are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
each of a1, b1, and c1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
L1 is —CH2—, lc—S(═O)2—lb, —O—, —S—, —NRL1—, —C(═O)—, lc—NRL1C(═O)—lb, lc—C(═O)NRL1—lb, lc—OC(═O)lb, or lc—C(═O)O—lb; wherein lb indicates the point of attachment is to Ring B; and lc indicates the point of attachment is to Ring C;
L2 is —O—, —S—, —NRL2—, lb—NRL2C(═O)—lm, lb—C(═O)NRL2—lm; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
X is xm—CH2CH2—xa, xm—CH═CH—xa, xm—CH2—NRLXxa, xm—CH2—O—CH2—xa, xm—CH2—NRLX—CH2—xa, —O—, —S—, —NRLX—, xm—O—CH2—xa, xm—S—CH2—xa, xm—S—C(═O)CH2—xa, or xm—NRLX—CH2—xa; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
each of RL1, RL2, and RLX is independently hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
R2 is any of Formulae (i-1)-(i-41):
Figure US20200172499A9-20200604-C00371
Figure US20200172499A9-20200604-C00372
Figure US20200172499A9-20200604-C00373
Figure US20200172499A9-20200604-C00374
Figure US20200172499A9-20200604-C00375
Figure US20200172499A9-20200604-C00376
wherein:
L3 is a bond or an optionally substituted C1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C═O—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(═S)NRL3a—, trans-CRL3b═CRL3b—, cis-CRL3b═CRL3b—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(═O)—, —S(═O)NRL3a—, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a—, or —NRL3aS(═O)2—, wherein RL3a is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group, and wherein each occurrence of RL3b is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
L4 is a bond or an optionally substituted, branched or unbranched C1-6 hydrocarbon chain;
each of RE1, RE2, and RE3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, and —SREE, wherein each occurrence of REE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two REE groups are joined to form an optionally substituted heterocyclic ring;
or RE1 and RE3, or RE2 and RE3, or RE1 and RE2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
RE4 is a leaving group;
RE5 is halogen;
RE6 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
each instance of Y is independently O, S, or NRE7, wherein RE7 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
a is 1 or 2; and
each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
2. (canceled)
3. The compound of claim 1, wherein the compound is of the formula:
Figure US20200172499A9-20200604-C00377
or a pharmaceutically acceptable salt thereof.
4. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the Ring B is optionally substituted monocyclic heterocyclyl.
5. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the Ring B is optionally substituted piperidinyl.
6. The compound of claim 5, wherein the compound is of Formula (I-i), (I-ii), (I-ii-a), (I-ii-b), (I-ii-c), (I-iii), or (I′-i):
Figure US20200172499A9-20200604-C00378
Figure US20200172499A9-20200604-C00379
or a pharmaceutically acceptable salt thereof.
7-11. (canceled)
12. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring B is optionally substituted monocyclic carbocyclyl.
13. (canceled)
14. The compound of claim 1, wherein the compound is of Formula (I-iv), (I-iv-a), or (I-iv-b):
Figure US20200172499A9-20200604-C00380
or a pharmaceutically acceptable salt thereof.
15-17. (canceled)
18. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring C is optionally substituted.bicyclic aryl or heteroaryl.
19-20. (canceled)
21. A compound of Formula (II′):
Figure US20200172499A9-20200604-C00381
or a pharmaceutically acceptable salt thereof, wherein:
R1 is hydrogen, halogen, or optionally substituted alkyl;
M is O, S, or NRM;
RM is hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group;
Ring A is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
Ring B is optionally substituted monocyclic carbocyclyl, optionally substituted monocyclic heterocyclyl, optionally substituted phenyl, or optionally substituted monocyclic heteroaryl;
each instance of RA and RB is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —ORa, —N(Ra)2, —SRa, —CN, —SCN, —C(═NRa)Ra, —C(═NRa)ORa, —C(═NRa)N(Ra)2, —C(═O)Ra, —C(═O)ORa, —C(═O)N(Ra)2, —NO2, —NRaC(═O)Ra, —NRaC(═O)ORa, —NRaC(═O)N(Ra)2, —OC(═O)Ra, —OC(═O)ORa, or —OC(═O)N(Ra)2;
each instance of Ra is independently hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Ra are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;
each of a1 and b1 is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits;
L2 is —O—, —S—, —NRL2—, lb—NRL2C(═O)—lm, lb—C(═O)NRL2—lm; wherein lb indicates the point of attachment is to Ring B; and lm indicates the point of attachment is to the heteroaryl ring with M;
X is a bond, —O—, —S—, —NRLX—, xm—O—CH2—xa, xm—S—CH2—xa, or xm—NRLX—CH2—xa; wherein xa indicates the point of attachment is to Ring A; and xm indicates the point of attachment is to the heteroaryl ring with M;
each of RL2 and RLX is independently hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
R2 is any of Formulae (i-1)-(i-41):
Figure US20200172499A9-20200604-C00382
Figure US20200172499A9-20200604-C00383
Figure US20200172499A9-20200604-C00384
Figure US20200172499A9-20200604-C00385
Figure US20200172499A9-20200604-C00386
Figure US20200172499A9-20200604-C00387
wherein:
L3 is a bond or an optionally substituted C1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C═O—, —O—, —S—, —NRL3a—, —NRL3aC(═O)—, —C(═O)NRL3a—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NRL3aC(═S)—, —C(═S)NRL3a—, trans-CRL3b═CRL3b—, cis-CRL3b═CRL3b—, —C≡C—, —S(═O)—, —S(═O)O—, —OS(—O)—, —S(—O)NRL3a—, —NRL3aS(═O)—, —S(═O)2—, —S(═O)2O—, —OS(═O)2—, —S(═O)2NRL3a—, or —NRL3aS(═O)2—, wherein RL3a is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group, and wherein each occurrence of RL3b is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two RL3b groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
L4 is a bond or an optionally substituted, branched or unbranched C1-6 hydrocarbon chain;
each of RE1, RE2, and RE3 is independently hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2OREE, —CH2N(REE)2, —CH2SREE, —OREE, —N(REE)2, —Si(REE)3, and —SREE, wherein each occurrence of REE is independently hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, or two REE groups are joined to form an optionally substituted heterocyclic ring;
or RE1 and RE3, or RE2 and RE3, or RE1 and RE2 are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;
RE4 is a leaving group;
RE5 is halogen;
RE6 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
each instance of Y is independently O, S, or NRE7, wherein RE7 is hydrogen, optionally substituted C1-6 alkyl, or a nitrogen protecting group;
a is 1 or 2; and
each instance of z is independently 0, 1, 2, 3, 4, 5, or 6, as valency permits.
22-30. (canceled)
31. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring A is optionally substituted monocyclic heteroaryl.
32-39. (canceled)
40. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring A is optionally substituted phenyl.
41-46. (canceled)
47. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring A is optionally substituted monocyclic carbocyclyl.
48. (canceled)
49. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring A is optionally substituted monocyclic heterocyclyl.
50-54. (canceled)
55. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein Ring A is optionally substituted 6-membered heteroaryl.
56. (canceled)
57. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein L1 is —CH2— or lc—S(═O)2—lb.
58-82. (canceled)
83. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein R2 is of Formula (i-1):
Figure US20200172499A9-20200604-C00388
84-90. (canceled)
91. The compound of claim 1, wherein the compound is of one of the following formulae:
Figure US20200172499A9-20200604-C00389
Figure US20200172499A9-20200604-C00390
Figure US20200172499A9-20200604-C00391
Figure US20200172499A9-20200604-C00392
Figure US20200172499A9-20200604-C00393
or a pharmaceutically acceptable salt thereof.
92. The compound of claim 1, wherein the compound is of one of the following formulae:
Figure US20200172499A9-20200604-C00394
Figure US20200172499A9-20200604-C00395
Figure US20200172499A9-20200604-C00396
Figure US20200172499A9-20200604-C00397
Figure US20200172499A9-20200604-C00398
Figure US20200172499A9-20200604-C00399
Figure US20200172499A9-20200604-C00400
Figure US20200172499A9-20200604-C00401
Figure US20200172499A9-20200604-C00402
Figure US20200172499A9-20200604-C00403
Figure US20200172499A9-20200604-C00404
Figure US20200172499A9-20200604-C00405
Figure US20200172499A9-20200604-C00406
Figure US20200172499A9-20200604-C00407
Figure US20200172499A9-20200604-C00408
Figure US20200172499A9-20200604-C00409
Figure US20200172499A9-20200604-C00410
or a pharmaceutically acceptable salt thereof.
93. The compound of claim 1, wherein the compound is of one of the following formulae:
Figure US20200172499A9-20200604-C00411
Figure US20200172499A9-20200604-C00412
Figure US20200172499A9-20200604-C00413
Figure US20200172499A9-20200604-C00414
Figure US20200172499A9-20200604-C00415
Figure US20200172499A9-20200604-C00416
Figure US20200172499A9-20200604-C00417
or a pharmaceutically acceptable salt thereof.
94-95. (canceled)
96. A pharmaceutical composition comprising a compound of claim 1, or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.
97. (canceled)
98. A method of treating a proliferative disease in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of claim 1, or a pharmaceutically acceptable salt thereof.
99-131. (canceled)
132. A method of inhibiting the activity of a cyclin-dependent kinase (CDK) in a biological sample or subject, the method comprising administering to the subject or contacting the biological sample with a therapeutically effective amount of a compound of claim 1, or a pharmaceutically acceptable salt thereof.
133-153. (canceled)
US15/758,982 2015-09-09 2016-09-09 Inhibitors of cyclin-dependent kinases Active 2037-09-13 US11142507B2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
US15/758,982 US11142507B2 (en) 2015-09-09 2016-09-09 Inhibitors of cyclin-dependent kinases

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562216271P 2015-09-09 2015-09-09
US15/758,982 US11142507B2 (en) 2015-09-09 2016-09-09 Inhibitors of cyclin-dependent kinases
PCT/US2016/051118 WO2017044858A2 (en) 2015-09-09 2016-09-09 Inhibitors of cyclin-dependent kinases

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2016/051118 A-371-Of-International WO2017044858A2 (en) 2015-09-09 2016-09-09 Inhibitors of cyclin-dependent kinases

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US17/378,622 Division US20220055998A1 (en) 2015-09-09 2021-07-16 Inhibitors of cyclin-dependent kinases

Publications (3)

Publication Number Publication Date
US20180362483A1 US20180362483A1 (en) 2018-12-20
US20200172499A9 true US20200172499A9 (en) 2020-06-04
US11142507B2 US11142507B2 (en) 2021-10-12

Family

ID=58240329

Family Applications (2)

Application Number Title Priority Date Filing Date
US15/758,982 Active 2037-09-13 US11142507B2 (en) 2015-09-09 2016-09-09 Inhibitors of cyclin-dependent kinases
US17/378,622 Abandoned US20220055998A1 (en) 2015-09-09 2021-07-16 Inhibitors of cyclin-dependent kinases

Family Applications After (1)

Application Number Title Priority Date Filing Date
US17/378,622 Abandoned US20220055998A1 (en) 2015-09-09 2021-07-16 Inhibitors of cyclin-dependent kinases

Country Status (6)

Country Link
US (2) US11142507B2 (en)
EP (2) EP3347018B1 (en)
JP (2) JP7028766B2 (en)
AU (1) AU2016319125B2 (en)
CA (1) CA2996978A1 (en)
WO (1) WO2017044858A2 (en)

Families Citing this family (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9180127B2 (en) 2009-12-29 2015-11-10 Dana-Farber Cancer Institute, Inc. Type II Raf kinase inhibitors
WO2013074986A1 (en) 2011-11-17 2013-05-23 Dana-Farber Cancer Institute, Inc. Inhibitors of c-jun-n-terminal kinase (jnk)
EP2909194A1 (en) 2012-10-18 2015-08-26 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinase 7 (cdk7)
US9758522B2 (en) 2012-10-19 2017-09-12 Dana-Farber Cancer Institute, Inc. Hydrophobically tagged small molecules as inducers of protein degradation
AU2014337044A1 (en) 2013-10-18 2016-05-05 Dana-Farber Cancer Institute, Inc. Polycyclic inhibitors of cyclin-dependent kinase 7 (CDK7)
CA2927917C (en) 2013-10-18 2022-08-09 Syros Pharmaceuticals, Inc. Heteroaromatic compounds useful for the treatment of proliferative diseases
CA2972239A1 (en) 2014-12-23 2016-06-30 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinase 7 (cdk7)
EP3273966B1 (en) 2015-03-27 2023-05-03 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinases
AU2016276963C1 (en) 2015-06-12 2021-08-05 Dana-Farber Cancer Institute, Inc. Combination therapy of transcription inhibitors and kinase inhibitors
EP3445760B1 (en) * 2016-04-22 2022-02-23 Dana-Farber Cancer Institute, Inc. Degradation of cyclin-dependent kinase 9 (cdk9) by conjugation of cdk9 inhibitors with e3 ligase ligand and methods of use
IL266181B2 (en) 2016-11-03 2024-04-01 Corvus Pharmaceuticals Inc Compounds and methods for modulating interleukin-2-inducible t-cell kinase
AU2017363307B2 (en) 2016-11-22 2021-07-29 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinase 12 (CDK12) and uses thereof
US10807951B2 (en) * 2017-10-13 2020-10-20 The Regents Of The University Of California mTORC1 modulators
TWI703149B (en) 2017-11-16 2020-09-01 美商美國禮來大藥廠 Compounds useful for inhibiting cdk7
US11447493B2 (en) 2018-05-02 2022-09-20 Kinnate Biopharma Inc. Inhibitors of cyclin-dependent kinases
SG11202013175SA (en) 2018-06-29 2021-01-28 Kinnate Biopharma Inc Inhibitors of cyclin-dependent kinases
WO2020046770A1 (en) * 2018-08-31 2020-03-05 Institute For Cancer Research D/B/A The Research Institute Of Fox Chase Cancer Center Kinase activity in tumors
TWI783480B (en) 2020-05-27 2022-11-11 美商美國禮來大藥廠 Compounds useful for inhibiting cdk7
EP4247808A1 (en) * 2020-11-20 2023-09-27 Yissum Research Development Company of the Hebrew University of Jerusalem Ltd. Inhibitors of igf2bp1-rna binding
WO2023283425A1 (en) 2021-07-09 2023-01-12 Plexium, Inc. Aryl compounds and pharmaceutical compositions that modulate ikzf2

Family Cites Families (280)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB796524A (en) 1956-03-21 1958-06-11 Hickson & Welch Ltd Improvements in or relating to optical whitening agents
US4231938A (en) 1979-06-15 1980-11-04 Merck & Co., Inc. Hypocholesteremic fermentation products and process of preparation
US4270537A (en) 1979-11-19 1981-06-02 Romaine Richard A Automatic hypodermic syringe
WO1984002131A1 (en) 1982-11-22 1984-06-07 Sandoz Ag Analogs of mevalolactone and derivatives thereof, processes for their production, pharmaceutical compositions containing them and their use as pharmaceuticals
US4828991A (en) 1984-01-31 1989-05-09 Akzo N.V. Tumor specific monoclonal antibodies
US4596556A (en) 1985-03-25 1986-06-24 Bioject, Inc. Hypodermic injection apparatus
CA1283827C (en) 1986-12-18 1991-05-07 Giorgio Cirelli Appliance for injection of liquid formulations
GB8704027D0 (en) 1987-02-20 1987-03-25 Owen Mumford Ltd Syringe needle combination
US4940460A (en) 1987-06-19 1990-07-10 Bioject, Inc. Patient-fillable and non-invasive hypodermic injection device assembly
US4941880A (en) 1987-06-19 1990-07-17 Bioject, Inc. Pre-filled ampule and non-invasive hypodermic injection device assembly
US4790824A (en) 1987-06-19 1988-12-13 Bioject, Inc. Non-invasive hypodermic injection device
US4885314A (en) 1987-06-29 1989-12-05 Merck & Co., Inc. Novel HMG-CoA reductase inhibitors
US4782084A (en) 1987-06-29 1988-11-01 Merck & Co., Inc. HMG-COA reductase inhibitors
US5339163A (en) 1988-03-16 1994-08-16 Canon Kabushiki Kaisha Automatic exposure control device using plural image plane detection areas
FR2638359A1 (en) 1988-11-03 1990-05-04 Tino Dalto SYRINGE GUIDE WITH ADJUSTMENT OF DEPTH DEPTH OF NEEDLE IN SKIN
US5064413A (en) 1989-11-09 1991-11-12 Bioject, Inc. Needleless hypodermic injection device
US5312335A (en) 1989-11-09 1994-05-17 Bioject Inc. Needleless hypodermic injection device
US5420245A (en) 1990-04-18 1995-05-30 Board Of Regents, The University Of Texas Tetrapeptide-based inhibitors of farnesyl transferase
US5190521A (en) 1990-08-22 1993-03-02 Tecnol Medical Products, Inc. Apparatus and method for raising a skin wheal and anesthetizing skin
US5527288A (en) 1990-12-13 1996-06-18 Elan Medical Technologies Limited Intradermal drug delivery device and method for intradermal delivery of drugs
US5747469A (en) 1991-03-06 1998-05-05 Board Of Regents, The University Of Texas System Methods and compositions comprising DNA damaging agents and p53
GB9118204D0 (en) 1991-08-23 1991-10-09 Weston Terence E Needle-less injector
SE9102652D0 (en) 1991-09-13 1991-09-13 Kabi Pharmacia Ab INJECTION NEEDLE ARRANGEMENT
US5328483A (en) 1992-02-27 1994-07-12 Jacoby Richard M Intradermal injection device with medication and needle guard
US5383851A (en) 1992-07-24 1995-01-24 Bioject Inc. Needleless hypodermic injection device
US5569189A (en) 1992-09-28 1996-10-29 Equidyne Systems, Inc. hypodermic jet injector
US5334144A (en) 1992-10-30 1994-08-02 Becton, Dickinson And Company Single use disposable needleless injector
EP0604181A1 (en) 1992-12-21 1994-06-29 Eli Lilly And Company Antitumor compositions and method of treatment
WO1994019357A1 (en) 1993-02-23 1994-09-01 Merrell Dow Pharmaceuticals Inc. Farnesyl:protein transferase inhibitors as anticancer agents
CA2118985A1 (en) 1993-04-02 1994-10-03 Dinesh V. Patel Heterocyclic inhibitors of farnesyl protein transferase
AU6909194A (en) 1993-05-14 1994-12-12 Board Of Regents, The University Of Texas System Preparation of n-cyanodithioimino-carbonates and 3-mercapto-5-amino-1h-1,2,4-triazole
US5602098A (en) 1993-05-18 1997-02-11 University Of Pittsburgh Inhibition of farnesyltransferase
EP0670314A4 (en) 1993-09-22 1996-04-10 Kyowa Hakko Kogyo Kk Farnesyltransferase inhibitor.
AU698960B2 (en) 1993-10-15 1998-11-12 Schering Corporation Tricyclic sulfonamide compounds useful for inhibition of g-protein function and for treatment of proliferative diseases
NZ274749A (en) 1993-10-15 1998-05-27 Schering Corp Tricyclic carbamate derivatives useful for inhibition of g-protein function and for treating proliferative diseases, medicaments
US5661152A (en) 1993-10-15 1997-08-26 Schering Corporation Tricyclic sulfonamide compounds useful for inhibition of G-protein function and for treatment of proliferative diseases
US5721236A (en) 1993-10-15 1998-02-24 Schering Corporation Tricyclic carbamate compounds useful for inhibition of G-protein function and for treatment of proliferative diseases
US5719148A (en) 1993-10-15 1998-02-17 Schering Corporation Tricyclic amide and urea compounds useful for inhibition of g-protein function and for treatment of proliferative diseases
IL111235A (en) 1993-10-15 2001-03-19 Schering Plough Corp Pharmaceutical compositions for inhibition of g-protein function and for treatment of proliferative diseases containing tricyclic compounds some such compounds and process for preparing part of them
ES2157994T3 (en) 1993-10-25 2001-09-01 Parke Davis & Co TETRA INHIBITORS AND SUBSTITUTED PENTAPEPTIDES OF THE PROTEIN FARNESILTRANSFERASA.
US5783593A (en) 1993-11-04 1998-07-21 Abbott Laboratories Inhibitors of squalene synthetase and protein farnesyltransferase
DE69417012T2 (en) 1993-11-04 1999-10-07 Abbott Lab CYCLOBUTAN DERIVATIVES AS INHIBITORS OF SQUALEN SYNTHETASE AND PROTEIN-FARNESYLTRANSFERASE
WO1995012612A1 (en) 1993-11-05 1995-05-11 Warner-Lambert Company Substituted di- and tripeptide inhibitors of protein:farnesyl transferase
US5484799A (en) 1993-12-09 1996-01-16 Abbott Laboratories Antifungal dorrigocin derivatives
WO1995024176A1 (en) 1994-03-07 1995-09-14 Bioject, Inc. Ampule filling device
US5466220A (en) 1994-03-08 1995-11-14 Bioject, Inc. Drug vial mixing and transfer device
US5840918A (en) 1994-03-15 1998-11-24 Eisai Co., Ltd. Isoprenyl transferase inhibitors
US6312699B1 (en) 1994-03-28 2001-11-06 Uab Research Foundation Ligands added to adenovirus fiber
IL113196A0 (en) 1994-03-31 1995-06-29 Bristol Myers Squibb Co Imidazole derivatives and pharmaceutical compositions containing the same
US5523430A (en) 1994-04-14 1996-06-04 Bristol-Myers Squibb Company Protein farnesyl transferase inhibitors
US5510510A (en) 1994-05-10 1996-04-23 Bristol-Meyers Squibb Company Inhibitors of farnesyl protein transferase
US5563255A (en) 1994-05-31 1996-10-08 Isis Pharmaceuticals, Inc. Antisense oligonucleotide modulation of raf gene expression
JPH10501259A (en) 1994-06-10 1998-02-03 ローン−プーラン・ロレ・ソシエテ・アノニム Novel farnesyltransferase inhibitors, their preparation and pharmaceutical compositions containing them
US5571792A (en) 1994-06-30 1996-11-05 Warner-Lambert Company Histidine and homohistidine derivatives as inhibitors of protein farnesyltransferase
CA2155448A1 (en) 1994-08-11 1996-02-12 Katerina Leftheris Inhibitors of farnesyl protein transferase
DE69514367T2 (en) 1994-08-11 2000-07-27 Banyu Pharma Co Ltd SUBSTITUTED AMID DERIVATIVES
EP0805154A1 (en) 1994-08-12 1997-11-05 Banyu Pharmaceutical Co., Ltd. N,n-disubstituted amic acid derivative
CA2204144A1 (en) 1994-12-09 1996-06-13 Francis J. Tinney Substituted tetra- and pentapeptide inhibitors of protein:farnesyl transferase
US5599302A (en) 1995-01-09 1997-02-04 Medi-Ject Corporation Medical injection system and method, gas spring thereof and launching device using gas spring
EP0794789A4 (en) 1995-01-12 1999-05-26 Univ Pittsburgh Inhibitors of prenyl transferases
FR2729390A1 (en) 1995-01-18 1996-07-19 Rhone Poulenc Rorer Sa NOVEL FARNESYL TRANSFERASE INHIBITORS, THEIR PREPARATION AND THE PHARMACEUTICAL COMPOSITIONS CONTAINING THEM
FR2730491B1 (en) 1995-02-09 1997-03-14 Rhone Poulenc Rorer Sa NOVEL FARNESYL TRANSFERASE INHIBITORS, THEIR PREPARATION AND THE PHARMACEUTICAL COMPOSITIONS CONTAINING THEM
FR2730492B1 (en) 1995-02-09 1997-03-14 Rhone Poulenc Rorer Sa NOVEL FARNESYL TRANSFERASE INHIBITORS, THEIR PREPARATION AND THE PHARMACEUTICAL COMPOSITIONS CONTAINING THEM
US5684013A (en) 1995-03-24 1997-11-04 Schering Corporation Tricyclic compounds useful for inhibition of g-protein function and for treatment of proliferative diseases
US5700806A (en) 1995-03-24 1997-12-23 Schering Corporation Tricyclic amide and urea compounds useful for inhibition of G-protein function and for treatment of proliferative diseases
IL117580A0 (en) 1995-03-29 1996-07-23 Merck & Co Inc Inhibitors of farnesyl-protein transferase and pharmaceutical compositions containing them
US5891872A (en) 1995-04-07 1999-04-06 Schering Corporation Tricyclic compounds
IL117798A (en) 1995-04-07 2001-11-25 Schering Plough Corp Tricyclic compounds useful for inhibition of g-protein function and for treatment of proliferative diseases and pharmaceutical compositions comprising them
US5712280A (en) 1995-04-07 1998-01-27 Schering Corporation Tricyclic compounds useful for inhibition of G-protein function and for treatment of proliferative diseases
DE69628559T2 (en) 1995-04-07 2004-04-29 Schering Corp. CARBONYL-PIPERAZNYL AND PIPERIDINYL DERIVATIVES FOR INHIBITING FARNESYL PROTEIN TRANSFERASE
US5831115A (en) 1995-04-21 1998-11-03 Abbott Laboratories Inhibitors of squalene synthase and protein farnesyltransferase
IL118101A0 (en) 1995-05-03 1996-09-12 Abbott Lab Inhibitors of farnesyltransferase
AU6034296A (en) 1995-06-16 1997-01-15 Warner-Lambert Company Tricyclic inhibitors of protein farnesyltransferase
FR2736641B1 (en) 1995-07-10 1997-08-22 Rhone Poulenc Rorer Sa NOVEL FARNESYL TRANSFERASE INHIBITORS, THEIR PREPARATION AND THE PHARMACEUTICAL COMPOSITIONS CONTAINING THEM
FR2736638B1 (en) 1995-07-12 1997-08-22 Rhone Poulenc Rorer Sa NOVEL FARNESYL TRANSFERASE INHIBITORS, THEIR PREPARATION AND THE PHARMACEUTICAL COMPOSITIONS CONTAINING THEM
CH690163A5 (en) 1995-07-28 2000-05-31 Symphar Sa Derivatives substituted gem-diphosphonates useful as anti-cancer.
CN1066147C (en) 1995-11-01 2001-05-23 诺瓦提斯公司 Purine derivatives and processes for their preparation
EP0873123B1 (en) 1995-11-06 2003-04-09 University Of Pittsburgh Inhibitors of protein isoprenyl transferases
CA2238081A1 (en) 1995-11-22 1997-05-29 S. Jane Desolms Inhibitors of farnesyl-protein transferase
ES2175137T3 (en) 1995-12-08 2002-11-16 Janssen Pharmaceutica Nv DERIVATIVES OF (IMIDAZOL-5-IL) METHYL-2-QUINOLINONE AS INHIBITORS OF LAPROTEIN FARNESIL-TRANSFERASE.
AU730194B2 (en) 1995-12-22 2001-03-01 Merck Sharp & Dohme Corp. Tricyclic amides useful for inhibition of G-protein function and for treatment of proliferative diseases
US5893397A (en) 1996-01-12 1999-04-13 Bioject Inc. Medication vial/syringe liquid-transfer apparatus
WO1997026246A1 (en) 1996-01-16 1997-07-24 Warner-Lambert Company Substituted histidine inhibitors of protein farnesyltransferase
US6673927B2 (en) 1996-02-16 2004-01-06 Societe De Conseils De Recherches Et D'applications Scientifiques, S.A.S. Farnesyl transferase inhibitors
JP2001519766A (en) 1996-04-03 2001-10-23 メルク エンド カンパニー インコーポレーテッド Inhibitors of farnesyl protein transferase
WO1997044350A1 (en) 1996-05-22 1997-11-27 Warner-Lambert Company Inhibitors of protein farnesyl transferase
CA2260216A1 (en) 1996-07-15 1998-01-22 Bristol-Myers Squibb Company Thiadioxobenzodiazepine inhibitors of farnesyl protein transferase
US5866702A (en) 1996-08-02 1999-02-02 Cv Therapeutics, Incorporation Purine inhibitors of cyclin dependent kinase 2
CA2276150A1 (en) 1996-12-30 1998-07-09 Steven D. Young Inhibitors of farnesyl-protein transferase
WO1998028980A1 (en) 1996-12-30 1998-07-09 Merck & Co., Inc. Inhibitors of farnesyl-protein transferase
US5993412A (en) 1997-05-19 1999-11-30 Bioject, Inc. Injection apparatus
US6040321A (en) 1997-11-12 2000-03-21 Bristol-Myers Squibb Company Aminothiazole inhibitors of cyclin dependent kinases
US6262096B1 (en) 1997-11-12 2001-07-17 Bristol-Myers Squibb Company Aminothiazole inhibitors of cyclin dependent kinases
US6214852B1 (en) * 1998-10-21 2001-04-10 Bristol-Myers Squibb Company N-[5-[[[5-alkyl-2-oxazolyl]methyl]thio]-2-thiazolyl]-carboxamide inhibitors of cyclin dependent kinases
CN1345334A (en) 1999-01-29 2002-04-17 伊姆克罗尼系统公司 Antibodies specific to KDR and uses thereof
GB9903762D0 (en) 1999-02-18 1999-04-14 Novartis Ag Organic compounds
GB9904387D0 (en) 1999-02-25 1999-04-21 Pharmacia & Upjohn Spa Antitumour synergistic composition
WO2000061186A1 (en) 1999-04-08 2000-10-19 Arch Development Corporation Use of anti-vegf antibody to enhance radiation in cancer therapy
PE20010306A1 (en) 1999-07-02 2001-03-29 Agouron Pharma INDAZOLE COMPOUNDS AND PHARMACEUTICAL COMPOSITIONS CONTAINING THEM USEFUL FOR THE INHIBITION OF PROTEIN KINASE
SK4772002A3 (en) * 1999-09-10 2002-11-06 Merck & Co Inc Tyrosine kinase inhibitors, pharmaceutical composition containing the same and their use
US6921763B2 (en) 1999-09-17 2005-07-26 Abbott Laboratories Pyrazolopyrimidines as therapeutic agents
ATE247657T1 (en) 1999-09-17 2003-09-15 Basf Ag PYRAZOLOPYRIMIDINES AS MEDICINAL PRODUCTS
MY125768A (en) 1999-12-15 2006-08-30 Bristol Myers Squibb Co N-[5-[[[5-alkyl-2-oxazolyl]methyl]thio]-2-thiazolyl]-carboxamide inhibitors of cyclin dependent kinases
TWI284639B (en) 2000-01-24 2007-08-01 Shionogi & Co A compound having thrombopoietin receptor agonistic effect
AU2001287654B2 (en) 2000-08-10 2006-12-14 Pfizer Italia S.R.I. Bicyclo-pyrazoles active as kinase inhibitors, process for their preparation and pharmaceutical compositions comprising them
MXPA03003774A (en) 2000-10-31 2003-07-28 Aventis Pharm Prod Inc Acyl and sulfonyl derivatives of 6,9-disubstituted 2-(trans-1,4-diaminocyclohexyl)-purines and their use as antiproliferative agents.
US7429599B2 (en) 2000-12-06 2008-09-30 Signal Pharmaceuticals, Llc Methods for treating or preventing an inflammatory or metabolic condition or inhibiting JNK
WO2002050071A1 (en) 2000-12-21 2002-06-27 Bristol-Myers Squibb Company Thiazolyl inhibitors of tec family tyrosine kinases
ES2265452T3 (en) 2000-12-21 2007-02-16 Vertex Pharmaceuticals Incorporated PIRAZOL COMPOUNDS USED AS INHIBITORS OF PROTEIN QUINASA.
FR2818642B1 (en) 2000-12-26 2005-07-15 Hoechst Marion Roussel Inc NOVEL DERIVATIVES OF PURINE, PROCESS FOR PREPARING THEM, THEIR USE AS MEDICAMENTS, PHARMACEUTICAL COMPOSITIONS AND THEIR NEW USE
MXPA03008560A (en) 2001-03-22 2004-06-30 Abbot Gmbh & Co Kg Single-stage pfc + ballast control circuit/general purpose power converter.
DE60223790T4 (en) 2001-03-29 2009-05-07 Vertex Pharmaceuticals Inc., Cambridge HEMMER OF C-JUN TERMINAL KINASE (JNK) AND OTHER PROTEIN KINASE
AU2002247847A1 (en) 2001-04-09 2002-10-21 Lorantis Limited Therapeutic use and identification of modulators of a hedgehog signalling pathway or one of its target pathways
US6881737B2 (en) 2001-04-11 2005-04-19 Amgen Inc. Substituted triazinyl acrylamide derivatives and methods of use
JP2002338537A (en) 2001-05-16 2002-11-27 Mitsubishi Pharma Corp Amide compound and its medicinal use
ES2274035T3 (en) 2001-06-01 2007-05-16 Vertex Pharmaceuticals Incorporated USEFUL TIAZOL COMPOUNDS AS PROTEIN QUINASE INHIBITORS.
JP4541695B2 (en) 2001-06-15 2010-09-08 バーテックス ファーマシューティカルズ インコーポレイテッド 5- (2-Aminopyrimidin-4-yl) benzisoxazole as a protein kinase inhibitor
US6939874B2 (en) 2001-08-22 2005-09-06 Amgen Inc. Substituted pyrimidinyl derivatives and methods of use
US7115617B2 (en) 2001-08-22 2006-10-03 Amgen Inc. Amino-substituted pyrimidinyl derivatives and methods of use
WO2003026664A1 (en) 2001-09-26 2003-04-03 Bayer Corporation 2-phenylamino-4- (5-pyrazolylamino) -pyramidine derivatives as kinase inhibitors, in particular, src kinase inhibitors
AU2002353186A1 (en) 2001-12-19 2003-06-30 Smithkline Beecham P.L.C. (1-h-indazol-3-yl) -amide derivatives as gsk-3 inhibitors
FR2836915B1 (en) 2002-03-11 2008-01-11 Aventis Pharma Sa AMINOINDAZOLE DERIVATIVES, PREPARATION METHOD AND INTERMEDIATES THEREOF AS MEDICAMENTS AND PHARMACEUTICAL COMPOSITIONS COMPRISING THE SAME
AU2003231231A1 (en) 2002-05-06 2003-11-11 Bayer Pharmaceuticals Corporation Pyridinyl amino pyrimidine derivatives useful for treating hyper-proliferative disorders
EP1506176B1 (en) 2002-05-17 2013-04-24 Pfizer Italia S.r.l. Aminoindazole derivatives active as kinase inhibitors, process for their preparation and pharmaceutical compositions comprising them
WO2004000214A2 (en) 2002-06-19 2003-12-31 Bristol-Myers Squibb Company Use of compounds having an amine nucleus in manufacture of a medicament useful for treating factor viia-associated conditions
TW200401638A (en) 2002-06-20 2004-02-01 Bristol Myers Squibb Co Heterocyclic inhibitors of kinases
US7361665B2 (en) 2002-07-09 2008-04-22 Vertex Pharmaceuticals Incorporated Inhibitors of c-Jun N-terminal kinases (JNK) and other protein kinases
TWI329112B (en) 2002-07-19 2010-08-21 Bristol Myers Squibb Co Novel inhibitors of kinases
GB0217757D0 (en) 2002-07-31 2002-09-11 Glaxo Group Ltd Novel compounds
DE10239042A1 (en) 2002-08-21 2004-03-04 Schering Ag New fused macrocyclic pyrimidine derivatives, useful as e.g. cyclin-dependent kinase inhibitors for treating e.g. cancer, autoimmune, cardiovascular or neurodegenerative diseases or viral infections
US7205308B2 (en) 2002-09-04 2007-04-17 Schering Corporation Trisubstituted 7-aminopyrazolopyrimidines as cyclin dependent kinase inhibitors
WO2004022561A1 (en) 2002-09-04 2004-03-18 Schering Corporation Pyrazolopyrimidines as cyclin-dependent kinase inhibitors
EP1534712B1 (en) 2002-09-04 2007-05-16 Schering Corporation Pyrazolo[1,5-a]pyrimidine compounds as cyclin dependent kinase inhibitors
CN1880317B (en) 2002-09-04 2012-10-10 先灵公司 Novel pyrazolopyrimidines as cyclin dependent kinase inhibitors
US7119200B2 (en) 2002-09-04 2006-10-10 Schering Corporation Pyrazolopyrimidines as cyclin dependent kinase inhibitors
US20050250837A1 (en) 2002-10-18 2005-11-10 D Mello Santosh R Use of C-Raf inhibitors for the treatment of neurodegenerative diseases
EP1562935B1 (en) 2002-10-28 2006-09-06 Bayer HealthCare AG Heteroaryloxy-substituted phenylaminopyrimidines as rho-kinase inhibitors
UA81790C2 (en) 2002-12-19 2008-02-11 Фармация Италия С.П.А. Substituted derivatives of pyrolopyrazol as kinaze inhibitors
FR2850022B1 (en) 2003-01-22 2006-09-08 Centre Nat Rech Scient NOVEL USE OF MIFEPRISTONE AND ITS DERIVATIVES AS MODULATORS OF THE HEDGEHOG PROTEIN SIGNALING PATH AND ITS APPLICATIONS
DE602004028907D1 (en) 2003-02-06 2010-10-14 Bristol Myers Squibb Co COMPOUNDS SUITABLE AS KINASEINHIBITORS ON THIAZOLYL BASIS
EP1597256A1 (en) 2003-02-21 2005-11-23 Pfizer Inc. N-heterocyclyl-substituted amino-thiazole derivatives as protein kinase inhibitors
EP1599482A4 (en) 2003-02-28 2008-10-01 Teijin Pharma Ltd Pyrazolo 1,5-a pyrimidine derivatives
GB0304665D0 (en) 2003-02-28 2003-04-02 Teijin Ltd Compounds
GB0305142D0 (en) 2003-03-06 2003-04-09 Eisai London Res Lab Ltd Synthesis
GB0305559D0 (en) 2003-03-11 2003-04-16 Teijin Ltd Compounds
WO2004087699A2 (en) 2003-03-25 2004-10-14 Vertex Pharmaceuticals Incorporated Thiazoles useful as inhibitors of protein kinases
EP1608652A1 (en) 2003-03-31 2005-12-28 Vernalis (Cambridge) Limited Pyrazolopyrimidine compounds and their use in medicine
WO2004100868A2 (en) 2003-04-23 2004-11-25 Abbott Laboratories Method of treating transplant rejection
JP4810427B2 (en) 2003-05-22 2011-11-09 アボット・ラボラトリーズ Indazole, benzisoxazole and benzisothiazole kinase inhibitors
SE0301906D0 (en) 2003-06-26 2003-06-26 Astrazeneca Ab New compounds
WO2005012256A1 (en) 2003-07-22 2005-02-10 Astex Therapeutics Limited 3, 4-disubstituted 1h-pyrazole compounds and their use as cyclin dependent kinases (cdk) and glycogen synthase kinase-3 (gsk-3) modulators
US7442698B2 (en) 2003-07-24 2008-10-28 Amgen Inc. Substituted heterocyclic compounds and methods of use
EP1651648A4 (en) 2003-07-29 2009-09-02 Irm Llc Compounds and compositions as protein kinase inhibitors
DK1660458T3 (en) 2003-08-15 2012-05-07 Irm Llc 2,4-Pyrimidine diamines useful in the treatment of neoplastic diseases, inflammatory disorders and disorders of the immune system.
EP1680431A1 (en) 2003-10-17 2006-07-19 Rigel Pharmaceuticals, Inc. Benzothiazole and thiazole'5,5-b!pyridine compositions and their use as ubiquitin ligase inhibitors
WO2005037797A1 (en) 2003-10-21 2005-04-28 Pharmacia Corporation Substituted pyrazole urea compounds for the treatment of inflammation
NZ546645A (en) 2003-10-23 2010-02-26 Ab Science 2-Aminoaryloxazole compounds as tyrosine kinase inhibitors
DE10357510A1 (en) 2003-12-09 2005-07-07 Bayer Healthcare Ag Heteroaryl-substituted benzenes
BRPI0418031A (en) 2003-12-22 2007-04-17 Gilead Sciences Inc phosphonate-substituted kinase inhibitors
AU2005229416B2 (en) 2004-04-02 2009-03-26 Novartis Ag Sulfonamide-thiazolpyridine derivatives as glucokinase activators useful the treatment of type 2 diabetes
DE102004017438A1 (en) 2004-04-08 2005-11-03 Bayer Healthcare Ag Hetaryloxy-substituted phenylaminopyrimidines
US20050228031A1 (en) * 2004-04-13 2005-10-13 Bilodeau Mark T Tyrosine kinase inhibitors
DE102004020570A1 (en) 2004-04-27 2005-11-24 Bayer Healthcare Ag Substituted phenylaminopyrimidines
GB0411791D0 (en) 2004-05-26 2004-06-30 Cyclacel Ltd Compounds
FR2871158A1 (en) 2004-06-04 2005-12-09 Aventis Pharma Sa SUBSTITUTED INDAZOLES, COMPOSITIONS CONTAINING SAME, METHOD OF MANUFACTURE AND USE
US7745437B2 (en) 2004-06-10 2010-06-29 Irm Llc Compounds and compositions as protein kinase inhibitors
DE102004028862A1 (en) 2004-06-15 2005-12-29 Merck Patent Gmbh 3-aminoindazoles
CA2577275A1 (en) 2004-08-31 2006-03-09 Astrazeneca Ab Quinazolinone derivatives and their use as b-raf inhibitors
WO2006031806A2 (en) 2004-09-10 2006-03-23 Atherogenics, Inc. 2-thiopyrimidinones as therapeutic agents
WO2006034341A2 (en) * 2004-09-20 2006-03-30 Xenon Pharmaceuticals Inc. Pyridazine derivatives for inhibiting human stearoyl-coa-desaturase
BRPI0518126A (en) 2004-10-15 2008-10-28 Astrazeneca Ab compound, process for preparing same, pharmaceutical composition, use of a compound, and methods for producing a b-raf inhibitory effect and an anti-cancer effect on a warm-blooded animal, and for treating a disease or condition
US7632854B2 (en) 2004-11-17 2009-12-15 Pfizer Italia S.R.L. Aminoindazole derivatives active as kinase inhibitors, process for their preparation and pharmaceutical compositions comprising them
ATE519759T1 (en) 2004-12-30 2011-08-15 Exelixis Inc PYRIMIDINE DERIVATIVES AS KINASE MODULATORS AND METHODS OF APPLICATION
KR100919905B1 (en) 2005-01-26 2009-10-06 아이알엠 엘엘씨 Compounds and compositions as protein kinase inhibitors
TW200639163A (en) 2005-02-04 2006-11-16 Genentech Inc RAF inhibitor compounds and methods
EP1847531A4 (en) 2005-02-09 2009-04-22 Takeda Pharmaceutical Pyrazole compound
BRPI0607062A2 (en) * 2005-02-28 2009-08-04 Japan Tobacco Inc aminopyridine compound with syk inhibitory activity, pharmaceutical composition and therapeutic agent comprising the same
FR2884516B1 (en) 2005-04-15 2007-06-22 Cerep Sa NPY ANTAGONISTS, PREPARATION AND USES
WO2006124731A2 (en) 2005-05-12 2006-11-23 Irm Llc Compounds and compositions as protein kinase inhibitors
ES2345629T3 (en) 2005-05-16 2010-09-28 Irm Llc PIRROLOPIRIDINE DERIVATIVES AS PROTEIN KINASE INHIBITORS.
RS52010B (en) 2005-06-22 2012-04-30 Plexxikon Inc. Pyrrolo [2, 3-b]pyridine derivatives as protein kinase inhibitors
WO2007024680A1 (en) 2005-08-22 2007-03-01 Amgen Inc. Pyrazolopyridine and pyrazolopyrimidine compounds useful as kinase enzymes modulators
WO2007035428A1 (en) 2005-09-15 2007-03-29 Bristol-Myers Squibb Company Met kinase inhibitors
US7799820B2 (en) 2005-09-30 2010-09-21 Banyu Pharmaceutical Co., Ltd. 2-Heterocycle-substituted indole derivatives for treating diabetes and associated conditions
GT200600429A (en) 2005-09-30 2007-04-30 ORGANIC COMPOUNDS
GB0520955D0 (en) 2005-10-14 2005-11-23 Cyclacel Ltd Compound
US8247556B2 (en) 2005-10-21 2012-08-21 Amgen Inc. Method for preparing 6-substituted-7-aza-indoles
US20070161645A1 (en) * 2005-11-02 2007-07-12 Targegen, Inc. Thiazole inhibitors targeting resistant kinase mutations
PT1979356E (en) 2005-12-21 2013-11-21 Pfizer Prod Inc Carbonylamino pyrrolopyrazoles, potent kinase inhibitors
JP5200939B2 (en) 2005-12-23 2013-06-05 アリアド・ファーマシューティカルズ・インコーポレイテッド Bicyclic heteroaryl compounds
WO2007076161A2 (en) * 2005-12-27 2007-07-05 Myriad Genetics, Inc Compounds with therapeutic activity
WO2007086584A1 (en) * 2006-01-30 2007-08-02 Meiji Seika Kaisha, Ltd. NOVEL INHIBITOR OF FabK AND FabI/K
WO2007129195A2 (en) 2006-05-04 2007-11-15 Pfizer Products Inc. 4-pyrimidine-5-amino-pyrazole compounds
US20070275963A1 (en) 2006-05-22 2007-11-29 Schering Corporation PYRAZOLO[1,5-a]PYRIMIDINES
WO2007138277A1 (en) 2006-05-26 2007-12-06 Astrazeneca Ab 2-carbocycloamino-4-imidaz0lylpyrimidines as agents for the inhbition of cell proliferation
CN102887900B (en) 2006-09-22 2015-04-29 药品循环公司 Inhibitors of bruton's tyrosine kinase
US8227472B2 (en) 2006-10-11 2012-07-24 Nerviano Medical Sciences S.R.L. Substituted pyrrolo-pyrazole derivatives as kinase inhibitors
US20080188524A1 (en) * 2006-10-25 2008-08-07 Martin Augustin Methods of treating pain
ES2403546T3 (en) 2006-11-03 2013-05-20 Pharmacyclics, Inc. Bruton tyrosine kinase activity probe and method of use
WO2008063888A2 (en) 2006-11-22 2008-05-29 Plexxikon, Inc. Compounds modulating c-fms and/or c-kit activity and uses therefor
WO2008068171A1 (en) 2006-12-08 2008-06-12 F. Hoffmann-La Roche Ag Substituted pyrimidines and their use as jnk modulators
PL2120932T3 (en) 2006-12-20 2015-02-27 Nerviano Medical Sciences Srl Indazole derivatives as kinase inhibitors for the treatment of cancer
EP2099794B1 (en) 2006-12-20 2013-05-15 Bristol-Myers Squibb Company Thiazolyl compounds useful as kinase inhibitors
RU2009122670A (en) 2006-12-21 2011-01-27 Плекссикон, Инк. (Us) COMPOUNDS AND METHODS FOR MODULATION OF KINASES AND INDICATIONS FOR THEIR USE
WO2008096260A1 (en) 2007-02-07 2008-08-14 Pfizer Inc. 3-amino-pyrrolo[3,4-c] pyrazole- 5 (1h, 4h, 6h) carbaldehyde derivatives as pkc inhibitors
WO2008112913A1 (en) 2007-03-14 2008-09-18 Exelixis, Inc. Inhibitors of the hedgehog pathway
WO2008124393A1 (en) 2007-04-04 2008-10-16 Irm Llc Benzothiazole derivatives and their use as protein kinase inhibitors
MX2009010951A (en) 2007-04-12 2009-10-29 Pfizer 3-amido-pyrrolo [3, 4-c] pyrazole-5 (1h, 4h, 6h) carbaldehyde derivatives as inhibitors of protein kinase c.
WO2008144253A1 (en) 2007-05-14 2008-11-27 Irm Llc Protein kinase inhibitors and methods for using thereof
US8242271B2 (en) 2007-06-04 2012-08-14 Avila Therapeutics, Inc. Heterocyclic compounds and uses thereof
EP2170073A4 (en) 2007-06-05 2011-07-27 Univ Emory Selective inhibitors for cyclin-dependent kinases
TW200911798A (en) 2007-08-02 2009-03-16 Amgen Inc PI3 kinase modulators and methods of use
US20090054392A1 (en) 2007-08-20 2009-02-26 Wyeth Naphthylpyrimidine, naphthylpyrazine and naphthylpyridazine analogs and their use as agonists of the wnt-beta-catenin cellular messaging system
WO2009032694A1 (en) 2007-08-28 2009-03-12 Dana Farber Cancer Institute Amino substituted pyrimidine, pyrollopyridine and pyrazolopyrimidine derivatives useful as kinase inhibitors and in treating proliferative disorders and diseases associated with angiogenesis
WO2009028655A1 (en) 2007-08-30 2009-03-05 Takeda Pharmaceutical Company Limited Heterocyclic compound and use thereof
TW200922564A (en) 2007-09-10 2009-06-01 Curis Inc CDK inhibitors containing a zinc binding moiety
US20100056524A1 (en) 2008-04-02 2010-03-04 Mciver Edward Giles Compound
GB0806419D0 (en) 2008-04-09 2008-05-14 Ineos Fluor Holdings Ltd Process
US20100197688A1 (en) 2008-05-29 2010-08-05 Nantermet Philippe G Epha4 rtk inhibitors for treatment of neurological and neurodegenerative disorders and cancer
TWI490214B (en) 2008-05-30 2015-07-01 艾德克 上野股份有限公司 Benzene or thiophene derivative and use thereof as vap-1 inhibitor
ES2554772T3 (en) 2008-05-30 2015-12-23 Merck Sharp & Dohme Corp. Novel Azabenzoxazoles Substituted
WO2009152027A1 (en) 2008-06-12 2009-12-17 Merck & Co., Inc. 5,7-dihydro-6h-pyrrolo[2,3-d]pyrimidin-6-one derivatives for mark inhibition
EP2303890A4 (en) 2008-06-19 2012-04-11 Progenics Pharm Inc Phosphatidylinositol 3 kinase inhibitors
US20110178070A1 (en) 2008-06-24 2011-07-21 Takeda Pharmaceutical Company Limited PI3K/mTOR INHIBITORS
GB0812031D0 (en) 2008-07-01 2008-08-06 7Tm Pharma As Thiazole derivatives
JP2011530511A (en) 2008-08-05 2011-12-22 メルク・シャープ・エンド・ドーム・コーポレイション Therapeutic compounds
CN102256966B (en) 2008-10-17 2016-02-10 白头生物医学研究所 Solubility mTOR mixture and its conditioning agent
CN101723936B (en) 2008-10-27 2014-01-15 上海睿星基因技术有限公司 Kinase suppressor and pharmaceutical application thereof
WO2010075542A1 (en) * 2008-12-23 2010-07-01 Curis, Inc. Cdk inhibitors
KR20110120286A (en) 2009-02-12 2011-11-03 아스텔라스세이야쿠 가부시키가이샤 Hetero ring derivative
TW201103943A (en) 2009-04-27 2011-02-01 Shionogi & Co Urea derivative having pi3k inhibitory activity
WO2010129053A2 (en) 2009-05-05 2010-11-11 Dana Farber Cancer Institute Egfr inhibitors and methods of treating disorders
TW201102387A (en) 2009-06-08 2011-01-16 Medicinova Inc Substituted pyrazolo[1,5-a]pyridine compounds having multi-target activity
US20120178758A1 (en) 2009-06-09 2012-07-12 California Capital Equity, Llc Styryl-triazine derivatives and their therapeutical applications
US8765747B2 (en) 2009-06-12 2014-07-01 Dana-Farber Cancer Institute, Inc. Fused 2-aminothiazole compounds
FR2948367A1 (en) 2009-07-24 2011-01-28 Centre Nat Rech Scient ACYL-GUANIDINE DERIVATIVES MODULATORS OF THE HEDGEHOG PROTEIN SIGNALING PATHWAY
JP2013508285A (en) 2009-10-14 2013-03-07 ブリストル−マイヤーズ スクイブ カンパニー Composition for the treatment of hepatitis C
US20110207736A1 (en) 2009-12-23 2011-08-25 Gatekeeper Pharmaceuticals, Inc. Compounds that modulate egfr activity and methods for treating or preventing conditions therewith
US9180127B2 (en) 2009-12-29 2015-11-10 Dana-Farber Cancer Institute, Inc. Type II Raf kinase inhibitors
KR20130006664A (en) 2010-03-16 2013-01-17 다나-파버 캔서 인스티튜트 인크. Indazole compounds and their uses
HUE031073T2 (en) 2010-05-14 2017-06-28 Dana Farber Cancer Inst Inc Thienotriazolodiazepine compounds for treating neoplasia
WO2012066061A1 (en) 2010-11-19 2012-05-24 F. Hoffmann-La Roche Ag Pyrazolopyridines and pyrazolopyridines and their use as tyk2 inhibitors
US8546443B2 (en) 2010-12-21 2013-10-01 Boehringer Ingelheim International Gmbh Benzylic oxindole pyrimidines
WO2012090219A2 (en) * 2010-12-31 2012-07-05 Jubilant Biosys Ltd. Thiazole compounds useful as acetyl-coa carboxylase (acc) inhibitors
WO2013014162A1 (en) 2011-07-28 2013-01-31 Cellzome Limited Heterocyclyl pyrimidine analogues as jak inhibitors
US20150017156A1 (en) 2011-09-16 2015-01-15 The Ohio State University Esx-mediated transcription modulators and related methods
AR088075A1 (en) * 2011-09-28 2014-05-07 Euro Celtique Sa NITROGEN MOSTAZA DERIVATIVES
WO2013074986A1 (en) 2011-11-17 2013-05-23 Dana-Farber Cancer Institute, Inc. Inhibitors of c-jun-n-terminal kinase (jnk)
GB201204384D0 (en) 2012-03-13 2012-04-25 Univ Dundee Anti-flammatory agents
WO2013154778A1 (en) 2012-04-11 2013-10-17 Dana-Farber Cancer Institute, Inc. Host targeted inhibitors of dengue virus and other viruses
EP2909194A1 (en) 2012-10-18 2015-08-26 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinase 7 (cdk7)
WO2014063054A1 (en) 2012-10-19 2014-04-24 Dana-Farber Cancer Institute, Inc. Bone marrow on x chromosome kinase (bmx) inhibitors and uses thereof
CN103319483B (en) 2012-10-19 2016-08-03 药源药物化学（上海）有限公司 A kind of preparation method of important intermediate of linagliptin
US9758522B2 (en) 2012-10-19 2017-09-12 Dana-Farber Cancer Institute, Inc. Hydrophobically tagged small molecules as inducers of protein degradation
TWI621618B (en) 2013-03-13 2018-04-21 比利時商健生藥品公司 Substituted 2-azabicycles and their use as orexin receptor modulators
CN105163738A (en) 2013-03-15 2015-12-16 西建阿维拉米斯研究公司 MK2 inhibitors and uses thereof
EP2976327B1 (en) 2013-03-20 2017-06-21 Bayer Pharma Aktiengesellschaft 3-acetylamino-1-(phenyl-heteroaryl-aminocarbonyl or phenyl-heteroaryl-carbonylamino)benzene derivatives for the treatment of hyperproliferative disorders
US9938279B2 (en) 2013-04-09 2018-04-10 Energenesis Biomedical Co., Ltd Method for treating disease or condition susceptible to amelioration by AMPK activators and compounds of formula which are useful to activate AMP-activated protein kinase (AMPK)
KR20160034379A (en) 2013-07-25 2016-03-29 다나-파버 캔서 인스티튜트 인크. Inhibitors of transcription factors and uses thereof
ES2792979T3 (en) * 2013-08-22 2020-11-12 Jubilant Biosys Ltd Substituted pyrimidine compounds, compositions and medical applications thereof
AU2014337044A1 (en) 2013-10-18 2016-05-05 Dana-Farber Cancer Institute, Inc. Polycyclic inhibitors of cyclin-dependent kinase 7 (CDK7)
CA2927917C (en) 2013-10-18 2022-08-09 Syros Pharmaceuticals, Inc. Heteroaromatic compounds useful for the treatment of proliferative diseases
WO2015117083A1 (en) 2014-01-31 2015-08-06 Dana-Farber Cancer Institute, Inc. Diazepane derivatives and uses thereof
EP3099693A4 (en) 2014-01-31 2017-08-16 Dana-Farber Cancer Institute, Inc. Uses of diazepane derivatives
MX2016009975A (en) 2014-01-31 2016-10-31 Dana Farber Cancer Inst Inc Dihydropteridinone derivatives and uses thereof.
CA2936865A1 (en) 2014-01-31 2015-08-06 Dana-Farber Cancer Institute, Inc. Diaminopyrimidine benzenesulfone derivatives and uses thereof
KR20170003553A (en) 2014-04-04 2017-01-09 사이로스 파마수티컬스, 인크. Inhibitors of cyclin-dependent kinase 7 (cdk7)
EP3805218A1 (en) * 2014-04-05 2021-04-14 Syros Pharmaceuticals, Inc. Inhibitors of cyclin-dependent kinase 7 (cdk7)
WO2015164604A1 (en) 2014-04-23 2015-10-29 Dana-Farber Cancer Institute, Inc. Hydrophobically tagged janus kinase inhibitors and uses thereof
WO2015164614A1 (en) 2014-04-23 2015-10-29 Dana-Farber Cancer Institute, Inc. Janus kinase inhibitors and uses thereof
CN104829610B (en) 2014-06-20 2017-03-15 中国科学院合肥物质科学研究院 A kind of novel cloth Shandong tyrosine kinase inhibitor
AU2015292827B2 (en) 2014-07-21 2019-11-14 Dana-Farber Cancer Institute, Inc. Macrocyclic kinase inhibitors and uses thereof
EP3171874B1 (en) 2014-07-21 2020-11-18 Dana-Farber Cancer Institute, Inc. Imidazolyl kinase inhibitors and uses thereof
US10308648B2 (en) 2014-10-16 2019-06-04 Syros Pharmaceuticals, Inc. Inhibitors of cyclin-dependent kinase 7 (CDK7)
US10131679B2 (en) 2014-10-31 2018-11-20 Ube Industries, Ltd. Substituted dihydropyrrolopyrazole compound
CA2972239A1 (en) 2014-12-23 2016-06-30 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinase 7 (cdk7)
EP3268000B1 (en) 2015-03-09 2021-08-04 Aurigene Discovery Technologies Limited Pyrazolo[1,5-a][1,3,5]triazine and pyrazolo[1,5-a]pyrimidine derivatives as cdk inhibitors
EP3273966B1 (en) 2015-03-27 2023-05-03 Dana-Farber Cancer Institute, Inc. Inhibitors of cyclin-dependent kinases
AU2016276963C1 (en) 2015-06-12 2021-08-05 Dana-Farber Cancer Institute, Inc. Combination therapy of transcription inhibitors and kinase inhibitors
JP2018526376A (en) 2015-08-28 2018-09-13 ノバルティス アーゲー Includes (A) the cyclin-dependent kinase 4/6 (CDK4 / 6) inhibitor LEE011 (= ribocyclib) and (B) the epidermal growth factor receptor (EGFR) inhibitor erlotinib for the treatment or prevention of cancer Pharmaceutical combination

Also Published As

Publication number Publication date
EP3347018A2 (en) 2018-07-18
EP3347018B1 (en) 2021-09-01
US20180362483A1 (en) 2018-12-20
US20220055998A1 (en) 2022-02-24
AU2016319125B2 (en) 2021-04-08
JP7028766B2 (en) 2022-03-02
WO2017044858A3 (en) 2017-04-27
JP2018526413A (en) 2018-09-13
WO2017044858A2 (en) 2017-03-16
US11142507B2 (en) 2021-10-12
CA2996978A1 (en) 2017-03-16
JP2022020611A (en) 2022-02-01
AU2016319125A1 (en) 2018-03-22
EP4019515A1 (en) 2022-06-29
EP3347018A4 (en) 2019-04-03

Similar Documents

Publication Publication Date Title
US20220055998A1 (en) Inhibitors of cyclin-dependent kinases
US11325910B2 (en) Inhibitors of cyclin-dependent kinases
US20220024929A9 (en) Inhibitors of cyclin-dependent kinase 7 (cdk7)
US20200338075A1 (en) 4,6-pyrimidinylene derivatives and uses thereof
US10342798B2 (en) Fused bicyclic pyrimidine derivatives and uses thereof
US20220089611A1 (en) Inhibitors of cyclin-dependent kinase 7 and uses thereof
US20240101559A1 (en) Tricyclic kinase inhibitors and uses thereof
US20230242534A9 (en) Inhibitors of cyclin-dependent kinase 7 and uses thereof

Legal Events

Date Code Title Description
FEPP Fee payment procedure

Free format text: ENTITY STATUS SET TO UNDISCOUNTED (ORIGINAL EVENT CODE: BIG.); ENTITY STATUS OF PATENT OWNER: SMALL ENTITY

FEPP Fee payment procedure

Free format text: ENTITY STATUS SET TO SMALL (ORIGINAL EVENT CODE: SMAL); ENTITY STATUS OF PATENT OWNER: SMALL ENTITY

AS Assignment

Owner name: DANA-FARBER CANCER INSTITUTE, INC., MASSACHUSETTS

Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:GRAY, NATHANAEL S.;ZHANG, TINGHU;KWIATKOWSKI, NICHOLAS PAUL;AND OTHERS;SIGNING DATES FROM 20161020 TO 20161024;REEL/FRAME:046939/0199

STPP Information on status: patent application and granting procedure in general

Free format text: DOCKETED NEW CASE - READY FOR EXAMINATION

FEPP Fee payment procedure

Free format text: PETITION RELATED TO MAINTENANCE FEES GRANTED (ORIGINAL EVENT CODE: PTGR); ENTITY STATUS OF PATENT OWNER: SMALL ENTITY

STPP Information on status: patent application and granting procedure in general

Free format text: RESPONSE TO NON-FINAL OFFICE ACTION ENTERED AND FORWARDED TO EXAMINER

STPP Information on status: patent application and granting procedure in general

Free format text: NON FINAL ACTION MAILED

STPP Information on status: patent application and granting procedure in general

Free format text: RESPONSE TO NON-FINAL OFFICE ACTION ENTERED AND FORWARDED TO EXAMINER

STPP Information on status: patent application and granting procedure in general

Free format text: EX PARTE QUAYLE ACTION MAILED

STPP Information on status: patent application and granting procedure in general

Free format text: RESPONSE TO EX PARTE QUAYLE ACTION ENTERED AND FORWARDED TO EXAMINER

STPP Information on status: patent application and granting procedure in general

Free format text: NOTICE OF ALLOWANCE MAILED -- APPLICATION RECEIVED IN OFFICE OF PUBLICATIONS

STPP Information on status: patent application and granting procedure in general

Free format text: PUBLICATIONS -- ISSUE FEE PAYMENT VERIFIED

AS Assignment

Owner name: NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT, MARYLAND

Free format text: CONFIRMATORY LICENSE;ASSIGNOR:DANA-FARBER CANCER INST;REEL/FRAME:057494/0408

Effective date: 20190207

STCF Information on status: patent grant

Free format text: PATENTED CASE

CC Certificate of correction