The present invention provides novel compounds of Formula (I), 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 or preventing proliferative diseases (e.g., cancers (e.g., leukemia, lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer), benign neoplasms, 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., cyclin-dependent kinase 7 (CDK7), cyclin-dependent kinase 12 (CDK12), or cyclin-dependent kinase 13 (CDK13)), and therefore, induce cellular apoptosis and/or inhibit transcription in the subject.

BACKGROUND OF THE INVENTION

The members of the cyclin-dependent kinase (CDK) family play critical regulatory roles in proliferation. There are currently 20 known mammalian CDKs. While CDK7-13 have been linked to transcription, only 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. Cell25, 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.”Nature374, 280-282 (1995); Shiekhattar et al., “CDK-activating kinase complex is a component of human transcription factor TFIIH.”Nature374, 283-287 (1995); Drapkin et al., “Human cyclin-dependent kinase-activating kinase exists in three distinct complexes.”Proc. Natl. Acad. Sci. U.S.A93, 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. Cell34, 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.

Disruption of RNAP II CTD phosphorylation has been shown to preferentially effect proteins with short half-lives, including those of the anti-apoptotic BCL-2 family (Konig et al., “The novel cyclin-dependent kinase inhibitor flavopiridol downregulates Bcl-2 and induces growth arrest and apoptosis in chronic B-cell leukemia lines.”Blood1, 4307-4312 (1997); Gojo et al., “The cyclin-dependent kinase inhibitor flavopiridol induces apoptosis in multiple myeloma cells through transcriptional repression and down-regulation of Mcl-1.” Clin. Cancer Res.8, 3527-3538 (2002)). Cancer cells have demonstrated ability to circumvent pro-cell death signaling through upregulation of BCL-2 family members (Llambi et al., “Apoptosis and oncogenesis: give and take in the BCL-2 family.”Curr. Opin. Genet. Dev.21, 12-20 (2011)). Therefore, inhibition of human CDK7 kinase activity is likely to result in anti-proliferative activity, and pharmacological inhibition could be used to treat proliferative disorders, including cancer. Indeed, flavopiridol, a non-selective pan-CDK inhibitor that targets CTD kinases, has demonstrated efficacy for the treatment of chronic lymphocytic leukemia (CLL), but suffers from a poor toxicity profile (Lin et al., “Phase II study of flavopiridol in relapsed chronic lymphocytic leukemia demonstrating high response rates in genetically high-risk disease.”J. Clin. Oncol.27, 6012-6018 (2009); Christian et al., “Flavopiridol in chronic lymphocytic leukemia: a concise review.”Clin. Lymphoma Myeloma9 Suppl. 3, S179-S185 (2009)). A selective CDK7 inhibitor may hold promise as a therapeutic agent for the treatment of CLL and other cancers.

SUMMARY OF THE INVENTION

Cyclin dependent kinases (CDKs) (e.g., cyclin-dependent kinase 7 (CDK7), cyclin-dependent kinase 12 (CDK12), and cyclin-dependent kinase 13 (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, cyclin H, and MAT1. The CAK complex containing CDK7 appears to constitute the major CAK activity in the cell. Besides its CAK function, CDK7 also plays a role in transcription and possibly in DNA repair. The trimeric CAK complex CDK7/cyclin H/MAT1 is also a component of TFIIH, the general transcription/DNA repair factor IIH. As a TFIIH subunit, CDK7 phosphorylates the carboxy-terminal-domain (CTD) of the largest subunit of RNAP II. This suggests that the CDK7 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 Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. The compounds of Formula (I), 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. In certain embodiments, the kinase is a CDK. In certain embodiments, the kinase is CDK7, CDK12, and/or CDK13. In certain embodiments, the compound of Formula (I) is selective for CDK7 compared to other kinases. The present invention further 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) and as therapeutics for the prevention and/or treatment of diseases associated with overexpression and/or aberrant activity of a kinase (e.g., CDK7). In certain embodiments, the inventive compounds are used for the prevention and/or treatment of proliferative diseases (e.g., cancers (e.g., leukemia, lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer), benign neoplasms, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject.

The compounds of Formula (I) may selectively inhibit the activity of a CDK. In some embodiments, the compounds of Formula (I) may selectively inhibit the activity of CDK7, CDK12, and/or CDK13. In certain embodiments, the compounds of Formula (I) may selectively inhibit the activity of CDK7 compared to other kinases. Since the discovery of selective inhibitors of CDK7 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 may be due to the compounds' ability to covalently modify the cysteine (Cys312) residue of CDK7, the Cys312 residue being largely unique among the CDKs and other kinases.

In certain embodiments, a compound of Formula (I) is of the formula:

In certain embodiments, a compound of Formula (I) is the formula:

In certain embodiments, a compound of Formula (I) is of the formula:

In certain embodiments, a compound of Formula (I) is of the formula:

In another aspect, the present invention provides pharmaceutical compositions comprising a compound of Formula (I), 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 compositions described herein include a therapeutically effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof. The pharmaceutical composition may be useful for treating and/or preventing a proliferative disease (e.g., cancer) or an infectious disease.

In another aspect, the present invention provides methods for treating and/or preventing proliferative diseases. Exemplary proliferative diseases include cancer (e.g., leukemia, lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer), benign neoplasm, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases. In other embodiments, the present invention provides methods for treating and/or preventing an infectious disease (e.g., a viral infection).

In still another aspect, the present invention provides methods of down-regulating the expression of a kinase (e.g., CDK (e.g., CDK7)) in a biological sample or subject. In certain embodiments, the method involves the specific down-regulation of the expression of CDK7.

Another aspect of the invention relates to methods of inhibiting the activity of a kinase (e.g., CDK (e.g., CDK7)) in a biological sample or subject. In certain embodiments, the method involves the selective inhibition of CDK7.

Also provided by the present invention are methods of inhibiting transcription in a biological sample or subject. The transcription of genes affected by the activity of CDK7 may be inhibited by the compounds of the invention.

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 a subject.

Another aspect of the invention relates to methods of screening a library of compounds (e.g., compounds of Formula (I)) to identify one or more compounds useful in the treatment of a proliferative disease (e.g., cancer (e.g., leukemia, lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer), benign neoplasm, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) or an infectious disease (e.g., viral infection) in a subject, in inhibiting a kinase (e.g., CDK, such as CDK7), in inhibiting cell growth, in inducing apoptosis of a cell, and/or in inhibiting transcription.

In yet another aspect, the present invention provides compounds of Formula (I), 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 proliferative disease in a subject.

In yet another aspect, the present invention provides compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof, for use in the treatment or prevention of an infectious disease in a subject. In certain embodiments, the infectious disease is a viral infection.

Another aspect of the present invention relates to kits comprising a container with a compound of Formula (I), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, or a pharmaceutical composition thereof. The kits of the invention may include a single dose or multiple doses of a compound of Formula (I), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, or a pharmaceutical composition thereof. The provided kits may be useful for the treatment and/or prevention of a proliferative disease (e.g., cancer (e.g., leukemia, lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer), benign neoplasm, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) or an infectious disease in a subject. In certain embodiments, the kits described herein further include instructions for administering the compound of Formula (I), or the pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, or the pharmaceutical composition thereof.

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, the Examples, and the Claims.

Definitions

“Hydrocarbon chain” refers to a substituted or unsubstituted divalent alkyl, alkenyl, or alkynyl group. A hydrocarbon chain includes at least one chain, each node (“carbon unit”) of which including at least one carbon atom, between the two radicals of the hydrocarbon chain. For example, hydrocarbon chain —CAH(CBH2CCH3)— includes only one carbon unit CA. The term “Cxhydrocarbon chain,” wherein x is a positive integer, refers to a hydrocarbon chain that includes x number of carbon unit(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 C1hydrocarbon chain, and

is a C3hydrocarbon chain. When a range of values is used, e.g., a C1-6hydrocarbon chain, the meaning of the range is as described herein. 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., —(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,

are all examples of a hydrocarbon chain. In contrast, in certain embodiments

are not within the scope of the hydrocarbon chains described herein.

“Alkyl” refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (“C1-20alkyl”). In some embodiments, an alkyl group has 1 to 10 carbon atoms (“C1-10alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C1-9alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C1-8alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C1-7alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C1-6alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“C1-5alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C1-4alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C1-3alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C1-2alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C1alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C2-6alkyl”). Examples of C1-6alkyl groups include methyl (C1), ethyl (C2), n-propyl (C3), isopropyl (C3), n-butyl (C4), tert-butyl (C4), sec-butyl (C4), isobutyl (C4), n-pentyl (C5), 3-pentanyl (C5), amyl (C5), neopentyl (C5), 3-methyl-2-butanyl (C5), tertiary amyl (C5), and n-hexyl (C6). 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 optionally substituted, i.e., unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is unsubstituted C1-10alkyl (e.g., —CH3). In certain embodiments, the alkyl group is substituted C1-10alkyl.

“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.

“Aralkyl” is a subset of alkyl and aryl and 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.

“Heteroaralkyl” is a subset of alkyl and heteroaryl and refers to an optionally substituted alkyl group substituted by an optionally substituted heteroaryl group.

“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) as herein defined. Likewise, “saturated” refers to a group that does not contain a double or triple bond, i.e., contains all single bonds.

The term “optionally substituted” refers to substituted or unsubstituted.

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;

“Alkoxy” or “alkoxyl” refers to a radical of the formula: —O-alkyl.

In certain embodiments, the substituent present on an sulfur atom is an sulfur protecting group (also referred to as a thiol protecting group). Sulfur protecting groups 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, —P(═O)2Raa, —P(═O)(Raa)2, —P(═O)(ORcc)2, —P(═O)2N(Rbb)2, and —P(═O)(NRbb)2, wherein Raa, Rbb, and Rccare as defined herein. Sulfur protecting groups are well known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rdedition, John Wiley & Sons, 1999, incorporated herein by reference.

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, pixyl, 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), 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. In some embodiments, the leaving group is a sulfonate-containing group. In some embodiments, the leaving group is a tosylate group. 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.

These and other exemplary substituents are described in more detail in the Detailed Description, Figures, Examples, and Claims. The invention is not intended to be limited in any manner by the above exemplary listing of substituents.

Other Definitions

The following definitions are more general terms used throughout the present application:

Tautomeric forms may be relevant to the attainment of the optimal chemical reactivity and biological activity of a compound of interest.

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 “prodrugs” refer to compounds, including derivatives of the compounds of Formula (I), which have cleavable groups and become by solvolysis or under physiological conditions the compounds of Formula (I) which are pharmaceutically active in vivo. Such examples include, but are not limited to, ester derivatives and the like. Other derivatives of the compounds of this invention have activity in both their acid and acid derivative forms, but in the acid sensitive form often offers 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 of this invention are particular prodrugs. In some cases it is desirable to prepare double ester type prodrugs such as (acyloxy)alkyl esters or ((alkoxycarbonyl)oxy)alkylesters. C1to C8alkyl, C2-C8alkenyl, C2-C8alkynyl, aryl, C7-C12substituted aryl, and C7-C12arylalkyl esters of the compounds of Formula (I) may be preferred.

A “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) and/or other non-human animals, for example, mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys). In certain embodiments, the animal is a mammal. The animal may be a male or female and at any stage of development. A non-human animal may be a transgenic animal.

The terms “administer,” “administering,” or “administration,” refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing an inventive compound, or a pharmaceutical composition thereof.

The terms “treatment,” “treat,” and “treating” refer to reversing, alleviating, delaying the onset of, or inhibiting the progress of a “pathological condition” (e.g., a disease, disorder, or condition, or one or more signs or symptoms thereof) described herein. In some embodiments, treatment may be administered after one or more signs or symptoms have developed or have been observed. In other embodiments, treatment may be administered in the absence of signs or symptoms of the disease or condition. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to delay or prevent recurrence.

An “effective amount” of a compound of Formula (I) 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 of Formula (I) 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 encompasses therapeutic and prophylactic treatment. For example, in treating cancer, an effective amount of an inventive compound may reduce the tumor burden or stop the growth or spread of a tumor.

A “therapeutically effective amount” of a compound of Formula (I) 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 or causes of the condition, or enhances the therapeutic efficacy of another therapeutic 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, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases.

The terms “neoplasm” and “tumor” are used interchangeably and refer to an abnormal mass of tissue wherein the growth of the mass surpasses and is not coordinated with the growth of a 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 “angiogenesis” refers to the formation and the growth of new blood vessels. Normal angiogenesis occurs in the healthy body of a subject for healing wounds and for restoring blood flow to tissues after injury. The healthy body controls angiogenesis through a number of means, e.g., angiogenesis-stimulating growth factors and angiogenesis inhibitors. Many disease states, such as cancer, diabetic blindness, age-related macular degeneration, rheumatoid arthritis, and psoriasis, are characterized by abnormal (i.e., increased or excessive) angiogenesis. Abnormal or pathological angiogenesis refers to angiogenesis greater than that in a normal body, especially angiogenesis in an adult not related to normal angiogenesis (e.g., menstruation or wound healing). Abnormal angiogenesis can provide new blood vessels that feed diseased tissues and/or destroy normal tissues, and in the case of cancer, the new vessels can allow tumor cells to escape into the circulation and lodge in other organs (tumor metastases). In certain embodiments, the angiogenesis is pathological angiogenesis.

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 arthritis, Guillain-Barré syndrome, Hashimoto's thyroiditis, and cardiomyopathy.

The term “autoinflammatory disease” refers to a category of diseases that are similar but different from autoimmune diseases. Autoinflammatory and autoimmune diseases share common characteristics in that both groups of disorders result from the immune system attacking a subject's own tissues and result in increased inflammation. In autoinflammatory diseases, a subject's innate immune system causes inflammation for unknown reasons. The innate immune system reacts even though it has never encountered autoantibodies or antigens in the subject. Autoinflammatory disorders are characterized by intense episodes of inflammation that result in such symptoms as fever, rash, or joint swelling. These diseases also carry the risk of amyloidosis, a potentially fatal buildup of a blood protein in vital organs. Autoinflammatory diseases include, but are not limited to, familial Mediterranean fever (FMF), neonatal onset multisystem inflammatory disease (NOMID), tumor necrosis factor (TNF) receptor-associated periodic syndrome (TRAPS), deficiency of the interleukin-1 receptor antagonist (DIRA), and Behçet's 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, mucus, 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 a first biological sample. Biological samples also include those biological samples that are transgenic, such as transgenic oocyte, sperm cell, blastocyst, embryo, fetus, donor cell, or cell nucleus.

A “protein” or “peptide” comprises a polymer of amino acid residues linked together by peptide bonds. The term refers to proteins, polypeptides, and peptides of any size, structure, or function. Typically, a protein will be at least three amino acids long. A protein may refer to an individual protein or a collection of proteins. Inventive proteins preferably contain only natural amino acids, although non-natural amino acids (i.e., compounds that do not occur in nature but that can be incorporated into a polypeptide chain) and/or amino acid analogs as are known in the art may alternatively be employed. Also, one or more of the amino acids in an inventive protein may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation or functionalization, or other modification. A protein may also be a single molecule or may be a multi-molecular complex. A protein may be a fragment of a naturally occurring protein or peptide. A protein may be naturally occurring, recombinant, or synthetic, or any combination of these.

The term “kinase” refers to any enzyme that catalyzes the addition of phosphate groups to an amino acid residue of a protein. For example, a serine kinase catalyzes the addition of a phosphate group to serine residue in a protein. In certain embodiments, the kinase is a protein kinase. Examples of kinases include, but are not limited to, a CMGC kinase (e.g., a cyclin-dependent kinase (CDK, e.g., CDK1, CDK2, CDK2, CDK4, CDK5, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13, CDK14, CDK16, CDK20), a mitogen-activated protein kinase (MAPK, e.g., MAPK1, MAPK3, MAPK4, MAPK6, MAPK7, MAPK8, MAPK9, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK15), a glycogen synthase kinase 3 (GSK3, e.g., GSK3α, GSK3β), or a CDC-like kinase (CLK, e.g., CLK1, CLK2, CLK3, CLK4)), an AGC kinase (e.g., protein kinase A (PKA), protein kinase C (PKC), protein kinase G (PKG)), a Ca2+/calmodulin-dependent protein kinase (CaM kinase, e.g., a specialized CaM kinase, a multifunctional CaM kinase), a casein kinase 1 (CK1, e.g., CK1alpha, CK1beta 1, CK1gamma 1, CK1gamma 2, CK1gamma 3, CK1delta, CK1epsilon), a STE kinase (e.g., a homolog of yeast Sterile 7, Sterile 11, or Sterile 20 kinase), a tyrosine kinase (TK, e.g., a receptor tyrosine kinase (RTK), a non-receptor tyrosine kinase (nRTK)), and a tyrosine-kinase-like kinase (TKL, e.g., a mixed lineage kinase (MLK), RAF, a serine threonine kinase receptor (STKR), a leucine rich repeat kinase (LRRK), a LIM domain kinase (LIMK), a testis expressed serine kinase (TESK), an IL1 receptor associated kinase (IRAK), a receptor interacting protein kinase (RIPK)).

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, CDK2, CDK4, CDK5, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK14, CDK16, and CDK20. CDK7 is a CDK wherein the substrate is Cyclin H, MAT1 (e.g., MNAT1), or Cyclin H and MAT1.

The present invention provides compounds, which inhibit the activity of a kinase, for the prevention and/or treatment of a proliferative disease of a subject. In certain embodiments, the inventive compounds inhibit the activity of cyclin-dependent kinase (CDK). In certain embodiments, the inventive compounds inhibit the activity of cyclin-dependent kinase 7 (CDK7). The present invention further 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)), and as therapeutics, e.g., in the prevention and/or treatment of diseases associated with the overexpression and/or aberrant activity of the kinase (e.g., CDK (e.g., CDK7)). In certain embodiments, the diseases are proliferative diseases. The proliferative diseases include, but are not limited to, cancer (e.g., leukemia, melanoma, multiple myeloma), benign neoplasm, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases. In certain embodiments, the cancer is associated with the overexpression and/or aberrant activity of a kinase (e.g., CDK (e.g., CDK7)).

Compounds

In one aspect of the present invention, provided are compounds of Formula (I):

Ring A is an optionally substituted heteroaryl ring of any one of the Formulae (i-1)-(i-6):

wherein:each instance of V1, V2, V3, V4, V5, V6, V7, V8, V9, V10, V11, V12, V13, V14, and V15is independently O, S, N, NRA1, C, or CRA2;each instance of RA1is independently selected from the group consisting of 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, and a nitrogen protecting group;each instance of RA2is independently selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —ORA2a, —N(RA2a)2, and —SRA2a, wherein each occurrence of RA2ais independently selected from the group consisting of 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, and a sulfur protecting group when attached to a sulfur atom, or two RA2agroups are joined to form an optionally substituted heterocyclic ring; andoptionally any two of RA1, RA2, and RA2agroups are joined to form an optionally substituted carbocyclic, optionally substituted heterocyclic, optionally substituted aryl, or optionally substituted heteroaryl ring;

RB1is selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —ORB1a, —N(RB1a)2, and —SRB1a, wherein each occurrence of RB1ais independently selected from the group consisting of 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, and a sulfur protecting group when attached to a sulfur atom, or RB1and RB2are joined to form an optionally substituted carbocyclic, optionally substituted heterocyclic, optionally substituted aryl, or optionally substituted heteroaryl ring;

WBis N or CRB2, wherein RB2is selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —ORB2a, —N(RB2a)2, and —SRB2a, or RB2and RB1are joined to form an optionally substituted carbocyclic, optionally substituted heterocyclic, optionally substituted aryl, or optionally substituted heteroaryl ring, wherein each occurrence of RB2ais independently selected from the group consisting of 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, and a sulfur protecting group when attached to a sulfur atom, or two RB2agroups are joined to form an optionally substituted heterocyclic ring;

L1is a bond or an optionally substituted C1-4hydrocarbon chain, optionally wherein one or more carbon units of the optionally substituted C1-4hydrocarbon chain are independently replaced with —O—, —S—, —NRL1—, —S(═O)—, or —S(═O)2—, wherein RL1is hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group, and optionally wherein two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;

L2is a bond or an optionally substituted C1-4hydrocarbon chain, optionally wherein one or more carbon units of the optionally substituted C1-4hydrocarbon chain are independently replaced with —O—, —S—, —NRL2—, —S(═O)—, or —S(═O)2—, wherein RL2is hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group, and optionally wherein two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;each instance of RCis independently selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, ═O, —CN, —ORC1, —N(RC1)2, and —SRC1; or two RCgroups are taken together to form an optionally substituted, heterocyclic, carbocyclic, aryl, or heteroaryl ring, wherein two substituents on the substituted heterocyclic ring or substituted carbocyclic ring, or one substituent on the substituted heterocyclic ring or substituted carbocyclic ring and a third RCgroup, are taken together to form another optionally substituted heterocyclic ring or optionally substituted carbocyclic ring; wherein each occurrence of RC1is independently selected from the group consisting of 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, and a sulfur protecting group when attached to a sulfur atom, or two RC1groups are joined to form an optionally substituted heterocyclic ring;

each instance of RDis independently selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —ORD1, —N(RD1)2, and —SRD1, wherein each occurrence of RD1is independently selected from the group consisting of 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, and a sulfur protecting group when attached to a sulfur atom, or two RD1groups are joined to form an optionally substituted heterocyclic ring;

REis of any one of the Formulae (ii-1)-(ii-20):

L4is a bond or an optionally substituted C1-4hydrocarbon chain;

RE1is selected from the group consisting of hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2ORE1a, —CH2N(RE1a)2, —CH2SRE1a, —ORE1a, —N(RE1a)2, —Si(RE1a)3, and —SRE1a, wherein each occurrence of RE1ais independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, or two RE1agroups are joined to form an optionally substituted heterocyclic ring;

RE2is selected from the group consisting of hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2ORE2a, —CH2N(RE2a)2, —CH2SRE2a, —ORE2a, —N(RE2a)2, and —SRE2a, wherein each occurrence of RE2ais independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, or two RE2agroups are joined to form an optionally substituted heterocyclic ring;

RE3is selected from the group consisting of hydrogen, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —CH2ORE3a, —CH2N(RE3a)2, —CH2SRE3a, —ORE3a, —N(RE3a)2, and —SRE3a, wherein each occurrence of RE3ais independently selected from the group consisting of hydrogen, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, or two RE3agroups are joined to form an optionally substituted heterocyclic ring;

optionally RE1and RE3, or RE2and RE3, or RE1and RE2are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;

Y is O, S, or NRE6, wherein RE6is hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group;

a is 1 or 2; and

Compounds of Formula (I) include Ring A attached to Ring B. Ring A may be an optionally substituted bicyclic heteroaryl ring. In certain embodiments, Ring A is an optionally substituted monocyclic heteroaryl ring fused with an optionally substituted monocyclic aryl ring. In certain embodiments, Ring A is an optionally substituted monocyclic heteroaryl ring fused with another optionally substituted monocyclic heteroaryl ring. Ring A may be an optionally substituted 6,5-membered heteroaryl ring or an optionally substituted 5,6-membered heteroaryl ring. In certain embodiments, Ring A is an optionally substituted monocyclic 5-membered heteroaryl ring fused with an optionally substituted monocyclic 6-membered aryl ring. In certain embodiments, Ring A is an optionally substituted monocyclic 5-membered heteroaryl ring fused with an optionally substituted monocyclic 6-membered heteroaryl ring. The point of attachment of Ring A to Ring B may be at any atom of Ring A, as valency permits. In certain embodiments, Ring A is of Formula (i-1):

In certain embodiments, Ring A is of Formula (i-2):

In certain embodiments, Ring A is of Formula (i-3):

In certain embodiments, Ring A is of Formula (i-4):

In compounds of Formula (I), V1, V2, V3, V4, V5, V6, V7, V8, and V9of Ring A may each independently be O, S, N, NRA1, C, or CRA2, as valency permits. In certain embodiments, V1is O, S, N or NRA1. In certain embodiments, V1is N or NRA1. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, only one of V1, V2, V3, V4, V5, V6, V7, V8, and V9is selected from the group consisting of O, S, N, and NRA1. In certain embodiments, only one of V1, V2, V3, V4, V5, V6, V7, V8, and V9is selected from the group consisting of N and NRA1. In certain embodiments, V1is N or NRA1; V2, V3, V4, V5, V6, V7, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted indole ring. In certain embodiments, Ring A is of Formula (iii-1):

In certain embodiments, Ring A is of Formula (iii-2):

In certain embodiments, Ring A is of Formula (iii-3):

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of Formula (iii-4):

In certain embodiments, Ring A is of Formula (iii-5):

In certain embodiments, Ring A is of Formula (iii-6):

In certain embodiments, Ring A is of Formula (iii-7):

In certain embodiments, only two of V1, V2, V3, V4, V5, V6, V7, V8, and V9are each independently selected from the group consisting of O, S, N, and NRA1. In certain embodiments, only two of V1, V2, V3, V4, V5, V6, V7, V8, and V9are each independently selected from the group consisting of N and NRA1. In certain embodiments, V1is N or NRA1; and only one of V2, V3, V4, V5, V6, V7, V8, and V9is N or NRA1. In certain embodiments, V1and V2are each independently N or NRA1; V3, V4, V5, V6, V7, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted indazole ring. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, V1and V3are each independently N or NRA1; V2, V4, V5, V6, V7, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted benzimidazole ring. In certain embodiments, Ring A is of Formula (iv-1):

In certain embodiments, Ring A is of Formula (iv-2):

In certain embodiments, Ring A is of Formula (iv-3):

In certain embodiments, Ring A is of Formula (iv-4):

In certain embodiments, Ring A is of Formula (iv-5):

In certain embodiments, Ring A is of Formula (iv-6):

In certain embodiments, V1and V4are each independently N or NRA1; V2, V3, V5, V6, V7, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted 4-azaindazole ring. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, V1and V5are each independently N or NRA1; V2, V3, V4, V6, V7, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted 5-azaindazole ring. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, V1and V6are each independently N or NRA1; V2, V3, V4, V5, V7, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted 6-azaindole ring. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, V1and V7are each independently N or NRA1; V2, V3, V4, V5, V6, V8, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted 7-azaindole ring. In certain embodiments, Ring A is of Formula (v-1):

In certain embodiments, Ring A is of Formula (v-2):

In certain embodiments, Ring A is of Formula (v-3):

In certain embodiments, Ring A is of Formula (v-4):

In certain embodiments, Ring A is of Formula (v-5):

In certain embodiments, Ring A is of Formula (v-6):

In certain embodiments, V1and V8are each independently N or NRA1, V2, V3, V4, V5, V6, V7, and V9are each independently C or CRA2; and therefore, Ring A is an optionally substituted 8-azaindole ring. In certain embodiments, Ring A is of Formula (vi-1):

In certain embodiments, Ring A is of Formula (vi-2):

In certain embodiments, Ring A is of Formula (vi-3):

In certain embodiments, Ring A is of Formula (vi-4):

In certain embodiments, Ring A is of Formula (vi-5):

In certain embodiments, Ring A is of Formula (vi-6):

In certain embodiments, V1and V9are each independently N or NRA1; V2, V3, V4, V5, V6, V7, and V8are each independently C or CRA2; and therefore, Ring A is an optionally substituted 9-azaindole ring. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, only three of V1, V2, V3, V4, V5, V6, V7, V8, and V9are each independently selected from the group consisting of O, S, N, and NRA1. In certain embodiments, only three of V1, V2, V3, V4, V5, V6, V7, V8, and V9are each independently selected from the group consisting of N and NRA1. In certain embodiments, V1is N or NRA1; and only two of V2, V3, V4, V5, V6, V7, V8, and V9are each independently N or NRA1.

In compounds of Formula (I), Ring A may also be an optionally substituted 5-membered heteroaryl ring. In certain embodiments, Ring A is of Formula (i-5):

In compounds of Formula (I), V10, V11, V12, V13, and V14of Ring A may each independently be O, S, N, NRA1, C, or CRA2, as valency permits. In certain embodiments, only one of V10, V11, V12, V13, and V14is selected from the group consisting of O, S, N, and NRA1. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, only two of V10, V11, V12, V13, and V14are each independently selected from the group consisting of O, S, N, and NRA1. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of Formula (vii):

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, only three of V10, V11, V12, V13, and V14are each independently selected from the group consisting of O, S, N, and NRA1. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, only four of V10, V11, V12, V13, and V14are each independently selected from the group consisting of N and NRA1. In certain embodiments, Ring A is of the formula:

In compounds of Formula (I), Ring A may also be an optionally substituted 6-membered heteroaryl ring. In certain embodiments, Ring A is of Formula (i-6):

In compounds of Formula (I), V10, V11, V12, V13, V14, and V15of Ring A may each independently be N, C, or CRA2, as valency permits. In certain embodiments, only one of V10, V11, V12, V13, V14, and V15is N. In certain embodiments, Ring A is of the formula:

In certain embodiments, only two of V10, V11, V12, V13, V14, and V15are N. In certain embodiments, Ring A is of the formula:

In certain embodiments, only three of V10, V11, V12, V13, V14, and V15are N. In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of Formula (i-1), (i-5), or (i-6). In certain embodiments, Ring A is of the formula:

In compounds of Formula (I), Ring A may be substituted with one or more RA1groups when the RA1group is attached to a nitrogen atom. In certain embodiments, at least one instance of RA1is H (hydrogen). In certain embodiments, at least one instance of RA1is halogen. In certain embodiments, at least one instance of RA1is F (fluorine). In certain embodiments, at least one instance of RA1is Cl (chlorine). In certain embodiments, at least one instance of RA1is Br (bromine). In certain embodiments, at least one instance of RA1is I (iodine). In certain embodiments, at least one instance of RA1is substituted acyl. In certain embodiments, at least one instance of RA1is unsubstituted acyl. In certain embodiments, at least one instance of RA1is acetyl. In certain embodiments, at least one instance of RA1is substituted acetyl. In certain embodiments, at least one instance of RA1is substituted alkyl. In certain embodiments, at least one instance of RA1is unsubstituted alkyl. In certain embodiments, at least one instance of RA1is C1-6alkyl. In certain embodiments, at least one instance of RA1is methyl. In certain embodiments, at least one instance of RA1is ethyl. In certain embodiments, at least one instance of RA1is propyl. In certain embodiments, at least one instance of RA1is butyl. In certain embodiments, at least one instance of RA1is substituted alkenyl. In certain embodiments, at least one instance of RA1is unsubstituted alkenyl. In certain embodiments, at least one instance of RA1is vinyl. In certain embodiments, at least one instance of RA1is substituted alkynyl. In certain embodiments, at least one instance of RA1is unsubstituted alkynyl. In certain embodiments, at least one instance of RA1is ethynyl. In certain embodiments, at least one instance of RA1is substituted carbocyclyl. In certain embodiments, at least one instance of RA1is unsubstituted carbocyclyl. In certain embodiments, at least one instance of RA1is substituted heterocyclyl. In certain embodiments, at least one instance of RA1is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RA1is substituted aryl. In certain embodiments, at least one instance of RA1is unsubstituted aryl. In certain embodiments, at least one instance of RA1is substituted phenyl. In certain embodiments, at least one instance of RA1is unsubstituted phenyl. In certain embodiments, at least one instance of RA1is substituted heteroaryl. In certain embodiments, at least one instance of RA1is unsubstituted heteroaryl. In certain embodiments, at least one instance of RA1is substituted pyridyl. In certain embodiments, at least one instance of RA1is unsubstituted pyridyl. In certain embodiments, at least one instance of RA1is a nitrogen protecting group. In certain embodiments, at least one instance of RA1is Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts.

In certain embodiments, at least one RA1is hydrogen, C1-6alkyl, or a nitrogen protecting group. In certain embodiments, all instances of RA1are each independently hydrogen, C1-6alkyl, or a nitrogen protecting group. In certain embodiments, all instances of RA1are hydrogen.

In compounds of Formula (I), Ring A may be substituted with one or more RA2groups when the RA2group is attached to a carbon atom. In certain embodiments, at least one RA2is H. In certain embodiments, at least one RA2is halogen. In certain embodiments, at least one RA2is F. In certain embodiments, at least one RA2is Cl. In certain embodiments, at least one RA2is Br. In certain embodiments, at least one RA2is I (iodine). In certain embodiments, at least one RA2is substituted acyl. In certain embodiments, at least one RA2is unsubstituted acyl. In certain embodiments, at least one RA2is acetyl. In certain embodiments, at least one RA2is substituted acetyl. In certain embodiments, at least one RA2is substituted alkyl. In certain embodiments, at least one RA2is unsubstituted alkyl. In certain embodiments, at least one RA2is C1-6alkyl. In certain embodiments, at least one RA2is methyl. In certain embodiments, at least one RA2is ethyl. In certain embodiments, at least one RA2is propyl. In certain embodiments, at least one RA2is butyl. In certain embodiments, at least one RA2is substituted alkenyl. In certain embodiments, at least one RA2is unsubstituted alkenyl. In certain embodiments, at least one RA2is vinyl. In certain embodiments, at least one RA2is substituted alkynyl. In certain embodiments, at least one RA2is unsubstituted alkynyl. In certain embodiments, at least one RA2is ethynyl. In certain embodiments, at least one RA2is substituted carbocyclyl. In certain embodiments, at least one RA2is unsubstituted carbocyclyl. In certain embodiments, at least one RA2is substituted heterocyclyl. In certain embodiments, at least one RA2is unsubstituted heterocyclyl. In certain embodiments, at least one RA2is substituted aryl. In certain embodiments, at least one RA2is unsubstituted aryl. In certain embodiments, at least one RA2is substituted phenyl. In certain embodiments, at least one RA2is unsubstituted phenyl. In certain embodiments, at least one RA2is substituted heteroaryl. In certain embodiments, at least one RA2is unsubstituted heteroaryl. In certain embodiments, at least one RA2is substituted pyridyl. In certain embodiments, at least one RA2is unsubstituted pyridyl. In certain embodiments, at least one RA2is —ORA2a. In certain embodiments, at least one RA2is —N(RA2a)2. In certain embodiments, at least one RA2is —SRA2a.

In certain embodiments, two RA2groups are each independently halogen, optionally substituted alkyl, or optionally substituted aryl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are each independently halogen or optionally substituted alkyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are halogen; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are optionally substituted alkyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are C1-6alkyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are methyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are ethyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are propyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are butyl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are optionally substituted aryl; and all other instances of RA2are hydrogen. In certain embodiments, two RA2groups are optionally substituted phenyl; and all other instances of RA2are hydrogen.

In certain embodiments, one RA2groups is halogen, optionally substituted alkyl, or optionally substituted aryl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is halogen or optionally substituted alkyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is halogen; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is optionally substituted alkyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is C1-6alkyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is methyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is ethyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is propyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is butyl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is optionally substituted aryl; and all other instances of RA2are hydrogen. In certain embodiments, one RA2is optionally substituted phenyl; and all other instances of RA2are hydrogen.

In certain embodiments, all instances of RA2are hydrogen.

In certain embodiments, when RA2is —ORA2a, —N(RA2a)2, or —SRA2a, at least one RA2ais H. In certain embodiments, at least one RA2ais halogen. In certain embodiments, at least one RA2ais F. In certain embodiments, at least one RA2ais Cl. In certain embodiments, at least one RA2ais Br. In certain embodiments, at least one RA2ais I (iodine). In certain embodiments, at least one RA2ais substituted acyl. In certain embodiments, at least one RA2ais unsubstituted acyl. In certain embodiments, at least one RA2ais acetyl. In certain embodiments, at least one RA2ais substituted acetyl. In certain embodiments, at least one RA2ais substituted alkyl. In certain embodiments, at least one RA2ais unsubstituted alkyl. In certain embodiments, at least one RA2ais C1-6alkyl. In certain embodiments, at least one RA2ais methyl. In certain embodiments, at least one RA2ais ethyl. In certain embodiments, at least one RA2ais propyl. In certain embodiments, at least one RA2ais butyl. In certain embodiments, at least one RA2is substituted alkenyl. In certain embodiments, at least one RA2ais unsubstituted alkenyl. In certain embodiments, at least one RA2ais vinyl. In certain embodiments, at least one RA2ais substituted alkynyl. In certain embodiments, at least one RA2ais unsubstituted alkynyl. In certain embodiments, at least one RA2ais ethynyl. In certain embodiments, at least one RA2ais substituted carbocyclyl. In certain embodiments, at least one RA2ais unsubstituted carbocyclyl. In certain embodiments, at least one RA2ais substituted heterocyclyl. In certain embodiments, at least one RA2ais unsubstituted heterocyclyl. In certain embodiments, at least one RA2is substituted aryl. In certain embodiments, at least one RA2ais unsubstituted aryl. In certain embodiments, at least one RA2ais substituted phenyl. In certain embodiments, at least one RA2ais unsubstituted phenyl. In certain embodiments, at least one RA2ais substituted heteroaryl. In certain embodiments, at least one RA2ais unsubstituted heteroaryl. In certain embodiments, at least one RA2ais substituted pyridyl. In certain embodiments, at least one RA2ais unsubstituted pyridyl. In certain embodiments, at least one RA2ais a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one RA2ais Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, at least one RA2ais an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one RA2ais silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom. In certain embodiments, at least one RA2ais a sulfur protecting group when attached to a sulfur atom. In certain embodiments, at least one RA2ais acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom. In certain embodiments, two RA2agroups are joined to form a substituted heterocyclic ring. In certain embodiments, two RA2agroups are joined to form an unsubstituted heterocyclic ring.

Compounds of Formula (I) include a substituted or unsubstituted heteroaryl ring of the formula:

In certain embodiments, WBis N. In certain embodiments, WBis CRB2; and thus Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

In compounds of Formula (I), RB1and RB2groups may be joined to form a ring fused to Ring B. In certain embodiments, RB1and RB2are joined to form a substituted carbocyclic ring. In certain embodiments, RB1and RB2are joined to form an unsubstituted carbocyclic ring. In certain embodiments, RB1and RB2are joined to form a substituted heterocyclic ring. In certain embodiments, RB1and RB2are joined to form an unsubstituted heterocyclic ring. In certain embodiments, RB1and RB2are joined to form a substituted aryl ring. In certain embodiments, RB1and RB2are joined to form an unsubstituted aryl ring. In certain embodiments, RB1and RB2are joined to form a substituted phenyl ring. In certain embodiments, RB1and RB2are joined to form an unsubstituted phenyl ring. In certain embodiments, RB1and RB2are joined to form a substituted heteroaryl ring. In certain embodiments, RB1and RB2are joined to form an unsubstituted heteroaryl ring. In certain embodiments, RB1and RB2are joined to form a substituted pyridyl ring. In certain embodiments, RB1and RB2are joined to form an unsubstituted pyridyl ring.

In certain embodiments, Ring B is of the formula:

In certain embodiments, Ring B is of the formula:

each instance of RB3is selected from the group consisting of hydrogen, halogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —ORB3a, —N(RB3a)2, and —SRB3a, wherein each occurrence of RB3ais independently selected from the group consisting of 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, and a sulfur protecting group when attached to a sulfur atom, or two RB3agroups are joined to form an optionally substituted heterocyclic ring; and q is 0, 1, 2, or 3.

In certain embodiments, q is 0. In certain embodiments, q is 1. In certain embodiments, q is 2. In certain embodiments, q is 3.

In compounds of Formula (I), L1is a divalent linker moiety connecting Ring B and Ring C. L1may be an optionally substituted C1-4hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL1—, —S(═O)—, or —S(═O)2—. In certain embodiments, L1is an optionally substituted C1-2hydrocarbon chain, optionally wherein one or two carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL1—, —S(═O)—, or —S(═O)2—. In certain embodiments, L1is an optionally substituted C1hydrocarbon chain, optionally wherein the carbon unit of the hydrocarbon chain is replaced with —O—, —S—, —NRL1—, —S(═O)—, or —S(═O)2—. In certain embodiments, L1is —O—, —S—, —NRL1—, —NRL1—C(RL1a)2—, —C(RL1a)2—NRL1—, or —C(RL1a)2—, wherein: each instance of RL1is independently hydrogen or unsubstituted C1-6alkyl; and each instance of RL1ais independently hydrogen, halogen, substituted or unsubstituted C1-6alkyl, —CN, —ORL1b, or —N(RL1b)2, wherein each instance of RL1bis independently hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, each instance of RL1ais independently hydrogen, halogen, —CN, —ORL1b, —N(RL1b)2, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more halogen, wherein each instance of RL1bis independently hydrogen, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more halogen. In certain embodiments, L1is —O—. In certain embodiments, L1is —S—. In certain embodiments, L1is —NRL1—. In certain embodiments, L1is —CH2—. In certain embodiments, L1is of the formula: —C(═O)NRL1— or —NRL1C(═O)—. In certain embodiments, L1is of the formula: —C(═O)NH— or —NH(═O)—. In certain embodiments, L1is an optionally substituted C3hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL1—, —S(═O)—, or —S(═O)2—. In certain embodiments, L1is an optionally substituted C4hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL1—, —S(═O)—, or —S(═O)2—. In certain embodiments, at least one carbon unit of the C1-4hydrocarbon chain is substituted with one or more substituents independently selected from the group consisting of halogen, unsubstituted C1-6alkyl, C1-6alkyl substituted with at least one instance of halogen, and oxo (═O). In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form an unsubstituted carbocyclic ring. In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form a substituted carbocyclic ring. In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form an unsubstituted heterocyclic ring. In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form a substituted heterocyclic ring.

In compounds of Formula (I), L2is a divalent linker moiety connecting Ring B and Ring C. L2may be an optionally substituted C1-4hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL2—, —S(═O)—, or —S(═O)2—. In certain embodiments, L2is an optionally substituted C1-2hydrocarbon chain, optionally wherein one or two carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL2—, —S(═O)—, or —S(═O)2—. In certain embodiments, L2is —NRL2C(═O)—, —C(═O)NRL2—, —NRL2S(═O)2—, —S(═O)2NRL2—, —NRL2(C1-2alkylene)-, or —(C1-2alkylene)NRL2—, wherein the C1-2alkylene is optionally substituted with 1 to 4 substituents independently selected from the group consisting of halogen, ═O, —CN, —ORL2, —N(RL2)2, —C(═O)N(RL2)2, —C(═O)ORL2, or substituted or unsubstituted C1-6alkyl, wherein each instance of RL2is independently hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, the C1-2alkylene is optionally substituted with 1 to 4 substituents independently selected from the group consisting of halogen, ═O, —CN, —ORL2, —N(RL2)2, —C(═O)N(RL2)2, —C(═O)ORL2, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —ORL2a, or —N(RL2a)2, wherein each instance of RL2and RL2ais independently hydrogen, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more halogen. In certain embodiments, L2is —NRL2C(═O)—, —C(═O)NRL2—, —NRL2S(═O)2—, —S(═O)2NRL2—, —NRL2(Cl1-2alkylene)- (e.g., —NRL2—CH2— (e.g., —NH—CH2—, —NMe-CH2—, or —N(Boc)-CH2—) or —NRL2—CH(substituted or unsubstituted C1-6alkyl)- (e.g., —NH—CH(CF3)—), —(C1-2alkylene)NRL2— (e.g., —CH2—NRL2— (e.g., —CH2—NH—, —CH2—NMe-, or —CH2—N(Boc)-) or —CH(substituted or unsubstituted C1-6alkyl)-NRL2— (e.g., —CH(CF3)—NH—), —NRL2— (e.g., —NH—), —O(C1-2alkylene)- (e.g., —O—CH2—), or —(C1-2alkylene)O— (e.g., —CH2—O—), wherein the C1-2alkylene is optionally substituted with 1 to 4 substituents independently selected from the group consisting of halogen, ═O, —CN, —ORL2, —N(RL2)2, —C(═O)N(RL2)2, —C(═O)ORL2, or substituted or unsubstituted C1-6alkyl, wherein each instance of RL2is independently hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group (e.g., Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts). In certain embodiments, L2is —NHC(═O)—, —C(═O)NH—, —NHS(═O)2—, —N(C(O)OC(CH3)3)—, —N(Boc)-CH2—, —NH—, —NHCH2—, —NMeCH2—, —OCH2—, or —NHCH(CF3)—. In certain embodiments, L2is an optionally substituted C1hydrocarbon chain, optionally wherein the carbon unit of the hydrocarbon chain is replaced with —O—, —S—, —NRL2—, —S(═O)—, or —S(═O)2—. In certain embodiments, L2is —O—, —S—, —NRL2—, —NRL2—C(RL2a)2—, —C(RL2a)2—NRL2—, or —C(RL2a)2—, wherein: each instance of RL2is independently hydrogen or unsubstituted C1-6alkyl; and each instance of RL2ais independently hydrogen, halogen, substituted or unsubstituted C1-6alkyl, —CN, —ORL2b, or —N(RL2b)2, wherein each instance of RL2bis independently hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, each instance of RL2ais independently hydrogen, halogen, —CN, —ORL2b, —N(RL2b)2, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more halogen, wherein each instance of RL2bis independently hydrogen, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more halogen. In certain embodiments, L2is —O—. In certain embodiments, L2is —S—. In certain embodiments, L2is —NRL2— (e.g., —NH— or —N(Me)—). In certain embodiments, L2is —CH2—. In certain embodiments, L2is of the formula: —C(═O)NRL2— or —NRL2C(═O)—. In certain embodiments, L2is of the formula: —C(═O)NH— or —NH(═O)—. In certain embodiments, L2is an optionally substituted C3hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL2—, —S(═O)—, or —S(═O)2—. In certain embodiments, L2is an optionally substituted C4hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NRL2—, —S(═O)—, or —S(═O)2—. In certain embodiments, at least one carbon unit of the C1-4hydrocarbon chain is substituted with one or more substituents independently selected from the group consisting of halogen, unsubstituted C1-6alkyl, C1-6alkyl substituted with at least one instance of halogen, and oxo (═O). In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form an unsubstituted carbocyclic ring. In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form a substituted carbocyclic ring. In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form an unsubstituted heterocyclic ring. In certain embodiments, two substituents on the optionally substituted C1-4hydrocarbon chain are taken together to form a substituted heterocyclic ring.

In compounds of Formula (I), Ring C is an optionally substituted cyclohexylene moiety. In certain embodiments, Ring C is an optionally substituted trans-cyclohexylene moiety. In certain embodiments, Ring C is an optionally substituted cis-cyclohexylene moiety. In certain embodiments, Ring C is an optionally substituted 1,2-cyclohexylene moiety. In certain embodiments, Ring C is an optionally substituted 1,3-cyclohexylene moiety. In certain embodiments, Ring C is an optionally substituted 1,4-cyclohexylene moiety. In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of the formula:

or a stereoisomeric form thereof. Ring C may be unsubstituted or may be substituted with one or more RCgroups. In certain embodiments, at least one RCis H. In certain embodiments, at least one RCis halogen. In certain embodiments, at least one RCis F. In certain embodiments, at least one RCis Cl. In certain embodiments, at least one RCis Br. In certain embodiments, at least one RCis I (iodine). In certain embodiments, at least one RCis substituted acyl. In certain embodiments, at least one RCis unsubstituted acyl. In certain embodiments, at least one RCis acetyl. In certain embodiments, at least one RCis substituted acetyl. In certain embodiments, at least one RCis substituted alkyl. In certain embodiments, at least one RCis unsubstituted alkyl. In certain embodiments, at least one RCis C1-6alkyl. In certain embodiments, at least one RCis methyl. In certain embodiments, at least one RCis ethyl. In certain embodiments, at least one RCis propyl. In certain embodiments, at least one RCis butyl. In certain embodiments, at least one RCis substituted alkenyl. In certain embodiments, at least one RCis unsubstituted alkenyl. In certain embodiments, at least one RCis vinyl. In certain embodiments, at least one RCis substituted alkynyl. In certain embodiments, at least one RCis unsubstituted alkynyl. In certain embodiments, at least one RCis ethynyl. In certain embodiments, at least one RCis substituted carbocyclyl. In certain embodiments, at least one RCis unsubstituted carbocyclyl. In certain embodiments, at least one RCis substituted heterocyclyl. In certain embodiments, at least one RCis unsubstituted heterocyclyl. In certain embodiments, at least one RCis substituted aryl. In certain embodiments, at least one RCis unsubstituted aryl. In certain embodiments, at least one RCis substituted phenyl. In certain embodiments, at least one RCis unsubstituted phenyl. In certain embodiments, at least one RCis substituted heteroaryl. In certain embodiments, at least one RCis unsubstituted heteroaryl. In certain embodiments, at least one RCis substituted pyridyl. In certain embodiments, at least one RCis unsubstituted pyridyl. In certain embodiments, at least one RCis ═O. In certain embodiments, at least one RCis —CN. In certain embodiments, at least one RCis —ORC1. In certain embodiments, at least one RCis —N(RC1)2. In certain embodiments, at least one RCis —SRC1. In certain embodiments, each instance of RCis independently halogen, ═O, —CN, —ORC1, —N(RC1)2, —C(═O)N(RC1)2, —C(═O)ORC1, or substituted or unsubstituted C1-6alkyl, wherein each instance of RC1is independently hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, each instance of RCis independently halogen, ═O, —CN, —ORC1, —N(RC1)2, —C(═O)N(RC1)2, —C(═O)ORC1, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more substituents independently selected from the group consisting of halogen, —CN, —ORC1a, or —N(RC1a)2, wherein each instance of RC1and RC1ais independently hydrogen, unsubstituted C1-6alkyl, or C1-6alkyl substituted with one or more halogen.

In certain embodiments, two instances of RCare joined to form a optionally substituted carbocyclic ring. In certain embodiments, two instances of RCare joined to form a optionally substituted heterocyclic ring. In certain embodiments, two instances of RCare joined to form a optionally substituted aryl ring (e.g., phenyl ring). In certain embodiments, two instances of RCare joined to form a optionally substituted heteroaryl ring. In certain embodiments, when two RCgroups are taken together to form an optionally substituted, heterocyclic or carbocyclic ring, two substituents on the substituted heterocyclic ring or substituted carbocyclic ring, or one substituent on the substituted heterocyclic ring or substituted carbocyclic ring and a third RCgroup, are taken together to form another optionally substituted heterocyclic ring or optionally substituted carbocyclic ring. In certain embodiments, Ring C and all instances of RCare taken together to form an unsubstituted 7- to 10-membered bicyclic carbocyclic ring consisting of 0, 1, or 2 double bonds in the carbocyclic ring system. In certain embodiments, Ring C and all instances of RCare taken together to form unsubstituted bicyclo[3.1.1]heptanyl (e.g.,

In certain embodiments, Ring C and all instances of RCare taken together to form an unsubstituted 8- to 14-membered tricyclic carbocyclic ring consisting of 0, 1, 2, 3, or 4 double bonds in the carbocyclic ring system. In certain embodiments, Ring C and all instances of RCare taken together to form unsubstituted adamantyl (e.g.,

In certain embodiments, each instance of RCis independently halogen, ═O, —CN, —ORC1, —N(RC1)2, —C(═O)N(RC1)2, —C(═O)ORC1, or substituted or unsubstituted C1-6alkyl, wherein each instance of RC1is independently hydrogen or substituted or unsubstituted C1-6alkyl, or two RCgroups are taken together to form an optionally substituted heterocyclic ring or optionally substituted carbocyclic ring, wherein two substituents on the substituted heterocyclic ring or substituted carbocyclic ring, or one substituent on the substituted heterocyclic ring or substituted carbocyclic ring and a third RCgroup, are taken together to form another optionally substituted heterocyclic ring or optionally substituted carbocyclic ring. In certain embodiments, each instance of RCis independently halogen, —ORC1, or unsubstituted C1-6alkyl, wherein each instance of RC1is independently hydrogen or substituted or unsubstituted C1-6alkyl, or two RCgroups are taken together to form an optionally substituted heterocyclic ring or optionally substituted carbocyclic ring, wherein two substituents on the substituted heterocyclic ring or substituted carbocyclic ring, or one substituent on the substituted heterocyclic ring or substituted carbocyclic ring and a third RCgroup, are taken together to form another optionally substituted heterocyclic ring or optionally substituted carbocyclic ring. In certain embodiments, each instance of RCis independently fluoro or —OH, or Ring C and all instances of RCare taken together to form:

wherein the carbon atom labeled with “2” attaches to L1and the carbon atom labeled with “3” attaches to L2

In certain embodiments, when RCis —ORC1, —N(RC1)2, or —SRC1, at least one RC1is H. In certain embodiments, at least one RC1is halogen. In certain embodiments, at least one RC1is F. In certain embodiments, at least one RC1is Cl. In certain embodiments, at least one RC1is Br. In certain embodiments, at least one RC1is I (iodine). In certain embodiments, at least one RC1is substituted acyl. In certain embodiments, at least one RC1is unsubstituted acyl. In certain embodiments, at least one RC1is acetyl. In certain embodiments, at least one RC1is substituted acetyl. In certain embodiments, at least one RC1is substituted alkyl. In certain embodiments, at least one RC1is unsubstituted alkyl. In certain embodiments, at least one RC1is C1-6alkyl. In certain embodiments, at least one RC1is methyl. In certain embodiments, at least one RC1is ethyl. In certain embodiments, at least one RC1is propyl. In certain embodiments, at least one RC1is butyl. In certain embodiments, at least one RC1is substituted alkenyl. In certain embodiments, at least one RC1is unsubstituted alkenyl. In certain embodiments, at least one RC1is vinyl. In certain embodiments, at least one RC1is substituted alkynyl. In certain embodiments, at least one RC1is unsubstituted alkynyl. In certain embodiments, at least one RC1is ethynyl. In certain embodiments, at least one RC1is substituted carbocyclyl. In certain embodiments, at least one RC1is unsubstituted carbocyclyl. In certain embodiments, at least one RC1is substituted heterocyclyl. In certain embodiments, at least one RC1is unsubstituted heterocyclyl. In certain embodiments, at least one RC1is substituted aryl. In certain embodiments, at least one RC1is unsubstituted aryl. In certain embodiments, at least one RC1is substituted phenyl. In certain embodiments, at least one RC1is unsubstituted phenyl. In certain embodiments, at least one RC1is substituted heteroaryl. In certain embodiments, at least one RC1is unsubstituted heteroaryl. In certain embodiments, at least one RC1is substituted pyridyl. In certain embodiments, at least one RC1is unsubstituted pyridyl. In certain embodiments, at least one RC1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one RC1is Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, at least one RC1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, at least one RC1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom. In certain embodiments, at least one RC1is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, at least one RC1is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom. In certain embodiments, two RC1groups are joined to form a substituted heterocyclic ring. In certain embodiments, two RC1groups are joined to form an unsubstituted heterocyclic ring.

Ring C may be unsubstituted or substituted with one or more RCgroups. In certain embodiments, Ring C is unsubstituted, and thus n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5. In certain embodiments, n is 6. In certain embodiments, n is 7. In certain embodiments, n is 8. In certain embodiments, n is 9. In certain embodiments, n is 10.

In compounds of Formula (I), Ring D is a substituted phenyl ring. Ring D is substituted with REand may also be substituted with one or more RDgroups. In certain embodiments, at least one RDis H. In certain embodiments, at least one RDis halogen. In certain embodiments, at least one RDis F. In certain embodiments, at least one RDis Cl. In certain embodiments, at least one RDis Br. In certain embodiments, at least one RDis I (iodine). In certain embodiments, at least one RDis substituted acyl. In certain embodiments, at least one RDis unsubstituted acyl. In certain embodiments, at least one RDis acetyl. In certain embodiments, at least one RDis substituted acetyl. In certain embodiments, at least one RDis substituted alkyl. In certain embodiments, at least one RDis unsubstituted alkyl. In certain embodiments, at least one RDis C1-6alkyl. In certain embodiments, at least one RDis methyl. In certain embodiments, at least one RDis ethyl. In certain embodiments, at least one RDis propyl. In certain embodiments, at least one RDis butyl. In certain embodiments, at least one RDis substituted alkenyl. In certain embodiments, at least one RDis unsubstituted alkenyl. In certain embodiments, at least one RDis vinyl. In certain embodiments, at least one RDis substituted alkynyl. In certain embodiments, at least one RDis unsubstituted alkynyl. In certain embodiments, at least one RDis ethynyl. In certain embodiments, at least one RDis substituted carbocyclyl. In certain embodiments, at least one RDis unsubstituted carbocyclyl. In certain embodiments, at least one RDis substituted heterocyclyl. In certain embodiments, at least one RDis unsubstituted heterocyclyl. In certain embodiments, at least one instance of RDis substituted or unsubstituted, 5- to 6-membered monocyclic heterocyclyl consisting of 0, 1, or 2 double bonds in the heterocyclic ring system, wherein 1, 2, or 3 atoms in the heterocyclic ring system are independently nitrogen, oxygen, or sulfur. In certain embodiments, at least one instance of RDis morpholinyl (e.g.,

In certain embodiments, each instance of RDis independently fluoro or morpholinyl. In certain embodiments, at least one RDis substituted aryl. In certain embodiments, at least one RDis unsubstituted aryl. In certain embodiments, at least one RDis substituted phenyl. In certain embodiments, at least one RDis unsubstituted phenyl. In certain embodiments, at least one RDis substituted heteroaryl. In certain embodiments, at least one RDis unsubstituted heteroaryl. In certain embodiments, at least one RDis substituted pyridyl. In certain embodiments, at least one RDis unsubstituted pyridyl. In certain embodiments, at least one RDis —CN. In certain embodiments, at least one RDis —ORD1. In certain embodiments, at least one RDis —N(RD1)2. In certain embodiments, at least one RDis —SRD1. In certain embodiments, each instance of RDis independently halogen, —CN, —ORC1, —N(RC1)2, —C(═O)N(RC1)2, —C(═O)ORC1, substituted or unsubstituted C1-6alkyl, or substituted or unsubstituted heterocyclyl, wherein each instance of RC1is independently hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, each instance of RDis independently halogen or substituted or unsubstituted heterocyclyl.

In certain embodiments, when RDis —ORD1, —N(RD1)2, or —SRD1, at least one RD1is H. In certain embodiments, at least one RD1is substituted acyl. In certain embodiments, at least one RD1is unsubstituted acyl. In certain embodiments, at least one RD1is acetyl. In certain embodiments, at least one RD1is substituted acetyl. In certain embodiments, at least one RD1is substituted alkyl. In certain embodiments, at least one RD1is unsubstituted alkyl. In certain embodiments, at least one RD1is C1-6alkyl. In certain embodiments, at least one RD1is methyl. In certain embodiments, at least one RD1is ethyl. In certain embodiments, at least one RD1is propyl. In certain embodiments, at least one RD1is butyl. In certain embodiments, at least one RD1is substituted alkenyl. In certain embodiments, at least one RD1is unsubstituted alkenyl. In certain embodiments, at least one RD1is vinyl. In certain embodiments, at least one RD1is substituted alkynyl. In certain embodiments, at least one RD1is unsubstituted alkynyl. In certain embodiments, at least one RD1is ethynyl. In certain embodiments, at least one RD1is substituted carbocyclyl. In certain embodiments, at least one RD1is unsubstituted carbocyclyl. In certain embodiments, at least one RD1is substituted heterocyclyl. In certain embodiments, at least one RD1is unsubstituted heterocyclyl. In certain embodiments, at least one RD1is substituted aryl. In certain embodiments, at least one RD1is unsubstituted aryl. In certain embodiments, at least one RD1is substituted phenyl. In certain embodiments, at least one RD1is unsubstituted phenyl. In certain embodiments, at least one RD1is substituted heteroaryl. In certain embodiments, at least one RD1is unsubstituted heteroaryl. In certain embodiments, at least one RD1is substituted pyridyl. In certain embodiments, at least one RD1is unsubstituted pyridyl. In certain embodiments, at least one RD1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one RD1is Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RD1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RD1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom. In certain embodiments, RD1is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, RD1is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom. In certain embodiments, two RD1groups are joined to form a substituted heterocyclic ring. In certain embodiments, two RD1groups are joined to form an unsubstituted heterocyclic ring.

Ring D may be unsubstituted or substituted with one or more RDgroups. In certain embodiments, Ring D is unsubstituted, and thus p is 0. In certain embodiments, p is 1. In certain embodiments, p is 2. In certain embodiments, p is 3. In certain embodiments, p is 4.

In certain embodiments, RDis halogen; and p is 1. In certain embodiments, RDis F; and p is 1. In certain embodiments, RDis Cl; and p is 1. In certain embodiments, RDis Br; and p is 1. In certain embodiments, RDis I (iodine); and p is 1. In certain embodiments, RDis substituted alkyl; and p is 1. In certain embodiments, RDis unsubstituted alkyl; and p is 1. In certain embodiments, RDis C1-6alkyl; and p is 1. In certain embodiments, RDis methyl; and p is 1. In certain embodiments, RDis ethyl, propyl, or butyl; and p is 1. In certain embodiments, each instance of RDis independently halogen or optionally substituted alkyl; and p is 2. In certain embodiments, each instance of RDis independently halogen or C1-6alkyl; and p is 2.

In compounds of Formula (I), Ring D also includes a substituent RE. In certain embodiments, REcomprises a Michael acceptor moiety. This Michael acceptor moiety may react with a cysteine residue of a kinase (e.g., CDK (e.g., CDK7)) to allow covalent attachment of the compound to the kinase. In certain embodiments, the covalent attachment is irreversible. In other embodiments, the covalent attachment is reversible.

In certain embodiments, REis of Formula (ii-1):

In certain embodiments, REis of Formula (ii-2):

In certain embodiments, REis of Formula (ii-3):

In certain embodiments, REis of Formula (ii-4):

In certain embodiments, REis of Formula (ii-5):

In certain embodiments, REis of Formula (ii-6):

In certain embodiments, REis of Formula (ii-7):

In certain embodiments, REis of Formula (ii-8):

In certain embodiments, REis of Formula (ii-9):

In certain embodiments, REis of Formula (ii-10):

In certain embodiments, REs of Formula (ii-11):

In certain embodiments, REis of Formula (ii-12):

In certain embodiments, REis of Formula (ii-13):

In certain embodiments, REis of Formula (ii-14):

In certain embodiments, REis of Formula (ii-15):

In certain embodiments, REis of Formula (ii-16):

In certain embodiments, REis of Formula (ii-17):

In certain embodiments, REis of Formula (ii-18):

In certain embodiments, REis of Formula (ii-19):

In certain embodiments, REis of Formula (ii-20):

In certain embodiments, REis of Formula (ii-1) or (ii-3).

In certain embodiment, REand L2are para or meta to each other. In certain embodiments, REand L2are meta to each other. In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, REand L2are para to each other. In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of the formula:

In certain embodiments, at least one RL3bis H. In certain embodiments, at least one RL3bis halogen. In certain embodiments, at least one RL3bis F. In certain embodiments, at least one RL3bis Cl. In certain embodiments, at least one RL3bis Br. In certain embodiments, at least one RL3bis I (iodine). In certain embodiments, at least one RL3bis substituted alkyl. In certain embodiments, at least one RL3bis unsubstituted alkyl. In certain embodiments, at least one RL3bis C1-6alkyl. In certain embodiments, at least one RL3bis methyl. In certain embodiments, at least one RL3bis ethyl. In certain embodiments, at least one RL3bis propyl. In certain embodiments, at least one RL3bis butyl. In certain embodiments, at least one RL3bis substituted alkenyl. In certain embodiments, at least one RL3bis unsubstituted alkenyl. In certain embodiments, at least one RL3bis vinyl. In certain embodiments, at least one RL3bis substituted alkynyl. In certain embodiments, at least one RL3bis unsubstituted alkynyl. In certain embodiments, at least one RL3bis ethynyl. In certain embodiments, at least one RL3bis substituted carbocyclyl. In certain embodiments, at least one RL3bis unsubstituted carbocyclyl. In certain embodiments, at least one RL3bis substituted heterocyclyl. In certain embodiments, at least one RL3bis unsubstituted heterocyclyl. In certain embodiments, at least one RL3bis substituted aryl. In certain embodiments, at least one RL3bis unsubstituted aryl. In certain embodiments, at least one RL3bis substituted phenyl. In certain embodiments, at least one RL3bis unsubstituted phenyl. In certain embodiments, at least one RL3bis substituted heteroaryl. In certain embodiments, at least one RL3bis unsubstituted heteroaryl. In certain embodiments, at least one RL3bis substituted pyridyl. In certain embodiments, at least one RL3bis unsubstituted pyridyl. In certain embodiments, two RL3bgroups are joined to form a substituted carbocyclic ring. In certain embodiments, two RL3bgroups are joined to form an unsubstituted carbocyclic ring. In certain embodiments, two RL3bgroups are joined to form a substituted heterocyclic ring. In certain embodiments, two RL3bgroups are joined to form an unsubstituted heterocyclic ring.

In compounds of Formula (I), RE1and RE3, or RE2and RE3, or RE1and RE2may be joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring. In certain embodiments, RE1and RE3are joined to form an optionally substituted carbocyclic ring. In certain embodiments, RE1and RE3are joined to form an optionally substituted heterocyclic ring. In certain embodiments, RE2and RE3are joined to form an optionally substituted carbocyclic ring. In certain embodiments, RE2and RE3are joined to form an optionally substituted heterocyclic ring. In certain embodiments, RE1and RE2are joined to form an optionally substituted carbocyclic ring. In certain embodiments, RE1and RE2are joined to form an optionally substituted heterocyclic ring.

In compounds of Formula (I), REmay include a Y group. In certain embodiments, Y is ═O. In certain embodiments, Y is —O—. In certain embodiments, Y is ═S. In certain embodiments, Y is —S—. In certain embodiments, Y is ═NRE6. In certain embodiments, Y is —NRE6—. In certain embodiments, Y is ═NH. In certain embodiments, Y is —NH—. In certain embodiments, RE6is H. In certain embodiments, RE6is substituted or unsubstituted C1-6alkyl (e.g., —CH3). In certain embodiments, RE6is a nitrogen protecting group (e.g., Bn, BOC, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts).

In compounds of Formula (I), REmay include a substituent RE5, which is halogen. In certain embodiments, RE5is F, Cl, Br, or I (iodine).

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. In certain embodiments, z is 4. In certain embodiments, z is 5. In certain embodiments, z is 6.

In certain embodiments, REis of Formula (ii-1); and RE1is hydrogen. In certain embodiments, REis of Formula (ii-1); and RE2is hydrogen. In certain embodiments, REis of Formula (ii-1); and RE3is hydrogen. In certain embodiments, REis of Formula (ii-1); and RE2and RE3are each hydrogen. In certain embodiments, REis of Formula (ii-1); and RE1, RE2and RE3are each hydrogen. In certain embodiments, REis of Formula (ii-1); and RE1is —CH2N(RE1a). In certain embodiments, REis of Formula (ii-1); RE1is —CH2N(RE1a); and RE1ais C1-6alkyl. In certain embodiments, REis of Formula (ii-1); RE1is —CH2N(RE1a); and RE1ais methyl. In certain embodiments, REis of Formula (ii-1); and RE2is —CH2N(RE2a). In certain embodiments, REis of Formula (ii-1); RE2is —CH2N(RE2a); and RE2ais C1-6alkyl. In certain embodiments, REis of Formula (ii-1); RE2is —CH2N(RE2a); and RE2ais methyl. In certain embodiments, REis of Formula (ii-1); and RE3is —CH2N(RE3a). In certain embodiments, REis of Formula (ii-1); RE3is —CH2N(RE3a); and RE3ais C1-6alkyl. In certain embodiments, REis of Formula (ii-1); RE3is —CH2N(RE3a); and RE3ais methyl. In certain embodiments, REis of Formula (ii-1); and Y is ═O. In certain embodiments, REis of Formula (ii-1); and L is —NRL3a—. In certain embodiments, REis of Formula (ii-1); and L3is —NH—. In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REs of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis of Formula (ii-3); and RE1is hydrogen. In certain embodiments, REis of Formula (ii-3); and RE1is —CH2N(RE1a). In certain embodiments, REis of Formula (ii-3); and RE1is —Si(RE1a)3(e.g., —Si(Me)3). In certain embodiments, REis of Formula (ii-3); RE1is —CH2N(RE1a); and RE1ais C1-6alkyl. In certain embodiments, REis of Formula (ii-3); RE1is —CH2N(RE1a); and RE1ais methyl. In certain embodiments, REis of Formula (ii-3); and Y is ═O. In certain embodiments, REis of Formula (ii-3); and L3is —NRL3a—. In certain embodiments, REis of Formula (ii-3); and L3is —NH—.

In certain embodiments, REis of the formula:

In certain embodiments, REis of the formula:

In certain embodiments, REis not of the formula:

Ring A is substituted or unsubstituted, 5- to 6-membered, monocyclic heteroaryl, or substituted or unsubstituted, 9- to 10-membered, bicyclic heteroaryl, wherein 1, 2, or 3 atoms in the heteroaryl ring system are independently oxygen, nitrogen, or sulfur;

each instance of RCis independently halogen, —ORC1, or substituted or unsubstituted C1-6alkyl, wherein each instance of RC1is independently hydrogen or substituted or unsubstituted C1-6alkyl, or two RCare taken together to form an optionally substituted heterocyclic ring or optionally substituted carbocyclic ring;

L2is —NRL2C(═O)—, —C(═O)NRL2—, —NRL2(substituted or unsubstituted C1-2alkylene)-, or —NRL2—, wherein each instance of RL2is independently hydrogen or substituted or unsubstituted C1-6alkyl;

each instance of RDis independently halogen;

REis of the formula:

n is 0, 1, or 2; and

p is 0 or 1.

In certain embodiments, in Formula (Ia):

Ring A is of the formula:

each instance of RCis independently halogen, —ORC1, or substituted or unsubstituted C1-6alkyl, wherein each instance of RC1is independently hydrogen or substituted or unsubstituted C1-6alkyl, or two RCare taken together to form an optionally substituted carbocyclic ring;

L2is —NRL2C(═O)—, —C(═O)NRL2—, —NRL2(substituted or unsubstituted C1-2alkylene)-, or —NRL2—, wherein each instance of RL2is independently hydrogen or substituted or unsubstituted C1-6alkyl;

each instance of RDis independently halogen;

REis of the formula:

each instance of RE1is independently hydrogen, substituted or unsubstituted C1-6alkyl, or —Si(RE1a)3, wherein each instance of RE1ais independently substituted or unsubstituted C1-6alkyl or substituted or unsubstituted phenyl;

RE2is hydrogen or substituted or unsubstituted C1-6alkyl;

RE3is hydrogen or substituted or unsubstituted C1-6alkyl;

n is 0, 1, or 2; and

p is 0 or 1.

In certain embodiments, in Formula (Ia), WBis CRB2and RB2is chloro, cyclopropyl, or —CN. In certain embodiments, in Formula (Ia), L1is —NH—. In certain embodiments, in Formula (Ia), each instance of RCis independently fluoro, —OH, or —CH3, or Ring C and all instances of RCare taken together to form

wherein the carbon atom labeled with “2” attaches to L1and the carbon atom labeled with “3” attaches to L2. In certain embodiments, in Formula (Ia), n is 0, 1, or 2. In certain embodiments, in Formula (Ia), L2is —NHC(═O)—, —C(═O)NH—, —NH(C1-2alkylene)-, or —NH—. In certain embodiments, in Formula (Ia), each instance of RDis independently fluoro. In certain embodiments, in Formula (Ia), p is 0 or 1. In certain embodiments, in Formula (Ia), REis of the formula:

In certain embodiments, a compound of Formula (I) is of the formula:

In certain embodiments, a compound of Formula (I) is the formula:

In certain embodiments, the compound of Formula (I) is a compound depicted inFIG. 1, 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 any one of Compounds 100-178 (e.g., Compound 102), 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 any one of Compounds 100-178 (e.g., Compound 102), or a pharmaceutically acceptable salt thereof.

In certain embodiments, a compound of Formula (I) is substantially pure. In certain embodiments, a compound of Formula (I) is a substantially pure stereoisomer. In certain embodiments, the compounds of the present invention are compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. In certain embodiments, the compounds of the present invention are compounds of Formula (I), and pharmaceutically acceptable salts and stereoisomers thereof. In certain embodiments, the compounds of the present invention are compounds of Formula (I), and pharmaceutically acceptable salts thereof. In certain embodiments, the compounds of the present invention are a stereoisomeric mixture of compounds of Formula (I), and pharmaceutically acceptable salts thereof. In certain embodiments, the compounds of the present invention are a racemic stereoisomeric mixture of compounds of Formula (I), and pharmaceutically acceptable salts thereof.

The compounds of the present invention may bear multiple binding motifs for binding to a CDK (e.g., CDK7, CDK12, and/or CDK13), specifically, CDK7. Ring A of the inventive compounds may be accommodated by a hydrophobic pocket in the ATP-binding site of the CDK (e.g., CDK7). Functionalities on Rings A and B may bind to residues of the CDK (e.g., CDK7). For example, Ring A may form a hydrogen bond with Asp155 of the CDK (e.g., CDK7). Functional groups of REmay form one or more hydrogen bonds with the CDK (e.g., CDK7). Moreover, the Michael acceptor moiety of REmay react with a cysteine residue (e.g., Cys312) of the CDK (e.g., CDK7) to allow covalent attachment of the compound to the CDK (e.g., CDK7).

The compounds of the present invention are thought to be kinase inhibitors. In certain embodiments, the inventive compounds are CDK inhibitors. In certain embodiments, the inventive compounds are CDK7 inhibitors. In certain embodiments, the inventive compounds are selective CDK inhibitors (e.g., being more active in inhibiting a CDK than a non-CDK kinase). In certain embodiments, the inventive compounds are selective CDK7 inhibitors (e.g., being more active in inhibiting CDK7 than a non-CDK7 kinase). In certain embodiments, the inventive compounds are selective CDK12 inhibitors. In certain embodiments, the inventive compounds are selective CDK13 inhibitors.

The selectivity of an inventive compound for a first kinase (e.g., CDK7) over a second kinase (e.g., a non-CDK7 kinase) may be measured by the quotient of the IC50(half maximal inhibitory concentration) value of the inventive compound in inhibiting the activity of the second kinase over the IC50value of the inventive compound in inhibiting the activity of the first kinase. The selectivity of an inventive compound for a first kinase over a second kinase may also be measured by the quotient of the Kd(dissociation constant) value of an adduct (covalent or non-covalent) of the inventive compound and the second kinase over the Kdvalue of an adduct of the inventive compound and the first kinase. In certain embodiments, the selectivity is at least about 1-fold, at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 30-fold, at least about 100-fold, at least about 300-fold, at least about 1,000-fold, at least about 3,000-fold, at least about 10,000-fold, at least about 30,000-fold, or at least about 100,000-fold. In certain embodiments, IC50values are measured by a functional antagonist assay. In certain embodiments, IC50values are measured by a competition binding assay. In certain embodiments, IC50values are measured by a method described herein. In certain embodiments, Kdvalues are measured by a nuclear magnetic resonance method (e.g., a linearization method and a curve fitting method). In certain embodiments, Kdvalues are measured by a mass spectrometry method (e.g., a one-ligand one-binding-site ESI-MS method).
Pharmaceutical Compositions, Kits, and Administration

The present invention provides pharmaceutical compositions comprising a compound of Formula (I), e.g., a compound of Formula (I), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, as described herein, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the compound of Formula (I), 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. In certain embodiments, the effective amount is a prophylactically effective amount.

Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the compound of Formula (I) (the “active ingredient”) into association with a carrier 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.

Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention 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. By way of example, the composition may comprise between 0.1% and 100% (w/w) active ingredient.

Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal 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.

Dosage forms for topical and/or transdermal administration of a compound of this invention 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 and/or any needed preservatives and/or buffers as can be required. Additionally, the present invention 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 such as those described in U.S. Pat. Nos. 4,886,499; 5,190,521; 5,328,483; 5,527,288; 4,270,537; 5,015,235; 5,141,496; and 5,417,662. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin, such as those described in PCT publication WO 99/34850 and functional equivalents thereof. Jet injection devices which deliver liquid vaccines 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. Jet injection devices are described, for example, in U.S. Pat. Nos. 5,480,381; 5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189; 5,704,911; 5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627; 5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880; 4,940,460; and PCT publications WO 97/37705 and WO 97/13537. 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. Alternatively or additionally, conventional syringes can be used in the classical mantoux method of intradermal administration.

Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition of the invention. 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.

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(s), mode of administration, and the like. The desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).

In certain embodiments, an effective amount of a compound for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosage form.

In certain embodiments, the compounds of Formula (I) may be at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.

It will be also appreciated that a compound or composition, as described herein, can be administered in combination with one or more additional pharmaceutical agents. The compounds or compositions can be administered in combination with additional pharmaceutical agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body. 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.

The compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional pharmaceutical agents, which may be useful as, e.g., combination therapies. Pharmaceutical agents include therapeutically active agents. Pharmaceutical agents also include prophylactically active agents. Each additional pharmaceutical agent may be administered at a dose and/or on a time schedule determined for that pharmaceutical agent. The additional pharmaceutical agents 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 inventive compound with the additional pharmaceutical agents and/or the desired therapeutic and/or prophylactic effect to be achieved. In general, it is expected that the additional pharmaceutical agents utilized 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.

Also encompassed by the invention are kits (e.g., pharmaceutical packs). The inventive kits may be useful for preventing and/or treating a proliferative disease (e.g., cancer (e.g., leukemia, lymphoma, melanoma, multiple myeloma, breast cancer, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma, lung cancer), benign neoplasm, angiogenesis, inflammatory disease, autoinflammatory disease, or autoimmune disease). The kits provided may comprise an inventive pharmaceutical composition or compound 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 an inventive pharmaceutical composition or compound. In some embodiments, the inventive pharmaceutical composition or compound provided in the container and the second container are combined to form one unit dosage form.

Thus, in one aspect, provided are kits including a first container comprising a compound described herein, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, and prodrug thereof, or a pharmaceutical composition thereof. In certain embodiments, the kit of the invention includes a first container comprising a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In certain embodiments, the kits are useful in preventing and/or treating a proliferative disease in a subject. In certain embodiments, the kits further include instructions for administering the compound, or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, and prodrug thereof, or a pharmaceutical composition thereof, to a subject to prevent and/or treat a proliferative disease.

Methods of Treatment and Uses

The present invention also provides methods for the treatment or prevention of a proliferative disease (e.g., cancer, benign neoplasm, angiogenesis, inflammatory disease, autoinflammatory disease, or autoimmune disease) or an infectious disease (e.g., a viral disease) in a subject.

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.

The proliferative disease to be treated or prevented using the compounds of Formula (I) 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, and activation 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 multisubunit protein complex identified as a factor required for RNA polymerase II (RNAP II)-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 of Formula (I) may be associated with overexpression of a CDK (e.g., CDK7). The compounds of Formula (I), or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, or pharmaceutical compositions thereof, may down-regulate the expression of a CDK (e.g., CDK7).

A proliferative disease may be associated with aberrant activity of a CDK (e.g., CDK7). Aberrant activity of a CDK (e.g., CDK7) 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) activity, frequently through elevated and/or inappropriate CDK activation. Inhibition of the catalytic activity of CDK7 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. The compounds of Formula (I), 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.

In other embodiments, the proliferative disease to be treated or prevented using the compounds of Formula (I) will typically be associated with aberrant activity of CDK12. Aberrant activity of CDK12 may be an elevated and/or an inappropriate (e.g., abnormal) activity of CDK12. In certain embodiments, CDK12 is not overexpressed, and the activity of CDK12 is elevated and/or inappropriate. In certain other embodiments, CDK12 is overexpressed, and the activity of CDK12 is elevated and/or inappropriate. The compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, tautomers, stereoisomers, isotopically labeled derivatives, and compositions thereof, may inhibit the activity of CDK12 and be useful in treating and/or preventing proliferative diseases.

In other embodiments, the proliferative disease to be treated or prevented using the compounds of Formula (I) will typically be associated with aberrant activity of CDK13. Aberrant activity of CDK13 may be an elevated and/or an inappropriate (e.g., abnormal) activity of CDK13. In certain 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 of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, tautomers, stereoisomers, isotopically labeled derivatives, and compositions thereof, may inhibit the activity of 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. CDK 7 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 of Formula (I), 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.

In certain embodiments, the proliferative disease to be treated or prevented using the compounds of Formula (I) 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 dependence on BCL-2 anti-apoptotic proteins (e.g., MCL-1 and/or XIAP). 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 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 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 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 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.

In certain embodiments, the infectious disease to be treated or prevented using the compounds of Formula (I) is a viral disease. Such viral infections are described in U.S. Provisional Patent Application, U.S. Ser. No. 61/622,828, filed Apr. 11, 2012, and international PCT application, PCT/US2013/032488, filed Mar. 15, 2013, each of which is incorporated herein in its entirety by reference.

The cell described herein may be an abnormal cell. The cell may be in vitro or in vivo. In certain embodiments, the cell is a proliferative cell. In certain embodiments, the cell is a blood cell. In certain embodiments, the cell is a lymphocyte. In certain embodiments, the cell is a B-cell. In certain embodiments, the cell is a T-cell. In certain embodiments, the cell is a cancer cell. In certain embodiments, the cell is a leukemia cell. In certain embodiments, the cell is a CLL cell. In certain embodiments, the cell is a melanoma cell. In certain embodiments, the cell is a multiple myeloma cell. In certain embodiments, the cell is a benign neoplastic cell. In certain embodiments, the cell is an endothelial cell. In certain embodiments, the cell is an immune cell.

In another aspect, the present invention provides methods of down-regulating the expression of a CDK (e.g., CDK7, CDK1, CDK2, CDK5, CDK8, CDK9, CDK12, CDK13) in a biological sample or subject. In another aspect, the present invention provides methods of down-regulating the expression of IRAK1, JNK1, JNK2, or MLK3 in a biological sample or subject.

Another aspect of the invention relates to methods of inhibiting the activity of a kinase in a biological sample or subject. In certain embodiments, the kinase is CDK. In certain embodiments, the kinase is CDK7. In other embodiments, the kinase is CDK12 or CDK13. In certain embodiments, the activity of the kinase is aberrant 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 of Formula (I) to the kinase.

Also provided in the present invention are methods of inhibiting transcription in a biological sample or subject.

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 a 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 of Formula (I), 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 of Formula (I), 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 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 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 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, ER-positive 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. 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.

Another aspect of the invention relates to methods of screening a library of compounds to identify one or more compounds that are useful in the treatment of a proliferative disease, in inhibiting a kinase (e.g., CDK, such as CDK7, CDK12, CDK13), in inhibiting cell growth, in inducing apoptosis of a cell, and/or in inhibiting transcription. In certain embodiments, the library of compounds is a library of compounds of Formula (I). The methods of screening a library include providing at least two different compounds of Formula (I), or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof, or pharmaceutical compositions thereof; and performing at least one assay using the different compounds of Formula (I), or pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, or prodrugs thereof, or pharmaceutical compositions thereof, to detect one or more characteristics associated with the proliferative disease. In certain embodiments, the methods of screening a library include providing at least two different compounds of Formula (I), or pharmaceutically acceptable salts thereof, or pharmaceutical compositions thereof; and performing at least one assay using the different compounds of Formula (I), or pharmaceutically acceptable salts thereof, or pharmaceutical compositions thereof, to detect one or more characteristics associated with the proliferative disease. The characteristic to be detected may be a desired characteristic associated with the proliferative disease. In certain embodiments, the desired characteristic is anti-proliferation. In certain embodiments, the desired characteristic is anti-cancer. In certain embodiments, the desired characteristic is inhibition of a kinase. In certain embodiments, the desired characteristic is inhibition of CDK. In certain embodiments, the desired characteristic is inhibition of CDK7. In certain embodiments, the desired characteristic is down-regulation of a kinase such as CDK (e.g., CDK7). In certain embodiments, the desired characteristic is induction of apoptosis of a cell. In certain embodiments, the desired characteristic is inhibition of transcription. The characteristic to be detected may also be an undesired characteristic associated with the proliferative disease, cell growth, apoptosis of a cell, and/or transcription. In certain embodiments, the undesired characteristic is induction of cell growth. In certain embodiments, the undesired characteristic is inhibition of apoptosis of a cell. In certain embodiments, the undesired characteristic is induction of transcription.

The different compounds of Formula (I) may be provided from natural sources (see, e.g., Sternberg et al.,Proc. Nat. Acad. Sci. USA,(1995) 92:1609-1613) or generated by synthetic methods such as combinatorial chemistry (see, e.g., Ecker et al.,Bio/Technology,(1995) 13:351-360 and U.S. Pat. No. 5,571,902). In certain embodiments, the different compounds are provided by liquid-phase or solution synthesis. In certain embodiments, the different compounds are provided by solid-phase synthesis. In certain embodiments, the different compounds are provided by a high-throughput, parallel, or combinatorial synthesis. In certain embodiments, the different compounds are provided by a low-throughput synthesis. In certain embodiments, the different compounds are provided by a one-pot synthesis. The different compounds may be provided robotically or manually. In certain embodiments, the step of providing at least two different compounds of the present invention include arraying into at least two vessels at least two different compounds of the present invention wherein the compounds are bound to solid supports, cleaving the compounds from the solid supports, and dissolving the cleaved compounds in a solvent. The solid supports include, but do not limit to, beads (e.g., resin beads and magnetic beads), hollow fibers, solid fibers, plates, dishes, flasks, meshes, screens, and membranes. In certain embodiments, the solid supports are beads. In certain embodiments, one solid support is capable of supporting at least 50 nmol of a compound. In certain embodiments, one solid support is capable of supporting at least 100 nmol of a compound. In certain embodiments, one solid support is capable of supporting at least 200 nmol of a compound. Each vessel may contain one or more support-bound compounds of the present invention. In certain embodiments, each vessel contains one support-bound compounds of the present invention. The solid supports and/or the compounds may be labeled with one or more labeling agents for the identification or detection of the compounds. The vessels may be wells of a microtiter plate. The solvent may be an inorganic solvent, organic solvent, or a mixture thereof. The steps of arraying, cleaving, and dissolving may be performed robotically or manually.

Typically, the methods of screening a library of compounds involve at least one assay. In certain embodiments, the assay is performed to detect one or more characteristics associated with the proliferative disease described herein. The assay may be an immunoassay, such as a sandwich-type assay, competitive binding assay, one-step direct test, two-step test, or blot assay. The step of performing at least one assay may be performed robotically or manually. In certain embodiments, the activity of a kinase is inhibited. In certain embodiments, the activity of CDK is inhibited. In certain embodiments, the activity of CDK7 is inhibited. In certain embodiments, the expression of a kinase such as CDK (e.g., CDK7) is down-regulated. In certain embodiments, apoptosis of a cell is induced. In certain embodiments, transcription is inhibited. In yet another aspect, the present invention provides the compounds of Formula (I), 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 proliferative disease in a subject. In certain embodiments, provided by the invention are the compounds described herein, and pharmaceutically acceptable salts and compositions thereof, for use in the treatment of a proliferative disease in a subject. In certain embodiments, provided by the invention are the compounds described herein, and pharmaceutically acceptable salts and compositions thereof, for use in inhibiting cell growth. In certain embodiments, provided by the invention are the compounds described herein, and pharmaceutically acceptable salts and compositions thereof, for use in inducing apoptosis in a cell. In certain embodiments, provided by the invention are the compounds described herein, and pharmaceutically acceptable salts and compositions thereof, for use in inhibiting transcription.

In another aspect, the present invention discloses a method for the design and/or identification of a potential binding compound for cyclin-dependent kinase 7 (CDK7) comprising the steps of:

(a) generating, on a computer, a three-dimensional representation of CDK7 having the coordinates of the solved X-ray structure, available publically as 1UA2 on PDB.org

(b) identifying amino acid residues forming a binding pocket in the three-dimensional structure of CDK7 from step (a), in proximity to cysteine-312;

(c) generating a three-dimensional model of the active site;

(d) designing and/or selecting a compound that potentially binds to the active site using the three-dimensional model of the active site; and

(e) synthesizing and/or choosing the potential binding compound.

In certain embodiments, the binding pocket comprises the CDK7 active site.

In certain embodiments, the binding pocket comprises the CDK7 amino acids phenylalanine-93, aspartic acid-92, aspartic acid-97, asparagine-142, and leucine-144, methionine-94, lysine-41, and phenylalanine-91.

In another aspect, the present invention discloses a method of identifying a compound that binds cyclin-dependent kinase 7 (CDK7), the method comprising computationally identifying a compound that binds to CDK7 using the atomic coordinates of cysteine-312, phenylalanine-93, aspartic acid-92, aspartic acid-97, asparagine-142, and leucine-144, methionine-94, lysine-41, and phenylalanine-91.

In another aspect, the present invention discloses a method of identifying a binding compound of cyclin-dependent kinase 7 (CDK7), the method comprising:

(a) providing a set of atomic coordinates for CDK7; and

(b) identifying in silico a binding compound that binds to CDK7 using the coordinates of step (a).

In another aspect, the present invention discloses a method of identifying a drug candidate for the treatment of a disease, the method comprising:

a) using the available atomic coordinates to form a three-dimensional structure of CDK7;

b) selecting a test compound having the best fit with the structure of CDK7; and

c) optionally, assaying the ability of the test compound to modulate CDK7 activity, wherein a test compound that modulates CDK7 activity is considered a drug candidate for treating a disease.

EXAMPLES

Synthesis of the Compounds

The compounds provided herein can be prepared from readily available starting materials using the following general methods and procedures. See, e.g., Scheme 1 below. It will be appreciated that where typical or preferred process conditions (i.e., reaction temperatures, times, mole ratios of reactants, solvents, pressures, etc.) are given, other process conditions can also be used unless otherwise stated. Optimum reaction conditions may vary with the particular reactants or solvents used, but such conditions can be determined by those skilled in the art by routine optimization procedures.

Additionally, as will be apparent to those skilled in the art, conventional protecting groups may be necessary to prevent certain functional groups from undergoing undesired reactions. The choice of a suitable protecting group for a particular functional group as well as suitable conditions for protection and deprotection are well known in the art. For example, numerous protecting groups, and their introduction and removal, are described in Greene et al.,Protecting Groups in Organic Synthesis, Second Edition, Wiley, New York, 1991, and references cited therein.

The compounds of the invention, such as those exemplified inFIG. 1, may be synthesized according to the methods described herein or in U.S. Provisional Patent Application, U.S. Ser. No. 61/561,078, filed Nov. 17, 2011, and international PCT Application, PCT/US2012/065618, filed Nov. 16, 2012, published on May 23, 2013 under Publication No. WO 2013/074986, each of which is incorporated herein in its entirety by reference. Detailed herein are exemplary syntheses of the compounds shown inFIG. 1.

To a solution of (1R,3S)-3-(tert-butoxycarbonylamino)cyclohexane-carboxylic acid (8.77 g, 36.1 mmol) in toluene (Tol) was added Et3N (5.53 mL, 39.7 mmol) and DPPA (7.7 mL, 36.1 mmol). The resulting solution was stirred for 2 h at 110° C. and cooled down to 80° C. Benzyl alcohol (4.66 mL, 45.1 mmol) and triethylamine (5.53 mL, 39.7 mmol) were added, and the mixture was stirred for 20 h at 80° C. The cooled solution was diluted with EtOAc (100 mL) and water (50 mL). The layers were separated, and the aqueous layer was extracted with EtOAc (2×50 mL). The combined organic layers were dried over MgSO4, filtered, and concentrated under reduced pressure. The residue was purified by SiO2chromatography (EtOAc in hexanes, 1 to 100% gradient) to afford the title compound (9.89 g, 28.4 mmol, 79% yield) as a white solid.

To a degassed solution of (1S,3R)-3-(benzyloxycarbonylamino) cyclohexylamino 2,2-dimethylpropionate (10 g, 28.4 mmol) in EtOH (473 mL) was added 10% w/w Pd/C (450 mg). The reaction mixture was stirred for 5 h under H2(1 atm.). The reaction mixture was filtered through a pad of Celite® (and washed with EtOH), and the filtrate was concentrated under reduced pressure to afford the title compound (6.08 g, 28.4 mmol, 100% yield) as a white solid.

To a solution of tert-butyl (1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamate (1.88 g, 3.23 mmol) in DCM (16.1 mL) was added a solution of HCl (4 N in dioxane, 12.11 mL, 48.44 mmol). The resulting mixture was stirred for 1.5 h at rt (room temperature) before being concentrated under reduced pressure to afford the title compound (1.72 g, 3.10 mmol, 96% yield) as a light yellow solid, which was used in the next step without further purification.

A solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (2.84 g, 4.05 mmol) and 5 M NaOH (12 mL, 60.8 mmol) in dioxane (40 mL) and water (10 mL) was heated for 3 h at 75° C. The cooled mixture was concentrated under reduced pressure to remove the dioxane. Water (5 mL) was added, and the resulting mixture was sonicated for 5 min. A solid formed and was filtrated and washed with water (3×5 mL). The solid was dried under high vacuum and afforded the title compound (2.27 g, 2.27 mmol, 100% yield) as a white solid.

A solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (2.27 g, 4.05 mmol) DCM (20 mL) was treated with TFA (3.10 mL, 40.53 mmol) and stirred overnight at rt. The mixture was concentrated under reduced pressure, diluted with DCM (1 mL), treated with sat. NaHCO3(2 mL) until basic pH (about 8), and sonicated for 5 min. A solid formed and was filtrated and washed with water (3×5 mL). The solid was dried under high vacuum and afforded the title compound (1.86 g, 4.05 mmol, 100% yield) as a yellow solid.

To a solution of 3-(2, 5-dichloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole (402 mg) in 1, 2-dimethoxylmethanol was added cyclohexane-1,3-diamine (114 mg, 1.0 equiv.) and diisopropylethylamine (129 mg, 1.0 equiv.). The solution was heated for 2 h at 120° C. The cooled solution was diluted with 100 mL of CHCl3/i-PrOH(4:1) and then washed with water. The volatiles were removed, and the crude residue was separated by silica gel chromatography with CH2Cl2/methanol (10:1) to give the title product (300 mg, 62% yield).

To a stirred solution of the product of the previous step (300 mg) in 10 mL of CH2Cl2was added 4-nitrobenzoyl chloride (113 mg, 1.0 equiv.) at room temperature. The reaction mixture was heated to 80° C. for 2 h and then concentrated under reduced pressure. The resulting crude product was purified by flash column chromatography with CH2Cl2/methanol (10:1) to provide the title compound (310 mg, 80% yield).

The nitro compound obtained from the previous step (310 mg) was suspended in 30 mL of ethyl acetate/methanol (5:1) and treated with SnCl2(232 mg, 2.5 equiv.). After stirring for 2 h at 80° C., the reaction mixture was cooled to room temperature and poured into saturated aqueous NaHCO3. The mixture was stirred for 10 min, and the aqueous phase was then extracted with 100 mL of chloroform/2-propanol (4:1). The combined organic layers were washed with water and brine, dried over MgSO4, filtered through a pad of Celite®, and concentrated under reduced pressure. The resulting crude product was purified by flash column chromatography with CH2Cl2/methanol (10:1) to provide the title compound (177 mg, 60% yield).

To the solution of the aniline product obtained from the previous step (60 mg) in 10 mL of acetonitrile was added diisopropylethylamine (13 mg, 1.0 equiv.). The reaction mixture was cooled to 0° C. and then treated with 4-chlorobut-2-enoyl chloride (54 mg, 3.0 equiv.) in CH2Cl2. The reaction mixture was stirred for 10 min at 0° C. and then treated with a solution of dimethylamine in THF. The reaction mixture was then warmed to room temperature, stirred for 1 h, and concentrated under reduced pressure. The resulting crude product was purified by preparative HPLC. The obtained product then was dissolved in 5 mL of 1,4-dioxane and 5 mL of 1 M NaOH. The solution was allowed to stir at room temperature for 2 h, and then 5 mL of 1 M HCl was added. The solution was then diluted with 30 mL of chloroform/2-propanol (4:1), and the organic layer was washed with water. The removal of solvent provides the crude product, which was purified by HPLC to give the final product (23 mg, 40% yield). MS 572 (M+1).

A solution of tricyclo[3.3.1.13,7]decane-1,3-dicarboxylic acid (500 mg, 2.230 mmol) in toluene (9 mL) was treated with Et3N (0.68 mL, 4.91 mmol) and DPPA (0.96 mL, 4.46 mmol) and heated at 110° C. for 1 h. The mixture was cooled down to 80° C., then treated with benzyl alcohol (0.580 mL, 5.574 mmol) and Et3N (0.68 mL, 4.91 mmol). The resulting mixture was heated at 80° C. for 20 h, and after cooling, the mixture was diluted with EtOAc (50 mL) and H2O (50 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×50 mL). The combined organics layers were washed with brine (50 mL), filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 70% gradient) and afforded the title compound (800 mg, 1.97 mmol, 88%) as a clear oil.

A degassed solution of dibenzyl tricyclo[3.3.1.13,7]decane-1,3-diyldicarbamate (773 mg, 0.223 mmol) in EtOH (45 mL) was treated with 10% w/w Pd/C (356 mg). The mixture was stirred 18 h under hydrogen (1 atm) before filtration over a pad of Celite® (EtOH). The filtrate was evaporated under reduced pressure and afforded the title compound (348 mg, 2.10 mmol, 94%) as a colorless oil which was used in the next step without further purification.

A solution of N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)tricyclo[3.3.1.13,7]decane-1,3-diamine (193 mg, 0.360 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (86 mg, 0.360 mmol) in 4:1 DCM/DMF (5 mL) was treated with HBTU (274 mg, 0.720 mmol) and DIPEA (0.19 mL, 1.08 mmol). The resulting mixture was stirred 18 h at rt and diluted with DCM (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the organic layer was extracted with DCM (3×10 mL). The combined organic layers were washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 50% gradient) and afforded the title compound (70 mg, 0.093 mmol, 26%) as a light yellow oil.

A solution of tert-butyl 4-(3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)tricyclo[3.3.1.13,7]decanylcarbamoyl)phenylcarbamate (70 mg, 0.093 mmoL) in DCM (2 mL) was treated with TFA (1.1 mL, 13.94 mmol). The resulting mixture was stirred 1 h at rt before being evaporated to dryness. The residue was dried under high vacuum and afforded the title compound (71 mg, 0.093 mmol, 100%) as a light yellow oil which was used in the next step without further purification.

A solution of 4-amino-N-(3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)tricyclo[3.3.1.13,7]decanyl)benzamide.TFA (47 mg, 0.072 mmol) in dioxane (1.5 mL) was treated with a 5M aqueous solution of NaOH (0.29 mL, 1.44 mmol) and heated 70° C. for 4 h. The cooled mixture was treated with a 1M aqueous solutution of HCl until ph=7, extracted with EtOAc (3×10 mL), dried over MgSO4, filtered and evaporated under reduced pressure. The residue was purified by C18chromatography (H2O/ACN+0.1% HCO2H 5 to 100% gradient) and afforded the title compound (9.5 mg, 0.019 mmol, 26%) as a white solid.

A degassed solution of tert-butyl((+/−)-3,5-diazidocyclohexyloxy)dimethylsilane (300 mg, 1.01 mmol) (prepared following New J. Chem., 2005, 29, 1152-1158) in MeOH (7 mL) was treated with 10% Pd/C (108 mg, 0.10 mmol) and stirred 2 h under hydrogen (1 atm). The resulting mixture was filtered over a pad of Celite® and the filtrate was evaporated to dryness leaving the title compound (227 mg, 0.930 mmol, 92%) as a beige solid which was used in the next step without further purification.

A solution of (+/−)-5-(tert-butyldimethylsilyloxy)-N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine (97 mg, 0.16 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (38 mg, 0.16 mmol) in DCM (1.1 mL) was treated with HBTU (120 mg, 0.32 mmol) and DIPEA (0.48 mmol). The resulting mixture was stirred 18 h at rt and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 50% gradient) and afforded the title compound (93 mg, 0.111 mmol, 71%) as a light yellow oil.

A solution of (+/−)-tert-butyl 4-(−3-(tert-butyldimethylsilyloxy)-5-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (93.0 mg, 0.112 mmol) in THF (4.5 mL) was treated with a 1M solution of TBAF in THF (0.168 mmol) and stirred for 2 days at rt. The resulting mixture was evaporated to dryness and the residue was purified by reverse phase chromatography (C18, H2O/ACN+0.1% HCO2H 10 to 100% gradient) and afforded the title compounds (32 mg, 0.067 mmol, 60%) as a yellow solid.

To a solution of (1R,3S)-3-(tert-butoxycarbonylamino)cyclohexanecarboxylic acid (prepared following Tetrahedron:Asymmetry2010 (21), 864-866) (8.77 g, 36.1 mmol) was added Et3N (5.53 mL, 39.7 mmol) and DPPA (7.7 mL, 36.1 mmol). The resulting solution was stirred 2 h at 110° C. then cooled down to 80° C. Benzyl alcohol (4.66 mL, 45.1 mmol) and triethylamine (5.53 mL, 39.7 mmol) were added and the mixture was stirred 20 h at 80° C. The cooled solution was diluted with EtOAc (100 mL) and H2O (50 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×50 mL). The combined organics were dried (MgSO4), filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 1 to 100% gradient), and afforded the title compound (9.89 g, 28.4 mmol, 79%) as a white solid.

To a degassed solution of (1S,3R)-3-(benzyloxycarbonylamino)cyclohexylamino 2,2-dimethylpropionate (10 g, 28.4 mmol) in EtOH (473 mL) was added 10% w/w Pd/C (450 mg). The reaction mixture was stirred 5 h under H2(1 atm). The reaction mixture was filtered through a pad of Celite® (EtOH), then the filtrate was evaporated to dryness and afforded the title compound (6.08 g, 28.4 mmol, 100%) as a white solid.

To a solution of tert-butyl (1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamate (1.88 g, 3.23 mmol) in DCM (16.1 mL) was added a solution of HCl 4 N in dioxane (12.11 mL, 48.44 mmol). The resulting mixture was stirred 1.5 h at rt before being evaporated to dryness and afforded the title compound (1.72 g, 3.10 mmol, 96%) as a light yellow solid which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl (840 mg, 1.62 mmol), 4-(tert-butoxycarbonylamino)benzoic acid (462 mg, 1.95 mmol), HBTU (924 mg, 2.44 mmol), Et3N (4.87 mmol) in DMF (8.0 mL) was stirred overnight at rt. The mixture was diluted with EtOAc (50 mL), washed with sat NaHCO3(10 mL), H2O (10 mL) and brine (10 mL). The organic layer was dried over MgSO4, filtered and concentrated under reduced pressure and afforded the title compound which was used in the next step without further purification (1.14 g, 1.62 mmol, 100%)

A solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (1.14 g, 1.62 mmol) in DCM (10 mL) was treated with a 4M solution of HCl in dioxane (8.1 mL, 32.4 mmol) and stirred 3 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (948 mg, 1.62 mmol, 100%) as a pale yellow solid which was used in the next step without further purification.

A solution of 4-amino-N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)benzamide.HCl (1.72 g, 3.10 mmol) and NaOH 5M (9.3 mL, 46.5 mmol) in dioxane (20 mL) was stirred 2.5 h at 75° C. The cooled mixture was concentrated, diluted with DCM (100 mL) and H2O (20 mL). The layers were separated and the aqueous layer was extracted with DCM (3×20 mL), dried over MgSO4, filtered, evaporated to dryness and afforded the title compound (1.20 g, 2.60 mmol, 84%) as a white solid which was used in the next step without further purification.

A solution of (1R,3S)-3-(tert-butoxycarbonylamino)cyclohexanecarboxylic acid (prepared following Tetrahedron:Asymmetry2010 (21), 864-866) (1.0 g, 4.11 mmol), K2CO3(474 mg, 3.43 mmol) and MeI (0.21 mL, 3.43 mmol) in DMF (8 mL) was stirred 72 h at rt. The resulting mixture was diluted with H2O (30 mL) and EtOAc (100 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×50 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness leaving the title compound (1.35 g, 4.11 mmol, 100%) as a light orange solid which was used in the next step without further purification.

A solution of (1S,3R)-methyl 3-(tert-butoxycarbonylamino)cyclohexanecarboxylate (1.058 g, 4.111 mmol) in DCM (20.6 mL) was treated with a 4M solution of HCl in dioxane (10.3 mL, 10.3 mmol) and stirred for 16 h. The mixture was concentrated to dryness leaving the title compound (739 mg, 3.81 mmol, 93%) as a light yellow solid which was used in the next step without further purification.

A solution of (1S,3R)-methyl 3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexanecarboxylate (200 mg, 0.38 mmol) in THF was treated with a 0.55M solution of LiOH.H2O in H2O (0.8 mL, 0.4 mmol) and stirred over the weekend at rt. The mixture was diluted with EtOAc (20 mL) and acidified with 1M HCl until the pH reached 2-3. The layers were separated and the aqueous layer was extracted with EtOAc (3×10 mL), dried over MgSO4, filtered and evaporated to dryness leaving the title compound (108 mg, 0.211 mmol, 56%) as a white solid which was used in the next step without further purification.

A solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexanecarboxamido)phenylcarbamate (144 mg, 0.21 mmol) in DCM (1 mL) was treated with TFA (0.16 mL, 2.05 mmol) and stirred 1 h at rt. The mixture was evaporated to dryness and afforded the title compound (142 mg, 0.811 mmol, 97%) as a yellow solid.

A solution of (1S,3R)—N-(4-aminophenyl)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexanecarboxamide.TFA (142 mg, 0.20 mmol) in dioxane (1.4 mL) was treated with a 5M solution of NaOH in H2O (0.81 mL, 4.07 mmol) and stirred at 75° C. for 3 h. The cooled mixture was evaporated to dryness and H2O (2 mL) was added to the residue. The resulting solid was filtered, washed with H2O (2×1 mL), dried under high vacuum leaving the title compound (90 mg, 0.195 mmol, 96%) as a white solid which was used in the next step without further purification.

A solution of (1R,3S)-3-(Benzyloxycarbonylamino)cyclohexylamino 2,2-dimethylpropionate prepared similarly to Example 1 (1.50 g, 4.31 mmol) in DCM (43 mL) was treated with a 4M solution of HCl in dioxane (16 mL, 64.6 mmol) and stirred 2 h at rt. The resulting solution was evaporated to dryness and afforded the title compound (1.23 g, 4.31 mmol, 100%) as a white solid which was used in the next step without further purification.

A degassed solution of benzyl (1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamate (prepared similarly to Example 1) (500 mg, 0.812 mmol), Cs2CO3(794 mg, 2.435 mmol) and potassium cyclopropyltrifluoroborate (360 mg, 2.435 mmol) in 2:1 tol/H2O (15 mL) was treated with a premixed solution of Pd(OAc)2(9 mg, 0.04 mmol) and butyldi-1-adamantylphosphine (29 mg, 0.08 mmol) in degassed tol (2 mL) and heated at 140° C. (microwave) for 2 h. The cooled mixture was diluted with EtOAc (50 mL) and saturated NaHCO3(20 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×20 mL). The combined organic layers were dried over Na2SO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 60% gradient) and afforded the title compound (324 mg, 0.521 mmol, 64%) as a pale yellow solid.

A degassed solution of Benzyl (1S,3R)-3-(5-cyclopropyl-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamate (778 mg, 1.250 mmol) in MeOH (60 mL) was treated with 10% wet Pd/C (150 mg) and stirred under H2(1 atm) for 6 h. The mixture was filtreted on Celite® (MeOH) and the filtrate was evaporated to dryness affording the title compound (610 mg, 1.25 mmol, 75%) as a white foam which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-cyclopropyl-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine (457 mg, 0.937 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (245 mg, 1.031 mmol) in DMF (10 mL) was treated with HBTU (533 mg, 1.406 mmol) and DIPEA (245 uL, 1.406 mmol). The resulting mixture was stirred overnight at rt and diluted with EtOAc (50 mL) and saturated NaHCO3(20 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×30 mL). The combined organic layers were dried over Na2SO4, filtered and evaporated to dryness leaving the title compound (662 mg, 0.936 mmol, 100%) as a yellow solid which was used in the next step without further purification.

A solution of tert-butyl 4-((1S,3R)-3-(5-cyclopropyl-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (663 mg, 0.938 mmol) in dioxane (10 mL) was treated with a 2M solution of NaOH (7 mL, 14 mmol) and heated at 70° C. for 1 h. The cooled mixture was diluted with MeTHF (20 mL) and the layers were separated. The aqueous layer was extracted with MeTHF (3×20 mL) and the combine organic layers were dried over Na2SO4, filtered and evaporated to dryness affording the title compound (531 mg, 0.937 mmol, 99.9%) as a pale yellow solid which was used in the next step without further purification.

A solution of tert-butyl 4-((1S,3R)-3-(5-cyclopropyl-4-(1H-indol-3-yl)pyrimidin-2-ylamino) cyclohexylcarbamoyl)phenylcarbamate (531 mg, 0.938 mmol) in DCM (10 mL) was treated with a 4M solution of HCl in dioxane (3.50 mL, 14.0 mmol) and stirred 2 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (471 mg, 0.938 mmol, 100%) as a white solid which was used in the next step without further purification.

A solution of tert-butyl (1S,3R)-3-(5-chloro-4-(pyridin-3-yl)pyrimidin-2-ylamino) cyclohexylcarbamate (210 mg, 0.520 mmol) in DCM (2.6 mL) was treated with a 4M solution of HCl in dioxane (1.3 mL, 5.130 mmol) and stirred 2 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (177 mg, 0.520 mmol, 100%) as a light yellow solid which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-chloro-4-(pyridin-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl (297 mg, 0.783 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (149 mg, 0.626 mmol) in DMF (5.2 mL) was treated with HBTU (297 mg, 0.783 mmol) and DIPEA (2.087 mmol). The resulting mixture was stirred overnight at rt and diluted with EtOAc (30 mL) and saturated NaHCO3(15 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×30 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 100% gradient) and afforded the title compound (227 mg, 0.434 mmol, 83%) as a light yellow solid.

A solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(pyridin-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (166 mg, 0.317 mmol) in DCM (3.2 mL) was treated with a 4M solution of HCl in dioxane (0.79 mL, 3.17 mmol) and stirred 16 h at rt. The resulting mixture was evaporated to dryness and diluted with EtOAc (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×15 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness affording the title compound (134 mg, 0.317 mmol, 100%) as a white solid which was used in the next step without further purification.

A solution of 4-amino-N-((1S,3R)-3-(5-cyano-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)benzamide (33 mg, 0.0549 mmol) in dioxane (3.8 mL) was treated with a 5M solution of NaOH (0.275 mmol) and heated at 50° C. for 43 h. The cooled mixture was treated with a 1M solution of HCl until a pH of 3 was reached and the mixture was evaporated to dryness. The residue was purified by reverse phase chromatography (C18, H2O/ACN+0.1% HCO2H 80 to 100% gradient) and afforded the title compound (48 mg, 0.106 mmol, 55%) as a white solid after lyophilisation.

A cooled (−78° C.) solution of (+/−)-3,5-diazidocyclohexanol (prepared following New J. Chem., 2005, 29, 1152-1158) in DCM (30 mL) was treated dropwise with Me-DAST (2.74 mmol) and stirred 18 h at this temperature. A saturated solution of NaHCO3(10 mL) was added, the layers were separated and the aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/Et2O 0 to 5% gradient) and afforded the title compound (141 mg, 0.349 mmol, 35%) as a colorless oil.

A degassed solution of (+/−)-1,3-diazido-5-fluorocyclohexane (141 mg, 0.77 mmol) in MeOH (5 mL) was treated with 10% Pd/C (81 mg, 0.08 mmol) and stirred under H2(1 atm) for 5 h. The resulting mixture was filtered over Celite® (MeOH) and the filtrate was evaporated to dryness affording the title compound (77 mg, 0.583 mmol, 76%) as a beige solid which was used in the next step without further purification.

A solution of 3-(2,5-dichloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole (180 mg, 0.45 mmol), (+/−)-5-fluorocyclohexane-1,3-diamine (77 mg, 0.58 mmol) and DIPEA (3.54 mmol) in NMP (3 mL) was heated at 135° C. (microwave) for 25 min. The cooled mixture was then treated with 4-(tert-butoxycarbonylamino)benzoic acid (93 mg, 0.45 mmol), HBTU (338 mg, 0.89 mmol) and DIPEA (0.23 mL, 1.34 mmol). The resulting mixture was stirred overnight at rt and then diluted with EtOAc (30 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layers were washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 100% gradient) and afforded the title compound (198 mg, 0.275 mmol, 62%) as a brownish solid.

A solution of (+/−)-tert-butyl 4-(−3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-5-fluorocyclohexylcarbamoyl)phenylcarbamate (198 mg, 0.28 mmol) in DCM (1.2 mL) was treated with TFA (2.75 mmol) and stirred 2 h at rt. The mixture was evaporated to dryness and afforded the title compound (205 mg, 0.28 mmol, 100%) as a pale yellow solid which was used in the next step without further purification.

A solution of (+/−)-4-amino-N-(3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-5-fluorocyclohexyl)benzamide.TFA (256 mg, 0.36 mmol) in dioxane (2.4 mL) was treated with a 5M solution of NaOH in H2O (1.43 mL, 7.15 mmol) and heated at 75° C. overnight. The cooled mixture was evaporated to dryness and the resulting solid was suspended in H2O (2 mL) and filtered. The solid was washed with H2O (2×2 ml) and dried under high vacuum affording the title compound (96 mg, 0.208 mmol, 58%) as a white solid which was used in the next step without further purification.

Compound 119 was prepared using the methods described herein in Example 15, except that 4-amino-N-((1S,3R,5R)-3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)-5-fluorocyclohexyl)benzamid was replaced with (+/−)-4-amino-N-(3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)-5-fluorocyclohexyl) benzamide.

A solution of N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)bicyclo[3.1.1]heptane-1,5-diamine (202 mg, 0.409 mmol) and 4-(tert-butoxycarbonylamino) benzoic acid (116 mg, 0.491 mmol) in DMF (5.0 mL) was treated with HBTU (233 mg, 0.613 mmol) and DIPEA (0.818 mmol). The resulting mixture was stirred overnight at rt and diluted with EtOAc (30 mL) and saturated NaHCO3(15 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×30 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness affording the title compound (291 mg, 0.408 mmol, 100%) as a brown oil which was used in the next step without further purification.

A solution of tert-butyl 4-(5-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)bicyclo[3.1.1]heptan-1-ylcarbamoyl)phenylcarbamate (291 mg, 0.408 mmol) in DCM (4 mL) was treated with TFA (1.56 mL, 20.4 mmol) and stirred 1 h at rt. The mixture was evaporated to dryness and afforded the title compound (250 mg, 0.408 mmol, 100%) as a yellowish oil.

A solution of 4-amino-N-(5-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)bicyclo[3.1.1]heptan-1-yl)benzamide.TFA (250 mg, 0.408 mmol) in dioxane (10 mL) was treated with a 1M solution of NaOH (6.0 mL, 6.0 mmol) and heated at 75° C. for 1 h. The cooled mixture was diluted with Me-THF (30 mL) and the organic layer was washed with H2O (10 mL), dried over MgSO4, filtered and evaporated to dryness affording the title compound (193 mg, 0.408 mmol, 100%) as a creamy solid which was used in the next step without further purification.

A solution of (+/−)-5,5-difluorocyclohexane-1,3-dicarboxylic acid (prepared as in WO2011005608) (454 mg, 2.18 mmol) in toluene (10 mL) was treated with Et3N (4.80 mmol) and DPPA (4.36 mmol) and heated at 110° C. for 1 h. The solution was cooled down to 80° C. and treated with Et3N (4.80 mmol) and BnOH (4.80 mmol) and stirred overnight at this temperature. The cooled mixture as diluted with EtOAc (50 mL) and H2O (20 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×20 mL). The combined organic layers were dried over MgSO4, filtered, and evaporated to dryness. The residue was triturated with Hex (10 mL) followed by Et2O (5 mL) and the solid was filtered and washed with Hex affording the title compound (694 mg, 1.66 mmol, 76%) as a creamy solid which was used in the next step without further purification.

A degassed solution of (+/−)-dibenzyl-5,5-difluorocyclohexane-1,3-diyldicarbamate (694 mg, 1.66 mmol) in MeOH (100 mL) was treated with 10% Pd/C (100 mg) and stirred 5 h under H2(1 atm). The resulting mixture was filtrated over Celite® (MeOH) and the filtrate was evaporated to dryness affording the title compound (249 mg, 1.66 mmol, 100%) as a colorless oil which was used in the next step without further purification.

A solution of (+/−)-N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)-5,5-difluorocyclohexane-1,3-diamine (192 mg, 0.370 mmol) and 4-(tert-butoxycarbonylamino) benzoic acid (105 mg, 0.444 mmol) in DMF (6.0 mL) was treated with HBTU (211 mg, 0.555 mmol) and DIPEA (0.740 mmol). The resulting mixture was stirred overnight at rt and diluted with EtOAc (30 mL) and saturated NaHCO3(15 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×30 mL). The combined organic layers were dried over MgSO4, filtered, and evaporated to dryness affording the title compound (272 mg, 0.370 mmol, 100%) as a brown oil which was used in the next step without further purification.

A solution of (+/−)-tert-butyl 4-(5-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-3,3-difluorocyclohexylcarbamoyl)phenylcarbamate (272 mg, 0.370 mmol) in DCM (4 mL) was treated with TFA (1.45 mL, 19.0 mmol) and stirred 2 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (235 mg, 0.370 mmol, 100%) as a brownish oil which was used in the next step without further purification.

A solution of (+/−)-4-amino-N-(5-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-3,3-difluorocyclohexyl)benzamide.TFA (235 mg, 0.370 mmol) in dioxane (10 mL) was treated with a 1M solution of NaOH in H2O (6.0 mL, 6.0 mmol) and heated at 75° C. for 2 h. The volatiles were removed by evaporation and the aqueous layer was extracted with MeTHF (30 mL). The organic layer was washed with H2O (10 mL), dried over Na2SO4, filtered and evaporated to dryness affording the title compound (157 mg, 0.316 mmol, 85%) as a yellow solid which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine prepared as in Example 1 (150 mg, 0.289 mmol) in pyr (2.2 mL) was treated with 4-nitrobenzene-1-sulfonyl chloride (64 mg, 0.289 mmol) and heated at 90° C. for 16 h. The cooled mixture was evaporated to dryness and the residue was purified by SiO2chromatography (DCM/EtOAc 0 to 100% gradient) and afforded the title compound (147 mg, 0.220 mmol, 76%) as a yellow foam.

A solution of N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)-4-nitrobenzenesulfonamide (147 mg, 0.223 mmol) in 5:1 EtOAc/MeOH (4 mL) was treated with SnCl2.10H2O (126 mg, 0.557 mmol) and heated at 90° C. in a sealed tube for 4 h. The cooled mixture was diluted with saturated NaHCO3(10 mL), then stirred 20 min at rt and the aqueous layer was extracted with 4:1 CHCl3/IPA (3×30 mL). The combined organic layers were washed with H2O (10 mL), brine (10 mL), dried over MgSO4, filtered through a pad of Celite® (4:1 CHCl3/IPA) and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 80% gradient) and afforded the title compound (109 mg, 0.171 mmol, 77%) as a colorless oil.

A solution of 4-amino-N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)benzenesulfonamide (109 mg, 0.171 mmol) in dioxane (3.4 mL) was treated with a 5M solution of NaOH in H2O (0.855 mmol) and heated at 50° C. overnight. The cooled mixture was treated with a 1M solution of HCl in H2O until the pH reached 7, then the mixture was evaporated to dryness. The residue was purified by SiO2chromatography (DCM/MeOH 0 to 20% gradient) and afforded the title compound (50 mg, 0.101 mmol, 59%) as a light yellow solid.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl prepared as in Example 1 (150 mg, 0.29 mmol) and 2-fluoro-4-nitrobenzoic acid (54 mg, 0.29 mmol) in DCM (1.9 mL) was treated with HBTU (219 mg, 0.58 mmol) and DIPEA (0.870 mmol). The resulting mixture was stirred overnight at rt and diluted with EtOAc (30 mL) and saturated NaHCO3(15 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×30 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 50% gradient) and afforded the title compound (174 mg, 0.268 mmol, 93%) as a beige solid.

A solution of N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)-2-fluoro-4-nitrobenzamide (174 mg, 0.27 mmol) in 5:1 EtOAc/MeOH (5 mL) was treated with SnCl2.10H2O (151 mg, 0.67 mmol) and heated at 80° C. in a sealed tube for 5 h. The cooled mixture was diluted with saturated NaHCO3(10 mL), then stirred 20 min at rt, followed by extraction of the aqueous layer with EtOAc (3×30 mL). The combined organic layers were washed with H2O (10 mL), brine (10 mL), dried over MgSO4, filtered, and evaporated to dryness affording the title compound (147 mg, 0.237 mmol, 88%) as a pale yellow solid which was used in the next step without further modification.

A solution of 4-amino-N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)-2-fluorobenzamide (146 mg, 0.24 mmol) in dioxane (1.6 mL) was treated with a 5M solution of NaOH in H2O (4.72 mmol) and heated at 75° C. overnight. The cooled mixture was diluted with MeTHF (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×15 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/THF 0 to 60% gradient) and afforded the title compound (98 mg, 0.205 mmol, 67%) as a white solid.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl prepared as in Example 1 (150 mg, 0.29 mmol) and 4-amino-3-fluorobenzoic acid (45 mg, 0.29 mmol) in DMF (1.9 mL) was treated with HBTU (219 mg, 0.58 mmol) and DIPEA (0.870 mmol). The resulting mixture was stirred overnight at rt and diluted with MeTHF (30 mL) and saturated NaHCO3(15 mL). The layers were separated and the aqueous layer was extracted with MeTHF (2×30 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 100% gradient) and afforded the title compound (178 mg, 0.287 mmol, 99%) as a pale yellow solid.

A solution of 4-amino-N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)-3-fluorobenzamide (179 mg, 0.29 mmol) in dioxane (1.9 mL) was treated with a 5M solution of NaOH in H2O (1.16 mL, 5.78 mmol) and heated at 75° C. overnight. The cooled mixture was diluted with MeTHF (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×15 mL). The combined organic layers were dried over MgSO4, filtered, and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/THF 0 to 60% gradient) and afforded the title compound (89 mg, 0.185 mmol, 64%) as a white solid.

A suspension of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl (295 mg, 0.57 mmol) in DCE (5.7 mL) was sequentially treated with DIPEA (0.57 mmol), AcOH (0.28 mmol), 4-nitrobenzaldehyde (86 mg, 0.57 mmol) and NaBH(OAc)3(181 mg, 0.85 mmol). The resulting mixture was stirred 48 h at rt before dilution with DCM (30 mL), saturated NaHCO3(5 ML) and brine (5 mL). The layers were separated and the organic layer was dried over MgSO4, filtered and evaporated to dryness affording the title compound (302 mg, 0.489 mmol, 86%) as a yellow solid which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)-N3-(4-nitrobenzyl)cyclohexane-1,3-diamine (302 mg, 0.489 mmol) and DIPEA (0.61 mmol) was treated with Boc2O (134 mg, 0.61 mmol) and stirred overnight at rt. The resulting mixture was diluted with DCM (30 mL) and saturated NaHCO3(5 mL) and brine (5 mL). The layers were separated and the organic layer was dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 25% gradient) and afforded the title compound (343 mg, 0.478 mmol, 98%) as a pale yellow solid.

A solution of tert-butyl (1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl(4-nitrobenzyl)carbamate (212 mg, 0.30 mmol) in 2:1 MeOH/THF (3.0 mL) was sequentially treated with NiCl2.6H2O (35 mg, 0.15 mmol) and NaBH4(45 mg, 1.18 mmol). The resulting mixture was stirred 15 min at rt before being diluted with EtOAc (15 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layers were washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 50% gradient) and afforded the title compound (106 mg, 0.154 mmol, 52%) as a pale yellow solid.

A solution of tert-butyl 4-aminobenzyl((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)carbamate (136 mg, 0.20 mmol) in dioxane (1.3 mL) was treated with a 5M solution of NaOH in H2O (0.40 mL, 1.98 mmol) and heated at 65° C. for 5 h. The cooled mixture was concentrated to dryness and the residue was purified by reverse phase chromatography (C18, H2O/ACN+0.1% HCO2H 0 to 60% gradient) and afforded the title compounds (100 mg, 0.183 mmol, 92%) as a beige solid.

A cooled (−60° C.) solution of 4-amino-N-((1S,3R)-3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)benzamide prepared as in eExample 1 (40 mg, 0.067 mmol) and DIPEA (0.200 mmol) in 1:6 NMP/THF (6.8 mL) was treated with a 54.2 mg/mL solution of (E)-4-bromobut-2-enoyl chloride in DCM (0.067 mmol). The resulting mixture was stirred 1 h at −60° C. before addition of methyl 2-(methylamino)acetate.HCl (18.7 mg, 0.134 mmol). The resulting mixture was warmed to rt and stirred overnight at this temperature before evaporation to dryness. The residue was purified by SiO2chromatography (DCM/MeOH 0 to 20% gradient) and afforded the title compound (25 mg, 0.032 mmol, 49%) as a white solid.

A degassed solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate prepared as in Example 1 (148 mg, 0.211 mmol) in MeOH (10 mL) was treated with 10% Pd/C (25 mg) and stirred overnight under H2(50 psi). The resulting mixture was filtered over Celite® (MeOH) and the filtrate was evaporated to dryness affording an inseparable mixture of the title compound and chlorinated pyrimidine which was used in the next step without purification.

A solution of tert-butyl 4-((1S,3R)-3-(4-(1H-indol-3-yl)pyrimidin-2-ylamino) cyclohexylcarbamoyl)phenylcarbamate (100 mg, as a mixture with chlorinated pyrimidine from previous step) in DCM (2.0 mL) was treated with a 4M solution of HCl in dioxane (750 mL, 3.0 mmol) and stirred 4 h at rt. The mixture was evaporated to dryness and the residue was purified by reverse phase chromatography (C18, H2O/ACN+0.1% HCO2H 5 to 60% gradient) and afforded the title compound (12.5 mg, 0.0081 mmol, 25%) as a white solid.

A solution of methyl 2-fluoro-4-nitrobenzoate (200 mg, 1.00 mmol) and morpholine (8.04 mmol) in NMP (2.1 mL) was heated at 140° C. (microwave) for 35 min. The cooled mixture was diluted with EtOAc (20 mL) and washed with H2O (10 mL) and brine (10 ml). The combined aqueous layers were acidified to pH=2 with a 1M solution of HCl in H2O and extracted with DCM (3×20 mL). The combined organic layers were dried by passing through a phase cartridge separator and evaporated to dryness affording the title compound as a mixture with morpholine which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine prepared as in Example 1 (50 mg, 0.104 mmol) and 2-morpholino-4-nitrobenzoic acid (29 mg, 0.114 mmol) in DMF (5.0 mL) was treated with Et3N (0.311 mmol) and HBTU (59 mg, 0.156 mmol). The resulting mixture was stirred overnight at rt, diluted with EtOAc (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the organic layer was washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 70% gradient) and afforded the title compound (48 mg, 0.067 mmol, 65%) as a pale yellow solid.

A cooled (0° C.) solution of N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)-2-morpholino-4-nitrobenzamide (76 mg, 0.106 mmol) in 2:1 MeOH/THF (1 mL) was sequentially treated with NiCl2.6H2O (12.6 mg, 0.053 mmol) and NaBH4(16.1 mg, 0.425 mmol). The resulting black mixture was stirred 15 min at rt before dilution with EtOAc (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layers were washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 70% gradient) and afforded the title compound (26 mg, 0.038 mmol, 36%) as a pale yellow solid.

A solution of 4-amino-N-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)-2-morpholinobenzamide (24 mg, 0.035 mmol) in dioxane (0.35 mL) was treated with a 2M solution of NaOH in H2O (0.525 mmol) and stirred overnight at rt and 2 h at 60° C. The cooled mixture was concentrated to remove volatiles and the resulting was diluted with MeTHF (15 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×10 mL). The combined organic layers were dried over Na2SO4, filtered and evaporated to dryness affording the title compound (19 mg, 0.0248 mmol, 71%) as a pale yellow solid which was used in the next step without further purification.

A solution of (trans)-N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,4-diamine (125 mg, 0.260 mmol) and 3-(tert-butoxycarbonylamino)benzoic acid (69 mg, 0.290 mmol) in DMF (2.5 mL) was treated with DIPEA (0.390 mmol) and HBTU (148 mg, 0.390 mmol). The resulting mixture was stirred overnight at rt, diluted with EtOAc (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×20 mL). The combined organic layers were washed with brine (10 mL), dried over Na2SO4, filtered and evaporated to dryness affording the title compound (182 mg, 0.290 mmol, 100%) as a yellow solid which was used in the next step without further purification.

A solution of tert-butyl 3-(trans-4-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (182 mg, 0.290 mmol) in dioxane (3.0 mL) was treated with a 2M solution of NaOH in H2O (2.5 mL, 5.00 mmol) and stirred at 70° C. for 1 h. The cooled mixture was evaporated to dryness and the residue was dissolved in MeTHF (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×10 mL). The combined organic layers were dried over Na2SO4, filtered and evaporated to dryness affording the title compound (163 mg, 0.290 mmol, 100%) as a yellow solid which was used in the next step without further purification.

A solution of tert-butyl 3-(trans-4-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (163 mg, 0.290 mmol) in DCM (3.0 mL) was treated with a 4M solution of HCl in dioxane (1.10 mL, 4.54 mmol) and stirred 30 min at rt. The resulting mixture was evaporated to dryness and afforded the title compound (144 mg, 0.290 mmol, 100%) as a yellow solid which was used in the next step without further purification.

A cooled (0° C.) solution of (1S,3R)-3-(tert-butoxycarbonylamino)cyclohexanecarboxylic acid (prepared following Tetrahedron:Asymmetry2010 (21), 864-866) (1.24 g, 5.09 mmol) in THF (34 mL) was treated with a 2M solution of BH3.Me2S in THF (3.7 mL, 7.38 mmol) and stirred overnight at rt. The resulting solution was treated with a 1M solution of HCl in H2O (20 mL) and extracted with EtOAc (3×20 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness affording the title compound (1.17 g, 5.09 mmol, 100%) as a colorless oil which was used in the next step without further purification.

A cooled (0° C.) solution of tert-butyl (1R,3S)-3-(hydroxymethyl)cyclohexylcarbamate (200 mg, 0.87 mmol) in Tol (6 mL) was sequentially treated with imidazole (148 mg, 2.18 mmol), PPh3(572 mg, 2.18 mmol) and I2(288 mg, 1.13 mmol). The resulting mixture was stirred overnight at rt before being diluted with a saturated solution of NaHCO3(10 mL), a 5% solution of Na2S2O3(10 mL) and DCM (30 mL). The layers were separated and the aqueous layer was extracted with DCM (2×30 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was dissolved in Tol (10 mL), treated with DBU (1.74 mmol) and heated overnight at 80° C. The cooled mixture was diluted with a saturated solution of NH4Cl (10 mL) and EtOAc (20 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×20 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 5 to 30% gradient) and afforded the title compound (72 mg, 0.341 mmol, 39%) as a white solid.

O3was bubbled into a cooled (−78° C.) solution of (R)-tert-butyl 3-methylenecyclohexylcarbamate (424 mg, 2.01 mmol) in DCM (40 mL) for 30 min, at which point PPh3(917 mg, 6.02 mmol) was added. The resulting mixture was warmed to rt and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 60% gradient) and afforded the title compound (415 mg, 1.95 mmol, 97%) as a white solid.

A solution of (R)-1-(4-bromophenyl)-2,2,2-trifluoroethanamine.HCl (prepared followingOrg. Lett.2005, 7, 2, 355-358) (501 mg, 1.72 mmol) in DCE (16.4 mL) was sequentially treated with DIPEA (1.81 mmol), AcOH (0.82 mmol), (R)-tert-butyl 3-oxocyclohexylcarbamate (350 mg, 1.64 mmol) and NaBH(OAc)3(522 mg, 2.46 mmol). The resulting mixture was stirred 16 at rt and then diluted with DCM (20 mL) and a saturated solution of NaHCO3(10 mL). The layers were separated and the organic layer was washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 5 to 50% gradient) and afforded the title compound (356 mg, 0.789 mmol, 48%) as a white solid together with the trans isomer (0.123 mg, 0.273, 17%) as white solid.

A solution of tert-butyl (1R,3S)-3-((R)-1-(4-bromophenyl)-2,2,2-trifluoroethylamino)cyclohexylcarbamate (144 mg, 0.32 mmol) in DCM (0.65 mL) was treated with a 4M solution of HCl in dioxane (1.60 mL, 6.38 mmol) and stirred 1 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (121 mg, 0.312 mmol, 98%) as a beige solid which was used in the next step without further purification.

A degassed solution of (1S,3R)—N1-((R)-1-(4-bromophenyl)-2,2,2-trifluoroethyl)-N3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine (141 mg, 0.196 mmol), t-butylcarbamate (28 mg, 0.24 mmol), Pd(OAc)2(1.3 mg, 0.01 mmol), Xphos (8.4 mg, 0.02 mmol) and Cs2CO3(90 mg, 0.27 mmol) in dioxane (2.0 mL) was heated at 90° C. for 12 h. The cooled mixture was filtered over Celite® (EtOAc) and the filtrate was evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 100% gradient) and afforded the title compound (191 mg as a mixture with an unknown impurity) as a pale yellow foam.

A solution of tert-butyl 4-((R)-1-((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylamino)-2,2,2-trifluoroethyl)phenylcarbamate (191 mg as a mixture with unknown impurity) in DCM (0.4 mL) was treated with a 4M solution of HCl in dioxane (2.94 mmol) and stirred 30 min at rt. The resulting mixture was evaporated to dryness, suspended in dioxane (1.3 mL) and treated with a 5M solution of NaOH in H2O (2.94 mmol). The resulting mixture was stirred 5 h at rt and diluted with MeTHF (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (2×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/THF 0 to 50% gradient) and afforded the title compound (59 mg, 0.115 mmol, 58% over 2 steps) as a pale yellow solid.

A degassed solution of 2,4-dichloro-5-fluoropyrimidine (500 mg, 2.99 mmol), 1-(phenylsulfonyl)-1H-indol-3-ylboronic acid (947 mg g, 3.14 mmol), Cs2CO3(1.95 g, 5.99 mmol) and Pd(PPh3)4(346 mg, 0.30 mmol) in 2:1 dioxane/H2O (30 ml) was heated overnight at 100° C. The cooled mixture was diluted with EtOAc (50 mL) and saturated NaHCO3(20 ml). The layers were separated and the aqueous layer was extracted with EtOAc (3×20 mL). The combined organic layers were washed with brine (20 mL), dried over MgSO4and evaporated to dryness. The residue was purified by SiO2chromatography (DCM) and afforded the title compound (599 mg, 1.55 mmol, 52%) as a pale orange oil.

A solution of tert-butyl (1S,3R)-3-(5-fluoro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamate (76 mg, 0.134 mmol) in dioxane (0.3 mL) was treated with a 4M solution of HCl in dioxane (1.34 mmol) and stirred 1 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (64 mg, 0.127 mmol, 95%) as a white solid which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-fluoro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl (64 mg, 0.127 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (27 mg, 0.130 mmol) in DMF (0.85 mL) was treated with DIPEA (0.51 mmol) and HBTU (97 mg, 0.256 mmol). The resulting mixture was stirred overnight at rt, diluted with EtOAc (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (2×20 mL). The combined organic layers were washed with brine (10 mL), dried over Na2SO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 100% gradient) and afforded the title compound (87 mg, 0.127 mmol, 100%) as a pale yellow solid.

A solution of tert-butyl 4-((1S,3R)-3-(5-fluoro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (87 mg, 0.127 mmol) in dioxane (0.85 ml) was treated with a 5M solution of NaOH in H2O (1.91 mmol) and heated at 65° C. for 5 h. The cooled mixture was evaporated to dryness and the residue was purified by SiO2chromatography (DCM/THF 0 to 50% gradient) and afforded the title compound (59 mg, 0.108 mmol, 85%) as a pale yellow solid.

A solution of tert-butyl 4-((1S,3R)-3-(5-fluoro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (59 mg, 0.108 mmol) in dioxane was treated with a 4M solution of HCl in dioxane (1.62 mmol) and stirred overnight at rt. The resulting mixture was evaporated to dryness and afforded the title compound (52 mg, 0.108 mmol, 100%) as a white solid which was used in the next step without further purification.

A solution of tert-butyl (1S,3R)-3-(5-chloro-4-(pyrazolo[1,5-a]pyridin-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamate (280 mg, 0.632 mmol) in DCM (4.1 mL) was treated with a 4M solution of HCl in dioxane (2.04 mL, 8.165 mmol) and stirred 5 h at rt. The mixture was diluted with EtOAc (5 mL) and H2O (5 mL) and the formed precipitate was filtrated and washed with EtOAc, affording the title compound (142 mg, 0.415 mmol, 66%) as a white solid which was used in the next step without further purification.

A solution of (1R,3S)—N1-(5-chloro-4-(pyrazolo[1,5-a]pyridin-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine.HCl (140 mg, 0.408 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (116 mg, 0.49 mmol) in DMF (4.1 mL) was treated with DIPEA (1.63 mmol) and HBTU (232 mg, 0.613 mmol). The resulting mixture was stirred overnight at rt, diluted with EtOAc (30 mL) and saturated NaHCO3(10 mL). The layers were separated and the organic layer was washed with brine (10 mL), dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 100% gradient) and afforded the title compound (229 mg, 0.408 mmol, 100%) as an orange oil.

A solution of tert-butyl 4-((1S,3R)-3-(5-chloro-4-(pyrazolo[1,5-a]pyridin-3-yl)pyrimidin-2-ylamino)cyclohexylcarbamoyl)phenylcarbamate (229 mg, 0.408 mmol) in DCM (1.0 mL) was treated with a 4M solution of HCl in dioxane (2.0 mL, 8.0 mmol) and stirred 1 h at rt. The resulting mixture was evaporated to dryness and the residue was triturated in EtOAc. The solid was filtered and washed with EtOAc affording the title compound (28 mg, 0.061 mmol, 15%) as a beige solid which was used in the next step without further purification.

To a mixture of 1H-indazole (5 g, 42.32 mmol) and NaOH (3.4 g, 84.6 mmol) in DMF (50 mL) was added I2(16.1 g, 63.4 mmol) in one portion at 25° C. and the mixture was stirred for 6 h. The mixture was concentrated, diluted with water (150 mL,) extracted with EA (100 mL×3), and the combined organic phase was washed with saturated brine (200 mL×2), dried with anhydrous Na2SO4and concentrated under vacuum. The residue was purified by silica gel chromatography to afford the title compound (8 g, 77.5%) as a white solid.

To a mixture of 3-iodo-1H-indazole (8 g, 32.7 mmol) and Boc2O (8.6 g, 39.2 mmol) in MeCN (100 mL) was added NaOH (2.0 g, 49.1 mmol) at 25° C. and the mixture was stirred for 12 h. The mixture was poured into water (150 mL), extracted with EA (50 mL×2), and the combined organic phase was washed with saturated brine (200 mL×2), dried with anhydrous Na2SO4and concentrated under vacuum. The residue was purified by silica gel chromatography to afford the title compound (11.2 g, 97.5%) as a white solid. MS (m/z): 477.2 [M+1]+.

A mixture of tert-butyl 3-iodoindazole-1-carboxylate (4.0 g, 11.6 mmol), Sn2Me6(5.7 g, 17.4 mmol) and Pd(PPh3)4(1.3 g, 1.2 mmol) in toluene (20 mL) was heated to 110° C. and stirred for 12 h. The mixture was concentrated under vacuum to give the title compound (4.43 g, crude), which was used directly in the next step. MS (m/z): 327.0 [M+1]+.

A mixture of tert-butyl 3-trimethylstannylindazole-1-carboxylate (5.0 g, 13.1 mmol), 2,4,5-trichloropyrimidine (2.4 g, 13.1 mmol) and Pd(PPh3)4(1.5 g, 1.3 mmol) in toluene (100 mL) was heated to 110° C. and stirred for 12 h. The mixture was concentrated under vacuum and the residue was purified by silica gel chromatography to afford the title compound (1.5 g, 31.3% for two steps).

A mixture of tert-butyl 3-(2,5-dichloropyrimidin-4-yl)indazole-1-carboxylate (1 g, 2.74 mmol), benzyl N-[(1S,3R)-3-aminocyclohexyl]carbamate (0.816 g, 3.3 mmol), and DIPEA (2.1 g, 16.2 mmol) in NMP (20 mL) was stirred at 135° C. for 45 min by micromave. The mixture was poured into water (20 mL), extracted with ethyl acetate (20 mL×2), and the combined organic phase was washed with saturated brine (20 mL×3), dried with anhydrous Na2SO4, and concentrated under vacuum. The residue was purified by prep-HPLC to afford the title compound (0.75 g, 57.3%) as a yellow solid. MS (m/z): 477.2 [M+1]+.

To a mixture of benzyl N-[(1S,3R)-3-[[5-chloro-4-(1H-indazol-3-yl)pyrimidin-2-yl]amino]cyclohexyl]carbamate (0.7 g, 1.5 mmol) in DCM (10 mL) was added TMSI (1.47 g, 7.3 mmol) at 25° C. and the mixture was stirred for 12 h. The mixture was poured into water (20 mL), extracted with ethyl acetate (10 mL×2), and the aqueous phase was concentrated under vacuum to afford the title compound (0.32 g, crude).

To a mixture of (1R,3S)—N1-[5-chloro-4-(1H-indazol-3-yl)pyrimidin-2-yl]cyclohexane-1,3-diamine (300 mg, 0.9 mmol) and 4-(tert-butoxycarbonylamino)benzoic acid (249.1 mg, 1.1 mmol) in DMF (10 mL) was added HATU (499.1 mg, 1.3 mmol) and DIPEA (226.2 mg, 1.8 mmol) at 30° C. and the mixture was stirred for 12 h. The mixture was poured into water (50 mL), extracted with EA (20 mL×2), and the combined organic phase was washed with saturated brine (50 mL×2), dried with anhydrous Na2SO4, and concentrated under vacuum. The residue was purified by silica gel chromatography to afford the title compound (200 mg, 25.8% for two steps). MS (m/z): 562.1 [M+1]+.

To a mixture of 2-methyl-1H-indole (20 g, 152.47 mmol) and KOH (21.39 g, 381.18 mmol) in DMF (200 mL) was added I2(38.7 g, 152.47 mmol) at 30° C. and the mixture was stirred for 12 h. The mixture was poured into water, extracted with EA, and the organic layer was dried over Na2SO4and concentrated. The residue was purified by column (PE: EA=15:1) to afford the title compound (25 g, 63.8%).

To a solution of 3-iodo-2-methyl-1H-indole (25 g, 97.25 mmol) in DMF (320 mL) was added NaH (4.67 g, 116.70 mmol) at 0° C. and the mixture was stirred at 30° C. for 1 h. Then benzenesulfonyl chloride (18.04 g, 102.11 mmol) was added and the mixture was stirred at 30° C. for 8 h. The mixture was poured into water, extracted with EA, and the organic layer was dried over Na2SO4and concentrated. The residue was purified by column (PE: EA=20:1) to afford the title compound (28 g, 72.8%).

To a solution of 3-iodo-2-methyl-1-(phenylsulfonyl)-1H-indole (20 g, 50.35 mmol) in THF (400 mL) was added i-PrMgCl.LiCl (14.63 g, 100.70 mmol) at −78° C. and the mixture was stirred under N2for 1 h. Then 2,5-dichloropyrimidine (15 g, 100.70 mmol) was added at −78° C. and the reaction was stirred at 30° C. for 3 h, at which point H2O (115.80 mmol) in THF (10 mL) was added at 0° C. Finally DDQ (22.86 g, 100.70 mmol) was added and the final mixture was stirred at 30° C. for 6 h. The mixture concentrated, diluted with water, extracted with EA, and the organic layer was concentrated. The residue was purified by column (PE:EA=10:1) to afford the title compound (6 g, 28.5%).

A mixture of benzyl ((1S,3R)-3-((5-chloro-4-(2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)amino)cyclohexyl)carbamate (5.0 g, 7.93 mmol) and Pd/C (0.80 g) in MeOH (100 mL) was stirred at 25° C. for 24 h under H2(40 psi). The mixture was filtered and the filtrate was concentrated to afford the title compound (2.7 g, crude).

To a solution of tert-butyl (4-(((1S,3R)-3-((5-chloro-4-(2-methyl-1H-indol-3-yl) pyrimidin-2-yl)amino)cyclohexyl)carbamoyl)phenyl)carbamate (700 mg, 1.22 mmol) in EA (5 mL) was added into a solution of HCl/EA (25 mL) and the mixture was stirred at 30° C. for 12 h. The mixture was concentrated to afford the title compound (500 mg, 80.1%).

To a solution of isobenzofuran-1,3-dione (25.0 g, 168 mmol) in DMF (160 mL) and toluene (160 mL) at 25° C. was added (1R,4R)-4-aminocyclohexanol (19.4 g, 168 mmol). The reaction was heated to 130° C. stirred at for 12 h. The reaction was diluted with H2O (200 mL), the mixture was filtered, and the filter cake was dried and evaporated under pressure to give the title compound (30.0 g, 72.5%).

To a solution of (3-nitrophenyl)methanol (12.0 g, 78.4 mmol) and DBU (2.4 g, 15.7 mmol) in DCM (200 mL) was added 3,3,3-trichloropropanenitrile (18.6 g, 117.5 mmol) at 0° C. The mixture was stirred at 25° C. for 12 h, after which the reaction was concentrated in vacuo and purified by silica gel column chromatography (PE/EA=20:1) to afford the title compound (20.0 g, 85.8%).

To a solution of 2-((1R,4R)-4-hydroxycyclohexyl)isoindoline-1,3-dione (20.0 g, 81.5 mmol) and 3-nitrobenzyl 2,2,2-trichloroacetimidate (36.4 g, 122.3 mmol) in DCM (200 mL) was added CF3SO3H (271.8 mg, 1.2 mmol) at 25° C. After 2 h, the reaction was quenched with NaHCO3solution (100 mL) and the aqueous was exacted with DCM (50 mL×4). The organic phase was dried over Na2SO4, concentrated and purified by silica gel column chromatography (PE/EA=10:1) to afford the title compound (8.0 g, 25.8%).

2-((1R,4R)-4-((3-nitrobenzyl)oxy)cyclohexyl)isoindoline-1,3-dione (8.0 g, 21 mmol) was dissolved in EtOH (100 mL), and then N2H4(1.35 g, 42 mmol) was added. The resulting mixture was heated at 80° C. for 12 h. The mixture then was filtered, and the filtrate was concentrated and purified by prep-HPLC (TFA condition) to give the title compound (0.3 g, 5.7%). MS (m/z): 251.3 [M+1]+.

To a solution of 3-(2,5-dichloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole (250 mg, 0.62 mmol) and (1R,4R)-4-((3-nitrobenzyl)oxy)cyclohexanamine (154.8 mg, 0.62 mmol) in EtOH (10 mL) and DMF (10 mL) was added DIPEA (0.4 mg, 3.09 mmol). The reaction was stirred at 25° C. for 10 min, then heated to 120° C. and stirred for 12 h. The reaction was concentrated, diluted with H2O (20 mL), and extracted with DCM (20 mL×3). The organic was concentrated, and the residue was purified by column (PE/EA=5:1) to afford the title compound (180 mg, 47.1%).

To a solution of 5-chloro-N-((1R,4R)-4-((3-nitrobenzyl)oxy)cyclohexyl)-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-amine (200 mg, 0.32 mmol) in EtOH (5 mL) and H2O (5 mL) were added Fe (90.4 mg, 1.60 mmol) and NH4Cl (17.3 mg, 0.32 mmol). The reaction was heated to 60° C. and stirred for 12 h. The mixture was filtered and the filtrate concentrated to give the title compound (150 mg, crude) as a yellow solid. MS (m/z): 588 [M+1]+.

To a solution of N-((1R,4R)-4-((3-aminobenzyl)oxy)cyclohexyl)-5-chloro-4-(1-(phenyl sulfonyl)-1H-indol-3-yl)pyrimidin-2-amine (150 mg, 0.25 mmol) in MeOH (5 mL) was added K2CO3(105.7 mg, 0.76 mmol). The mixture was stirred at 25° C. for 12 h. The reaction was concentrated, then the residue was diluted with H2O (20 mL), extrated with DCM (20 mL×3), and the organic was dried, filtered, and concentrated to give the title compound (120 mg, crude) as a light yellow solid. MS (m/z): 448 [M+1]+.

A mixture of (1R,3S)—N1-(5-chloro-4-(1H-indazol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine (500 mg, 1.3 mmol) and 4-nitrobenzaldehyde (294 mg, 1.9 mmol) in DMF (10 mL) and AcOH (0.5 mL) was stirred at 30° C. for 12 h. Then NaBH3CN (163 mg, 2.6 mmol) was added, and the mixture was stirred at 30° C. for 2 h. The mixture was poured into water (100 mL), extracted with EA (50 mL×3), and the organic layer was concentrated. The residue was directly purified by prep-HPLC (TFA conditions) to afford the title compound (200 mg, 31.7%). MS (m/z): 478.2 [M+1]+.

To a mixture of tert-butyl ((1S,3R)-3-((5-chloro-4-(1H-indazol-3-yl)pyrimidin-2-yl) amino)cyclohexyl)(4-nitrobenzyl)carbamate (400 mg, 0.7 mmol) and NH4Cl (74 mg, 1.4 mmol) in EtOH (10 mL) and H2O (1 mL) was added Fe (193 mg, 3.5 mmol) at 25° C. The mixture was heated to 80° C. and stirred for 12 h. The mixture was poured into water (20 mL), extracted with EA (10 mL×2), and the organic layer was concentrated in vacuum and purified by flash column to give the title compound (230 mg, 60.6%) as a brown solid.

To a mixture of tert-butyl4-aminobenzyl((1S,3R)-3-((5-chloro-4-(1H-indazol-3-yl) pyrimidin-2-yl)amino)cyclohexyl)carbamate (200 mg, 0.36 mmol) and DIPEA (47.2 g, 0.36 mmol) in DCM (10 mL) was added acryloyl chloride (29.7 mg, 0.32 mmol) at 30° C. under N2and the mixture was stirred for 2 h. The mixture was poured into water (20 mL), extracted with DCM (10 mL×2), and the organic layer was concentrated to give the title compound (200 mg, crude), which was used directly in next step.

A solution of (1S,3R)-3-(tert-butoxycarbonylamino)-1-methylcyclohexanecarboxylic acid prepared as in WO2010/148197 (100 mg, 0.389 mmol) in toluene (1.5 mL) was treated with Et3N (0.43 mmol) and DPPA (0.39 mmol) and heated at 110° C. for 1 h. The mixture was cooled down to 80° C., treated with benzyl alcohol (0.41 mmol) and Et3N (0.43 mmol). The resulting mixture was heated at 80° C. for 20 h. The cooled mixture was then diluted with EtOAc (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with EtOAc (3×10 mL). The combined organics layers were washed with brine (10 mL), filtered and evaporated to dryness. The residue was purified by SiO2chromatography (Hex/EtOAc 0 to 50% gradient) and afforded the title compound (59 mg, 0.180 mmol, 46%) as a colorless oil.

A solution of tert-butyl (1R,3S)-3-(Benzyloxycarbonylamino)-3-methylcyclohexylcarbamate (45 mg, 0.124 mmol) in DCM (0.6 mL) was treated with a 4M solution of HCl in dioxane (2.48 mmol) and stirred 1 h at rt. The mixture was evaporated to dryness and afforded the title compound (37 mg, 0.124 mmol, 100%) as a white solid that was used in the next step without further purification.

A cooled (−78° C.) solution of (+/−)-benzyl-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-1-methylcyclohexylcarbamate (51 mg, 0.081 mmol) in DCM (0.32 mL) was treated with a 1M solution of BBr3in DCM (0.097 mmol) and was slowly warmed to rt. MeOH (1 ML) was added to the mixture was the resulting solution was stirred 1 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (40 mg, 0.081 mmol, 100%) as a yellow solid which was used in the next step without further purification.

A solution of (+/−)-benzyl-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-1-methylcyclohexylcarbamate (40 mg, 0.81 mmol) and 4-(tert-butoxycarbonylamino) benzoic acid (23 mg, 0.97 mmol) in DMF (0.4 mL) was treated with HBTU (46 mg, 0.121 mmol) and Et3N (0.242 mmol). The resulting mixture was stirred overnight at rt and diluted with EtOAc (10 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with AtOAc (2×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/EtOAc 0 to 100% gradient) and afforded the title compound (48 mg, 0.067 mmol, 83%) as a beige solid.

A solution of (+/−)-tert-butyl 4-(3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)-1-methylcyclohexylcarbamoyl)phenylcarbamate (45 mg, 0.063 mmol) in dioxane (0.6 mL) was treated with a 2M solution of NaOH in H2O (0.944 mmol) and heated at 60° C. for 1 h. The cooled mixture was diluted with MeTHF (20 mL) and H2O (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness affording the title compound (36 mg, 0.063 mmol, 100%) as a yellow solid which was used in the next step without further purification.

A solution of (+/−)-tert-butyl 4-(3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)-1-methylcyclohexylcarbamoyl)phenylcarbamate (36 mg, 0.063 mmol) in DCM was treated with a 4M solution of HCl in dioxane (0.939 mmol) and stirred overnight at rt. The resulting mixture was diluted with MeTHF (10 mL) and saturated NaHCO3(5 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness affording the title compound (30 mg, 0.063 mmol, 100%) as a pale yellow solid which was used in the next step without further purification.

A cooled (−60° C.) solution of (+/−)-4-amino-N-(3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)-1-methylcyclohexyl)benzamide (29 mg, 0.0611 mmol) and DIPEA (0.183 mmol) in THF (0.4 mL) was treated with a 54.2 mg/mL solution of (E)-4-bromobut-2-enoyl chloride in DCM (0.055 mmol). The resulting mixture was stirred 2 h at −60° C. before addition of a 2M solution of dimethylamine in THF (0.244 mmol). The resulting mixture was warmed to rt and stirred 45 min at this temperature before being evaporated to dryness. The residue was purified by reverse phase chromatography (C18, H2O/ACN+0.1% HCO2H 0 to 60% gradient) and afforded the title compound (15 mg, 0.026 mmol, 41%) as a white solid after lyophilisation.

A solution of (1R,3S)—N1-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-yl)cyclohexane-1,3-diamine prepared as in Example 1 (180 mg, 0.373 mmol), tert-butyl 4-formylphenylcarbamate (124 mg, 0.822 mmol) and AcOH (0.221 mmol) in DCM (3.7 mL) was treated with NaBH(OAc)3(198 mg, 0.934 mmol) and stirred overnight at rt. The resulting mixture was diluted with DCM (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with DCM (2×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/MeOH 0 to 12% gradient) and afforded the title compound (178 mg, 0.259 mmol, 69%) as a white foam.

A solution of tert-butyl 4-(((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexylamino)methyl)phenylcarbamate (178 mg, 0.259 mmol), paraformaldehyde (14 mg, 0.466 mmol) and AcOH (0.259 mmol) in DCM (4.3 mL) was treated with NaBH(OAc)3(132 mg, 0.622 mmol) and stirred 40 h at rt. The resulting mixture was diluted with DCM (20 mL) and saturated NaHCO3(10 mL). The layers were separated and the aqueous layer was extracted with DCM (2×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/MeOH 0 to 12% gradient) and afforded the title compound (96 mg, 0.137 mmol, 53%) as a white foam.

A solution of tert-butyl 4-((((1S,3R)-3-(5-chloro-4-(1-(phenylsulfonyl)-1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)(methyl)amino)methyl)phenylcarbamate (96 mg, 0.137 mmol) in dioxane (2.7 mL) was treated with a 5M solution of NaOH in H2O (0.55 mL, 2.74 mmol) and heated at 65° C. for 2 h. The cooled mixture was diluted with H2O (5 mL) and MeTHF (10 mL). The layers were separated and the aqueous layer was extracted with MeTHF (3×10 mL). The combined organic layers were dried over MgSO4, filtered and evaporated to dryness. The residue was purified by SiO2chromatography (DCM/MeOH 0 to 12% gradient) and afforded the title compound (57 mg, 0.102 mmol, 74%) as a pale yellow foam.

A solution of tert-butyl 4-((((1S,3R)-3-(5-chloro-4-(1H-indol-3-yl)pyrimidin-2-ylamino)cyclohexyl)(methyl)amino)methyl)phenylcarbamate (57 mg, 0.101 mmol) in DCM (2.0 mL) was treated with a 4M solution of HCl in dioxane (1.0 mL, 4.06 mmol) and stirred 18 h at rt. The resulting mixture was evaporated to dryness and afforded the title compound (50 mg, 0.101 mmol, 100%) as a bright yellow solid which was used in the next step without further purification.

Synthesis of Other Exemplary Compounds of the Invention

Other exemplary compounds of the invention were synthesized using modification to or one or more of the foregoing examples. In Table 1B, the specific examples and modifications are indicated for each compound, as well as the1H NMR (δ(ppm)) and MS (m/z [M+1]+) characterization data. Compound numbers (“Compound No.”) correspond to the compound numbers (“Compound No.”) shown inFIG. 1.

Inhibition of Kinase Activity

Compounds of the invention were assayed for activity against a variety of different kinases at Life Technologies™ (Grand Island, N.Y.) using their commercially available Adapta® (for CDK7, CDK9/cyclin T1, and IRAK1 kinases), Z′-Lyte® (for CDK1, CDK2, CDK5/p25, CDK5/p35, JNK1 and JNK2 kinases), and LanthaScreen Eu® (for CDK8, CDK9/cyclin K and MLK3) kinase assay services. Test compounds were tested at 100 nM and 1 μM final concentrations in 1% DMSO against all kinases except CDK7. For CDK7, test compounds were tested at concentrations ranging from 10 μM to 0.514 nM in a series of 3-fold serial dilutions. Detailed protocols of these assays, including substrates used for each kinase, are known in the art, such as on the Life Technologies web site (www.lifetechnologies.com/us/en/home/life-science/drug-discovery/target-and-lead-identification-and-validation/kinasebiology/kinase-activity-assays.html). Exemplary results are presented as calculated IC50values (Tables 1C and 2) or as percent inhibitions of activity (Tables 3A to 3C). In Tables 1C and 2, “A” represents a calculated IC50value of less than 100 nM; “B” represents a calculated IC50value of greater than or equal to 100 nM and less than 1 μM; and “C” represents a calculated IC50value of 1 μM or greater. In Tables 3A to 3C, “A” represents greater than 70% inhibition of a kinase by the test compound, “B” represents between 50% and 70% inhibition, inclusive; and “C” represents less than 50% inhibition. The co-factors used for each kinase in the assays were as follows: CDK1: cyclin B; CDK2: cyclin A; CDK5: p25 or p35 as indicated; CDK7: cyclin H and MNAT1; CDK8: cyclin C; CDK9: cyclin K or cyclin T1 as indicated; IRAK1: Histone H3 (1-20) peptide; JNK1: none required; JNK2: none required; MLK3: none required.

TABLE 1CCalculated IC50values of exemplary compoundsof the invention against CDK7CompoundCDK7No.IC50100A101B102A103B104A105A106A108B109A110A111A112A113B114A115A116B117A118B119A120B121A122A123B124A125A126A127B128A129A130A131A132C133B134C135A136C137B138A139C140A141A142B143A144B145AB146B147AB148A149A150A151A152B153A154A155C160B

TABLE 2Calculated IC50values of exemplary compoundsof the invention against various kinasesCompoundNo.CDK7CDK2CDK5cCDK8CDK9eCDK9fMLK3100ACCBBB101BCC102ACC103BCC104ACC105A

TABLE 3APercent inhibition of various kinases by exemplary compounds of theinventionCom-poundNo.CDK1aCDK1bCDK2aCDK2bCDK5a,cCDK5b,c102CCCCCC103CCCCCC

TABLE 3BPercent inhibition of various kinases by exemplary compounds of theinventionCompoundNo.CDK5a,dCDK5b,dCDK8aCDK8bCDK9a,eCDK9b,e102CCCCCC103CCCCCB

TABLE 3CPercent inhibition of various kinases by exemplary compounds of theinventionCompoundNo.IRAK1aIRAK1bJNK1aJNK1bJNK2aJNK2bMLK3a102CCCBCBC103CCCBCACaCompound tested at 100 nM.bCompound tested at 1 μM.cCDK5 tested using p25 co-factor.dCDK5 tested using p35 co-factor.eCDK9 tested using cyclin T1 co-factor.fCDK9 tested using cyclin K co-factor.

Exemplary compounds of the invention were further tested for inhibitory activity against CDK7 using an assay developed using a Caliper/LabChip EZ Reader (Perkin Elmer, Waltham, Mass.). In this protocol, the concentration of phosphorylated peptide substrate produced as a fraction of total peptide activity is monitored following an incubation period (30 minutes), which was selected such that the total fraction of phosphorylated peptide produced was less than 20% for the uninhibited kinase. Compounds of the invention were assayed at concentrations ranging from 10 μM to 0.514 nM in a series of 3-fold serial dilutions, and were incubated with CDK7/Cyclin H/MAT1 trimeric complex (10 nM), ATP (2 mM), and “FAM-CDK7tide” peptide substrate (2 μM, synthesized fluorophore-labeled peptide with the following sequence: 5-FAM-YSPTSPSYSPTSPSYSPTSPSKKKK) in a buffer comprising 20 mM MES, pH 6.75; 6 mM MgCl2; 0.01% Tween 20; and 0.05 mg/mL BSA. IC50values were recorded for selected test compounds and are reported in Table 4, wherein “A” represents a calculated IC50of less than 100 nM, “B” represents a calculated IC50of between 100 nM and 1 μM, inclusive and “C” represents a calculated IC50of greater than 1 μM.

TABLE 4Calculated IC50values of exemplary compounds ofthe invention against CDK7CompoundCDK7No.IC50135B155C156C157B158A159C

Inhibition of Cell Proliferation

Exemplary compounds of the invention were tested at different concentrations (from 10 μM to 316 pM; 0.5 log serial dilutions) for their ability to inhibit the proliferation of various cancer cell lines. Known CDK inhibitors flavopiridol and triptolide were used as positive controls. Cells were grown in the indicated media below. All cell lines were supplemented with FBS (Life Technologies) and 100 U·mL−1penicillin, 100 μg·mL−1streptomycin (Invitrogen) and cultured at 37° C. in a humidified chamber in the presence of 5% CO2. Proliferation assays were conducted over a 72 hour time period. CellTiter-Glo® (Promega Corporation, Madison, Wis. USA) was used to assess the anti-proliferative effects of the compounds following manufacturer's directions and utilizing the reagents supplied with the CellTiter-Glo® kit.

The following cancer cell lines were tested with the media conditions indicated:

Blood cancer cell lines

Exemplary results of these assays are set forth in Tables 5A to 5D, where “A” represents an IC50value of less than 500 nM; “B” represents an IC50value of between 500 nM and 5 μM, inclusive; and “C” represents an IC50value of greater than 5 μM.

TABLE 5AInhibition of proliferation of various blood cancer cell lines byexemplary compounds of the inventionCompound No.HL60THP-1MV4-11RS4-11102AAAA103BBABFlavopiridolAAAATriptolideAAAA

TABLE 5BInhibition of proliferation of various breast cancer cell lines byexemplary compounds of the inventionCompoundhTERT-MDA-No.HME1MB231MCF7MCF10AT47DSKBR3102AACACC103BBBACCFlavopiridolAABACATriptolideAAAACA

TABLE 5CInhibition of proliferation of various cancer cell lines by exemplarycompounds of the inventionOsteosarcomaMNNG-CompoundEwing's SarcomaHOSNo.A673Hs822THs863TRD-ESSK-ES-1SAOSCl#5143B102ACCAAACC103ACCBBBCCFlavopiridolACCAAABBTriptolideABCAAAAA

TABLE 5DInhibition of proliferation of Jurkat cells by exemplarycompounds of the inventionCompoundJurkatNo.IC50101B102A103B104A108B109A110A111A112A113B114A115A116A117A118B119A120B121A122A123A124A125A126A127B128A129A130A131A133A134C135A137A138A139B140A141A142A143A144A145A146B147A152A

EQUIVALENTS AND SCOPE