Inhibitors of transcription factors and uses thereof

The present invention provides novel compounds of any one of Formulae (I) to (IV), and pharmaceutically compositions thereof. Compounds of any one of Formulae (I) to (IV) are believed to be inhibitors of bromodomain-containing proteins (e.g., bromo and extra terminal proteins (BETs)). Also provided are methods, uses, and kits using the inventive compounds and pharmaceutical compositions for inhibiting the activity of the bromodomain-containing proteins and for treating and/or preventing in a subject in need thereof diseases associated with bromodomain-containing proteins, such as proliferative diseases.

BACKGROUND OF THE INVENTION

Bromodomain-containing proteins are of substantial biological interest, as components of transcription factor complexes and determinants of epigenetic memory. For example, the bromo and extra terminal protein (BET) family (e.g., bromodomain-containing protein 2 (BRD2), bromodomain-containing protein 3 (BRD3), bromodomain-containing protein 4 (BRD4), and bromodomain testis-specific protein (BRDT)) shares a common domain architecture featuring two amino-terminal bromodomains that exhibit high levels of sequence conservation, and a more divergent carboxy-terminal recruitment domain (Filippakopoulos et al.,Nature2010, 468, 1067-1073). BRD2 and BRD3 are reported to associate with histones along actively transcribed genes and may be involved in facilitating transcriptional elongation (Leroy et al.,Mol. Cell.2008, 30, 51-60). It has also been reported that BRD4 or BRD3 may fuse with nuclear protein in testis (NUT), forming novel fusion oncogenes BRD4-NUT or BRD3-NUT, in a highly malignant form of epithelial neoplasia (French et al.,Cancer Res.,2003, 63, 304-307; French et al.,J. Clin. Oncol.2004, 22, 4135-4139). Data suggests that BRD-NUT fusion proteins contribute to carcinogenesis (French et al.,Oncogene2008, 27, 2237-2242). BRDT is uniquely expressed in the testes and ovary. All family members of BET have been reported to have some function in controlling or executing aspects of the cell cycle and have been shown to remain in complex with chromosomes during cell division, suggesting a role in the maintenance of epigenetic memory. In addition, some viruses make use of BET proteins to tether their genomes to the host cell chromatin, as part of the process of viral replication (You et al.,Cell2004, 117, 349-360). BRD4 appears to be involved in the recruitment of the pTEF-b complex to inducible genes, resulting in phosphorylation of RNA polymerase and increased transcriptional output (Hargreaves et al.,Cell2009, 138, 129-145). In humans, BRD2, BRD3, BRD4, and BRDT exhibit similar gene arrangements, domain organizations, and some functional properties (Wu et al.,J. Biol. Chem.2007, 282, 13141-13145).

Recently, some compounds have been reported to be bromodomain binding agents, e.g., WO 2012/075383, WO 2011/054553, WO 2011/054841, WO 2011/054844, WO 2011/054845, WO 2011/054846, WO 2011/054848, WO 2011/143669, and WO 2011/161031. Moreover, Japanese patent application publication JP 2008/156311 discloses a benzimidazole derivative which is said to be a BRD2 bromodomain binding agent which has utility with respect to virus infection and/or proliferation. International PCT publication WO 2009/084693 discloses a series of thienotriazolodiazepine derivatives that are said to inhibit the binding between an acetylated histone and a bromodomain-containing protein which are said to be useful as anti-cancer agents. International PCT publication WO 2011/054843 suggests compounds which inhibit the binding of a bromodomain with its cognate acetylated proteins may have utility in the treatment of a range of autoimmune and inflammatory diseases or conditions.

BET proteins, however, are just one branch of the bromodomain containing protein family. There are dozens of undrugged bromodomains, and novel probe molecules against these targets would be invaluable tools both for improved biological studies and potential leads for drug development. Transcription initiation factor TFIID subunit 1 (TAF1) and TAF1L are two such proteins. As a part of the STAGA complex containing TRRAP, GCN5, TFIID, CBP/P300, mediator (Liu et al.,Molecular Cell Biology2008, 28, 108), and Sp1 (Schroder et al.,J. Biol. Chem.2012, 287, 1090), TAF1 is susceptible to oncogenic activation by MYC. Moreover, TAF1 has been shown to block p53 activity (Li et al.,Molecular Cell.2004, 13, 867), and inactivation of TAF1 triggers a DNA damage response (Buchmann et al.,Molecular Cell Biology2004, 24, 5332). In addition, the TFIID complex, of which TAF1 is a significant member, is vital to stem cell reprogramming (Pijnappel et al.,Nature2013, 495, 516). Inhibitors of TAF1 may help further elucidate its biological role and potentially be an inhibitor of cancer cell growth. With such promising studies related to drugging the epigenome, it is of the utmost importance to develop new chemistry capable of reaching these targets.

SUMMARY OF THE INVENTION

Compound JQ1 (e.g., (+)-JQ1, (−)-JQ1, or a mixture thereof; below) and certain compounds related to JQ1 have been reported as inhibitors of bromodomain-containing proteins (e.g., BET proteins). See, e.g., international PCT patent application publication, WO 2011/143669. It has been demonstrated that JQ1 may bind to the acetyl-lysine binding cavity of a bromodomain-containing protein (e.g., BRD4). Binding of JQ1 to the tandem bromodomains of BRD4 has been shown to be acetyl-lysine competitive and able to displace BRD4 from chromatin in human cells. It is expected that JQ1 may be useful in treating a disease associated with bromodomain-containing proteins, such as cancer (e.g., human squamous cell carcinoma). Similar properties of compound I-BET (below), another bromodomain inhibitor, have also been reported (Nicodeme et al.,Nature2010, 468, 1119-1123).

The present invention provides novel compounds of Formulae (I)-(IV). The inventive compounds are thought to be inhibitors of transcription factors, such as bromodomain-containing proteins (e.g., BET proteins) and may be useful in treating diseases associated with bromodomain-containing proteins, such as proliferative diseases (e.g., cancers, benign neoplasms, angiogenesis, inflammatory diseases, and autoimmune diseases). Also provided in the present invention are pharmaceutical compositions, kits, methods, and uses involving a compound of the invention.

Exemplary compounds of Formula (I) include, but are not limited to:

The compounds of the invention are thought to be able to bind bromodomain-containing proteins. In certain embodiments, the compounds of the invention bind to a bromodomain of the bromodomain-containing proteins. The compounds of the invention may inhibit the activity of the bromodomain-containing proteins. The compounds of the invention may also inhibit the function of a bromodomain of the bromodomain-containing proteins.

In another aspect, the present invention provides the compound of Formula (II):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. The compound of Formula (II) is also referred to as compound UMB17.

In yet another aspect, the present invention provides the compound of Formula (III):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. The compound of Formula (III) is also referred to as compound UMB18.

In still another aspect, the present invention provides the compound of Formula (IV):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. The compound of Formula (IV) is also referred to as compound UMB27.

In still another aspect, the present invention provides pharmaceutical compositions including a compound of the invention, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical compositions described herein include a therapeutically or prophylactically effective amount of a compound of the invention. The pharmaceutical composition may be useful for treating and/or preventing a disease associated with a bromodomain-containing protein in a subject in need thereof. The pharmaceutical composition may also be useful in inhibiting the activity of a bromodomain-containing protein, in inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and/or in modulating (e.g., down-regulating) the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell.

In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with the activity of the bromodomain-containing protein. In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with the function of a bromodomain of the bromodomain-containing protein. In certain embodiments, the disease associated with a bromodomain-containing protein is a proliferative disease (e.g., cancer, benign neoplasm, angiogenesis, an inflammatory disease, or an autoimmune disease).

In certain embodiments, the subject is a human. In certain embodiments, the subject is a non-human mammal. In certain embodiments, the cell is an in vitro cell.

Another aspect of the present invention relates to methods of treating a disease associated with a bromodomain-containing protein in a subject in need thereof. In another aspect, the present invention provides methods of preventing a disease associated with a bromodomain-containing protein in a subject in need thereof.

Another aspect of the present invention relates to methods of reducing the risk of having a disease associated with a bromodomain-containing protein in a subject in need thereof.

In another aspect, the present invention provides methods of inhibiting the activity of a bromodomain-containing protein in a subject or cell.

In yet another aspect, the present invention provides methods of inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell.

In still another aspect, the present invention provides methods of modulating the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the methods of modulating the transcription of a gene are methods of down-regulating the transcription of the gene.

The methods of the present invention include administering to the subject an effective amount of a compound or pharmaceutical composition of the invention. In certain embodiments, the effective amount is a therapeutically effective amount. In certain embodiments, the effective amount is a prophylactically effective amount.

Another aspect of the invention relates to methods of screening a library of compounds to identify a compound that is useful in the methods of the invention (e.g., useful for inhibiting the activity of a bromodomain-containing protein).

Another aspect of the present invention relates to kits comprising a container with a compound or pharmaceutical composition of the invention. The kits of the invention may include a single dose or multiple doses of the inventive compound, or pharmaceutical compositions thereof. The provided kits may be useful in treating and/or preventing a disease associated with a bromodomain-containing protein in a subject in need thereof. The kits may also be useful in inhibiting the activity of a bromodomain-containing protein, in inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and/or in modulating (e.g., down-regulating) the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the kit further includes instructions for administering the compound, or pharmaceutical composition, to the subject.

In yet another aspect, the present invention provides compounds and pharmaceutical compositions of the invention for use in the treatment of a disease associated with a bromodomain-containing protein in a subject in need thereof.

In still another aspect, the present invention provides compounds and pharmaceutical compositions of the invention for use in the prevention of a disease associated with a bromodomain-containing protein in a subject in need thereof.

In still another aspect, the present invention provides compounds and pharmaceutical compositions of the invention for use in reducing the risk of having a disease associated with a bromodomain-containing protein in a subject in need thereof.

The present application refers to various issued patent, published patent applications, journal articles, and other publications, all of which are incorporated herein by reference. 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 Figures, 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 optionally substituted with one or more functional groups. As will be appreciated by one of ordinary skill in the art, “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. Thus, the term “alkyl” includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl”, and the like. Furthermore, the terms “alkyl”, “alkenyl”, “alkynyl”, and the like encompass both substituted and unsubstituted groups. In certain embodiments, “lower alkyl” is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention 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.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to 10-membered non-romatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 membered heterocyclyl”). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged, or spiro ring system, such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or can be partially unsaturated. Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings. “Heterocyclyl” also includes ring systems wherein the heterocyclic ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclic ring, or ring systems wherein the heterocyclic ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclic ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclic ring system. Unless otherwise specified, each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents. In certain embodiments, the heterocyclyl group is unsubstituted 3-10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3-10 membered heterocyclyl.

“Aralkyl” is a subset of alkyl and aryl and refers to an optionally substituted alkyl group substituted by an optionally substituted aryl group. In certain embodiments, the aralkyl is optionally substituted benzyl. In certain embodiments, the aralkyl is benzyl. In certain embodiments, the aralkyl is optionally substituted phenethyl. In certain embodiments, the aralkyl is phenethyl.

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

“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) as herein defined. 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.

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

Exemplary sulfur atom substituents include, but are not limited to, —Raa, —C(═O)SRaa, —C(═O)Raa, —CO2Raa, —C(═O)N(Rbb)2, —C(═NRbb)Raa, —C(═NRbb)ORaa,—C(═NRbb)N(Rbb)2, —S(═O)Raa, —SO2Raa, —Si(Raa)3, —P(Rcc)2, —P(Rcc)3, —P(═O)2Raa, —P(═O)(Raa)2, —P(═O)(ORcc)2, —P(═O)2N(Rbb)2, and —P(═O)(NRbb)2, wherein Raa, Rbb, and Rccare as defined herein. In certain embodiments, the sulfur atom substituent present on a sulfur atom is a sulfur protecting group (also referred to as a thiol protecting group). Sulfur protecting groups are well known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rdedition, John Wiley & Sons, 1999, incorporated herein by reference.

The invention is not intended to be limited in any manner by the above exemplary listing of substituents.

Other Definitions

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

The term “tautomers” or “tautomeric” refers to two or more interconvertable 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 “prodrugs” refer to compounds, including derivatives of the compounds described herein, which 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 of this invention 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 of this invention are particular prodrugs. In some cases it is desirable to prepare double ester type prodrugs such as (acyloxy)alkyl esters or ((alkoxycarbonyl)oxy)alkylesters. C1-C8alkyl, C2-C8alkenyl, C2-C8alkynyl, aryl, C7-C12substituted aryl, and C7-C12arylalkyl esters of the compounds described herein may be preferred.

The term “lipophilic” or “hydrophobic” refers to the ability of a compound to dissolve, or the ability of a moiety of a compound to assist the compound in dissolving in fats, oils, lipids, and/or non-polar solvents (e.g., hexane or toluene). Lipophilic moieties include, but are not limited to, substituted or unsubstituted, branched or unbranched alkyl groups having 1 to 50 carbon atoms. In certain embodiments, the lipophilic moiety is an alkyl group including at least 1, at least 6, at least 12, at least 18, at least 24, at least 36, or at least 50 carbon atoms. In certain embodiments, the lipophilic moiety is an alkyl group including at most 50, at most 36, at most 24, at most 18, at most 12, or at most 6 carbon atoms. Combinations of the above-referenced ranges (e.g., at least about 1 and at most about 24 carbon atoms) are also within the scope of the invention. In certain embodiments, the lipophilic moiety is unsubstituted alkyl. In certain embodiments, the lipophilic moiety is unsubstituted and unbranched alkyl. In certain embodiments, the lipophilic moiety is unsubstituted and unbranched C1-24alkyl. In certain embodiments, the lipophilic moiety is unsubstituted and unbranched C6-24alkyl. In certain embodiments, the lipophilic moiety is unsubstituted and unbranched C12-24alkyl.

The term “small molecule” refers to molecules, whether naturally-occurring or artificially created (e.g., via chemical synthesis) that have a relatively low molecular weight.

Typically, a small molecule is an organic compound (i.e., it contains carbon). The small molecule may contain multiple carbon-carbon bonds, stereocenters, and other functional groups (e.g., amines, hydroxyl, carbonyls, and heterocyclic rings, etc.). In certain embodiments, the molecular weight of a small molecule is at most about 1,000 g/mol, at most about 900 g/mol, at most about 800 g/mol, at most about 700 g/mol, at most about 600 g/mol, at most about 500 g/mol, at most about 400 g/mol, at most about 300 g/mol, at most about 200 g/mol, or at most about 100 g/mol. In certain embodiments, the molecular weight of a small molecule is at least about 100 g/mol, at least about 200 g/mol, at least about 300 g/mol, at least about 400 g/mol, at least about 500 g/mol, at least about 600 g/mol, at least about 700 g/mol, at least about 800 g/mol, or at least about 900 g/mol, or at least about 1,000 g/mol. Combinations of the above ranges (e.g., at least about 200 g/mol and at most about 500 g/mol) are also possible. In certain embodiments, the small molecule is a therapeutically active agent such as a drug (e.g., a molecule approved by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (C.F.R.)). The small molecule may also be complexed with one or more metal atoms and/or metal ions. In this instance, the small molecule is also referred to as a “small organometallic molecule.” Preferred small molecules are biologically active in that they produce a biological effect in animals, preferably mammals, more preferably humans. Small molecules include, but are not limited to, radionuclides and imaging agents. In certain embodiments, the small molecule is a drug. Preferably, though not necessarily, the drug is one that has already been deemed safe and effective for use in humans or animals by the appropriate governmental agency or regulatory body. For example, drugs approved for human use are listed by the FDA under 21 C.F.R. §§ 330.5, 331 through 361, and 440 through 460, incorporated herein by reference; drugs for veterinary use are listed by the FDA under 21 C.F.R. §§ 500 through 589, incorporated herein by reference. All listed drugs are considered acceptable for use in accordance with the present invention.

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

The term “gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” or “chimeric construct” refers to any gene or a construct, not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene or chimeric construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but which is introduced into the host organism by gene transfer.

Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.

The term “histone” refers to highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation.

The term “bromodomain” refers to a protein domain that recognizes acetylated lysine residues such as those on the N-terminal tails of histones. In certain embodiments, a bromodomain of a BET protein comprises about 110 amino acids and shares a conserved fold comprising a left-handed bundle of four alpha helices linked by diverse loop regions that interact with chromatin.

The term “bromodomain-containing protein” or “bromodomain protein” refers to a protein, whether wild-type or mutant, natural or synthetic, truncated or complete, or a variant thereof, that possesses the minimum amino acid sequence sufficient for a functional bromodomain capable of mediating molecular recognition of acetyl-lysine of acetylated lysine residues on the tails of histones. Bromodomain-containing proteins include, for example, fusion proteins comprising a bromodomain and an additional portion having desired functionality (e.g., a reporter portion).

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

A “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) and/or other non-human animals, for example, mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys). In certain embodiments, the animal is a mammal. The animal may be a male or female at any stage of development. The animal may be a transgenic animal or genetically engineered animal. In certain embodiments, the subject is non-human animal. In certain embodiments, the animal is fish. A “patient” refers to a human subject in need of treatment of a disease. The subject may also be a plant. In certain embodiments, the plant is a land plant. In certain embodiments, the plant is a non-vascular land plant. In certain embodiments, the plant is a vascular land plant. In certain embodiments, the plant is a seed plant. In certain embodiments, the plant is a cultivated plant. In certain embodiments, the plant is a dicot. In certain embodiments, the plant is a monocot. In certain embodiments, the plant is a flowering plant. In some embodiments, the plant is a cereal plant, e.g., maize, corn, wheat, rice, oat, barley, rye, or millet. In some embodiments, the plant is a legume, e.g., a bean plant, e.g., soybean plant. In some embodiments, the plant is a tree or shrub.

The terms “administer,” “administering,” or “administration” refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing an inventive compound, or a composition thereof, 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. An effective amount encompasses therapeutic and prophylactic treatment.

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

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, Goodspature'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, perphigus vulgaris, ANCA-associated vasculitis (e.g., Wegener's granulomatosis, microscopic polyangiitis), urveitis, Sjogren's syndrome, Crohn's disease, Reiter's syndrome, ankylosing spondylitis, Lyme disease, Guillain-Barre syndrome, Hashimoto's thyroiditis, and cardiomyopathy.

Inhibitors (e.g., JQ1 and I-BET) of bromodomain-containing proteins (e.g., BET proteins) are useful for treating diseases (such as cancer (e.g., human squamous cell carcinoma)) associated with bromodomain-containing proteins.

The present invention provides compounds of Formulae (I)-(IV), which are novel inhibitors of bromodomain-containing proteins. The compounds of the invention may be able to bind to in a binding pocket of a bromodomain of a bromodomain-containing protein. In certain embodiments, the compounds of the invention bind to the binding pocket of the bromodomain by mimicking the contact between a histone acetyl-lysine residue and the binding pocket. In certain embodiments, the compounds of the invention bind to the apo binding pocket of the bromodomain. Also provided in the present invention are pharmaceutical compositions and kits useful in inhibiting the activity of a transcription factor (e.g., a bromodomain-containing protein). The compounds, pharmaceutical compositions, and kits of the invention may be useful in treating diseases associated with a bromodomain-containing protein, such as proliferative diseases (e.g., cancers, benign neoplasms, angiogenesis, inflammatory diseases, and autoimmune diseases).

Compounds

The present invention provides compounds of Formula (I):

wherein no more than two of XA, XB, and XCcan be N;

Ring A is of the formula:

L is a bond or of the formula:

each instance of RA1is 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 RA1are joined to form a substituted or unsubstituted heterocyclic ring;

RBis 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, —C(═O)RB1, —C(═O)ORB1, —C(═O)N(RB1)2, or a nitrogen protecting group, or RBand RCare joined to form a substituted or unsubstituted heterocyclic ring;

each instance of RB1is 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, or an oxygen protecting group when attached to an oxygen atom, or two instances of RB1are joined to form a substituted or unsubstituted heterocyclic ring;

RCis 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, —C(═O)RC1, —C(═O)ORC1, —C(═O)N(RC1)2, or a nitrogen protecting group, or RCand RBare joined to form a substituted or unsubstituted heterocyclic ring;

each instance of RC1is 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, or an oxygen protecting group when attached to an oxygen atom, or two instances of RC1are joined to form a substituted or unsubstituted heterocyclic ring;

each instance of RD1is 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 RD1are joined to form a substituted or unsubstituted heterocyclic ring;

each instance of RE1is 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, or an oxygen protecting group when attached to an oxygen atom, or two instances of RE1are joined to form a substituted or unsubstituted heterocyclic ring;

each instance of RF1is 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 RF1are joined to form a substituted or unsubstituted heterocyclic ring;

d is 0, 1, or 2;

In certain embodiments, the present invention provides compounds of Formula (I) and pharmaceutically acceptable salts thereof.

Compounds of Formula (I) include Ring A. 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, 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, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

In certain embodiments, Ring A is of the formula:

Ring A of Formula (I) may include one or more substituent RA. In certain embodiments, at least one instance of RAis H. In certain embodiments, at least one instance of RAis halogen. In certain embodiments, at least one instance of RAis F. In certain embodiments, at least one instance of RAis Cl. In certain embodiments, at least one instance of RAis Br. In certain embodiments, at least one instance of RAis I (iodine). In certain embodiments, at least one instance of RAis substituted acyl. In certain embodiments, at least one instance of RAis unsubstituted acyl. In certain embodiments, at least one instance of RAis substituted alkyl. In certain embodiments, at least one instance of RAis unsubstituted alkyl. In certain embodiments, at least one instance of RAis C1-12alkyl. In certain embodiments, at least one instance of RAis C1-6alkyl. In certain embodiments, at least one instance of RAis unsubstituted methyl. In certain embodiments, at least one instance of RAis substituted methyl. In certain embodiments, at least one instance of RAis —CH2F. In certain embodiments, at least one instance of RAis —CHF2. In certain embodiments, at least one instance of RAis —CF3. In certain embodiments, at least one instance of RAis Bn. In certain embodiments, at least one instance of RAis unsubstituted ethyl. In certain embodiments, at least one instance of RAis substituted ethyl. In certain embodiments, at least one instance of RAis —(CH2)2Ph. In certain embodiments, at least one instance of RAis propyl. In certain embodiments, at least one instance of RAis butyl. In certain embodiments, at least one instance of RAis pentyl. In certain embodiments, at least one instance of RAis hexyl. In certain embodiments, at least one instance of RAis substituted alkenyl. In certain embodiments, at least one instance of RAis unsubstituted alkenyl. In certain embodiments, at least one instance of RAis vinyl. In certain embodiments, at least one instance of RAis substituted alkynyl. In certain embodiments, at least one instance of RAis unsubstituted alkynyl. In certain embodiments, at least one instance of RAis ethynyl. In certain embodiments, at least one instance of RAis substituted carbocyclyl. In certain embodiments, at least one instance of RAis unsubstituted carbocyclyl. In certain embodiments, at least one instance of RAis saturated carbocyclyl. In certain embodiments, at least one instance of RAis unsaturated carbocyclyl. In certain embodiments, at least one instance of RAis carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RAis monocyclic carbocyclyl. In certain embodiments, at least one instance of RAis 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RAis cylcopropyl. In certain embodiments, at least one instance of RAis cyclobutyl. In certain embodiments, at least one instance of RAis cyclopentyl. In certain embodiments, at least one instance of RAis cyclohexyl. In certain embodiments, at least one instance of RAis cycloheptyl. In certain embodiments, at least one instance of RAis bicyclic carbocyclyl. In certain embodiments, at least one instance of RAis 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RAis substituted heterocyclyl. In certain embodiments, at least one instance of RAis unsubstituted heterocyclyl. In certain embodiments, at least one instance of RAis saturated heterocyclyl. In certain embodiments, at least one instance of RAis unsaturated heterocyclyl. In certain embodiments, at least one instance of RAis heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RAis heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RAis monocyclic heterocyclyl. In certain embodiments, at least one instance of RAis 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RAis bicyclic heterocyclyl. In certain embodiments, at least one instance of RAis 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RAis substituted aryl. In certain embodiments, at least one instance of RAis unsubstituted aryl. In certain embodiments, at least one instance of RAis 6- to 14-membered aryl. In certain embodiments, at least one instance of RAis 6- to 10-membered aryl. In certain embodiments, at least one instance of RAis substituted phenyl. In certain embodiments, at least one instance of RAis unsubstituted phenyl. In certain embodiments, at least one instance of RAis substituted naphthyl. In certain embodiments, at least one instance of RAis unsubstituted naphthyl. In certain embodiments, at least one instance of RAis substituted heteroaryl. In certain embodiments, at least one instance of RAis unsubstituted heteroaryl. In certain embodiments, at least one instance of RAis heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RAis monocyclic heteroaryl. In certain embodiments, at least one instance of RAis 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RAis 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RAis pyridyl. In certain embodiments, at least one instance of RAis bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RAis 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RAis 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RAis ORA1. In certain embodiments, at least one instance of RAis —OMe. In certain embodiments, at least one instance of RAis —OEt. In certain embodiments, at least one instance of RAis —OPr. In certain embodiments, at least one instance of RAis —OBu. In certain embodiments, at least one instance of RAis —O(pentyl). In certain embodiments, at least one instance of RAis —O(hexyl). In certain embodiments, at least one instance of RAis —OPh. In certain embodiments, at least one instance of RAis —OBn. In certain embodiments, at least one instance of RAis —O(CH2)2Ph. In certain embodiments, at least one instance of RAis —OH. In certain embodiments, at least one instance of RAis —SRA1. In certain embodiments, at least one instance of RAis —SMe. In certain embodiments, at least one instance of RAis —SH. In certain embodiments, at least one instance of RAis —N(RA1)2. In certain embodiments, at least one instance of RAis —NMe2. In certain embodiments, at least one instance of RAis —NH2. In certain embodiments, at least one instance of RAis —CN. In certain embodiments, at least one instance of RAis —SCN. In certain embodiments, at least one instance of RAis —C(═NRA1)RA1, —C(═NRA1)ORA1, or —C(═NRA1)N(RA1)2. In certain embodiments, at least one instance of RAis —C(═O)RA1, —C(═O)ORA1, or —C(═O)N(RA1)2. In certain embodiments, at least one instance of RAis —NO2.

In certain embodiments, at least one instance of RAis —NRA1C(═O)RA1, —NRA1C(═O)ORA1or —NRA1C(═O)N(RA1)2. In certain embodiments, at least one instance of RAis —OC(═O)RA1, —OC(═O)ORA1, or —OC(═O)N(RA1)2.

In compounds of Formula (I), two RAgroups may be joined to form a substituted or unsubstituted carbocyclic ring. In certain embodiments, two instances of RAare joined to form a saturated or unsaturated carbocyclic ring. In certain embodiments, two instances of RAare joined to form a carbocyclic ring including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 3- to 7-membered, monocyclic carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 3-membered carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 4-membered carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 5-membered carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 6-membered carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 7-membered carbocyclic ring. In certain embodiments, two instances of RAare joined to form a 5- to 13-membered, bicyclic carbocyclic ring.

In certain embodiments, two instances of RAare joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RAare joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RAare joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RAare joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RAare joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RAare joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

In certain embodiments, two instances of RAare joined to form a substituted or unsubstituted aryl ring. In certain embodiments, two instances of RAare joined to form a 6- to 14-membered aryl ring. In certain embodiments, two instances of RAare joined to form a 6-to 10-membered aryl ring. In certain embodiments, two instances of RAare joined to form a monocyclic aryl ring. In certain embodiments, two instances of RAare joined to form a phenyl. In certain embodiments, two instances of RAare joined to form a bicyclic aryl ring. In certain embodiments, two instances of RAare joined to form a naphthyl.

In certain embodiments, two instances of RAare joined to form a substituted or unsubstituted heteroaryl ring. In certain embodiments, two instances of RAare joined to form a monocyclic heteroaryl ring, wherein one, two, or three atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RAare joined to form a 5-membered, monocyclic heteroaryl ring. In certain embodiments, two instances of RAare joined to form a 6-membered, monocyclic heteroaryl ring. In certain embodiments, two instances of RAare joined to form a pyridyl. In certain embodiments, two instances of RAare joined to form a bicyclic heteroaryl ring, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RAare joined to form a 9-membered, bicyclic heteroaryl ring. In certain embodiments, two instances of RAare joined to form a 10-membered, bicyclic heteroaryl ring.

In certain embodiments, at least one instance of RAis halogen or substituted or unsubstituted alkyl. In certain embodiments, at least one instance of RAis halogen or unsubstituted alkyl. In certain embodiments, at least one instance of RAis halogen or unsubstituted C1-6alkyl.

In certain embodiments, at least one instance of RA1is H. 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 alkyl. In certain embodiments, at least one instance of RA1is unsubstituted alkyl. In certain embodiments, at least one instance of RA1is C1-12alkyl. 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 pentyl. In certain embodiments, at least one instance of RA1is hexyl. 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 saturated carbocyclyl. In certain embodiments, at least one instance of RA1is unsaturated carbocyclyl. In certain embodiments, at least one instance of RA1is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RA1is 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RA1is cylcopropyl. In certain embodiments, at least one instance of RA1is cyclobutyl. In certain embodiments, at least one instance of RA1is cyclopentyl. In certain embodiments, at least one instance of RA1is cyclohexyl. In certain embodiments, at least one instance of RA1is cycloheptyl. In certain embodiments, at least one instance of RA1is 5- to 13-membered, bicyclic 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 saturated heterocyclyl. In certain embodiments, at least one instance of RA1is unsaturated heterocyclyl. In certain embodiments, at least one instance of RA1is heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RA1is heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RA1is 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RA1is 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RA1is substituted or unsubstituted aryl. In certain embodiments, at least one instance of RA1is 6- to 14-membered aryl. In certain embodiments, at least one instance of RA1is 6- to 10-membered aryl. In certain embodiments, at least one instance of RA1is monocyclic aryl. In certain embodiments, at least one instance of RA1is phenyl. In certain embodiments, at least one instance of RA1is bicyclic aryl. In certain embodiments, at least one instance of RA1is naphthyl. In certain embodiments, at least one instance of RA1is substituted or unsubstituted heteroaryl. In certain embodiments, at least one instance of RA1is heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RA1is monocyclic heteroaryl. In certain embodiments, at least one instance of RA1is 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RA1is 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RA1is pyridyl. In certain embodiments, at least one instance of RA1is bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RA1is 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RA1is 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RA1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one instance of RA1is Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RA1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RA1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom. In certain embodiments, RA1is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, RA1is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom.

In certain embodiments, two instances of RA1are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RA1are joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RA1are joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RA1are joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RA1are joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RA1are joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

In certain embodiments, a is 0. In certain embodiments, a is 1. In certain embodiments, a is 2. In certain embodiments, a is 3. In certain embodiments, a is 4. In certain embodiments, a is 5.

In certain embodiments, at least one instance of RAis halogen or substituted or unsubstituted alkyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis halogen or unsubstituted alkyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis halogen or unsubstituted C1-6alkyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis halogen or methyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis substituted or unsubstituted alkyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis unsubstituted alkyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis unsubstituted C1-6alkyl; and a is 1 or 2. In certain embodiments, at least one instance of RAis methyl; and a is 1 or 2.

When Ring A is of the formula:

compounds of Formula (I) include substituent RE. In certain embodiments, REis H. In certain embodiments, REis substituted acyl. In certain embodiments, REis unsubstituted acyl. In certain embodiments, REis substituted alkyl. In certain embodiments, REis unsubstituted alkyl. In certain embodiments, REis C1-12alkyl. In certain embodiments, REis C1-6alkyl. In certain embodiments, REis unsubstituted methyl. In certain embodiments, REis substituted methyl. In certain embodiments, REis —CH2F. In certain embodiments, REis —CHF2. In certain embodiments, REis —CF3. In certain embodiments, REis Bn. In certain embodiments, REis unsubstituted ethyl. In certain embodiments, REis substituted ethyl. In certain embodiments, REis —(CH2)2Ph. In certain embodiments, REis propyl. In certain embodiments, REis butyl. In certain embodiments, REis pentyl. In certain embodiments, REis hexyl. In certain embodiments, REis substituted alkenyl. In certain embodiments, REis unsubstituted alkenyl. In certain embodiments, REis vinyl. In certain embodiments, REis substituted alkynyl. In certain embodiments, REis unsubstituted alkynyl. In certain embodiments, REis ethynyl. In certain embodiments, REis substituted carbocyclyl. In certain embodiments, REis unsubstituted carbocyclyl. In certain embodiments, REis saturated carbocyclyl. In certain embodiments, REis unsaturated carbocyclyl. In certain embodiments, REis carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, REis monocyclic carbocyclyl. In certain embodiments, REis 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, REis cylcopropyl. In certain embodiments, REis cyclobutyl. In certain embodiments, REis cyclopentyl. In certain embodiments, REis cyclohexyl. In certain embodiments, REis cycloheptyl. In certain embodiments, REis bicyclic carbocyclyl. In certain embodiments, REis 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, REis substituted heterocyclyl. In certain embodiments, REis unsubstituted heterocyclyl. In certain embodiments, REis saturated heterocyclyl. In certain embodiments, REis unsaturated heterocyclyl. In certain embodiments, REis heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, REis heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, REis monocyclic heterocyclyl. In certain embodiments, REis 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, REis bicyclic heterocyclyl. In certain embodiments, REis 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, REis substituted aryl. In certain embodiments, REis unsubstituted aryl. In certain embodiments, REis 6- to 14-membered aryl. In certain embodiments, REis 6- to 10-membered aryl. In certain embodiments, REis substituted phenyl. In certain embodiments, REis unsubstituted phenyl. In certain embodiments, REis substituted naphthyl. In certain embodiments, REis unsubstituted naphthyl. In certain embodiments, REis substituted heteroaryl. In certain embodiments, REis unsubstituted heteroaryl. In certain embodiments, REis heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, REis monocyclic heteroaryl. In certain embodiments, REis 5-membered, monocyclic heteroaryl. In certain embodiments, REis 6-membered, monocyclic heteroaryl. In certain embodiments, REis pyridyl. In certain embodiments, REis bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, REis 9-membered, bicyclic heteroaryl. In certain embodiments, REis 10-membered, bicyclic heteroaryl. In certain embodiments, REis —C(═O)RE1. In certain embodiments, REis —C(═O)ORE1. In certain embodiments, REis —C(═O)N(RE1)2. In certain embodiments, REis a nitrogen protecting group. In certain embodiments, REis Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts.

In certain embodiments, REis hydrogen or substituted or unsubstituted alkyl. In certain embodiments, REis hydrogen or unsubstituted alkyl. In certain embodiments, REis hydrogen or unsubstituted C1-6alkyl.

In certain embodiments, at least one instance of RE1is H. In certain embodiments, at least one instance of RE1is substituted acyl. In certain embodiments, at least one instance of RE1is unsubstituted acyl. In certain embodiments, at least one instance of RE1is acetyl. In certain embodiments, at least one instance of RE1is substituted alkyl. In certain embodiments, at least one instance of RE1is unsubstituted alkyl. In certain embodiments, at least one instance of RE1is C1-12alkyl. In certain embodiments, at least one instance of RE1is C1-6alkyl. In certain embodiments, at least one instance of RE1is methyl. In certain embodiments, at least one instance of RE1is ethyl. In certain embodiments, at least one instance of RE1is propyl. In certain embodiments, at least one instance of RE1is butyl. In certain embodiments, at least one instance of RE1is pentyl. In certain embodiments, at least one instance of RE1is hexyl. In certain embodiments, at least one instance of RE1is substituted alkenyl. In certain embodiments, at least one instance of RE1is unsubstituted alkenyl. In certain embodiments, at least one instance of RE1is vinyl. In certain embodiments, at least one instance of RE1is substituted alkynyl. In certain embodiments, at least one instance of RE1is unsubstituted alkynyl. In certain embodiments, at least one instance of RE1is ethynyl. In certain embodiments, at least one instance of RE1is substituted carbocyclyl. In certain embodiments, at least one instance of RE1is unsubstituted carbocyclyl. In certain embodiments, at least one instance of RE1is saturated carbocyclyl. In certain embodiments, at least one instance of RE1is unsaturated carbocyclyl. In certain embodiments, at least one instance of RE1is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RE1is 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RE1is cylcopropyl. In certain embodiments, at least one instance of RE1is cyclobutyl. In certain embodiments, at least one instance of RE1is cyclopentyl. In certain embodiments, at least one instance of RE1is cyclohexyl. In certain embodiments, at least one instance of RE1is cycloheptyl. In certain embodiments, at least one instance of RE1is 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RE1is substituted heterocyclyl. In certain embodiments, at least one instance of RE1is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RE1is saturated heterocyclyl. In certain embodiments, at least one instance of RE1is unsaturated heterocyclyl. In certain embodiments, at least one instance of RE1is heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RE1is heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RE1is 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RE1is 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RE1is substituted or unsubstituted aryl. In certain embodiments, at least one instance of RE1is 6- to 14-membered aryl. In certain embodiments, at least one instance of RE1is 6- to 10-membered aryl. In certain embodiments, at least one instance of RE1is monocyclic aryl. In certain embodiments, at least one instance of RE1is phenyl. In certain embodiments, at least one instance of RE1is bicyclic aryl. In certain embodiments, at least one instance of RE1is naphthyl. In certain embodiments, at least one instance of RE1is substituted or unsubstituted heteroaryl. In certain embodiments, at least one instance of RE1is heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RE1is monocyclic heteroaryl. In certain embodiments, at least one instance of RE1is 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RE1is 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RE1is pyridyl. In certain embodiments, at least one instance of RE1is bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RE1is 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RE1is 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RE1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one instance of RE1is Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RE1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RE1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom.

In certain embodiments, two instances of RE1are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RE1are joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RE1are joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RE1are joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RE1are joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RE1are joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

Compounds of Formula (I) includes linker moiety L. In certain embodiments, L is a bond. In certain embodiments, L is a single bond. In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is

When linker moiety L of compounds of Formula (I) is of the formula:

L may include one or more substituent RF. In certain embodiments, at least one instance of RFis H. In certain embodiments, at least one instance of RFis halogen. In certain embodiments, at least one instance of RFis F. In certain embodiments, at least one instance of RFis Cl. In certain embodiments, at least one instance of RFis Br. In certain embodiments, at least one instance of RFis I (iodine). In certain embodiments, at least one instance of RFis substituted acyl. In certain embodiments, at least one instance of RFis unsubstituted acyl. In certain embodiments, at least one instance of RFis substituted alkyl. In certain embodiments, at least one instance of RFis unsubstituted alkyl. In certain embodiments, at least one instance of RFis C1-12alkyl. In certain embodiments, at least one instance of RFis C1-6alkyl. In certain embodiments, at least one instance of RFis unsubstituted methyl. In certain embodiments, at least one instance of RFis substituted methyl. In certain embodiments, at least one instance of RFis —CH2F. In certain embodiments, at least one instance of RFis —CHF2. In certain embodiments, at least one instance of RFis —CF3. In certain embodiments, at least one instance of RFis Bn. In certain embodiments, at least one instance of RFis unsubstituted ethyl. In certain embodiments, at least one instance of RFis substituted ethyl. In certain embodiments, at least one instance of RFis —(CH2)2Ph. In certain embodiments, at least one instance of RFis propyl.In certain embodiments, at least one instance of RFis butyl. In certain embodiments, at least one instance of RFis pentyl. In certain embodiments, at least one instance of RFis hexyl. In certain embodiments, at least one instance of RFis substituted alkenyl. In certain embodiments, at least one instance of RFis unsubstituted alkenyl. In certain embodiments, at least one instance of RFis vinyl. In certain embodiments, at least one instance of RFis substituted alkynyl. In certain embodiments, at least one instance of RFis unsubstituted alkynyl. In certain embodiments, at least one instance of RFis ethynyl. In certain embodiments, at least one instance of RFis substituted carbocyclyl. In certain embodiments, at least one instance of RFis unsubstituted carbocyclyl. In certain embodiments, at least one instance of RFis saturated carbocyclyl. In certain embodiments, at least one instance of RFis unsaturated carbocyclyl. In certain embodiments, at least one instance of RFis carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RFis monocyclic carbocyclyl. In certain embodiments, at least one instance of RFis 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RFis cylcopropyl. In certain embodiments, at least one instance of RFis cyclobutyl. In certain embodiments, at least one instance of RFis cyclopentyl. In certain embodiments, at least one instance of RFis cyclohexyl. In certain embodiments, at least one instance of RFis cycloheptyl. In certain embodiments, at least one instance of RFis bicyclic carbocyclyl. In certain embodiments, at least one instance of RFis 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RFis substituted heterocyclyl. In certain embodiments, at least one instance of RFis unsubstituted heterocyclyl. In certain embodiments, at least one instance of RFis saturated heterocyclyl. In certain embodiments, at least one instance of RFis unsaturated heterocyclyl. In certain embodiments, at least one instance of RFis heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RFis heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RFis monocyclic heterocyclyl. In certain embodiments, at least one instance of RFis 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RFis bicyclic heterocyclyl. In certain embodiments, at least one instance of RFis 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RFis substituted aryl. In certain embodiments, at least one instance of RFis unsubstituted aryl. In certain embodiments, at least one instance of RFis 6- to 14-membered aryl. In certain embodiments, at least one instance of RFis 6- to 10-membered aryl. In certain embodiments, at least one instance of RFis substituted phenyl. In certain embodiments, at least one instance of RFis unsubstituted phenyl. In certain embodiments, at least one instance of RFis substituted naphthyl. In certain embodiments, at least one instance of RFis unsubstituted naphthyl. In certain embodiments, at least one instance of RFis substituted heteroaryl. In certain embodiments, at least one instance of RFis unsubstituted heteroaryl. In certain embodiments, at least one instance of RFis heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RFis monocyclic heteroaryl. In certain embodiments, at least one instance of RFis 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RFis 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RFis pyridyl. In certain embodiments, at least one instance of RFis bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RFis 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RFis 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RFis —ORF. In certain embodiments, at least one instance of RFis —OMe. In certain embodiments, at least one instance of RFis —OEt. In certain embodiments, at least one instance of RFis —OPr. In certain embodiments, at least one instance of RFis —OBu. In certain embodiments, at least one instance of RFis —O(pentyl). In certain embodiments, at least one instance of RFis —O(hexyl). In certain embodiments, at least one instance of RFis —OPh. In certain embodiments, at least one instance of RFis —OBn. In certain embodiments, at least one instance of RFis —O(CH2)2Ph. In certain embodiments, at least one instance of RFis —OH. In certain embodiments, at least one instance of RFis —SRF1. In certain embodiments, at least one instance of RFis —SMe. In certain embodiments, at least one instance of RFis —SH. In certain embodiments, at least one instance of RFis —N(RF1)2. In certain embodiments, at least one instance of RFis —NMe2. In certain embodiments, at least one instance of RFis —NH2. In certain embodiments, at least one instance of RFis —CN. In certain embodiments, at least one instance of RFis —SCN. In certain embodiments, at least one instance of RFis —C(═NRF1)RF1, —C(═NRF1)ORF1, or —C(═NRF1)N(RF1)2. In certain embodiments, at least one instance of RFis —C(═O)RF1, —C(═O)ORF1, or —C(═O)N(RF1)2. In certain embodiments, at least one instance of RFis —NO2. In certain embodiments, at least one instance of RFis —NRF1C(═O)RF1, —NRF1C(═O)ORF1, or NRF1C(═O)N(RF)2. In certain embodiments, at least one instance of RFis OC(═O)RF1, —OC(═O)ORF1, or —OC(═O)N(RF1)2.

In compounds of Formula (I), two RFgroups may be joined to form a substituted or unsubstituted carbocyclic ring. In certain embodiments, two instances of RFare joined to form a saturated or unsaturated carbocyclic ring. In certain embodiments, two instances of RFare joined to form a carbocyclic ring including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 3- to 7-membered, monocyclic carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 3-membered carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 4-membered carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 5-membered carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 6-membered carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 7-membered carbocyclic ring. In certain embodiments, two instances of RFare joined to form a 5- to 13-membered, bicyclic carbocyclic ring.

In certain embodiments, two instances of RFare joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RFare joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RFare joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RFare joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RFare joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RFare joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

In certain embodiments, two instances of RFare joined to form a substituted or unsubstituted aryl ring. In certain embodiments, two instances of RFare joined to form a 6- to 14-membered aryl ring. In certain embodiments, two instances of RFare joined to form a 6-to 10-membered aryl ring. In certain embodiments, two instances of RFare joined to form a monocyclic aryl ring. In certain embodiments, two instances of RFare joined to form a phenyl. In certain embodiments, two instances of RFare joined to form a bicyclic aryl ring. In certain embodiments, two instances of RFare joined to form a naphthyl.

In certain embodiments, two instances of RFare joined to form a substituted or unsubstituted heteroaryl ring. In certain embodiments, two instances of RFare joined to form a monocyclic heteroaryl ring, wherein one, two, or three atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RFare joined to form a 5-membered, monocyclic heteroaryl ring. In certain embodiments, two instances of RFare joined to form a 6-membered, monocyclic heteroaryl ring. In certain embodiments, two instances of RFare joined to form a pyridyl. In certain embodiments, two instances of RFare joined to form a bicyclic heteroaryl ring system, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RFare joined to form a 9-membered, bicyclic heteroaryl ring system. In certain embodiments, two instances of RFare joined to form a 10-membered, bicyclic heteroaryl ring system.

In certain embodiments, at least one instance of RFis halogen, substituted or unsubstituted alkyl, or —ORF1. In certain embodiments, at least one instance of RFis halogen, unsubstituted alkyl, or —O-(unsubstituted alkyl). In certain embodiments, at least one instance of RFis halogen, unsubstituted C1-6alkyl, or —O-(unsubstituted C1-6alkyl).

In certain embodiments, at least one instance of RF1is H. In certain embodiments, at least one instance of RF1is substituted acyl. In certain embodiments, at least one instance of RF1is unsubstituted acyl. In certain embodiments, at least one instance of RF1is acetyl. In certain embodiments, at least one instance of RF1is substituted alkyl. In certain embodiments, at least one instance of RF1is unsubstituted alkyl. In certain embodiments, at least one instance of RF1is C1-12alkyl. In certain embodiments, at least one instance of RF1is C1-6alkyl. In certain embodiments, at least one instance of RF1is methyl. In certain embodiments, at least one instance of RF1is ethyl. In certain embodiments, at least one instance of RF1is propyl. In certain embodiments, at least one instance of RF1is butyl. In certain embodiments, at least one instance of RF1is pentyl. In certain embodiments, at least one instance of RF1is hexyl. In certain embodiments, at least one instance of RF1is substituted alkenyl. In certain embodiments, at least one instance of RF1is unsubstituted alkenyl. In certain embodiments, at least one instance of RF1is vinyl. In certain embodiments, at least one instance of RF1is substituted alkynyl. In certain embodiments, at least one instance of RF1is unsubstituted alkynyl. In certain embodiments, at least one instance of RF1is ethynyl. In certain embodiments, at least one instance of RF1is substituted carbocyclyl. In certain embodiments, at least one instance of RF1is unsubstituted carbocyclyl. In certain embodiments, at least one instance of RFis saturated carbocyclyl. In certain embodiments, at least one instance of RF1is unsaturated carbocyclyl. In certain embodiments, at least one instance of RF1is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RF1is 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RF1is cylcopropyl. In certain embodiments, at least one instance of RF1is cyclobutyl. In certain embodiments, at least one instance of RF1is cyclopentyl. In certain embodiments, at least one instance of RF1is cyclohexyl. In certain embodiments, at least one instance of RF1is cycloheptyl. In certain embodiments, at least one instance of RF1is 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RF1is substituted heterocyclyl. In certain embodiments, at least one instance of RF1is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RF1is saturated heterocyclyl. In certain embodiments, at least one instance of RF1is unsaturated heterocyclyl. In certain embodiments, at least one instance of RF1is heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RF1is heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RF1is 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RF1is 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RF1is substituted or unsubstituted aryl. In certain embodiments, at least one instance of RF1is 6- to 14-membered aryl. In certain embodiments, at least one instance of RF1is 6- to 10-membered aryl. In certain embodiments, at least one instance of RF1is monocyclic aryl. In certain embodiments, at least one instance of RF1is phenyl. In certain embodiments, at least one instance of RF1is bicyclic aryl. In certain embodiments, at least one instance of RF1is naphthyl. In certain embodiments, at least one instance of RF1is substituted or unsubstituted heteroaryl. In certain embodiments, at least one instance of RF1is heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RF1is monocyclic heteroaryl. In certain embodiments, at least one instance of RF1is 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RF1is 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RF1is pyridyl. In certain embodiments, at least one instance of RF1is bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RF1is 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RF1is 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RF1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one instance of RF1is Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RF1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RF1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom. In certain embodiments, RF1is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, RF1is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom.

In certain embodiments, two instances of RF1are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RF1are joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RF1are joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RF1are joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RF1are joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RF1are joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

In certain embodiments, f is 0. In certain embodiments, f is 1. In certain embodiments, f is 2. In certain embodiments, f is 3. In certain embodiments, f is 4.

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

In certain embodiments, RFis halogen, substituted or unsubstituted alkyl, or —ORF1; and f or g is 1. In certain embodiments, RFis halogen, unsubstituted alkyl, or —O- (unsubstituted alkyl); and f or g is 1. In certain embodiments, RFis halogen, unsubstituted C1-6alkyl, or —O-(unsubstituted C1-6alkyl); and f or g is 1. In certain embodiments, RFis —ORF1; and f or g is 1. In certain embodiments, RFis —O-(unsubstituted alkyl); and f or g is 1. In certain embodiments, RFis —O-(unsubstituted C1-6alkyl); and f or g is 1. In certain embodiments, RFis —OMe; and f or g is 1.

Compounds of Formula (I) include substituent RBon the amino moiety. In certain embodiments, RBis H. In certain embodiments, RBis substituted acyl. In certain embodiments, RBis unsubstituted acyl. In certain embodiments, RBis substituted alkyl. In certain embodiments, RBis unsubstituted alkyl. In certain embodiments, RBis C1-12alkyl. In certain embodiments, RBis C1-6alkyl. In certain embodiments, RBis unsubstituted methyl. In certain embodiments, RBis substituted methyl. In certain embodiments, RBis —CH2F. In certain embodiments, RBis CHF2. In certain embodiments, RBis CF3. In certain embodiments, RBis Bn. In certain embodiments, RBis unsubstituted ethyl. In certain embodiments, RBis substituted ethyl. In certain embodiments, RBis —(CH2)2Ph. In certain embodiments, RBis propyl. In certain embodiments, RBis n-propy. In certain embodiments, RBis iso-propyl. In certain embodiments, RBis butyl. In certain embodiments, RBis n-butyl. In certain embodiments, RBis iso-butyl. In certain embodiments, RBis t-butyl. In certain embodiments, RBis pentyl. In certain embodiments, RBis hexyl. In certain embodiments, RBis substituted alkenyl. In certain embodiments, RBis unsubstituted alkenyl. In certain embodiments, RBis vinyl. In certain embodiments, RBis substituted alkynyl. In certain embodiments, RBis unsubstituted alkynyl. In certain embodiments, RBis ethynyl. In certain embodiments, RBis substituted carbocyclyl. In certain embodiments, RBis unsubstituted carbocyclyl. In certain embodiments, RBis saturated carbocyclyl. In certain embodiments, RBis unsaturated carbocyclyl. In certain embodiments, RBis carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, RBis monocyclic carbocyclyl. In certain embodiments, RBis 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, RBis cylcopropyl. In certain embodiments, RBis cyclobutyl. In certain embodiments, RBis cyclopentyl. In certain embodiments, RBis cyclohexyl. In certain embodiments, RBis cycloheptyl. In certain embodiments, RBis bicyclic carbocyclyl. In certain embodiments, RBis 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, RBis substituted heterocyclyl. In certain embodiments, RBis unsubstituted heterocyclyl. In certain embodiments, RBis saturated heterocyclyl. In certain embodiments, RBis unsaturated heterocyclyl. In certain embodiments, RBis heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, RBis heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, RBis monocyclic heterocyclyl. In certain embodiments, RBis 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, RBis bicyclic heterocyclyl. In certain embodiments, RBis 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, RBis substituted aryl. In certain embodiments, RBis unsubstituted aryl. In certain embodiments, RBis 6- to 14-membered aryl. In certain embodiments, RBis 6- to 10-membered aryl. In certain embodiments, RBis substituted phenyl. In certain embodiments, RBis para-substituted phenyl. In certain embodiments, RBis of the formula:

In certain embodiments, RBis of the formula:

In certain embodiments, RB is unsubstituted phenyl. In certain embodiments, RBis substituted naphthyl. In certain embodiments, RBis unsubstituted naphthyl. In certain embodiments, RBis substituted heteroaryl. In certain embodiments, RBis unsubstituted heteroaryl. In certain embodiments, RBis heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, RBis monocyclic heteroaryl. In certain embodiments, RBis 5-membered, monocyclic heteroaryl. In certain embodiments, RBis 6-membered, monocyclic heteroaryl. In certain embodiments, RBis pyridyl. In certain embodiments, RBis bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, RBis 9-membered, bicyclic heteroaryl. In certain embodiments, RBis 10-membered, bicyclic heteroaryl. In certain embodiments, RBis —C(═O)RB1. In certain embodiments, RBis —C(═O)-(substituted or unsubstituted alkyl). In certain embodiments, RBis —C(═O)-(unsubstituted C1-6alkyl). In certain embodiments, RBis —C(═O)-(t-Bu). In certain embodiments, RBis —C(═O)-(substituted or unsubstituted phenyl). In certain embodiments, RBis —C(═O)Ph. In certain embodiments, RBis of the formula:

In certain embodiments, RBand RCare joined to form a substituted heterocyclic ring. In certain embodiments, RBand RCare joined to form an unsubstituted heterocyclic ring. In certain embodiments, RBand RCare joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, RBand RCare joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, RBand RCare joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, RBand RCare joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, RBand RCare joined to form a 5- or 6-membered, monocyclic heterocyclic ring wherein one or two atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen or oxygen. In certain embodiments, RBand RCare joined to form a heterocyclic ring of the formula:

In certain embodiments, RBand RCare joined to form a heterocyclic ring of the formula:

In certain embodiments, RBand RCare joined to form a heterocyclic ring of the formula:

In certain embodiments, RBand RCare joined to form a heterocyclic ring of the formula:

In certain embodiments, RBand RCare joined to form a heterocyclic ring of the formula:

In certain embodiments, RBand RCare joined to form a 5- to 13-membered, bicyclic heterocyclic ring system.

In certain embodiments, at least one instance of RB1is H. In certain embodiments, at least one instance of RB1is substituted acyl. In certain embodiments, at least one instance of RB1is unsubstituted acyl. In certain embodiments, at least one instance of RBis acetyl. In certain embodiments, at least one instance of RB1is substituted alkyl. In certain embodiments, at least one instance of RB1is unsubstituted alkyl. In certain embodiments, at least one instance of RB1is C1-12alkyl. In certain embodiments, at least one instance of RB1is C1-6alkyl. In certain embodiments, at least one instance of RB1is methyl. In certain embodiments, at least one instance of RB1is ethyl. In certain embodiments, at least one instance of RB1is propyl. In certain embodiments, at least one instance of RB1is butyl. In certain embodiments, at least one instance of RB1is pentyl. In certain embodiments, at least one instance of RB1is hexyl. In certain embodiments, at least one instance of RB1is substituted alkenyl. In certain embodiments, at least one instance of RB1is unsubstituted alkenyl. In certain embodiments, at least one instance of RB1is vinyl. In certain embodiments, at least one instance of RB1is substituted alkynyl. In certain embodiments, at least one instance of RB1is unsubstituted alkynyl. In certain embodiments, at least one instance of RB1is ethynyl. In certain embodiments, at least one instance of RB1is substituted carbocyclyl. In certain embodiments, at least one instance of RBis unsubstituted carbocyclyl. In certain embodiments, at least one instance of RB1is saturated carbocyclyl. In certain embodiments, at least one instance of RB1is unsaturated carbocyclyl. In certain embodiments, at least one instance of RB1is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RB1is 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RB1is cylcopropyl. In certain embodiments, at least one instance of RB1is cyclobutyl. In certain embodiments, at least one instance of RB1is cyclopentyl. In certain embodiments, at least one instance of RB1is cyclohexyl. In certain embodiments, at least one instance of RB1is cycloheptyl. In certain embodiments, at least one instance of RB1is 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RB1is substituted heterocyclyl. In certain embodiments, at least one instance of RB1is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RB1is saturated heterocyclyl. In certain embodiments, at least one instance of RB1is unsaturated heterocyclyl. In certain embodiments, at least one instance of RB1is heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RB1is heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RB1is 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RB1is 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RB1is substituted or unsubstituted aryl. In certain embodiments, at least one instance of RB1is 6- to 14-membered aryl. In certain embodiments, at least one instance of RB1is 6- to 10-membered aryl. In certain embodiments, at least one instance of RBis monocyclic aryl. In certain embodiments, at least one instance of RB1is phenyl. In certain embodiments, at least one instance of RB1is bicyclic aryl. In certain embodiments, at least one instance of RBI is naphthyl. In certain embodiments, at least one instance of RB1is substituted or unsubstituted heteroaryl. In certain embodiments, at least one instance of RB1is heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RB1is monocyclic heteroaryl. In certain embodiments, at least one instance of RB1is 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RB1is 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RB1is pyridyl. In certain embodiments, at least one instance of RB1is bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RB1is 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RB1is 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RB1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one instance of RB1is Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RB1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RB1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom.

In certain embodiments, two instances of RB1are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RB1are joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RB1are joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RB1are joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RB1are joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RB1are joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

In certain embodiments, at least one instance of RC1is H. In certain embodiments, at least one instance of RC1is substituted acyl. In certain embodiments, at least one instance of RC1is unsubstituted acyl. In certain embodiments, at least one instance of RC1is acetyl. In certain embodiments, at least one instance of RC1is substituted alkyl. In certain embodiments, at least one instance of RC1is unsubstituted alkyl. In certain embodiments, at least one instance of RC1is C1-12alkyl. In certain embodiments, at least one instance of RC1is C1-6alkyl. In certain embodiments, at least one instance of RC1is methyl. In certain embodiments, at least one instance of RC1is ethyl. In certain embodiments, at least one instance of RC1is propyl. In certain embodiments, at least one instance of RC1is butyl. In certain embodiments, at least one instance of RC1is pentyl. In certain embodiments, at least one instance of RC1is hexyl. In certain embodiments, at least one instance of RC1is substituted alkenyl. In certain embodiments, at least one instance of RC1is unsubstituted alkenyl. In certain embodiments, at least one instance of RC1is vinyl. In certain embodiments, at least one instance of RC1is substituted alkynyl. In certain embodiments, at least one instance of RC1is unsubstituted alkynyl. In certain embodiments, at least one instance of RC1is ethynyl. In certain embodiments, at least one instance of RC1is substituted carbocyclyl. In certain embodiments, at least one instance of RC1is unsubstituted carbocyclyl. In certain embodiments, at least one instance of RC1is saturated carbocyclyl. In certain embodiments, at least one instance of RC1is unsaturated carbocyclyl. In certain embodiments, at least one instance of RC1is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RC1is 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RC1is cylcopropyl. In certain embodiments, at least one instance of RC1is cyclobutyl. In certain embodiments, at least one instance of RC1is cyclopentyl. In certain embodiments, at least one instance of RC1is cyclohexyl. In certain embodiments, at least one instance of RC1is cycloheptyl. In certain embodiments, at least one instance of RC1is 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RCis substituted heterocyclyl. In certain embodiments, at least one instance of RC1is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RC1is saturated heterocyclyl. In certain embodiments, at least one instance of RCis unsaturated heterocyclyl. In certain embodiments, at least one instance of RC1is heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RC1is heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RC1is 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RC1is 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RC1is substituted or unsubstituted aryl. In certain embodiments, at least one instance of RC1is 6- to 14-membered aryl. In certain embodiments, at least one instance of RC1is 6- to 10-membered aryl. In certain embodiments, at least one instance of RC1is monocyclic aryl. In certain embodiments, at least one instance of RC1is phenyl. In certain embodiments, at least one instance of RC1is bicyclic aryl. In certain embodiments, at least one instance of RC1is naphthyl. In certain embodiments, at least one instance of RCis substituted or unsubstituted heteroaryl. In certain embodiments, at least one instance of RC1is heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RC1is monocyclic heteroaryl. In certain embodiments, at least one instance of RC1is 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RC1is 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RC1is pyridyl. In certain embodiments, at least one instance of RC1is bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RC1is 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RC1is 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RC1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one instance of RC1is Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RC1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RC1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom.

In certain embodiments, two instances of RC1are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RC1are joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RC1are joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RC1are joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RC1are joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RC1are joined to form a 5- to 13-membered, bicyclic heterocyclic ring.

Compounds of Formula (I) may include one or more substituent RD. In certain embodiments, at least one instance of RDis H. In certain embodiments, at least one instance of RDis halogen. In certain embodiments, at least one instance of RDis F. In certain embodiments, at least one instance of RDis Cl. In certain embodiments, at least one instance of RDis Br. In certain embodiments, at least one instance of RDis I (iodine). In certain embodiments, at least one instance of RDis substituted acyl. In certain embodiments, at least one instance of RDis unsubstituted acyl. In certain embodiments, at least one instance of RDis substituted alkyl. In certain embodiments, at least one instance of RDis unsubstituted alkyl. In certain embodiments, at least one instance of RDis C1-12alkyl. In certain embodiments, at least one instance of RDis C1-6alkyl. In certain embodiments, at least one instance of RDis unsubstituted methyl. In certain embodiments, at least one instance of RDis substituted methyl. In certain embodiments, at least one instance of RDis —CH2F. In certain embodiments, at least one instance of RDis —CHF2. In certain embodiments, at least one instance of RDis —CF3. In certain embodiments, at least one instance of RDis Bn. In certain embodiments, at least one instance of RDis unsubstituted ethyl. In certain embodiments, at least one instance of RDis substituted ethyl. In certain embodiments, at least one instance of RDis —(CH2)2Ph. In certain embodiments, at least one instance of RDis propyl. In certain embodiments, at least one instance of RDis butyl. In certain embodiments, at least one instance of RDis pentyl. In certain embodiments, at least one instance of RDis hexyl. In certain embodiments, at least one instance of RDis substituted alkenyl. In certain embodiments, at least one instance of RDis unsubstituted alkenyl. In certain embodiments, at least one instance of RDis vinyl. In certain embodiments, at least one instance of RDis substituted alkynyl. In certain embodiments, at least one instance of RDis unsubstituted alkynyl. In certain embodiments, at least one instance of RDis ethynyl. In certain embodiments, at least one instance of RDis substituted carbocyclyl. In certain embodiments, at least one instance of RDis unsubstituted carbocyclyl. In certain embodiments, at least one instance of RDis saturated carbocyclyl. In certain embodiments, at least one instance of RDis unsaturated carbocyclyl. In certain embodiments, at least one instance of RD is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RDis monocyclic carbocyclyl. In certain embodiments, at least one instance of RDis 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RDis cylcopropyl. In certain embodiments, at least one instance of RDis cyclobutyl. In certain embodiments, at least one instance of RDis cyclopentyl. In certain embodiments, at least one instance of RDis cyclohexyl. In certain embodiments, at least one instance of RDis cycloheptyl. In certain embodiments, at least one instance of RDis bicyclic carbocyclyl. In certain embodiments, at least one instance of RDis 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RDis substituted heterocyclyl. In certain embodiments, at least one instance of RDis unsubstituted heterocyclyl. In certain embodiments, at least one instance of RDis saturated heterocyclyl. In certain embodiments, at least one instance of RDis unsaturated heterocyclyl. In certain embodiments, at least one instance of RDis heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RDis heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RDis monocyclic heterocyclyl. In certain embodiments, at least one instance of RDis 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RDis bicyclic heterocyclyl. In certain embodiments, at least one instance of RDis 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RDis substituted aryl. In certain embodiments, at least one instance of RDis unsubstituted aryl. In certain embodiments, at least one instance of RDis 6- to 14-membered aryl. In certain embodiments, at least one instance of RDis 6- to 10-membered aryl. In certain embodiments, at least one instance of RDis substituted phenyl. In certain embodiments, at least one instance of RDis unsubstituted phenyl. In certain embodiments, at least one instance of RDis substituted naphthyl. In certain embodiments, at least one instance of RDis unsubstituted naphthyl. In certain embodiments, at least one instance of RDis substituted heteroaryl. In certain embodiments, at least one instance of RDis unsubstituted heteroaryl. In certain embodiments, at least one instance of RDis heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RDis monocyclic heteroaryl. In certain embodiments, at least one instance of RDis 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RDis 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RDis pyridyl. In certain embodiments, at least one instance of RDis bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RDis 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RDis 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RDis —ORD1. In certain embodiments, at least one instance of RDis —O-(substituted or unsubstituted alkyl). In certain embodiments, at least one instance of RDis —O-(unsubstituted C1-6-alkyl). In certain embodiments, at least one instance of RDis —OMe. In certain embodiments, at least one instance of RDis —OEt. In certain embodiments, at least one instance of RDis —OPr. In certain embodiments, at least one instance of RDis —OBu. In certain embodiments, at least one instance of RDis —O(pentyl). In certain embodiments, at least one instance of RDis —O(hexyl). In certain embodiments, at least one instance of RDis —OPh. In certain embodiments, at least one instance of RDis —OBn. In certain embodiments, at least one instance of RDis —O(CH2)2Ph. In certain embodiments, at least one instance of RDis —OH. In certain embodiments, at least one instance of RDis —SRD1. In certain embodiments, at least one instance of RDis —SMe. In certain embodiments, at least one instance of RDis —SH. In certain embodiments, at least one instance of RDis —N(RD1)2. In certain embodiments, at least one instance of RDis —NMe2. In certain embodiments, at least one instance of RDis —NH2. In certain embodiments, at least one instance of RDis —CN. In certain embodiments, at least one instance of RDis —SCN. In certain embodiments, at least one instance of RDis —C(═NRD1)RD1, —C(═NRD1)ORD1, or —C(═NRD1)N(RD1)2. In certain embodiments, at least one instance of RDis —C(═O)RD1, —C(═O)ORD1, or —C(═O)N(RD1)2. In certain embodiments, at least one instance of RDis —NO2. In certain embodiments, at least one instance of RDis —NRD1C(═O)RD1, —NRD1C(═O)ORD1or —NRD1C(═O)N(RD1)2. In certain embodiments, at least one instance of RDis —OC(═O)RD, —OC(═O)ORD1, or —OC(═O)N(RD1)2.

In compounds of Formula (I), two RDgroups may be joined to form a substituted or unsubstituted carbocyclic ring. In certain embodiments, two instances of RDare joined to form a saturated or unsaturated carbocyclic ring. In certain embodiments, two instances of RDare joined to form a carbocyclic ring including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 3- to 7-membered, monocyclic carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 3-membered carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 4-membered carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 5-membered carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 6-membered carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 7-membered carbocyclic ring. In certain embodiments, two instances of RDare joined to form a 5- to 13-membered, bicyclic carbocyclic ring system.

In certain embodiments, two instances of RDare joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RDare joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RDare joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RDare joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RDare joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RDare joined to form a 5- to 13-membered, bicyclic heterocyclic ring system.

In certain embodiments, two instances of RDare joined to form a substituted or unsubstituted aryl ring. In certain embodiments, two instances of RDare joined to form a 6- to 14-membered aryl ring. In certain embodiments, two instances of RDare joined to form a 6-to 10-membered aryl ring. In certain embodiments, two instances of RDare joined to form a monocyclic aryl ring. In certain embodiments, two instances of RDare joined to form a phenyl. In certain embodiments, two instances of RDare joined to form a bicyclic aryl ring system. In certain embodiments, two instances of RDare joined to form a naphthyl.

In certain embodiments, two instances of RDare joined to form a substituted or unsubstituted heteroaryl ring. In certain embodiments, two instances of RDare joined to form a monocyclic heteroaryl ring, wherein one, two, or three atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RDare joined to form a 5-membered, monocyclic heteroaryl ring. In certain embodiments, two instances of RDare joined to form a 6-membered, monocyclic heteroaryl ring. In certain embodiments, two instances of RDare joined to form a pyridyl ring. In certain embodiments, two instances of RDare joined to form a bicyclic heteroaryl ring system, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RDare joined to form a 9-membered, bicyclic heteroaryl ring system. In certain embodiments, two instances of RDare joined to form a 10-membered, bicyclic heteroaryl ring system.

In certain embodiments, at least one instance of RDis halogen, substituted or unsubstituted alkyl, or —ORD1. In certain embodiments, at least one instance of RDis halogen, unsubstituted alkyl, or —O-(unsubstituted alkyl). In certain embodiments, at least one instance of RDis halogen, unsubstituted C1-6alkyl, or —O-(unsubstituted C1-6alkyl). In certain embodiments, at least one instance of RDis Cl or —OMe. In certain embodiments, all instances of RDare hydrogen.

In certain embodiments, at least one instance of RD1is H. In certain embodiments, at least one instance of RD1is substituted acyl. In certain embodiments, at least one instance of RD1is unsubstituted acyl. In certain embodiments, at least one instance of RD1is acetyl. In certain embodiments, at least one instance of RD1is substituted alkyl. In certain embodiments, at least one instance of RD1is unsubstituted alkyl. In certain embodiments, at least one instance of RD1is C1-12alkyl. In certain embodiments, at least one instance of RD1is C1-6alkyl. In certain embodiments, at least one instance of RD1is methyl. In certain embodiments, at least one instance of RD1is ethyl. In certain embodiments, at least one instance of RD1is propyl. In certain embodiments, at least one instance of RD1is butyl. In certain embodiments, at least one instance of RD1is pentyl. In certain embodiments, at least one instance of RD1is hexyl. In certain embodiments, at least one instance of RD1is substituted alkenyl. In certain embodiments, at least one instance of RD1is unsubstituted alkenyl. In certain embodiments, at least one instance of RD1is vinyl. In certain embodiments, at least one instance of RD1is substituted alkynyl. In certain embodiments, at least one instance of RD1is unsubstituted alkynyl. In certain embodiments, at least one instance of RD1is ethynyl. In certain embodiments, at least one instance of RD1is substituted carbocyclyl. In certain embodiments, at least one instance of RD1is unsubstituted carbocyclyl. In certain embodiments, at least one instance of RD1is saturated carbocyclyl. In certain embodiments, at least one instance of RD1is unsaturated carbocyclyl. In certain embodiments, at least one instance of RD1is carbocyclyl including one, two, or three double bonds in the carbocyclic ring. In certain embodiments, at least one instance of RD1is 3- to 7-membered, monocyclic carbocyclyl. In certain embodiments, at least one instance of RD1is cylcopropyl. In certain embodiments, at least one instance of RD1is cyclobutyl. In certain embodiments, at least one instance of RD1is cyclopentyl. In certain embodiments, at least one instance of RD1is cyclohexyl. In certain embodiments, at least one instance of RDis cycloheptyl. In certain embodiments, at least one instance of RD1is 5- to 13-membered, bicyclic carbocyclyl. In certain embodiments, at least one instance of RD1is substituted heterocyclyl. In certain embodiments, at least one instance of RD1is unsubstituted heterocyclyl. In certain embodiments, at least one instance of RD1is saturated heterocyclyl. In certain embodiments, at least one instance of RD1is unsaturated heterocyclyl. In certain embodiments, at least one instance of RD1is heterocyclyl including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, at least one instance of RD1is heterocyclyl, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RD1is 3- to 7-membered, monocyclic heterocyclyl. In certain embodiments, at least one instance of RD1is 5- to 13-membered, bicyclic heterocyclyl. In certain embodiments, at least one instance of RD1is substituted or unsubstituted aryl. In certain embodiments, at least one instance of RD1is 6- to 14-membered aryl. In certain embodiments, at least one instance of RD1is 6- to 10-membered aryl. In certain embodiments, at least one instance of RD1is monocyclic aryl. In certain embodiments, at least one instance of RD1is phenyl. In certain embodiments, at least one instance of RD1is bicyclic aryl. In certain embodiments, at least one instance of RD1is naphthyl. In certain embodiments, at least one instance of RD1is substituted or unsubstituted heteroaryl. In certain embodiments, at least one instance of RD1is heteroaryl, wherein one, two, three, or four atoms in the heteroaryl ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, at least one instance of RD1is monocyclic heteroaryl. In certain embodiments, at least one instance of RD1is 5-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RD1is 6-membered, monocyclic heteroaryl. In certain embodiments, at least one instance of RD1is pyridyl. In certain embodiments, at least one instance of RD1is bicyclic heteroaryl, wherein the point of attachment may be on any atom of the bicyclic heteroaryl ring system, as valency permits. In certain embodiments, at least one instance of RD1is 9-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RD1is 10-membered, bicyclic heteroaryl. In certain embodiments, at least one instance of RD1is a nitrogen protecting group when attached to a nitrogen atom. In certain embodiments, at least one instance of RD1is Bn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to a nitrogen atom. In certain embodiments, RD1is an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RD1is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, or benzoyl when attached to an oxygen atom. In certain embodiments, RD1is a sulfur protecting group when attached to a sulfur atom. In certain embodiments, RD1is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom.

In certain embodiments, two instances of RD1are joined to form a substituted or unsubstituted heterocyclic ring. In certain embodiments, two instances of RD1are joined to form a saturated or unsaturated heterocyclic ring. In certain embodiments, two instances of RD1are joined to form a heterocyclic ring including one, two, or three double bonds in the heterocyclic ring. In certain embodiments, two instances of RD1are joined to form a heterocyclic ring, wherein one, two, or three atoms in the heterocyclic ring are independently selected from the group consisting of nitrogen, oxygen, and sulfur. In certain embodiments, two instances of RD1are joined to form a 3- to 7-membered, monocyclic heterocyclic ring. In certain embodiments, two instances of RD1are joined to form a 5- to 13-membered, bicyclic heterocyclic ring system.

In certain embodiments, d is 0. In certain embodiments, d is 1. In certain embodiments, d is 2.

In certain embodiments, RDis halogen, substituted or unsubstituted alkyl, or —ORD1; and d is 1. In certain embodiments, RDis halogen, unsubstituted alkyl, or —O-(unsubstituted alkyl); and d is 1. In certain embodiments, RDis halogen, unsubstituted C1-6alkyl, or —O-(unsubstituted C1-6alkyl); and d is 1. In certain embodiments, RDis halogen; and d is 1. In certain embodiments, RDis Cl; and d is 1. In certain embodiments, RDis —ORD1; and d is 1. In certain embodiments, RDis —OMe; and d is 1.

The present invention also provides the compound of Formula (II):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. In certain embodiments, the present invention provides the compound of Formula (II), and pharmaceutically acceptable salts thereof.

The present invention also provides the compound of Formula (III):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. In certain embodiments, the present invention provides the compound of Formula (III), and pharmaceutically acceptable salts thereof.

The present invention also provides the compound of Formula (IV):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. In certain embodiments, the present invention provides the compound of Formula (IV), and pharmaceutically acceptable salts thereof.

In certain embodiments, compounds of the invention are compounds described herein, and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. In certain embodiments, compounds of the invention are compounds described herein, and pharmaceutically acceptable salts thereof. In certain embodiments, compounds of the invention are compounds of any one of Formulae (I) to (IV), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof. In certain embodiments, compounds of the invention are compounds of any one of Formulae (I) to (IV), and pharmaceutically acceptable salts thereof. In certain embodiments, compounds of the 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, compounds of the invention are compounds of Formula (I), and pharmaceutically acceptable salts thereof.

Compounds of the invention are inhibitors of bromodomain-containing proteins. In certain embodiments, the compounds of the invention bind to a bromodomain-containing protein. Without wishing to be bound by any particular theory, the compounds of the invention are thought to bind in a binding pocket of a bromodomain of a bromodomain-containing protein. In certain embodiments, the compounds of the invention bind to the binding pocket of the bromodomain by mimicking the contact between a histone acetyl-lysine residue and the binding pocket. In certain embodiments, the compounds of the invention bind to the apo binding pocket of the bromodomain. In certain embodiments, the compounds of the invention covalently bind to the bromodomain-containing protein. In certain embodiments, the compounds of the invention non-covalently bind to the bromodomain-containing protein. In certain embodiments, the compounds of the invention reversibly bind to the bromodomain-containing protein. In certain embodiments, the compounds of the invention non-reversibly bind to the bromodomain-containing protein. In certain embodiments, the compounds of the invention inhibit the activity of a bromodomain-containing protein. In certain embodiments, the compounds of the invention inhibit the activity of a bromodomain-containing protein because of the binding of the compound to the bromodomain-containing protein. In certain embodiments, the compounds of the invention inhibit the activity of a bromodomain-containing protein because of the binding of the compounds to a bromodomain of the bromodomain-containing protein. In certain embodiments, the inventive compounds specifically bind to a bromodomain-containing protein. In certain embodiments, the inventive compounds specifically bind to a bromodomain of a bromodomain-containing protein. In certain embodiments, the inventive compounds that specifically bind to a bromodomain-containing protein show a greater binding affinity to the bromodomain-containing protein than to one or more other proteins or one or more other bromodomain-containing proteins. In certain embodiments, the inventive compounds non-specifically bind to a bromodomain-containing protein. In certain embodiments, the inventive compounds non-specifically bind to a bromodomain of a bromodomain-containing protein. In certain embodiments, the compounds of the invention reduce transcriptional elongation. In certain embodiments, the compounds of the invention disrupt the subcellular localization of a bromodomain-containing protein. In certain embodiments, the compounds of the invention reduce chromatin binding. In certain embodiments, the compounds of the invention inhibit the binding of Histone H4 Kac peptide to a bromodomain of a bromodomain-containing protein. In certain embodiments, the compounds of the invention form one or more hydrogen bonds with an evolutionarily conserved asparagine in a bromodomain of a bromodomain-containing protein. In certain embodiments, the bromodomain-containing protein is BRD4 or BRD2; and the asparagine is Asnl40 in BRD4(1) and Asn429 in BRD2(2). In certain embodiments, the compounds of the invention bind competitively with chromatin in a cellular environment. It is thus expected that the compounds of the invention may be useful in the treatment of a disease associated with the activity a bromodomain-containing protein (e.g., a proliferative disease).

The bromodomain-containing proteins that may be bound, and whose activity may be inhibited, by the inventive compounds include, but are not limited to, the bromodomain-containing proteins described herein. In certain embodiments, the bromodomain-containing protein is a bromo and extra terminal protein (BET). In certain embodiments, the bromodomain-containing protein is BRD2. In certain embodiments, the bromodomain-containing protein is BRD2(1). In certain embodiments, the bromodomain-containing protein is BRD2(2). In certain embodiments, the bromodomain-containing protein is BRD3. In certain embodiments, the bromodomain-containing protein is BRD3(1). In certain embodiments, the bromodomain-containing protein is BRD3(2). In certain embodiments, the bromodomain-containing protein is BRD4. In certain embodiments, the bromodomain-containing protein is BRD4(1). In certain embodiments, the bromodomain-containing protein is BRD4(2). In certain embodiments, the bromodomain-containing protein is BRDT. In certain embodiments, the bromodomain-containing protein is BRDT(1). In certain embodiments, the bromodomain-containing protein is BRDT(2). In certain embodiments, the bromodomain-containing protein is a TBP (TATA box binding protein)-associated factor protein (TAF). In certain embodiments, the bromodomain-containing protein is TAF1. In certain embodiments, the bromodomain-containing protein is TAF1L. In certain embodiments, the bromodomain-containing protein is CREB-binding protein (CBP). In certain embodiments, the bromodomain-containing protein is E1A binding protein p300 (EP300).

The binding affinity of a compound of the invention to a bromodomain-containing protein may be measured by the dissociation constant (Kd) value of an adduct of the compound of the invention and the bromodomain-containing protein using methods known in the art (e.g., isothermal titration calorimetry (ITC)). In certain embodiments, the adduct comprises the compound of the invention and the bromodomain-containing protein, which are bound (e.g., covalently or non-covalently) to each other. In certain embodiments, the Kdvalue of the adduct is at most about 100 μM, at most about 30 μM, at most about 10 μM, at most about 3 μM, at most about 1 μM, at most about 300 nM, at most about 100 nM, at most about 30 nM, at most about 10 nM, at most about 3 nM, or at most about 1 nM. In certain embodiments, the Kdvalue of the adduct is at least about 1 nM, at least about 10 nM, at least about 100 nM, at least about 1 μM, at least about 10 μM, or at least about 100 μM. Combinations of the above-referenced ranges (e.g., at most about 10 μM and at least about 1 nM) are also within the scope of the invention. Other ranges are also possible. In certain embodiments, the Kdvalue of the adduct is at most about 10 μM. In certain embodiments, the Kdvalue of the adduct is at most about 300 nM. In certain embodiments, the Kdvalue of the adduct is at most about 100 nM.

In certain embodiments, the activity of the bromodomain-containing proteins described herein is inhibited by the inventive compounds. The inhibition of the activity of a bromodomain-containing protein by an inventive compound may be measured by the half maximal inhibitory concentration (IC50) value of a compound of the invention when the inventive compound, or a pharmaceutical composition thereof, is contacted, directly or indirectly, with the bromodomain-containing protein. The IC50values may be obtained using methods known in the art, e.g., by competing the PEG-biotinylated JQ1 off from a BRD protein in an alpha assay. In certain embodiments, the IC50value of a compound of the invention is at most about 1 mM, at most about 300 μM, at most about 100 μM, at most about 30 μM, at most about 10 μM, at most about 3 μM, at most about 1 μM, at most about 300 nM, at most about 100 nM, at most about 30 nM, at most about 10 nM, at most about 3 nM, or at most about 1 nM. In certain embodiments, the IC50value of a compound of the invention is at least about 1 nM, at least about 3 nM, at least about 10 nM, at least about 30 nM, at least about 100 nM, at least about 300 nM, at least about 1 μM, at least about 3 μM, at least about 10 μM, at least about 30 μM, at least about 100 μM, at least about 300 μM, or at least 1 mM. Combinations of the above-referenced ranges (e.g., at most about 300 μM and at least about 1 μM) are also within the scope of the invention. Other ranges are also possible. In certain embodiments, the IC50value of a compound of the invention is at most about 300 μM. In certain embodiments, the IC50value of a compound of the invention is at most about 30 μM. In certain embodiments, the IC50value of a compound of the invention is at most about 10 μM.

The compounds of the invention may selectively inhibit the activity of a bromodomain-containing protein. In certain embodiments, the inventive compounds that selectively inhibit the activity of a bromodomain-containing protein show a greater inhibitory activity against the bromodomain-containing protein than against one or more other proteins or one or more other bromodomain-containing proteins.

The selectivity of an inventive compound for a bromodomain-containing protein over another protein (e.g., another bromodomain-containing protein) may be measured by the quotient of the IC50value of the inventive compound in inhibiting the activity of the another protein over the IC50value of the inventive compound in inhibiting the activity of the bromodomain-containing protein. The selectivity of an inventive compound for a bromodomain-containing protein over another protein (e.g., another bromodomain-containing protein) may also be measured by the quotient of the Kdvalue of an adduct of the inventive compound and the another protein over the Kdvalue of an adduct of the inventive compound and the bromodomain-containing protein. 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, the selectivity is at most about 100,000-fold, at most about 10,000-fold, at most about 1,000-fold, at most about 100-fold, at most about 10-fold, or at most about 1-fold. Combinations of the above-referenced ranges (e.g., and at least about 2-fold and at most about 10,000-fold) are also within the scope of the invention. Other ranges are also possible. In certain embodiments, the selectivity is at least about 2-fold. In certain embodiments, the selectivity is at least about 10-fold. In certain embodiments, the selectivity is at least about 100-fold. In certain embodiments, the compounds of the invention selectively inhibit a bromodomain-containing protein described herein. In certain embodiments, the compounds of the invention selectively inhibit a BET protein. In certain embodiments, the compounds of the invention selectively inhibit BRD2. In certain embodiments, the compounds of the invention selectively inhibit BRD3. In certain embodiments, the compounds of the invention selectively inhibit BRD4. In certain embodiments, the compounds of the invention selectively inhibit BRDT. In certain embodiments, the compounds of the invention selectively inhibit a TAF protein (e.g., TAF1 or TAF1L), CBP, and/or EP300. In certain embodiments, the compound of the inventions are non-selective inhibitors of two or more bromodomain-containing proteins.

It is known in the art that a bromodomain-containing protein is implicated in a wide range of diseases. For example, BRD3 and BRD4 are related to BRD3 NUT midline carcinoma and BRD4 NUT midline carcinoma, respectively, BRDT is related to sperm formation, and CBP is related to mixed-lineage leukemia (MLL). Therefore, the inventive compounds are expected to be useful in treating and/or preventing diseases associated with bromodomain-containing proteins or as a male contraceptive drug.

Pharmaceutical Compositions, Kits, and Administration

The present invention provides pharmaceutical compositions comprising a compound of the invention (e.g., a compound of any one of Formulae (I)-(IV), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof), and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises a compound of Formula (I), or a pharmaceutically acceptable salt thereof, 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 a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises the compound of Formula (II), or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises the compound of Formula (II), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises the compound of Formula (III), or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises the compound of Formula (III), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises the compound of Formula (IV), or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient. In certain embodiments, the pharmaceutical composition of the invention comprises the compound of Formula (IV), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

In certain embodiments, the compound of the invention 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. In certain embodiments, the effective amount is an amount effective for treating and/or preventing a disease (e.g., a disease described herein). In certain embodiments, the effective amount is an amount effective for treating a disease. In certain embodiments, the effective amount is an amount effective for treating and/or preventing a disease associated with a bromodomain-containing protein. In certain embodiments, the effective amount is an amount effective for treating a disease associated with a bromodomain-containing protein. In certain embodiments, the effective amount is an amount effective for treating and/or preventing a proliferative disease (e.g., a proliferative disease described herein). In certain embodiments, the effective amount is an amount effective for treating a proliferative disease. In certain embodiments, the effective amount is an amount effective for treating and/or preventing cancer (e.g., a cancer described herein). In certain embodiments, the effective amount is an amount effective for treating cancer. In certain embodiments, the effective amount is an amount effective for treating and/or preventing lung cancer (e.g., small-cell lung cancer or non-small-cell lung cancer). In certain embodiments, the effective amount is an amount effective for treating lung cancer. In certain embodiments, the effective amount is an amount effective for treating and/or preventing a benign neoplasm (e.g., a benign neoplasm described herein). In certain embodiments, the effective amount is an amount effective for treating a benign neoplasm. In certain embodiments, the effective amount is an amount effective for treating and/or preventing a diseases or process associated with angiogenesis. In certain embodiments, the effective amount is an amount effective for treating a disease or process associated angiogenesis. In certain embodiments, the effective amount is an amount effective for treating and/or preventing an inflammatory disease (e.g., an inflammatory disease described herein). In certain embodiments, the effective amount is an amount effective for treating an inflammatory disease. In certain embodiments, the effective amount is an amount effective for treating and/or preventing an autoimmune disease (e.g., an autoimmune disease described herein). In certain embodiments, the effective amount is an amount effective for treating an autoimmune disease. In certain embodiments, the effective amount is an amount effective for treating and/or preventing diabetes (e.g., type 1 diabetes, type 2 diabetes, and gestational diabetes), obesity, fatty liver (NASH or otherwise), multiple myoloma, neuroblastoma, medullo, therosclerosis, arterial stent occlusion, heart failure, cachexia, graft versus host disease, an infection disease associated with a bromodomain-containing protein, an infection disease caused by a parasite, malaria, trypanosomes, an inflammatory disease, or male fertility.

An effective amount of a compound may vary from about 0.001 mg/kg to about 1000 mg/kg in one or more dose administrations for one or several days (depending on the mode of administration). In certain embodiments, the effective amount per dose varies from about 0.001 mg/kg to about 1000 mg/kg, from about 0.01 mg/kg to about 750 mg/kg, from about 0.1 mg/kg to about 500 mg/kg, from about 1.0 mg/kg to about 250 mg/kg, and from about 10.0 mg/kg to about 150 mg/kg.

An effective amount of a compound of the invention may be an amount effective for inhibiting the activity of a bromodomain-containing protein in a subject or cell. An effective amount of a compound of the invention may also be an amount effective for inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell. An effective amount of a compound of the invention may further be an amount effective for modulating (e.g., down-regulating) the expression (e.g., transcription) of a gene that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a bromodomain-containing protein, the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and/or the transcription of a gene that is regulated by a bromodomain-containing protein by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%. In certain embodiments, the effective amount is an amount effective for inhibiting the activity of a bromodomain-containing protein, the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and/or the transcription of a gene that is regulated by a bromodomain-containing protein by at most about 90%, at most about 80%, at most about 70%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 20%, or at most about 10%. Combinations of the ranges described herein (e.g., at least about 20% and at most about 50%) are also within the scope of the invention. In certain embodiments, the activity of a bromodomain-containing protein, the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and/or the transcription of a gene that is regulated by a bromodomain-containing protein are inhibited by a percentage or a range of percentage described herein by an effective amount of a compound of the invention.

In certain embodiments, the gene regulated by a bromodomain-containing protein is a gene regulated by a bromo and extra terminal protein (BET). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD2. In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD2(1). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD2(2). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD3. In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD3(1). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD3(2). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD4. In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD4(1). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRD4(2). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRDT. In certain embodiments, the gene regulated by a bromodomain-containing protein is BRDT(1). In certain embodiments, the gene regulated by a bromodomain-containing protein is BRDT(2). In certain embodiments, the gene regulated by a bromodomain-containing protein is a gene regulated by a TBP (TATA box binding protein)-associated factor protein (TAF). In certain embodiments, the gene regulated by a bromodomain-containing protein is TAF1. In certain embodiments, the gene regulated by a bromodomain-containing protein is TAF1L. In certain embodiments, the gene regulated by a bromodomain-containing protein is a gene regulated by a CREB-binding protein (CBP). In certain embodiments, the gene regulated by a bromodomain-containing protein is a gene regulated by an E1A binding protein p300 (EP300).

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 described herein (i.e., the “active ingredient”) into association with a carrier or excipient, and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping, and/or packaging the product into a desired single- or multi-dose unit.

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. The composition may comprise between 0.1% and 100% (w/w) active ingredient.

Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, antiprotozoan preservatives, alcohol preservatives, acidic preservatives, and other preservatives. In certain embodiments, the preservative is an antioxidant. In other embodiments, the preservative is a chelating agent.

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 or excipient and/or any needed preservatives and/or buffers as can be required. Additionally, the present invention contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body. Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium. Alternatively or additionally, the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.

Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices such as those described in U.S. Pat. Nos. 4,886,499; 5,190,521; 5,328,483; 5,527,288; 4,270,537; 5,015,235; 5,141,496; and 5,417,662. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin, such as those described in PCT publication WO 99/34850 and functional equivalents thereof. Alternatively or additionally, conventional syringes can be used in the classical mantoux method of intradermal administration. Jet injection devices which deliver liquid vaccines to the dermis via a liquid jet injector and/or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable. Jet injection devices are described, for example, in U.S. Pat. Nos. 5,480,381; 5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189; 5,704,911; 5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627; 5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880; 4,940,460; and PCT publications WO 97/37705 and WO 97/13537. Ballistic powder/particle delivery devices which use compressed gas to accelerate the compound in powder form through the outer layers of the skin to the dermis are suitable.

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

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

In certain embodiments, the compounds described herein 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 and/or prophylactic 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 (e.g., therapeutically and/or prophylactically active agents). The compounds or compositions can be administered in combination with additional pharmaceutical agents that improve their activity (e.g., activity (e.g., potency and/or efficacy) in treating a disease associated with a bromodomain-containing protein in a subject in need thereof, in preventing a disease associated with a bromodomain-containing protein in a subject in need thereof, in reducing the risk to have a disease associated with a bromodomain-containing protein in a subject in need thereof, in inhibiting the activity of a bromodomain-containing protein in a subject or cell, in inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell, in modulating the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell), bioavailability, and/or safety, reduce drug resistance, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body of a subject. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects. In certain embodiments, an inventive pharmaceutical composition including a compound of the invention and an additional pharmaceutical agent shows a synergistic effect that is absent in a pharmaceutical composition including one of the compound and the additional pharmaceutical agent, but not both.

The compound or composition can be administered concurrently with, prior to, or subsequent to one or more additional pharmaceutical agents, which may be useful as, e.g., combination therapies. Pharmaceutical agents include therapeutically active agents. Pharmaceutical agents also include prophylactically active agents. Pharmaceutical agents include small organic molecules such as drug compounds (e.g., compounds approved for human or veterinary use by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In certain embodiments, the additional pharmaceutical agent is a pharmaceutical agent useful for treating and/or preventing a disease described herein. 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 agent(s) and/or the desired therapeutic and/or prophylactic effect to be achieved. In general, it is expected that the additional pharmaceutical agent(s) utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.

The additional pharmaceutical agents include, but are not limited to, anti-proliferative agents, anti-cancer agents, anti-angiogenesis agents, anti-inflammatory agents, immunosuppressants, anti-bacterial agents, anti-viral agents, anti-diabetic agents, anti-allergic agents, and pain-relieving agents. In certain embodiments, the additional pharmaceutical agent is an inhibitor of a bromodomain-containing protein. In certain embodiments, the additional pharmaceutical agent is selected from the group consisting of (+)-JQ1, (−)-JQ1, I-BET, and PFI-1. See, e.g., international PCT patent application publication, WO 2011/143669. In certain embodiments, the additional pharmaceutical agent is selected from the group consisting of 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 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 inventive compounds or pharmaceutical compositions can be administered in combination with an anti-cancer therapy including, but not limited to, surgery, radiation therapy, and chemotherapy.

Also encompassed by the invention are kits (e.g., pharmaceutical packs). 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 first 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, or prodrug thereof, or a pharmaceutical composition thereof. In certain embodiments, the kits are useful for treating and/or preventing a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits are useful for treating a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits are useful for preventing a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits are useful for reducing the risk of having a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits are useful for inhibiting the activity of a bromodomain-containing protein in a subject or cell. In certain embodiments, the kits are useful for inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell. In certain embodiments, the kits are useful for modulating (e.g., down-regulating) the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the kits are useful for screening a library of compounds to identify a compound that is useful in the methods of the invention (e.g., useful for inhibiting the activity of a bromodomain-containing protein). In certain embodiments, the kits further include instructions for administering the compound or pharmaceutical composition of the invention. The kits may also include information as required by a regulatory agency such as the U.S. Food and Drug Administration (FDA). In certain embodiments, the information included in the kits is prescribing information. In certain embodiments, the kits and instructions provide for treating and/or preventing a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for treating a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for preventing a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for reducing the risk of having a disease described herein (e.g., a disease associated with bromodomain-containing proteins, such as a proliferative disease) in a subject in need thereof. In certain embodiments, the kits and instructions provide for inhibiting the activity of a bromodomain-containing protein in a subject or cell. In certain embodiments, the kits and instructions provide for inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell. In certain embodiments, the kits and instructions provide for modulating (e.g., down-regulating) the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the kits and instructions provide for screening a library of compounds to identify a compound that is useful in the methods of the invention (e.g., useful for inhibiting the activity of a bromodomain-containing protein). The kit of the invention may include one or more additional pharmaceutical agents described herein as a separate composition.

Methods of Treatment and Uses

The present invention provides methods that are useful for the treatment of a disease associated with a bromodomain-containing protein, such as a proliferative disease. The invention also provides methods of inhibiting the activity of a bromodomain-containing protein, methods of inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and methods of modulating the expression (e.g., transcription) of a gene that is regulated by a bromodomain-containing protein.

It has been reported that compound JQ1 is a cell-permeable, potent, small-molecule bromodomain inhibitor with biochemical selectivity for the BET family of bromodomain-containing proteins and that compounds related to JQ1 are capable of regulating bromodomain-containing proteins. See, e.g., international PCT patent application publication, WO 2011/143669. Lysine acetylation has emerged as a signaling modification of broad relevance to cellular and disease biology. Targeting the enzymes which reversibly mediate side-chain acetylation has been an active area of drug discovery for many years. To date, successful efforts have been limited to the “writers” (acetyl transferases) and “erasers” (histone deacetylases) of covalent modifications arising in the context of nuclear chromatin. Inhibitors of acetyl-lysine recognition modules, or bromodomains, are less studied. The recent characterization of a co-crystal structure of JQ1-BRD4 revealed excellent shape complementarity of JQ1 with the acetyl-lysine binding cavity of BRD4. Binding of JQ1 to the tandem bromodomains of BRD4 is acetyl-lysine competitive and displaces BRD4 from chromatin in human cells. Recurrent translocation of BRD4 has been observed in an incurable, genetically-defined subtype of human squamous cell carcinoma. Competitive binding of JQ1 to the BRD4 fusion oncoprotein has resulted in immediate squamous differentiation and specific anti-proliferative effects in patient-derived cell lines and in a murine model of BRD4-dependent carcinoma. Similar properties of compound I-BET, another bromodomain inhibitor, have also been reported (Nicodeme et al.,Nature2010, 468, 1119-1123). These data have established the feasibility of targeting protein-protein interactions of epigenetic “readers” and have suggested a versatile chemical scaffold for the development of chemical probes more broadly throughout the bromodomain protein family.

Gene regulation is fundamentally governed by reversible, non-covalent assembly of macromolecules. Signal transduction to RNA polymerase requires higher-ordered protein complexes, spatially regulated by assembly factors capable of interpreting the post-translational modification states of chromatin. Epigenetic readers are structurally diverse proteins, and each of the epigenetic readers possesses one or more evolutionarily conserved effector modules, which recognize covalent modifications of histone proteins or DNA. The ϵ-N-acetylation of lysine residues (Kac) on histone tails is associated with an open chromatin architecture and transcriptional activation. Context-specific molecular recognition of acetyl-lysine is principally mediated by bromodomains.

Bromodomain-containing proteins are of substantial biological interest, as components of transcription factor complexes (e.g., TBP (TATA box binding protein)-associated factor 1 (TAF1), CREB-binding protein (CBP or CREBBP), P300/CBP-associated factor (PCAF), and Gcn5) and determinants of epigenetic memory. There are 41 human proteins containing a total of 57 diverse bromodomains. Despite large sequence variations, all bromodomains share a conserved fold comprising a left-handed bundle of four alpha helices (αz, αA, αB, and αC), linked by diverse loop regions (ZA and BC loops) that determine substrate specificity. Co-crystal structures with peptidic substrates showed that the acetyl-lysine is recognized by a central hydrophobic cavity and is anchored by a hydrogen bond with an asparagine residue present in most bromodomains. The bromo and extra-terminal (BET) family (e.g., BRD2, BRD3, BRD4 and BRDT) shares a common domain architecture comprising two N-terminal bromodomains that exhibit high level of sequence conservation, and a more divergent C-terminal recruitment domain.

Recent research has established a compelling rationale for targeting BRD4 in cancer. BRD4 functions to facilitate cell cycle progression and knock-down in cultured cancer cell lines prompts G1 arrest. BRD4 is an important mediator of transcriptional elongation, functioning to recruit the positive transcription elongation factor complex (P-TEFb). Cyclin dependent kinase-9, a core component of P-TEFb, is a validated target in chronic lymphocytic leukemia, and has recently been linked to c-Myc dependent transcription. Bromodomains present in BRD4 recruit P-TEFb to mitotic chromosomes resulting in increased expression of growth promoting genes. BRD4 remains bound to transcriptional start sites of genes expressed during M/G1 but has not been found present at start sites that are expressed later in the cell cycle. Knockdown of BRD4 in proliferating cells has been shown to lead to G1 arrest and apoptosis by decreasing expression levels of genes important for mitotic progression and survival.

Importantly, BRD4 has recently been identified as a component of a recurrent t(15;19) chromosomal translocation in an aggressive form of human squamous cell carcinoma. Such translocations express the tandem N-terminal bromodomains of BRD4 as an in-frame chimera with the nuclear protein in testis (NUT) protein, genetically defining the NUT midline carcinoma (NMC). Functional studies in patient-derived NMC cell lines have validated the essential role of the BRD4-NUT oncoprotein in maintaining the characteristic proliferation advantage and differentiation block of this malignancy. Notably, RNA silencing of BRD4-NUT gene expression arrests proliferation and prompts squamous differentiation with a marked increase in cytokeratin expression. A bromodomain may also down-regulates Myc and other transcripitional factors, such as interleukin 7 receptor (IL7R). These observations underscore the utility and therapeutic potential of an inhibitor of bromodomain-containing proteins.

In one aspect, the present invention provides methods of inhibiting the activity of a bromodomain-containing protein in a subject or cell. In certain embodiments, the bromodomain-containing protein is a bromodomain-containing protein described herein (e.g., a BET protein, such as BRD2, BRD3, BRD4, or BRDT). In certain embodiments, the activity of a bromodomain-containing protein in a subject or cell is inhibited by the inventive methods. In certain embodiments, the activity of a bromodomain-containing protein in a subject or cell is inhibited by the inventive methods by at least about 1%, at least about 3%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%. In certain embodiments, the activity of a bromodomain-containing protein in a subject or cell is inhibited by the inventive methods by at most about 90%, at most about 80%, at most about 70%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 20%, at most about 10%, at most about 3%, or at most about 1%. Combinations of the above-referenced ranges (e.g., at least about 10% and at most about 50%) are also within the scope of the invention. Other ranges are also possible. In some embodiments, the activity of a bromodomain-containing protein in a subject or cell is selectively inhibited by the inventive methods. In other embodiments, the activity of a bromodomain-containing protein in a subject or cell is non-selectively inhibited by the inventive methods. In certain embodiments, the cytokine level and/or histamine release are reduced by the inventive methods.

In certain embodiments, the subject described herein is a human. In certain embodiments, the subject is a human diagnosed as having a disease associated with a bromodomain-containing protein. In certain embodiments, the subject is a human diagnosed as being at a higher-than-normal risk to have a disease associated with a bromodomain-containing protein. In certain embodiments, the subject is a human suspected of having a disease associated with a bromodomain-containing protein. In certain embodiments, the subject is an animal. The animal may be of either sex and may be at any stage of development. In certain embodiments, the subject is a fish. In certain embodiments, the subject is a mammal. In certain embodiments, the subject is a non-human mammal. In certain embodiments, the subject is a human or non-human mammal. 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 (e.g., mouse, rat), dog, pig, or non-human primate. In certain embodiments, the animal is a genetically engineered animal. In certain embodiments, the animal is a transgenic animal.

In certain embodiments, the cell is in vitro. In certain embodiments, the cell is ex vivo. In certain embodiments, the cell is in vivo.

In certain embodiments, the methods of the invention include administering to a subject in need thereof an effective amount of a compound or pharmaceutical composition of the invention. In certain embodiments, the methods of the invention include administering to a subject in need thereof a therapeutically effective amount of a compound or pharmaceutical composition of the invention. In certain embodiments, the methods of the invention include administering to a subject in need thereof an effective amount of a pharmaceutical composition of the invention. In certain embodiments, the methods of the invention include administering to a subject in need thereof a therapeutically effective amount of a pharmaceutical composition of the invention. In certain embodiments, the methods of the invention include contacting a cell with an effective amount of a compound or pharmaceutical composition of the invention. In certain embodiments, the methods of the invention include contacting a cell with an effective amount of a pharmaceutical composition of the invention.

In certain embodiments, the inventive methods are in vitro methods. In certain embodiments, the inventive methods are ex vivo methods. In certain embodiments, the inventive methods are in vivo methods.

Another aspect of the present invention relates to methods of inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell. In certain embodiments, the histone is selected from the group consisting of H1, H2A, H2B, H3, H4, and H5. In certain embodiments, the binding of a bromodomain of the bromodomain-containing protein to an acetyl-lysine residue of the histone is inhibited by the inventive methods.

In another aspect, the present invention provides methods of modulating the transcription of a gene (e.g., a gene described herein) that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the present invention provides methods of down-regulating the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell. Without wishing to be bound by any particular theory, the inventive compounds and pharmaceutical compositions may be able to interfere with the binding of a bromodomain-containing protein to a transcriptional start site of the gene. In certain embodiments, the inventive compounds and pharmaceutical compositions interfere with the acetyl-lysine recognition during the transcription of the gene. In certain embodiments, the inventive compounds and pharmaceutical compositions interfere with the acetyl-lysine anchoring during the transcription of the gene. In certain embodiments, the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell is modulated by the inventive methods. In certain embodiments, the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell is down-regulated by the inventive methods. In certain embodiments, the gene that is regulated by a bromodomain-containing protein is an oncogene.

Another aspect of the present invention relates to methods of treating a disease associated with a bromodomain-containing protein in a subject in need thereof. In certain embodiments, the disease associated with a bromodomain-containing protein is treated by the inventive methods.

In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with the activity of the bromodomain-containing protein. In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with the function of a bromodomain of the bromodomain-containing protein. In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with a bromodomain of the bromodomain-containing protein. In certain embodiments, the disease associated with a bromodomain-containing protein is driven by a transcriptional activator. In certain embodiments, the transcriptional activator is Myc. In certain embodiments, the disease associated with a bromodomain-containing protein is associated with a NUT rearrangement. In certain embodiments, the disease associated with a bromodomain-containing protein is a proliferative disease (e.g., a proliferative disease described herein). In certain embodiments, the disease associated with a bromodomain-containing protein is cancer (e.g., a cancer described herein). In certain embodiments, the disease associated with a bromodomain-containing protein is lung cancer, multiple myoloma, neuroblastoma, colon cancer, or ovary cancer. In certain embodiments, the disease associated with a bromodomain-containing protein is lung cancer (e.g., small-cell lung cancer or non-small-cell lung cancer). In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of Burkitt's lymphoma, breast cancer, colon cancer, neuroblastoma, glial blastoma multiforme, MLL-driven leukemia, chronic lymphocytic leukemia, NUT midline carcinoma, and squamous cell carcinoma. In certain embodiments, the disease associated with a bromodomain-containing protein is a benign neoplasm (e.g., a benign neoplasm described herein). In certain embodiments, the disease associated with a bromodomain-containing protein is an inflammatory disease (e.g., an inflammatory disease described herein). In certain embodiments, the disease associated with a bromodomain-containing protein is a disease that involves an inflammatory response to an infection with a bacterium, virus, fungus, parasite, and/or protozoon. In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of osteoarthritis, acute gout, multiple sclerosis, an inflammatory bowel disease (e.g., Crohn's disease and ulcerative colitis), neuroinflammation, asthma, a chronic obstructive airways disease, pneumonitis, myocarditis, pericarditis, myositis, eczema, dermatitis, acne, cellulitis, an occlusive disease, a cardiac valvular disease, stenosis, restenosis, in-stent-stenosis, a coronary arterial disease, congestive heart failure, angina pectoris, myocardial ischemia, thrombosis, alopecia, nephritis, vasculitis, atherosclerosis, retinitis, uveitis, scleritis, sclerosing cholangitis, hypophysitis, thyroiditis, sepsis, sepsis syndrome, septic shock, systemic inflammatory response syndrome (SIRS), toxic shock syndrome, acute lung injury, ARDS (adult respiratory distress syndrome), acute renal failure, hepatitis (e.g., fulminant hepatitis), burns, pancreatitis (e.g., acute pancreatitis), post-surgical syndromes, sarcoidosis, Herxheimer reactions, encephalitis, myelitis, meningitis, malaria, and SIRS associated with viral infections (such as influenza, herpes zoster, herpes simplex, and coronavirus). In certain embodiments, the disease associated with a bromodomain-containing protein is acute or chronic pancreatitis. In certain embodiments, the disease associated with a bromodomain-containing protein is burns. In certain embodiments, the disease associated with a bromodomain-containing protein is an inflammatory bowel disease. In certain embodiments, the disease associated with a bromodomain-containing protein is neuroinflammation. In certain embodiments, the disease associated with a bromodomain-containing protein is an autoimmune disease (e.g., an autoimmune disease described herein). In certain embodiments, the disease associated with a bromodomain-containing protein is rheumatoid arthritis. In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of psoriasis, systemic lupus erythematosus, vitiligo, a bullous skin disease, hepatic cirrhosis, biliary cirrhosis, Addison's disease, acute rejection of transplanted organs, endotoxemia, and multi-organ dysfunction syndrome. In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with ischemia-reperfusion injury. In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of myocardial infarction, cerebrovascular ischemia (stroke), acute coronary syndromes, renal reperfusion injury, organ transplantation, coronary artery bypass grafting, a cardio-pulmonary bypass procedure, or pulmonary, renal, hepatic, gastro-intestinal, or peripheral limb embolism. In certain embodiments, the disease associated with a bromodomain-containing protein is a disorder of lipid metabolism via the regulation of apolipoprotein A1 (APOA1). In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of hypercholesterolemia, atherosclerosis, and Alzheimer's disease. In certain embodiments, the disease associated with a bromodomain-containing protein is a viral infection. In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of infectious diseases caused by herpes virus, human papilloma virus, adenovirus, and/or poxvirus. In certain embodiments, the disease associated with a bromodomain-containing protein is a fibrotic condition. In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of idiopathic pulmonary fibrosis, renal fibrosis, post-operative stricture, keloid formation, scleroderma, and cardiac fibrosis. In certain embodiments, the disease associated with a bromodomain-containing protein is selected from the group consisting of diabetes (e.g., type 1 diabetes, type 2 diabetes, and gestational diabetes), obesity, fatty liver (NASH or otherwise), therosclerosis, arterial stent occlusion, heart failure, cachexia, graft versus host disease, an infection disease associated with a bromodomain-containing protein, an infection disease caused by a parasite, malaria, trypanosomes, an inflammatory disease, and male fertility. In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with aberrant Myc function. In certain embodiments, the disease associated with a bromodomain-containing protein is a disease associated with interleukin 7 receptor (IL7R).

In yet another aspect, the present invention provides methods of reducing the risk to have a disease associated with a bromodomain-containing protein in a subject in need thereof. In certain embodiments, the risk to have the disease associated with a bromodomain-containing protein is reduced by the inventive methods.

Another aspect of the invention relates to methods of inhibiting the interaction between a bromodomain-containing protein and an immunoglobulin (Ig) regulatory element in a subject or cell.

Another aspect of the invention relates to methods of screening a library of compounds, and pharmaceutical acceptable salts thereof, to identify a compound, or a pharmaceutical acceptable salt thereof, that is useful in the methods of the invention. In certain embodiments, the compound identified is useful for treating and/or preventing a disease associated with a bromodomain-containing protein in a subject in need thereof. In certain embodiments, the compound identified is useful for treating a disease associated with a bromodomain-containing protein in a subject in need thereof. In certain embodiments, the compound identified is useful for treating a proliferative disease in a subject in need thereof. In certain embodiments, the compound identified is useful for treating cancer in a subject in need thereof. In certain embodiments, the compound identified is useful for treating a benign neoplasm in a subject in need thereof. In certain embodiments, the compound identified is useful for treating pathological angiogenesis in a subject in need thereof. In certain embodiments, the compound identified is useful for treating an inflammatory disease in a subject in need thereof. In certain embodiments, the compound identified is useful for treating an autoimmune disease in a subject in need thereof. In certain embodiments, the compound identified is useful for reducing the risk to have a disease associated with a bromodomain-containing protein in a subject in need thereof. In certain embodiments, the compound identified is useful for inhibiting the activity of a bromodomain-containing protein in a subject or cell. In certain embodiments, the compound identified is useful for inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell. In certain embodiments, the compound identified is useful for modulating the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell. In certain embodiments, the library of compounds is a library of the compounds of the invention. In certain embodiments, the methods of screening a library include obtaining at least two different compounds of the invention; and performing at least one assay using the different compounds of the invention. In certain embodiments, at least one assay is useful in identifying a compound that is useful in the inventive methods.

Typically, the methods of screening a library of compounds involve at least one assay. In certain embodiments, the assay is performed to detect one or more characteristics associated with the treatment and/or prevention of a disease described herein, with the inhibition of the activity of a bromodomain-containing protein, with the inhibition of the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone, and/or with the modulation the transcription of a gene that is regulated by a bromodomain-containing protein. The characteristics may be desired characteristics (e.g., a disease having been treated, a disease having been prevented, the risk to have a disease having been reduced, the activity of a bromodomain-containing protein having been inhibited, the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone having been inhibited, or the transcription of a gene that is regulated by a bromodomain-containing protein having been modulated). The characteristics may be undesired characteristics (e.g., a disease not having been treated, a disease not having been prevented, the risk to have a disease not having been reduced, the activity of a bromodomain-containing protein not having been inhibited, the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone not having been inhibited, or the transcription of a gene that is regulated by a bromodomain-containing protein not having been modulated). The assay may be an immunoassay, such as a sandwich-type assay, competitive binding assay, one-step direct test, two-step test, or blot assay. The step of performing at least one assay may be performed robotically or manually. In certain embodiments, the assay comprises (a) contacting a library of compounds with a bromodomain-containing protein; and (b) detecting the binding of the library of compounds to the bromodomain-containing protein. In certain embodiments, the assay comprises detecting the specific binding of the library of compounds to the bromodomain-containing protein. In certain embodiments, the assay comprises detecting the specific binding of the library of compounds to a bromodomain of the bromodomain-containing protein. In certain embodiments, the detected binding of the library of compounds to the bromodomain-containing protein is useful in identifying the compound that is useful in the methods of the invention. In certain embodiments, the step of detecting the binding comprises using differential scanning fluorimetry (DSF), isothermal titration calorimetry (ITC), and/or an amplified luminescence proximity homogeneous assay (ALPHA). The step of performing at least one assay may be performed in a cell (e.g., a cancer cell) in vitro, ex vivo, or in vivo. In certain embodiments, the step of performing at least one assay is performed in a cell (e.g., a cancer cell) in vitro. In certain embodiments, the assay comprises (a) contacting a library of compounds with a cell; and (b) detecting a decrease in cell proliferation, an increase in cell death, and/or an increase in cell differentiation. In certain embodiments, the cell death is apoptotic cell death. In certain embodiments, the cell differentiation is identified by detecting an increase in cytokeratin expression. In certain embodiments, the step of performing at least one assay further comprises detecting a reduction in transcriptional elongation.

In another aspect, the present invention provides uses of the inventive compounds and pharmaceutical compositions in treating and/or preventing a disease described herein in a subject in need thereof. In certain embodiments, the invention provides uses of the inventive compounds and pharmaceutical compositions in treating a disease described herein in a subject in need thereof.

Another aspect of the present invention relates to uses of the inventive compounds and pharmaceutical compositions in reducing the risk to have a disease described herein in a subject in need thereof.

In yet another aspect, the present invention provides uses of the inventive compounds and pharmaceutical compositions in inhibiting the activity of a bromodomain-containing protein in a subject or cell.

Another aspect of the present invention relates to uses of the inventive compounds and pharmaceutical compositions in inhibiting the binding of a bromodomain of a bromodomain-containing protein to an acetyl-lysine residue of a histone in a subject or cell.

In still another aspect, the present invention provides uses of the inventive compounds and pharmaceutical compositions in modulating the transcription of a gene that is regulated by a bromodomain-containing protein in a subject or cell.

EXAMPLES

Preparation of Compounds

Compounds of Formula (I) (e.g., compounds of Formula (I-A)), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, may be prepared by methods similar to the one reported in Lu et al.,QSAR Comb. Sci.2004, 23, 827-835, such as the synthetic sequence outlined below in Scheme 1, wherein XA, XB, Ring A, RB, RD, RF, d, and f are as defined herein. The compounds of Formula (I) (e.g., compounds of Formula (I-B)), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, may also be synthesized according to the method shown in Scheme 2. Alternatively, compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, and prodrugs thereof, may be prepared by other methods described herein or known in the art.

The compound of Formula (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, may be prepared by methods similar to the one reported in Zhang et al.,Tetrahedron Lett.2005, 46, 1807-1810, such as the synthetic sequence outlined below in Scheme 3. Alternatively, the compound of Formula (II), or a pharmaceutically acceptable salt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer, isotopically labeled derivative, or prodrug thereof, may be prepared by other methods described herein or known in the art.

Isoxazole probe compounds were prepared using Suzuki-type coupling reactions followed by purification of reaction intermediates using fluorous-solid phase extraction (F-SPE). In this case, aryl perfluorooctylsulfonates (ArOSO2(CF2)7CF3) were reacted with 3,5-dimethylisoxazole-4-boronic acid pinacol esters to produce a low-molecular weight chemical series. The resulting compounds were purified using F-SPE. Initial compounds included positional isomers of carbonyl functionalities around the phenyl ring system.

General Methods

All chemical reagents (including solvents) were purchased from commercial suppliers and used as received.1H NMR (300 MHz) and13C NMR (75 MHz) spectra were recorded on a Varian NMR spectrometer. LC-MS were performed on an Agilent 2100 system with a C18LC column (5.0 μm, 6.0×50 mm). The mobile phase was a mixture of MeOH (containing 0.05% trifluoroacetic acid) and water (containing 0.05% trifluoroacetic acid). A linear gradient was started from 75:25 MeOH—H2O to 100% MeOH in 5.0 min at a flow rate of 0.7 mL/min. The chromatograms were recorded at UV 210 nm, 254 nm, and 365 nm. Low resolution mass spectra (LRMS) were recorded in APCI (atmospheric pressure chemical ionization). Flash chromatography separations were performed on a YAMAZEN AI-580 system with Agela silica gel (12 g or 20 g, 230-400 μm) cartridges. The microwave reactions were performed on a Biotage Initiator 8 system.

Procedures for the Synthesis of Compounds 1a-5a.

These compounds were prepared by direct Suzuki coupling of fluorous arylsulfonates with the boronic ester. The Suzuki coupling reactions were carried out following the general procedure as shown.

Additional UMB Analog Synthesis and Characterization

Compound 24a (0.284 g, 0.677 mmol, 1 eq) was dissolved in DCM (2.7 mL) and TFA (2.7 mL) and stirred at room temperature. After 12 hours, the mixture was concentrated, and purified by preparative HPLC (5 to 95% MeCN/water with 0.1% TFA) and lyophilized to yield the product as an orange powder (187 mg, 0.515 mmol, 76%).

Aminopyrazine (95.2 mg, 1.00 mmol, 1 eq), 4-bromobenzaldehyde (278 mg, 1.50 mmol, 1.5 eq) and methyl isocyanoacetate (0.105 mL, 1.15 mmol, 1.15 eq) were dissolved in methanol (2 mL). A IM solution of perchloric acid in methanol (0.20 mL, 0.10 eq) was added and the solution was stirred for 12 hours at room temperature. The mixture was then diluted with EtOAc and washed with saturated sodium bicarbonate, water and brine. The crude material was purified by automated column chromatography (50 to 100% EtOAc/hexanes) to yield a cream colored solid (0.21 g, 0.581 mmol, 58%).

Biochemical and Cellular Assays of the Compounds

In Vitro AlphaScreen® Protein Binding Assay

Assays were performed with minor modifications from the manufacturer's protocol (PerkinElmer, USA). All reagents were diluted in 50 mM HEPES, 150 mM NaCl, 0.1% w/v BSA, and 0.01% w/v Tween® 20 at pH 7.5 and allowed to equilibrate to room temperature prior to addition to plates. After addition of Alpha beads to master solutions, all subsequent steps were performed in low light conditions. A 2× solution of components with final concentrations of a BRD protein (e.g., BRD4) at 40 nM, Ni-coated Acceptor Bead at 25 μg/ml, and 20 nM biotinylated JQ1 was added in 10 μL to 384-well plates (AlphaPlate-384, PerkinElmer, USA). Biotinylated JQ1 was synthesized as described herein or according to methods known in the art. After a 1000-rpm spin-down for 1 minute, 100 nL of the solutions of compounds of the invention in DMSO from stock plates were added by pin transfer using a Janus Workstation (PerkinElmer, USA). The streptavidin-coated donor beads (25 μg/ml final) were added as with previous solution in a 2×, 10 μL volume. Following this addition, the plates were sealed with foil to block light exposure and to prevent evaporation. The plates were spun down again at 1000 rpm for 1 minute. Next, the plates were incubated in the room with the plate reader (for temperature equilibration) for 1 hour prior to reading the assay. Signal is stable for up to 3 hours after donor bead addition. AlphaScreen® measurements were performed on an Envision 2104 (PerkinElmer, USA) utilizing the manufacturer's protocol.

Assays were performed with minor modifications from the manufacturer's protocol (PerkinElmer, USA). All reagents were diluted in 50 mM HEPES, 150 mM NaCl, 0.1% w/v BSA, and 0.01% w/v Tween® 20 at pH 7.5 and allowed to equilibrate to room temperature prior to addition to plates. After addition of Alpha beads to master solutions, all subsequent steps were performed in low light conditions. A 2× solution of components with final concentrations of BRD4.1 at 80 nM, Ni-coated Acceptor Bead at 25 μg/ml, and 80 nM biotinylated H4-tetra acetyl was added in 10 μL to 384-well plates (AlphaPlate-384, PerkinElmer, USA). Biotinylated peptide for BRD4.1 was synthesized in-house on a CEM Liberty 9008005 microwave peptide synthesizer: H4-tetra acetyl, biotin-PEG2-SGRGKacGGKacGLGKacGGAKacRHRK—COOH. Addition to wells was performed with either a multichannel pipet (for optimization experiments) or a Biotek EL406 liquid handler. After a 1000-rpm spin-down for 1 minute, 100 nL of the solutions of the compounds of the invention from stock plates were added by pin transfer using a Janus Workstation (PerkinElmer, USA). The streptavidin-coated donor beads (25 μg/ml final) were added as with previous solution in a 2×, 10 μL volume. Following this addition, the plates were sealed with foil to block light exposure and to prevent evaporation. The plates were spun down again at 1000 rpm for 1 minute. Next, the plates were incubated in the room with the plate reader (for temperature equilibration) for 1.5 hour prior to reading the assay. AlphaScreen® measurements were performed on an Envision 2104 (PerkinElmer, USA) utilizing the manufacturer's protocol.

Cellular Assay

The compounds of the invention are also evaluated in the BRD4 dependant cell line for the cellular activity to generate cellular IC50values.

Cells (e.g., BRD4 dependant cells) were counted and adjusted to 60,000 cells/mL. Using a Biotek EL406, 50 μL of the cells in media were distributed into 384 well white plates from Thermo. Immediately after plating, compounds of the invention in DMSO were distributed to plates. For large plate sets, cells were returned to a 37° C. incubator while not in use. The compounds were added to plates using a 100 nL 384 well pin transfer manifold on a Janus workstation. Stocks were arrayed in 10 point quadruplicate dose response in DMSO stock in 384-well Greiner compound plates. After addition of the compounds, plates were incubated for three days in a 37° C. incubator. Cell viability was read out using ATPlite from Perkin Elmer. Plates were removed from the incubator and brought to room temperature prior to use. Lyophilized powder was resuspended in lysis buffer and diluted 1:2 with DI water. 25 μL of this solution was added to each well using the Biotek liquid handler. Plates were sealed with adherent aluminum seals prior to vortexing and spinning down at 1000 g for 1 minute. Plates were incubated for 15 minutes at room temperature before signal was read on an Envision Plate Reader.

Biologic and Biochemical Compound Evaluation Reagents

Endogenous BRD4-NUT-expressing midline carcinoma cell lines, 797 was described previously (Toretsky et al.,Am. J. Clin. Oncol.2003, 26, 300). Media, trypsin, and antibiotics for tissue culture were purchased from MediatechCloning. cDNA encoding human BRD2, BRD3, BRD4, BRDT, CREBBP and WDR9 (NCBI accession number NP 005095, NP 031397.1, NP 055114.1, NP 001717.2, NP 004371.1, NP 061836.2) were obtained from different sources (BRD2: Synthetic, BRD3: Origene, BRD4: FivePrime, BRDT: IMAGE collection, CREBBP: Synthetic, WDR9: synthetic) and used as templates to amplify the bromodomain regions of the above proteins, using the polymerase chain reaction (PCR) in the presence of Platinum® Pfx DNA polymerase (Invitrogen™, UK). PCR products were purified (QIAquick PCR Purification Kit, Qiagen Ltd. UK) and further sub-cloned into a pET28 derived expression vector, pNIC28-Bsa4, using ligation independent cloning (Stols et al.,Protein Expr. Purif2002, 25, 8). The constructs were transformed into competent Mach1™ cells (Invitrogen™, UK) to yield the final plasmid DNA. This vector includes sites for ligation-independent cloning and a Tobacco Etch Virus (TEV)-cleavable N-terminal His6-tag (extension MHHHHHHSSGVDLGTENLYFQ*SM-) After digestion with TEV protease, the protein retains an additional serine and methionine on the N-terminus.

Protein Expression and Purification

The first bromodomain of Brd4 (Brd4-BD1, residues 42-168) was subcloned into a modified pET-15b(+) vector with an N-terminal His6tag followed by a Tobacco Etch Virus cleavage site. The encoded protein was expressed in theE. coliBL21(DE3) strain.E. colicells transformed with the vector were grown 4 hours at 37° C. to an OD600of 1.0, in 1 liter LB media containing ampicillin (0.1 mg/ml). After 0.1 mM IPTG induction at 20° C., cells were cultured overnight, and collected by centrifugation at 4,000 g. The pellet was suspended in 40 ml lysis buffer containing 50 mM HEPES, pH 7.4, 500 mM NaCl, 5 mM 3-mercaptoethanol, and 1 mM PMSF. Cells were lysed on ice by sonication and cell debris was precipitated by centrifugation at 15,000 g for 30 minutes. Brd4-BD1 was purified by affinity chromatography on an Ni-NTA agarose column (Qiagen), using an elution buffer of 50 mM HEPES, pH 7.4, 500 mM NaCl, 5 mM b-mercaptoethanol, and 50 mM of imidazole. After overnight TEV cleavage of the His6-tag, the cleaved tag was captured on affinity resin, and Brd4-BD1 was then purified to homogeneity by gel filtration before concentration to roughly 12 mg/ml in storage buffer (20 mM HEPES, pH 7.4, and 150 mM NaCl). Samples for isothermal calorimetry were dialysed over night at 4° C. in a D-Tube™ Dialyser Midi, MWCO 3.5 kDa to a final buffer of 50 mM HEPES, pH 7.4 (at 25° C.), 150 mM NaCl. Protein handling was carried out on ice or in a cold room in all the above steps.

Experiments were carried out on a VP-ITC titration microcalorimeter from MicroCal™, LLC (Northampton, Mass.). All experiments were carried out at 15° C. while stirring at 295 rpm, in ITC buffer (50 mM HEPES pH 7.4 at 25° C., 150 mM NaCl). The microsyringe (250 μL) was loaded with a solution of the protein sample (300 μM protein for the BETs, 950 μM protein for CREBBP and 600 μM for WDR9(2), in ITC buffer). All titrations were conducted using an initial control injection of 2 μl followed by 34 identical injections of 8 μl with a duration of 16 sec (per injection) and a spacing of 250 sec between injections. The heat of dilution was determined by independent titrations (protein into buffer) and was subtracted from the experimental data. The collected data were implicated in the MicroCal™ Origin software supplied with the instrument to yield enthalpies of binding (ΔH) and binding constants (KB) as previously described by Wiseman and co-workers (Wiseman et al.,Anal. Biochem.1989, 179, 131). Thermodynamic parameters were calculated (ΔG=ΔH−TΔS=−RTlnKB, where ΔG, ΔH and ΔS are the changes in free energy, enthalpy and entropy of binding respectively). In all cases a single binding site model was employed.

Results

Shown in Table 1 are in vitro IC50values, obtained through AlphaScreen®, of exemplary compounds of Formula (I) or (IV) in inhibiting the activity of BRD4. All compounds in Table 1 inhibit the activity of BRD4.

TABLE 1In vitro IC50values of exemplary compounds of Formula(I) or (IV) in inhibiting the activity of BRD4.CompoundIC50(M)UMB111.10E−05UMB201.18E−05UMB211.88E−05UMB226.83E−05UMB233.15E−05UMB242.89E−06UMB257.86E−06UMB265.10E−06UMB272.05E−06UMB289.04E−07UMB294.79E−07UMB302.76E−06UMB311.17E−06UMB322.56E−07

Table 2 shows in vitro IC50values, obtained through AlphaScreen®, of exemplary compounds of Formula (I) or (II) in inhibiting BRD and CBP, and cellular IC50values of the compounds in lung carcinoma cell line H2171. Compound UMB11 shows good selectivity toward BRD4 over CBP. Compounds UMB11 and UMB17 show cellular activity in H2171.

TABLE 2In vitro IC50values of exemplary compounds of Formula (I)or (II) in inhibiting BRD and CBP, and cellular IC50valuesof the compounds in lung carcinoma cell line H2171.CompoundBRD4 IC50(μM)CBP IC50(μM)H2171 IC50(μM)UMB110.51110.76UMB171223055

Table 3 shows the in vitro IC50value, obtained through AlphaScreen®, of an exemplary compound of Formula (I) in inhibiting the activity of BRD4. Also shown in Table 3 is the compound's cellular EC50value obtained from a cellular assay where a BRD4 dependant cell line was treated with the compound. Compound UMB32 is active in inhibiting the activity of BRD4 in vitro and also shows cellular activity in the BRD4 dependant cell line.

TABLE 3In vitro IC50value of an exemplary compound of Formula(I) in inhibiting the activity of BRD4, and cellular EC50value of the compound in a BRD4 dependant cell line.CompoundBRD4 IC50(μM)BRD4 EC50(μM)UMB320.261.1

Shown in Table 4 are cellular EC50values obtained from a cellular assay where a BRD4 (site 1) dependant cell line was treated with exemplary compounds of Formula (I) or (IV). All compounds tested show cellular activity in the BRD4 dependant cell line.

TABLE 4Cellular EC50values of exemplary compounds of Formula(I) or (IV) in a BRD4 dependant cell line.CompoundEC50(M)UMB111.41E−05UMB201.84E−05UMB214.91E−05UMB221.24E−05UMB232.07E−05UMB241.18E−05UMB253.28E−05UMB262.02E−05UMB272.07E−04UMB285.07E−06UMB292.04E−06UMB307.36E−06UMB312.19E−06UMB321.13E−06

A diverse set of molecules was synthesized using reactions previously developed around fluorous-tagged multicomponent reactions. These reactions created structural diversity by changing the substituent groups on each fractional component, allowing generation of diverse small-molecule libraries around a biasing element. The perfluoroalkyl tags can substituted with a binding motif of choice via Suzuki coupling. Synthesized compounds included tertiary amines, pyrimidines and fused heterocyclic ring systems in order to explore the optimal shape for exploiting protein-inhibitor contour interactions. In addition to biochemical IC50, these compounds were selectively evaluated in a BRD4-dependent cell viability study (see Table 5). The EC50s were collected by assessing viability using PerkinElmer ATPlite kits against the BRD4-dependent Nut-Midline Carcinoma line 797. The use of a fluorous-tagged Groebke-Blackburn-Bienayme multi-component reaction was used to develop the para-imidazo[1,2-a]pyridine scaffold (UMB11), which was found have biochemical and cellular inhibitory values of 11.0 μM and 14.1 μM, respectively. In addition, the UMB11 scaffold is accessible at a variety of positions for diversification to drive potency and develop understanding of SAR.

TABLE 5Exploration of Compound Scaffold Region.CompoundArBRD4--IC50(μM)797--EC50(μM)II>1009.42III13.09.91IV2.05>100UMB1111.014.1

Further analogs were synthesized to explore the functional role of both sterics and electronics of the fused bicyclic scaffold on inhibitor function (see Table 6). Variations of RBfrom the benzyl group to bulky, non-aromatic groups like cyclohexane and t-Bu improved potency. Ring-nitrogens at the 7 and 8 position resulted in little biochemical potency change. Cellular potency, however, modestly improved upon substitution of a 7-N.

TABLE 6Exploration of Compound Scaffold Region.Com-BRD4--IC50poundRBRDX(μM)797--EC50(μM)12aHHCH3.8913aBn6-MeCH>100UMB20Bn6-ClCH11.818.4UMB21BnH7-N18.849.1UMB28cyclohexaneHCH0.9045.07UMB304-(OMe)PhHCH2.767.36UMB234-(OMe)Ph6-ClCH31.520.7UMB244-(OMe)Ph7-OMe6-N2.8911.8UMB254-(OMe)PhH7-N7.8632.821a(S)-1-PhEtH7-N2.8622a—CH2CO2HH7-N>10023a—CH2CO2EtH7-N4.5324a—CH2CO2tBuH7-N4.96UMB29t-BuHCH0.4792.04UMB31t-Bu6-ClCH1.172.1927at-Bu6-MeCH3.1728at-Bu8-CF3CH11.929at-Bu6-CO2CH2CH1.6230at-Bu6-COOHCH0.968UMB56t-BuH6-N20.72.06UMB32t-BuH7-N0.6370.72433at-BuH8-N0.860UMB57i-PrH7-N0.8070.49435an-BuH7-N1.66

Limited structural study around the linking phenyl ring is shown below (see Table 7). Electron-donating methoxy substituents appear to be mildly beneficial in biochemical assays. Additional work regarding this linking region of the molecule will be a focus of continued medicinal chemistry.

Selectivity of the Compounds for Different Bromodomain-Containing Proteins

The compounds of the invention (e.g., UMB11 and UMB32) were profiled with a panel of bromodomain-containing proteins for selectivity and were also fully characterized by isothermal titration calorimetry (ITC) (FIG. 12). The results show that the compounds of the invention are active against bromodomain-containing proteins such as TAF1 and TAF1L, which may be validated targets for cancer therapy (Tables 8 and 9 andFIGS. 3A-3B).

Computational Methods

Computational Methods

All computational work was performed in Schrodinger Suite (Schrodinger, LLC). Conformational analysis of lead compounds was performed using Schrodinger's Conformational Search function. Possible poses were prepared for docking by Ligprep. In both cases, default settings were used (OPLS2005 force field, water solvent). Docking was conducted using Glide. The co-crystal of BRD4 and JQ1 (PDB: 3MXF) was used to define the ligand receptor grid. Water molecules outside the binding pocket were excluded, and hydrogen bonding interactions were optimized prior to docking.

Results

Computational modeling was performed to better understand the modality of binding and inform further medicinal chemistry. Using previously published crystal structures of both JQ1 and iBET151, fragments were docked into the structure. As is the case with iBET151, compound 5a is thought to bind through a conserved hydrogen bond with N-140 through the ring oxygen, while the ring nitrogen coordinates through a structured water interacting with the hydroxyl group of Y-97. Based on this interaction, further analogs were built off the 4-position of the phenyl ring to improve potency by optimizing protein surface interactions near the BC loop region.

Crystallization and Diffraction Data Collection

Crystallization was conducted using the sitting drop vapor diffusion method at 22° C. Crystals of inhibitor-free BRD4-BD1 were first obtained in a drop with equal volumes of BD1 at 12 mg/ml and a precipitant solution containing 100 mM sodium nitrate, 5% ethylene glycol, and 18% (w/v) PEG3350, as precipitant. Rod-like crystals were typically grown in 10 days reaching a maximal size of 0.05×0.05×0.4 mm3. Then, native crystals were transferred and soaked in 1 mM UMB32 in the same crystallization buffer for 7 days. For data collection, a single crystal was flash frozen with a precipitant solution containing 20% (v/v) glycerol. Diffraction data for BD1-UMB32 complex were collected from a flash-cooled crystal at 100° K using the 24ID-E beam lines at the NE-CAT, Argonne National Laboratory and were processed, integrated, and scaled together with HKL2000 (Otwinowski et al.,Methods Enzymol1997, 276, 307).

Structure Determination and Refinement

The structure of the BD1-UMB32 complex was solved by molecular replacement (MR) as implemented in Phenix5using the previous BD1-JQ1 structure (PDB 3MXF) as the search model. Structure refinement was carried out using conjugate-gradient energy minimization, torsion-constrained molecular dynamics simulated annealing, group B factor refinement, and individual B factor refinement protocols in Phenix5with 5% of the reflections omitted for free R factor calculation. Electron density peaks in difference Fourier maps at a height of above 3σ were assigned as water molecules in later refinement stages if they had reasonable geometry in relation to hydrogen bond donors or acceptors and their B-factors did not rise above 50 Å2during subsequent refinement. Model building was performed in Coot6guided by σA-weighted 2Fo-Fc and Fo-Fc maps and composite omit maps.

Data Collection and Refinement Statistics

EQUIVALENTS AND SCOPE

In the claims articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process. Furthermore, it is to be understood that the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Furthermore, where the claims recite a composition, it is to be understood that methods of using the composition for any of the purposes disclosed herein are included, and methods of making the composition according to any of the methods of making disclosed herein or other methods known in the art are included, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise.

Where elements are presented as lists, e.g., in Markush group format, it is to be understood that each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements, features, etc., certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements, features, etc. For purposes of simplicity those embodiments have not been specifically set forth in haec verba herein. It is also noted that the term “comprising” is intended to be open and permits the inclusion of additional elements or steps.

All cited sources, for example, references, publications, databases, database entries, and art cited herein, are incorporated into this application by reference, even if not expressly stated in the citation. In case of conflicting statements of a cited source and the instant application, the statement in the instant application shall control.