Compositions, systems and methods for modulating target genes

Abstract

Methods of modulating expression of a target gene in a cell are provided. Aspects of the methods contact the cell with a compound having a first moiety covalently linked to a second moiety wherein: (i) the first moiety exhibits specific binding to a first endogenous 10 protein; (ii) the second moiety exhibits specific binding to a second endogenous protein, the second endogenous protein being different from the first endogenous protein; and (iii) upon contact with the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a function in the cell and thereby activating a process that is generally not controlled by any of the first endogenous protein and the second endogenous protein. Wherein the first moiety is targeted to BCL-6; and the second moiety targets any one of an estrogen receptor, an androgen receptor, BRD4, or a cyclin dependent kinase.

Description

[0001] Government rights

[0002] This invention was made with government support under Contracts CA163915, CA276167, and MH126720 awarded by the National Institutes of Health. The government has certain rights in this invention.

[0003] CROSS-REFERENCE TO RELATED APPLICATIONS

[0004] This application claims the benefit of U.S. Provisional Application No. 63 / 337,330, filed on May 2, 2022; U.S. Provisional Application No. 63 / 388,386, filed on July 12, 2022; U.S. Provisional Application No. 63 / 406,128, filed on September 13, 2022; U.S. Provisional Application No. 63 / 406,602, filed on September 14, 2022; and U.S. Provisional Application No. 63 / 406,570, filed on September 14, 2022, each of which is incorporated herein by reference in its entirety. Background Art

[0005] The method for controlled regulation gene expression is more and more important in a wide range of fields, and described field includes but is not limited to gene therapy, synthetic biology, plant management, environmental cleaning, bacteria and microorganism management and synthetic gene circuit.The control of gene expression has great potential in reforming treatment, animal model and biotechnology process, and can be used for integrating the multiple input signals of cell-based therapy and animal model development.Although progress has been rapid in recent years, the precise control of gene expression still has challenges owing to the unpredictability of the unexpected interaction between biological components such as transcription factors.The basic goal of cell engineering is to express gene efficiently in a predictive manner and under precise control with the expected level.This type of cell through genetic engineering has great hope to advancing treatment, diagnosis, animal model and biotechnology process.

[0006] To date, various gene regulation technologies for regulating gene expression in cells have been developed. Such gene regulation technologies include RNA interference, DNA editing and expression, and chemical compounds that inhibit, enhance, or modify gene expression. These gene regulation technologies can be in the form of RNA, DNA, or protein and can be introduced into cells in culture by direct application to culture medium, liposome transfection, electroporation, or viral transduction.

[0007] However, due to the broad applicability of gene regulation for both research and therapeutic applications, there has been interest in developing new ways to regulate the transcription of target genes in cells, specifically to regulate the expression of genes without genetic modification. Summary of the Invention

[0008] Methods and compositions for regulating the expression of a target gene in a cell are provided. Aspects of the method include contacting the cell with a compound having a first portion covalently linked to a second portion, wherein: (i) the first portion exhibits specific binding to a first endogenous protein that binds to the target gene (or a region near the target gene), such as a promoter or regulatory region; (ii) the second portion exhibits specific binding to a second endogenous protein that is different from the first endogenous protein; and (iii) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell. In some embodiments, the gain of function is characterized by regulating the expression of the target gene in a manner that is dependent on the presence of the second endogenous protein bound to the compound. Embodiments of the method provide one or more beneficial characteristics, including but not limited to: achieving the gain of function by utilizing less than about 50% of the amount of the first endogenous protein and / or the second endogenous protein present in the cell; mediating the gain of function with an EC50 of less than about 1 micromolar; and regulating the expression of the target gene in less than or equal to about 16 hours.

[0009] Thus, in one aspect, provided herein is a compound of formula I:

[0010] BR–L–BC (I)

[0011] in:

[0012] BR is a ligand that specifically binds to bromodomain-containing protein 4 (BRD4);

[0013] BC is a ligand that specifically binds to B-cell lymphoma 6 (BCL-6) (or a homolog thereof); and

[0014] L is a linker;

[0015] or a pharmaceutically acceptable salt thereof.

[0016] In another aspect, provided herein is a method of treating a malignancy in a subject, the method comprising administering to the subject an effective amount of a transcriptional chemical proximity inducer (TCIP) that links BCL-6 to BRD4, to treat the malignancy in the subject.

[0017] In another aspect, provided herein is a pharmaceutical composition comprising: a transcriptional chemical proximity inducer (TCIP) for treating malignant diseases, wherein the TCIP comprises a first ligand and a second ligand, wherein the first ligand specifically binds to BCL-6 and the second ligand specifically binds to BRD4; and a delivery vehicle.

[0018] In yet another aspect, provided herein is a method of treating diffuse large B-cell lymphoma (DLBCL) in a subject, comprising administering to the subject an effective amount of a chemical proximity inducer (CIP) that ligates BCL-6 to an estrogen receptor, thereby treating the DLBCL in the subject.

[0019] In yet another aspect, provided herein is a method of treating a malignancy in a subject, the method comprising administering to the subject an effective amount of a transcriptional chemical proximity inducer (TCIP) that links BCL-6 (or a homolog thereof) to a cyclin-dependent kinase, to treat the malignancy in the subject.

[0020] In yet another aspect, provided herein is a transcriptional chemical proximity inducer (TCIP) for treating a malignant disease, wherein the TCIP comprises a first ligand and a second ligand, wherein the first ligand specifically binds to BCL-6 (or a homolog thereof), and the second ligand specifically binds to CDK.

[0021] In yet another aspect, provided herein is a pharmaceutical composition comprising: a transcriptional chemical proximity inducer (TCIP) for treating malignant diseases, wherein the TCIP comprises a first ligand and a second ligand, wherein the first ligand specifically binds to BCL-6 (or a homolog thereof), and the second ligand specifically binds to CDK; and a delivery vehicle.

[0022] In yet another aspect, provided herein is a method for treating a malignancy in a subject, the method comprising administering to the subject an effective amount of a transcriptional chemical proximity inducer (TCIP), the TCIP linking BCL-6 (or a homolog thereof) to an androgen receptor (AR), to treat the malignancy in the subject. In yet another aspect, provided herein is a transcriptional chemical proximity inducer (TCIP) for treating a malignancy, the TCIP comprising a first ligand that specifically binds to BCL-6 (or a homolog thereof), the BCL-6 being linked to a second ligand via a linker, the second ligand specifically binding to AR.

[0023] In yet another aspect, provided herein is a pharmaceutical composition comprising: a transcriptional chemical proximity inducer (TCIP) for treating malignant diseases, wherein the TCIP comprises a first ligand that specifically binds to BCL-6 (or a homolog thereof), wherein the BCL-6 is linked to a second ligand via a linker, and wherein the second ligand specifically binds to AR; and a delivery vehicle.

[0024] In yet another aspect, provided herein is a method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first portion covalently linked to a second portion, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, which binds to the target gene or a region near the target gene (e.g., a promoter, a regulatory region); (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein bound to the compound, and wherein the gain of function is achieved by utilizing less than about 50% of the amount of the second endogenous protein present in the cell.

[0025] In yet another aspect, provided herein is a method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first portion covalently linked to a second portion, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, which binds to the target gene; (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein to which the compound binds, and wherein the compound has an EC of less than about 1 micromolar. 50 The gain of function is mediated by

[0026] In yet another aspect, provided herein is a method for regulating the expression of multiple target genes in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first portion covalently linked to a second portion, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, which reduces expression of the target gene in the absence of the compound; (b) the second portion exhibits specific binding to the second endogenous protein, which enhances expression of an additional target gene in the absence of the compound; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially paired with each other by the compound, thereby producing a gain of function in the cell, and wherein the gain of function is characterized by: (i) increased expression of the target gene compared to expression in the absence of the compound, and (ii) decreased expression of the additional target gene compared to expression in the absence of the compound.

[0027] In yet another aspect, provided herein is a method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with an effective amount of a compound having a first portion covalently linked to a second portion, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, which binds to the target gene; (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein bind to the compound to form a complex, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating the expression of the target gene in a manner that is dependent on the presence of the second endogenous protein bound to the compound, and wherein the expression of the target gene is regulated within less than or equal to about 16 hours after the contacting.

[0028] In yet another aspect, provided herein is a compound of formula (I):

[0029] AB (I),

[0030] in:

[0031] (a) A is a first portion, wherein the first portion specifically binds to a first endogenous protein in a cell, and the first endogenous protein binds to a target gene;

[0032] (b) B is a second portion that exhibits specific binding to a second endogenous protein in the cell, the second endogenous protein being different from the first endogenous protein; and

[0033] (c) the compound causes the first endogenous protein and the second endogenous protein to sterically complex with each other, thereby producing a gain of function in the cell,

[0034] wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein to which the compound binds, and

[0035] in:

[0036] (i) the gain of function is achieved by utilizing less than about 50% of the amount of the second endogenous protein present in the cell;

[0037] (ii) the compound has an EC of less than about 1 micromolar 50 mediating the gain of function; and / or

[0038] (iii) the first endogenous protein reduces the expression of the target gene in the absence of the compound, and the second endogenous protein enhances the expression of an additional target gene in the absence of the compound, wherein the gain of function is characterized in that: (iii(a)) expression of the target gene is enhanced compared to expression in the absence of the compound, and (iii(b)) expression of the additional target gene is reduced compared to expression in the absence of the compound.

[0039] In yet another aspect, provided herein is a compound of formula (I):

[0040] AB (I),

[0041] in:

[0042] (a) A is a first portion, wherein the first portion specifically binds to a first endogenous protein in a cell, and the first endogenous protein binds to a target gene;

[0043] (b) B is a second portion that exhibits specific binding to a second endogenous protein in the cell, the second endogenous protein being different from the first endogenous protein; and

[0044] (c) the compound binds to the first endogenous protein and the second endogenous protein to form a complex, wherein the complex is capable of regulating the expression of the target gene in a manner that is dependent on the presence of the second endogenous protein in the complex, and

[0045] wherein the complex modulates expression of the target gene in less than or equal to about 16 hours. BRIEF DESCRIPTION OF THE DRAWINGS

[0046] Figure 1 A non-limiting example of a design in which compounds of the present disclosure (e.g., CIP or TCIP) hijack BCL-6 to kill BRD4-positive DLBCL cells, SLCL cells, or ER-positive DLBCL cells according to embodiments provided herein is shown. BCL-6 is a transcription factor and oncogene that prevents the death of a variety of cancer cells, including SLCL cancer cells and DLBCL cancer cells, by binding to epigenetic repressors BCOR, NCOR, and SMRT (PMID 18280243, 15531890, 10898795). Chemical linkage of inhibitors of BCL6 (and / or its homologs), such as BI3812 (PMID 33208943), to ligands or estrogenic compounds of BRD4, which then bind to and induce proximity to cell death (pro-apoptotic) promoters, such as those of TP53, PUMA, BIM, etc., converts cell death inhibitors into potent cell death activators, demonstrating the gain of function provided by the compounds of the present disclosure (e.g., TCIP).

[0047] Figure 2 The structure of TCIP JWZ-7-7 is provided.

[0048] Figure 3 TCIP JWZ-7-7 kills CHOP-resistant p53-negative Karpas422 DLBCL at 1.3 nM. Data are the average of 4 biological replicates performed by 3 experimenters.

[0049] Figure 4A It is shown that TCIP JWZ-7-7 uses endogenous BCL6 and BRD4 levels to rapidly upregulate gene expression in DLBCL cells. Karpas 422 cells were transfected with a GFP reporter gene containing a high-fidelity BCL6 binding site and treated with JWZ-7-7 for 8 hours.

[0050] Figure 4B This demonstrates that TCIP JWZ-7-7 rapidly and specifically regulates genes critical for DLBCL at <1 NM. Karpas 422 cells were treated with the indicated concentrations of JWZ-7-7 for 24 hours, and extracts were prepared and Western blotted. BCL6 (long isoform) is the upper band, and the short isoform is the lower band. Note the "hook effect" (decreased activity at higher concentrations), a characteristic of ternary complex formation.

[0051] Figure 5Provided are dose-response curves for JWZ-7-7, BI-3812, JQ1, and their combination on three small cell lung cancer lines (NCI-H1105, DMS-79, NCI-H2196).

[0052] Figure 6 Provided are the results of a TR-FRET (time-resolved fluorescence resonance energy transfer) assay detecting ternary complex formation between JWZ-7-7, BRD4, and BCL6.

[0053] Figure 7A and 7B The nanoBRET assay of JWZ-7-7 and the results obtained from the assay are shown, respectively.

[0054] Figure 8 The researchers showed that TCIP1 is 100 times more potent in DLBCL than the recently FDA-approved selinexor and is less toxic.

[0055] Figure 9 Depicted are non-limiting examples of the structure and activity of ER-BCL6 TCIPs. Panel A: Non-limiting examples of the structures of compounds of the present disclosure (e.g., TCIPs) based on estrone and BI3812. Also shown are the structures of molecules synthesized to test the effects of linkers on estrone and BI3812, as well as negative controls that do not bind to ER (XFL-01-190 and 106) or BCL6 (XFL-03-004). Panel B: Viability of Karpas DLBCLs 48 hours after addition of estrone, BI3812, BI3802 (BCL6 degrader), and XFL-01-92. Note that XFL-01-92 is more active than either parent compound in specifically killing these cells that overexpress ER and BCL6. Neither the androgen (XFL-01-108) nor the linker compound nor the two negative control compounds are active.

[0056] Figure 10 It was shown that XFL-01-92 specifically kills DLBCL cells.Dose-response curves for lymphocytes and three breast cancer cell lines that do not express BCL6 are shown.

[0057] Figure 11 CIP-induced apoptosis is rapid and robust. XFL-01-92 induces apoptosis within 8 hours of addition to Karpas 422 cells. Annexin V and 7AAD staining identify early and late apoptotic cells.

[0058] Figure 12It is shown that the compounds of the present disclosure (e.g., TCIP) hijack BCL-6 to kill CDK-positive cancer cells in a non-limiting example of a design. BCL-6 is a transcription factor and oncogene that prevents the death of a variety of cancer cells, including prostate cancer cells, by binding to epigenetic inhibitors BCOR, NCOR, and SMRT (PMID 18280243, 15531890, 10898795). Chemical connection of BCL-6 inhibitors (such as BI-3812 (PMID33208943)) to the ligands of CDK9 converts the cell death inhibitor into a powerful cell death activator, which then binds to and induces cell death (pro-apoptosis) promoters (such as TP53, PUMA, BIM, etc.) in the vicinity of the promoter. Figure 12 As shown, a small molecule that binds to the transcriptional activator CDK9 is used to recruit CDK9 to the promoter of a gene that activates the expression of a cell death gene. BCL6 and some of its homologs are typically cell death suppressors, but TCIP described herein according to embodiments of the present disclosure prevents this inhibitory effect and becomes ready for activation by the CDK9 molecule.

[0059] Figure 13 This demonstrates the advantages of the TCIP method according to embodiments of the present disclosure. Conventional therapeutics such as inhibitors, degraders, RNAi, and CRISPR must inhibit nearly all of the activity of the target protein, which inevitably leads to mechanism-based toxicity due to loss of function of the target protein's normal function. In contrast, TCIP only requires a small portion of the target to activate the cell death mechanism, which is a TCIP-induced gain of function. This method avoids the mechanism-based toxicity inherent in conventional therapeutics.

[0060] Figure 14 Provided are the structure of CDK9 inhibitor SNS-032 (A), the structure of a BCL6 binder (B), and the structure of TCIP prepared from these ligands (C), according to embodiments of the present disclosure.

[0061] Figure 15 CDK9-BCL6 TCIP was shown to be effective in killing human lymphoma cells. Figure 14 The molecules shown in the figure were used to treat different lymphoma cell lines, such as SUDHL5 shown here. Death was recorded after 72 hours. Additional data are available in Figure 26 Supplied with controls.

[0062] Figure 16 The results showed that CDK9-BCL6 TCIP (BAK_04_21) was more effective than the component molecules and competitor molecules in killing lymphoma cells.

[0063] Figure 17 This demonstrates that CDK9-BCL6 TCIP BAK04-21 forms a ternary complex in cells that can compete with BCL6 inhibitors. Cell death was recorded 72 hours after adding increasing concentrations of the BCL6 inhibitor BI3812 shown on the X-axis to TCIP BAK04-21.

[0064] Figure 18A Provided are structures of CDK ligands that can be used with TCIP according to embodiments of the present disclosure, and Figure 18B Provided are structures of additional BCL6 ligands that can be used with TCIP according to embodiments of the present disclosure.

[0065] Figure 19 The design of TCIP hijacking BCL-6 to kill androgen receptor (AR) driven prostate cancer cells is shown. BCL-6 is a transcription factor and oncogene that prevents the death of a variety of cancer cells, including prostate cancer cells, by binding to epigenetic inhibitors BCOR, NCOR and SMRT (PMID18280243, 15531890, 10898795). Chemical connection of BCL-6 inhibitors (such as BI-3812 (PMID33208943)) to AR ligands converts cell death inhibitors into powerful cell death activators, which then bind to cell death (pro-apoptosis) promoters (such as TP53, PUMA, BIM, etc.) and induce proximity to them. Normally, androgens will bind to AR and induce proliferation. As Figure 19 As shown, TCIP, which links AR to BCL6, leads to robust and rapid death of prostate cancer cells by binding to and coordinately activating killer genes. The methods shown provide a therapy for AR-driven prostate cancer, which comprises more than 80% of human prostate cancers.

[0066] Figure 20 Examples of gain-of-function provided by compounds of the present disclosure (e.g., TCIP) are shown. Typically, cancer drivers promote the proliferation, spread, and survival of cancer cells. In this example, TCIP diverts signals from cancer drivers to evolutionarily conserved cell death pathways that cancer drivers would not normally engage.

[0067] Figure 21 Compounds of the present disclosure (e.g., TCIP, such as Figure 22A non-limiting example of a method by which the androgen receptor can acquire a function it does not normally possess (e.g., cell killing) is provided by the compounds described in

[0014] . By using an AR portion on one side and a BCL6 protein or a prostate-specific transcription factor to engage the androgen-dependent proliferation pathway and then using a second portion to control cell death genes, a proliferation signal is induced that leads to cell death.

[0068] Figure 22 Components for the design and synthesis of AR-TCIP according to embodiments of the present disclosure are provided. A: BCL6 BTB inhibitors and degraders. These molecules can be used to generate an AR-TCIP arm that binds to endogenous BCL6 or its homologs. B: Steroidal androgen agonists and nonsteroidal androgen agonists, which can be used to form an AR-TCIP arm that binds to the endogenous androgen receptor in prostate cancer cells. C: Androgen receptor antagonists, which can be used as described in B. D: Linkers, which can be used to construct AR-BCL6 TCIP.

[0069] Figure 23 The structures of AR-BCL6 TCIPs according to embodiments of the present disclosure that were synthesized and tested for their ability to kill human prostate cancer are depicted. Each structure includes an androgen receptor binder, a linker, and a BCL6 binder / inhibitor that binds to the conserved BTB domain present in functionally related proteins. Each of the components is shown in the figure, and these components are examples of TCIPs according to embodiments of the present disclosure. The molecules labeled RCS-02-075 (AR-BCL6 negative, control 1) and RCS-02-155 (AR-BCL6 negative, control 2) are negative binding controls, which have minor but significant chemical modifications on the AR binding side and the BCL6 binding site, respectively.

[0070] Figure 24 AR-TCIP demonstrated rapid and potent killing of human prostate cancer cell lines. Four different androgen-dependent cell lines were used. AR-TCIP was added at the indicated concentrations, and viable cell counts were determined after 72 hours of exposure. RCS-02-063 demonstrated potent killing of prostate cancer cell lines at an IC50 of approximately 1.5 μM.

[0071] Figure 25Depicts target engagement achieved in vivo by TCIP RCS-02-063. A: A nanoBRET assay was constructed using nanoluc-labeled AR and Halotag-labeled BCL6. BRET signals were then detected after exciting HEK293 cells infected with the labeled fusion proteins at 460 nm. TCIP RCS-02-063 induces a robust BRET signal, indicating target engagement in vivo.

[0072] Figure 26 Demonstrating that the gain of function described herein (e.g., regulating the expression of a target gene that would not otherwise be achieved in the absence of a ternary complex between a first endogenous protein, a second endogenous protein, and a compound of the present disclosure) is achieved by recruiting a portion of the available second endogenous protein present in the cell, thereby avoiding mechanism-based toxicity. In this example, less than 10% of BRD4 was recruited to the promoter of a cell death gene by a compound disclosed herein (e.g., a TCIP1 compound) to activate a pro-apoptotic BCL6 target. The gain of function is due to BCL6 activating a pro-apoptotic pathway rather than inhibiting it, which is the normal role of BCL6.

[0073] Figure 27 A-27F depicts non-limiting examples of the production of compounds of the present disclosure and data associated therewith.

[0074] Figure 28 A-28D depicts data demonstrating the efficacy of compounds of the present disclosure in cancer cell lines and correlation with BCL6 levels.

[0075] Figure 29 A-29G depicts data demonstrating that compounds of the present disclosure act by inducing ternary complex formation.

[0076] Figure 30 A-30E depicts data on the rescue of cell death induced by compounds of the present disclosure by competitive titration of a BCL6 inhibitor.

[0077] Figure 31 A-31F depicts data demonstrating that compounds of the present disclosure induce apoptosis at each stage of the cell cycle.

[0078] Figure 32 A-32F depicts biochemical studies of ternary complex binding affinities of compounds of the present disclosure.

[0079] Figure 33 A-33G depicts data demonstrating that compounds of the present disclosure inhibit MYC and its targets while activating pro-apoptotic genes.

[0080] Figure 34Cell cycle blockade and apoptosis induction by compounds of the present disclosure are depicted.

[0081] Figure 35 A-35M depicts rapid activation of BCL6 target genes through recruitment of BRD4.

[0082] Figure 36 A-36E depicts robust and dose-dependent gene regulation by the compounds of the present disclosure.

[0083] Figure 37 A-37L demonstrates the toxicity of the disclosed compounds in mice and primary human cells as well as their general activity against ER-positive cancers.

[0084] Figure 38 A-38C depicts specific activation of gene expression by a compound of the present disclosure but not a relevant control.

[0085] Figure 39 A-39E depicts ChIP-seq analysis of BRD4, H3K27ac, and RNA Pol II in response to compounds of the present disclosure.

[0086] Figure 40 A-40D depicts the conversion of the BCL6 autoinhibitory pathway to a feedforward loop. DETAILED DESCRIPTION

[0087] As used herein, the term "alkyl" by itself or as part of another substituent refers to a saturated, branched or straight-chain monovalent hydrocarbon radical derived by removing one hydrogen atom from a single carbon atom of a parent alkane. Typical alkyl groups include, but are not limited to, methyl; ethyl; propyl, such as prop-1-yl or prop-2-yl; and butyl, such as but-1-yl, but-2-yl, 2-methyl-prop-1-yl, or 2-methyl-prop-2-yl. In some embodiments, the alkyl group contains 1 to 20 carbon atoms. In other embodiments, the alkyl group contains 1 to 10 carbon atoms. In still other embodiments, the alkyl group contains 1 to 6 carbon atoms, such as 1 to 4 carbon atoms.

[0088] "Alkanyl" by itself or as part of another substituent refers to a saturated branched, straight-chain or cyclic alkyl group derived by removing one hydrogen atom from a single carbon atom of an alkane. Typical alkanyl groups include, but are not limited to, methane; ethyl; propane, such as prop-1-yl, prop-2-yl (isopropyl), cycloprop-1-yl, etc.; butane, such as but-1-yl, but-2-yl (sec-butyl), 2-methyl-prop-1-yl (isobutyl), 2-methyl-prop-2-yl (tert-butyl), cyclobut-1-yl, etc.; and the like.

[0089] "Alkylene" refers to a branched or unbranched saturated hydrocarbon chain typically having from 1 to 40 carbon atoms, more typically from 1 to 10 carbon atoms, and even more typically from 1 to 6 carbon atoms. This term is exemplified by groups such as methylene (-CH2-), ethylene (-CH2CH2-), propylene isomers (e.g., -CH2CH2CH2- and -CH(CH3)CH2-), and the like.

[0090] "Alkenyl" by itself or as part of another substituent refers to an unsaturated branched, straight chain, or cyclic alkyl group having at least one carbon-carbon double bond derived by removing one hydrogen atom from a single carbon atom of an alkene. The group can be in either a cis or trans configuration about the double bond. Typical alkenyl groups include, but are not limited to, ethenyl; propenyl groups, such as prop-1-en-1-yl, prop-1-en-2-yl, prop-2-en-1-yl (allyl), prop-2-en-2-yl; cycloprop-1-en-1-yl; cycloprop-2-en-1-yl; butenyl groups, such as but-1-en-1-yl, but-1-en-2-yl, 2-methyl-prop-1-en-1-yl, but-2-en-1-yl, but-2-en-1-yl, but-2-en-2-yl, but-1,3-dien-1-yl, but-1,3-dien-2-yl, cyclobut-1-en-1-yl, cyclobut-1-en-3-yl, cyclobut-1,3-dien-1-yl, and the like; and so forth.

[0091] "Alkynyl" by itself or as part of another substituent refers to an unsaturated branched, straight-chain, or cyclic alkyl group having at least one carbon-carbon triple bond derived by removing one hydrogen atom from a single carbon atom of an alkyne. Typical alkynyl groups include, but are not limited to, ethynyl; propynyl, such as prop-1-yn-1-yl, prop-2-yn-1-yl, etc.; butynyl, such as but-1-yn-1-yl, but-1-yn-3-yl, but-3-yn-1-yl, etc.; and the like.

[0092] "Acyl" by itself or as part of another substituent refers to the group -C(O)R 30 , where R 30 is hydrogen, alkyl, cycloalkyl, cycloheteroalkyl, aryl, arylalkyl, heteroalkyl, heteroaryl, heteroarylalkyl, and substituted versions thereof as defined herein. Representative examples include, but are not limited to, formyl, acetyl, cyclohexylcarbonyl, cyclohexylmethylcarbonyl, benzoyl, benzylcarbonyl, piperonyl, propionyl, succinyl, and malonyl.

[0093] The term "aminoacyl" refers to the group -C(O)NR 21 R 22 , where R 21 and R 22are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, heteroaryl, substituted heteroaryl, heterocycle, and substituted heterocycle, and wherein R 21 and R 22 and optionally linked, together with the nitrogen to which it is bound, to form a heterocycle or a substituted heterocycle, and wherein alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycle and substituted heterocycle are as defined herein.

[0094] "Alkoxy" by itself or as part of another substituent refers to the group -OR 31 , where R 31 represents an alkyl or cycloalkyl group as defined herein. Representative examples include, but are not limited to, methoxy, ethoxy, propoxy, butoxy, cyclohexyloxy, and the like.

[0095] "Alkoxycarbonyl" by itself or as part of another substituent refers to the group -C(O)OR 31 , where R 31 represents an alkyl or cycloalkyl group as defined herein. Representative examples include, but are not limited to, methoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl, cyclohexyloxycarbonyl, and the like.

[0096] "Aryl" by itself or as part of another substituent refers to a monovalent aromatic hydrocarbon radical derived by removing one hydrogen atom from a single carbon atom of an aromatic ring system. Typical aryl groups include, but are not limited to, radicals derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, In some embodiments, the aryl group comprises 6 to 20 carbon atoms. In certain embodiments, the aryl group contains 6 to 12 carbon atoms.Examples of aryl groups are phenyl and naphthyl.

[0097] "Arylalkyl" by itself or as part of another substituent refers to a group in which the carbon atoms (typically, terminal carbon atoms or sp 3 An acyclic alkyl group in which one of the hydrogen atoms bonded to a (C-C) carbon atom is replaced by an aryl group. Typical arylalkyl groups include, but are not limited to, benzyl, 2-phenylethyl-1-yl, 2-phenylethyl-1-yl, naphthylmethyl, 2-naphthylethyl-1-yl, 2-naphthylethyl-1-yl, naphthylbenzyl, 2-naphthylphenylethyl-1-yl, and the like. Where a specific alkyl moiety is the objective, the nomenclature arylalkyl, arylalkenyl, and / or arylalkynyl is used. In certain embodiments, arylalkyl is (C-C 30 ) arylalkyl, for example, the alkanyl, alkenyl or alkynyl portion of the arylalkyl is (C1-C 10 ), and the aryl moiety is (C6-C 20 In certain embodiments, the arylalkyl group is (C7-C 20 ) arylalkyl, for example, the alkanyl, alkenyl or alkynyl portion of the arylalkyl is (C1-C8) and the aryl portion is (C6-C 12 ).

[0098] "Arylaryl" by itself or as part of another substituent refers to a monovalent hydrocarbon radical derived by removing one hydrogen atom from a single carbon atom of a ring system in which two or more identical or non-identical aromatic ring systems are directly linked together by a single bond, wherein the number of such direct ring attachment points is one less than the number of aromatic ring systems involved. Typical arylaryl groups include, but are not limited to, diphenyl, triphenyl, phenyl-naphthyl, binaphthyl, diphenyl-naphthyl, and the like. When the number of carbon atoms in an arylaryl group is specified, the number refers to the carbon atoms included in each aromatic ring. For example, (C5-C 14 )Arylaryl is an arylaryl group wherein each aromatic ring contains 5 to 14 carbon atoms, for example, diphenyl, triphenyl, binaphthyl, phenylnaphthyl, etc. In certain embodiments, each aromatic ring system of the arylaryl group is independently (C5-C 14 In certain embodiments, each aromatic ring system of the arylaryl group is independently (C5-C 10 ) aromatic compounds. In certain embodiments, each aromatic ring system is the same, for example, diphenyl, triphenyl, binaphthyl, trinaphthyl, etc.

[0099] "Cycloalkyl" by itself or as part of another substituent refers to a saturated or unsaturated cyclic alkyl group. When a specific level of saturation is intended, the nomenclature "cycloalkane" or "cycloalkenyl" is used. Typical cycloalkyl groups include, but are not limited to, groups derived from cyclopropane, cyclobutane, cyclopentane, cyclohexane, and the like. In certain embodiments, a cycloalkyl group is (C3-C 10 In certain embodiments, the cycloalkyl group is a (C3-C7)cycloalkyl group.

[0100] "Cycloheteroalkyl" or "heterocyclyl" by itself or as part of another substituent refers to a saturated or unsaturated cyclic alkyl group in which one or more carbon atoms (and any associated hydrogen atoms) are independently replaced by the same or different heteroatoms. Typical heteroatoms used to replace carbon atoms include, but are not limited to, N, P, O, S, Si, and the like. When a specific level of saturation is desired, the nomenclature "cycloheteroalkane" or "cycloheteroalkenyl" is used. Typical cycloheteroalkyl groups include, but are not limited to, groups derived from epoxides, azirines, thiirane, imidazolidine, morpholine, piperazine, piperidine, pyrazolidine, pyrrolidine, quinuclidine, and the like.

[0101] "Heteroalkyl, heteroalkyl, heteroalkenyl and heteroalkynyl" by themselves or as part of another substituent refer to alkyl, alkanyl, alkenyl and alkynyl groups, respectively, in which one or more of the carbon atoms (and any associated hydrogen atoms) are independently replaced by the same or different heteroatom groups. Typical heteroatom groups that can be included in these groups include, but are not limited to, -O-, -S-, -SS-, -OS-, -NR- 37 R 38 -,=NN=,-N=N-,-N=N-NR 39 R 40 、-PR 41 -、-P(O)2-、-POR 42 -, -OP(O)2-, -SO-, -S-(O)-, -SO2-, -SnR 43 R 44 - etc., where R 37 、R 38 、R 39 、R 40 、R 41 、R 42 、R 43 and R 44 and alkyl, substituted alkyl, aryl, substituted aryl, arylalkyl, substituted arylalkyl, cycloalkyl, substituted cycloalkyl, cycloheteroalkyl, substituted cycloheteroalkyl, heteroalkyl, substituted heteroalkyl, heteroaryl, substituted heteroaryl, heteroarylalkyl, or substituted heteroarylalkyl.

[0102] "Heteroaryl" by itself or as part of another substituent refers to a monovalent heteroaryl group derived by removing one hydrogen atom from a single atom of a heteroaromatic ring system. Typical heteroaryl groups include, but are not limited to, groups derived from acridine (arsindole), carbazole, β-carboline, chroman, chromene, cinnoline, furan, imidazole, indazole, indole, indoline, indolizine, isobenzofuran, isochromene, isoindole, isoindoline, isoquinoline, isothiazole, isoxazole, naphthyridine, oxadiazole, oxazole, piperidine, phenanthridine, phenanthroline, phenazine, phthalazine, pteridine, purine, pyran, pyrazine, pyrazole, pyridazine, pyridine, pyrimidine, pyrrole, pyrrolizine, quinazoline, quinoline, quinolinazine, quinoxaline, tetrazole, thiadiazole, thiazole, thiophene, triazole, xanthene, benzodioxole, and the like. In certain embodiments, heteroaryl is a 5-20 membered heteroaryl group. In certain embodiments, the heteroaryl group is a 5-10 membered heteroaryl group. In certain embodiments, the heteroaryl group is a group derived from thiophene, pyrrole, benzothiophene, benzofuran, indole, pyridine, quinoline, imidazole, oxazole, and pyrazine.

[0103] "Heteroarylalkyl" by itself or as part of another substituent refers to a group in which the carbon atoms (typically, terminal carbon atoms or sp3 In some embodiments, heteroarylalkyl is a 6-30 membered heteroarylalkyl, for example, the alkanyl, alkenyl or alkynyl moiety of the heteroarylalkyl is 1-10 membered, and the heteroaryl moiety is a 5-20 membered heteroaryl. In some embodiments, heteroarylalkyl is a 6-20 membered heteroarylalkyl, for example, the alkanyl, alkenyl or alkynyl moiety of the heteroarylalkyl is 1-8 membered, and the heteroaryl moiety is a 5-12 membered heteroaryl.

[0104] "Aromatic ring system" by itself or as part of another substituent refers to an unsaturated cyclic or polycyclic ring system having a conjugated pi electron system. Specifically included within the definition of "aromatic ring system" are fused ring systems in which one or more of the rings is aromatic and one or more of the rings is saturated or unsaturated, such as fluorene, indane, indene, pinene, etc. Typical aromatic ring systems include, but are not limited to, aceanthrene, acenaphthylene, acephenanthren, anthracene, azulene, benzene, Coronene, fluoranthene, fluorene, hexacene, hexalene, asymmetric indacene, symmetric indacene, indane, indene, naphthalene, octacene, octalene, octalene, octalene, pentadiene, pentacene, cyclopentadiene, pentaphene, perylene, cinnamate, phenanthrene, cinnamate, septalene, pyrene, pyranthrene, pyridine, triphenylene, ternaphthalene, etc.

[0105] "Heteroaromatic ring system" by itself or as part of another substituent refers to an aromatic ring system in which one or more carbon atoms (and any associated hydrogen atoms) are independently replaced by the same or different heteroatoms. Typical heteroatoms replacing carbon atoms include, but are not limited to, N, P, O, S, Si, and the like. Specifically included within the definition of "aromatic ring system" are fused ring systems in which one or more of the rings is aromatic and one or more of the rings is saturated or unsaturated, such as acridine, benzodioxane, benzofuran, chroman, chromene, indole, indoline, xanthene, and the like. Typical heteroaromatic ring systems include, but are not limited to, acridine, carbazole, β-carboline, chroman, chromene, cinnoline, furan, imidazole, indazole, indole, indoline, indolizine, isobenzofuran, isochromene, isoindole, isoindoline, isoquinoline, isothiazole, isoxazole, naphthyridine, oxadiazole, oxazole, piperidine, phenanthridine, phenanthroline, phenazine, phthalazine, pteridine, purine, pyran, pyrazine, pyrazole, pyridazine, pyridine, pyrimidine, pyrrole, pyrrolizine, quinazoline, quinoline, quinolinazine, quinoxaline, tetrazole, thiadiazole, thiazole, thiophene, triazole, xanthene, and the like.

[0106] "Substituted" refers to a group in which one or more hydrogen atoms are independently replaced by the same or different substituents. Typical substituents include, but are not limited to, alkylenedioxy (such as methylenedioxy), -M, -R 60 、-O - ,=O,-OR 60 、-SR 60 、-S - , =S, -NR 60 R 61 、=NR 60 , -CF3, -CN, -OCN, -SCN, -NO, -NO2, =N2, -N3, -S(O)2O - 、-S(O)2OH、-S(O)2R 60 、-OS(O)2O - 、-OS(O)2R 60 、-P(O)(O - )2、-P(O)(OR 60 )(O - )、-OP(O)(OR 60 )(OR 61 ),-C(O)R 60 、-C(S)R 60 、-C(O)OR 60 、-C(O)NR 60 R 61 ,-C(O)O - 、-C(S)OR 60 、-NR 62 C(O)NR 60 R 61 、-NR 62 C(S)NR 60 R 61 、-NR 62 C(NR 63 )NR 60 R 61 and -C(NR 62 )NR 60 R 61 , wherein M is halogen; R 60 、R 61 、R 62 and R 63 R is independently hydrogen, alkyl, substituted alkyl, alkoxy, substituted alkoxy, cycloalkyl, substituted cycloalkyl, cycloheteroalkyl, substituted cycloheteroalkyl, aryl, substituted aryl, heteroaryl or substituted heteroaryl, or optionally R 60 and R 61 Together with the nitrogen atom to which it is bound, it forms a cycloheteroalkyl ring or a substituted cycloheteroalkyl ring, and R64 and R 65 is independently hydrogen, alkyl, substituted alkyl, aryl, cycloalkyl, substituted cycloalkyl, cycloheteroalkyl, substituted cycloheteroalkyl, aryl, substituted aryl, heteroaryl or substituted heteroaryl, or optionally R 64 and R 65 Together with the nitrogen atom to which it is bonded, they form a cycloheteroalkyl or substituted cycloheteroalkyl ring. In certain embodiments, the substituents include -M, -R 60 ,=O,-OR 60 、-SR 60 、-S - , =S, -NR 60 R 61 、=NR 60 , -CF3, -CN, -OCN, -SCN, -NO, -NO2, =N2, -N3, -S(O)2R 60 、-OS(O)2O - 、-OS(O)2R 60 、-P(O)(O - )2、-P(O)(OR 60 )(O - )、-OP(O)(OR 60 )(OR 61 ),-C(O)R 60 、-C(S)R 60 、-C(O)OR 60 、-C(O)NR 60 R 61 、-C(O)O - 、-NR 62 C(O)NR 60 R 61 In certain embodiments, the substituents include -M, -R 60 ,=O,-OR 60 、-SR 60 、-NR 60 R 61 , -CF3, -CN, -NO2, -S(O)2R 60 、-P(O)(OR 60 )(O - )、-OP(O)(OR 60 )(OR 61 ),-C(O)R 60 、-C(O)OR 60 、-C(O)NR 60 R 61 、-C(O)O - In certain embodiments, the substituents include -M, -R60 ,=O,-OR 60 、-SR 60 、-NR 60 R 61 , -CF3, -CN, -NO2, -S(O)2R 60 、-OP(O)(OR 60 )(OR 61 ),-C(O)R 60 、-C(O)OR 60 、-C(O)O - , where R 60 、R 61 and R 62 As defined above. For example, a substituted group may carry a methylenedioxy substituent or one, two or three substituents selected from halogen atoms, (1-4C)alkyl and (1-4C)alkoxy groups.

[0107] Provided herein are compositions, systems, and methods for regulating the expression of a target gene in a target cell. The compositions, systems, and methods can be used to regulate the expression of a target gene in a target cell by allowing different endogenous proteins expressed by the target cell to approach each other spatially so that the target gene can be regulated by protein regulation, and the target gene, in the absence of a compound, will generally not be regulated by the protein regulation. The compositions, systems, and methods generally relate to compounds that specifically bind to at least one first endogenous protein and a second different endogenous protein, each endogenous protein being expressed by the target cell. The first endogenous protein is generally a protein that can bind to the target gene or a region near the target gene (such as a promoter or regulatory region) and acts as an anchor for the complex. The second endogenous protein is a protein that does not substantially regulate the expression of the target gene in the absence of the compound, but can regulate the expression of the target gene when recruited to the target gene or a region near the target gene by the compound. Advantageously, the compositions, systems, and methods provided herein do not require any genetic modification of the target cell. In contrast, the compositions, systems, and methods provided herein rely on the presence of proteins endogenously expressed in the target cell. In addition, the compound is generally a small molecule that can be administered to a subject (e.g., by oral administration, intravenous administration, etc.).

[0108] It should be understood that the present disclosure is not limited to the particular embodiments described, as such embodiments may, of course, vary. It should also be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting, as the scope of the present disclosure will be limited only by the appended claims.

[0109] Where a range of values ​​is provided, it will be understood that each intervening value (to the tenth of the unit of the lower limit, unless otherwise expressly stated) between the upper and lower limits of the range, as well as any other stated or intermediate values ​​within the range, is encompassed within the present invention. The upper and lower limits of these smaller ranges may independently be included in smaller ranges and are also encompassed within the present invention, subject to any specifically excluded limits in the stated ranges. Where a stated range includes one or both of the limits, ranges excluding either or both of those included limits are also encompassed within the present invention.

[0110] The term "about" or "approximately" generally means within an acceptable error range for a particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., limitations of the measurement system. For example, according to practice in the art, "about" can mean within 1 or more than 1 standard deviation. Alternatively, "about" can mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude of a value, preferably within 5-fold and more preferably within 2-fold. When describing specific values ​​in the application and claims, unless otherwise indicated, it should be assumed that the term "about" means within an acceptable error range for the specific value.

[0111] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, representative illustrative methods and materials are now described.

[0112] All publications and patents cited in this specification are incorporated herein by reference as if each individual publication or patent was specifically and individually indicated to be incorporated by reference, and are incorporated herein by reference to disclose and describe the methods and / or materials in connection with the cited publication. Citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Additionally, the publication dates provided may be different from the actual publication dates, which may need to be independently confirmed.

[0113] It should be noted that, as used herein and in the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Furthermore, it should be noted that claims can be drafted to exclude any optional elements. Thus, this statement is intended to presuppose the use of exclusive terminology such as "solely," "only," and the like in connection with the recitation of claim elements or the use of a "negative" limitation.

[0114] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

[0115] As will be apparent to those skilled in the art after reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features that can be readily separated or combined with the features of any other several embodiments without departing from the scope or spirit of the invention. Any recited method can be executed in the order of events recited or in any other logically possible order.

[0116] Although devices and methods have been or will be described for purposes of grammatical fluency and functional explanation, it is to be expressly understood that, unless expressly formulated pursuant to 35 U.S.C. § 112, the claims shall not be construed as necessarily limiting in any manner by constructing “means” or “step” limitations, but shall be given the full meaning and scope of equivalents provided by the defined claims under the doctrine of equivalents, and, if the claims are expressly formulated pursuant to 35 U.S.C. § 112, the full statutory equivalents under 35 U.S.C. § 112 shall apply.

[0117] Systems, compositions, and methods for regulating the expression of target genes

[0118] In one aspect, provided herein is a method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first portion (e.g., covalently) linked to a second portion, wherein (a) the first portion exhibits specific binding to the first endogenous protein, wherein the first endogenous protein binds to the target gene or a region (e.g., a promoter, a regulatory region) near the target gene; (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein bound to the compound. The method further provides that the gain of function is achieved by utilizing less than about 50% of the amount of the second endogenous protein present in the cell.

[0119] In another aspect, provided herein is a method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first portion covalently linked to a second portion, wherein (a) the first portion exhibits specific binding to the first endogenous protein, wherein the first endogenous protein binds to the target gene or a region near the target gene (e.g., a promoter, a regulatory region); (b) the second portion exhibits specific binding to a second endogenous protein, which is different from the first endogenous protein; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein bound to the compound. The method further provides that the compound mediates the gain of function at an EC50 of less than about 1 micromolar.

[0120] In another aspect, provided herein is a method for regulating the expression of multiple target genes in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first portion covalently linked to a second portion, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, wherein the first endogenous protein reduces expression of the target gene in the absence of the compound; (b) the second portion exhibits specific binding to the second endogenous protein, wherein the second endogenous protein enhances expression of an additional target gene in the absence of the compound; and (c) upon contacting the cell, the first endogenous protein and the second endogenous protein are spatially paired with each other by the compound, thereby producing a gain of function in the cell, and the method further provides that the gain of function is characterized by: (i) expression of the target gene is enhanced compared to expression in the absence of the compound; and (ii) expression of the additional target gene is reduced compared to expression in the absence of the compound.

[0121] In another aspect, provided herein is a method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with an effective amount of a compound having a first portion covalently linked to a second portion, wherein (a) the first portion exhibits specific binding to the first endogenous protein, wherein the first endogenous protein binds to the target gene or a region near the target gene (e.g., a promoter, a regulatory region); (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) after contacting the cell, the first endogenous protein and the second endogenous protein bind to the compound to form a complex, thereby generating a gain of function in the cell, wherein the gain of function is characterized by regulating the expression of the target gene in a manner dependent on the presence of the second endogenous protein bound to the compound. The method further provides for regulating the expression of the target gene within less than or equal to about 16 hours after the contact.

[0122] Further provided herein are compositions and systems suitable for performing any of the foregoing methods further described herein.

[0123] As summarized above, the present disclosure provides a method for regulating the expression of a target gene in a cell, and a system and composition for realizing the method. The method can be regarded as an inductive method for regulating the expression of a target gene. Since the method is inductive, the expression of the target gene is not constitutive, but on the contrary occurs in response to an applied stimulus (e.g., providing a compound described in more detail below in a cell). Since the method is a method for regulating the expression of a target gene inductively, the method is a method for changing the expression or expression spectrum of the target gene in some way (e.g., enhancing the expression of the target gene or reducing the expression of the target gene). The magnitude of the expression change (relative to a suitable control, e.g., the same system but without compound) may change, wherein in some instances, the magnitude of the change (e.g., enhancing or reducing) is 2 times or greater, such as 5 times or greater, e.g., 10 times or greater. The target gene can be any gene described herein or known in the art. The target gene can be a wild-type gene or a mutated gene.

[0124] As summarized above, the present disclosure provides methods for regulating the expression of target genes (including but not limited to BCL6 target genes). The term gene refers to a genomic region encoding a functional RNA, including non-coding RNA, microRNA, enhancer RNA, or RNA that can be translated into a protein product. The term gene is used in its conventional sense to refer to a region or domain of a chromosome that includes not only a coding sequence (e.g., in the form of exons separated by introns), but also includes a regulatory sequence (e.g., enhancer / silencer, promoter, terminator, non-coding RNA, microRNA, etc.).

[0125] The specific target gene that is the focus of a given method can vary. The target gene can be any gene whose expression will be regulated by the compositions, systems and methods provided herein. In some instances, the target gene is a gene whose expression is to be enhanced. Non-limiting examples of genes whose expression is to be enhanced by the compositions, systems and methods provided herein include pro-apoptotic genes (e.g., PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA (PMAIP1)). In some instances, the target gene is a gene whose expression is to be suppressed or reduced. Non-limiting examples of genes whose expression is to be suppressed or reduced by the compositions, systems and methods provided herein include anti-apoptotic genes (e.g., BCL6) and genes that promote cell survival and proliferation (e.g., MYC). In some instances, the target gene is a therapeutic gene whose expression (e.g., increase or enhance) can have a beneficial effect in cells or on subjects, such as, but not limited to, rate-limiting enzymes (e.g., TPH2), haploinsufficient genes (e.g., ARID1B) etc. In some instances, a target gene is a gene whose expression has a deleterious effect on a cell or subject and / or causes a disease or condition in a subject (e.g., a mutated gene) and whose expression is to be inhibited or reduced by the compositions, systems, and methods provided herein. In some instances, a target gene is an overexpressed gene whose expression is to be inhibited or reduced by the compositions, systems, and methods provided herein, such as, but not limited to, oncogenes (e.g., MYC), trisomic genes (e.g., chromosome 21 genes), amplified genes, and the like.

[0126] The above gene categories are merely examples of gene types that can be target genes for the subject methods. Any gene whose expression is to be regulated (e.g., enhanced, reduced) by the compositions, systems, and methods provided herein can be a target gene. Additional examples of target genes include, but are not limited to, developmental genes (e.g., adhesion molecules, cyclin kinase inhibitors, cytokines / lymphokines and their receptors, determinants of tumor immunogenicity, growth / differentiation factors and their receptors, immune checkpoint receptors and ligands, neurotransmitters and their receptors); oncogenes (e.g., ABLI, BCLI, BCL2, BCL6, CBFA2, CBL, CSFIR, ERBA, ERBB, EBRB2, ETSI, ETS1, ETV6, FOR, FOS, FYN, HCR, HRAS, JUN, KRAS, LCK, LYN, MDM2, MLL, MYB, MYC, MYCLI, MYCN, NRAS, PIM 1, PML, RET, SRC, TALI, TCL3, and YES); tumor suppressor genes (e.g., APC, BRCA 1, BRCA2, MADH4, MCC, NF1, NF2, RB1, TP53, and WTI); enzymes (e.g., ACC synthase and oxidase, ACP desaturase and hydroxylase, ADP-glucose pyrophosphorylase, ATPase, alcohol dehydrogenase, amylase, amyloglucosidase, catalase, cellulase, chalcone synthases, chitinase, cyclooxygenase, decarboxylase, dextrinase, DNA and RNA polymerase, galactosidase, glucanase, glucose oxidase, granule-bound starch synthase, GTPase, helicase, hemicellulase, integrase, inulinase, invertase, isomerase, kinase, lactase, upase, lipoxygenase, lysozyme, nopaline synthase, octopine synthase, pectinesterase, peroxidase, phosphatase, phospholipase, phosphorylase, phytase, plant growth regulator synthase, polygalacturonase, protease, and peptidases, pullulanases, recombinases, reverse transcriptases, RUBISCO, topoisomerases, and xylanases); chemokines (e.g., CXCR4, CCR5), the RNA component of telomerase, vascular endothelial growth factor (VEGF), VEGF receptors, tumor necrosis factor nuclear factor kappa B, transcription factors, cell adhesion molecules, insulin-like growth factor, transforming growth factor beta family members, cell surface receptors, RNA binding proteins (e.g., small nucleolar RNAs, RNA transport factors), translation factors, telomerase reverse transcriptase); and the like.

[0127] As described above, in some instances, the target gene is a therapeutic gene (e.g., a gene that has a beneficial effect on a cell or subject when expressed). Examples of therapeutic target genes suitable for regulation using the compositions, systems, and methods provided herein include, but are not limited to, the therapeutic target genes provided in Table 1 below.

[0128] Table 1: Examples of therapeutic target genes

[0129]

[0130]

[0131] In some instances, the target gene is a non-coding gene. The non-coding genes of interest include, but are not limited to, the genes provided in Table 2.

[0132] Table 2: Non-limiting examples of non-coding genes.

[0133] MIR663AHG LINC00847 LINC00641 Snhg16 MIR663A LINC01089 LINC02035 Snhg3 MIR663B LINC01963 LINC02447 Snhg4 MIR3648-1 LINC02413 LINC00672 Snhg5 MIR3648-2 LINC01588 LINC01232 Snhg6 MIR22HG LINC01176 LINC01004 Snhg8 LINC00273 LINC00894 SNORD3B-2 LINC02202 LINC01145 SNORD3B-1 LINC00868 LINC00926 Mir22hg LINC00476 LINC00910 Snhg1 LINC02137 LINC00293 Snhg12

[0134] Genes that can be targeted by one or more compounds provided herein (e.g., chemical proximity inducers (CIPs), transcriptional chemical proximity inducers (TCIPs), etc.) are also provided in PCT application serial number PCT / US2021 / 058231 published as WO 2022 / 098989; the disclosure of which is hereby incorporated by reference in its entirety.

[0135] In some cases, the target gene that can be regulated and controlled by the system, composition and method that this paper provides can be a chromosomal gene or an epichromosomal gene.In some cases, the target gene can be an endogenous gene.Alternately or in addition, the target gene can be a heterologous gene, for example, be present in the gene that is introduced into (for example, by transfection agent transfection, with viral mode transduction etc.) to cell on plasmid or carrier.Before the system, composition and method that this paper provides regulate and control, this heterologous gene can or can not be integrated in the genome of cell.

[0136] As described herein, the compositions, systems, and methods provided herein involve the use of a compound having at least a first portion and a second portion, wherein the first portion specifically binds to a first endogenous protein expressed in a target cell, and the second portion specifically binds to a second endogenous protein expressed in a target cell. Portions of a compound may be referred to as ligands throughout this disclosure, and the terms "portion" and "ligand" (or "portions" and "ligands") are used interchangeably herein. The first endogenous protein and the second endogenous protein are each derived from a cell and expressed in the cell. Specifically, upon administration of a compound disclosed herein (e.g., including CIP or TCIP), both the first endogenous protein and the second endogenous protein are present in the cell or expressed in the cell. The compositions, systems, and methods provided herein generally do not require the exogenous introduction (e.g., transfection, transduction, etc.) of the first endogenous protein and / or the second endogenous protein into the cell to which the subject compound is administered to achieve gain of function. The compositions, systems, and methods provide specificity such that gain of function is achieved only in the specific target cells where the first endogenous protein and the second endogenous protein are expressed. In some embodiments, the compounds of the present disclosure comprise at least a first portion and a second portion, wherein the first portion and the second portion bind to at least a first endogenous protein and a second endogenous protein, thereby forming a ternary complex between the compound, the first endogenous protein, and the second endogenous protein. The first endogenous protein and the second endogenous protein are spatially adjacent and associated with each other.

[0137] A ternary complex (e.g., between a compound, a first endogenous protein, and a second endogenous protein) is a non-naturally occurring complex that would not be present in a cell in the absence of both the compound and the first endogenous protein and the second endogenous protein. Thus, this compound may be referred to herein as a "chemical proximity inducer" or "CIP." In some cases, such as when the compound binds to an endogenous anchor transcription factor and an endogenous transcriptional regulator, the compound may be referred to herein as a "transcriptional chemical proximity inducer," "transcriptional chemical proximity inducer," or "TCIP." The first and second parts of the compound may be derived from naturally occurring substances and / or synthetic substances. Applicable and readily observable or readily measurable criteria for selecting a portion may include, but are not limited to: (A) the portion is physiologically acceptable (e.g., not overly toxic to the cells or animals to be used); (B) the portion has a reasonable therapeutic dose range (e.g., determined by producing a desired expression profile of a target gene or desired cellular activity in a cell); (C) the portion can pass through the cell membrane and other membranes, if necessary; and / or (D) the portion binds to one or more target domains of the first endogenous protein and / or the second endogenous protein (e.g., an endogenous anchor transcription factor and / or an endogenous transcriptional regulator as provided herein). For example, a desired criterion is that the compound is chemically stable and capable of forming a complex. In some instances, a portion of the compound (e.g., the first portion and / or the second portion) may be non-peptide and non-nucleic acid. Alternatively or in addition, at least a portion of the first portion and / or the second portion of the compound may be a peptide and / or a nucleic acid.

[0138] The composition (e.g., pharmaceutical composition) comprising at least a compound can be administered to a subject, e.g., to treat a condition or disease in the subject. Administration can be, for example, intra-articular, oral, parenteral, intravenous, intramuscular, rectal, dermal, subcutaneous, topical, transdermal, sublingual, nasal, vaginal, intracapsular, intraurethral, ​​intrathecal, epidural, ear, and / or eye administration. For example, the composition can be taken orally (e.g., a compound that is stable in the gastrointestinal system and can be absorbed into the vascular system).

[0139] The compound can be a small molecule. The compound can be non-toxic. Small molecules refer to molecules having a molecular weight of 5000 g / mole (Daltons) or less, such as 2500 g / mole (Daltons) or less (including 1000 g / mole (Daltons) or less, for example, 500 g / mole (Daltons) or less). In some examples, the molecular weight of the CIP used in the embodiments of the present disclosure is in the range of 250 g / mole to 1500 g / mole (such as 300 g / mole to 1200 g / mole).

[0140] The compound can include multiple parts (such as a first part and a second part), and the multiple parts are used to bind to multiple endogenous proteins respectively. In a single compound, the first part and the second part can be coupled to or connected to each other by a linker (for example, a linker with at least one atom). A linker can exist to provide a certain distance (for example, a desired distance) between the two parts. Alternatively, in the absence of a linker, the two parts can be directly coupled to each other (for example, the two parts can be coupled to each other by a direct chemical bond between the two atoms of the two parts). For example, a compound can include two parts and a chemical bond directly between the two parts so that the two parts of the compound form two sides (or two surfaces) of the compound, and the two sides are each bound to their corresponding protein.

[0141] The compound can comprise multiple parts, each part binding to a different endogenous protein. For example, the compound can comprise at least or at most about 2 parts, at least or at most about 3 parts, at least or at most about 4 parts, at least or at most about 5 parts, at least or at most about 6 parts, at least or at most about 7 parts, at least or at most about 8 parts, at least or at most about 9 parts, or at least or at most about 10 parts. The compound can bind to and form a complex with at least or at most 2 endogenous proteins, at least or at most 3 endogenous proteins, at least or at most 4 endogenous proteins, at least or at most 5 endogenous proteins, at least or at most 6 endogenous proteins, at least or at most 7 endogenous proteins, at least or at most 8 endogenous proteins, at least or at most 9 endogenous proteins, or at least or at most 10 endogenous proteins. In some cases, at least one of the endogenous proteins may be a wild-type protein or a mutated protein comprising one or more amino acid mutations (e.g., one or more point mutations, one or more amino acid insertions, one or more amino acid deletions, one or more amino acid translocations, etc.) that cause the mutated protein to exhibit a function or activity different from that of the wild-type protein. For example, the mutated protein may be a disease-causing protein, such as a mutated protein whose activity promotes the survival, proliferation, and / or spread of diseased cells (e.g., cancer cells). In some cases, a protein may be expressed by a wild-type gene or a mutated gene or by a mutated protein produced by a fusion transcript (e.g., due to chromosomal rearrangements, spliced ​​transcription errors, inversions, inter- or intra-chromosomal translocations, chromothripsis, etc.).

[0142] In some cases, the first endogenous protein is a protein that binds to a target gene or a region near the target gene (such as a promoter or regulatory region). In the absence of a compound, the first endogenous protein can bind to a target gene or a region near the target gene. In some cases, the binding of the first endogenous protein to the target gene (or the region near the target gene) can be direct binding. In other cases, the binding of the first endogenous protein to the target gene (or the region near the target gene) can be indirect binding, such as by binding to one or more cofactors, which directly bind to the target gene. The first endogenous protein can bind to part of the compound and form a ternary complex with the compound and the second endogenous protein. In this case, the first endogenous protein (in the ternary complex) can bind to the target gene or the region near the target gene and make the second endogenous protein closely adjacent to the target gene or the region near the target gene. In some embodiments, the first endogenous protein can serve as an "anchor protein" because the first endogenous protein anchors the ternary complex to the target gene, and, specifically, when the first endogenous protein is a transcription factor, it can serve as an "anchor transcription factor". In some cases, in the absence of a compound, the first endogenous protein can regulate the expression of the target gene. For example, in the absence of the compound, the first endogenous protein can enhance the expression of the target gene or can reduce or inhibit the expression of the target gene. In other examples, the first endogenous protein may have no effect on the expression of the target gene (e.g., the first endogenous protein can bind to the target gene (or a region near the target gene) but have no effect on the expression of the target gene. The first endogenous protein can be any protein that can bind to the target gene or a region near the target gene (e.g., directly or indirectly), regardless of whether the first endogenous protein has any effect on the expression of the target gene. In some instances, the first endogenous protein can be a transcriptional regulator, such as a transcription factor, a transcriptional activator, a transcriptional repressor and / or an epigenetic regulator and / or a signaling intermediate, such as, but not limited to, a kinase or a phosphatase.

[0143] The first endogenous protein can (e.g., directly or indirectly) bind to the coding sequence (or a portion of the coding sequence) of the target gene. Alternatively or additionally, the first endogenous protein can (e.g., directly or indirectly) bind to a non-coding sequence of the target gene (e.g., a regulatory region of the coding sequence, such as an enhancer sequence, a promoter sequence, a CCAAT box, a TATA box, etc.). Alternatively or additionally, the first endogenous protein can (e.g., directly or indirectly) bind to a sequence near the coding sequence of the target gene. For example, the first endogenous protein can be at least or at most about 1 nucleobase, at least or at most about 2 nucleobases, at least or at most about 5 nucleobases, at least or at most about 10 nucleobases, at least or at most about 15 nucleobases, at least or at most about 20 nucleobases, at least or at most about 30 nucleobases, at least or at most about 40 nucleobases, at least or at most about 50 nucleobases, at least or at most about 100 nucleobases, at least or at most about 200 nucleobases, at least or at most about 300 nucleobases, at least or at most about 400 nucleobases, at least or at most about 500 nucleobases, at least or at most about 1,000 nucleobases, at least or at most about 2,000 nucleobases, or at least or at most about 3,000 nucleobases from the coding sequence of the target gene. In some embodiments, the present invention relates to a sequence of at least or at most about 3,000 nucleobases, at least or at most about 4,000 nucleobases, at least or at most about 5,000 nucleobases, at least or at most about 6,000 nucleobases, at least or at most about 7,000 nucleobases, at least or at most about 8,000 nucleobases, at least or at most about 9,000 nucleobases, at least or at most about 10,000 nucleobases, at least or at most about 11,000 nucleobases, at least or at most about 12,000 nucleobases, at least or at most about 13,000 nucleobases, at least or at most about 14,000 nucleobases, at least or at most about 15,000 nucleobases, or at least or at most about 20,000 nucleobases.

[0144] In some cases, the second endogenous protein is a protein that has no effect on the expression of the target gene in the absence of the compound or in the formation of a ternary complex with the compound, but is recruited to the target gene and can regulate the expression of the target gene in the presence of the compound (for example, when it forms a ternary complex with the compound and the first endogenous protein). In some cases, the second endogenous protein is a transcriptional regulator, such as a transcription factor, a transcription activator, a transcription repressor and / or an epigenetic regulator and / or a signaling intermediate, such as, but not limited to, a kinase or a phosphatase, as described herein. In some cases, the second endogenous protein can be a cofactor of a transcriptional regulator, such as a component of an auxiliary transcriptional regulator of a mediator complex. An epigenetic regulator can be a protein or domain that causes epigenetic modification of DNA (for example, chromosomal DNA). Epigenetic modification can include, but is not limited to, DNA methylation and demethylation; histone modification, including methylation and demethylation (for example, monomethylation, dimethylation, trimethylation), histone acetylation and deacetylation, and histone ubiquitination, phosphorylation, and SUMOylation.

[0145] In some cases, the compound can include a first portion that is linked (e.g., covalently) to a second portion, wherein: (i) the first portion exhibits specific binding to a first endogenous protein that binds to a target gene or a region near the target gene (e.g., a promoter, a regulatory region, etc.); and (ii) the second portion exhibits specific binding to a second endogenous protein that is different from the first endogenous protein.

[0146] In some cases, in the absence of a compound or in the absence of a ternary complex, the second endogenous protein can regulate the expression or activity level of another target gene different from the target gene of the first endogenous protein. Compound (e.g., CIP or TCIP) is applied to cells to recruit a second endogenous protein to form a ternary complex comprising the compound, the first endogenous protein, and the second endogenous protein, which can be combined with the target gene of the first endogenous protein and regulate the expression and / or activity level of the target gene, as mentioned above. The administration of the compound can also regulate the expression of another target gene. For example, the second endogenous protein is recruited away from another target gene (of the second endogenous protein) and recruited to the ternary complex to reduce the presence (e.g., amount, concentration, probability) of the second endogenous protein at another target gene or adjacent to another target gene, thereby destroying the regulatory effect of the second endogenous protein on the expression or activity level of another target gene. In this example, the second endogenous protein can be recruited to the target gene away from another target gene and can regulate the expression of the target gene. In yet another example, a complex can also be formed at or adjacent to an additional target gene to recruit the first endogenous protein to the additional target gene, and the first endogenous protein can modulate the expression or activity level of the additional target gene (e.g., partially or completely reverse the effect of the second endogenous protein on the additional target gene before the complex is formed). For example, the second endogenous protein can reduce (e.g., inhibit) the expression or activity level of the additional target gene in the absence of the compound, and in the presence of the compound (and formation of a complex), the expression or activity level of the additional target gene can be increased (e.g., because the second endogenous protein has been recruited away from the additional target gene); at the same time, the expression of the target gene can now be regulated by the second endogenous protein as part of the complex. Alternatively, treatment with the compound (e.g., CIP) and the resulting formation of a complex may not or need not affect the regulation of the expression or activity level of the additional target gene of the second endogenous protein.

[0147] In some cases, the second endogenous protein may not be configured to regulate the expression or activity level of any target gene in the absence of the compound.

[0148] Further provided herein are compounds suitable for performing the methods provided herein.

[0149] In various aspects, provided are compounds of formula (I) or compounds of formula (II):

[0150] A-Linker-B (I); or

[0151] AB (II)

[0152] in:

[0153] (a) A is a first portion, which exhibits specific binding to a first endogenous protein in a cell, wherein the first endogenous protein binds to a target gene or a region near the target gene (e.g., a promoter, a regulatory region);

[0154] (b) B is a second portion that exhibits specific binding to a second endogenous protein in the cell, the second endogenous protein being different from the first endogenous protein; and

[0155] (c) the compound causes the first endogenous protein and the second endogenous protein to sterically complex with each other, thereby producing a gain of function in the cell,

[0156] Wherein the gain of function is characterized in that: the expression of the target gene is regulated in a manner that is dependent on the presence of the second endogenous protein that binds to the compound. In some cases, the gain of function is achieved by utilizing less than about 50% of the amount of the second endogenous protein present in the cell. In some cases, the compound mediates gain of function at an EC50 of less than about 1 micromolar. In some cases, the first endogenous protein reduces the expression of the target gene in the absence of the compound, and the second endogenous protein enhances the expression of another target gene in the absence of the compound, wherein the gain of function is characterized in that: (iii (a)) the expression of the target gene is enhanced compared to the expression in the absence of the compound, and (iii (b)) the expression of the other target gene is reduced compared to the expression in the absence of the compound. In some cases, the expression of the target gene is regulated in less than or equal to about 16 hours.

[0157] In some cases, the linker is any linker described herein. In some cases, no linker is present, such that moiety A and moiety B are directly linked to each other (eg, compounds of formula (II)).

[0158] The terms "specific binding," "specifically binds," and the like refer to the ability of a first or second ligand or moiety to preferentially bind directly to its corresponding first endogenous protein and second endogenous protein relative to other molecules or moieties in the cell. In certain embodiments, the affinity of a given ligand or moiety and its corresponding endogenous protein when they specifically bind to each other in a binding complex is characterized by a KD (dissociation constant) of 10 -5 M or smaller, 10 -6 M or smaller, 10 -7 M or smaller, 10 -8 M or smaller, 10 -9 M or smaller, 10 -10 M or smaller, 10 -11 M or smaller, 10 -12 M or smaller, 10 -13M or smaller, 10 -14 M or smaller or 10 -15 M or less (it should be noted that in certain embodiments, these values ​​can be applied to other specific binding pair interactions mentioned elsewhere in this description). The first portion, second portion, and linker that can be used in embodiments of the present disclosure are described in more detail below. When provided in a cell, for example, by contacting the cell with a compound (e.g., CIP), the first endogenous protein and the second endogenous protein are spatially paired with each other (e.g., spatially complexed) by the compound, thereby producing a gain of function in the cell, for example, as described in more detail below.

[0159] The compounds provided herein (e.g., chemical proximity inducers or "CIPs") can bind to a variety of different proteins (e.g., a variety of different endogenous proteins) to allow the multiple different proteins to spatially complex (or form a complex with the multiple different proteins), thereby generating a gain of function in the cell that would otherwise not exist in the absence of the compound. As used herein, the term "gain of function" refers to a function that is achieved in the presence of a compound, which can result in the formation of a ternary complex formed between a first endogenous protein, a second endogenous protein, and a compound of the present disclosure (e.g., CIP), that would otherwise not be achieved in the absence of the compound. Gain of function is not achieved when the first endogenous protein or the second endogenous protein is not expressed in the cell, in which case a ternary complex cannot be formed. As used herein, a non-limiting example of gain of function is the use of a compound provided herein to recruit a second endogenous protein to a target gene, such that the second endogenous protein is able to regulate the expression of the target gene in the presence of the compound, a function that the second endogenous protein would not have in the absence of the compound. In some embodiments, the second endogenous protein has substantially no effect on the expression or activity level of the target gene. In some other embodiments, the second endogenous protein regulates the target gene in a manner opposite to that achieved by the compounds disclosed herein. In some other embodiments, the second endogenous protein can be an endogenous cancer driver, which is recruited to the target pro-apoptotic gene by forming a ternary complex between an endogenous cancer driver, a first endogenous protein bound to the target pro-apoptotic gene, and the compound, so that the expression of the pro-apoptotic gene is enhanced. The number of different proteins bound to form a ternary complex by the compound can be at least or at most about 2 different proteins, at least or at most about 3 different proteins, at least or at most about 4 different proteins, at least or at most about 5 different proteins, at least or at most about 6 different proteins, at least or at most about different 7 proteins, at least or at most about 8 different proteins, at least or at most about 9 different proteins, at least or at most about 10 different proteins, at least or at most about 15 different proteins, or at least or at most about 20 different proteins. The plurality of different proteins may be different proteins that exhibit different activities (eg, innate or natural activities) in a cell (such as, but not limited to, binding to and regulating different genes in the cell).

[0160] Conventional drug development involves identifying the target, and then constructing a method for inhibiting, degrading, removing the RNA or the gene encoding the target. The conventional method of this drug development then needs to remove the target to a great extent. In contrast, the function acquisition method described herein only uses a portion of the target to provide a new therapeutic function for the cell. Advantageously, the function acquisition described herein does not need to recruit all the second endogenous proteins present in the cell. In some instances, only a small portion of the second endogenous protein present in the cell needs to be recruited to the target gene to achieve function acquisition. Without wishing to be bound by any particular theory, compared with other conventional therapies that require large bioavailability or exposure to be effective, using a small amount of the second endogenous protein makes the subject composition more effective and the treatment window is larger. In some examples, gain of function can be achieved by recruiting to the target gene or utilizing less than or equal to about 50%, less than or equal to about 45%, less than or equal to about 40%, less than or equal to about 35%, less than or equal to about 30%, less than or equal to about 25%, less than or equal to about 20%, less than or equal to about 15%, less than or equal to about 10%, less than or equal to about 9%, less than or equal to about 8%, less than or equal to about 7%, less than or equal to about 6%, less than or equal to about 5%, less than or equal to about 4%, less than or equal to about 3%, less than or equal to about 2%, or less than or equal to about 1% of the amount of the second endogenous protein present in the cell (e.g., the target gene is regulated by the second endogenous protein in the presence of the compound, but not regulated by the second endogenous protein in the absence of the compound).

[0161] In some cases, gain of function can be achieved by recruiting to the target gene or utilizing less than or equal to about 50% of the amount of the second endogenous protein present in the cell (e.g., the target gene is regulated by the second endogenous protein in the presence of the compound, and in the absence of the compound, the target gene cannot be regulated by the second endogenous protein). In some cases, gain of function can be achieved by recruiting to the target gene or utilizing less than or equal to about 10% of the amount of the second endogenous protein present in the cell. In some instances, gain of function can be achieved by recruiting to the target gene or utilizing about 1% to about 30%, about 1% to about 20%, about 1% to about 15%, or about 1% to about 10% of the amount of the second endogenous protein present in the cell. In some cases, gain of function can be achieved by recruiting to the target gene or utilizing about 2% to about 20% of the amount of the second endogenous protein present in the cell. In some cases, gain of function can be achieved by recruiting to the target gene or utilizing about 2% to about 10% of the amount of the second endogenous protein present in the cell.

[0162] In some examples, the gain of function can be achieved by utilizing at least or at most about 1%, at least or at most about 2%, at least or at most about 3%, at least or at most about 4%, at least or at most about 5%, at least or at most about 6%, at least or at most about 7%, at least or at most about 8%, at least or at most about 9%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 25%, at least or at most about 30%, at least or at most about 35%, at least or at most about 40%, at least or at most about 45%, at least or at most about 50%, at least or at most about 55%, at least or at most about 60%, at least or at most about 65%, at least or at most about 70%, at least or at most about 75%, at least or at most about 80%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150%, at least or at most about 20%, at least or at most about 25%, at least or at most about 30%, at least or at most about 35%, at least or at most about 40%, at least or at most about 45%, at least or at most about 50%, at least or at most about 55%, at least or at most about 60%, at least or at most about 65%, at least or at most about or up to about 10%, about 2% to about 50%, about 2% to about 45%, about 2% to about 40%, about 2% to about 35%, about 2% to about 30%, about 1% to about 25%, about 1% to about 20%, about 1% to about 15%, about 1% to about 10%, about 2% to about 50%, about 2% to about 45%, about 2% to about 40%, about 2% to about 35%, about 2% to about 30%, about 2% to about 25%, about 2% to about 20%, about 1% to about 15%, or about 2% to about 10%.

[0163] The amount of the first endogenous protein and / or the second endogenous protein required to produce the gain of function provided herein can be determined by various methods, for example, chromatin immunoprecipitation (ChIP) sequencing, which can identify (i) the amount of the first endogenous protein that is spatially associated (e.g., bound) with the target gene of the second protein and / or (ii) the amount of the second protein that is spatially associated (e.g., bound) with the target gene of the first protein. This information can be used together with the total amount of the first endogenous protein and / or the second endogenous protein to determine the proportion (e.g., percentage) of the first endogenous protein and / or the second endogenous protein required to produce the gain of function.

[0164] The compounds provided herein (e.g., chemical proximity inducers or "CIPs") can bind to a plurality of different proteins (e.g., a plurality of different endogenous proteins) to spatially complex (or form a complex with) the plurality of different proteins, thereby producing a gain of function in a cell. Gain of function can be characterized by inducing or promoting a property in the cell that would not otherwise be achieved in the absence of the compound. Non-limiting examples of such properties in cells can include cell death (e.g., inducing cell death within up to about 5 days, up to about 4 days, up to about 3 days, up to about 2 days, up to about 1 day, up to about 18 hours, up to about 12 hours, up to about 8 hours, etc., after contacting the cells with the compound, compared to the absence of the compound), cell survival (enhancing cell survival for at least about 12 hours, at least about 18 hours, at least about 1 day, at least about 2 days, at least about 7 days, at least about 2 weeks, at least about 4 weeks, etc., after contacting the cells with the compound, compared to the absence of the compound), cell proliferation (enhancing cell proliferation by at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 2 ... The invention further provides the invention to enhance the expression or activity level of the target gene (compared to the situation in the absence of compound, by at least about 1%, at least about 5%, at least about 10%, at least about 20%, at least about 50%, at least about 100%, at least about 200%, at least about 400%, etc.), increase the expression or activity level of the target gene (compared to the situation in the absence of compound, by at least about 1%, at least about 5%, at least about 10%, at least about 20%, at least about 50%, at least about 100%, at least about 200%, at least about 400%, etc.), reduce the expression or activity level of the target gene (for example, compared to the situation in the absence of compound, by at least about 1%, at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90% or substantially about 100%).

[0165] In some cases, the compound may be present at less than or equal to about 10 micromolar, less than or equal to about 5 micromolar, less than or equal to about 2 micromolar, less than or equal to about 1 micromolar, less than or equal to about 900 nanomolar, less than or equal to about 800 nanomolar, less than or equal to about 700 nanomolar, less than or equal to about 600 nanomolar, less than or equal to about 500 nanomolar, less than or equal to about 400 nanomolar, less than or equal to about 300 nanomolar, less than or equal to about 200 nanomolar, less than or equal to about 100 nanomolar, less than or equal to about 90 nanomolar, less than or equal to about 80 nanomolar, less than or equal to about 70 nanomolar, less than or equal to about 60 nanomolar, less than or equal to about 50 nanomolar, less than or equal to about 40 nanomolar, less than or equal to about 3 ... The compound can mediate gain of function (e.g., for eliciting a property in a cell) at an EC50 of about 20 nanomolar, about 10 nanomolar or less, about 9 nanomolar or less, about 8 nanomolar or less, about 7 nanomolar or less, about 6 nanomolar or less, about 5 nanomolar or less, about 4 nanomolar or less, about 3 nanomolar or less, about 2 nanomolar or less, about 1 nanomolar or less, about 0.9 nanomolar or less, about 0.8 nanomolar or less, about 0.7 nanomolar or less, about 0.6 nanomolar or less, about 0.5 nanomolar or less, about 0.4 nanomolar or less, about 0.3 nanomolar or less, about 0.2 nanomolar or less, or about 0.1 nanomolar or less. In one example, the compound can mediate gain of function at an EC50 of about 1 micromolar or less. In another example, the compound can mediate gain of function at an EC50 of about 500 nanomolar or less. In another example, the compound can mediate gain of function at an EC50 of less than or equal to about 200 nanomolar. In another example, the compound can mediate gain of function at an EC50 of less than or equal to about 100 nanomolar. In another example, the compound can mediate gain of function at an EC50 of less than or equal to about 50 nanomolar. In another example, the compound can mediate gain of function at an EC50 of less than or equal to about 20 nanomolar. As used herein in the context of in vitro or in vivo assays, the term "EC50" generally refers to the concentration of a test portion (e.g., a compound as described herein, such as a small molecule) that induces a response (e.g., a desired response or target response) that is about 50% of the maximum response (i.e., halfway between the maximum response and the baseline in the absence of the test portion).

[0166] In some cases, the gain of function can be characterized by inhibiting a property of a cell as provided herein. Thus, the compound can be present at a concentration of less than or equal to about 10 micromolar, less than or equal to about 5 micromolar, less than or equal to about 2 micromolar, less than or equal to about 1 micromolar, less than or equal to about 900 nanomolar, less than or equal to about 800 nanomolar, less than or equal to about 700 nanomolar, less than or equal to about 600 nanomolar, less than or equal to about 500 nanomolar, less than or equal to about 400 nanomolar, less than or equal to about 300 nanomolar, less than or equal to about 200 nanomolar, less than or equal to about 100 nanomolar, less than or equal to about 90 nanomolar, less than or equal to about 80 nanomolar, less than or equal to about 70 nanomolar, less than or equal to about 60 nanomolar, less than or equal to about 50 nanomolar, less than or equal to about 40 nanomolar, less than or equal to about 30 nanomolar, less than or equal to about

[0015] In some embodiments, the present invention mediates a gain of function (e.g., for inhibiting a property of a cell) at an IC50 of less than or equal to about 20 nanomolar, less than or equal to about 10 nanomolar, less than or equal to about 9 nanomolar, less than or equal to about 8 nanomolar, less than or equal to about 7 nanomolar, less than or equal to about 6 nanomolar, less than or equal to about 5 nanomolar, less than or equal to about 4 nanomolar, less than or equal to about 3 nanomolar, less than or equal to about 2 nanomolar, less than or equal to about 1 nanomolar, less than or equal to about 0.9 nanomolar, less than or equal to about 0.8 nanomolar, less than or equal to about 0.7 nanomolar, less than or equal to about 0.6 nanomolar, less than or equal to about 0.5 nanomolar, less than or equal to about 0.4 nanomolar, less than or equal to about 0.3 nanomolar, less than or equal to about 0.2 nanomolar, or less than or equal to about 0.1 nanomolar. As used herein in the context of in vitro or in vivo assays, the term "IC50" generally refers to the concentration of a test moiety (e.g., a compound described herein, such as a small molecule) that reduces a response (e.g., a desired response or target response) to about 50% of the maximal response in the absence of the test moiety.

[0167] The compounds provided herein (e.g., chemical proximity inducers or "CIPs") can bind to a plurality of different proteins (e.g., a plurality of different endogenous proteins) to spatially complex (or form a complex with) the plurality of different proteins, thereby producing a gain of function in a cell. The gain of function can be characterized by modulation (e.g., enhancement or reduction) of the expression or activity level of a target gene by a second endogenous protein that, in the absence of the compound, does not substantially affect the expression or activity level of the target gene. In some cases, the gain of function can be characterized in that the expression or activity level of the target gene is enhanced by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150%, at least or at most about 200%, at least or at most about 300%, at least or at most about 400%, at least or at most about 500%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150%, at least or at most about 200%, at least or at most about 300%, at least or at most about 400%, at least or at most about 500%, at least or at most about 60 or up to about 90 times, at least or up to about 100 times, at least or up to about 110 times, at least or up to about 120 times, at least or up to about 130 times, at least or up to about 140 times, at least or up to about 150 times, at least or up to about 200 times, or at least or up to about 500 times.In some cases, the gain of function can be characterized by a decrease in the expression or activity level of the target gene by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150 ... or up to about 100% more, at least or at most about 0.1 times, at least or at most about 0.5 times, at least or at most about 1 times, at least or at most about 2 times, at least or at most about 3 times, at least or at most about 4 times, at least or at most about 5 times, at least or at most about 10 times, at least or at most about 15 times, at least or at most about 20 times, at least or at most about 30 times, at least or at most about 40 times, at least or at most about 50 times, at least or at most about 60 times, at least or at most about 70 times, at least or at most about 80 times, at least or at most about 90 times, or at least or at most about 100 times.

[0168] In some cases, the compound can include multiple different parts that exhibit specific binding to multiple different endogenous proteins. The multiple different endogenous proteins can include (i) a first endogenous protein that affects the reduced (or enhanced) expression of a first target gene; and (ii) a second endogenous protein that affects the enhanced (or reduced) expression of a second target gene. In such cases, the function gained by the compound can be characterized by: changing (e.g., reversing or inducing the effect on) the expression profile of the first target gene and / or the second target gene.

[0169] In some cases, the gain of function can be characterized by: (1) expression of the first target gene is enhanced by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150%, at least or at most about 200%, at least or at most about 300%, at least or at most about 400%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150%, at least or at most about 200%, at least or at most about 300%, at least or up to about 400%, at least or up to about 500%, at least or up to about 0.1 times, at least or up to about 0.5 times, at least or up to about 1 times, at least or up to about 2 times, at least or up to about 3 times, at least or up to about 4 times, at least or up to about 5 times, at least or up to about 10 times, at least or up to about 15 times, at least or up to about 20 times, at least or up to about 30 times, at least or up to about 40 times, at least or up to about 50 times, at least or up to about 60 times, at least or up to about 70 times, at least or up to about 80 times, at least or up to about 90 times, at least or up to about 100 times, at least or up to about 11 times. 0-fold, at least or at most about 120-fold, at least or at most about 130-fold, at least or at most about 140-fold, at least or at most about 150-fold, at least or at most about 200-fold, or at least or at most about 500-fold, and / or (2) expression of a second target gene is reduced by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or up to about 90%, at least or up to about 95%, substantially about 100%, at least or up to about 0.1 times, at least or up to about 0.5 times, at least or up to about 1 times, at least or up to about 2 times, at least or up to about 3 times, at least or up to about 4 times, at least or up to about 5 times, at least or up to about 10 times, at least or up to about 15 times, at least or up to about 20 times, at least or up to about 30 times, at least or up to about 40 times, at least or up to about 50 times, at least or up to about 60 times, at least or up to about 70 times, at least or up to about 80 times, at least or up to about 90 times, or at least or up to about 100 times.

[0170] Vice versa, a gain of function can be characterized in that: (1) expression of the first target gene is reduced by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 100%, at least or at most about 150%, at least or at most about 200%, at least or at most about 300%, at least or at most about 400%, at least or up to about 400%, at least or up to about 500%, at least or up to about 0.1 times, at least or up to about 0.5 times, at least or up to about 1 times, at least or up to about 2 times, at least or up to about 3 times, at least or up to about 4 times, at least or up to about 5 times, at least or up to about 10 times, at least or up to about 15 times, at least or up to about 20 times, at least or up to about 30 times, at least or up to about 40 times, at least or up to about 50 times, at least or up to about 60 times, at least or up to about 70 times, at least or up to about 80 times, at least or up to about 90 times, at least or up to about 100 times, at least or up to about 110 times. fold, at least or at most about 120-fold, at least or at most about 130-fold, at least or at most about 140-fold, at least or at most about 150-fold, at least or at most about 200-fold, or at least or at most about 500-fold, and / or (2) expression of the second target gene is enhanced by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or up to about 90%, at least or up to about 95%, substantially about 100%, at least or up to about 0.1 times, at least or up to about 0.5 times, at least or up to about 1 times, at least or up to about 2 times, at least or up to about 3 times, at least or up to about 4 times, at least or up to about 5 times, at least or up to about 10 times, at least or up to about 15 times, at least or up to about 20 times, at least or up to about 30 times, at least or up to about 40 times, at least or up to about 50 times, at least or up to about 60 times, at least or up to about 70 times, at least or up to about 80 times, at least or up to about 90 times, or at least or up to about 100 times.

[0171] In some cases, the gain-of-function achieved by the compositions, systems, and methods provided herein can be characterized by: modulating (e.g., increasing or decreasing) the expression or activity level of a target gene (e.g., by a second endogenous protein in the presence of a compound, wherein in the absence of the compound, the second endogenous protein has substantially no effect on the expression or activity level of the target gene). In some other cases, the second endogenous protein regulates the target gene in a manner opposite to that achieved by the compounds disclosed herein. In some cases, the expression or activity level of the target gene can be modulated (e.g., enhanced or decreased) within less than or equal to about 16 hours, less than or equal to about 15 hours, less than or equal to about 14 hours, less than or equal to about 13 hours, less than or equal to about 12 hours, less than or equal to about 11 hours, less than or equal to about 10 hours, less than or equal to about 9 hours, less than or equal to about 8 hours, less than or equal to about 7 hours, less than or equal to about 6 hours, less than or equal to about 5 hours, less than or equal to about 4 hours, less than or equal to about 3 hours, less than or equal to about 2 hours, or less than or equal to about 1 hour after the cell is contacted with the compound, compared to the absence of the compound. In one example, the expression or activity level of the target gene can be modulated (e.g., enhanced or decreased) within less than or equal to about 16 hours after the cell is contacted with the compound, compared to the absence of the compound. In another example, the expression or activity level of the target gene can be modulated (e.g., enhanced or decreased) within less than or equal to about 8 hours after the cell is contacted with the compound, compared to the absence of the compound.

[0172] Any modulation of the expression level of a target gene provided herein can be induced or observed (e.g., experimentally) in less than or equal to about 48 hours, less than or equal to about 42 hours, less than or equal to about 36 hours, less than or equal to about 30 hours, less than or equal to about 24 hours, less than or equal to about 18 hours, less than or equal to about 12 hours, less than or equal to about 10 hours, less than or equal to about 9 hours, less than or equal to about 8 hours, less than or equal to about 7 hours, less than or equal to about 6 hours, less than or equal to about 5 hours, less than or equal to about 4 hours, less than or equal to about 3 hours, less than or equal to about 2 hours, less than or equal to about 1 hour, less than or equal to about 45 minutes, less than or equal to about 30 minutes, less than or equal to about 20 minutes, less than or equal to about 15 minutes, or less than or equal to about 10 minutes.

[0173] The first endogenous protein, the second endogenous protein, or both can affect an activity in the cell or exhibit an activity in the cell in the absence and / or presence of the compound. Non-limiting examples of such activities can include one or more members selected from the group consisting of transcriptional activation activity, transcriptional repression activity, methyltransferase activity, demethylase activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity or glycosylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylation activity, deSUMOylation activity, ribosylation activity, deribosylation activity, myristoylation activity, remodeling activity, protease activity, oxidoreductase activity, transferase activity, hydrolase activity, lyase activity, isomerase activity, synthase activity, synthase activity, and / or demyristoylation activity. The first endogenous protein, the second endogenous protein, or both can exhibit this activity in the absence of a compound (e.g., a chemical proximity inducer or "CIP"). Alternatively, or in addition, the first endogenous protein, the second endogenous protein, or both can exhibit this activity in the presence of a compound. Upon binding to the compound, the first endogenous protein, the second endogenous protein, or both can exhibit at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 25%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 95%, or substantially about 100% of the activity of the first endogenous protein, the second endogenous protein, or both in the absence of the compound.

[0174] The first endogenous protein, the second endogenous protein, or both (e.g., forming a ternary complex with the compound) can be any protein of interest having any desired activity. Non-limiting examples of the first endogenous protein and / or the second endogenous protein can include secretory proteins, non-secretory proteins, chaperones, transposases, integrases, recombinases, resolvases, invertases, proteases, helicases, methyltransferases, demethylases, acetylases, deacetylases, phosphatases, kinases, nucleases, transcription repressors, transcription activators, transcription coactivators, transcription protein recruitment proteins, cellular uptake activity-related proteins, nucleic acid binding proteins, nucleic acid structuring proteins, signal peptides or proteins, nuclear proteins, cell plasticity or cytoplasmic proteins, membrane proteins (e.g., transmembrane proteins or intracellular membrane proteins), non-membrane proteins, any fragments thereof, any variants thereof, and any combinations thereof. In some cases, the first endogenous protein, the second endogenous protein, or both can be transcription factors, such as transcription repressors, transcription activators, and / or transcription coactivators. In some cases, the first endogenous protein, the second endogenous protein or both can be an epigenetic regulator showing enzymatic activity, and the epigenetic regulator causes epigenetic modification to a target gene (for example, DNA, such as chromosomal DNA). Epigenetic modification can include but is not limited to DNA methylation and demethylation; Histone modification, including methylation and demethylation (for example, monomethylation, dimethylation, trimethylation), histone acetylation and deacetylation, histone ubiquitination, histone phosphorylation and histone SUMOylation (histone sumoylation). In some cases, protein used herein can refer to all or part of (for example, fragmented part) of a protein or a protein in a functional domain of a protein. In some cases, protein (for example, the first endogenous protein and / or the second endogenous protein) is a non-viral protein (for example, a mammalian protein). Alternatively, protein (for example, the first endogenous protein and / or the second endogenous protein) can be a viral protein (for example, derived from a viral genome).

[0175] In some cases, the protein bound by the compound (e.g., the first endogenous protein and / or the second endogenous protein) is not a protease and / or does not affect the degradation of another protein. For example, the first endogenous protein and the second endogenous protein can be bound by the compound to form a ternary complex, and (i) the first endogenous protein in the ternary complex does not directly or indirectly induce the degradation of the second endogenous protein, and / or (ii) the second endogenous protein in the ternary complex does not directly or indirectly induce the degradation of the first endogenous protein. Alternatively, the first endogenous protein bound in the ternary complex can be a protease and / or can affect the degradation of the second endogenous protein in the same complex.

[0176] In some cases, the protein (e.g., the first endogenous protein and / or the second endogenous protein) that binds to the compounds provided herein can be a functional protein, e.g., that exhibits its innate or natural function (e.g., binding to a target gene, associating with a target gene, and / or regulating the expression of a target gene) prior to being complexed with the compound. Thus, upon complexing with the compound, at least a portion of this activity can be reduced (e.g., reduced by at least or at most about 1%, at least or at most about 2%, at least or at most about 5%, at least or at most about 10%, at least or at most about 15%, at least or at most about 20%, at least or at most about 25%, at least or at most about 30%, at least or at most about 40%, at least or at most about 50%, at least or at most about 60%, at least or at most about 70%, at least or at most about 80%, at least or at most about 90%, at least or at most about 95%, or substantially about 100%).

[0177] In some cases, the first endogenous protein provided herein can be, for example, an anchor transcription factor, and the second endogenous protein provided herein can be, for example, a transcriptional regulator. In such cases, the compound can be referred to as "TCIP".

[0178] In certain non-limiting embodiments, the first endogenous protein includes a BTB domain. The terms "BTB domain," "BR-C, ttk, and bab domains," "POZ domain," and "poxvirus and zinc finger domains" are used interchangeably herein and generally refer to domains (e.g., structural domains) of proteins that mediate protein multimerization (e.g., homodimerization, heterodimerization, etc.). Specific examples of such proteins are provided in greater detail below (e.g., see Table 3 for example proteins containing a BTB domain).

[0179] In certain non-limiting embodiments, the second endogenous protein can be varied. Examples of the second endogenous protein include, but are not limited to, BET proteins, such as BRD2, BRD3, BRD4, BRD5, BRD7, BRD9, and BRDT; intracellular receptors, hormone receptors, such as estrogen receptors, androgen receptors, kinases, phosphatases, and the like.

[0180] Part I and Part II (A and B)

[0181] The properties of the first and second parts of the CIP compound (also referred to herein as the first ligand and the second ligand) and the linker component (when used) can vary. In any given CIP compound, the first and second ligands are selected based on the properties of the corresponding first and second endogenous proteins to which the moieties are bound. Some non-limiting examples of corresponding anchors (e.g., first endogenous proteins) and transcriptional regulators (e.g., second endogenous proteins) and their corresponding ligands are provided below. Specificity for activity relative to a particular cell type can be provided by selecting the first and second ligands of the CIP, which can be configured to recruit the first and second endogenous proteins in a manner that provides the desired cell or condition specificity. For example, a CIP can be engineered to induce proximity of a first and second endogenous protein that is primarily present in a target cell of interest, such that the CIP exhibits highly selective activity against the cell. The selectivity of a given CIP can be described by the following formula:

[0182] (Selectivity of expression of the first endogenous protein) x (selectivity of expression of the second endogenous protein) x (genomic specificity of the first endogenous protein) = selectivity of the induced activity

[0183] Examples of first and second moieties that can be used in various CIPs (e.g., A and B in the compound formulae provided herein, also referred to as first and second ligands) are reviewed in more detail below. Suitable first and second moieties that can be used in CIPs according to embodiments of the present disclosure, as well as methods for identifying the first and second moieties, are also provided in PCT application serial number PCT / US2021 / 058231, disclosed as WO2022 / 098989, the disclosure of which is incorporated herein by reference.

[0184] Linker

[0185] As described above, the present disclosure provides a compound (e.g., CIP) having two ligands (e.g., a BCL-6 (B cell lymphoma 6) ligand and a second ligand (e.g., a BRD4 (bromodomain-containing 4) ligand, an ER ligand, an AR ligand, a CDK ligand, etc.) covalently bonded via a linker. When used, any convenient linker can be used to link the first ligand and the second ligand to each other. The linker of interest is one that provides a stable association of the first ligand and the second ligand in a manner that enables the first ligand and the second ligand to specifically bind to the corresponding endogenous factor in the cell. Since the linker stabilizes the association of the first ligand and the second ligand, the first ligand and the second ligand are able to bind to each other in the cell. The linkers may be provided to provide a stable association of the first ligand and the second ligand using any convenient binding (e.g., covalent or non-covalent), wherein in some instances, the linker component is covalently bound to both the first ligand and the second ligand. Linking schemes of interest include, but are not limited to, addition reactions, elimination reactions, substitution reactions, pericyclic reactions, photochemical reactions, redox reactions, free radical reactions, reactions occurring through carbene intermediates, metathesis reactions, and other types of bonding reactions. In some embodiments, the linker employs a reactive linking chemistry, such as one in which a reactive linker pair (e.g., consisting of a ligand and a moiety on the linker) is formed. Reactive linking chemistries provided include, but are not limited to, maleimide / thiol; thiol / thiol; pyridyldithiol / thiol; succinimidyl iodoacetic acid / thiol; N-succinimidyl ester (NHS ester), sulfodichlorophenol ester (SDP ester), or pentafluorophenyl ester (PFP ​​ester) / amine; disuccinimidyl ester / amine; imidoester / amine; hydrazine or amine / aldehyde, dialdehyde, or benzaldehyde; isocyanate / hydroxyl or amine; carbohydrate-periodate / hydrazine or amine; bis(aziridine) / aryl azide chemistry; pyridyldithiol / aryl azide chemistry; alkyne / azide; carboxyl-carbodiimide / amine; amine / sulfo-SMCC (sulfosuccinimidyl 4-[N-maleimidomethyl] ] cyclohexane-1-carboxylate) / thiol and amine / BMPH (N-[β-maleimidopropionic acid] hydrazine.TFA) / thiol; azide / triarylphosphine; nitrone / cyclooctyne; azide / tetrazine and formylbenzamide / hydrazino-nicotinamide. In certain embodiments, the linker employs a cycloaddition reaction, such as a [1+2]-cycloaddition, a [2+2]-cycloaddition, a [3+2]-cycloaddition, a [2+4]-cycloaddition, a [4+6]-cycloaddition, or a chelate reaction, including linkers that undergo a 1,3-dipolar cycloaddition (e.g., azide-alkyne Huisgen cycloaddition), a Diels-Alder reaction, a reverse electron demand Diels-Alder cycloaddition, an ene reaction, or a [2+2] photochemical cycloaddition reaction.In some embodiments, the linker can include an alkyl chain, an alkoxy chain, an alkenyl chain, or an alkynyl chain, wherein the number of carbon atoms in the chain can vary, and in some instances, ranges from 2 to 25, such as 5 to 20, wherein one or more carbon atoms are replaced by NH or CH3-N as a covalently bonded reactive functional group.

[0186] In some examples, the linker is selected from the group consisting of (where n refers to the total number of carbon or carbon substituent atoms that may be present, counted as k, m, and / or p):

[0187] In some examples, the linker is selected from the group consisting of (where n refers to the total number of carbon or carbon substituent atoms that may be present, counted as k, m, and / or p):

[0188] a) Cn alkyl chain L, including one or more carbon atoms substituted by NH or CH3-N

[0189] b) Cn alkoxy chains L, including those in which one or more carbon atoms are replaced by NH or CH3-N

[0190] c) Cn alkenyl or alkenyloxy chain L, including one or more carbon atoms substituted by NH or CH3-N

[0191] d) Cn alkynyl or alkynyloxy chain L, including one or more carbon atoms substituted by NH or CH3-N

[0192] e)L 1 -Ar-L 2 or L 1 -Het-L 2 , where L1 and L 2 It can be, for example, a bond of 1 to 10 atoms (which are carbon or optionally substituted nitrogen), an alkenyl, alkynyl, alkynyloxy, alkenyloxy, alkoxy or alkyl chain such as CH2N(H)CH2, CH2OCH2, C5H 10 OCH2, etc.; Ar is 6-membered optionally substituted aryl; and Het is 4- to 6-membered heterocycloalkyl or 9- to 10-membered spirobicyclic heterocycloalkyl or 3- to 6-membered optionally substituted heteroaryl.

[0193] In some embodiments, the linker comprises a C(1-16) alkyl chain. In some instances, the linker comprises a C(1-16) alkyl chain in which one or more methylene groups are replaced by NH or CH3-N. In some instances, the linker comprises a C(1-16) alkoxy chain. In some instances, the linker comprises a C(1-16) alkoxy chain in which one or more methylene groups are replaced by NH or CH3-N. In certain instances, the linker comprises L 1 -Ring-L 2 , L1 -Heterocyclic-L 2 , L 1 -Ar-L 2 or L 1 -Het-L 2 , where L 1 and L 2 can be a bond, alkenyl, alkynyl, alkynyloxy, alkenyloxy, alkoxy, or an alkyl chain, wherein:

[0194] Ring is C(3-8)cycloalkyl or substituted C(3-8)cycloalkyl;

[0195] Heterocycle is C(3-8)heterocycloalkyl or substituted C(3-8)heterocycloalkyl;

[0196] Ar is aryl or substituted aryl; and

[0197] Het is heteroaryl or substituted heteroaryl.

[0198] In certain embodiments, linker A is selected from:

[0199]

[0200]

[0201] wherein m, n and p are independently selected from 0 or an integer from 1-12.

[0202] Suitable linkers that may be used in embodiments of the present disclosure are further described in International Patent Publication Nos. WO2020219650 and WO2017185023, as well as U.S. Patent No. 10,532,103 and U.S. Patent Application Publication No. 20190111143; the disclosures of which are hereby incorporated by reference.

[0203] In some embodiments, the linker of interest includes the linker described in International Patent Publication No. WO2020 / 264499, the disclosure of which is incorporated herein by reference. For example, the linker can be selected from:

[0204]

[0205]

[0206]

[0207]

[0208]

[0209]

[0210]

[0211]

[0212]

[0213]

[0214]

[0215]

[0216]

[0217]

[0218]

[0219]

[0220]

[0221]

[0222]

[0223]

[0224]

[0225]

[0226]

[0227]

[0228]

[0229]

[0230]

[0231]

[0232]

[0233] In some embodiments, linkers suitable for use with the compounds of the present disclosure (e.g., CIP, TCIP) are provided in U.S. Publication No. 2019 / 0076540A1, which is incorporated herein by reference for its disclosure of such linkers.

[0234] In some embodiments, the linker of the compounds suitable for use in the present disclosure (e.g., CIP, TCIP) may include one or more members selected from the group consisting of:

[0235]

[0236]

[0237]

[0238] In some embodiments, the linker is selected from the group consisting of Formula LI, Formula LII, Formula LIII, Formula LIV, Formula LV, Formula LVI, and Formula LVII:

[0239]

[0240] in:

[0241] X 1 and X 2 are independently selected from a bond, NH, NR 25 , CH2, CHR 25 、C(R 25 )2, O and S;

[0242] R 20 、R 21 、R 22 、R 23 and R 24 independently selected from a bond, alkyl, -C(O)-, -C(O)O-, -OC(O)-, -C(O)alkyl, -C(O)Oalkyl, -C(S)-, -SO2-, -S(O)-, -C(S)-, -C(O)NH-, -NHC(O)-, -N(alkyl)C(O)-, -C(O)N(alkyl)-, -O-, -S-, -NH-, -N(alkyl)-, -CH(-OR 26 )-、-CH(-NHR 25 )-、-CH(-NH2)-、-CH(-NR 25 2)-、-C(-OR 26 )alkyl-, -C(-NHR 25 )alkyl-、-C(-NH2)alkyl-、-C(-NR 25 2) Alkyl-, -C(R 4 R 4)-、-alkyl(R 27 )-alkyl(R 28 )-、-C(R 27 R 28 )-、-P(O)(OR 26 )O-、-P(O)(OR 26 )-、-NHC(O)NH-、-N(R 25 )C(O)N(R 25 )-、-N(H)C(O)N(R 25 )-, polyethylene glycol, poly(lactic-co-glycolic acid), olefins, alkyl halides, alkoxy groups, and alkynes;

[0243] Or in addition to the above, R 20 、R 21 、R 22 、R 23 and R 24 It can also be independently selected from heteroarylalkyl, aryl, arylalkyl, heterocycle, aliphatic, heteroaliphatic, heteroaryl, polypropylene glycol, lactic acid, glycolic acid, carbocycle, or -O-(CH2) 1-12 -O-, -NH-(CH2) 1-12 -NH-, -NH-(CH2) 1-12 -O- or -O-(CH2) 1-12 -NH-, -S-(CH2) 1-12 -O-, -O-(CH2) 1-12 -S-, -S-(CH2) 1-12 -S-, -S-(CH2) 1-12 -NH-, -NH-(CH2) 1-12 -S- (and wherein 1-12 can independently be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12, and wherein one or more of CH2 or NH may be substituted by substitution with H as described herein for methyl, ethyl, cyclopropyl, F (if on carbon), etc., and optionally, heteroatoms, heteroalkyl, aryl, heteroaryl or cycloaliphatic groups are interspersed in the chain).

[0244] Some non-limiting examples include -O-CH(CH3)-CH(CH3)CH-O-, -O-CH2-CH(CH3)CH-O-, -O-CH(CH3)-CH2CH-O-, and the like.

[0245] R 20 、R 21 、R 22 、R 23 and R 24 Each of which is optionally replaced by one or more selected from R 101or alternatively substituted with a substituent as described herein;

[0246] R 25 is in each instance selected from: alkyl, -C(O)H, -C(O)OH, -C(O)alkyl, -C(O)Oalkyl, alkenyl, or alkynyl, or alternatively may be an aliphatic, heteroaliphatic, aryl, heteroaryl, or heterocycle;

[0247] R 26 is hydrogen, alkyl, silane, arylalkyl, heteroarylalkyl, alkene and alkyne; or in addition to these, may be selected from aryl, heteroaryl, heterocycle, aliphatic compound and heteroaliphatic compound;

[0248] R 27 and R 28 Independently selected from hydrogen, alkyl, amine, or together with the carbon atom to which it is attached, form C(O), C(S), C═CH2, C3-C6 spirocarbocycle or a 4-membered, 5-membered or 6-membered spiroheterocycle containing 1 or 2 heteroatoms selected from N and O, or form 1 or 2 carbon bridged rings;

[0249] R 101 is independently selected at each occurrence from hydrogen, alkyl, alkene, alkyne, haloalkyl, alkoxy, hydroxy, aryl, heteroaryl, heterocycle, arylalkyl, heteroarylalkyl, heterocycloalkyl, arylcation, heteroaryloxy, CN, -COOalkyl, COOH, NO2, F, Cl, Br, I, CF3, NH2, NHalkyl, N(alkyl)2, NR 25 R 25 、NHR 25 , aliphatic compounds, heteroaliphatic compounds and COR 4 ;and

[0250] R 4 is selected from hydrogen, alkyl, aliphatic, heteroaliphatic, aryl, heteroaryl, carbocycle, hydroxy, alkoxy, amine, -NHalkyl or -Nalkyl2.

[0251] In a further embodiment, the linker can be selected from the group consisting of: Formula LVIII, LIX and LX:

[0252]

[0253] wherein each variable is as defined in formula LI. In alternative embodiments of LVIII, LIX, and LX, a carbocycle is used in place of a heterocycle.

[0254] The following are non-limiting examples of linkers that can be used in the present disclosure. As some non-limiting examples, Formula LI, Formula LII, Formula LIII, Formula LIV, Formula LV, Formula LVI or Formula LVII include:

[0255]

[0256]

[0257]

[0258]

[0259]

[0260] In some embodiments, the linker can be selected from:

[0261]

[0262] In some embodiments, the linker can be selected from:

[0263]

[0264]

[0265] In some embodiments, X 1 Can be attached to the first and / or second moiety (of the compound of the present disclosure). In other embodiments, X 2 Can be attached to the first moiety and / or the second moiety (of the compound of the present disclosure).

[0266] Non-limiting examples of moieties for R20, R21, R22, R23, and R24 include:

[0267]

[0268] R 20 、R 21 、R 22 、R 23 and R 24 Additional non-limiting examples of portions include:

[0269]

[0270]

[0271]

[0272]

[0273] R20 、R 21 、R 22 、R 23 and R 24 Additional non-limiting examples of portions include:

[0274]

[0275]

[0276] In some embodiments, the linker group can be an optionally substituted (poly)ethylene glycol having at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10 ethylene glycol units or an optionally substituted alkyl group interspersed with optionally substituted O, N, S, P or Si atoms. In some embodiments, the linker can be flanked by, substituted by, or interspersed with aryl, phenyl, benzyl, alkyl, alkylene or heterocyclic groups. In some embodiments, the linker can be asymmetric or symmetric. In some embodiments, the linker can be a substituted or unsubstituted polyethylene glycol group ranging in size from about 1 to about 12 ethylene glycol units, 1 to about 10 ethylene glycol units, about 2 to about 6 ethylene glycol units, about 2 to about 5 ethylene glycol units, or about 2 to about 4 ethylene glycol units. In any of the embodiments of the compounds described herein, the linker group can be any suitable moiety described herein.

[0277] In some embodiments, the linker can be selected from:

[0278] -NR 61 (CH2) n1 -(lower alkyl)-, -NR 61 (CH2) n1 -(lower alkoxy)-, -NR 61 (CH2) n1 -(lower alkoxy)-OCH2-, -NR 61 (CH2) n1 -(lower alkoxy)-(lower alkyl)-OCH2-, -NR 61 (CH2) n1 -(cycloalkyl)-(lower alkyl)-OCH2-, -NR 61 (CH2) n1 -(heterocycloalkyl)-, -NR 61 (CH2CH2O) n1 -(lower alkyl)-O-CH2-, -NR 61 (CH2CH2O)n1 -(Heterocycloalkyl)-O-CH2-, -NR 61 (CH2CH2O) n1 -Aryl-O-CH2-, -NR 61 (CH2CH2O) n1 -(heteroaryl)-O-CH2-, -NR 61 (CH2CH2O) n1 -(cycloalkyl)-O-(heteroaryl)-O-CH2-, -NR 61 (CH2CH2O) n1 -(cycloalkyl)-O-aryl-O-CH2-, -NR 61 (CH2CH2O) n1 -(lower alkyl)-NH-aryl-O-CH2-, -NR 61 (CH2CH2O) n1 -(lower alkyl)-O-aryl-CH2, -NR 61 (CH2CH2O) n -cycloalkyl-O-aryl-, -NR 61 (CH2CH2O) n -cycloalkyl-O-heteroaryl-, -NR 61 (CH2CH2) n1 -(cycloalkyl)-O-(heterocycle)-CH2, -NR 61 (CH2CH2) n1 -(heterocycle)-(heterocycle)-CH2 and -NR 61 -(heterocyclic)-CH2;

[0279] wherein n1 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10; and

[0280] R 61 is H, methyl or ethyl.

[0281] In some embodiments, the linker can be selected from:

[0282] -N(R 61 )-(CH2) m1 -O(CH2) n2 -O(CH2) o1 -O(CH2) p1 -O(CH2) q1 -O(CH2) r1 -OCH2-;

[0283] -O-(CH2) m1 -O(CH2) n2 -O(CH2) o1-O(CH2) p1 -O(CH2) q1 -O(CH2) r1 -OCH2-;

[0284] -O-(CH2) m1 -O(CH2) n2 -O(CH2) o1 -O(CH2) p1 -O(CH2) q1 -O(CH2) r1 -O-;

[0285] -N(R 61 )-(CH2) m1 -O(CH2) n2 -O(CH2) o1 -O(CH2) p1 -O(CH2) q1 -O(CH2) r1 -O-;

[0286] -(CH2) m1 -O(CH2) n2 -O(CH2) o1 -O(CH2) p1 -O(CH2) q1 -O(CH2) r1 -O-;

[0287] -(CH2) m1 -O(CH2) n2 -O(CH2) o1 -O(CH2) p1 -O(CH2) q1 -O(CH2) r1 -OCH2-;

[0288] -O(CH2) m1 -O(CH2) n2 O(CH2) p1 O(CH2) q1 OCH2-; -O(CH2) m1 O(CH2) n2 O(CH2) p1 O(CH2) q1 OCH2-;

[0289] in

[0290] m1, n2, o1, p1, q1 and r1 are independently 1, 2, 3, 4 or 5; and

[0291] R61 is H, methyl or ethyl.

[0292] In some embodiments, the linker can be selected from:

[0293]

[0294]

[0295] wherein m1, n2, o1, p1, q2 and r1 are independently 1, 2, 3, 4 or 5.

[0296] In some embodiments, the linker can be selected from:

[0297]

[0298]

[0299]

[0300]

[0301]

[0302]

[0303]

[0304]

[0305]

[0306]

[0307]

[0308]

[0309]

[0310]

[0311]

[0312]

[0313]

[0314]

[0315]

[0316]

[0317]

[0318]

[0319]

[0320]

[0321]

[0322]

[0323]

[0324] where R 71 It is -O-, -NH, -NMe, -N alkyl, N(aliphatic compound), -N(heteroaliphatic compound).

[0325] In some embodiments, the linker can be a non-linear chain and can be or can include an aliphatic or aromatic or heteroaromatic ring moiety.

[0326] In some embodiments, the linker can include continuous, partially continuous, or non-continuous ethylene glycol unit groups ranging in size from about 1 to about 12 ethylene glycol units, about 1 to about 10 ethylene glycol units, about 2 to about 6 ethylene glycol units, about 2 to about 5 ethylene glycol units, about 2 to about 4 ethylene glycol units (e.g., 1, 2, 3, 4, 6, 6, 7, 8, 9, 10, 11, or 12 ethylene glycol units).

[0327] In some embodiments, the linker can have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or fluorine substituents. In another embodiment, the linker can be perfluorinated. In yet another embodiment, the linker can be a partially or fully fluorinated polyether. Non-limiting examples of fluorinated linkers include:

[0328]

[0329] Providing a compound of the present disclosure (e.g., TCIP) in a cell

[0330] The present disclosure provides methods for providing a compound of the present disclosure (e.g., TCIP or CIP) to a cell (e.g., as described above) in a manner sufficient to induce proximity of a first endogenous protein and a second endogenous protein (e.g., as described above). Any convenient protocol for providing the CIP compound to the cell can be employed. The specific protocol employed can vary, for example, depending on whether the target cell is in vitro or in vivo. In certain instances, the CIP compound is provided to the cell by contacting the cell with the CIP compound. For in vitro protocols, contacting the CIP compound with the target cell can be achieved using any convenient protocol. For example, the target cell can be maintained in a suitable culture medium and introduced into the CIP compound in the culture medium as specifically described in the figure.

[0331] For in vivo protocols, any convenient administration protocol can be adopted. Depending on the binding affinity of the CIP compound, the desired response, mode of administration, half-life, the number of cells present, various protocols can be adopted. Therefore, CIP can be incorporated into various preparations, for example, a pharmaceutically acceptable vehicle (also referred to herein as a drug delivery vehicle or carrier) for therapeutic administration. More specifically, the CIP of the present disclosure can be formulated as a pharmaceutical composition to be administered intravenously over a period of several days or weeks. This can be accomplished by combining with an appropriate pharmaceutically acceptable vehicle or diluent, and can be formulated into preparations in solid, semisolid, liquid or gaseous form, such as tablets, capsules, powders, granules, ointments (e.g., skin emulsions), solutions, suppositories, injections, inhalants, and aerosols. Therefore, the administration of a medicament (e.g., a compound of the present disclosure) can be achieved in various ways, including oral, buccal, rectal, parenteral, intraperitoneal, intradermal, transdermal, intratracheal, intravenous, intravesical, subcutaneous, intramuscular administration. In terms of pharmaceutical dosage forms, CIP can be administered alone or in combination with other pharmaceutically active compounds as appropriate. The following examples are illustrative and not limiting. In some cases, the compounds of the present disclosure can be formulated and / or administered in such a manner that they can cross the blood-brain barrier.

[0332] For oral preparations, the pharmaceutical agent (e.g., a compound of the present disclosure) can be used alone or in combination with appropriate additives to prepare tablets, powders, granules, or capsules, for example, with conventional additives (such as lactose, mannitol, corn starch, or potato starch); with binders (such as crystalline cellulose, cellulose derivatives, gum arabic, corn starch, or gelatin); with disintegrants (such as corn starch, potato starch, or sodium carboxymethylcellulose); with lubricants (such as talc or magnesium stearate); and, if desired, with diluents, buffers, wetting agents, preservatives, and flavorings.

[0333] The pharmaceutical agent (e.g., the compound of the present disclosure) can be formulated into a preparation for injection by dissolving, suspending or emulsifying the pharmaceutical agent in an aqueous or non-aqueous solvent (such as vegetable oil or other similar oils, synthetic fatty acid glycerides, esters of higher fatty acids or propylene glycol); and if desired, using conventional additives such as solubilizers, isotonic agents, suspending agents, emulsifiers, stabilizers and preservatives.

[0334] Medicaments (e.g., compounds of the present disclosure) can be used in aerosol formulations to be administered by inhalation. Compounds of the present disclosure can be formulated into pressurized acceptable propellants such as dichlorodifluoromethane, propane, nitrogen, and the like.

[0335] In addition, the medicament (e.g., compound of the present disclosure) can be made into a suppository by mixing with a variety of bases such as emulsifying bases or water-soluble bases. The compound of the present disclosure can be administered rectally via a suppository. Suppositories can include vehicles such as cocoa butter, carbowax, and polyethylene glycol, which melt at body temperature but solidify at room temperature.

[0336] Unit dosage forms for oral or rectal administration, such as syrups, elixirs, and suspensions, can be provided, wherein each dosage unit (e.g., teaspoonful, tablespoonful, tablet, or suppository) contains a predetermined amount of a composition comprising one or more inhibitors. Similarly, unit dosage forms for injection or intravenous administration may contain the inhibitor in a composition as a solution in sterile water, normal saline, or another pharmaceutically acceptable carrier.

[0337] As used herein, the term "unit dosage form" refers to physically discrete units suitable as unit dosages for human and animal subjects, each unit containing a predetermined quantity of a compound of the present disclosure sufficient to produce the desired effect in association with a pharmaceutically acceptable diluent, carrier, or vehicle. The specifications for the novel unit dosage forms of the present disclosure depend on the specific compound employed and the effect to be achieved, as well as the pharmacodynamics associated with each compound in the host.

[0338] Pharmaceutically acceptable excipients such as vehicles, adjuvants, carriers or diluents are readily available to the public. In addition, pharmaceutically acceptable auxiliary substances such as pH adjusting agents and buffers, tonicity adjusting agents, stabilizers, wetting agents are readily available to the public.

[0339] Those skilled in the art will readily appreciate that dosage levels may vary depending on the function of the specific compound, the nature of the delivery vehicle, etc. Preferred dosages for a given compound can be readily determined by those skilled in the art in a variety of ways.

[0340] In those embodiments where an effective amount of an active agent (e.g., a compound of the present disclosure) is administered to a living subject, the amount or dose is effective when administered for a suitable period of time (e.g., one week or longer, including two weeks or longer, such as three weeks or longer, four weeks or longer, eight weeks or longer, etc.) to demonstrate the desired therapeutic effect. For example, an effective dose is a dose that will produce the desired therapeutic effect when administered for a suitable period of time (e.g., a period of at least about one week, and possibly about two weeks or longer, up to about three weeks, four weeks, eight weeks or longer). In some instances, an effective amount or dose of an active agent (e.g., a compound of the present disclosure) will not only slow or stop the progression of a disease condition, but will also induce reversal of the condition, i.e., cause an improvement in one or more symptoms of the condition. For example, in some instances, an effective amount is one that will improve one or more symptoms in a subject suffering from a disease condition when administered for a suitable period of time (generally at least about one week and can be for a period of about two weeks or longer, up to about 3 weeks, 4 weeks, 8 weeks or longer), wherein in some instances, the magnitude of the improvement (e.g., as measured using a suitable regimen with a relevant control) can vary, for example, by 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold or more.

[0341] In certain embodiments, the method comprises removing the CIP from the cells at some point after providing the CIP. Removal of the CIP from the cells can be accomplished using any convenient protocol, for example, by removing the CIP from the culture medium in which the cells are present, by ceasing administration of the CIP to an animal containing the cells, by contacting the cells with a proximity inhibitor of CIP induction, by contacting the cells with a molecule that displaces the CIP and binds to only one of the first endogenous protein or the second endogenous protein, etc. A specific type of inhibitor of CIP action would be a one-sided molecule consisting of a ligand for the first endogenous protein or the second endogenous protein without a linker or other moiety.

[0342] As summarized above, the present disclosure further provides a method for inducibly regulating the transcription of a target gene. In a non-limiting example, the target gene is a pro-apoptotic gene. As described above, a pro-apoptotic gene is a gene whose expression product promotes or causes apoptosis (i.e., programmed cell death occurring in multicellular organisms), which can be characterized by: various cellular changes, such as blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal DNA fragmentation, overall mRNA decay and death. Specific pro-apoptotic genes of interest for transcription that can be enhanced in embodiments of the present disclosure include, but are not limited to: PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA, etc. In such examples, the magnitude of the enhancement can vary, in which case examples include from substantially no expression to certain expression, and in some instances, the magnitude can be 2 times or greater, such as 5 times or greater, including 10 times or greater. In another non-limiting example, the target gene is a survival factor (eg, BCL-2, BCLX, and other factors that promote cell proliferation), and the expression of the survival factor can be reduced using the compositions, systems, and methods provided herein.

[0343] In some examples, the cell is a malignant cell, for example, a cell of a subject having a malignant condition (such as cancer), i.e., a cell obtained from such a subject or a cell as part of such a subject. For example, the cell can be a cell having elevated levels of BCL6 (or another BTB domain-containing protein) and normal or higher levels of other factors (e.g., ER, BRD4, target CDK (e.g., CDK9, CDK8 and / or CDK7), AR, etc.), such as a malignant / cancer cell, such as, but not limited to, a lung cancer cell (e.g., SCLC) or a lymphoma cell (e.g., DCBCL) cell, a prostate cancer cell, a leukemia cell, a breast cancer cell, etc.

[0344] As summarized above, the present disclosure further provides a method for inductively regulating the transcription of a target gene. Such methods are included under conditions sufficient to regulate the transcription of the target gene, and provide a chemical proximity inducer (CIP) to a cell (e.g., eukaryotic cell) containing the first endogenous protein and the second endogenous protein, for example, as described above. CIP and cells can be as described above. Transcriptional regulation can vary. In some instances, regulation includes enhancing the transcription of a gene, for example, when a gene is beneficial to a disease condition, for example, by enhancing the activity of the expectation in the cell, such as increasing the expression of a pro-apoptotic gene when the desired cell death is desired, increasing the expression of a gene beneficial in the treatment of a given disease condition, etc., in the case where the product of the increased amount of this gene is beneficial to a given disease condition. In such instances, the magnitude of the enhancement can vary, in which case, examples include from substantially no expression to certain expression, and in some instances, magnitude can be 2 times or greater, such as 5 times or greater, including 10 times or greater. In some instances, regulation includes reducing the transcription of a target gene, for example, when a gene is harmful, such as c-myc or a triple-expanded gene, for example, such as Huntington's disease, etc. In such instances, the amount of reduction can vary, in which case examples include from some expression to essentially no expression (if any), and in some instances the amount of reduction can be 2-fold or greater, such as 5-fold or greater, including 10-fold or greater.

[0345] In some examples, the cell is a cell of a subject suffering from, diagnosed as suffering from, having, or suspected of having a disease condition, i.e., a cell obtained from such a subject or a cell that is part of such a subject. The disease condition that a subject may have, may be diagnosed as having, may have, or may be suspected of having can vary, in which case examples of such disease conditions include, but are not limited to, neoplastic disease conditions, such as cancer; neurological conditions, neurodevelopmental disorders, immune disorders, gastrointestinal diseases, cardiovascular diseases, etc.

[0346] The compositions, systems and methods of the present disclosure can be used to treat various different conditions in which it is desired to regulate the transcription of a target gene in a host. "Treatment" means at least achieving an improvement in one or more of the symptoms associated with the condition of illness that plagues the host (e.g., symptoms associated with the condition of illness being treated), wherein improvement is broadly used to refer to at least a decrease in the magnitude of a parameter. Thus, treatment also includes a situation in which a pathological condition or at least a symptom associated therewith is completely suppressed (e.g., prevented from occurring) or stopped (e.g., terminated) such that the host no longer suffers from the condition of illness or at least no longer suffers from the symptoms that characterize the condition of illness.

[0347] Where the method is a method of treating a condition in a subject, the method may further comprise assessing the subject for the given condition, e.g., to confirm that the given CIP is suitable for treating the condition in the subject. Any convenient diagnostic protocol suitable for the given condition may be employed, in which case the choice of such protocol will necessarily depend on the specific condition to be treated.

[0348] Non-limiting examples of conditions or diseases of subjects (e.g., patients) that can be treated or improved by the compositions, systems, and methods of the present disclosure may include multiple sclerosis, various malignancies, ciliopathies, cleft palate, diabetes, heart disease, hypertension, inflammatory bowel disease, mental retardation, mood disorders, obesity, refractive errors, infertility, Angelman syndrome, Canavan disease, celiac disease, Shillero-Marus, and other inflammatory bowel diseases. Figure 3 Charcot-Marie-Tooth disease, cystic fibrosis, Duchenne muscular dystrophy, hemochromatosis, hemophilia, Klinefelter's syndrome, neurofibromatosis, phenylketonuria, polycystic kidney disease, (PKD1) or 4 (PKD2), Prader-Willi syndrome, sickle cell disease, Tay-Sachs disease, and Turner syndrome.

[0349] Additional non-limiting examples of such conditions or diseases can include conditions or diseases caused by microbial agents or other exogenous agents such as viruses, bacteria, fungi, protozoa, or other microorganisms.

[0350] In some cases, the condition or disease of the subject can be cancer. Non-limiting examples of cancer can include adrenocortical carcinoma, AIDS-related cancers (e.g., Kaposi's sarcoma, lymphoma, etc.), anal cancer, appendix cancer, astrocytoma, atypical teratoma / rhabdoid tumor, basal cell carcinoma, bile duct cancer (extrahepatic bile duct cancer and intrahepatic bile duct cancer), bladder cancer, bone cancer (e.g., Ewing's sarcoma, osteosarcoma and malignant fibrous histiocytoma, etc.), brain stem glioma, brain tumor (e.g., astrocytoma, central nervous system embryonal tumor, central nervous system germ cell tumor, craniopharyngioma, ependymoma, etc.), breast cancer (e.g., female breast cancer, male breast cancer, childhood breast cancer, etc.), bronchial tumor, carcinoid tumor (e.g., childhood carcinoid tumor, gastrointestinal carcinoid tumor, etc.), carcinoma of unknown primary site (Carcinoma ofUnknown Primary), Cardiac / Heart tumors, Central nervous system (e.g., atypical teratoma / rhabdoid tumor, embryonal tumor, germ cell tumor, lymphoma, etc.), Cervical cancer, Childhood cancer, Chordoma, Colon cancer, Colorectal cancer, Craniopharyngioma, Ductal carcinoma in situ (DCIS), Embryonic tumor, Endometrial cancer, Ependymoma, Esophageal cancer, Olfactory neuroblastoma, Ewing's sarcoma, Extracranial germ cell tumor, Extragonadal germ cell tumor, Extrahepatic bile duct cancer, Eye cancer (e.g., intraocular melanoma, retinoblastoma, etc.), Fibrous histiocytoma of bone (e.g., malignant fibrous histiocytoma of bone, osteosarcoma, etc.), Gallbladder cancer, gastric (Gastric / Stomach) cancer, gastrointestinal carcinoid, gastrointestinal stromal tumor (GIST), germ cell tumor (e.g., extracranial germ cell tumor, extragonadal germ cell tumor, ovarian germ cell tumor, testicular germ cell tumor, etc.), gestational trophoblastic disease, glioma, head and neck cancer, heart cancer, hepatocellular (liver) cancer, histiocytosis (e.g., Langerhans cell histiocytosis, etc.), hypopharyngeal cancer, intraocular melanoma, islet cell tumor (e.g., pancreatic neuroendocrine tumor, etc.), Kaposi's sarcoma, kidney cancer (e.g., renal cell carcinoma, Wilms tumor, pediatric kidney tumor, etc.), Langerhans cell histiocytosis, laryngeal cancer, leukemia (e.g.,Acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), nonleukemic leukemia, acute nonlymphocytic leukemia, acute monocytic leukemia, acute granulocytic leukemia, acute promyelocytic leukemia, chronic lymphocytic leukemia (CLL), chronic myeloid leukemia (CML), chronic myeloid leukemia, adult T-cell leukemia, basophilic leukemia, eosinophilic leukemia, histiocytic leukemia, mast cell leukemia, megakaryocyte leukemia, blast cell leukemia, leukemia cutis, hairy cell leukemia, stem cell leukemia, leukopenic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphoblastic leukemia, lymphoid leukemia Leukemia), lymphosarcoma cell leukemia, monocytic leukemia, myeloblastic leukemia, myeloid leukemia, plasma cell leukemia, multiple myeloma, plasma cell leukemia, promyelocytic leukemia), lip and oral cancer, liver cancer (primary liver cancer), lobular carcinoma in situ (LCIS), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer, etc.), lymphoma (non-Hodgkin lymphoma or Hodgkin's lymphoma): e.g., small lymphocytic lymphoma, mantle cell lymphoma, follicular lymphoma, marginal zone lymphoma, extranodal (MALT) lymphoma, nodal (monocytic B cell) lymphoma, T cell lymphoma, splenic lymphoma, diffuse large cell B cell lymphoma, Burkitt's lymphoma Lymphoma), lymphoblastic lymphoma, immunoblastic large cell lymphoma or precursor B lymphoblastic lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, anaplastic large cell lymphoma, mycosis fungoides, primary central nervous system (CNS) lymphoma, and precursor T-lymphoblastic lymphoma), macroglobulinemia (eg, Waldenstrom, macroglobulinemia, etc.), male breast cancer, malignant fibrous histiocytoma of bone and osteosarcoma, melanoma, Merkel cell carcinoma, mesothelioma, metastatic squamous neck cancer with occult primary, midline tract cancer involving the NUT gene, oral cancer, multiple endocrine neoplasia syndrome, multiple myeloma / plasma cell neoplasms, myelodysplastic syndrome, myelodysplasia / myeloproliferative neoplasms, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, non-small cell lung cancer, oral cancer, Cancer (e.g., lip cancer, etc.), oropharyngeal cancer, osteosarcoma and malignant fibrous histiocytoma of bone, ovarian cancer (e.g., epithelial cancer, germ cell tumor, low malignant potential tumor, etc.), pancreatic cancer, pancreatic neuroendocrine tumor (islet cell tumor), papillomatosis, paraganglioma, paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pituitary tumor, pleuropulmonary blastoma, prostate cancer, rectal cancer, renal cell (kidney) cancer, renal pelvis and ureter, transitional cell cancer, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, sarcoma (e.g., Ewing's sarcoma, Kaposi's sarcoma, osteosarcoma, rhabdomyosarcoma, soft tissue sarcoma, uterine sarcoma, etc.), Sézary syndrome Syndrome), skin cancer (e.g., childhood skin cancer, melanoma, Merkel cell carcinoma, non-melanoma, etc.), small cell lung cancer, small intestinal cancer, soft tissue sarcoma, squamous cell carcinoma, squamous neck cancer (e.g., squamous neck cancer with occult primary, metastatic squamous neck cancer, etc.), stomach (Stomach / Gastric) cancer, testicular cancer, laryngeal cancer, thymoma and thymic cancer, thyroid cancer, transitional cell carcinoma of the renal pelvis and ureter, ureter and renal pelvis cancer, urethral cancer, uterine cancer (e.g., endometrial cancer, etc.), uterine sarcoma, vaginal cancer, vulvar cancer, Waldenstrom's macroglobulinemia, Wilm's tumor, etc.Cancers that may further be treated include epithelial cancers, such as carcinomas, e.g., acinar carcinoma, acinar cell carcinoma, acinar carcinoma, glandular cystic carcinoma, adenoid cystic carcinoma, adenosquamous carcinoma, adnexal carcinoma, adrenocortical carcinoma, alveolar carcinoma, ameloblastic carcinoma, apocrine carcinoma, basal cell carcinoma, bronchioloalveolar carcinoma, bronchogenic carcinoma, cholangiocellular carcinoma, choriocarcinoma, clear cell carcinoma, colloid carcinoma, cribriform carcinoma, ductal carcinoma in situ, embryonal carcinoma, carcinoma en cuirasse, endometrioid carcinoma, epidermoid carcinoma, carcinoma ex mixed tumor, carcinoma ex pleomorphic adenoma, follicular thyroid carcinoma, hepatocellular carcinoma, carcinoma in situ, intraductal carcinoma, Hürthle cell carcinoma, carcinoma), inflammatory breast cancer, large cell carcinoma, invasive lobular carcinoma, lobular carcinoma, lobular carcinoma in situ (LCIS), medullary carcinoma, meningeal carcinoma, Merkel cell carcinoma, mucinous carcinoma, mucoepidermoid carcinoma, nasopharyngeal carcinoma, non-small cell carcinoma, non-small cell lung cancer (NSCLC), oat cell carcinoma, papillary carcinoma, renal cell carcinoma, scirrhous carcinoma, sebaceous carcinoma, simple carcinoma, signet ring cell carcinoma, small cell carcinoma, small cell lung cancer, spindle cell carcinoma, squamous cell carcinoma, terminal duct carcinoma, transitional cell carcinoma, tubular carcinoma, verrucous carcinoma, etc.

[0351] Various subjects can be treated according to the subject methods. In some instances, the subject is a "mammal" or "mammal-like," wherein these terms are broadly used to describe organisms within the class Mammalia, including carnivores (e.g., dogs and cats), rodents (e.g., mice, guinea pigs, and rats), and primates (e.g., humans, chimpanzees, and monkeys). In some instances, the subject is a human.

[0352] Chemical proximity inducers and the treatment of malignant diseases

[0353] In various aspects, the compositions, systems and methods provided herein are particularly useful for treating malignancies (eg, cancer). In some aspects of the present disclosure, the compositions, systems and methods are used to treat malignancies (eg, cancer).

[0354] Malignancy is a term for diseases in which abnormal cells divide uncontrollably and can invade nearby tissues. Malignant cells can also spread to other parts of the body through the blood and lymphatic systems. There are several main types of malignancies. Carcinomas are malignancies that begin in the skin or tissues lining or covering internal organs. Sarcomas are malignancies that begin in bone, cartilage, fat, muscle, blood vessels, or other connective or supporting tissues. Leukemias are malignancies that begin in blood-forming tissues such as the bone marrow and cause the production of too many abnormal blood cells. Lymphomas and multiple myeloma are malignancies that begin in cells of the immune system. Central nervous system cancers are malignancies that begin in the tissues of the brain and spinal cord.

[0355] Lung cancer is the leading cause of cancer death worldwide, with 2.2 million new cases and 1.8 million deaths in 2020 alone (Sung et al., CA Cancer J. Clin. (2021) 71: 209-249). Although pharmacological and surgical advances have improved the survival of most subtypes of lung cancer, small cell lung cancer (SCLC) remains the most lethal, with a median survival of less than 2 years after diagnosis in the case of early identification, and a median survival of about 1 year for patients with metastatic disease (Rudin et al., Nat. Rev. Dis. Primers (2021) 7: 3). Therefore, new therapeutic agents for SCLC patients are urgently needed.

[0356] SCLC is a high-grade neuroendocrine cancer that accounts for 15% of all lung cancer cases, which is close to 250,000 new cases and 200,000 deaths worldwide each year. About 98% of patients with SCLC have a history of smoking to some extent, and are also associated with exposure to environmental toxins (Varghese et al., J. Thorac. Oncol. (2014) 9:892-896). Up to 70% of patients present at TNM IV stage at diagnosis, with 8% surviving 24 months (Nicholson et al., J. Thorac. Oncol. (2016) 11:300-311). At the time of initial diagnosis, the mass is usually centrally located with lymph node and / or metastatic involvement, which results in limited surgical options (Rudin, supra). Genomic characterization of SCLC has identified that, in a significant proportion of SCLC cases, the tumor suppressors TP53 and RB are simultaneously inactivated (George et al., Nature (2015) 524:47-53). Furthermore, other cellular mechanisms involved in cell cycle arrest and apoptosis are occasionally dysregulated in SCLC, such as MYC amplification and BCL-2 amplification (Little et al., Nature (1983) 306:194-196; Ikegaki et al., Cancer Res. (1994) 54:6-8). However, to date, no single pathway or molecular target has been robustly pursued for therapeutic development.

[0357] Non-Hodgkin's lymphoma (NHL) is a different group of blood cancers that includes any type of lymphoma except Hodgkin's lymphoma. The types of NHL vary significantly in severity, from indolent to very aggressive. Less aggressive non-Hodgkin's lymphomas have long survival periods, while more aggressive non-Hodgkin's lymphomas may quickly become fatal without treatment. They can be formed by B cells or T cells. B-cell non-Hodgkin's lymphomas include Burkitt's lymphoma, chronic lymphocytic leukemia / small lymphocytic lymphoma (CLL / SLL), diffuse large B-cell lymphoma, follicular lymphoma, immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, and mantle cell lymphoma. T-cell non-Hodgkin's lymphomas include mycosis fungoides, anaplastic large cell lymphoma, and precursor T-lymphoblastic lymphoma. Prognosis and treatment depend on the stage and type of the disease.

[0358] Diffuse large cell B-cell lymphoma (DLBCL) DLBCL is the most common lymphoma and originates from germinal center B cells. First-line treatment with R-CHOP, an aggressive and highly toxic regimen, is successful in approximately 60% of patients, but leaves some with permanent neurological or cardiovascular damage. DLBCL that is resistant to R-CHOP is difficult to treat and represents an area of ​​great need. BCL6, MYC, BCL2, and STAT3 are established drivers of DLBCL that are targeted by gene translocations and amplifications that activate these drivers or increase their expression (Pasqualucci and Dalla-Favera, “Genetics of diffuse large B-cell lymphoma,” Blood (2018) 131:2307-2319; Schmitz et al., “Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma,” N Engl J Med (2018) 378:1396-1407; and Reddy et al., “Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma,” These driver events occur in combination with each other in the setting of double-hit / triple-hit lymphomas and along with numerous other genetic alterations that define no fewer than five genetic subtypes of DLBCL (Schmitz et al., supra; Chapuy et al., “Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes,” Nat Med (2018) 24:679-690). Clearly, new treatments are needed that are less toxic and address the multiple drivers of DLBCL.

[0359] Prostate cancer is the second most commonly diagnosed cancer and the sixth leading cause of cancer death in men, accounting for 14% (903,500) of all new cancer cases and 6% (258,400) of all cancer deaths in men worldwide. The progression of prostate cancer from diagnosis to death is best categorized into a series of clinical stages based on the extent of the disease, hormonal status, and the presence or absence of detectable metastases: localized disease, rising prostate-specific antigen (PSA) levels after radiation therapy or surgery and no detectable metastases, and clinical metastases in the non-castration or castration-resistant stage. Although surgery, radiation, or a combination of both can be curative for patients with localized disease, a significant proportion of these patients experience disease recurrence, as evidenced by rising PSA levels, which can lead to the development of metastases, particularly in high-risk populations, which is a transition to the lethal stage of the disease.

[0360] The incidence of cancer continues to rise as the general population ages, new cancers develop, and the susceptible population grows. Therefore, there is a great need for new methods and compositions that can be used to treat patients suffering from cancer.

[0361] CIP for the treatment of malignant diseases

[0362] The present disclosure provides methods for treating a malignancy (e.g., lung cancer, upper aerodigestive cancer, hematological malignancies such as lymphoma, leukemia, sarcoma, GI cancer (e.g., bile duct cancer, pancreatic cancer, liver cancer, colorectal cancer, esophageal cancer, gastric cancer), breast cancer, prostate cancer, CNS malignancies (e.g., glioblastoma, astrocytoma), renal cancer, urinary tract cancer, thyroid cancer, melanoma, ovarian cancer, soft tissue malignancies, uterine cancer, cervical cancer, etc.) in a subject. As summarized above, embodiments of the methods employ a CIP, such as a transcriptional chemical proximity inducer (TCIP). TCIP is a compound that induces the proximity of a first endogenous anchor transcription factor (e.g., BCL-6 (and / or its functional homolog)) to a second endogenous transcriptional regulator (e.g., a cancer cell driver, e.g., SCLC or DLBCL driver, prostate cancer driver, e.g., androgen receptor (AR), estrogen receptor, etc.) under intracellular conditions, wherein the first endogenous anchor transcription factor binds to the promoter of a target gene (e.g., a pro-apoptotic gene). Because some CIPs of the present disclosure induce the proximity of at least one endogenous transcription factor or epigenetic regulator to another endogenous transcriptional regulator (e.g., BRD4, CDK, estrogen receptor, AR, etc.), such CIPs of the present disclosure may be referred to as transcriptional chemical proximity inducers (TCIPs). The TCIPs of the present disclosure may be considered transcriptional and epigenetic chemical proximity inducers. When used with respect to the compounds of the present disclosure (CIP or TCIP), "induced proximity" means that a first endogenous protein and a second endogenous protein are spatially associated with each other through a binding event mediated by a compound, and the compound is configured to bind to both endogenous proteins simultaneously, so that the compound can be considered a bifunctional compound or molecular glue. Spatial association is characterized by the presence of a ternary complex comprising CIP, a first endogenous protein, and a second endogenous protein (e.g., BRD4, CDK, estrogen receptor, AR, etc.). In the ternary complex, each member or component of the ternary complex is bound to at least one other member of the ternary complex. In this ternary complex, the binding between the various components may be different. For example, CIP can simultaneously bind to the domains of a first endogenous factor or protein and a second endogenous factor or protein, thereby generating a ternary complex and a desired spatial association, such as ultimately resulting in a spatial association of desired transcriptional regulation of a target gene. This ternary complex is composed of three different non-covalently bound components (e.g., a first endogenous protein, a second endogenous protein, and CIP). In the case of TCIP, the ternary complex is composed of three different non-covalently bound components (eg, an endogenous anchor transcription factor, an endogenous transcriptional regulator, and TCIP).Additional details regarding CIP and TCIP can be found in pending PCT application serial number PCT / US2021 / 058231 published as WO 2022 / 098989, the disclosure of which is hereby incorporated by reference.

[0363] The TCIP compound used in the embodiments of the present disclosure may include a first ligand and a second ligand, wherein the first ligand specifically binds to an anchor transcription factor (e.g., BCL-6 (and / or its functional homolog)), and the second ligand may be a second covalently linked second ligand that specifically binds to a transcriptional regulator (e.g., BRD4, CDK, estrogen receptor, AR, etc.). The first ligand and the second ligand may be stably associated with each other, for example, by being linked, and the link may be a bond or a linking group, for example, a bond or a linking group that provides a covalent bond between the first ligand and the second ligand directly or through a linking group as needed. In other words, in an embodiment, the TCIP compound includes a linker component, which may be a bond or a linking moiety that covalently links the first ligand that specifically binds to the anchor transcription factor and the second ligand that specifically binds to the transcriptional regulator. When used with respect to TCIP, the terms "specifically bind," "specifically bind," and the like refer to the ability of the first ligand and the second ligand to preferentially bind directly to their corresponding anchor and transcriptional regulator relative to other molecules or moieties in the cell.

[0364] In some instances, the first ligand and the second ligand of TCIP are small molecules, and in some instances, the molecular weight of each small molecule is in the range of 50 daltons to 1000 daltons, such as 400 daltons to 800 daltons. The chemical structures of the first ligand and the second ligand can vary greatly, wherein the first ligand and the second ligand can be selected to provide the desired specific binding to the target anchor transcription factor or transcriptional regulatory factor. The first ligand and the second ligand can be selected so that they have little, if any, effect on the activity of the endogenous factor (e.g., anchor transcription factor or transcriptional regulatory factor) to which they are configured to bind.

[0365] As summarized above, the present disclosure provides compounds that are chemical proximity inducers. The following are specific examples of compounds that can be used in the compositions, systems, and methods provided herein. In specific embodiments, the compounds of interest include BCL-6 (B cell lymphoma 6) inhibitors and BRD4 (bromodomain-containing 4) ligands. In some embodiments, the BCL-6 inhibitor and the BRD4 ligand are covalently bonded via a linker. In some embodiments, the chemical proximity inducer includes a compound of formula I:

[0366] (BR, or EL, or CL, or AL)–L–BC(I)

[0367] in:

[0368] EL is a ligand that specifically binds to the estrogen receptor;

[0369] BR is a ligand that specifically binds to bromodomain-containing protein 4 (BRD4);

[0370] CL is a ligand that specifically binds to a CDK (e.g., CDK9, CDK8, and / or CDK7);

[0371] AL is a ligand that specifically binds to the androgen receptor;

[0372] BC is a ligand that specifically binds to B-cell lymphoma 6 (BCL-6) or a BCL6 BTB domain family member; and

[0373] L is a linker (optional),

[0374] or a pharmaceutically acceptable salt thereof.

[0375] In some embodiments, the "salts" of the compounds of the present disclosure may include: (1) acid addition salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, etc.; or with organic acids such as acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethane-disulfonic acid, 2-hydroxyethylsulfonic acid, benzenesulfonic acid or (2) salts formed when the acidic protons in the compound are replaced by metal ions (e.g., alkali metal ions, alkaline earth ions, or aluminum ions) or coordinated with organic bases such as ethanolamine, diethanolamine, triethanolamine, N-methylglucamine, etc.

[0376] As used herein, the term "solvate" refers to a complex or aggregate formed by one or more molecules of a solute (e.g., a compound of Formula I (BR-L-BC) or a salt thereof) and one or more molecules of a solvent. Such a solvate can be a crystalline solid having a substantially fixed molar ratio of solute to solvent. For example, representative solvents include water, methanol, ethanol, isopropanol, acetic acid, and the like. When the solvent is water, the solvate formed is a hydrate.

[0377] In some embodiments, the compounds described herein exist in their isotopically labeled form. For example, the compounds disclosed herein include isotopically labeled compounds that are identical to the compounds described herein, but this is in response to the fact that one or more atoms are replaced by atoms having an atomic mass or mass number different from the atomic mass or mass number of the atoms typically found in nature. Examples of isotopes incorporated into the compounds described herein include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur, fluorine, and chlorine, such as 2H, 3H, 13C, 14C, 15N, 17O, 18O, 31P, 32P, 35S, 18F, and 36Cl, respectively. Compounds described herein and pharmaceutically acceptable salts, esters, solvates, hydrates, or derivatives thereof containing the aforementioned isotopes and / or other isotopes of other atoms are within the scope of the present invention. Certain isotopically labeled compounds (e.g., compounds into which radioactive isotopes such as 3H and 14C are incorporated) can be used in drug and / or substrate tissue distribution assays. Tritiated isotopes (i.e., 3H) and carbon-14 isotopes (i.e., 14C) are particularly preferred due to their ease of preparation and detectability. In addition, substitution with heavy isotopes such as deuterium (i.e., 2H) can produce certain therapeutic advantages that result in greater metabolic stability, for example, increased in vivo half-life or reduced dosage requirements. In some embodiments, isotopically labeled compounds, pharmaceutically acceptable salts, esters, solvates, hydrates, or derivatives thereof are prepared by any suitable method.

[0378] The compounds disclosed herein encompass prodrugs thereof. As used herein, "prodrug" refers to a compound that can be converted under physiological conditions or by solvolysis to a biologically active compound described herein. The term "prodrug" refers to a pharmaceutically acceptable precursor of a biologically active compound. A prodrug may be inactive when administered to a subject but is converted to an active compound in vivo, for example, by hydrolysis. Prodrug compounds may provide advantages in solubility, tissue compatibility, and / or delayed release in mammalian organisms (see, e.g., Bundgard, H., Design of Prodrugs (1985), pp. 7, 9, 21, 24 (Elsevier, Amsterdam). A discussion of prodrugs is provided in Higuchi, T. et al., Prodrugs as Novel Delivery Systems, ACS Symposium Series, Vol. 14, and Bioreversible Carriers in Drug Design, ed. Edward B. Roche, American Pharmaceutical Association and Pergamon Publishers.

[0014] See, e.g., J. Am. Chem. Appl. Rev. USA, 1996, 1996, both of which are incorporated herein by reference in their entirety. Prodrugs of the active compounds described herein can be prepared by modifying functional groups present in the active compounds in such a way that the modifications are cleaved to the parent active compound during routine manipulation or in vivo.

[0379] BR: bromodomain-containing 4 (BRD4) ligand

[0380] Methods of treating a malignancy (e.g., lung cancer (e.g., small cell lung cancer (SCLC)) or lymphoma (e.g., diffuse large B-cell lymphoma (DLBCL))) in a subject are provided. In some cases, the methods can include administering a transcriptional chemical proximity inducer (TCIP) that links a BTB domain-containing protein (e.g., BCL-6 or a related family member) to BRD4 to treat the subject's malignancy, e.g., SCLC or DLBCL. Compositions for practicing the methods of the disclosure are also provided.

[0381] The TCIPs employed in these embodiments of the present disclosure include ligands for transcriptional regulators (e.g., oncogenic transcription factors, such as BRD4). This embodiment is particularly significant in the treatment of cancer, where CIPs enable cancer cells to kill themselves using their own driver factors. Oncogenic transcription factors are transcription factors whose activity contributes to neoplasms (e.g., cancerous disease conditions). Oncogenic transcription factors can vary, and examples of oncogenic transcription factors that can be used to treat SCLC include, but are not limited to, BRD4, c-myc, oncogenic fusions, and the like. Any convenient ligand for these oncogenic transcription factors can be employed, wherein suitable ligands include small molecule ligands that can specifically bind to the target oncogenic transcription factor and, when forming a complex with the anchoring transcription factor via TCIP, do not negatively affect the target oncogenic transcription factor's ability to enhance transcription of the target pro-apoptotic gene (i.e., the transcriptional activation activity of the oncogenic transcription factor). The molecular weight of these ligands can vary, and in some instances, ranges from 150 to 500 daltons, such as 250 to 400 daltons.

[0382] Suitable ligands for BRD4 include, but are not limited to, those described in U.S. Patent Nos. 11,279,703; 11,267,820; 11,117,865; 11,020,404; 10,975,059; 10,738,016; 10,689,395; 10,526,291; 10,328,074; 10,300,073; 10,106,507; 10,071,129; 9,840,526; 9,814,728; 9,610,332; 9,387,231; 9,2 No. 66,891; No. 9,255,089; No. 9,249,161; No. 9,108,953; and the ligands described below: U.S. Patent Application Publication Nos. 20220185820; 20220177459; 20220119370; 20220047596; 20210355088; 20210221821; 20210147419; 20200407328; 20200405809; 20200385408; 20200339595; 20200338065; 202002 No. 55450; No. 20200095252; No. 20200046726; No. 20190367530; No. 20190381013; No. 20190359573; No. 20190292168; No. 20190262355; No. 20190055203; No. 20180290984; No. 20180282316; No. 20180237453; No. 20180050043; No. 20170304315; No. 20170226065; No. 20160129001; No. 20160075695; No. 2016 No. 0060260; No. 20160031868; No. 20150148344; No. 20150148333; No. 20150133436; No. 20150087636; No. 20140371157; No. 20140336190; No. 20140296246; No. 20140296243; No. 20140243322; No. 20140243286; No. 20140005169; No. 20140044770; No. 20120208800; No. 20120157428; the disclosures of said documents are incorporated herein by reference.Suitable ligands for BRD4 include, but are not limited to, JQ1, AZD5153, ABBV-075, BMS-986158, CPI-0610, GSK525762, OTX-015, PLX51107, INCB054329, INCB057643, I-BET151, RVX-208, etc. The structure is provided below:

[0383]

[0384] In some embodiments, the bromodomain-containing 4 ligand (BR) is of Formula IA:

[0385]

[0386] in:

[0387] n is an integer from 0 to 12;

[0388] m is an integer from 0 to 5;

[0389] p is an integer from 0 to 5;

[0390] A is 5-8 membered cycloalkyl, substituted cycloalkyl, heterocycloalkyl, substituted heterocycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heteroarylalkyl, and substituted heteroarylalkyl;

[0391] B is 3-12 membered cycloalkyl, substituted cycloalkyl, heterocycloalkyl, substituted heterocycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heteroarylalkyl, and substituted heteroarylalkyl;

[0392] W is C, N, O or S;

[0393] X is oxygen or sulfur, or: R 3 and X, taken together with its intermediate atoms, form optionally substituted 5-6 membered cycloalkyl, substituted cycloalkyl, heterocycloalkyl, substituted heterocycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heteroarylalkyl, and substituted heteroarylalkyl;

[0394] Y is a covalent bond, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, or a substituted divalent C(1-6) hydrocarbon chain in which one or more methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R)-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-;

[0395] Z is -CH2, -NH, -O- or -S-;

[0396] Indicates a single bond or a double bond;

[0397] represents a bond to the linker;

[0398] Each of R1, R2, R3, R4 and R5 is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine and substituted sulfoximine.

[0399] In some embodiments, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen or oxygen. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms selected from nitrogen and oxygen. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen and sulfur. In certain instances, A is selected from thiazolo, isothiazolo, oxazolo, isoxazolo, pyrazolo, and imidazo rings. In certain instances, A is isothiazolo.

[0400] In some embodiments, A is benzo or a 5-6 membered fused heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having 2-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 6-membered fused heteroaryl ring having 2-3 nitrogen atoms. In some instances, A is benzo. In some instances, A is a 5-6 membered fused heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 6-membered fused heteroaryl ring having 1-3 nitrogen atoms. In certain instances, A is selected from pyrido, pyrimido, pyrazino, pyridazino, and triazino rings. In certain instances, A is a 5-membered fused heteroaryl ring having 1 heteroatom selected from nitrogen, oxygen, or sulfur. In certain instances, A is thieno. In certain instances, A is furano. In certain instances, A is pyrrolo.

[0401] In some embodiments, B is a 3-7 membered saturated or partially unsaturated carbocyclic ring, a phenyl group, an 8-10 membered bicyclic saturated, partially unsaturated, or aryl ring, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is phenyl. In some instances, B is a 3-7 membered saturated or partially unsaturated monocyclic ring. In certain instances, B is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl. In certain instances, B is cyclopentyl, cyclohexyl, or cycloheptyl.

[0402] In some embodiments, B is a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is a 5-6 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydropyranyl, tetrahydrothiopyranyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolane, diazepinyl, oxazepinyl, thiazepinyl, or morpholinyl.

[0403] In some embodiments, B is a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur; in some instances, R is a 6 membered heteroaryl ring having 1-3 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 1 nitrogen atom. In some instances, B is a 6 membered heteroaryl ring having 2 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 3 nitrogen atoms.

[0404] In some embodiments, B is a 5-membered heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and oxygen. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and sulfur. In some instances, B is a 5-membered heteroaryl ring having 1-3 nitrogen atoms. In certain instances, B is selected from thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, or pyrazinyl.

[0405] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused aromatic bicyclic ring. In some instances, B is naphthyl, indanyl, or indenyl.

[0406] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocycle having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, or quinuclidinyl. In some examples, B is selected from indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, 2-azabicyclo[2.2.1]heptyl, octahydroindolyl, or tetrahydroquinolinyl.

[0407] In some embodiments, B is an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain instances, B is a 5,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain embodiments, B is pyrrolizine, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, imidazopyridinyl, indazolyl, purinyl, cinnolinyl, quinazolinyl, phthalazinyl, naphthyridinyl, quinoxalinyl, thiazolinyl or benzofuranyl. In certain embodiments, B is selected from indolizinyl, purinyl, naphthyridinyl or pteridinyl.

[0408] In some embodiments, R 3 and X together with its intermediate atoms form a heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen or sulfur. In certain embodiments, R 3and X together with its intermediate atom form an optionally substituted triazolyl ring. In some instances, R3 is an optionally substituted C(1-6) aliphatic compound. In some embodiments, R3 is substituted. In some embodiments, R3 is unsubstituted. In certain embodiments, R3 is C(1-6) alkyl. In certain embodiments, R3 is C(1-4) alkyl. In certain embodiments, R3 is methyl, ethyl, propyl, or isopropyl.

[0409] In some embodiments, X is oxygen or sulfur, or R3 and X together with its intermediate atoms form an optionally substituted 5-membered heteroaryl ring with 1-4 heteroatoms independently selected from nitrogen, oxygen or sulfur. In some embodiments, X is oxygen. In some embodiments, X is sulfur. In some embodiments, R3 and X together with its intermediate atoms form an optionally substituted 5-membered heteroaryl ring with 1-4 heteroatoms independently selected from nitrogen, oxygen or sulfur. In some embodiments, R3 and X together with its intermediate atoms form a substituted 5-membered heteroaryl ring with 1-4 heteroatoms independently selected from nitrogen, oxygen or sulfur. In some embodiments, R3 and X together with its intermediate atoms form an unsubstituted 5-membered heteroaryl ring with 1-4 heteroatoms independently selected from nitrogen, oxygen or sulfur. In certain embodiments, R3 and X together with its intermediate atoms form an optionally substituted 5-membered heteroaryl ring with 1-2 heteroatoms independently selected from nitrogen, oxygen or sulfur. In certain embodiments, R3 and X, together with their intervening atoms, form an optionally substituted pyrrolyl, pyrazolyl, imidazolyl, triazolyl, tetrazolyl, thienyl, furanyl, thiazolyl, isothiazolyl, thiadiazolyl, oxazolyl, isoxazolyl, or oxadiazolyl.

[0410] In some embodiments, R 4 is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 4 In certain embodiments, R 4In certain other embodiments, R 4 In some embodiments, R 4 is -OR, -SR or -N(R')2-. In certain embodiments, R 4 In some embodiments, R 4 is CN or -NO2. In certain embodiments, R 4 is -C(O)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, or -C(S)OR. In certain embodiments, R 4 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 4 is -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')SO2R, -N(R')SO2N(R')2, -N(R')N(R')2, or -N(R')C(=N(R'))N(R')2. In certain embodiments, R 4 In some embodiments, R 4 is -OC(O)R or -OC(O)N(R')2.

[0411] In some embodiments, m is an integer from 0 to 5. In some instances, m is 1. In some instances, m is 2. In some instances, m is 3. In some instances, m is 4. In some instances, m is 5.

[0412] In some embodiments, R 5 is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 5 In certain embodiments, R5 In certain other embodiments, R 5 In some embodiments, R 4 In some embodiments, R 5 In other embodiments, R 5 In some embodiments, R 5 In other embodiments, R 5 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 5 In certain other embodiments, R 5 In yet other embodiments, R 5 is -OC(O)R or -OC(O)N(R')2.

[0413] In some embodiments, p is an integer from 0 to 5. In some instances, p is 1. In some instances, p is 2. In some instances, p is 3. In some instances, p is 4. In some instances, p is 5.

[0414] In some embodiments, Y is a covalent bond. In some instances, Y is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some instances, Y is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, Y is a C1-3 hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0415] In some embodiments, each R1 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R x is halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R1 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R1 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is independently selected from a C(1-6) aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0416] In some embodiments, each R2 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R x is halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R2 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R2 is independently selected from a C(1-6)aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0417] In some embodiments, n is an integer from 0 to 12. In some instances, n is 1. In some instances, n is 2. In some instances, n is 3. In some instances, n is 4. In some instances, n is 5. In some instances, n is 6.

[0418] In some embodiments, Z is -CH2. In some instances, Z is -NH. In some instances, Z is -O-. In some instances, Z is -S-.

[0419] In some embodiments, the bromodomain-containing 4 ligand (BR) is of Formula IA1:

[0420]

[0421] in:

[0422] X1 is C, N, O or S;

[0423] X2 is C, N, O or S;

[0424] X3 is C or N;

[0425] represents a single bond or a double bond; and

[0426] R6 is hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0427] In some instances, X1 is N or O; X2 is N; and X3 is C or N. In some instances, X1 is N; X2 is N; and X3 is N. In some instances, X1 is O; X2 is N; and X3 is C.

[0428] In some instances, R6 is hydrogen or C(1-6) alkyl. In some instances, R6 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, R6 is methyl.

[0429] In some embodiments, n is an integer from 0 to 4. In some instances, n is 1. In some instances, n is 2. In some instances, n is 3. In some instances, n is 4. In some instances, n is 5. In some instances, n is 6.

[0430] In some embodiments, each R1 is independently selected from hydrogen and C(1-6) alkyl. In some instances, each R1 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is independently selected from C(1-6) aliphatic compounds, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -C02R. In some instances, each R1 is hydrogen or C(1-6) alkyl. In some instances, each R1 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is methyl.

[0431] In some embodiments, each R2 is independently selected from hydrogen and C (1-6) alkyl. In some instances, each R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, each R2 is independently selected from C (1-6) aliphatic compounds, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR' or -C02R. In some instances, each R2 is hydrogen or C (1-6) alkyl. In some instances, each R2 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, each R2 is methyl.

[0432] In certain embodiments, n is an integer from 1 to 4; and each of R1 and R2 is independently selected from hydrogen and C(1-6) alkyl. In certain instances, n is an integer from 1 to 4, and each of R1 and R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, n is an integer from 1 to 4, and each of R1 and R2 is methyl. In certain instances, n is 1, and each of R1 and R2 is hydrogen. In certain instances, n is 1, and each of R1 and R2 is methyl.

[0433] In some embodiments, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen or oxygen. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms selected from nitrogen and oxygen. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen and sulfur. In certain instances, A is selected from thiazolo, isothiazolo, oxazolo, isoxazolo, pyrazolo, and imidazo rings. In certain instances, A is isothiazolo.

[0434] In some embodiments, A is benzo or a 5-6 membered fused heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having 2-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 6-membered fused heteroaryl ring having 2-3 nitrogen atoms. In some instances, A is benzo. In some instances, A is a 5-6 membered fused heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 6-membered fused heteroaryl ring having 1-3 nitrogen atoms. In certain instances, A is selected from pyrido, pyrimido, pyrazino, pyridazino, and triazino rings. In certain instances, A is a 5-membered fused heteroaryl ring having 1 heteroatom selected from nitrogen, oxygen, or sulfur. In certain instances, A is thieno. In certain instances, A is furano. In certain instances, A is pyrrolo.

[0435] In some embodiments, B is a 3-7 membered saturated or partially unsaturated carbocyclic ring, a phenyl group, an 8-10 membered bicyclic saturated, partially unsaturated, or aryl ring, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is phenyl. In some instances, B is a 3-7 membered saturated or partially unsaturated monocyclic ring. In certain instances, B is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl. In certain instances, B is cyclopentyl, cyclohexyl, or cycloheptyl.

[0436] In some embodiments, B is a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is a 5-6 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydropyranyl, tetrahydrothiopyranyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolane, diazepinyl, oxazepinyl, thiazepinyl, or morpholinyl.

[0437] In some embodiments, B is a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur; in some instances, R is a 6 membered heteroaryl ring having 1-3 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 1 nitrogen atom. In some instances, B is a 6 membered heteroaryl ring having 2 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 3 nitrogen atoms.

[0438] In some embodiments, B is a 5-membered heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and oxygen. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and sulfur. In some instances, B is a 5-membered heteroaryl ring having 1-3 nitrogen atoms. In certain instances, B is selected from thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, or pyrazinyl.

[0439] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused aromatic bicyclic ring. In some instances, B is naphthyl, indanyl, or indenyl.

[0440] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocycle having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, or quinuclidinyl. In some examples, B is selected from indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, 2-azabicyclo[2.2.1]heptyl, octahydroindolyl, or tetrahydroquinolinyl.

[0441] In some embodiments, B is an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain instances, B is a 5,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain embodiments, B is pyrrolizine, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, imidazopyridinyl, indazolyl, purinyl, cinnolinyl, quinazolinyl, phthalazinyl, naphthyridinyl, quinoxalinyl, thiazolinyl or benzofuranyl. In certain embodiments, B is selected from indolizinyl, purinyl, naphthyridinyl or pteridinyl.

[0442] In some embodiments, R 4 is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 4 In certain embodiments, R 4 In certain other embodiments, R 4 In some embodiments, R 4 is -OR, -SR or -N(R')2-. In certain embodiments, R 4 In some embodiments, R 4 In some embodiments, R 4is -C(O)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, or -C(S)OR. In certain embodiments, R 4 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 4 is -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')SO2R, -N(R')SO2N(R')2, -N(R')N(R')2, or -N(R')C(=N(R'))N(R')2. In certain embodiments, R 4 In some embodiments, R 4 is -OC(O)R or -OC(O)N(R')2.

[0443] In some embodiments, m is an integer from 0 to 5. In some instances, m is 1. In some instances, m is 2. In some instances, m is 3. In some instances, m is 4. In some instances, m is 5.

[0444] In some embodiments, R 5 is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 5 In certain embodiments, R 5 In certain other embodiments, R 5 In some embodiments, R 4 In some embodiments, R 5 In other embodiments, R 5In some embodiments, R 5 In other embodiments, R 5 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 5 In certain other embodiments, R 5 In yet other embodiments, R 5 is -OC(O)R or -OC(O)N(R')2.

[0445] In some embodiments, p is an integer from 0 to 5. In some instances, p is 1. In some instances, p is 2. In some instances, p is 3. In some instances, p is 4. In some instances, p is 5.

[0446] In some embodiments, Y is a covalent bond. In some instances, Y is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some instances, Y is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, Y is a C1-3 hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0447] In some embodiments, each R1 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R x is halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R1 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R1 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is independently selected from a C(1-6) aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0448] In some embodiments, each R2 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R x is halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R2 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R2 is independently selected from a C(1-6)aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0449] In some embodiments, n is an integer from 0 to 12. In some instances, n is 1. In some instances, n is 2. In some instances, n is 3. In some instances, n is 4. In some instances, n is 5. In some instances, n is 6.

[0450] In some embodiments, Z is -CH2. In some instances, Z is -NH. In some instances, Z is -O-. In some instances, Z is -S-.

[0451] In some embodiments, the bromodomain-containing 4 ligand (BR) is of Formula IA2:

[0452]

[0453] in:

[0454] X1 is C, N, O or S;

[0455] X2 is C, N, O or S;

[0456] X3 is C or N;

[0457] X4 is derived from CH2, NH, O or S;

[0458] represents a single bond or a double bond; and

[0459] Each of R6, R7 and R8 is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0460] In some embodiments, X4 is S. In certain instances, represents a double bond. In some embodiments, X1 is N or O; X2 is N; and X3 is C or N. In some embodiments, X1 is N; X2 is N; and X3 is N.

[0461] In some instances, R6 is hydrogen or C(1-6) alkyl. In some instances, R6 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, R6 is methyl. In some instances, R7 is hydrogen or C(1-6) alkyl. In some instances, R7 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, R7 is methyl. In some instances, R8 is hydrogen or C(1-6) alkyl. In some instances, R8 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, R8 is methyl. In certain instances, each of R6, R7 and R8 is methyl.

[0462] In some embodiments, B is a 3-7 membered saturated or partially unsaturated carbocyclic ring, a phenyl group, an 8-10 membered bicyclic saturated, partially unsaturated, or aryl ring, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is phenyl. In some instances, B is a 3-7 membered saturated or partially unsaturated monocyclic ring. In certain instances, B is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl. In certain instances, B is cyclopentyl, cyclohexyl, or cycloheptyl.

[0463] In some embodiments, B is a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is a 5-6 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydropyranyl, tetrahydrothiopyranyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolane, diazepinyl, oxazepinyl, thiazepinyl, or morpholinyl.

[0464] In some embodiments, B is a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur; in some instances, R is a 6 membered heteroaryl ring having 1-3 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 1 nitrogen atom. In some instances, B is a 6 membered heteroaryl ring having 2 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 3 nitrogen atoms.

[0465] In some embodiments, B is a 5-membered heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and oxygen. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and sulfur. In some instances, B is a 5-membered heteroaryl ring having 1-3 nitrogen atoms. In certain instances, B is selected from thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, or pyrazinyl.

[0466] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused aromatic bicyclic ring. In some instances, B is naphthyl, indanyl, or indenyl.

[0467] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocycle having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, or quinuclidinyl. In some examples, B is selected from indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, 2-azabicyclo[2.2.1]heptyl, octahydroindolyl, or tetrahydroquinolinyl.

[0468] In some embodiments, B is an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain instances, B is a 5,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain embodiments, B is pyrrolizine, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, imidazopyridinyl, indazolyl, purinyl, cinnolinyl, quinazolinyl, phthalazinyl, naphthyridinyl, quinoxalinyl, thiazolinyl or benzofuranyl. In certain embodiments, B is selected from indolizinyl, purinyl, naphthyridinyl or pteridinyl.

[0469] In some embodiments, R 5is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 5 In certain embodiments, R 5 In certain other embodiments, R 5 In some embodiments, R 4 In some embodiments, R 5 In other embodiments, R 5 In some embodiments, R 5 In other embodiments, R 5 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 5 In certain other embodiments, R 5 In yet other embodiments, R 5 is -OC(O)R or -OC(O)N(R')2.

[0470] In some embodiments, p is an integer from 0 to 5. In some instances, p is 1. In some instances, p is 2. In some instances, p is 3. In some instances, p is 4. In some instances, p is 5.

[0471] In some embodiments, Y is a covalent bond. In some instances, Y is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some instances, Y is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, Y is a C1-3 hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0472] In some embodiments, each R1 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R xis halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R1 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R1 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is independently selected from a C(1-6) aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0473] In some embodiments, each R2 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R xis halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R2 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R2 is independently selected from a C(1-6)aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0474] In some embodiments, n is an integer from 0 to 12. In some instances, n is 1. In some instances, n is 2. In some instances, n is 3. In some instances, n is 4. In some instances, n is 5. In some instances, n is 6.

[0475] In some embodiments, Z is -CH2. In some instances, Z is -NH. In some instances, Z is -O-. In some instances, Z is -S-.

[0476] In some embodiments, the bromodomain-containing 4 ligand (BR) is of Formula IA3:

[0477]

[0478] in:

[0479] X1 is C, N, O or S;

[0480] X2 is C, N, O or S;

[0481] X3 is C or N;

[0482] represents a single bond or a double bond; and

[0483] R6, R7, R8, R9 and R 10Each of the groups is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0484] In some instances, X1 is N or O; X2 is N; and X3 is C or N. In some instances, X1 is N; X2 is N; and X3 is N. In some instances, X1 is O; X2 is N; and X3 is C.

[0485] In some instances, R6 is hydrogen or C(1-6) alkyl. In some instances, R6 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, R6 is methyl. In certain instances, R7 is hydrogen or C(1-6) alkyl. In certain instances, R7 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, R7 is hydrogen. In certain instances, R8 is hydrogen or C(1-6) alkyl. In certain instances, R8 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, R8 is hydrogen. In certain instances, R9 is hydrogen or C(1-6) alkyl. In certain instances, R9 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, R9 is hydrogen. In some instances, R 10 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 10 In certain embodiments, R6 is methyl, and R7, R8, R9 and R 10 Each of is hydrogen.

[0486] In some instances, CR6 X2 represents a double bond; and CX3 X1 represents a single bond.

[0487] In some embodiments, B is a 3-7 membered saturated or partially unsaturated carbocyclic ring, a phenyl group, an 8-10 membered bicyclic saturated, partially unsaturated, or aryl ring, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is phenyl. In some instances, B is a 3-7 membered saturated or partially unsaturated monocyclic ring. In certain instances, B is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl. In certain instances, B is cyclopentyl, cyclohexyl, or cycloheptyl.

[0488] In some embodiments, B is a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is a 5-6 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In certain embodiments, Ring B is tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydropyranyl, tetrahydrothiopyranyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolane, diazepinyl, oxazepinyl, thiazepinyl, or morpholinyl.

[0489] In some embodiments, B is a 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur; in some instances, R is a 6 membered heteroaryl ring having 1-3 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 1 nitrogen atom. In some instances, B is a 6 membered heteroaryl ring having 2 nitrogen atoms. In some instances, B is a 6 membered heteroaryl ring having 3 nitrogen atoms.

[0490] In some embodiments, B is a 5-membered heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and oxygen. In some instances, B is a 5-membered heteroaryl ring having 2 heteroatoms independently selected from nitrogen and sulfur. In some instances, B is a 5-membered heteroaryl ring having 1-3 nitrogen atoms. In certain instances, B is selected from thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, or pyrazinyl.

[0491] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused aromatic bicyclic ring. In some instances, B is naphthyl, indanyl, or indenyl.

[0492] In some embodiments, B is a 7-10 membered saturated or partially unsaturated bicyclic heterocycle having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 7-8 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered saturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 9-10 membered partially unsaturated bicyclic heterocycle having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, or quinuclidinyl. In some examples, B is selected from indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, 2-azabicyclo[2.2.1]heptyl, octahydroindolyl, or tetrahydroquinolinyl.

[0493] In some embodiments, B is an 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused saturated, partially unsaturated, or aromatic bicyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain instances, B is a 5,5-fused, 5,6-fused, or 6,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain instances, B is a 5,6-fused heteroaryl ring having 1-4 nitrogen atoms. In certain embodiments, B is pyrrolizine, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, imidazopyridinyl, indazolyl, purinyl, cinnolinyl, quinazolinyl, phthalazinyl, naphthyridinyl, quinoxalinyl, thiazolinyl or benzofuranyl. In certain embodiments, B is selected from indolizinyl, purinyl, naphthyridinyl or pteridinyl.

[0494] In some embodiments, R 5is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 5 In certain embodiments, R 5 In certain other embodiments, R 5 In some embodiments, R 4 In some embodiments, R 5 In other embodiments, R 5 In some embodiments, R 5 In other embodiments, R 5 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 5 In certain other embodiments, R 5 In yet other embodiments, R 5 is -OC(O)R or -OC(O)N(R')2.

[0495] In some embodiments, p is an integer from 0 to 5. In some instances, p is 1. In some instances, p is 2. In some instances, p is 3. In some instances, p is 4. In some instances, p is 5.

[0496] In some embodiments, Y is a covalent bond. In some instances, Y is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some instances, Y is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, Y is a C1-3 hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0497] In some embodiments, each R1 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R xis halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R1 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R1 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is independently selected from a C(1-6) aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0498] In some embodiments, each R2 is independently selected from hydrogen, halogen, optionally substituted C(1-6) aliphatic, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -S02R, -S02N(R')2, -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')SO2R, -N(R')S02N(R')2, -N(R')N(R')2 , -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, -OC(O)N(R')2 or -(CH2) q R x , where q is 0-3, and R xis halogen, optionally substituted C(1-6) aliphatic compounds, -OR, -SR, -CN, -N(R')2, -C(O)R, -C(S)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R') C(O)R, -N(R')C(O)N(R')2, -N(R')C(S)N(R')2, -N(R')S02R, -N(R')S02N(R')2, -N(R')N(R')2, -N(R')C(=N(R'))N(R')2, -C=NN(R')2, -C=NOR, -C(=N(R'))N(R')2, -OC(O)R, or -OC(O)N(R')2. In some embodiments, each R2 is independently selected from hydrogen and C(1-6)alkyl. In some instances, each R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R2 is independently selected from a C(1-6)aliphatic, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -CO2R.

[0499] In some embodiments, n is an integer from 0 to 12. In some instances, n is 1. In some instances, n is 2. In some instances, n is 3. In some instances, n is 4. In some instances, n is 5. In some instances, n is 6.

[0500] In some embodiments, Z is -CH2. In some instances, Z is -NH. In some instances, Z is -O-. In some instances, Z is -S-.

[0501] In some embodiments, the bromodomain-containing 4 ligand (BR) is of Formula IA4:

[0502]

[0503] in:

[0504] n is an integer from 0 to 12;

[0505] m is an integer from 0 to 5;

[0506] X1 is C, N, O or S;

[0507] X2 is C, N, O or S;

[0508] X3 is C or N;

[0509] Indicates a single bond or a double bond;

[0510] represents a bond to the linker; and

[0511] R1, R2, R4, R6, R 11 、R 12 、R 13 、R 14 and R 15 Each of the groups is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0512] In some instances, X1 is N or O; X2 is N; and X3 is C or N. In some instances, X1 is N; X2 is N; and X3 is N. In some instances, X1 is O; X2 is N; and X3 is C.

[0513] In some instances, R6 is hydrogen or C(1-6) alkyl. In some instances, R6 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, R6 is methyl.

[0514] In some instances, R 11 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 11 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 11 In some examples, R 12 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 12 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 12 In some examples, R 13 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 13 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 13 In certain embodiments, R 13 In certain embodiments, R 13 is selected from fluorine, chlorine, bromine and iodine. In certain embodiments, R 13 In some examples, R 14is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 14 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 14 In some examples, R 15 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 15 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 15 In certain embodiments, R 11 、R 12 、R 14 and R 15 Each of is hydrogen, and R 13 is selected from fluorine, chlorine, bromine and iodine. 11 、R 12 、R 14 and R 15 Each of is hydrogen, and R 13 For chlorine.

[0515] In some embodiments, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen or oxygen. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms selected from nitrogen and oxygen. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having two heteroatoms independently selected from nitrogen and sulfur. In certain instances, A is selected from thiazolo, isothiazolo, oxazolo, isoxazolo, pyrazolo, and imidazo rings. In certain instances, A is isothiazolo.

[0516] In some embodiments, A is benzo or a 5-6 membered fused heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 5-membered fused heteroaryl ring having 2-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 6-membered fused heteroaryl ring having 2-3 nitrogen atoms. In some instances, A is benzo. In some instances, A is a 5-6 membered fused heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some instances, A is a 6-membered fused heteroaryl ring having 1-3 nitrogen atoms. In certain instances, A is selected from pyrido, pyrimido, pyrazino, pyridazino, and triazino rings. In certain instances, A is a 5-membered fused heteroaryl ring having 1 heteroatom selected from nitrogen, oxygen, or sulfur. In certain instances, A is thieno. In certain instances, A is furano. In certain instances, A is pyrrolo.

[0517] In some embodiments, R 4 is -R, halogen, -OR, -SR, -N(R')2, -CN, -NO2, -C(O)R, -C(S)R, -CO2R, -C(O)N(R')2, -C(O)SR, -C(O)C(O )R, -C(O)CH2C(O)R, -C(S)N(R')2, -C(S)OR, -S(O)R, -SO2R, -SO2N(R')2, -N(R')C(O)R, -N(R')C( In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. In some embodiments, R is an integer from 1 to 2, wherein R and R' are as defined and described herein. 4 In certain embodiments, R 4 In certain other embodiments, R 4 In some embodiments, R 4 is -OR, -SR or -N(R')2-. In certain embodiments, R 4 In some embodiments, R 4 is CN or -NO2. In certain embodiments, R 4 is -C(O)R, -C02R, -C(O)N(R')2, -C(O)SR, -C(O)C(O)R, -C(O)CH2C(O)R, -C(S)N(R')2, or -C(S)OR. In certain embodiments, R 4 is -S(O)R, -SO2R or -SO2N(R')2. In certain embodiments, R 4 is -N(R')C(O)R, -N(R')C(O)N(R')2, -N(R')SO2R, -N(R')SO2N(R')2, -N(R')N(R')2, or -N(R')C(=N(R'))N(R')2. In certain embodiments, R 4 In some embodiments, R 4 is -OC(O)R or -OC(O)N(R')2.

[0518] In some embodiments, m is an integer from 0 to 5. In some instances, m is 1. In some instances, m is 2. In some instances, m is 3. In some instances, m is 4. In some instances, m is 5.

[0519] In some embodiments, each R1 is independently selected from hydrogen and C(1-6) alkyl. In some instances, each R1 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is independently selected from C(1-6) aliphatic compounds, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR', ​​or -C02R. In some instances, each R1 is hydrogen or C(1-6) alkyl. In some instances, each R1 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, each R1 is methyl.

[0520] In some embodiments, each R2 is independently selected from hydrogen and C (1-6) alkyl. In some instances, each R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, each R2 is independently selected from C (1-6) aliphatic compounds, -OR, -N(R')2, -C(O)R, -OC(O)R, -N(R')C(O)R, -C(O)NR' or -C02R. In some instances, each R2 is hydrogen or C (1-6) alkyl. In some instances, each R2 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. In certain instances, each R2 is methyl.

[0521] In certain embodiments, n is an integer from 1 to 4; and each of R1 and R2 is independently selected from hydrogen and C(1-6) alkyl. In certain instances, n is an integer from 1 to 4, and each of R1 and R2 is independently selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, or tert-butyl. In certain instances, n is an integer from 1 to 4, and each of R1 and R2 is methyl. In certain instances, n is 1, and each of R1 and R2 is hydrogen. In certain instances, n is 1, and each of R1 and R2 is methyl.

[0522] In some embodiments, Z is -CH2. In some instances, Z is -NH. In some instances, Z is -O-. In some instances, Z is -S-.

[0523] In certain embodiments, the bromodomain-containing 4 ligand (BR) is a compound described in International Patent Publication No. WO2012 / 075456, the disclosure of which is incorporated by reference.

[0524] In certain embodiments, the bromodomain-containing 4 ligand (BR) is selected from:

[0525]

[0526] in Represents the bond to the linker.

[0527] In certain embodiments, the bromodomain-containing 4 ligand (BR) is of Formula IA5:

[0528]

[0529] in Represents the bond to the linker.

[0530] In certain embodiments, the bromodomain-containing 4 ligand (BR) is selected from:

[0531]

[0532] in Represents the bond to the linker.

[0533] In certain embodiments, the bromodomain-containing 4 ligand (BR) is selected from:

[0534]

[0535] in Represents the bond to the linker.

[0536] In certain embodiments, the bromodomain-containing 4 ligand (BR) is selected from:

[0537]

[0538]

[0539]

[0540] In some examples, the ligand is JQ1.

[0541] EL: estrogen receptor ligand

[0542] Provided are methods for treating diffuse large B-cell lymphoma (DLBCL) in a subject. In some cases, the methods may include administering a chemical proximity inducer (CIP) to treat DLBCL in the subject. Also provided are compositions for practicing the methods of the present disclosure.

[0543] The CIPs employed in the embodiments of the present disclosure include ligands of oncogenic transcription factors (e.g., estrogen receptors). This embodiment is particularly significant in the treatment of cancer, where the CIPs cause cancer cells to kill themselves using their own drivers. Oncogenic transcription factors are transcription factors whose activity contributes to neoplasms (e.g., cancerous disease conditions). Oncogenic transcription factors can vary, for example, depending on the specific nature of the disease condition being treated, with examples of oncogenic transcription factors including, but not limited to, hormone receptors (e.g., estrogen receptors, androgen receptors, and progesterone receptors), oncogene drivers (e.g., MYC, MLL fusion proteins, ETS fusion proteins, SS18-SSX fusion proteins, etc.), translocated fusion oncogenes, and proteins that regulate cell cycle entry (e.g., E2F family members, etc.). In some instances, the oncogenic transcription factor is a hormone receptor. Hormone receptors that can be used as oncogenic transcription factors in the embodiments of the present disclosure include, but are not limited to, estrogen receptors (ER), etc. Any convenient ligand for these hormone receptors can be used, wherein suitable ligands include small molecule ligands that can specifically bind to the target hormone receptor, and when forming a complex with the anchor transcription factor through CIP, these ligands will not have any negative impact on the ability of the hormone receptor to enhance the transcription of the target pro-apoptotic gene (i.e., the transcriptional activation activity of the oncogenic transcription factor). The molecular weight of these ligands can vary, and in some instances, range from 150 Daltons to 500 Daltons, such as 250 Daltons to 400 Daltons. Suitable ligands for estrogen receptors include, but are not limited to:

[0544]

[0545] In some instances, the ligand is estrone.

[0546] CDK ligands

[0547] Methods of treating a malignancy (e.g., lymphoma (e.g., DLBCL), lung cancer (e.g., SCLC), breast cancer, etc.) in a subject are provided. In some cases, the methods can include administering a transcriptional chemical proximity inducer (TCIP) that links a BTB domain-containing protein (e.g., BCL-6 or a related family member) to a cyclin-dependent kinase (CDK) to treat the subject's malignancy. Compositions for practicing the methods of the present disclosure are also provided.

[0548] The TCIP used in the embodiments of the present disclosure can include a ligand of a transcriptional regulator (such as CDK, for example, CDK9, CDK8, CDK12 or CDK7). This embodiment has special significance in the treatment of cancer, wherein CIP causes cancer cells to kill themselves with their own CDK driver factors. Any convenient CDK ligand can be used, wherein suitable ligands include small molecule ligands that can specifically bind to the target CDK, and when forming a complex with the anchoring transcription factor through TCIP, these ligands will not have any negative impact on the ability of CDK to enhance the transcription of the target pro-apoptotic gene (that is, the transcriptional activation activity of CDK). The molecular weight of these ligands can vary, and in some instances, the range is 150 daltons to 500 daltons, such as 250 daltons to 400 daltons.

[0549] In some embodiments, the CDK is CDK9. Suitable ligands for CDK9 include, but are not limited to, ligands described in the following published PCT application publications: WO / 2022 / 098843; WO / 2022 / 028556; WO / 2021 / 260578; WO / 2021 / 227904; WO / 2021 / 172359; WO / 2020 / 259 ... No. 0 / 244612; No. WO / 2020 / 228513; No. WO / 2020 / 202232; No. WO / 2020 / 117988; No. WO / 2020 / 092 No. 314; No. WO / 2019 / 242471; No. WO / 2019 / 209825; No. WO / 2019 / 058348; No. WO / 2018 / 192273; No. WO / 2017 / 185023; No. WO / 2017 / 001354; No. WO / 2016 / 061144; No. WO / 2015 / 119712; No. WO / 2 No. 014 / 160028; No. WO / 2014 / 159999; No. WO / 2014 / 160017; No. WO / 2014 / 151444; No. WO / 2014 / 1 No. 39328; No. WO / 2013 / 059634; No. WO / 2013 / 026874; No. WO / 2012 / 101062; No. WO / 2012 / 101065; No. WO / 2007 / 117653; and No. WO / 2005 / 027902; No. WO / 2004 / 002226; the disclosures of which are incorporated herein by reference.

[0550] Specific CDK9 ligands of interest include, but are not limited to:

[0551]

[0552]

[0553]

[0554]

[0555] In some embodiments, the CDK is CDK8. Suitable ligands for CDK8 include, but are not limited to, those described in the following published PCT application publications: WO / 2021 / 108581; WO / 2020 / 071550; WO / 2020 / 027704; WO / 2019 / 068613; WO / 2019 / 031990; WO / 2018 / 156858; WO / 2018 / 136202; WO / 2018 / 027082; WO / 2017 / 202719; WO / 2017 / No. 185034; No. WO / 2017 / 091836; No. WO / 2016 / 100782; No. WO / 2016 / 009076; No. WO / 2015 / 049325; No. WO / 2014 / 194245; No. WO / 2014 / 194201; No. WO / 2014 / 134169; No. WO / 2013 / 122609; No. WO / 2013 / 116786; and No. WO / 2013 / 001310; the disclosures of which are incorporated herein by reference.

[0556] Specific CDK8 ligands of interest include, but are not limited to:

[0557]

[0558]

[0559]

[0560] In some embodiments, the CDK is CDK7. Suitable ligands for CDK7 include, but are not limited to, ligands described in the following published PCT application publications: WO / 2022 / 136174; WO / 2022 / 084930; WO / 2022 / 082056; WO / 2022 / 064009; WO / 2022 / 061155; WO / 2022 / 017533; WO / 2021 / 242602; WO / 2021 / 182914; WO / 2021 / 087138; WO / 2020 / 186196; WO / 2020 / 093006; WO / 2020 / 093011; WO / 2019 / No. 143730; No. WO / 2019 / 143719; No. WO / 2019 / 099298; No. WO / 2018 / 231859; No. WO / 2018 / 187357; No. WO / 2018 / 013867; No. WO / 2017 / 160797; No. WO / 2016 / 105528; No. WO / 2016 / 058544; No. WO / 2015 / 154022; No. WO / 2015 / 154038; No. WO / 2015 / 154039; No. WO / 2015 / 058140; and No. WO / 2014 / 063068; the disclosures of which are incorporated herein by reference.

[0561] Specific CDK7 ligands of interest include, but are not limited to:

[0562]

[0563]

[0564]

[0565]

[0566] AR ligands

[0567] Methods for treating a malignancy (e.g., prostate cancer) in a subject are provided. In some cases, the methods may include administering a transcriptional chemical proximity inducer (TCIP) that links a BTB domain-containing protein (e.g., BCL-6 or a related family member) to an androgen receptor (AR) to treat the subject's malignancy. Compositions for practicing the methods of the present disclosure and procedures for selecting susceptible patient populations are also provided.

[0568] The TCIP used in the embodiments of the present disclosure may include a ligand of a transcriptional regulator (such as an oncogenic transcription factor, such as AR). This embodiment has special significance in the treatment of cancer, wherein CIP causes cancer cells to kill themselves with their own driving factors. An oncogenic transcription factor is a transcription factor whose activity contributes to neoplasms (e.g., cancerous disease symptoms). The oncogenic transcription factor may vary, and examples of oncogenic transcription factors that may be used include AR. Any convenient ligand of these oncogenic transcription factors may be used, wherein suitable ligands include small molecule ligands that can specifically bind to the target oncogenic transcription factor, and when forming a complex with the anchoring transcription factor through TCIP, these ligands will not have any negative impact on the ability of the target oncogenic transcription factor to enhance the transcription of the target pro-apoptotic gene (i.e., the transcriptional activation activity of the oncogenic transcription factor). The molecular weight of these ligands may vary, and in some instances, range from 150 daltons to 500 daltons, such as 250 daltons to 400 daltons.

[0569] Suitable ligands for use with the AR include, but are not limited to, those described in the following U.S. Patents: 11,358,938; 11,332,465; 11,242,324; 11,185,549; 10,934,271; 10,815,221; 10,766,875; 10,662,148; 10,556,882; 10,526,310 ; No. 10,434,075; No. 10,308,630; No. 10,150,739; No. 10,053,418; No. 9,994,545; No. 9,969,683; No. 9,889,110; No. 9,884,038; No. 9,744,149; No. 9,963,433; No. 9,622,992; No. 9,611,225; No. 9,604,9 16; 9,481,663; 9,359,285; 9,340,524; 9,085,539; 9,809,583; 8,865,918; 8,802,689; 8,580,811; 8,519,158; 8,445,507; 8,420,694; 8,193,357; 8,183,38 No. 8; No. 7,816,372; No. 7,727,980; No. 7,365,202; No. 7,288,553; No. 7,214,690; No. 7,026,484; No. 6,960,474; No. 6,534,516; No. 6,462,038; No. 6,017,924; and No. 5,677,336; the disclosures of which are incorporated herein by reference.

[0570] Suitable ligands for AR include, but are not limited to, AR agonists, such as steroidal AR agonists, including but not limited to:

[0571]

[0572] Also of interest are nonsteroidal AR agonists, such as, but not limited to:

[0573]

[0574] In some examples, the AR ligand is an AR antagonist, such as a nonsteroidal AR antagonist, examples of which include but are not limited to:

[0575]

[0576] In some embodiments, the AR antagonist is a steroidal AR antagonist, examples of which include but are not limited to:

[0577]

[0578] Anchor transcription factor ligand

[0579] Any of the methods of the present disclosure can include providing a transcriptional chemical proximity inducer (TCIP) in a cell, for example, by a protocol as described below, wherein the TCIP connects a first endogenous anchor transcription factor (e.g., BCL-6) (and / or its functional homologs, Table 3) and a second endogenous transcriptional regulator (e.g., ER, CDK, BRD4, AR, etc.), wherein the first endogenous anchor transcription factor binds to the promoter of a pro-apoptotic gene, wherein the CIP-mediated connection of these factors enhances transcription of the pro-apoptotic gene in the cell. In some examples, the TCIPs employed in these embodiments are generally as described above and include a first ligand that specifically binds to an anchor transcription factor (e.g., BCL-6) and a second ligand that specifically binds to a transcriptional regulator (e.g., ER, BRD4, CDK9, AR), wherein these first ligands and the second ligand are connected by a bond or a suitable linker, for example, as described below.

[0580] A variety of different anchor transcription factors can be sampled in the methods of these embodiments. Anchor transcription factors of interest include, but are not limited to, BCL-6, TFAP2A, TFAP2C, SP3, TFDP1, ELK3, SREBF1, SREBF2, THRA, SMAD2, TFDP1, TCF3, USF1, USF2, VEZF1, PBX1, HIF1A, RARA, FOXO3A, MAZ, E2F1, E2F2, PAX9, STAT1, SPDEF, CREB3L1, BATF, XBP1, SIX4, AR, LEF1, MYB, RUNX1, and PPARG. In some instances, the anchor transcription factor is BCL-6.

[0581] In certain embodiments, BTB domain-containing proteins, such as BCL-6 and related family members, are of interest. Small molecules that bind to BTB domains (such as BI3812 and the other small molecules mentioned above) can exert their effects by binding to BCL6 and / or any one or more of the 131 BTB domain-containing proteins encoded in the human genome listed in Table 3. Generally, these BTB domain proteins also possess a DNA binding domain. Because they are typically expressed in a tissue-specific manner, they allow TCIP to activate diverse biological programs in different cell types. In the case of specific cancers, selective expression of BTB domain-containing proteins may lead to cell death, for example, by removing inhibition caused by various epigenetic mechanisms, including removal of the polycomb repressive complex, removal of histone deacetylation complexes, or other means. Furthermore, recruitment to the locus occupied by the BTB domain-containing protein may lead to the death of the cancer cell due to steric interference or other mechanisms. Furthermore, recruitment of BTB domain-containing proteins to form ternary complexes can confer novel therapeutic activities. For example, cell-type-specific BTB domain proteins can prevent BRD4 from binding to chromatin in specific types of cancer cells (such as SCLC), thereby providing tissue-specific inhibition of the effects of BRD4.

[0582] The BTB domain-containing proteins and BCL6 homologs shown in Table 3 include family members known to repress cell death genes, including p53, Puma, and Bim (doi:10.4049 / jimmunol.1600013; doi:10.4049 / Jimmunol.1101451; doi:10.3389 / fimmu.2021.713294; ​​dx.doi.org / 10.1016 / j.molcel.2014.02.017). This repression of cell death genes is due to the binding of epigenetic repressors such as BCOR, SMRT, and NCOR. The BTB domain of this family is crucial for this repression, and point mutations in the BTB domain close to the corepressor binding site release repression and lead to aberrant cell death (doi:10.4049 / jimmunol.1600013). Since the BTB family shares functional similarities with BCL6, ligands for their BTB domains can be used to construct TCIPs similar to those described for BCL6 in this application.

[0583]

[0584]

[0585] In the TCIP of these embodiments, any ligand convenient for these anchor transcription factors can be used, wherein suitable ligands include small molecule ligands that can specifically bind to the target anchor transcription factor but do not have any relevant negative impact on the binding ability of the anchor transcription factor to the target DNA binding site. The molecular weight of these ligands may vary, and in some examples, range from 50 daltons to 1200 daltons, such as 200 daltons to 500 daltons. Ligands suitable for anchor transcription factors can be selected using any convenient scheme, such as in silico screening protocols, etc., as described below.

[0586] When the anchor transcription factor is BCL-6, suitable ligands include, but are not limited to, those described in U.S. Patent Nos. 11,242,351; 11,192,880; 11,161,839; 11,001,570; 9,943,506; 8,791,075; 8,703,503; 8,338,464; and 7,919,578, and those described in U.S. Patent Application Publication Nos. 20210330672; No. 20210206756; No. 20210163497; No. 20210147382; No. 20210053978; No. 20200331921; No. 20200325119; No. 20200308147; No. 20200071297; No. 20160166549; No. 20120014979; No. 20100130564; No. 20090018083; the disclosures of the said documents are hereby incorporated by reference.

[0587] In some embodiments, the B-cell lymphoma 6 ligand (BC) is of Formula IB:

[0588]

[0589] in:

[0590] D is selected from a bond, alkyl, amide, ester, carbamate, acyl, substituted acyl, carboxyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, and substituted acylamino;

[0591] E is -CH or nitrogen;

[0592] G is nitrogen or CR 23 , where R 23 is selected from hydrogen, -C(1-4)alkyl, -OC(1-14)alkyl, -OC(1-4)haloalkyl, -C(1-4)haloalkyl and halogen;

[0593] J is -CH or nitrogen;

[0594] M is -CH or nitrogen;

[0595] K is -CH2, O, S or -NH;

[0596] represents a bond to the linker; and

[0597] R 16 、R 17 、R 18 、R 19、R 20 、R 21 、R 22 Each of the groups is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0598] In some instances, D is an amide. In some embodiments, D is an optionally substituted C(1-6) aliphatic compound. In some embodiments, D is substituted. In some embodiments, D is unsubstituted. In certain embodiments, D is a C(1-6) alkyl group. In certain embodiments, D is a C(1-4) alkyl group. In certain embodiments, D is methyl, ethyl, propyl, or isopropyl. In some instances, D is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, D is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, D is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0599] In certain instances, E is nitrogen. In certain instances, E is -CH.

[0600] In some instances, R 16 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 16 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 16 In certain embodiments, R 16 In some examples, R 16 is selected from fluorine, chlorine, bromine and iodine. 16 For chlorine.

[0601] In some instances, R 17 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 17 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 17 In certain embodiments, R 17 In some examples, R 17 is selected from fluorine, chlorine, bromine and iodine. 17 In certain embodiments, R 16 is hydrogen, and R 17 For chlorine.

[0602] In some embodiments, R 18 is selected from hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. 18 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 18 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 18 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 18 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 18 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 18 is selected from fluorine, chlorine, bromine and iodine.

[0603] In some instances, R 19 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 19 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 19 In certain embodiments, R 19 In some examples, R19 is selected from fluorine, chlorine, bromine and iodine. 19 In certain embodiments, R 16 is hydrogen, R 17 is chlorine, and R 19 For hydrogen.

[0604] In some embodiments, G is CR 23 , and R 23 is selected from hydrogen, C(1-4)alkyl, -OC(1-4)alkyl, -OC(1-4)haloalkyl and halogen. 23 is hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. In some examples, R 23 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 23 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 23 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 23 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 23 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 23 is selected from fluorine, chlorine, bromine and iodine.

[0605] In some instances, J is -CH. In some instances, J is nitrogen. In some instances, M is -CH. In some instances, m is nitrogen. In some instances, K is -CH2. In some instances, K is oxygen. In some instances, K is sulfur. In some instances, K is -NH.

[0606] In some embodiments, R 21 is selected from hydrogen, -C(1-6)alkyl optionally substituted by a group selected from -OH, -NH2, -OC 1-4Alkyl, -NH-C(1-4)alkyl, -N(C 1-4 alkyl) 2, -C (3-6) cycloalkyl and 4- to 7-membered heterocyclyl, wherein each cycloalkyl and heterocyclyl is optionally and independently substituted with a group selected from -C (1-3) alkyl, or R 21 is -C(3-6)cycloalkyl, 4-membered to 7-membered heterocyclyl, wherein each group is optionally substituted by a group selected from -C(1-3)alkyl. 21 is selected from -C(1-4)alkyl, -C(3-6)cycloalkyl and -N(C 1-4 In some embodiments, R 21 is selected from -CH3, -CH2CH3, -CH2CH2CH3, -CH(CH3)2, -(CH2)3OH, -(CH2)2(CH3)2, -CH2-cyclopropyl and -(CH2)2N(CH3)2. In some examples, R 21 is hydrogen or C(1-6) alkyl. In some examples, R 21 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 21 It is a methyl group.

[0607] In some embodiments, R 20 is selected from hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. In certain embodiments, R 20 In some examples, R 20 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 20 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 20 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 20 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 20is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 20 is selected from fluorine, chlorine, bromine and iodine.

[0608] In some embodiments, R 22 -L1-C(R 24 R 25 )-R 26 or -CH═CH-R 26 , where L1 is -O- or -S-; R 24 is hydrogen or C(1-4) alkyl; R 25 is hydrogen or C(1-4)alkyl; or R together form -C(3-5)cycloalkyl 24 and R 25 ; R 26 -COOH, -CONH2, -C(O)R 27 、-C(O)OR 27 、-C(O)NR 27 R 28 、-S(O)-C 1-6 Alkyl, -S(O)2-C(1-6)alkyl, -P(O)-(C 1-6 Alkyl)2, -C(NH)NH2, R 27 is a 3-6 membered heterocyclic group or a -C(1-4)alkyl group optionally substituted by one or more identical or different groups selected from -OH, -CF3, -N(C 1-4 alkyl)2, -C(3-6)cycloalkyl, 3-6 membered heterocyclic group, -C(2-4)alkenyl, -C 2-4 Alkynyl; and R 28 is hydrogen or C(1-4)alkyl. In certain embodiments, R 22 Selected from:

[0609]

[0610]

[0611] In some embodiments, R 22 for:

[0612] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of the formula IB1:

[0613]

[0614] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of formula IB2:

[0615]

[0616] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of formula IB3:

[0617]

[0618] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of formula IB4:

[0619]

[0620] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of the formula IB5:

[0621]

[0622] in:

[0623] D is selected from a bond, alkyl, amide, ester, carbamate, acyl, substituted acyl, carboxyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, and substituted acylamino;

[0624] E is -CH or nitrogen;

[0625] G is nitrogen or CR 23 , where R 23 is selected from hydrogen, -C(1-4)alkyl, -OC(1-14)alkyl, -OC(1-4)haloalkyl, -C(1-4)haloalkyl and halogen;

[0626] J is -CH or nitrogen;

[0627] M is -CH or nitrogen;

[0628] Q is -CH or nitrogen;

[0629] K is -CH2, O, S or NH;

[0630] represents a bond to the linker; and

[0631] R 16 、R 17 、R 18 、R 19 、R 20 and R 21Each of the groups is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0632] In some instances, D is an amide. In some embodiments, D is an optionally substituted C(1-6) aliphatic compound. In some embodiments, D is substituted. In some embodiments, D is unsubstituted. In certain embodiments, D is a C(1-6) alkyl group. In certain embodiments, D is a C(1-4) alkyl group. In certain embodiments, D is methyl, ethyl, propyl, or isopropyl. In some instances, D is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, D is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, D is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0633] In certain instances, E is nitrogen. In certain instances, E is -CH.

[0634] In some instances, R 16 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 16 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 16 In certain embodiments, R 16 In some examples, R 16 is selected from fluorine, chlorine, bromine and iodine. 16 For chlorine.

[0635] In some instances, R 17is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 17 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 17 In certain embodiments, R 17 In some examples, R 17 is selected from fluorine, chlorine, bromine and iodine. 17 In certain embodiments, R 16 is hydrogen, and R 17 For chlorine.

[0636] In some embodiments, R 18 is selected from hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. 18 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 18 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 18 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 18 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 18 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 18 is selected from fluorine, chlorine, bromine and iodine.

[0637] In some instances, R 19 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 19 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 19 In certain embodiments, R 19 In some examples, R 19 is selected from fluorine, chlorine, bromine and iodine.19 In certain embodiments, R 16 is hydrogen, R 17 is chlorine, and R 19 For hydrogen.

[0638] In some embodiments, G is CR 23 , and R 23 is selected from hydrogen, C(1-4)alkyl, -OC(1-4)alkyl, -OC(1-4)haloalkyl and halogen. 23 is hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. In some examples, R 23 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 23 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 23 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 23 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 23 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 23 is selected from fluorine, chlorine, bromine and iodine.

[0639] In some instances, J is -CH. In some instances, J is nitrogen. In some instances, M is -CH. In some instances, m is nitrogen. In some instances, K is -CH2. In some instances, K is oxygen. In some instances, K is sulfur. In some instances, K is -NH.

[0640] In some embodiments, R 20 is selected from hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. In certain embodiments, R 20 In some examples, R 20is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 20 In some examples, R 20 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 20 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 20 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 20 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 20 is selected from fluorine, chlorine, bromine and iodine.

[0641] In some embodiments, R 21 is selected from hydrogen, -C(1-6)alkyl optionally substituted by a group selected from -OH, -NH2, -OC 1-4 Alkyl, -NH-C(1-4)alkyl, -N(C 1-4 alkyl) 2, -C (3-6) cycloalkyl and 4- to 7-membered heterocyclyl, wherein each cycloalkyl and heterocyclyl is optionally and independently substituted with a group selected from -C (1-3) alkyl, or R 21 is -C(3-6)cycloalkyl, 4-membered to 7-membered heterocyclyl, wherein each group is optionally substituted by a group selected from -C(1-3)alkyl. 21 is selected from -C(1-4)alkyl, -C(3-6)cycloalkyl and -N(C 1-4 In some examples, R 21 In certain embodiments, R 21 for In some instances, R 21 is selected from -C(1-4)alkyl, -C(3-6)cycloalkyl and -N(C 1-4 In some embodiments, R 21 is selected from -CH3, -CH2CH3, -CH2CH2CH3, -CH(CH3)2, -(CH2)3OH, -(CH2)2(CH3)2, -CH2-cyclopropyl and -(CH2)2N(CH3)2. In some examples, R 21 is hydrogen or C(1-6) alkyl. In some examples, R 21 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 21 It is a methyl group.

[0642] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of the formula IB6:

[0643]

[0644] in Represents the bond to the linker.

[0645] In some embodiments, the B-cell lymphoma 6 ligand (BC) is of formula IB7:

[0646]

[0647] in:

[0648] D is selected from a bond, alkyl, amide, ester, carbamate, acyl, substituted acyl, carboxyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, and substituted acylamino;

[0649] E is -CH or nitrogen;

[0650] G is nitrogen or CR 23 , where R 23 is selected from hydrogen, -C(1-4)alkyl, -OC(1-14)alkyl, -OC(1-4)haloalkyl, -C(1-4)haloalkyl and halogen;

[0651] J is -CH or nitrogen;

[0652] M is -CH or nitrogen;

[0653] K is -CH2, O, S or NH;

[0654] represents a bond to the linker; and

[0655] R 16 、R 17 、R 18 、R 19 and R 21 Each of the groups is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0656] In some instances, D is an amide. In some embodiments, D is an optionally substituted C(1-6) aliphatic compound. In some embodiments, D is substituted. In some embodiments, D is unsubstituted. In certain embodiments, D is a C(1-6) alkyl group. In certain embodiments, D is a C(1-4) alkyl group. In certain embodiments, D is methyl, ethyl, propyl, or isopropyl. In some instances, D is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, D is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, D is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0657] In certain instances, E is nitrogen. In certain instances, E is -CH.

[0658] In some instances, R 16 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 16 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 16 In certain embodiments, R 16 In some examples, R 16is selected from fluorine, chlorine, bromine and iodine. 16 For chlorine.

[0659] In some instances, R 17 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 17 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 17 In certain embodiments, R 17 In some examples, R 17 is selected from fluorine, chlorine, bromine and iodine. 17 In certain embodiments, R 16 is hydrogen, and R 17 For chlorine.

[0660] In some embodiments, R 18 is selected from hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. 18 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 18 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 18 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 18 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 18 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 18 is selected from fluorine, chlorine, bromine and iodine.

[0661] In some instances, R 19 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 19 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl.19 In certain embodiments, R 19 In some examples, R 19 is selected from fluorine, chlorine, bromine and iodine. 19 In certain embodiments, R 16 is hydrogen, R 17 is chlorine, and R 19 For hydrogen.

[0662] In some embodiments, G is CR 23 , and R 23 is selected from hydrogen, C(1-4)alkyl, -OC(1-4)alkyl, -OC(1-4)haloalkyl and halogen. 23 is hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. In some examples, R 23 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 23 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 23 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 23 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 23 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 23 is selected from fluorine, chlorine, bromine and iodine.

[0663] In some instances, J is -CH. In some instances, J is nitrogen. In some instances, M is -CH. In some instances, m is nitrogen. In some instances, K is -CH2. In some instances, K is oxygen. In some instances, K is sulfur. In some instances, K is -NH.

[0664] In some embodiments, R 21is selected from hydrogen, -C(1-6)alkyl optionally substituted by a group selected from -OH, -NH2, -OC 1-4 Alkyl, -NH-C(1-4)alkyl, -N(C 1-4 alkyl) 2, -C (3-6) cycloalkyl and 4- to 7-membered heterocyclyl, wherein each cycloalkyl and heterocyclyl is optionally and independently substituted with a group selected from -C (1-3) alkyl, or R 21 is -C(3-6)cycloalkyl, 4-membered to 7-membered heterocyclyl, wherein each group is optionally substituted by a group selected from -C(1-3)alkyl. 21 is selected from -C(1-4)alkyl, -C(3-6)cycloalkyl and -N(C 1-4 In some embodiments, R 21 is selected from -CH3, -CH2CH3, -CH2CH2CH3, -CH(CH3)2, -(CH2)3OH, -(CH2)2(CH3)2, -CH2-cyclopropyl and -(CH2)2N(CH3)2. In some examples, R 21 is hydrogen or C(1-6) alkyl. In some examples, R 21 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 21 It is a methyl group.

[0665] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of formula IB8:

[0666]

[0667] in represents a bond to the linker.

[0668] In some embodiments, the B-cell lymphoma 6 ligand (BC) is of the formula IB9:

[0669]

[0670] in:

[0671] D is selected from a bond, alkyl, amide, ester, carbamate, acyl, substituted acyl, carboxyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, and substituted acylamino;

[0672] E is -CH or nitrogen;

[0673] J is -CH or nitrogen;

[0674] M is -CH or nitrogen;

[0675] K is -CH2, O, S or NH;

[0676] represents a bond to the linker; and

[0677] R 16 、R 17 、R 18 、R 19 and R 21 Each of the groups is independently selected from hydrogen, halogen, hydroxy, alkoxy, cyano, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, acyl, substituted acyl, carbonyl, alkoxycarbonyl, substituted alkoxycarbonyl, aminoacyl, substituted aminoacyl, amino, substituted amino, acylamino, substituted acylamino, thiol, substituted thiol, sulfoxide, substituted sulfoxide, sulfone, substituted sulfone, sulfoximine, or substituted sulfoximine.

[0678] In some instances, D is an amide. In some embodiments, D is an optionally substituted C(1-6) aliphatic compound. In some embodiments, D is substituted. In some embodiments, D is unsubstituted. In certain embodiments, D is a C(1-6) alkyl group. In certain embodiments, D is a C(1-4) alkyl group. In certain embodiments, D is methyl, ethyl, propyl, or isopropyl. In some instances, D is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, D is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, D is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-.

[0679] In certain instances, E is nitrogen. In certain instances, E is -CH.

[0680] In some instances, R 16 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 16is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 16 In certain embodiments, R 16 In some examples, R 16 is selected from fluorine, chlorine, bromine and iodine. 16 For chlorine.

[0681] In some instances, R 17 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 17 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 17 In certain embodiments, R 17 In some examples, R 17 is selected from fluorine, chlorine, bromine and iodine. 17 In certain embodiments, R 16 is hydrogen, and R 17 For chlorine.

[0682] In some embodiments, R 18 is selected from hydrogen, -C(1-4)alkyl, -OC(1-4)alkyl and halogen. 18 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 18 is selected from methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy or tert-butoxy. 18 is an optionally substituted divalent C(1-6) hydrocarbon chain in which one or two methylene units are optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R')-, -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In some examples, R 18 is an optionally substituted divalent C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NR'-, -N(R')C(O)-, -C(O)N(R), -N(R')SO2-, -SON(R')-, -O-, -C(O)-, -OC(O)-, -C(O)O-, -S-, -SO-, or -SO2-. In certain embodiments, R 18 is a C(1-3) hydrocarbon chain in which one methylene unit is optionally replaced by -NH-, -O-, -S-, -S(O)-, or -SO2-. 18 is selected from fluorine, chlorine, bromine and iodine.

[0683] In some instances, R 19 is selected from hydrogen, halogen or C(1-6) alkyl. In some examples, R 19 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 19 In certain embodiments, R 19 In some examples, R 19 is selected from fluorine, chlorine, bromine and iodine. 19 In certain embodiments, R 16 is hydrogen, R 17 is chlorine, and R 19 For hydrogen.

[0684] In some instances, J is -CH. In some instances, J is nitrogen. In some instances, M is -CH. In some instances, m is nitrogen. In some instances, K is -CH2. In some instances, K is oxygen. In some instances, K is sulfur. In some instances, K is -NH.

[0685] In some embodiments, R 21 is selected from hydrogen, -C(1-6)alkyl optionally substituted by a group selected from -OH, -NH2, -OC 1-4 Alkyl, -NH-C(1-4)alkyl, -N(C 1-4 alkyl) 2, -C (3-6) cycloalkyl and 4- to 7-membered heterocyclyl, wherein each cycloalkyl and heterocyclyl is optionally and independently substituted with a group selected from -C (1-3) alkyl, or R 21 is -C(3-6)cycloalkyl, 4-membered to 7-membered heterocyclyl, wherein each group is optionally substituted by a group selected from -C(1-3)alkyl. 21 is selected from -C(1-4)alkyl, -C(3-6)cycloalkyl and -N(C 1-4 In some embodiments, R 21 is selected from -CH3, -CH2CH3, -CH2CH2CH3, -CH(CH3)2, -(CH2)3OH, -(CH2)2(CH3)2, -CH2-cyclopropyl and -(CH2)2N(CH3)2. In some examples, R 21 is hydrogen or C(1-6) alkyl. In some examples, R 21 is selected from methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl or tert-butyl. 21 It is a methyl group.

[0686] Wherein the anchor transcription factor is BCL-6, suitable ligands may include but are not limited to:

[0687]

[0688]

[0689] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is of the formula IB10:

[0690]

[0691] in Represents the bond to the linker.

[0692] In certain embodiments, the B-cell lymphoma 6 ligand (BC) is a compound such as a compound described in U.S. Patent Publication No. 2020 / 0071297, the disclosure of which is incorporated herein by reference.

[0693] In certain embodiments, BCL6 ligands are capable of binding to other BTB domain-containing proteins (e.g., the BTB domain-containing proteins listed in Table 3). These ligands can be generated based on the crystal structure of the BCL6 BTB domain occupied by any of the compounds listed above and the primary sequence of a specific BTB domain-containing protein. In other embodiments, the BCL6 BTB ligands described above bind to different BTB domain-containing proteins and thereby produce their therapeutic effects.

[0694] Linker

[0695] As described above, the present disclosure provides chemical proximity inducing agents having two ligands (e.g., a BCL-6 (B-cell lymphoma 6) ligand and a second ligand (e.g., a BRD4 (bromodomain-containing 4) ligand, an ER ligand, an AR ligand, a CDK ligand, etc.) covalently bonded via a linker. When used, any convenient linker can be used to link the first ligand and the second ligand to each other. The linker of interest is one that provides a stable association of the first ligand and the second ligand in a manner that enables the first ligand and the second ligand to specifically bind to the corresponding endogenous factor in the cell. Because the linker stably associates the first ligand and the second ligand with each other, the first ligand and the second ligand do not dissociate from each other under cellular conditions (e.g., conditions on the cell surface, conditions inside the cell, etc.). The linker can use any convenient binding (e.g., covalent binding or non-covalent binding) to provide a stable association of the first ligand and the second ligand, wherein in some examples, the linker component is covalently bound to both the first ligand and the second ligand. Suitable linkers include, but are not limited to, the linkers described below.

[0696] Additional details

[0697] The TCIP used in the embodiments of the present disclosure is, for example, Figure 1 The TCIP that enhances the transcription of pro-apoptotic genes in cells is shown. Enhancing the transcription of pro-apoptotic genes means that the transcription of pro-apoptotic genes is increased. The magnitude of the increase in transcription can vary. In instances where the transcription of pro-apoptotic genes is not detectable by suitable assays, embodiments of the method enhance transcription so that transcription, for example, can be detected by detecting the expression product of the pro-apoptotic gene or its activity (e.g., apoptosis or its indicator). In instances where a baseline level of transcription can be detected, the magnitude of the increase can vary, and in some instances, can be 1.5 times or more, 2 times or more, such as 5 times or more, including 10 times or more.

[0698] The method can enhance the transcription of a variety of different pro-apoptotic genes. Pro-apoptotic genes are genes whose expression products promote or cause apoptosis (i.e., programmed cell death occurring in multicellular organisms), which can be characterized by: various cellular changes, such as blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal DNA fragmentation, overall mRNA decay and death. Specific pro-apoptotic genes of interest for transcription that can be enhanced in the embodiments of the present disclosure include, but are not limited to: PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA, etc. Table 4 shows the relative ability of specific pro-apoptotic genes to kill breast cancer cells when only overexpressed. These measurements can be used to select transcription factors and ligands to target TCIP to specific effective pro-apoptotic genes (such as BMF, BIM and HRK).

[0699]

[0700]

[0701] *The values ​​shown on the right are actual experimental values ​​found after induced expression in MCF7 ER-positive breast cancer (see Experimental Section).

[0702] Pro-apoptotic genes are of particular interest because they are expressed at levels that balance anti-apoptotic genes, allowing cells to survive in this balanced steady state. Another example is the master transcriptional cell death activator FOXO3, which activates other pro-apoptotic genes (Akt promotes cell survival by phosphorylating and inhibiting forkhead transcription factors). Brunet A, Bonni A, Zigmond MJ, Lin MZ, Juo P, Hu LS, Anderson MJ, Arden KC, Blenis J, Greenberg ME. Cell. 1999 Mar 19;96(6):857-68. Doi:10.1016 / s0092-8674(00)80595-4. PMID:10102273).

[0703] BRD4-BCL6 TCIP

[0704] As reviewed above, in some embodiments, the chemical proximity inducing agent comprises a compound of Formula I:

[0705] BR–L–BC (I)

[0706] in:

[0707] BR is a ligand that specifically binds to bromodomain-containing protein 4 (BRD4);

[0708] BC is a ligand that specifically binds to B-cell lymphoma 6 (BCL-6) or a BCL6 BTB domain family member; and

[0709] L is a linker (optional),

[0710] or a pharmaceutically acceptable salt thereof.

[0711] Figure 1 Instructions are provided on how to construct TCIPs by rational design using existing components. Figure 1 As shown, a design in which TCIP is configured to hijack BCL6 to kill BRD4-positive DCBCL or SLCL cells is shown. BCL6 is a transcription factor and oncogene that prevents the death of a variety of cancer cells, including lymphoma and SCLC cells, by binding to the inhibitory factors BCOR, NCO, and SMRT (PMID: 30335946) on the promoters of cell death genes. Several inhibitors of BCL6 inhibitory function have been produced, which prevent BCOR, NCOR, and SMRT from binding to sites formed on the surface of BCL6 dimers (PMID: 18280243). However, the activity of these inhibitors is not yet sufficient for therapeutic use (PMID: 30335946).

[0712] In cells expressing BRD4 (e.g., DCBLC or SCLC cells), chemical linkage of a BCL-6 inhibitor, such as BI3812 (PMID 32275432), to a BRD4 ligand compound (e.g., JQ1) converts the cell death inhibitor into a cell death activator, which then binds to and induces cell death (pro-apoptotic) promoters, such as those of TP53, PUMA, and BIM.

[0713] In certain embodiments, chemical proximity inducers of interest having a BCL-6 (B-cell lymphoma 6...

Claims

1. A method of treating diffuse large B-cell lymphoma (DLBCL) in a subject, the method comprising: An effective amount of a chemical proximity inducer (CIP) that links BCL-6 to an estrogen receptor is administered to the subject to treat DLBCL in the subject.

2. The method of claim 1, wherein the CIP comprises a first ligand covalently linked to a second ligand, the first ligand specifically binds to BCL-6, and the second ligand specifically binds to the estrogen receptor.

3. The method of claim 1, wherein the administration of the CIP activates transcription of pro-apoptotic genes to treat DLBCL in the subject.

4. The method of claim 3, wherein the pro-apoptotic gene is selected from the group consisting of TP53, PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA.

5. The method of claim 1, wherein the DLBCL is refractory DLBCL, optionally wherein the refractory DLBCL is CHOP-resistant DLBCL.

6. A method of treating a malignancy in a subject, the method comprising: An effective amount of a transcriptional chemical proximity inducer (TCIP) that links BCL-6 to BRD4 is administered to the subject to treat the malignancy in the subject.

7. The method of claim 6, wherein administration of the CIP activates transcription of pro-apoptotic genes to treat the malignancy in the subject.

8. The method of claim 7, wherein the pro-apoptotic gene is selected from the group consisting of TP53, PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA.

9. The method of claim 6, wherein the malignancy is small cell lung cancer (SCLC) or diffuse large B-cell lymphoma (DLBCL).

10. The method of claim 1, measuring the level of at least one of BRD4 and BCL6 in malignant cells of the subject, thereby evaluating the subject to determine whether the malignancy is susceptible to treatment with the TCIP.

11. A method of treating a malignancy in a subject, the method comprising: An effective amount of a transcriptional chemical proximity inducer (TCIP) that links BCL-6 (or a homolog thereof) to an androgen receptor (AR) is administered to the subject to treat the malignancy in the subject.

12. The method of claim 11, wherein the second ligand comprises an AR agonist.

13. The method of claim 11, wherein the second ligand comprises an AR antagonist.

14. The method of claim 11, wherein the administration of TCIP activates transcription of pro-apoptotic genes to treat the malignancy in the subject.

15. The method of claim 14, wherein the pro-apoptotic gene is selected from the group consisting of TP53, PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA.

16. A method of treating a malignancy in a subject, the method comprising: An effective amount of a transcriptional chemical proximity inducer (TCIP) that links BCL-6 (or a homolog thereof) to a cyclin-dependent kinase is administered to the subject to treat the malignancy in the subject.

17. The method of claim 16, wherein the second ligand is selected from the group consisting of a CDK9 ligand, a CDK8 ligand, and a CDK7 ligand. The method of claim 17 , wherein the second ligand is the CDK9 ligand.

19. The method of claim 16, wherein administration of the CIP activates transcription of pro-apoptotic genes to treat the malignancy in the subject.

20. The method of claim 19, wherein the pro-apoptotic gene is selected from the group consisting of TP53, PUMA (BBC3), BIM (BCL2L11), BID, BAX, BAK, BOK, BAD, HRK, BIK, BMF and NOXA.

21. A method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first moiety covalently linked to a second moiety, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, and the first endogenous protein binds to the target gene or a region near the target gene (e.g., a promoter, a regulatory region); (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) after contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein that binds to the compound, and wherein said gain of function is achieved by utilizing less than about 50% of the amount of said second endogenous protein present in said cell.

22. The method of claim 21, wherein the gain of function is achieved by utilizing about 1% to about 30%, about 1% to about 20%, about 1% to about 15%, or about 1% to about 10% of the amount of the second endogenous protein present in the cell.

23. The method of claim 21, wherein the gain of function is achieved by utilizing about 2% to about 20% of the amount of the second endogenous protein present in the cell.

24. The method of claim 21, wherein the gain of function is achieved by utilizing about 2% to about 10% of the amount of the second endogenous protein present in the cell.

25. A method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first moiety covalently linked to a second moiety, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, and the first endogenous protein binds to the target gene; (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) after contacting the cell, the first endogenous protein and the second endogenous protein are spatially complexed with each other by the compound, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein that binds to the compound, and wherein the compound has an EC of less than about 1 micromolar 50 The above-mentioned gain of function is mediated by the following.

26. The method of claim 25, wherein the EC 50 Less than about 500 nanomolar, less than about 200 nanomolar, or less than about 100 nanomolar.

27. The method of claim 25, wherein the EC 50 Less than about 50 nanomoles.

28. The method of claim 25, wherein the EC 50 Less than about 20 nanomoles.

29. A method for regulating the expression of multiple target genes in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with a compound having a first moiety covalently linked to a second moiety, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, and the first endogenous protein reduces the expression of the target gene in the absence of the compound; (b) the second moiety exhibits specific binding to the second endogenous protein, which enhances expression of an additional target gene in the absence of the compound; and (c) after contacting the cell, the first endogenous protein and the second endogenous protein are spatially paired with each other by the compound, thereby generating a gain of function in the cell, and The gain of function is characterized by: (i) increased expression of the target gene compared to expression in the absence of the compound, and (ii) decreased expression of the additional target gene compared to expression in the absence of the compound.

30. The method of claim 29, wherein (i) the expression of the target gene is enhanced by at least about 10%, at least about 20%, at least about 50%, or at least about 80% compared to expression in the absence of the compound.

31. The method of claim 29, wherein (ii) the expression of the additional target gene is reduced by at least about 10%, at least about 20%, at least about 50%, or at least about 80% compared to expression in the absence of the compound.

32. The method of claim 29, wherein (i) the expression of the target gene is enhanced by at least about 20% compared to expression in the absence of the compound, and (ii) the expression of the additional target gene is reduced by at least about 20% compared to expression in the absence of the compound.

33. The method of claim 29, wherein (i) the expression of the target gene is enhanced by at least about 50% compared to expression in the absence of the compound, and (ii) the expression of the additional target gene is reduced by at least about 50% compared to expression in the absence of the compound.

34. A method for regulating expression of a target gene in a cell comprising a first endogenous protein and a second endogenous protein, the method comprising: contacting the cell with an effective amount of a compound having a first moiety covalently linked to a second moiety, wherein: (a) the first portion exhibits specific binding to the first endogenous protein, and the first endogenous protein binds to the target gene; (b) the second portion exhibits specific binding to the second endogenous protein, which is different from the first endogenous protein; and (c) after contacting the cell, the first endogenous protein and the second endogenous protein bind to the compound to form a complex, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating the expression of the target gene in a manner that is dependent on the presence of the second endogenous protein that binds to the compound, and wherein expression of said target gene is modulated within less than or equal to about 16 hours after said contacting.

35. The method of claim 34, wherein the complex modulates expression of the target gene in less than or equal to about 8 hours after the contacting.

36. The method of any one of the preceding claims, wherein the expression level of the target gene is enhanced by at least about 5%, at least about 10%, or at least about 20% compared to the expression level in the absence of the compound.

37. The method of any one of the preceding claims, wherein the expression level of the target gene is enhanced by at least about 30% compared to the expression level in the absence of the compound.

38. The method of any one of the preceding claims, wherein the method causes death of the cell.

39. The method of any of the preceding claims, wherein the first endogenous protein reduces expression of the target gene in the absence of the compound, and the gain of function is characterized by enhancing expression of the target gene in a manner that is dependent on the presence of the second endogenous protein that binds to the compound.

40. The method of any of the preceding claims, wherein the first endogenous protein enhances expression of the target gene in the absence of the compound, and the gain of function is characterized by reducing expression of the target gene in a manner that is dependent on the presence of the second endogenous protein that binds to the compound.

41. The method of any of the preceding claims, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the spatial association of the second endogenous protein with the target gene.

42. The method of any one of the preceding claims, wherein the first endogenous protein is a transcription factor or an epigenetic regulator.

43. The method of any one of the preceding claims, wherein the second endogenous protein is a transcription factor or an epigenetic regulator.

44. The method of any of the preceding claims, wherein the first endogenous protein comprises a BTB domain.

45. The method of claim 44, wherein the first portion of the compound binds to at least a portion of the BTB domain of the first endogenous protein.

46. ​​The method of claim 44, wherein the first endogenous protein is selected from Table 3.

47. The method of claim 46, wherein the first endogenous protein is BCL6.

48. The method of any of the preceding claims, wherein the second endogenous protein is a BET family protein selected from the group consisting of BRD2, BRD3, BRD4, BRD5, BRD7, BRD9 and BRDT.

49. The method of claim 48, wherein the second endogenous protein is BRD4.

50. The method of any one of the preceding claims, wherein the second endogenous protein is an intracellular receptor.

51. The method of claim 50, wherein the intracellular receptor is a hormone receptor.

52. The method of claim 51, wherein the hormone receptor is an estrogen receptor.

53. The method of claim 51, wherein the hormone receptor is an androgen receptor.

54. The method of claim 51, wherein the hormone receptor is a progesterone receptor.

55. The method of any one of the preceding claims, wherein the target gene is a pro-apoptotic gene or an anti-apoptotic gene.

56. The method of claim 55, wherein the pro-apoptotic gene is a late apoptotic gene.

57. The method of claim 55, wherein the pro-apoptotic gene is an early apoptotic gene.

58. The method of any one of the preceding claims, wherein the target gene is a therapeutic gene.

59. The method of any of the preceding claims, wherein the cell overexpresses at least one of the first endogenous protein and the second endogenous protein compared to non-diseased cells.

60. The method of any of the preceding claims, wherein the cell overexpresses both the first endogenous protein and the second endogenous protein compared to non-diseased cells.

61. The method of any of the preceding claims, wherein the cell is a diseased cell.

62. The method of any one of the preceding claims, wherein the cell is a cancer cell.

63. The method of any of the preceding claims, wherein the compound is in a composition during the contacting, and wherein the concentration of the compound in the composition is less than about 1 micromolar, less than about 500 nanomolar, less than about 200 nanomolar, less than about 100 nanomolar, less than about 50 nanomolar, or less than about 20 nanomolar.

64. The method of claim 63, wherein the concentration of the compound in the composition is less than about 10 nanomolar.

65. The method of any of the preceding claims, wherein when the first endogenous protein and the second endogenous protein are bound to the compound, the first endogenous protein does not induce post-translational modification of the second endogenous protein, and vice versa.

66. The method of claim 65, wherein the post-translational modification comprises ubiquitination, deubiquitination, acetylation, deacetylation, phosphorylation, dephosphorylation, methylation, or demethylation.

67. The method of any of the preceding claims, wherein the contacting comprises administering the composition to a subject comprising the cell to treat diffuse large B-cell lymphoma (DLBCL) in the subject.

68. A compound of formula (I): AB(I), in: (a) A is a first part, wherein the first part specifically binds to a first endogenous protein in a cell, and the first endogenous protein binds to a target gene; (b) B is a second portion, the second portion exhibits specific binding to a second endogenous protein in the cell, the second endogenous protein being different from the first endogenous protein; and (c) the compound causes the first endogenous protein and the second endogenous protein to spatially complex with each other, thereby producing a gain of function in the cell, wherein the gain of function is characterized by regulating expression of the target gene in a manner that is dependent on the presence of the second endogenous protein that binds to the compound, and in: (i) the gain of function is achieved by utilizing less than about 50% of the amount of the second endogenous protein present in the cell; (ii) the compound has an EC of less than about 1 micromolar 50 Mediating the gain of function; and / or (iii) the first endogenous protein reduces the expression of the target gene in the absence of the compound, and the second endogenous protein enhances the expression of an additional target gene in the absence of the compound, wherein the gain of function is characterized in that: (iii(a)) the expression of the target gene is enhanced compared to the expression in the absence of the compound, and (iii(b)) the expression of the additional target gene is reduced compared to the expression in the absence of the compound.

69. The compound of claim 68, wherein (i) the gain of function is achieved by utilizing less than about 50% of the amount of the second endogenous protein present in the cell.

70. The compound of claim 68, wherein (i), and wherein the gain of function is achieved by utilizing about 1% to about 30%, about 1% to about 20%, about 1% to about 15%, or about 1% to about 10% of the amount of the second endogenous protein present in the cell.

71. The compound of claim 68, wherein (i), and wherein the gain of function is achieved by utilizing about 2% to about 20% of the amount of the second endogenous protein present in the cell.

72. The compound of claim 68, wherein (i), and wherein the gain of function is achieved by utilizing about 2% to about 10% of the amount of the second endogenous protein present in the cell.

73. The compound of claim 68, wherein (ii) the compound has an EC of less than about 1 micromolar. 50 The above-mentioned gain of function is mediated by the following.

74. The compound of claim 68, wherein (ii), and wherein the EC 50 Less than about 500 nanomolar, less than about 200 nanomolar, or less than about 100 nanomolar.

75. The compound of claim 68, wherein (ii), and wherein the EC 50 Less than about 50 nanomoles.

76. The compound of claim 68, wherein (ii), and wherein the EC 50 Less than about 20 nanomoles.

77. The compound of claim 68, wherein (iii) the first endogenous protein reduces the expression of the target gene in the absence of the compound, and the second endogenous protein enhances the expression of the additional target gene in the absence of the compound, wherein the gain of function is characterized in that: (iii(a)) the expression of the target gene is enhanced compared to the expression in the absence of the compound, and (iii(b)) the expression of the additional target gene is reduced compared to the expression in the absence of the compound.

78. The compound of claim 68, wherein (iii), and wherein in (iii(a)), the expression of the target gene is enhanced by at least about 10%, at least about 20%, at least about 50%, or at least about 80% compared to expression in the absence of the compound.

79. The compound of claim 68, wherein (iii), and wherein in (iii(b)), the expression of the additional target gene is reduced by at least about 10%, at least about 20%, at least about 50%, or at least about 80% compared to expression in the absence of the compound.

80. The compound of claim 68, wherein (iii), and wherein in (iii(a)), the expression of the target gene is enhanced by at least about 20% compared to expression in the absence of the compound, and in (iii(b)), the expression of the additional target gene is reduced by at least about 20% compared to expression in the absence of the compound.

81. The compound of claim 68, wherein (iii), and wherein in (iii(a)), the expression of the target gene is enhanced by at least about 50% compared to expression in the absence of the compound, and in (iii(b)), the expression of the additional target gene is reduced by at least about 50% compared to expression in the absence of the compound.

82. A compound of formula (I): AB(I), in: (a) A is a first part, wherein the first part specifically binds to a first endogenous protein in a cell, and the first endogenous protein binds to a target gene; (b) B is a second portion, the second portion exhibits specific binding to a second endogenous protein in the cell, the second endogenous protein being different from the first endogenous protein; and (c) the compound binds to the first endogenous protein and the second endogenous protein to form a complex, wherein the complex is capable of regulating the expression of the target gene in a manner that is dependent on the presence of the second endogenous protein in the complex, and wherein the complex regulates expression of the target gene in less than or equal to about 16 hours.

83. The compound of claim 82, wherein the complex modulates expression of the target gene in less than or equal to about 8 hours.

84. The compound of any of the preceding claims, wherein the modulation is characterized by enhancing the expression level of the target gene by at least about 5%, at least about 10%, or at least about 20% compared to the expression level in the absence of the compound.

85. The compound of any of the preceding claims, wherein the modulation is characterized by increasing the expression level of the target gene by at least about 30% compared to the expression level in the absence of the compound.

86. The compound of any of the preceding claims, wherein the modulation is characterized by death of the cell.

87. A compound according to any of the preceding claims, wherein the first endogenous protein reduces the target gene expression in the absence of the compound, and the modulation is characterized by enhancing the target gene expression in a manner that is dependent on the presence of the second endogenous protein that binds to the compound.

88. A compound according to any of the preceding claims, wherein the first endogenous protein enhances the target gene expression in the absence of the compound, and the modulation is characterized by reducing the target gene expression in a manner that is dependent on the presence of the second endogenous protein that binds to the compound.

89. A compound according to any of the preceding claims, wherein the modulation is dependent on the spatial association of the second endogenous protein with the target gene.

90. The compound of any one of the preceding claims, wherein the first endogenous protein is a transcription factor or an epigenetic regulator.

91. The compound of any of the preceding claims, wherein the second endogenous protein is a transcription factor or an epigenetic regulator.

92. The compound of any of the preceding claims, wherein the first endogenous protein comprises a BTB domain.

93. The compound of claim 92, wherein the first portion of the compound binds to at least a portion of the BTB domain of the first endogenous protein.

94. The compound of claim 92, wherein the first endogenous protein is selected from Table 3.

95. The compound of claim 94, wherein the first endogenous protein is BCL6.

96. The compound of any of the preceding claims, wherein the second endogenous protein is a BET family protein selected from the group consisting of BRD2, BRD3, BRD4, BRD5, BRD7, BRD9 and BRDT.

97. The compound of claim 96, wherein the second endogenous protein is BRD4.

98. The compound of any of the preceding claims, wherein the second endogenous protein is an intracellular receptor.

99. The compound of claim 98, wherein the intracellular receptor is a hormone receptor.

100. The compound of claim 99, wherein the hormone receptor is an estrogen receptor.

101. The compound of claim 99, wherein the hormone receptor is an androgen receptor.

102. The compound of any one of the preceding claims, wherein the target gene is a pro-apoptotic gene or an anti-apoptotic gene.

103. The compound of claim 102, wherein the pro-apoptotic gene is a late apoptotic gene.

104. The compound of claim 102, wherein the pro-apoptotic gene is an early apoptotic gene.

105. The compound of any one of the preceding claims, wherein the target gene is a therapeutic gene.

106. The compound of any of the preceding claims, wherein the cell overexpresses at least one of the first endogenous protein and the second endogenous protein compared to non-diseased cells.

107. The compound of any of the preceding claims, wherein the cell overexpresses both the first endogenous protein and the second endogenous protein compared to non-diseased cells.

108. The compound of any of the preceding claims, wherein the cell is a diseased cell.

109. The compound of any one of the preceding claims, wherein the cell is a cancer cell.

110. The compound of any of the preceding claims, wherein when the first endogenous protein and the second endogenous protein are bound to the compound, the first endogenous protein does not induce post-translational modification of the second endogenous protein, and vice versa.

111. The compound of claim 110, wherein the post-translational modification comprises ubiquitination, deubiquitination, acetylation, deacetylation, phosphorylation, dephosphorylation, methylation, or demethylation.

112. A composition comprising a compound according to any one of the preceding claims.

113. The composition of claim 112, wherein the composition comprises a therapeutically effective amount of the compound.

114. A composition according to any of the preceding claims, wherein the concentration of the compound in the composition is less than about 1 micromolar, less than about 500 nanomolar, less than about 200 nanomolar, less than about 100 nanomolar, less than about 50 nanomolar, or less than about 20 nanomolar.

115. The composition of any of the preceding claims, wherein the concentration of the compound in the composition is less than about 10 nanomolar.

116. The composition of any of the preceding claims, wherein the first moiety (A) is directly conjugated to the second moiety (B) in the absence of a linker.

117. A composition according to any one of the preceding claims, wherein the compound comprises a structure of formula (II): A-Linker-B(II), wherein the linker comprises at least one atom that is heterologous to the first portion (A) and the second portion (B).

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