4,6-pyrimidinylene derivatives and uses thereof

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., lung cancer, breast cancer, leukemia, lymphoma, melanoma, multiple myeloma, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma), 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 (e.g. a protein kinase (e.g. a cyclin-dependent kinase (CDK) (e.g. CDK7, CDK12, or CDK13) or a lipid kinase such as a phosphatidylinositol-5-phosphate 4-kinase (PIP4K) (e.g., PI5P4Kα, PI5P4Kβ, or PI5P4Kγ)) in the subject.

BACKGROUND OF THE INVENTION

Lung cancer is the leading cancer killer worldwide accounting for 1.37 million deaths annually. In the United States, lung cancer causes more deaths than the next three most common cancers combined (colon, breast and pancreatic) and in 2014, an estimated 159,260 Americans will die from lung cancer. Lung cancer arises as a result of environmental exposures, such as smoking, combined with genetic alterations such as deregulation of oncoproteins, including Myc and RAS, and loss of tumor suppressors, such as p53. The vast majority of patients that develop lung cancer will have non-small cell lung cancer (NSCLC), and 50% of patients will initially present with advanced NSCLC, which is incurable using currently available therapies. The median survival of patients with advanced NSCLC treated with chemotherapy is 8-10 months.

A major therapeutic goal in lung cancer is to identify agents against targets that are critical to the growth of lung cancers. This has been clinically achieved for patients that harbor activating mutations in EGFR or chromosomal translocations such as EML4-ALK using selective ATP-competitive kinase inhibitors. Unfortunately the duration of response to targeted kinase inhibitors is typically less than 2 years, and most lung tumors do not express an oncogene that is targeted by an available drug. For example, loss of p53 is a common event in lung cancer, but there are currently limited drugs that can exploit its loss.

Phosphatidylinositol 4,5-bisphosphate (PIP2) is a membrane bound lipid molecule with the ability to affect a wide array of signaling pathways that regulate different cellular processes (Camilli et al.,Science,1996, 271: 1533-1539). PIP2is used as a precursor to generate the second messengers PIP3, DAG, and IP3, indispensable molecules for signaling events generated by membrane receptors. However, PIP2can also directly regulate a vast array of proteins and is emerging as a crucial messenger with the potential to distinctly modulate biological processes critical for both normal and pathogenic cell physiology (Martin, T. F. J. (1998)Annu. Rev. Cell Dev. Biol.14, 231-264). PIP2directly associates with effector proteins via unique phosphoinositide binding domains, altering their localization and/or enzymatic activity. The spatial and temporal generation of PIP2synthesized by the phosphatidylinositol phosphate kinases (PIPKs) tightly regulates the activation of receptor signaling pathways, endocytosis and vesicle trafficking, cell polarity, focal adhesion dynamics, actin assembly, and 3′ mRNA processing (Balla et al., Phosphoinositides I: Enzymes of Synthesis and Degradation, 2012, Chapter 2, PIP Kinases from the Cell Membrane to the Nucleus, p 25). Two types of PIP kinases have been identified, type I and type II PI(4)P 5-kinases (Fruman et al.,Annu. Rev. Biochem.,1998, 67: 481-507). Type I phosphorylates PI(4)P at the 5-position to make PI(4,5)P2 and type II can phosphorylate PI(5)P and PI(3)P at the 4-position to make PI(4,5)P2 and PI(3,4)P2.

Recently, it has been discovered that RNAi-mediated depletion of two type II PIP kinases, PIP4K2A and PIP4K2B, selectively inhibited the proliferation of TP53 mutant breast cancer cell line (BT474 cells) while cells that were wild-type for TP53 were unaffected (Emerling et al.,Cell,2013, 155: 844-857). These kinases phosphorylate the lipid phosphatidylinositol-5-phosphate (PI-5-P) at the 4-position of the inositol ring to generate phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) and are in the same kinase family as the PI3 kinases which are now targeted by a number of clinical stage drugs. Genetic studies in mice demonstrate that homozygous germline deletion of PIP4K2B results in healthy mice with a normal life span, while combined deletion of PIP4K2B and TP53 results in early embryonic lethality (FIG. 1) (Rameh et al.,Nature,1997, 390: 192-196). Mice expressing one allele of PIP4K2B and homozygous deletion of PIP4K2A and TP53 are viable and exhibit a dramatic reduction in cancers and an extended lifespan compared to their littermates that were TP53 deleted with wild type PIP4K2A. These studies suggest that PIP4K2A/B becomes essential when TP53 function is lost. Therefore, small molecule inhibitors of PIP4K2A/B may hold promise as a therapeutic agent for treating cancer.

SUMMARY OF THE INVENTION

The phosphoinositide family of lipids includes seven derivatives of hosphatidylinositol (PI) that are formed through the phosphorylation of the 3-, 4-, and 5-positions on the inositol ring (Emerling et al., Cell, 2013, 155: 844-857). Phosphoinositides have distinct biological roles and regulate many cellular processes, including proliferation survival, glucose uptake, and migration. Phosphoinositide kinases, phosphatases and phospholipases, spatially and temporally regulate the generation of the different phosphoinositide species, which localize to different subcellular compartments. phosphorylation of lipid phosphatidylinositol-5-phosphate (PI-5-P) at the 4-position to generate phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) is catalyzed by the enzymes PIP4K2A, B and C. Germ line deletion of PIP4K2A and PIP4K2B in mice suppresses tumor formation in the context of TP53 deletion (Rameh et al., Nature, 1997, 390: 192-196). Loss or mutations in the tumor suppressor gene TP53 (encoding p53) are one of the most frequent events in cancer. Clinical and functional studies have unequivocally validated the functional importance of the loss of p53 in cancer. Therefore, it is advantageous to develop PIP4K2A and/or PIP4K2B inhibitors to provide therapeutic benefit in cancers, for example, TP53-deleted tumors.

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, can inhibit the activity of a kinase. In certain embodiments, the kinase is a protein kinase. In certain embodiments, the protein kinase is a CDK (e.g. cyclin-dependent kinases (CDKs)). In certain embodiments, the kinase is a lipid kinase. In certain embodiments, the lipid kinase is a phosphatidylinositol phosphate kinase (PIPK). In certain embodiments, the PIPK is PIP4K, catalyzing phosphorylation of lipid phosphatidylinositol-5-phosphate (PI-5-P) at the 4-position to generate phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2). In some embodiments, the PIP4K is class I PIP4K, i.e. PIP4K1. In some embodiments, the PIP4K is class II PIP4K, i.e. PIP4K2. In some embodiments, the PIP4K2 is PIP4K2A protein. In some embodiments, the PIP4K2 is PIP4K2B protein. In some embodiments, the PIP4K2 is PIP4K2C protein. In certain embodiments, the compound of Formula (I) is selective for a lipid kinase compared to other kinases. In certain embodiments, the compound of Formula (I) is selective for PIP4K 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., PIP4K) and as therapeutics for the prevention and/or treatment of diseases associated with overexpression and/or aberrant activity of a kinase (e.g., PIP4K). In certain embodiments, the inventive compounds are used for the prevention and/or treatment of proliferative diseases (e.g., cancers (e.g., lung cancer, breast cancer, leukemia, lymphoma, melanoma, multiple myeloma, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma), benign neoplasms, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject.

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

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

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

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

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

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., lung cancer, breast cancer, leukemia, lymphoma, melanoma, multiple myeloma, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma), benign neoplasm, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases. In certain embodiments, the cancer has one or more mutations. In certain embodiments, the cancer is TP53-deleted cancer. In other embodiments, the present invention provides methods for treating and/or preventing an infectious disease (e.g., a viral infection).

Another aspect of the invention relates to methods of modulating the activity of a kinase (e.g., PIP4K (e.g., PIP4K2) enzyme) in a biological sample or subject. In certain embodiments, the method involves the selective inhibition of the PIP4K enzyme over other kinases. In certain embodiments, the method involves the selective inhibition of the PIP4K2 enzyme over other kinases.

The present invention also provides methods of inhibiting cell growth in a biological sample or 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., lung cancer, breast cancer, leukemia, lymphoma, melanoma, multiple myeloma, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma), 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., PIP4K enzyme), or in inhibiting cell growth.

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., lung cancer, breast cancer, leukemia, lymphoma, melanoma, multiple myeloma, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma), 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

The term “aliphatic” includes both saturated and unsaturated, straight chain (i.e., unbranched), branched, acyclic, cyclic, or polycyclic aliphatic hydrocarbons, which are substituted or unsubstituted with one or more functional groups. As will be appreciated by one of ordinary skill in the art, “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. Thus, the term “alkyl” includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl”, and the like. Furthermore, the terms “alkyl”, “alkenyl”, “alkynyl”, and the like encompass both substituted and unsubstituted groups. In certain embodiments, “lower alkyl” is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the disclosure contain 1-4 carbon atoms. Illustrative aliphatic groups thus include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH2-cyclopropyl, vinyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, cyclobutyl, —CH2-cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl, cyclopentyl, —CH2-cyclopentyl, n-hexyl, sec-hexyl, cyclohexyl, —CH2-cyclohexyl moieties and the like, which again, may bear one or more substituents. Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and the like. Representative alkynyl groups include, but are not limited to, ethynyl, 2-propynyl (propargyl), 1-propynyl, and the like.

The term “alkyl” refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms (“C1-10alkyl”). 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), propyl (C3) (e.g., n-propyl, isopropyl), butyl (C4) (e.g., n-butyl, tert-butyl, sec-butyl, iso-butyl), pentyl (C5) (e.g., n-pentyl, 3-pentanyl, amyl, neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C6) (e.g., n-hexyl). Additional examples of alkyl groups include n-heptyl (C7), n-octyl (C8), and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents (e.g., halogen, such as F). In certain embodiments, the alkyl group is an unsubstituted C1-10alkyl (such as unsubstituted C1-6alkyl, e.g., —CH3(Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstituted n-propyl (n-Pr), unsubstituted isopropyl (i-Pr)), unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (n-Bu), unsubstituted tert-butyl (tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu or s-Bu), unsubstituted isobutyl (i-Bu)). In certain embodiments, the alkyl group is a substituted C1-10alkyl (such as substituted C1-6alkyl, e.g., benzyl (Bn) or —CF3).

may be an (E)- or (Z)-double bond.

“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” refers to a substituted or unsubstituted alkyl group substituted by a substituted or unsubstituted aryl group. In certain embodiments, the aralkyl is substituted or unsubstituted benzyl. In certain embodiments, the aralkyl is benzyl. In certain embodiments, the aralkyl is substituted or unsubstituted phenethyl. In certain embodiments, the aralkyl is phenethyl.

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

“Unsaturated” or “partially unsaturated” refers to a group that includes at least one double or triple bond. A “partially unsaturated” ring system is further intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl groups). Likewise, “saturated” refers to a group that does not contain a double or triple bond, i.e., contains all single bonds.

An atom, moiety, or group described herein may be unsubstituted or substituted, as valency permits, unless otherwise provided expressly. The term “optionally substituted” refers to substituted or unsubstituted.

A group is substituted or unsubstituted unless expressly provided otherwise. The term “optionally substituted” refers to being substituted or unsubstituted. In certain embodiments, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups are substituted or unsubstituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or “unsubstituted” heteroaryl group). In general, the term “substituted”, whether preceded by the term “optionally” or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term “substituted” is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound. The present disclosure contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this disclosure, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety. In certain embodiments, the substituent is a carbon atom substituent. In certain embodiments, the substituent is a nitrogen atom substituent. In certain embodiments, the substituent is an oxygen atom substituent. In certain embodiments, the substituent is a sulfur atom substituent.

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;

The term “hydroxyl” or “hydroxy” refers to the group —OH. The term “substituted hydroxyl” or “substituted hydroxyl,” by extension, refers to a hydroxyl group wherein the oxygen atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from —ORaa, —ON(Rbb)2, —OC(═O)SRaa, —OC(═O)Raa, —OCO2Raa, —OC(═O)N(Rbb)2, —OC(═NRbb)Raa, —OC(═NRbb)ORaa, —OC(═NRbb)N(Rbb)2, —OS(═O)Raa, —OSO2Raa, —OSi(Raa)3, —OP(Rcc)2, —OP(Rcc)3+X−, —OP(ORcc)2, —OP(ORcc)3+X−, —OP(═O)(Raa)2, —OP(═O)(ORcc)2, and —OP(═O)(N(Rbb))2, wherein Raa, Rbb, and Rccare as defined herein.

A “hydrocarbon chain” refers to a substituted or unsubstituted divalent alkyl, alkenyl, or alkynyl group. A hydrocarbon chain includes (1) one or more chains of carbon atoms immediately between the two radicals of the hydrocarbon chain; (2) optionally one or more hydrogen atoms on the chain(s) of carbon atoms; and (3) optionally one or more substituents (“non-chain substituents,” which are not hydrogen) on the chain(s) of carbon atoms. A chain of carbon atoms consists of consecutively connected carbon atoms (“chain atoms” or “carbon units”) and does not include hydrogen atoms or heteroatoms. However, a non-chain substituent of a hydrocarbon chain may include any atoms, including hydrogen atoms, carbon atoms, and heteroatoms. For example, hydrocarbon chain —CAH(CBH2CCH3)— includes one chain atom CA, one hydrogen atom on CA, and non-chain substituent —(CBH2CCH3). The term “Cxhydrocarbon chain,” wherein x is a positive integer, refers to a hydrocarbon chain that includes x number of chain atom(s) between the two radicals of the hydrocarbon chain. If there is more than one possible value of x, the smallest possible value of x is used for the definition of the hydrocarbon chain. For example, —CH(C2H5)— is a C1hydrocarbon chain, and

is a C3hydrocarbon chain. When a range of values is used, the meaning of the range is as described herein. For example, a C3-10hydrocarbon chain refers to a hydrocarbon chain where the number of chain atoms of the shortest chain of carbon atoms immediately between the two radicals of the hydrocarbon chain is 3, 4, 5, 6, 7, 8, 9, or 10. A hydrocarbon chain may be saturated (e.g., —(CH2)4—). A hydrocarbon chain may also be unsaturated and include one or more C═C and/or C≡C bonds anywhere in the hydrocarbon chain. For instance, —CH═CH—(CH2)2—, —CH2—C≡C—CH2—, and —C≡C—CH═CH— are all examples of a unsubstituted and unsaturated hydrocarbon chain. In certain embodiments, the hydrocarbon chain is unsubstituted (e.g., —C≡C— or —(CH2)4—). In certain embodiments, the hydrocarbon chain is substituted (e.g., —CH(C2H5)— and —CF2—). Any two substituents on the hydrocarbon chain may be joined to form a substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, or substituted or unsubstituted 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. When a chain atom of a Cxhydrocarbon chain is replaced with a heteroatom, the resulting group is referred to as a Cxhydrocarbon chain wherein a chain atom is replaced with a heteroatom, as opposed to a Cx-1hydrocarbon chain. For example,

is a C3hydrocarbon chain wherein one chain atom is replaced with an oxygen atom.

The term “leaving group” is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile. Examples of suitable leaving groups include, but are not limited to, halogen (such as F, Cl, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O-dimethylhydroxylamino, 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), —OS(═O)2(CF2)3CF3(nonaflate, -ONf), or trifluoromethanesulfonate (triflate, -OTf). In some cases, the leaving group is a brosylate, such as p-bromobenzenesulfonyloxy. In some cases, the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy. The leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate. Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties. Further exemplary leaving groups include, but are not limited to, halo (e.g., chloro, bromo, iodo) and activated substituted hydroxyl groups (e.g., —OC(═O)SRaa, —OC(═O)Raa, —OCO2Raa, —OC(═O)N(Rbb)2, —OC(═NRbb)Raa, —OC(═NRbb)ORaa, —OC(═NRbb)N(Rbb)2, —OS(═O)Raa, —OSO2Raa, —OP(Rcc)2, —OP(Rcc)3, —OP(═O)2Raa, —OP(═O)(Raa)2, —OP(═O)(ORcc)2, —OP(═O)2N(Rbb)2, and —OP(═O)(NRbb)2, wherein Raa, Rbb, and Rccare as defined herein).

Other Definitions

The term “tautomers” or “tautomeric” refers to two or more interconvertible compounds resulting from at least one formal migration of a hydrogen atom and at least one change in valency (e.g., a single bond to a double bond, a triple bond to a single bond, or vice versa). The exact ratio of the tautomers depends on several factors, including temperature, solvent, and pH. Tautomerizations (i.e., the reaction providing a tautomeric pair) may catalyzed by acid or base. Exemplary tautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim, enamine-to-imine, and enamine-to-(a different enamine) tautomerizations.

The term “polymorphs” refers to a crystalline form of a compound (or a salt, hydrate, or solvate thereof) in a particular crystal packing arrangement. All polymorphs have the same elemental composition. Different crystalline forms usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Various polymorphs of a compound can be prepared by crystallization under different conditions.

The term “co-crystal” refers to a crystalline structure composed of at least two components. In certain embodiments, a co-crystal may contain a compound of the present invention and one or more other component, including but not limited to, atoms, ions, molecules, or solvent molecules. In certain embodiments, a co-crystal may contain a compound of the present invention and one or more components related to said compound, including not limited to, an isomer, tautomer, salt, solvate, hydrate, synthetic precursor, synthetic derivative, fragment or impurity of said compound.

The term “isotopically labeled derivative” or “isotopically labeled” refers to a compound wherein one or more atoms in the compound (or in an associated ion or molecule of a salt, hydrate, or solvate) has been replaced with an isotope of the same element. For the given element or position in the molecule the isotope will be enriched, or present in a higher percentage of all atoms of the element or of all atoms at the position in the molecule in a sample, relative to an unlabeled variant. In certain embodiments, the enriched isotope will be a stable isotope. In certain embodiments, the enriched isotope will be an unstable or radioactive isotope (e.g., a radionuclide). In certain embodiments, the enriched isotope may be detected by a measurement technique, including but not limited to nuclear magnetic resonance, mass spectrometry, infrared spectroscopy, or a technique that measures radioactive decay.

The term “prodrugs” refers to compounds that have cleavable groups and become by solvolysis or under physiological conditions the compounds described herein, which are pharmaceutically active in vivo. Such examples include, but are not limited to, choline ester derivatives and the like, N-alkylmorpholine esters and the like. Other derivatives of the compounds described herein have activity in both their acid and acid derivative forms, but in the acid sensitive form often offer advantages of solubility, tissue compatibility, or delayed release in the mammalian organism (see, Bundgard, H.,Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well known to practitioners of the art, such as, for example, esters prepared by reaction of the parent acid with a suitable alcohol, or amides prepared by reaction of the parent acid compound with a substituted or unsubstituted amine, or acid anhydrides, or mixed anhydrides. Simple aliphatic or aromatic esters, amides, and anhydrides derived from acidic groups pendant on the compounds described herein are particular prodrugs. In some cases it is desirable to prepare double ester type prodrugs such as (acyloxy)alkyl esters or ((alkoxycarbonyl)oxy)alkylesters. C1-C8alkyl, C2-C8alkenyl, C2-C8alkynyl, aryl, C7-C12substituted aryl, and C7-C12arylalkyl esters of the compounds described herein may be preferred.

The term “inhibition”, “inhibiting”, “inhibit,” or “inhibitor” refer to the ability of a compound to reduce, slow, halt or prevent activity of a particular biological process (e.g., activity of a bromodomain and/or a bromodomain-containing protein) in a cell relative to vehicle.

When a compound, pharmaceutical composition, method, use, or kit is referred to as “selectively,” “specifically,” or “competitively” binding a first protein or a first chromatin, the compound, pharmaceutical composition, method, use, or kit binds the first protein or the first chromatin with a higher binding affinity (e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold) than binding a second protein or second chromatin that is different from the first protein and the first chromatin. When a compound, pharmaceutical composition, method, use, or kit is referred to as “selectively,” “specifically,” or “competitively” modulating (e.g., increasing or inhibiting) the activity of a bromodomain-containing protein, the compound, pharmaceutical composition, method, use, or kit modulates the activity of the bromodomain-containing protein to a greater extent (e.g., not less than about 2-fold, not less than about 5-fold, not less than about 10-fold, not less than about 30-fold, not less than about 100-fold, not less than about 1,000-fold, or not less than about 10,000-fold) than the activity of at least one protein that is different from the bromodomain-containing protein.

The term “aberrant activity” refers to activity deviating from normal activity, that is, abnormal activity. The term “increased activity” refers to activity higher than normal activity.

The terms “composition” and “formulation” are used interchangeably.

A “subject” to which administration is contemplated refers to a human (i.e., male or female of any age group, e.g., pediatric subject (e.g., infant, child, or adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) or non-human animal. In certain embodiments, the non-human animal is a mammal (e.g., primate (e.g., cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g., cattle, pig, horse, sheep, goat, cat, or dog), or bird (e.g., commercially relevant bird, such as chicken, duck, goose, or turkey)). In certain embodiments, the non-human animal is a fish, reptile, or amphibian. The non-human animal may be a male or female at any stage of development. The non-human animal may be a transgenic animal or genetically engineered animal. A “patient” refers to a human subject in need of treatment of a disease.

The term “biological sample” refers to any sample including tissue samples (such as tissue sections and needle biopsies of a tissue); cell samples (e.g., cytological smears (such as Pap or blood smears) or samples of cells obtained by microdissection); samples of whole organisms (such as samples of yeasts or bacteria); or cell fractions, fragments or organelles (such as obtained by lysing cells and separating the components thereof by centrifugation or otherwise). Other examples of biological samples include blood, serum, urine, semen, fecal matter, cerebrospinal fluid, interstitial fluid, mucous, tears, sweat, pus, biopsied tissue (e.g., obtained by a surgical biopsy or needle biopsy), nipple aspirates, milk, vaginal fluid, saliva, swabs (such as buccal swabs), or any material containing biomolecules that is derived from another biological sample.

The terms “administer,” “administering,” or “administration” refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing a compound described herein, or a composition thereof, into, in, or on a subject.

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

An “effective amount” of a compound described herein refers to an amount sufficient to elicit the desired biological response, i.e., treating the condition. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound described herein may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject. In certain embodiments, an effective amount is a therapeutically effective amount. In certain embodiments, an effective amount is a prophylactic treatment. In certain embodiments, an effective amount is the amount of a compound described herein in a single dose. In certain embodiments, an effective amount is the combined amounts of a compound described herein in multiple doses.

A “therapeutically effective amount” of a compound described herein is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the condition. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms, signs, or causes of the condition, and/or enhances the therapeutic efficacy of another therapeutic agent.

A “proliferative disease” refers to a disease that occurs due to abnormal growth or extension by the multiplication of cells (Walker,Cambridge Dictionary of Biology; Cambridge University Press: Cambridge, UK, 1990). A proliferative disease may be associated with: 1) the pathological proliferation of normally quiescent cells; 2) the pathological migration of cells from their normal location (e.g., metastasis of neoplastic cells); 3) the pathological expression of proteolytic enzymes such as the matrix metalloproteinases (e.g., collagenases, gelatinases, and elastases); or 4) the pathological angiogenesis as in proliferative retinopathy and tumor metastasis. Exemplary proliferative diseases include cancers (i.e., “malignant neoplasms”), benign neoplasms, diseases associated with angiogenesis, inflammatory diseases, and autoimmune diseases.

The term “angiogenesis” refers to the physiological process through which new blood vessels form from pre-existing vessels. Angiogenesis is distinct from vasculogenesis, which is the de novo formation of endothelial cells from mesoderm cell precursors. The first vessels in a developing embryo form through vasculogenesis, after which angiogenesis is responsible for most blood vessel growth during normal or abnormal development. Angiogenesis is a vital process in growth and development, as well as in wound healing and in the formation of granulation tissue. However, angiogenesis is also a fundamental step in the transition of tumors from a benign state to a malignant one, leading to the use of angiogenesis inhibitors in the treatment of cancer. Angiogenesis may be chemically stimulated by angiogenic proteins, such as growth factors (e.g., VEGF). “Pathological angiogenesis” refers to abnormal (e.g., excessive or insufficient) angiogenesis that amounts to and/or is associated with a disease.

The terms “neoplasm” and “tumor” are used herein interchangeably and refer to an abnormal mass of tissue wherein the growth of the mass surpasses and is not coordinated as in the growth of normal tissue. A neoplasm or tumor may be “benign” or “malignant,” depending on the following characteristics: degree of cellular differentiation (including morphology and functionality), rate of growth, local invasion, and metastasis. A “benign neoplasm” is generally well differentiated, has characteristically slower growth than a malignant neoplasm, and remains localized to the site of origin. In addition, a benign neoplasm does not have the capacity to infiltrate, invade, or metastasize to distant sites. Exemplary benign neoplasms include, but are not limited to, lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheic keratoses, lentigos, and sebaceous hyperplasias. In some cases, certain “benign” tumors may later give rise to malignant neoplasms, which may result from additional genetic changes in a subpopulation of the tumor's neoplastic cells, and these tumors are referred to as “pre-malignant neoplasms.” An exemplary pre-malignant neoplasm is a teratoma. In contrast, a “malignant neoplasm” is generally poorly differentiated (anaplasia) and has characteristically rapid growth accompanied by progressive infiltration, invasion, and destruction of the surrounding tissue. Furthermore, a malignant neoplasm generally has the capacity to metastasize to distant sites. The term “metastasis,” “metastatic,” or “metastasize” refers to the spread or migration of cancerous cells from a primary or original tumor to another organ or tissue and is typically identifiable by the presence of a “secondary tumor” or “secondary cell mass” of the tissue type of the primary or original tumor and not of that of the organ or tissue in which the secondary (metastatic) tumor is located. For example, a prostate cancer that has migrated to bone is said to be metastasized prostate cancer and includes cancerous prostate cancer cells growing in bone tissue.

An “autoimmune disease” refers to a disease arising from an inappropriate immune response of the body of a subject against substances and tissues normally present in the body. In other words, the immune system mistakes some part of the body as a pathogen and attacks its own cells. This may be restricted to certain organs (e.g., in autoimmune thyroiditis) or involve a particular tissue in different places (e.g., Goodpasture's disease which may affect the basement membrane in both the lung and kidney). The treatment of autoimmune diseases is typically with immunosuppression, e.g., medications which decrease the immune response. Exemplary autoimmune diseases include, but are not limited to, glomerulonephritis, Goodpasture's syndrome, necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemic lupus erythematosis, rheumatoid arthritis, psoriatic arthritis, systemic lupus erythematosis, psoriasis, ulcerative colitis, systemic sclerosis, dermatomyositis/polymyositis, anti-phospholipid antibody syndrome, scleroderma, pemphigus vulgaris, ANCA-associated vasculitis (e.g., Wegener's granulomatosis, microscopic polyangiitis), uveitis, Sjogren's syndrome, Crohn's disease, Reiter's syndrome, ankylosing spondylitis, Lyme disease, Guillain-Barré syndrome, Hashimoto's thyroiditis, and cardiomyopathy.

The term “CDK” refers to a cyclin-dependent kinase. A CDK binds a cyclin (e.g., Cyclin H), which is a regulatory protein. CDKs phosphorylate their substrates at serines and threonines. The consensus sequence for the phosphorylation site in the amino acid sequence of a CDK substrate is [S/T*]PX[K/R], where S/T* is the phosphorylated serine or threonine, P is proline, X is any amino acid, K is lysine, and R is arginine. CDKs include CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, CDK11, CDK12, CDK13, CDK14, CDK15, CDK16, CDK17, CDK18, CDK19 and CDK20.

CDK7, cyclin-dependent kinase 7, is a CDK, wherein the substrate is Cyclin H, MAT1 (e.g., MNAT1), or Cyclin H and MAT1. CDK7 is alternatively referred to as CAK1, HCAK, MO15, STK1, CDKN7, and p39MO15. Non-limiting examples of the nucleotide and protein sequences for human CDK7 are described in GenBank Accession Number NP_001790, incorporated herein by reference. The amino acid sequence of this CDK7 is as follows:

CDK12, cyclin-dependent kinase 12, is a CDK, wherein the substrate is Cyclin K or Flavopiridol. CDK12 is alternatively referred to as Cdc2-related kinase, CDC2-related protein kinase 7, Cell division cycle 2-related protein kinase 7, Cell division protein kinase 12, CRK7, CRKR, CRKRS, cyclin-dependent kinase 12, or KIAA0904. Non-limiting examples of the nucleotide and protein sequences for human CDK12 are described in Uniprot Number Q9NYV4, which is incorporated herein by reference. The amino acid sequence of this CDK12 is as follows:

CDK13, cyclin-dependent kinase 13, is a CDK, wherein the relevant cyclin is cyclin K and a reference inhibitor is the pan-CDK inhibitor Flavopiridol and the c-terminal domain (CTD) of RNA-polymerase II is a physiological substrate. CDK13 is alternatively referred to as CHED; CDC2L; CDC2L5; or hCDK13. Non-limiting examples of the nucleotide and protein sequences for human CDK12 are described in GenBank Accession Number M80629, which is incorporated herein by reference. The amino acid sequence of this CDK13 is as follows:

The term “PIP kinases”, also known as “PIPKs,” refers to phosphatidylinositol phosphate kinases or phosphatidylinositol-5-phosphate 4-kinases, a class of enzymes that catalyzes the chemical reaction: ATP+1-phosphatidyl-1D-myo-inositol 4-phosphateADP+1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate. PIP kinases are divided into two classes, type I and type II. The type I and type II PIP kinases are 35% identical at the kinase domain. Their sequences are significantly divergent for a stretch of about 25 amino acids in the region of the kinase domain that corresponds to the activation loop of protein kinases. There are three isoforms of type II PIP4-kinase in mammalian cells, namely α (PIP4K2A), β (PIP4K2B), and γ (PIP4K2C) isoforms (Liu et al., Nat. Rev. Drug. Discov., 2009, 8(8): 627-644). At the protein level, the α and β isoforms are 83% identical and the γ isoform is about 60% identical to either one of them. All isoforms are ubiquitously expressed, but the α isoform is found predominantly in brain and platelets, the β isoform in brain and muscle, and the γ isoform in brain and kidney. Although the type II PIP4-kinase isoforms are ubiquitously expressed, changes in protein levels may play a role in the regulation of their cellular function. The type II PIP4-kinase β isoform gene, which localizes to the chromosome 17q11-12, was found to be amplified in primary breast cancer samples with Heregulin 2 gene amplifications and in a subset of breast cancer cell lines. These gene amplifications resulted in increased protein expression, which correlated with increased breast cancer cell proliferation and anchorage-independent growth (Emerling et al., Cell, 2013, 155(4): 844-857). In certain embodiments, the PIPK is PI5P4K (i.e. PIP4K2A enzyme) encoded by PIP4K2A gene. In certain embodiments, the PIPK is PI5P4Kβ (i.e. PIP4K2B enzyme) encoded by PIP4K2B gene. In certain embodiments, the PIPK is PI5P4Kγ (i.e. PIP4K2C enzyme) encoded by PIP4K2C gene. As used herein, type II PIP4Ks enzymes are referred as follows: PI5P4K is interchangeable with PIP4K; PI5P4Kα is interchangeable with PIP4Kα, PIP4K2A, PIP4K2A enzyme, and PIP4K2A protein; PI5P4Kβ is interchangeable with PIP4Kβ, PIP4K2B, PIP4K2B enzyme, and PIP4K2B protein; PI5P4Kγ is interchangeable with PIP4Kγ, PIP4K2C, PIP4K2C enzyme, and PIP4K2C protein.

In certain embodiments, the PIP4K2A enzyme is sp|P48426|PI42A_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (OS=Homo sapiens, GN=PIP4K2A, PE=1, and SV=2) and of the following sequence:

In certain embodiments, the PIP4K2B enzyme is sp|P78356|PI42B_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (OS=Homo sapiens, GN=PIP4K2B, PE=1, and SV=1) and of the following sequence:

In certain embodiments, the PIP4K2C enzyme is sp|Q8TBX8|PI42C_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma (OS=Homo sapiens, GN=PIP4K2C, PE=1, and SV=3) and of the following sequence:

In certain embodiments, the PIP4K2A gene of Gene ID: 5305 and HGNC:8997 and has the cDNA sequence as follows:

In certain embodiments, the PIP4K2B gene of Gene ID: 8396 and HGNC:8998, and has the cDNA sequence as follows:

In certain embodiments, the PIP4K2C gene of Gene ID: 79837 and HGNC:23786, and has the cDNA sequence as follows:

Recent studies have shown that lipid kinases play an essential role in inhibiting cancer cell growth when the TP53 function is absent. Depletion of two lipid kinases, PIP4K2A and PIP4K2B, selectively inhibited the proliferation of TP53 mutant breast cancer cell line (BT474 cells) while cells that were wild-type for TP53 were unaffected (Emerling et al., Cell, 2013, 155: 844-857). Further research has shown that mice expressing one allele of PIP4K2B and homozygous deletion of PIP4K2A and TP53 are viable and exhibit a dramatic reduction in cancers and extended lifespan compared to their littermates that were TP53 deleted with wild type PIP4K2A. Therefore, small molecule inhibitors of lipid kinases may hold promise as a therapeutic agent for treating proliferative diseases.

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 a lipid kinase, such as PIP4K. The present invention further provides methods of using the compounds described herein, e.g., as biological probes to study the modulation of the activity of a kinase (e.g., a lipid kinase such as PIP4K), 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., a lipid kinase such as PIP4K). In certain embodiments, the disease being treated and/or prevented is a proliferative disease. Exemplary proliferative diseases include, but are not limited to, cancers (e.g., lung cancer, breast cancer, leukemia, melanoma, multiple myeloma), benign neoplasms, 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., a lipid kinase such as PIP4K).

Compounds

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

or a pharmaceutically acceptable salt thereof, wherein:

Ring A is a substituted or unsubstituted heteroaryl ring;

each instance of Rais independently hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Raare joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;

each instance of Rbis independently hydrogen, halogen, or substituted or unsubstituted C1-6alkyl;

each instance of Rcis independently hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group;

Ring C is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, substituted or unsubstituted, monocyclic heterocyclic ring, or substituted or unsubstituted, monocyclic heteroaryl ring;

Ring D is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring; provided that at least one of Ring C and Ring D is a substituted or unsubstituted phenyl ring;

REis of the formula:

L4is a bond or substituted or unsubstituted C1-6hydrocarbon chain;

RE6is hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group;

each instance of Y is independently O, S, or NRc;

a is 1 or 2; and

In certain embodiments, the compound described herein is of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein:

Ring A is a substituted or unsubstituted heteroaryl ring;

each instance of Rais independently hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of Raare joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;

each instance of Rbis independently hydrogen, halogen, or substituted or unsubstituted C1-6alkyl;

each instance of Rcis independently hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group;

Ring C is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring;

Ring D is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring;

provided that at least one of Ring C and Ring D is a substituted or unsubstituted phenyl ring;

REis of the formula:

L4is a bond or substituted or unsubstituted C1-6hydrocarbon chain;

RE6is hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group;

each instance of Y is independently O, S, or NRc;

a is 1 or 2; and

Compounds of Formula (I) include Ring A attached to Ring B through linker L1. In certain embodiments, Ring A is a substituted or unsubstituted bicyclic heteroaryl ring. In certain embodiments, Ring A is a substituted or unsubstituted, 9- or 10-membered, bicyclic heteroaryl ring, wherein one, two, three, or four atoms in the heteroaryl ring system are independently oxygen, nitrogen, or sulfur, as valency permits. In certain embodiments, Ring A is a substituted or unsubstituted bicyclic heteroaryl ring with one nitrogen. In certain embodiments, Ring A is a substituted or unsubstituted bicyclic heteroaryl ring with two nitrogen. In certain embodiments, Ring A is a substituted or unsubstituted monocyclic heteroaryl ring fused with a substituted or unsubstituted monocyclic aryl ring. In certain embodiments, Ring A is a substituted or unsubstituted monocyclic heteroaryl ring fused with another substituted or unsubstituted monocyclic heteroaryl ring. Ring A may be a substituted or unsubstituted 6,5-membered heteroaryl ring or a substituted or unsubstituted 5,6-membered heteroaryl ring. In certain embodiments, Ring A is a substituted or unsubstituted, 5- or 6-membered, monocyclic heteroaryl ring, wherein one, two, three, or four atoms in the heteroaryl ring system are independently oxygen, nitrogen, or sulfur, as valency permits. In certain embodiments, Ring A is a substituted or unsubstituted monocyclic 5-membered heteroaryl ring fused with a substituted or unsubstituted monocyclic 6-membered aryl ring. In certain embodiments, Ring A is a substituted or unsubstituted monocyclic 5-membered heteroaryl ring fused with a substituted or unsubstituted 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 a substituted or unsubstituted indole ring. In certain embodiments, Ring A is of Formula (A-i):

wherein RA1, RA2, and k are as defined herein. 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 a substituted or unsubstituted indazole ring. In certain embodiments, Ring A is of Formula (A-ii):

wherein RA1, RA2, and k are as defined herein. 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 Formula (A-iii):

(A-iii), wherein RA1, RA2, and k are as defined herein. 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, 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 a substituted or unsubstituted 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 a substituted or unsubstituted 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 a substituted or unsubstituted 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 a substituted or unsubstituted 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 a substituted or unsubstituted 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 a substituted or unsubstituted 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 a substituted or unsubstituted 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 a substituted or unsubstituted monocyclic heteroaryl ring. In compounds of Formula (I), Ring A may also be a substituted or unsubstituted 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, V1, V2, 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, V2, 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 a substituted or unsubstituted 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 Formula (A-v):

wherein RA2and k are as defined herein. 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 the formula:

In compounds of Formula (I), Ring A may be substituted with one or more RAgroups when the RAgroup is attached to a carbon atom. In certain embodiments, at least one RAis halogen. In certain embodiments, at least one RAis F. In certain embodiments, at least one RAis Cl. In certain embodiments, at least one RAis Br. In certain embodiments, at least one RAis I (iodine). In certain embodiments, at least one RAis substituted alkyl. In certain embodiments, at least one RAis unsubstituted alkyl. In certain embodiments, at least one RAis C1-6alkyl. In certain embodiments, at least one RAis methyl. In certain embodiments, at least one RAis ethyl. In certain embodiments, at least one RAis propyl. In certain embodiments, at least one RAis substituted alkenyl. In certain embodiments, at least one RAis unsubstituted alkenyl. In certain embodiments, at least one RAis vinyl. In certain embodiments, at least one RAis substituted alkynyl. In certain embodiments, at least one RAis unsubstituted alkynyl. In certain embodiments, at least one RAis ethynyl. In certain embodiments, at least one RAis substituted carbocyclyl. In certain embodiments, at least one RAis unsubstituted carbocyclyl. In certain embodiments, at least one RAis substituted heterocyclyl. In certain embodiments, at least one RAis unsubstituted heterocyclyl. In certain embodiments, at least one RAis substituted aryl. In certain embodiments, at least one RAis unsubstituted aryl. In certain embodiments, at least one RAis substituted phenyl. In certain embodiments, at least one RAis unsubstituted phenyl. In certain embodiments, at least one RAis substituted heteroaryl. In certain embodiments, at least one RAis —ORa, wherein Rais as defined herein. In certain embodiments, at least one RAis —ORa, wherein RAais hydrogen. In certain embodiments, at least one RAis —ORa, wherein Rais hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, at least one RAis —ORa, wherein Rais unsubstituted C1-6alkyl. In certain embodiments, at least one RAis —OCH3. In certain embodiments, at least one RAis —N(Ra)2, wherein Rais hydrogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, at least one RAis —NHRa. In certain embodiments, at least one RAis —SRa.

In compounds of Formula (I), Ring A may be substituted with one or more RAgroups as valency permits. In certain embodiments, k is 0. In certain embodiments, k is 1. In certain embodiments, k is 2. In certain embodiments, k is 3. In certain embodiments, k is 5. In certain embodiments, k is 6.

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, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group. In certain embodiments, all instances of RA1are each independently hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group. In certain embodiments, all instances of RA1are hydrogen.

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, wherein RA2ais as defined herein. In certain embodiments, at least one RA2is —ORA2a, wherein RA2ais hydrogen. In certain embodiments, at least one RA2is —ORA2a, wherein RA2ais substituted or unsubstituted C1-6alkyl. In certain embodiments, at least one RA2is —ORA2a, wherein RA2ais unsubstituted C1-6alkyl. In certain embodiments, at least one RA2is —OCH3. In certain embodiments, at least one RA2is —N(RA2a)2. In certain embodiments, at least one RA2is —SRA2a. In certain embodiments, all instances of RA2are hydrogen.

In certain embodiments, all RA1and RA2are hydrogen. In certain embodiments, RA1is hydrogen; and at least one RA2is substituted or unsubstituted alkyl. In certain embodiments, RA1is hydrogen; and at least one RA2is unsubstituted alkyl. In certain embodiments, RA1is hydrogen; and at least one RA2is methyl, ethyl, or n-propyl. In certain embodiments, RA1is hydrogen; and at least one RA2is-ORA2a, wherein RA2ais as defined herein. In certain embodiments, RA1is hydrogen; and at least one RA2is-ORA2a, wherein RA2ais substituted or unsubstituted C1-6alkyl. In certain embodiments, RA1is hydrogen; and at least one RA2is-ORA2a, wherein RA2ais unsubstituted C1-6alkyl. In certain embodiments, RA1is hydrogen; and at least one RA2is-OCH3.

In certain embodiments, Rais H. In certain embodiments, Rais halogen. In certain embodiments, Rais F. In certain embodiments, Rais Cl. In certain embodiments, Rais Br. In certain embodiments, Rais I (iodine). In certain embodiments, Rais substituted C1-6alkyl. In certain embodiments, Rais unsubstituted C1-6alkyl. In certain embodiments, Rais methyl. In certain embodiments, Rais ethyl. In certain embodiments, at least one Rais H. In certain embodiments, each Rais H. In certain embodiments, at least one Rais halogen (e.g., F, Cl, Br, or I (iodine)). In certain embodiments, at least one Rais substituted or unsubstituted alkyl. In certain embodiments, at least one Rais substituted C1-6alkyl. In certain embodiments, at least one Rais unsubstituted C1-6alkyl. In certain embodiments, at least one Rais Me. In certain embodiments, at least one Rais substituted methyl (e.g., —CF3or Bn), Et, substituted ethyl (e.g., fluorinated ethyl), Pr, substituted propyl (e.g., fluorinated propyl), Bu, or substituted butyl (e.g., fluorinated butyl). In certain embodiments, at least one Rais substituted or unsubstituted alkenyl or substituted or unsubstituted alkynyl. In certain embodiments, at least one Rais substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In certain embodiments, at least one Rais a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom. In certain embodiments, two instances of Raare joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring.

In certain embodiments, RB1and RB2are the same. In certain embodiments, RB1and RB2are different. In certain embodiments, both RB1and RB2are hydrogen. In certain embodiments, RB1is hydrogen and RB2is hydrogen, halogen, substituted or unsubstituted alkyl, —ORaa, or —N(Ra)2, wherein each instance of Rais independently hydrogen or substituted or unsubstituted alkyl. In certain embodiments, RB1is hydrogen and RB2is halogen. In certain embodiments, RB1is hydrogen and RB2is substituted or unsubstituted alkyl. In certain embodiments, RB1is hydrogen and RB2is unsubstituted alkyl. In certain embodiments, RB1is hydrogen and RB2is methyl or ethyl. In certain embodiments, RB2is hydrogen and RB1is hydrogen, halogen, substituted or unsubstituted alkyl, —ORaa, or —N(Ra)2, wherein each instance of Rais independently hydrogen, substituted or unsubstituted alkyl, an oxygen protecting group when attached to oxygen, or a nitrogen protecting group when attached to nitrogen. In certain embodiments, RB2is hydrogen and RB1is halogen. In certain embodiments, RB2is hydrogen and RB1is substituted or unsubstituted alkyl. In certain embodiments, RB2is hydrogen and RB1is unsubstituted alkyl. In certain embodiments, RB2is hydrogen and RB1is methyl or ethyl. In certain embodiments, RB2is hydrogen and RB1is —ORaa, wherein Rais independently hydrogen, substituted or unsubstituted alkyl, or an oxygen protecting group. In certain embodiments, RB2is hydrogen and RB1is —N(Ra), wherein each instance of Rais independently hydrogen, substituted or unsubstituted alkyl, or a nitrogen protecting group.

In certain embodiments, Rbis H. In certain embodiments, Rbis halogen. In certain embodiments, Rbis F. In certain embodiments, Rbis Cl. In certain embodiments, Rbis Br. In certain embodiments, Rbis I (iodine). In certain embodiments, Rbis substituted C1-6alkyl. In certain embodiments, Rbis unsubstituted C1-6alkyl. In certain embodiments, Rbis methyl. In certain embodiments, Rbis ethyl. In certain embodiments, at least one Rbis H. In certain embodiments, each Rbis H. In certain embodiments, at least one Rbis halogen (e.g., F, Cl, Br, or I (iodine)). In certain embodiments, at least one Rbis substituted C1-6alkyl. In certain embodiments, at least one Rbis unsubstituted C1-6alkyl. In certain embodiments, at least one Rbis Me. In certain embodiments, at least one Rbis substituted methyl (e.g., —CF3or Bn), Et, substituted ethyl (e.g., fluorinated ethyl), Pr, substituted propyl (e.g., fluorinated propyl), Bu, or substituted butyl (e.g., fluorinated butyl).

In certain embodiments, Rcis H. In certain embodiments, Rcis substituted C1-6alkyl. In certain embodiments, Rcis unsubstituted C1-6alkyl. In certain embodiments, Rcis methyl. In certain embodiments, Rcis ethyl. In certain embodiments, Rcis a nitrogen protecting group. In certain embodiments, Rcis BOC, acetyl, or Ts. In certain embodiments, at least one Rcis H. In certain embodiments, each Rcis H. In certain embodiments, at least one Rcis halogen (e.g., F, Cl, Br, or I (iodine)). In certain embodiments, at least one Rcis substituted C1-6alkyl. In certain embodiments, at least one Rcis unsubstituted C1-6alkyl. In certain embodiments, at least one Rcis Me. In certain embodiments, at least one Rcis substituted methyl (e.g., —CF3or Bn), Et, substituted ethyl (e.g., fluorinated ethyl), Pr, substituted propyl (e.g., fluorinated propyl), Bu, or substituted butyl (e.g., fluorinated butyl). In certain embodiments, at least one Rcis a nitrogen protecting group.

In certain embodiments, L1is a bond, —O—, —S—, or —NRc—; and X is —C(Rb)2—, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O)2—, or —NRc—, wherein Rband Rcare as defined herein. In certain embodiments, L1is a bond and X is —C(Rb)2—, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O)2—, or —NRc—, wherein Rband Rcare as defined herein. In certain embodiments, L1is a bond and X is —O—. In certain embodiments, L1is a bond and X is —S—. In certain embodiments, L1is a bond and X is-NRc—, wherein Rcis as defined herein. In certain embodiments, L1is a bond and X is-NH—. In certain embodiments, L1is —O— and X is —C(Rb)2—, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O)2—, or —NRc—, wherein Rband Rcare as defined herein. In certain embodiments, L1is —O— and X is —O—. In certain embodiments, L1is —O— and X is —S—. In certain embodiments, L1is —O— and X is-NRc—, wherein Rcis as defined herein. In certain embodiments, L1is —O— and X is-NH—.

In certain embodiment, X and L2are para to each other. In certain embodiments, X and L2are meta to each other. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring. In certain embodiments, Ring C is a substituted phenyl ring. In certain embodiments, Ring C is an unsubstituted phenyl ring. In certain embodiments, Ring C is a substituted or unsubstituted 1,2-phenylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted 1,3-phenylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted 1,4-phenylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted substituted or unsubstituted, monocyclic carbocyclic ring. In certain embodiments, wherein Ring C is a substituted or unsubstituted, 3- to 7-membered, monocyclic carbocyclic ring, wherein there are zero, one, or two double bonds in the carbocyclic ring system, as valency permits. In certain embodiments, Ring C is a substituted or unsubstituted cyclopentylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted cyclohexylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted trans-cyclohexylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted cis-cyclohexylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted 1,2-cyclohexylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted 1,3-cyclohexylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted 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 a substituted or unsubstituted, monocyclic heterocyclic ring. In certain embodiments, Ring C is a substituted or unsubstituted, 5-membered heterocyclic ring. In certain embodiments, Ring C is a substituted or unsubstituted, 6-membered heterocyclic ring. In certain embodiments, Ring C is a substituted or unsubstituted, 3- to 7-membered, monocyclic heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring system are independently oxygen, nitrogen, or sulfur, as valency permits. In certain embodiments, Ring C is a substituted or unsubstituted piperidinylene moiety. In certain embodiments, Ring C is of the formula:

wherein x indicates the point of attachment to linker X and 1 indicates the point of attachment to linker L2. In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of one of the formulae:

In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of one of the formulae:

In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of one of the formulae:

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 one of the formulae:

In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of one of the formulae:

In certain embodiments, Ring C is of the formula:

In certain embodiments, Ring C is of one of the formulae:

In certain embodiments, Ring C is of the formula:

wherein RCNis hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group. In certain embodiments, Ring C is a substituted or unsubstituted, monocyclic heteroaryl ring. In certain embodiments, Ring C is a substituted or unsubstituted, 5- or 6-membered, monocyclic heteroaryl ring, wherein one, two, three, or four atoms in the heteroaryl ring system are independently oxygen, nitrogen, or sulfur, as valency permits. In certain embodiments, Ring C is substituted or unsubstituted pyridinylene. In certain embodiments, Ring C is substituted or unsubstituted 2-pyridinylene, wherein X is attached to the 1-position of the substituted or unsubstituted 2-pyridinylene.

Ring C may be unsubstituted or may be substituted with one or more RCgroups. 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 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 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, each instance of RCis independently halogen, substituted or unsubstituted C1-6alkyl, or —ORa(e.g., —OH or —O(substituted or unsubstituted C1-6alkyl)).

In certain embodiments, Ring C is a substituted phenyl ring and at least one RCis independently halogen or substituted or unsubstituted C1-6alkyl. In certain embodiments, Ring C is a substituted phenyl ring and at least one RCis independently halogen. In certain embodiments, Ring C is a substituted phenyl ring and at least one RCis substituted or unsubstituted C1-6alkyl. In certain embodiments, Ring C is a substituted phenyl ring and one RCis substituted or unsubstituted C1-6alkyl. In certain embodiments, Ring C is a substituted phenyl ring and one RCis unsubstituted C1-6alkyl (e.g. methyl or ethyl).

Ring C may be unsubstituted or substituted with one or more RCgroups as valency permits. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring and n is 0, 1, 2, 3, or 4. In certain embodiments, Ring C is a substituted or unsubstituted, monocyclic carbocyclic ring and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, as valency permits. In certain embodiments, Ring C is a substituted or unsubstituted cyclohexylene moiety and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, as valency permits. In certain embodiments, Ring C is a substituted or unsubstituted, monocyclic heterocyclic ring and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, as valency permits. In certain embodiments, Ring C is a substituted or unsubstituted, 6-membered monocyclic heterocyclic ring and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, as valency permits.

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 or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring. In certain embodiments, Ring D is a substituted phenyl ring. In certain embodiments, Ring D is an unsubstituted phenyl ring. In certain embodiments, Ring D is a substituted or unsubstituted 1,2-phenylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted 1,3-phenylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted 1,4-phenylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted substituted or unsubstituted, monocyclic carbocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted, 3- to 7-membered, monocyclic carbocyclic ring, wherein there are zero, one, or two double bonds in the carbocyclic ring system, as valency permits. In certain embodiments, Ring D is a substituted or unsubstituted cyclopentylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted cyclohexylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted trans-cyclohexylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted cis-cyclohexylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted 1,2-cyclohexylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted 1,3-cyclohexylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted 1,4-cyclohexylene moiety. 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 a substituted or unsubstituted, monocyclic heterocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted, 5-membered heterocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted, 6-membered heterocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted, 3- to 7-membered, monocyclic heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring system are independently oxygen, nitrogen, or sulfur, as valency permits. In certain embodiments, Ring D is a substituted or unsubstituted piperidinylene moiety. In certain embodiments, Ring D is of the formula:

wherein l′ indicates the point of attachment to linker L2and e indicates the point of attachment to RE. In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of one of the formulae:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of one of the formulae:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of one of the formulae:

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 one of the formulae:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of one of the formulae:

In certain embodiments, Ring D is of the formula:

In certain embodiments, Ring D is of one of the formulae:

In certain embodiments, Ring D is of the formula:

wherein RDNis hydrogen, substituted or unsubstituted C1-6alkyl, or a nitrogen protecting group.

In certain embodiments, at least one of Ring C and Ring D is a substituted or unsubstituted phenyl ring. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring and Ring D is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring and Ring C is a substituted or unsubstituted phenyl ring, substituted or unsubstituted, monocyclic carbocyclic ring, or substituted or unsubstituted, monocyclic heterocyclic ring. In certain embodiments, each of Ring C and Ring D is independently a substituted or unsubstituted phenyl ring. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring and Ring D is a substituted or unsubstituted, monocyclic carbocyclic ring. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring and Ring D is a substituted or unsubstituted cyclohexylene moiety. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring and Ring D is a substituted or unsubstituted heterocyclic ring. In certain embodiments, Ring C is a substituted or unsubstituted phenyl ring and Ring D is a substituted or unsubstituted piperidinylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring and Ring C is a substituted or unsubstituted, monocyclic carbocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring and Ring C is a substituted or unsubstituted cyclohexylene moiety. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring and Ring C is a substituted or unsubstituted heterocyclic ring. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring and Ring C is a substituted or unsubstituted piperidinylene moiety.

In compounds of Formula (I), 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 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, each instance of RDis independently halogen, substituted or unsubstituted C1-6alkyl, or —ORa(e.g., —OH or —O(substituted or unsubstituted C1-6alkyl)).

Ring D may be unsubstituted or substituted with one or more RDgroups as valency permits. In certain embodiments, Ring D is a substituted or unsubstituted phenyl ring and p is 0, 1, 2, 3, or 4. In certain embodiments, Ring D is a substituted or unsubstituted, monocyclic carbocyclic ring and p is 0, 1, 2, 3, 4, 5, 6, 7, 8, or 9, as valency permits. In certain embodiments, Ring D is a substituted or unsubstituted cyclohexylene moiety and p is 0, 1, 2, 3, 4, 5, 6, 7, 8, or 9, as valency permits. In certain embodiments, Ring D is a substituted or unsubstituted, monocyclic heterocyclic ring and p is 0, 1, 2, 3, 4, 5, 6, 7, 8, or 9, as valency permits. In certain embodiments, Ring D is a substituted or unsubstituted, 6-membered monocyclic heterocyclic ring and p is 0, 1, 2, 3, 4, 5, 6, 7, 8, or 9, as valency permits.

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 substituted or unsubstituted 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., PIP4K) 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.

As generally defined herein, REmay be any one of Formulae (i-1)-(i-41). In certain embodiments, REis of Formula (i-1):

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

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

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

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

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

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

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

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

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

In certain embodiments, REis of Formula (i-11):

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

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

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

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

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

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

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

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

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

In certain embodiments, REis of Formula (i-21):

In certain embodiments, REis of Formula (i-22):

In certain embodiments, REis of Formula (i-23):

In certain embodiments, REis of Formula (i-24):

In certain embodiments, REis of Formula (i-25):

In certain embodiments, REis of Formula (i-26):

In certain embodiments, REis of Formula (i-27):

In certain embodiments, REis of Formula (i-28):

In certain embodiments, REis of Formula (i-29):

In certain embodiments, REis of Formula (i-30):

In certain embodiments, REis of Formula (i-31):

In certain embodiments, REis of Formula (i-32):

In certain embodiments, REis of Formula (i-33):

In certain embodiments, REis of Formula (i-34):

In certain embodiments, REis of Formula (i-35):

In certain embodiments, REis of Formula (i-36):

In certain embodiments, REis of Formula (i-37):

In certain embodiments, REis of Formula (i-38):

In certain embodiments, REis of Formula (i-39):

In certain embodiments, REis of Formula (i-40):

In certain embodiments, REis of Formula (i-41):

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

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

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

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

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

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

RE3(i-1f). In certain embodiments, REis of Formula (i-1g):

In certain embodiments, REis

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

In certain embodiments, REis

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

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

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

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

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

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

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

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

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

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, Ring D is of the formula:

In certain embodiments, Ring D is of one of the following formulae:

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 one of the following formulae:

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 one of the following formulae:

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 R is unsubstituted 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 a substituted or unsubstituted carbocyclic or substituted or unsubstituted heterocyclic ring. In certain embodiments, RE1and RE3are joined to form a substituted or unsubstituted carbocyclic ring. In certain embodiments, RE1and RE3are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, RE2and RE3are joined to form a substituted or unsubstituted carbocyclic ring. In certain embodiments, RE2and RE3are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, RE1and RE2are joined to form a substituted or unsubstituted carbocyclic ring. In certain embodiments, RE1and RE2are joined to form a substituted or unsubstituted 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 (i-1); and RE1is hydrogen. In certain embodiments, REis of Formula (i-1); and RE2is hydrogen. In certain embodiments, REis of Formula (i-1); and RE3is hydrogen. In certain embodiments, REis of Formula (i-1); and RE2and RE3are each hydrogen. In certain embodiments, REis of Formula (i-1); and RE1, RE2and RE3are each hydrogen. In certain embodiments, REis of Formula (i-1); and RE1is —CH2N(RE1a). In certain embodiments, REis of Formula (i-1); RE1is —CH2N(RE1a); and RE1ais C1-6alkyl. In certain embodiments, REis of Formula (i-1); RE1is —CH2N(RE1a); and RE1ais methyl. In certain embodiments, REis of Formula (i-1); and RE2is —CH2N(RE2a). In certain embodiments, REis of Formula (i-1); RE2is —CH2N(RE2a); and RE2ais C1-6alkyl. In certain embodiments, REis of Formula (i-1); RE2is —CH2N(RE2a); and RE2ais methyl. In certain embodiments, REis of Formula (i-1); and RE3is —CH2N(RE3a). In certain embodiments, REis of Formula (i-1); RE3is —CH2N(RE3a); and RE3ais C1-6alkyl. In certain embodiments, REis of Formula (i-1); RE3is —CH2N(RE3a); and RE3ais methyl. In certain embodiments, REis of Formula (i-1); and Y is ═O. In certain embodiments, REis of Formula (i-1); and L3is —NRL3a—. In certain embodiments, REis of Formula (i-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, 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 the formula:

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

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of Formula (II-b):

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is one of the following formulae:

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of Formula (V-b):

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

or a pharmaceutically acceptable salt thereof.

In certain embodiments, the compound of Formula (I) is of one of the following formulae:

or a pharmaceutically acceptable salt thereof.

In certain embodiments of Formulae (I)-(VI), REis of Formula (i-1); and L3is —NRL3a—. In certain embodiments of Formulae (I)-(VI), REis of Formula (i-1); and L3is —NH—. In certain embodiments of Formulae (I)-(VI), REis of the formula:

In certain embodiments of Formulae (I)-(VI), REis of the formula:

In certain embodiments, REis of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

or a pharmaceutically acceptable salt thereof. In certain embodiments, the compound of Formula (I) is of the formula:

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 kinase. The compounds of the present invention may also inhibit a kinase. In certain embodiments, the kinase is a protein kinase. In certain embodiments, the protein kinase is a CDK (e.g., CDK7, CDK12, and/or CDK13). In certain embodiments, the kinase is a lipid kinase. In certain embodiments, the protein kinase is a PIP4K. In certain embodiments, the PIP4K is a PIP4K2. In certain embodiments, the PIP4K2 is PIP4K2A protein. In certain embodiments, the PIP4K2 is PIP4K2B protein. In certain embodiments, the PIP4K2 is PIPK2C protein. Ring A of the inventive compounds may be accommodated by a hydrophobic pocket in the ATP-binding site of the kinase (e.g., a lipid kinase such as PIP4K2 enzyme). Functionalities on Rings A and B may bind to residues of the kinase (e.g., a lipid kinase such as PIP4K2 enzyme). For example, Ring A may form a hydrogen bond with a Cys residue of PIP4K (e.g. Cys293 of PIP4K2A enzyme or Cys307 and/or Cys318 of PIP4K2B enzyme). Functional groups of REmay form one or more hydrogen bonds with the kinase (e.g., a lipid kinase such as PIP4K2 enzyme). Moreover, the Michael acceptor moiety of REmay react with a cysteine residue of the kinase (e.g., a lipid kinase such as PIP4K2 enzyme) to allow covalent attachment of the compound to the kinase (e.g., a lipid kinase such as a PIP4K2 enzyme).

In certain embodiments, the provided compound is capable of covalently modifying Cys293 of PI5P4Kα. In certain embodiments, the provided compound is capable of covalently modifying Cys307 and/or Cys318 of PI5P4Kβ. In certain embodiments, the provided compound is capable of covalently modifying Cys313 of PI5P4Kγ while Cys313 is based on the sequence alignment.

The compounds of the present invention are thought to be kinase inhibitors. In certain embodiments, the inventive compounds are inhibitors of protein kinases. 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 CDK12 inhibitors. In certain embodiments, the inventive compounds are CDK13 inhibitors. In certain embodiments, the inventive compounds are inhibitors of lipid kinases. In certain embodiments, the inventive compounds are PIPK inhibitors. In certain embodiments, the inventive compounds are PIP4K2 inhibitors. In certain embodiments, the inventive compounds are PIP4K2A inhibitors. In certain embodiments, the inventive compounds are PIP4K2B inhibitors. In certain embodiments, the inventive compounds are PIP4K2C 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. In certain embodiments, the inventive compounds are selective PIPK inhibitors (e.g., being more active in inhibiting a PIPK than a non-PIPK kinase). In certain embodiments, the inventive compounds are selective PIP4K2 inhibitors (e.g., being more active in inhibiting PIP4K2 than a non-PIP4K2 kinase). In certain embodiments, the inventive compounds are selective PIP4K2A inhibitors. In certain embodiments, the inventive compounds are selective PIP4K2B inhibitors. In certain embodiments, the inventive compounds are selective PIP4K2C inhibitors.

The selectivity of an inventive compound for a first kinase (e.g., lipid kinase) over a second kinase (e.g., a non-lipid 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).

The compounds as described herein differ in the Ring B moiety from the compounds disclosed in WO2014/063068 published Apr. 24, 2014. The compounds as described herein are also differ in the Ring A moiety from the compounds disclosed in International Application No. PCT/US2015/027312 filed Apr. 23, 2015.

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. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin. 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. 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). An effective amount may be included in a single dose (e.g., single oral dose) or multiple doses (e.g., multiple oral doses). In certain embodiments, when multiple doses are administered to a subject or applied to a tissue or cell, any two doses of the multiple doses include different or substantially the same amounts of a compound described herein. In certain embodiments, when multiple doses are administered to a subject or applied to a tissue or cell, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses a day, two doses a day, one dose a day, one dose every other day, one dose every third day, one dose every week, one dose every two weeks, one dose every three weeks, or one dose every four weeks. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is one dose per day. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is two doses per day. In certain embodiments, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses per day. In certain embodiments, when multiple doses are administered to a subject or applied to a tissue or cell, the duration between the first dose and last dose of the multiple doses is one day, two days, four days, one week, two weeks, three weeks, one month, two months, three months, four months, six months, nine months, one year, two years, three years, four years, five years, seven years, ten years, fifteen years, twenty years, or the lifetime of the subject, tissue, or cell. In certain embodiments, the duration between the first dose and last dose of the multiple doses is three months, six months, or one year. In certain embodiments, the duration between the first dose and last dose of the multiple doses is the lifetime of the subject, tissue, or cell. In certain embodiments, a dose (e.g., a single dose, or any dose of multiple doses) described herein includes independently between 0.1 μg and 1 μg, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg, between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg, between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and 300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 1 mg and 3 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 3 mg and 10 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 10 mg and 30 mg, inclusive, of a compound described herein. In certain embodiments, a dose described herein includes independently between 30 mg and 100 mg, inclusive, of a compound described herein.

In certain embodiments, a dose described herein is a dose to an adult human whose body weight is 70 kg. 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 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.

Exemplary additional pharmaceutical agents include, but are not limited to, anti-proliferative agents, anti-cancer agents, anti-diabetic agents, anti-inflammatory agents, immunosuppressant agents, and a pain-relieving agent. Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In certain embodiments, the additional pharmaceutical agent is selected from the group consisting of cytotoxic agents, epigenetic or transcriptional modulators (e.g., DNA methyltransferase inhibitors, histone deacetylase inhibitors (HDAC inhibitors), lysine methyltransferase inhibitors), antimitotic drugs (e.g., taxanes and vinca alkaloids), hormone receptor modulators (e.g., estrogen receptor modulators and androgen receptor modulators), cell signaling pathway inhibitors (e.g., tyrosine protein kinase inhibitors), modulators of protein stability (e.g., proteasome inhibitors), Hsp90 inhibitors, glucocorticoids, all-trans retinoic acids, and other agents that promote differentiation. In certain embodiments, the compounds described herein or pharmaceutical compositions can be administered in combination with an anti-cancer therapy including, but not limited to, surgery, radiation therapy, transplantation (e.g., stem cell transplantation, bone marrow transplantation), immunotherapy, and chemotherapy.

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. The proliferative disease to be treated or prevented using the compounds of Formula (I) may be associated with aberrant activity of a kinase. In certain embodiments, the kinase is a lipid kinase. In certain embodiments, the lipid kinase is a PIP kinase. In certain embodiments, the PIPK is PIP4K, catalyzing phosphorylation of lipid phosphatidylinositol-5-phosphate (PI-5-P) at the 4-position to generate phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2). In some embodiments, the PIP4K is class I PIP4K, i.e. PIP4K1. In some embodiments, the PIP4K is class II PIP4K, i.e. PIP4K2. In some embodiments, the PIP4K2 is PIP4K2A protein. In some embodiments, the PIP4K2 is PIP4K2B protein. In some embodiments, the PIP4K2 is PIP4K2C protein.

In certain embodiments, the kinase is a protein kinase. In certain embodiments, the protein kinase is a 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. In certain embodiments, the CDK is CDK7. In certain embodiments, the CDK is CDK12. In certain embodiments, the CDK is CDK13.

In certain embodiments, 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.

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 some embodiments, the cancer has one or more mutations. In certain embodiments, the cancer has EGFR mutation. In certain embodiments, the cancer has TP53 mutation. In certain embodiments, the cancer has loss of TP53 mutation. In certain embodiments, the cancer has KRAS mutation. In certain embodiments, the cancer has ALK mutation. 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 lung cancer has one or more mutations. In certain embodiments, the lung cancer has EGFR mutation. In certain embodiments, the lung cancer has TP53 mutation. In certain embodiments, the lung cancer has loss of TP53 mutation. In certain embodiments, the lung cancer has KRAS mutation. In certain embodiments, the lung cancer has ALK mutation. 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 and published on Oct. 17, 2011, 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 modulating the activity of a kinase (e.g. a lipid kinase such as PIPK (e.g. PIP4K2A, PIP4K2B, or PIP4K2C protein) enzyme or a protein kinase such as CDK (e.g., CDK7, CDK1, CDK2, CDK5, CDK8, CDK9, CDK12, CDK13) enzyme) in a biological sample or subject. 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 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 additional pharmaceutical agent is an anti-macroglobulinemia agent.

In certain embodiments, the additional pharmaceutical agent is an inhibitor of a lipid kinase. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a PIP4K. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a PIP4K2. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a PIP4K2A. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a PIP4K2B. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a PIP4K2C. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a protein kinase. 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 an inhibitor of CDK12. In certain embodiments, the additional pharmaceutical agent is an inhibitor of CDK13. 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 certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of IRAK1, IRAK4, BMX, and PI3K. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of BUB1B, CDK2, CDK9, CHEK2, FGR, HIPK4, PRKCQ, RET, SRC, or MELK. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL, ARG, BLK, CSK, EphB1, EphB2, FGR, FRK, FYN, SRC, YES, LCK, LYN, MAP2K5, NLK, p38a, SNRK, and TEC. In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL1(H396P)-phosphorylated, ABL1-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, FGR, JAK3(JH domain-catalytic), KIT, KIT(L576P), KIT(V559D), PDGFRB, SRC, YES, ABL1(H396P)-nonphosphorylated, ABL1(Y253F)-phosphorylated, ABL1-nonphosphorylated, FRK, LYN, ABL1(Q252H)-nonphosphorylated, DDR1, EPHB 1, ERBB4, p38-alpha, ABL2, ABL(Q252H)-phosphorylated, SIK, EPHA8, MEK5, ABL1(E255K)-phosphorylated, ABL1(F317L)-nonphosphorylated, FYN, LCK, EPHA2, ABL(M351T)-phosphorylated, TXK, EGFR(L858R), EGFR(L861Q), ERBB2, ERBB3, EPHA5, ABL1 (F317I)-nonphosphorylated, EGFR(L747-E749del, A750P), CSK, EPHA1, ABL1(F317L)-phosphorylated, BRAF(V600E), EGFR, KIT-autoinhibited, and EGFR(E746-A750del). In certain embodiments, the additional pharmaceutical agent is an inhibitor of one or more protein kinases selected from the group consisting of ABL1(F317L)-nonphosphorylated, AB L (H396P)-nonphosphorylated, AB L (H396P)-phosphorylated, ABL-phosphorylated, BLK, EPHA4, EPHB2, EPHB3, EPHB4, JAK3(JH1domain-catalytic), KIT, KIT(L576P), KIT(V559D), LYN, PDGFRB, SRC, YES, ABL1-nonphosphorylated, ABL1(Y253F)-phosphorylated, ERBB3, FGR, FRK, p38-alpha, ABL1(F317I)-nonphosphorylated, DDR1, EPHA2, ABL1(Q252H)-phosphorylated, MEK5, ABL1(Q252H)-nonphosphorylated, ABL2, FYN, EPHB 1, ABL1(E255K)-phosphorylated, ABL1(F317L)-phosphorylated, EPHA1, ABL1(M351T)-phosphorylated, ERBB4, TXK, LCK, EPHA8, SIK, EPHA5, EGFR(L861Q), CSF1R-autoinhibited, BRAF(V600E), BRK, CSK, KIT(D816V), KIT-autoinhibited, EGFR(L747-T751del, Sins), EGFR(L858R), EGFR(L747-E749del, A750P), and CSF1R. In certain embodiments, the additional pharmaceutical agent is an anti-angiogenesis agent, anti-inflammatory agent, immunosuppressant, anti-bacterial agent, anti-viral agent, cardiovascular agent, cholesterol-lowering agent, anti-diabetic agent, anti-allergic agent, pain-relieving agent, or a combination thereof. In certain embodiments, the compounds described herein or pharmaceutical compositions can be administered in combination with an anti-cancer therapy including, but not limited to, transplantation (e.g., bone marrow transplantation, stem cell transplantation), surgery, radiation therapy, immunotherapy, and chemotherapy.

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., PIPK or CDK (e.g CDK7, CDK12, CDK13) enzyme), in inhibiting cell growth. 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 a lipid kinase. In certain embodiments, the desired characteristic is inhibition of PIPK. In certain embodiments, the desired characteristic is inhibition of PIP4K. In certain embodiments, the desired characteristic is inhibition of PIP4K2. In certain embodiments, the desired characteristic is inhibition of PIP4K2A. In certain embodiments, the desired characteristic is inhibition of PIP4K2B. In certain embodiments, the desired characteristic is inhibition of PIP4K2C. In certain embodiments, the desired characteristic is inhibition of a protein 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 inhibition of CDK12. In certain embodiments, the desired characteristic is inhibition of CDK13. In certain embodiments, the desired characteristic is down-regulation of a kinase such as PIPK or CDK.

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.

Example 1. The synthesis of (E)-N-(3-((6-(1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)-4-(4-(dimethylamino)but-2-enamido)benzamide

Compound 8 was prepared according to the method described in Scheme 1 or the method described below.

Compound numbers 1 to 8 recited in Example 1 apply only to Example 1, andFIGS. 2, 3A to 3D, 4A, 4B, 5A, and 5B. To a solution of 5-bromo-1H-pyrrolo[2,3-b]pyridine (10 g, 50.7 mmol) in pyridine (100 mL) was added benzenesulfonyl chloride (44.8 g, 253.8 mmol). The resulting mixture was heated to 80° C. for 4h and then concentrated under vacuum. The residue was diluted with EtOAc (300 mL). The pH of the solution was adjusted to 3 with 1M HCl and the resulting mixture was washed with NaHCO3and water. The organic layer washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (15 g, 88%) of the title compound (1) as a slightly yellow solid. MS m/z 339.19 [M+H]+.

To a solution of 5-bromo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]Pyridine (15 g, 44.5 mmol) in 1,4-dioxane (100 mL) was added 4,4,4′,4′,5,5,5′,5′-octamethyl-2,2′-bi(1,3,2-dioxaborolane)(13.5 g, 53.4 mmol), Pd(dppf)Cl2(1.6 g, 2.2 mmol) and KOAc (6.5g, 66.7 mmmol). The reaction mixture was heated to 100° C. for 12h under the N2. The resulting mixture was concentrated to dryness. The residue was purified by a silica gel column to afford (14 g, 82%) of the title compound (2) as a slightly yellow solid. MS m/z 385.26 [M+H]+.

To a solution of 1-(phenylsulfonyl)-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridine (1 g, 2.6 mmol) in MeCN and H2O (20 mL, 4/1, v/v) was added 4,6-dichloropyrimidine (0.38 g, 2.6 mmol), NaHCO3(0.21 g, 2.6 mmol) and Pd(PPh3)2Cl2(91 mg, 0.013 mmol). The reaction mixture was heated to 90° C. for 12h under the N2. Then the resulting mixture was diluted with EtOAc (100 mL) at room temperature, washed with water and brine and dried (Na2SO4). The residue was purified by a silica gel column to afford (0.8 g, 83%) of the title compound (3) as a slightly yellow solid. MS m/z 371.81 [M+H]+.

To a solution of 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo-[2,3-b]pyridine (0.5 g, 1.3 mmol) in NMP (10 mL) was added benzene-1,3-diamine (0.72 g, 6.7 mmol). The reaction mixture was heated to 150° C. for 5h. Then resulting mixture was diluted with EtOAc (150 mL) at room temperature, washed with water and brine, dried (Na2SO4). The residue was purified by a silica gel column to afford (0.3 g, 50%) of the title compound (4) as a slightly yellow solid. MS m/z 443.49 [M+H]+.

To a solution of N1-(6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)benzene-1,3-diamine (0.3 g, 0.67 mmol) in DCM (10 mL) was added TEA (83.0 mg, 0.81 mmol) and 4-nitrobenzoyl chloride (151 mg, 0.81 mmol) at 0° C. during 3 min. Then resulting mixture was diluted with DCM (50 mL), washed with water and brine, dried (Na2SO4). The residue was purified by a silica gel column to afford the title compound (5) (0.3 g, 75.0%) as a slightly yellow solid. MS m/z 592.60 [M+H]+.

To a solution of 4-nitro-N-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)benzamide (0.3 g, 0.50 mmol) in MeOH (10 mL) was added 10% Pd/C (50 mg). The reaction mixture was stirred at room temperature for 2h under a balloon of H2. Then resulting mixture was then filtered through a short pad of CELITE. The filtrate was concentrated to afford the title compound (6) (0.24 g, 84%) as a slightly yellow solid. MS m/z 562.60 [M+H]+.

To a solution of 4-amino-N-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)benzamide (0.24 g, 0.42 mmol) in MeCN (10 mL) was added DIEA (66.7 mg, 0.51 mmol) and (E)-4-bromobut-2-enoyl chloride (12.21 mg, 0.51 mmol) at 0° C. during 3 min. Then 2 mL of dimethylamine (4.0M in THF) was added. The reaction mixture was stirred at room temperature for 2h. Then it was concentrated and purified by a silica gel column to afford the title compound (7) (0.2 g, 71%) as a slightly yellow solid. MS m/z 673.76 [M+H]+.

Example 2. The Synthesis of THZ-CE-A-4-1

Compound numbers 1 to 8 recited in Example 2 apply only to Example 2. To a stirred suspension of 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (2.0 g, 54 mmol) in NMP, cyclohexane-1,3-diamine (0.74 g, 65 mmol) and DIEA (0.85 g, 65 mmol) was added and the solution was then heated at 150° C. overnight. The solution was cooled down to room temperature and then was diluted with 300 mL of ethyl acetate. The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (50/1) as eluent (1 g, yield 42%).

To a dichloromethane solution of free amine compound (3) (0.7 g, 1.5 mmol) was added 4-nitrobenzoyl chloride (0.35 g, 1.2 equiv). After stirring for 1 hour, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (30/1) as eluent (0.7 g, yield 75%).

The nitro compound (5) (0.65 g, 1.1 mmol) was dissolve in ethyl acetate/methanol (1:1, vol/vol, 70 ml), and the resulted suspension was treated with Pd/C (0.15 g). After nitrogen replacement three times, the reaction mixture was stirred at the room temperature overnight. The reaction mixture was filtered over CELITE, the solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate/NH3=(3/1/0.1) as eluent (0.4 g, yield 60%).

To a dichloromethane solution of free amine compound (6) (1.0 g, 1.76 mmol) was added (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (0.35 g, 2.11 mmol), DIEA (0.8 g, 6.16 mmol) and HATU (0.8 g, 2.11 mol). After stirring for 12 hours at room temperature, the solution was diluted with 100 mL of water, and extracted with dichloromethane (3×50 ml). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (50/1-30/1) as eluent (0.5 g, yield 30%)

The compound 8 (0.1 g) was dissolved in 1,4-dioxane (10.0 mL) and 1M NaOH solution (3.0 mL). The solution was stirred at room temperature for 6 hours and then extracted with chloroform/2-propanol (4/1, vol/vol, 300 mL). The organic layer was washed with water, brine and dried over Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (10/1-5/1) as eluent (10 mg, yield 10%). M/Z 539.28 [M+H]+.

Example 3. The Synthesis of THZ-CE-A-4-2

Compound numbers 1 to 6 recited in Example 3 apply only to Example 3. To a stirred suspension of 3-bromo-1-(phenylsulfonyl)-1H-indole (5.0 g, 14.87 mmol) in THF (50 mL) was added n-BuLi (2.5 M, 13 mL) at −98° C. and stirred for 5 minutes. Triisopropyl borate (3.37 g, 17.85 mmol) was then added dropwise at the same temperature. After 5 minutes, the reaction was quenched with aqueous HCl (10%), and the pH was adjusted to 6-7 with Na2CO3(3.6 g, 29.74 mmol), and tetrakis(triphenylphosphine)platinum (1 g) and 4,6-dichloropyrimidine (2.44 g, 16.36 mmol) were added directly, and the solution was refluxed overnight under nitrogen. Ethyl acetate and water were added, and the reaction mixture was filtered over CELITE. The ethyl acetate layer was dried by Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/dichloromethane=(1/2) as eluent (2.8 g, yield 51%).

3-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-indole (2) (1.4 g, 3.78 mmol) and benzene-1,3-diamine (0.82 g, 2.0 equiv) was dissolved in 30 mL of NMP. DIEA (0.51 g, 3.89 mmol) was added, and then the solution was heated at 150° C. overnight. The solution was cooled down to room temperature and was diluted with 300 mL of ethyl acetate. The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (10/1) as eluent (1.6 g, yield 95%).

To a pyridine solution of free amine compound (3) (1.6 g, 3.62 mmol) was added 4-nitrobenzoyl chloride (0.74 g, 1.2 equiv). After stirring for 3 hours at 80° C., The solution was cooled down to room temperature and then was diluted with 100 mL of water and extracted with ethyl acetate (3×100 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was used to the next step directly.

The compound (4) (2 g, 3.38 mmol) was dissolve in ethyl acetate/methanol (4:1, vol/vol, 70 ml), and the resulted suspension was treated with Pd/C (0.3 g). After nitrogen replacement three times the reaction mixture was stirred at the room temperature overnight. The reaction mixture was filtered over CELITE, the solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate/NH3=(3/1/0.1) as eluent (1.4 g, yield 74%)

To a solution of free amino compound (5) (1.4 g, 2.5 mmol) in dried acetonitrile (60 mL) was added N,N-Diisopropylethylamine (0.4 g, 3 mmol) and (E)-4-bromobut-2-enoyl chloride (0.55 g, 3 mmol) in dichloromethane (15 mL) at 0° C. dropwise. After stirring for 5 min, the solution of dimethylamine (2 M, 25 mL) in THF was added, and the reaction mixture was then stirred at the room temperature for 2 hours. The solution was diluted with 100 mL of water, and extracted with dichloromethane (3×100 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (20/1-10/1) as eluent (0.4 g, yield 24%)

Example 4. The Synthesis of THZ-CE-A-4-3

Compound numbers 1 to 7 recited in Example 4 apply only to Example 4. To a solution of 5-bromo-1H-pyrrolo[2,3-b]pyridine (50 g, 0.254 mol) in pyridine (300 mL) was added benzene sulfonyl chloride (224 g, 1.27 mol). The resulted mixture was heated at 85° C. for 4 hours and then concentrated under vacuum. The residue was diluted with EtOAc (1500 mL). The pH of the solution was adjusted to 3 with 1M HCl, and the resulted mixture was washed with NaHCO3and water. The organic layer was washed with water and brine, dried (Na2SO4) and concentrated. The residue was purified by a silica gel column to afford (85 g, 99.2%) of the title compound as a slightly yellow solid.

To a solution of 5-bromo-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (70 g, 0.208 mol) in 1,4-dioxane (560 mL) was added 4,4,4′,4′,5,5,5′,5′-octamethyl-2,2′-bi(1,3,2-dioxaborolane) (63 g, 0.25 mmol), Pd(dppf)Cl2(7.5 g, 12.5 mmol), and KOAc (98 g, 0.374 mol). The resulted mixture was heated at 100° C. for 12 hours under N2. The residue was concentrated and purified by a silica gel column to afford (79.2 g, 99.0%) of the title compound as a slightly yellow solid.

To a solution of 1-(phenylsulfonyl)-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridine (60g, 0.156 mol) in 1,4-Dioxane and H2O (600 mL, 1/1, v/v) was added 4,6-dichloropyrimidine (25.6 g, 0.172 mol), Na2CO3(19.8 g, 0.187 mol), and Pd(PPh3)4(9 g, 7.8 mmol). The resulted mixture was heated at 104° C. for 2.5 hours under N2. Then it was diluted with EtOAc (1500 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (42 g, 72.6%) of the title compound as a slightly yellow solid.

To a solution of 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo-[2,3-b]pyridine (1.85 g, 5 mmol) in NMP (5 mL) was added benzene-1,3-diamine (1.1 g, 10 mmol). The resulted mixture was heated at 150° C. for 8 hours. Then it was diluted with EtOAc (300 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (1 g, 46.0%) of the title compound as a slightly yellow solid.

To a solution of N1-(6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)benzene-1,3-diamine (0.88 g, 2 mmol) in DCM (10 mL) was added DIEA (390 mg, 3 mmol) and 3-nitrobenzoyl chloride (0.45 g, 2.4 mmol) at 0° C. for 5 min. Then it was diluted with DCM (100 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.8 g, 68.0%) of the title compound as a slightly yellow solid.

To a solution of 3-nitro-N-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)benzamide (0.8 g, 1.35 mmol) in MeOH (30 mL) was added Pd/C (100 mg). The resulted mixture was stirred at room temperature for 12 hours under H2. Then it was filtered through a short pad of CELITE, and purified by a silica gel column to afford (0.4 g, 53.0%) of the title compound as a slightly yellow solid.

To a solution of 3-amino-N-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)benzamide (0.4 g, 0.71 mmol) in DCM (20 mL) was added DIEA (0.2 g, 1.42 mmol) and (E)-4-bromobut-2-enoyl chloride (0.26 g, 1.42 mmol) at 0° C. for 30 min. Then it was added 2.0 M dimethylamine in THF (7 mL). The resulted mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by a silica gel column to afford (0.28 g, 59.0%) of the title compound as a slightly yellow solid.

Example 5. The Synthesis of THZ-CE-A-4-4

Compound numbers 1 to 5 recited in Example 5 apply only to Example 5. 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (11 g, 30 mmol) and tert-butyl 3-aminopiperidine-1-carboxylate (7.2 g, 36 mmol), DIEA (4.3 g, 33 mmol) was dissolved in 200 mL of NMP and was heated to 110° C. for overnight. The reaction mixture was poured into water and ethyl acetate. The solid was filtrated, and the filtrate was separated, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (8 g, 50%) of the title compound.

Compound (1) (8 g, 15 mmol) was dissolved in dry DCM (80 mL) and was the added TFA (40 mL) in an ice bath. The resulted mixture was stirred at room temperature for overnight. Concentration to remove TFA to afford the crude title compound which was used directly in the next step.

Compound (2) (1.5 g, 3.45 mmol) in DCM (50 ml) was added TEA (0.42 g, 4.14 mmol) and 4-nitrobenzoyl chloride (0.77 g, 4.14 mmol) at 0° C. After 3 hours stirring, it was diluted with DCM, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (1.2 g, 60%) of the title compound.

Compound (3) (1.2 g, 2 mmol) in methanol (40 mL) was added Pd/C (0.2 g), and the resulted mixture was stirred at room temperature for 12 hours under H2. Then it was filtered through a short pad of CELITE and purified by a silica gel column to afford (0.8 g, 73%) of the title compound.

Compound (4) (0.22 g, 0.4 mmol) and DIEA (0.08 g, 0.6 mmol) were dissolved in 10 mL of dry acetonitrile at 0° C. (E)-4-bromobut-2-enoyl chloride (0.11 g, 0.6 mmol) in 5 mL of DCM was then added. After 5 min stirring, a solution of dimethylamine in THF (2N, 4 mL) was added, and the solution was stirred for 1 hour. The reaction solution was diluted with DCM, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.17 g, 64%) of the title compound.

Compound (5) (0.17 g, 0.25 mmol) in 10 mL of 1,4-dioxane was added 1N aqueous solution of sodium hydroxide. The solution was stirred at room temperature for 4 hours. Then the pH of the solution was adjusted to 7.0 with 4M HCl. The solution was concentrated, and the residue was purified by a silica gel column to afford (68 mg, 52%) of the title compound MS m/z 525.26[M+H].

Example 6. The Synthesis of THZ-CE-A-4-5

Compound numbers 1 to 5 recited in Example 6 apply only to Example 6. In a sealed tube, 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (11 g, 30 mmol) and tert-butyl 3-aminopiperidine-1-carboxylate (7.2 g, 36 mmol), DIEA (4.3 g, 33 mmol) in 200 mL of NMP was heated to 110° C. for overnight. The reaction mixture was then cooled down and poured into water and ethyl acetate. The solution was filtrated and then was dried (Na2SO4) and concentrated. The residue was purified by a silica gel column to afford (8 g, 50%) of the title compound.

Compound (1) (8 g, 15 mmol) was dissolved in dry DCM (80 mL) and was the added TFA (40 mL) in an ice bath. The resulting mixture was stirred at room temperature for overnight. Concentration to remove TFA to afford the crude title compound which was used directly in the next step.

To a solution of Triphosgene (0.24 g, 0.8 mmol), TEA (0.71 g, 7 mmol) in DCM (30 mL) was added 3-nitroaniline (0.33 g, 2.4 mmol) in 10 mL of DCM. The mixture was stirred for 2 hours at 0° C. and a solution of compound (2) (0.87 g, 2 mmol) in DCM was added dropwise. Reaction solution was allowed to stir overnight. After cooling down to room temperature, the product precipitated as solid (1 g, yield 83.3%).

Compound (3) (1.29 g, 2.15 mmol), SnCl2(3.3 g, 17.24 mmol) in ethyl acetate/methanol (4/1) (50 mL) was refluxed overnight. The solution was then cooled down to room temperature and then was diluted with chloroform/isopropyl alcohol (4/1). The solution was washed with saturated sodium bicarbonate solution and then filtered by CELITE pad. The filtrate was dried over sodium sulfate and concentrated, and the product was obtained by flash chromatography with dichloromethane/methanol/ammonia (20/1/0.1-10/1/0.1) as eluent (0.9 g, yield 74%).

To solution of compound (4) (0.32 g, 0.56 mmol) and DIEA (0.11 g, 0.84 mmol) in acetonitrile (18 mL) was add (E)-4-bromobut-2-enoyl chloride (0.154 g, 0.84 mmol) in DCM (9 mL). The reaction solution was stirred for 5 min and then was added 2N solution of dimethylamine in THF (6 mL). After stirring for 1 hour, the solution was diluted with DCM, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.26 g, 68%) of the title compound.

To a solution of compound (5) (0.26 g, 0.38 mmol) in 1,4-dioxane (15 mL), 1M NaOH solution (15.0 mL) was added dropwise at 10° C., and then solution was stirred at room temperature for 4 hours. The solution was extracted with chloroform/2-propanol (4/1, vol/vol, 100 mL). The organic layer was washed with water, brine, and dried over Na2SO4. The solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (20/1-10/1) as eluent (0.06 g, yield 30%). MS m/z 540.28[M+H]+.

Example 7. The Synthesis of THZ-CE-A-4-6

Compound numbers 1 to 5 recited in Example 7 apply only to Example 7. In a sealed tube, 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (0.925 g, 2.5 mmol) and tert-butyl 4-aminopiperidine-1-carboxylate (1 g, 5 mmol), DIEA (0.48 g, 3.75 mmol) was dissolved in 20 mL of NMP, and the solution was heated to 130° C. for overnight. The solution was cooled down to room temperature and then was diluted with ethyl acetate (100 mL). The solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the residue was purified by a silica gel column to afford (0.72 g, 54%) of the title compound.

To a solution of compound (1) (0.72 g, 1.34 mmol) in dry CH2Cl2(8 mL) was added TFA (4 mL) in an ice bath and the mixture was stirred at room temperature for 3 hours. TFA was then removed under a reduced pressure. The residue then was dissolved again in CH2Cl2and then was washed with saturated sodium bicarbonate solution. The solution was dried (Na2SO4) and concentrated to afford (0.52 g, 90%) of the title compound as crude.

To a solution of compound (2) (0.72 g, 1.657 mmol) in CH2Cl2(25 mL) was added TEA (0.2 g, 1.99 mmol) and 4-nitrobenzoyl chloride (0.37 g, 1.99 mmol), and the solution was stirred at 0° C. for 4 hours. The reaction solution was filtered to give a solid which was washed by petrol ether to give compound as crude (0.9 g, yield 93%).

The nitro compound (3) (0.9 g, 1.54 mmol), SnCl2(2.34 g, 12.34 mmol) in ethyl acetate/methanol (4/1) (50 mL) was stirred and refluxed overnight. Reaction solution was then diluted with chloroform/isopropyl alcohol (4:1) and then washed with saturated sodium bicarbonate solution. The solution was then filtered, dried with sodium sulfate, and concentrated. The product was obtained by flash chromatography with dichloromethane/methanol/ammonia (20/1/0.1-10/1/0.1) as eluent (0.7 g, yield 82%)

To a solution of free amino compound (4) (0.4 g, 0.72 mmol) in dried acetonitrile (18 mL) was added DIEA (0.14 g, 1.08 mmol) and (E)-4-bromobut-2-enoyl chloride (0.2 g, 1.08 mmol) in dichloromethane (9 mL) at 0° C. dropwise. After stirring for 5 min, the solution of dimethylamine (2 M, 25 mL)) in THF was added, and the reaction mixture was then stirred at the room temperature for 2 hours. The solution was diluted with water (100 mL), extracted with dichloromethane (3×100 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (20/1-10/1) as eluent (0.37 g, yield 77%).

Example 8. The Synthesis of THZ-CE-A-4-7

Compound numbers 1 to 10 recited in Example 8 apply only to Example 8. To a solution of 3-nitroaniline (2.76 g, 20 mmol) and 4,6-dichloropyrimidine (4.5 g, 30 mmol) was dissolved in NMP (30 mL), DIEA (3.9 g, 30 mmol) was added and then was heated at 130° C. overnight. The solution was cooled down to room temperature and then was diluted with ethyl acetate. The resulted solution was washed with brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate (5/1) as eluent (2.4g, yield 48%).

6-chloro-N-(3-nitrophenyl)pyrimidin-4-amine (3) (2.4g, 9.6 mmol), SnCl2(15g, 76.8 mmol) was dissolved in ethyl acetae/methanol (4/1) (125 mL) and was refluxed overnight. The solution was extracted by chloroform: isopropyl alcohol (4:1) and washed with saturated sodium bicarbonate solution. The pH was adjusted to about 8.0 and filtered through CELITE pad. The filtrate was dried over sodium sulfate. Concentrated to dryness to give the crude product (1.47g, yield 70%).

N1-(6-chloropyrimidin-4-yl)benzene-1,3-diamine (1.47g, 6.7 mmol), 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (2.75g, 13.4 mmol), Na2CO3(1.42g, 13.4 mmol) was dissolved in 40/20 ml acetonitrile/water and then was added Pd (dppf)2Cl2CH2Cl2(1 g). The solution was then degassed and was refluxed under nitrogen overnight. The solution was cooled down to room temperature, and the solid was washed with petroleum ether. The solid was dissolved in dichloromethane and then filtered. The filtrate was concentrated to dryness to give the crude product (0.72g, yield 41%).

N1-(6-(pyridin-4-yl)pyrimidin-4-yl)benzene-1,3-diamine(6) (0.72g, 2.73 mmol) was dissolved DCM (30 ml) and TEA (0.42g, 4.1 mmol) and 4-nitrobenzoyl chloride (0.76g, 4.1 mmol) was then added. The reaction was stirred at 0° C. for 3 hours. The solid was then washed with petroleum ether to give the crude product (0.5g, yield 45%).

To a solution of 4-nitro-N-(3-((6-(pyridin-4-yl)pyrimidin-4-yl)amino)phenyl)benzamide (8) (0.72 g, 1.746 mmol) in ethyl acetate/methanol (4:1) (30 mL) was added SnCl2(2.65 g, 13.97 mmol). The resulting mixture was heated at 80° C. for 8 hours. The pH of the solution was adjusted to 7 with 1 M NaOH. It was concentrated to afford (0.59 g, 88%) of the title compound (9) as a solid. MS m/z 382.15 [M+H]+.

4-amino-N-(3-((6-(pyridin-4-yl)pyrimidin-4-yl)amino)phenyl)benzamide (0.12g, 0.3 mmol), (E)-4-(dimethylamino)but-2-enoic acid (60 mg, 0.36 mmol), and DIEA (60 mg, 0.45 mmol) were dissolved in DMF (2 mL), and HATU was added (0.171g, 0.45 mmol). The solution was stirred at room temperature for 1 hour. The solution was diluted with ethyl acetate and water. The organic layer was washed twice with saturated sodium bicarbonate, dried over sodium sulfate, concentrated, and the product was obtained by flash chromatography with DCM/MeOH/NH3=(8/1/0.1) as eluent (41 mg, yield 28%). MS m/z 494.23 [M+H]+.

Example 9. The Synthesis of THZ-CE-A-4-8

Compound numbers 1 to 5 recited in Example 9 apply only to Example 9. In a sealed tube, 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (11 g, 30 mmol) and tert-butyl 3-aminopiperidine-1-carboxylate (7.2 g, 36 mmol), DIEA (4.3 g, 33 mmol) in NMP (200 mL) were heated to 110° C. overnight. The reaction mixture was cooled down and poured into water and ethyl acetate. The solution was filtrated and was washed with water, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (8 g, 50%) of the title compound.

To a solution of compound (1) (8 g, 15 mmol) in dry CH2Cl2(80 ml) was added dropwise TFA (40 mL). The resulted mixture was stirred at room temperature for overnight. The solution was then concentrated to remove TFA. The residue was dissolved again in CH2Cl2(80 mL). The solution was then washed with saturated sodium bicarbonate solution, water, dried (Na2SO4), and concentrated to afford (5.5 g, 84.6%) of the title compound as crude.

To Compound (2) (1.5 g, 3.45 mmol) in CH2Cl2(50 ml) was added TEA (0.42 g, 4.14 mmol) and 1-(chloromethyl)-4-nitrobenzene (0.77 g, 4.14 mmol) at 0° C., and then solution was stirred overnight. The solvent was then removed, and the residue was dissolved in CH2Cl2. Then product was precipitated by adding petroleum ether to the solution (1.7 g, yield 87%).

Compound (3) (2.7 g, 4.7 mmol), and SnCl2(7.2 g, 38 mmol) were dissolved in ethyl acetate/methanol (4/1) (80 mL), and the solution was stirred and refluxed overnight. The solution was extracted with chloroform/isopropyl alcohol (4:1) and then washed with saturated sodium bicarbonate solution, and water, dried (Na2SO4), and concentrated. The product was obtained by flash chromatography with dichloromethane/methanol/ammonia (20/1/0.1-10/1/0.1) as eluent (2.0 g, yield 79%).

To Compound (4) (0.43 g, 0.8 mmol) and DIEA (0.16 g, 1.2 mmol) in dry acetonitrile (15 mL) was added (E)-4-bromobut-2-enoyl chloride (0.22 g, 1.2 mmol) in CH2Cl2(5 mL). After 5 min stirring, 2 N solution of dimethylamine in THF (8 mL) was added and then was stirred for 1 hour. The reaction solution was extracted with CH2Cl2, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.13 g, 25%) of the title compound.

To Compound (5) (70 mg, 0.11 mmol) in 1,4-dioxane (5 mL) was added 1 N aqueous solution of sodium hydroxide (5 mL). The reaction was stirred for 4 hours at room temperature. Then pH of the solution was adjusted to 7.0 with 4 M HCl and diluted with CH2Cl2. The solution was dried (Na2SO4) and concentrated. The product was obtained by a prep TLC (DCM:MeOH=5:1) (15 mg, 26%). MS m/z 511.26[M+H]+.

Example 10. The Synthesis of THZ-CE-A-4-9

Compound numbers 1 to 5 recited in Example 10 apply only to Example 10. 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (1) (10 g, 27 mmol) and benzene-1,3-diamine (4.73 g, 2.0 equiv) were dissolved in NMP (30 mL). DIEA (7 g, 54 mmol) was added, and then the solution was heated at 150° C. overnight. The solution was cooled down to room temperature and then was diluted with ethyl acetate (100 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (30/1) as eluent (5.5 g, yield 46%).

To a dichloromethane solution of free amine compound (2) (1.5 g, 3.39 mmol) was added 3-((tert-butoxycarbonyl)amino)cyclohexane-1-carboxylic acid (cis and trans, 0.9 g, 3.73 mmol) and HATU (1.55 g, 4.07 mol). After stirring for 3 hours at room temperature, the solution was diluted with water (100 mL), extracted with dichloromethane (3×50 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (50/1) as eluent (1.5 g, yield 60%).

To a methanol solution of compound (3) (1.5 g, 2.25 mmol) was added hydrochloric ether, and the reaction solution was allowed to stir at room temperature overnight. The solvent was then removed and ether was added. The filtering to give title compound as HCl salt (1.2 g, 90%).

To a dichloromethane solution of free amine compound (4) (1.0 g, 1.76 mmol) was added (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (0.35 g, 2.11 mmol), DIEA (0.8g, 6.16 mmol) and HATU (0.8 g, 2.11 mol). After stirring for 12 hours at room temperature, the solution was diluted with water (100 mL), and extracted with dichloromethane (3×50 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (50/1-30/1) as eluent (0.5 g, 30%)

To a solution of (E)-3-(4-(dimethylamino)but-2-enamido)-N-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)cyclohexane-1-carboxamide (5) (0.5 g, 0.7 mmol) in 1,4-dioxane (26.0 mL), 1M Sodium hydroxide solution (26.0 mL) was added dropwise at 10° C. After stirring at room temperature for 6 hours, the solution was extracted with chloroform/2-propanol (4/1, vol/vol, 300 mL). The organic layer was washed with water and brine, and dried over Na2SO4. The solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (20/1-10/1) as eluent (0.15 g, 30%). MS m/z 539.28 [M+H]+.

Example 11. The Synthesis of THZ-CE-A-4-10

Compound numbers 1 to 4 recited in Example 11 apply only to Example 11. To a dichloromethane solution of free amine compound (1) (1.5 g, 3.39 mmol) was added 4-((tert-butoxycarbonyl)amino)cyclohexane-1-carboxylic acid (0.9 g, 3.73 mmol) and HATU (1.55 g, 4.07 mol). After stirring for 3 hours at room temperature, the solution was diluted with water (100 mL) and then was extracted with dichloromethane (3×50 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (50/1) as eluent (1.5 g, yield 60%).

To a methanol solution of compound (2) (1.5 g, 2.25 mmol) was added hydrochloric ether, and the solution was stirred at room temperature overnight. The solvent was then removed, and ether was then added. The product was then obtained as HCl salt (1.2 g, yield 90%).

To a dichloromethane solution of free amine compound (3) (1.0 g, 1.76 mmol) was added (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (0.35 g, 2.11 mmol), DIEA (0.8 g, 6.16 mmol), and HATU (0.8 g, 2.11 mmol). After stirring for 12 hours at room temperature, the solution was diluted with water (100 mL) and then extracted with dichloromethane (3×50 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (50/1-30/1) as eluent (0.5 g, yield 30%).

To a solution of (E)-4-(4-(dimethylamino)but-2-enamido)-N-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)cyclohexane-1-carboxamide (4) (0.5 g, 0.7 mmol) in 1,4-dioxane (26.0 mL), 1 M Sodium hydroxide solution (26.0 mL) was added dropwise at 10° C. Then the solution was stirred at room temperature for 6 hours and was extracted with chloroform/2-propanol (4/1, vol/vol, 300 mL). The organic layer was washed with water and brine, and dried over Na2O4. The solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (20/1-10/1) as eluent (0.15 g, yield 30%). MS m/z 539.28 [M+H]+.

Example 12. The Synthesis of THZ-CE-A-4-12

Compound numbers 1 to 5 recited in Example 12 apply only to Example 12. To a solution of 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo-[2,3-b]pyridine (3.7 g, 10 mmol) in NMP (10 mL) was added 2-(3-aminophenyl)acetic acid (1.83 g, 12 mmol). The resulted mixture was heated at 140° C. for 12 hours. Then it was diluted with EtOAc (200 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.3 g, 6.1%) of the title compound as a slightly yellow solid.

To a solution of 2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)acetic acid (0.3 g, 0.62 mmol) in DMF (2 mL) was added HATU (0.35 g, 0.93 mmol), tert-butyl piperidin-4-ylcarbamate (0.19 g, 0.93 mmol), and DIEA (0.22 mL, 1.24 mmol). The resulting mixture was stirred at room temperature for 30 min. Then it was diluted with ethyl acetate (150 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.21 g, 51.2%) of the title compound as a white solid.

To a solution of tert-butyl(1-(2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)acetyl)piperidin-4-yl)carbamate (0.21 g, 0.31 mmol) in ethyl acetate (5 mL) was added 4 M HCl. The resulted mixture was stirred at room temperature for 30 min. Then it was diluted with EtOAc (100 mL). The pH of the solution was adjusted to 7.0 with 1 M NaOH. The organic layer was washed with water and brine, dried (Na2SO4), and concentrated to afford (0.15 g, 90.0%) of the title compound as a white solid.

To a solution of 1-(4-aminopiperidin-1-yl)-2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)ethan-1-one (0.5 g, 0.88 mmol) in DMF (2 mL) was added HATU (0.5 g, 1.32 mmol), (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (0.18 g, 1.06 mmol), and DIEA (0.34 g, 2.7 mmol). The resulted mixture was stirred at room temperature for 30 min. Then it was diluted with DCM (200 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.3 g, 50%) of the title compound as a white solid.

Example 13. The Synthesis of THZ-CE-A-4-13

Compound numbers 1 to 4 recited in Example 13 apply only to Example 13. To a solution of 2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)acetic acid (0.3 g, 0.62 mmol) in DMF (2 mL) was added HATU (0.35 g, 0.93 mmol), tert-butyl (4-aminocyclohexyl)carbamate (0.8 g, 3.75 mmol), and DIEA (0.65 g, 5 mmol). The resulting mixture was stirred at room temperature for 30 min. Then it was diluted with ethyl acetate (300 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (1.52 g, 89.2%) of the title compound as a white solid.

A solution of tert-butyl(4-(2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)acetamido)cyclohexyl)carbamate (1.52 g, 2.23 mmol) in 4 M HCl of EtOAc (20 mL) was stirred at room temperature for 30 min. Then it was diluted with EtOAc (300 mL). The pH of the solution was adjusted to 7.0 with 1 M NaOH. The organic layer was washed with water and brine, dried (Na2SO4), and concentrated to afford (1.3g, 100%) of the title compound as a white solid.

To a solution of N-(4-aminocyclohexyl)-2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)acetamide (0.93 g, 1.5 mmol) in DMF (5 mL) was added HATU (0.9 g, 2.3 mmol), (E)-4-(dimethylamino)but-2-enoic acid hydrochloride (0.3 g, 1.8 mmol), and DIEA (0.58 g, 4.5 mmol). The resulting mixture was stirred at room temperature for 30 min. Then it was diluted with DCM (200 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.6 g, 58%) of the title compound as a white solid.

A solution of (E)-4-(dimethylamino)-N-(1-(2-(3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)acetyl)piperidin-4-yl)but-2-enamide (0.6 g, 0.87 mmol) in 1 M NaOH and 1,4-dioxane (10 mL, 1/1, v/v) was stirred at room temperature for 4 hours. Then the pH of the solution was adjusted to 7.0 with 1 M HCl, and the resulted mixture was concentrated. The residue was purified by a silica gel column to afford (230 mg, 48%) of the title compound as a white solid. MS m/z 553.30 [M+H]+.

Example 14. The Synthesis of THZ-CE-A-4-14

Compound numbers 1 to 6 recited in Example 14 apply only to Example 14. To a solution of 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (1.5 g, 4 mmol) in 1,4-Dioxane was added 2-methyl-5-nitroaniline (1.23 g, 8 mmol), Cs2CO3(1.4 g, 4.4 mmol), Pd2(dba)3(0.07 g, 0.08 mmol), and 2-dicyclohexylphosphino-2′,4′,6′-triipropyl-1,1′-biphenyl(0.14 g, 0.24 mmol). The resulted mixture was heated at 104° C. for 3 hours under N2. Then it was diluted with EtOAc (1500 mL) at room temperature, washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (0.81 g, 42%) of the title compound as a slightly yellow solid.

To a solution of N-(2-methyl-5-nitrophenyl)-6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-amine (4.2 g, 8.63 mmol) in MeOH (200 mL) was added SnCl2(16.4 g, 86.3 mmol). The resulted mixture was heated at 80° C. for 8 hours. The pH of the solution was then adjusted to 7.0 with 1 M NaOH. The solution was concentrated. The residue was purified by a silica gel column to afford (2.4 g, 61%) of the title compound as a slightly yellow solid.

To a solution of 6-methyl-N-(6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)benzene-1,3-diamine (0.91 g, 2.0 mmol) in DMF (5.0 mL) was added HATU (1.14 g, 3.0 mmol), 4-((tert-butoxycarbonyl)amino)benzoic acid (0.71 g, 3.0 mmol), and DIEA (0.59 g, 4.0 mmol). The resulted mixture was stirred at room temperature for 30 min. Then it was diluted with ethyl acetate (300 mL), washed with water and brine, dried (Na2SO4), and concentrated. The residue was purified by a silica gel column to afford (1 g, 74%) of the title compound as a slightly yellow solid.

A solution of tert-butyl(4-((4-methyl-3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)carbamoyl)phenyl)carbamate (1 g, 1.5 mmol) in 4 M HCl of EtOAc (5.0 mL) was stirred at room temperature for 30 min. Then it was diluted with EtOAc (100 mL). The pH of the solution was adjusted to 7 with 1 M NaOH. The organic layer was washed with water and brine, dried (Na2SO4), and concentrated to afford (0.8 g, 85%) of the title compound as a white solid.

To a solution of 4-amino-N-(4-methyl-3-((6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-4-yl)amino)phenyl)benzamide (0.4 g, 0.7 mmol) in DCM (10 mL) was added DIEA (0.27 g, 2.1 mmol) and (E)-4-bromobut-2-enoyl chloride (0.23 g, 1.25 mmol) at 0° C. for 30 min. Then it was added 2.0 M dimethylamine in THF (3.5 mL). The resulted mixture was stirred at room temperature for 2 hours. Then it was concentrated and purified by a silica gel column to afford (0.2 g, 42%) of the title compound as a slightly yellow solid.

Example 15. The Synthesis of THZ-CE-A-4-15

Compound numbers 1 to 7 recited in Example 15 apply only to Example 15. To a stirred suspension of 1-(phenylsulfonyl)-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridine (6.0 g, 15 mmol) in acetonitrile and water (50 mL) was added tert-butyl (4,6-dichloropyrimidin-2-yl)carbamate (5 g, 19 mmol), NaHCO3(2g, 29.74 mmol), and Bis(triphenylphosphine)palladium(II) chloride (0.2 g), and the solution was refluxed overnight under N2. Ethyl acetate and water were added, and the reaction mixture was filtered over CELITE. The organic layer was dried by Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with Hexane/Ethyl acetate=(10/1) as eluent (3 g, yield 30%).

Tert-butyl(4-chloro-6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-2-yl)carbamate (2) (1.5 g, 3.1 mmol), benzene-1,3-diamine (0.38 g, 2.0 equiv), Cesium carbonate (1.5g, 0.06 eq), and Pd2(dba)3(0.06 g, 0.05 eq) were dissolved in 1,4-dioxane (30 mL) and then were refluxed overnight under nitrogen. The solution was cooled down to room temperature and then was diluted with 300 mL of ethyl acetate. The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (100/1) as eluent (1 g, yield 50%).

To a dichloromethane solution of free amine compound (3) (1.6 g, 2.9 mmol) was added 4-nitrobenzoyl chloride (0.64 g, 1.2 equiv), and triethylamine (0.5 g). After stirring for 3 hours at room temperature, the solution was diluted with of water (100 mL), and extracted with ethyl acetate (3×100 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (50/1) as eluent (1.5 g, yield 70%).

The nitro compound (4) (2.4 g, 3.38 mmol) was dissolve in ethyl acetate/methanol (10:1, vol/vol, 70 mL), and the resulted suspension was treated with Pd/C (0.5 g). After nitrogen replacement three times, the reaction mixture was stirred at the room temperature overnight. The reaction mixture was filtered over CELITE, the solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate/NH3=(3/1/0.1) as eluent (2.2 g, yield 90%).

To a dichloromethane solution of free amine compound (5) (1.0 g, 1.5 mmol) was added (E)-4-(dimethylamino)but-2-enoic acid (0.35 g, 2.11 mmol), DIEA (0.8g, 6.16 mmol) and HATU (0.8 g, 2.11 mol). After stirring for 12 hours at room temperature, the solution was diluted with water, and extracted with dichloromethane (3×50 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the crude product was obtained by flash chromatography with dichloromethane/methanol (50/1-30/1) as eluent (0.2 g, yield 20%).

To a solution of tert-butyl (E)-(4-((3-(4-(4-(dimethylamino)but-2-enamido)benzamido)phenyl)amino)-6-(1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)pyrimidin-2-yl)carbamate (6) (0.2 g) in methanol (26.0 mL), 1M HCl of diethyl ether solution (26.0 mL) was added dropwise at 10° C. The solution was then stirred at room temperature for 12 hours. The solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (50/1-10/1) as eluent (0.18 g, yield 95%).

Example 16. The Synthesis of THZ-CE-A-4-19

Compound numbers 1 to 11 recited in Example 16 apply only to Example 16. To a stirred suspension of 6-bromo-1-methyl-1H-indazole (1.0 g, 4.7 mmol) in 1,4-Dioxane (20 mL) was added 4,4,4′,4′,5,5,5′,5′-octamethyl-2,2′-bi(1,3,2-dioxaborolane) (1.43 g, 5.64 mmol), potassium acetate (0.69 g, 7.0 mmol), and [1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II) (0.17 g, 0.23 mmol), and the solution was then refluxed overnight under nitrogen. The solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate=(10/1) as eluent (1.2 g, yield 70%).

To a stirred suspension of 1-methyl-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-indazole (1.2 g, 4.7 mmol) in acetonitrile (20 mL) and water (5 mL) was added 4,6-dichloropyrimidine (0.7 g, 4.65 mmol), sodium bicarbonate (0.69 g, 7.05 mmol), and bis(triphenylphosphine)palladium(II) dichloride (0.016 g, 0.0235 mmol), and then the solution was refluxed overnight under nitrogen. The solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate=(3/1) as eluent (0.8 g, yield 70%).

6-(6-chloropyrimidin-4-yl)-1-methyl-1H-indazole (5) (0.8 g, 3.27 mmol) and benzene-1,3-diamine (0.7 g, 4.9 mmol) were dissolved in NMP (30 mL) and then were heated at 150° C. overnight. The solution was cooled down to room temperature and then was diluted with ethyl acetate. The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained (0.5 g, yield 50%).

To a dichloromethane solution of free amine compound (7) (0.5 g, 1.58 mmol) and TEA (0.2 g, 1.89 mmol) was added 4-nitrobenzoyl chloride (0.45 g, 2.3 mmol). After stirring for 5 hours at room temperature, the solution was filtered, and the crude product was washed with dichloromethane (0.6 g, yield 99%).

The nitro compound (9) (0.6 g) was dissolve in ethyl acetate/methanol (10:1, vol/vol, 20 mL), and the resulted suspension was treated with Pd/C (0.3 g). After nitrogen replacement three times, the reaction mixture was stirred at the room temperature overnight. The reaction mixture was filtered over CELITE, the solvent was then removed, and the product was obtained by flash chromatography with petroleum dichloromethane/methanol (20/1) as eluent (0.6 g, yield 100%).

Example 17. The Synthesis of THZ-CE-A-4-17

Compound numbers 1 to 9 recited in Example 17 apply only to Example 17. To a stirred suspension of 6-methoxypyridin-3-ol (1.0 g, 8 mmol) in acetonitrile (50 mL) was added 4,6-dichloropyrimidine (1.4 g, 9.6 mmol), sodium bicarbonate (0.8 g, 9.6 mmol), and the solution was refluxed overnight under nitrogen. The solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate=(20/1) as eluent (1.85 g, yield 80%).

4-chloro-6-((6-methoxypyridin-3-yl)oxy)pyrimidine (3) (1.85 g, 7.8 mmol) and benzene-1,3-diamine (1 g, 9.37 mmol) were dissolved in NMP (30 mL) and then were heated at 150° C. overnight. The solution was cooled down to room temperature and then was diluted with ethyl acetate (300 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (100/1-50/1) as eluent (1.75 g, yield 65%).

To a dichloromethane solution of free amine compound (5) (1.75 g, 5.66 mmol) and TEA (1.23 g, 5.66 mmol) was added 4-nitrobenzoyl chloride (1 g, 5.66 mmol). After stirring for 5 hours at room temperature, the solution was filtered, and the crude product was wash with dichloromethane (0.89 g, yield 33%).

The nitro compound (7) (0.89 g, 3.38 mmol) was dissolve in ethyl acetate/methanol (0:1, vol/vol, 70 mL), and the resulted suspension was treated with Pd/C (0.3 g). After nitrogen replacement three times, the reaction mixture was stirred at the room temperature overnight. The reaction mixture was filtered over CELITE, the solvent was then removed, and the product was obtained (0.85 g, yield 100%).

Example 18. The Synthesis of THZ-CE-A-4-18

Compound numbers 1 to 5 recited in Example 18 apply only to Example 18. To a solution of 5-(6-chloropyrimidin-4-yl)-1-(phenylsulfonyl)-1H-pyrrolo[2,3-b]pyridine (5) (1.85 g, 5 mmol) and benzene-1,4-diamine (0.81 g, 1.5 equiv) in NMP, DIEA (0.97 g, 7.5 mmol) was added, and then the solution was heated at 150° C. overnight. The solution was cooled down to room temperature and then was diluted with ethyl acetate. The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (100/1) as eluent (1.3 g, yield 60%).

To a dichloromethane solution of free amine compound (2) (0.6 g, 1.36 mmol) and TEA (0.2 g, 1.63 mmol) was added 4-nitrobenzoyl chloride (0.3 g, 1.2 equiv). After stirring for 1.5 hours at room temperature. The solution was filtered, the crude product was wash with dichloromethane (0.65 g, yield 85%).

The nitro compound (3) (0.65 g, 1.1 mmol) was dissolved in ethyl acetate/methanol (0:1, vol/vol, 70 mL) and the resulted suspension was treated with Pd/C (0.15 g). After nitrogen replacement three times, the reaction mixture was stirred at the room temperature overnight. The reaction mixture was filtered over CELITE, the solvent was then removed, and the product was obtained by flash chromatography with petroleum ether/ethyl acetate/NH3=(3/1/0.1) as eluent (0.4 g, yield 60%).

To a solution of free amino compound (10) (0.4 g, 0.7 mmol) in dried acetonitrile (60 mL) was added N,N-Diisopropylethylamine (0.11 g, 0.84 mmol) and (E)-4-bromobut-2-enoyl chloride (0.15 g, 0.84 mmol) in dichloromethane (15 mL) at 0° C. dropwise. After stirring for 5 min, the solution of dimethylamine (2 M, 7 mL) in THF was added, and the reaction mixture was then stirred at the room temperature for 2 hours. The solution was diluted with water and extracted with dichloromethane (3×100 mL). The resulted solution was washed with water and brine. After drying with Na2SO4, the solvent was then removed, and the product was obtained by flash chromatography with dichloromethane/methanol (50/1) as eluent (0.17 g, yield 30%).

Biological Evaluation

Example 19. Kinase Assay

PIP4K in vitro kinase assay was carried out as described in Rameh et al (Nature, 1997). Briefly, 0.1 ug (μg) of GST-PI5P4Ka or 0.4 ug of GST-PI5P4Ka resuspended in 70 uL (μL) of kinase buffer containing 20 mM HEPES pH 7.4, 100 mM NaCl, 0.5 mM EGTA was stabilized at room temperature for 10 minutes and incubated with 1 uM of DMSO or indicated compound for 30 minutes. Then the kinase reaction was carried out in a total volume of 100 ul (μL) for 10 minutes by adding 20 uL of lipid substrates (4 ug of phosphatidylserine and 2 ug of PI5P) in buffer containing 30 mM HEPES pH 7.4 and 1 mM EGTA, and 10 uL of ATP mix (500 uM (μM) non-radiolabeled ATP, 10 uCi [g-32P]-ATP, 65 mM HEPES pH 7.4 and 100 mM MgCl2). The reaction was terminated by adding 50 uL of HCl. Phosphoinositides were extracted by adding 100 uL methanol/chloroform (1:1, vol:vol) mix and subjected to thin layer chromatography separation using heat-activated 1% potassium oxalate-coated silica gel 60 plates (EMD Chemicals Inc., Billerica, Mass., USA) and a 1-propanol/2 M acetic acid (65:35, vol:vol) solvent system. The radiolabeled PI(4,5)P2was quantified with a Phosphorimager (Molecular Dynamics, STORM840, GE Healthcare, Waukesha, Wis., USA).

Example 20. Cell Proliferation Assay

To determine cell proliferation, cells were plated at 2×103cells per well of 96-well plate. Cells were incubated and assayed at indicated times using Cell TITER-GLO Luminescent Cell Viability assay (Promega). Cells were allowed to equilibrate to room temperature for 15 minutes, then an equal volume of the Cell TITER-GLO reagent was added to wells and incubated for 15 minutes on an orbital shaker. Luminescence was recorded according to the manufacturer's protocol.

PIP5K2A enzyme (diluted in 12.5 mM Glycine-NaOH (pH 8.5), 50 mM KCl, 2.5 mM MgCl2, 1 mM DTT, 0.25% Na-Cholate, and 1 mg/ml BSA) was assayed in total volume of 20 μl containing 12.5 mM Glycine-NaOH (pH 8.5), 50 mM KCl, 2.5 mM MgCl2, 1 mM DTT, 0.25% Na-Cholate, 0.01 mM ATP, and 0.05 mM diC8 PI(5)P. The enzyme was assayed for 15 min after which 20 μl of ADP-GLO reagent was added. After a further incubation of 40 minutes, 40 μl of Kinase Detection Buffer was added. After a further incubation of 40 min, the enzyme was read on PERKINELMER ENVISION for 1 sec/well. Exemplary results are shown in Table 1.

TABLE 1Exemplary IC50values of select compounds on PIP4K2ACompoundTHZ-CE-THZ-CE-THZ-CE-THZ-CE-THZ-CE-NumberA-4-2A-4-3A-4-9A-4-18A-4IC50(μM)0.060.010.250.050.33

EQUIVALENTS AND SCOPE