Indole amino ketone histone deacetylase inhibitors and uses thereof

Abstract

Provided herein is a method of treating a kidney injury in a patient comprising administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury.

Description

Attorney Docket No.06527-2409107 INDOLE AMINO KETONE HISTONE DEACETYLASE INHIBITORS AND USES THEREOF CROSS REFERENCE TO RELATED APPLICATION

[0001] The present application claims priority to United States Provisional Patent Application No.63 / 551,649, filed February 9, 2024, the disclosure of which is hereby incorporated by reference in its entirety. BACKGROUND OF THE INVENTION Field of the Invention

[0002] Provided herein are compounds and methods of using such compounds for the treatment of kidney injury. Description of Related Art

[0003] Kidney injury, e.g., acute kidney injury (AKI) is remarkably common and has an unacceptably high mortality that has been unchanged for the last twenty years. AKI therapies that have been developed in experimental models when administered prior to the onset of injury have failed to show therapeutic benefit in humans. However, the kidney has an innate capacity to undergo epithelial regeneration following injury, suggesting that drugs that enhance this regenerative capacity are more likely to be of benefit when given after the onset of injury.

[0004] AKI is a multi-factorial disorder that occurs in approximately 7% of in- patients’ hospital admissions. It is an independent predictor of in-hospital mortality. Severe AKI requiring renal replacement therapy occurs in 4% of critically ill patients and has 50% in-patient mortality. Long term studies in survivors of severe AKI indicate that approximately 12.5% become dialysis-dependent. Accordingly, there is an urgent need to develop effective therapies that will accelerate the rate of recovery following induction of renal injury. SUMMARY OF THE INVENTION

[0005] Provided herein is a method of treating a kidney injury in a patient including administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury, the HDAC inhibitor including a compound as set forth in Formula (1): 1 61R3271.DOCXAttorney Docket No.06527-2409107

[0006] wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; and R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0007] Also provided herein is a method of treating a kidney injury in a patient including administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury, the HDAC inhibitor including a compound as set forth in Formula (2):

[0008] wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl, heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0009] Also provided herein is a method of treating fibrosis in a patient including: administering an amount of a histone deacetylase (HDAC) inhibitor effective to treat the fibrosis in the patient, the HDAC inhibitor including a compound as set forth in Formula (1): 2 61R3271.DOCXAttorney Docket No.06527-2409107

[0010] wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof; or a compound as set forth in Formula (2):

[0011] wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0012] Also provided herein is a composition including a compound as set forth in Formula (1):

[0013] wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more 3 61R3271.DOCXAttorney Docket No.06527-2409107 of S, N, or O; R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0014] Also provided herein is a composition including a compound as set forth in Formula (2):

[0015] wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0016] Further non-limiting embodiments are set forth in the following clauses:

[0017] 1. A method of treating a kidney injury in a patient comprising administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury, the HDAC inhibitor comprising a compound as set forth in Formula (1):

[0018] wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; and R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 4 61R3271.DOCXAttorney Docket No.06527-2409107 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0019] 2. The method of clause 1, the compound having the structure:, or a

[0021] 4. The method of any of clauses 1-3, the compound having the structure:and / or pharmaceutically-acceptable salt thereof.

[0022] 5. The method of any of clauses 1-4, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0023] 6. The method of any of clauses 1-5, wherein the HDAC inhibitor is selective for HDAC8.

[0024] 7. The method of any of clauses 1-6, wherein the HDAC inhibitor is administered to the patient orally, intravenously, subcutaneously, intramuscularly, intradermally, via inhalation, and / or via insufflation. 5 61R3271.DOCXAttorney Docket No.06527-2409107

[0025] 8. The method of any of clauses 1-7, wherein the kidney injury is acute kidney injury (AKI).

[0026] 9. The method of any of clauses 1-8, wherein the HDAC inhibitor is administered within 1-24 hours of the AKI.

[0027] 10. The method of any of clauses 1-9, wherein the kidney injury is associated with trauma in the patient.

[0028] 11. The method of any of clauses 1-10, wherein the kidney injury is associated with: chronic kidney disease; decreased blood flow to the kidneys; blood or fluid loss; use medications; heart attack; heart disease; infection; liver failure; sepsis; severe allergic reaction; burns; dehydration; blood clots in the veins and arteries in and around the kidneys; cholesterol deposits that block blood flow in the kidneys; glomerulonephritis; inflammation of the glomeruli; hemolytic uremic syndrome; lupus; use of dyes used during imaging tests; scleroderma; thrombotic thrombocytopenic purpura; toxins; rhabdomyolysis; tumor lysis syndrome; bladder cancer; blood clots in the urinary tract; cervical cancer; colon cancer; enlarged prostate; kidney stones; nerve damage involving the nerves that control the bladder; and / or prostate cancer.

[0029] 12. A method of treating a kidney injury in a patient comprising administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury, the HDAC inhibitor comprising a compound as set forth in Formula (2):

[0030] wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl, heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof. 6 61R3271.DOCXAttorney Docket No.06527-2409107

[0031] 13. The method of clause 12, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0032] 14. The method of clause 12 or clause 13, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0033] 15. The method of any of clauses 12-14 wherein the HDAC inhibitor is a selective HDAC8 inhibitor.

[0034] 16. The method of any of clauses 12-15, wherein the HDAC inhibitor is administered to the patient orally, intravenously, subcutaneously, intramuscularly, intradermally, via inhalation, and / or via insufflation.

[0035] 17. The method of any of clauses 12-16, wherein the injury is an acute kidney injury (AKI).

[0036] 18. The method of any of clauses 12-17, wherein the HDAC inhibitor is administered within 1-24 hours of the AKI.

[0037] 19. The method of any of clauses 12-18, wherein the injury is associated with trauma in the patient.

[0038] 20. The method of any of clauses 12-19, wherein the kidney injury is associated with: chronic kidney disease; decreased blood flow to the kidneys; blood or fluid loss; use medications; heart attack; heart disease; infection; liver failure; sepsis; severe allergic reaction; burns; dehydration; blood clots in the veins and arteries in and around the kidneys; cholesterol deposits that block blood flow in the kidneys; glomerulonephritis; inflammation of the glomeruli; hemolytic uremic syndrome; lupus; use of dyes used during imaging tests; scleroderma; thrombotic thrombocytopenic purpura; toxins; rhabdomyolysis; tumor lysis syndrome; bladder 7 61R3271.DOCXAttorney Docket No.06527-2409107 cancer; blood clots in the urinary tract; cervical cancer; colon cancer; enlarged prostate; kidney stones; nerve damage involving the nerves that control the bladder; and / or prostate cancer.

[0039] 21. A method of treating fibrosis in a patient comprising:

[0040] administering an amount of a histone deacetylase (HDAC) inhibitor effective to treat the fibrosis in the patient, the HDAC inhibitor comprising a compound as set forth in Formula (1):

[0041] wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof; or a compound as set forth in Formula (2):

[0042] wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0043] 22. A compound of Formula (1): 8 61R3271.DOCXAttorney Docket No.06527-2409107

[0044] wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; and R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0045] 23. The compound of clause 22, having the structure:, or a

[0047] 25. The compound of any of clauses 22-24, having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0048] 26. The compound of any of clauses 22-25, having the structure: 9 61R3271.DOCXAttorney Docket No.06527-2409107, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0049] 27. A composition comprising the compound of any of clauses 22-26 and a pharmaceutically-acceptable excipient.

[0050] 28. A compound of Formula (2):

[0051] wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

[0052] 29. The compound of clause 28, having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0053] 30. The compound of clause 28 or clause 29, having the structure: 10 61R3271.DOCXAttorney Docket No.06527-2409107, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

[0054] 31. A composition comprising the compound of any of clauses 28-30 and a pharmaceutically-acceptable excipient. BRIEF DESCRIPTION OF THE DRAWINGS

[0055] FIG. 1 shows a non-limiting embodiment of a synthesis pathway for compounds as disclosed herein;

[0056] FIG.2 shows an exemplary generic structure, with moieties, of compounds as disclosed herein;

[0057] FIG. 3 shows the structure of compounds UPHH-276 and UPHH-274 as disclosed herein;

[0058] FIGS.4A-4J show exemplary HDAC8 inhibitors as disclosed herein;

[0059] FIGS.5A-5B show results of binding assays for UPHH-276 (5A) and UPHH- 274 (5B);

[0060] FIG.6 shows survival assays for in vivo zebrafish experiments using UPHH- 276, with the hazard ratio shown;

[0061] FIG.7 shows results of UPHH-276 in a human organoid hemin injury model;

[0062] FIGS. 8A-8D show results of UPHH-276 in a human kidney organoid doxorubicin injury model; and

[0063] FIGS.9A-9B show NMR spectra for UPHH-276 (9A) and UPHH-274 (9B). DESCRIPTION OF THE INVENTION

[0064] The use of numerical values in the various ranges specified in this application, unless expressly indicated otherwise, are stated as approximations as though the minimum and maximum values within the stated ranges are both preceded by the word "about". In this manner, slight variations above and below the stated ranges can be used to achieve substantially the same results as values within the ranges. Also, unless indicated otherwise, the disclosure of these ranges is intended as a continuous range including every value between the minimum and maximum 11 61R3271.DOCXAttorney Docket No.06527-2409107 values. For definitions provided herein, those definitions refer to word forms, cognates and grammatical variants of those words or phrases. As used herein “a” and “an” refer to one or more.

[0065] As used herein, the term “comprising” is open-ended and may be synonymous with “including”, “containing”, or “characterized by”. As used herein, embodiments “comprising” one or more stated elements or steps also include but are not limited to embodiments “consisting essentially of” and “consisting of” these stated elements or steps.

[0066] A “moiety” (pl. “moieties”) is a part of a chemical compound, and includes groups, such as functional groups.

[0067] As used herein, "alkyl" refers to straight, branched chain, and / or cyclic hydrocarbon groups including, for example, from 1 to about 20 carbon atoms, for example and without limitation C1-C3, C1-C6, C1-C10 groups, for example and without limitation, straight, branched chain alkyl groups such as methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl, dodecyl, and the like. An alkyl group can be, for example, a C1, C2, C3, C4, C5, C6, C7, C8, C9, or C10 group that is substituted or unsubstituted. “lower alkyl” refers to C1-C6 alkyl. Non-limiting examples of straight alkyl groups include methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, and decyl. Branched alkyl groups comprise any straight alkyl group substituted with any number of alkyl groups. Non-limiting examples of branched alkyl groups include isopropyl, n-butyl, isobutyl, sec-butyl, and t-butyl. “Unsaturated alkyl” may comprise one or more, e.g., 1, 2, 3, 4, or 5, carbon-to-carbon double bonds and alternatively may be referred to as alkene or alkenyl, as described below. "Substituted alkyl" can include alkyl substituted at 1 or more (e.g., 1, 2, 3, 4, 5, 6, or more) positions, which substituents are attached at any available atom to produce a stable compound, with substitution as described herein. "Optionally substituted alkyl" refers to alkyl or substituted alkyl. "Halogen," "halide," and "halo" refers to -F, -CI, -Br, and / or -I. "Alkylene" and "substituted alkylene" can include divalent alkyl and divalent substituted alkyl, respectively, including, without limitation, methylene, ethylene, trimethylene, tetramethylene, pentamethylene, hexamethylene, hepamethylene, octamethylene, nonamethylene, or decamethylene. "Optionally substituted alkylene" can include alkylene or substituted alkylene.

[0068] Non-limiting examples of cyclic alkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptlyl, and cyclooctyl groups. Cyclic alkyl groups also 12 61R3271.DOCXAttorney Docket No.06527-2409107 comprise fused-, bridged-, and spiro-bicycles and higher fused-, bridged-, and spiro- systems. A cyclic alkyl group can be substituted with any number of straight, branched, or cyclic alkyl groups. A cycloalkyl group may be attached via any atom. Cycloalkyl also contemplates fused rings where the cycloalkyl is fused to an aryl or heteroaryl ring. A cycloalkyl group can be unsubstituted or optionally substituted with one or more substituents as described herein below. “Cycloalkylene" refers to divalent cycloalkyl. The term "optionally substituted cycloalkylene" refers to cycloalkylene that is substituted with at least 1, 2 or 3 substituents, attached at any available atom to produce a stable compound, wherein the substituents are as described herein. A cycloalkylene may be formed by two “R groups” taken together, such as with “R2 and R3 taken together,” as referenced below.

[0069] "Alkene or alkenyl" can include straight, branched chain, or cyclic hydrocarbyl groups including, e.g., from 2 to about 20 carbon atoms having one or more, e.g., 1, 2, 3, 4, or 5, carbon-to-carbon double bonds, and may be referred to as “unsaturated alkyl”. The olefin or olefins of an alkenyl group can be, for example, E, Z, cis, trans, terminal, or exo-methylene. An alkenyl or alkenylene group can be, for example, a C2, C3, C4, C5, C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, or C20 group that is substituted or unsubstituted. A halo-alkenyl group can be any alkenyl group substituted with any number of halogen atoms. "Substituted alkene" can include alkene substituted at 1 or more, e.g., 1, 2, 3, 4, or 5 positions, which substituents are attached at any available atom to produce a stable compound, with substitution as described herein. "Optionally substituted alkene" can include alkene or substituted alkene. Likewise, "alkenylene" can refer to divalent alkene. Examples of alkenylene include without limitation, ethenylene (-CH=CH-) and all stereoisomeric and conformational isomeric forms thereof. "Substituted alkenylene" can refer to divalent substituted alkene. "Optionally substituted alkenylene" can refer to alkenylene or substituted alkenylene.

[0070] Alkyne or "alkynyl" refers to a straight, branched chain, or cyclic unsaturated hydrocarbon having the indicated number of carbon atoms and at least one triple bond. The triple bond of an alkyne or alkynyl group can be internal or terminal. Examples of a (C2-C8)alkynyl group include, but are not limited to, acetylene, propyne, 1-butyne, 2-butyne, 1-pentyne, 2-pentyne, 1-hexyne, 2-hexyne, 3-hexyne, 1-heptyne, 2- heptyne, 3-heptyne, 1-octyne, 2-octyne, 3-octyne and 4-octyne. An alkynyl group can be unsubstituted or optionally substituted with one or more substituents as described 13 61R3271.DOCXAttorney Docket No.06527-2409107 herein below. An alkyne or alkynyl group can be, for example, a C2, C3, C4, C5, C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, or C20 group that is substituted or unsubstituted. A halo-alkynyl group can be any alkynyl group substituted with any number of halogen atoms. The term "alkynylene" refers to divalent alkyne. Examples of alkynylene include without limitation, ethynylene, propynylene. "Substituted alkynylene" refers to divalent substituted alkyne.

[0071] “Carboxyl” or “carboxylic” refers to group having an indicated number of carbon atoms, where indicated, and terminating in a –C(O)OH group, thus having the structure –R–C(O)OH, where R is an unsubstituted or substituted divalent organic group that can include linear, branched, or cyclic hydrocarbons. Non-limiting examples of these include: C1-C8 carboxylic groups, such as ethanoic, propanoic, 2- methylpropanoic, butanoic, 2,2-dimethylpropanoic, pentanoic, etc. “Amine” or “amino” refers to group having the indicated number of carbon atoms, where indicated, and terminating in a –NH2 group, thus having the structure –R–NH2, where R is an unsubstituted or substituted divalent organic group that, e.g., includes linear, branched, or cyclic hydrocarbons, and optionally comprises one or more heteroatoms. The term “alkylamino” refers to a radical of the formula -NHRx or -NRxRx where each Rx is, independently, an alkyl radical as defined above. “Alkoxyl” or “alkoxy” refers to an -O-alkyl group, such as methoxyl, ethoxyl, propyloxyl, etc.

[0072] “Aryl," alone or in combination refers to an aromatic ring system such as phenyl or naphthyl. "Aryl" also can include aromatic ring systems that are optionally fused with a cycloalkyl ring. A "substituted aryl" is an aryl that is independently substituted with one or more substituents attached at any available atom to produce a stable compound, wherein the substituents are as described herein. The substituents can be, for example, hydrocarbyl groups, alkyl groups, alkoxy groups, and halogen atoms. "Optionally substituted aryl" refers to aryl or substituted aryl. An aryloxy group can be, for example, an oxygen atom substituted with any aryl group, such as phenoxy. An arylalkoxy group can be, for example, an oxygen atom substituted with any aralkyl group, such as benzyloxy. "Arylene" denotes divalent aryl, and "substituted arylene" refers to divalent substituted aryl. "Optionally substituted arylene" refers to arylene or substituted arylene. A “polycyclic aryl group” and related terms, such as “polycyclic aromatic group” refers to a group composed of at least two fused aromatic rings. “Heteroaryl” or “hetero-substituted aryl” refers to an aryl group substituted with one or more heteroatoms, such as N, O, P, and / or S. Examples of heteroaryl groups include, 14 61R3271.DOCXAttorney Docket No.06527-2409107 but are not limited to, thienyl, furyl, pyridyl, oxazolyl, quinolyl, thiophenyl, thiopyranyl, benzothiophenyl, benzothiopyranyl, isoquinolyl, indolyl, triazinyl, triazolyl, isothiazolyl, isoxazolyl, imidazolyl, benzothiazolyl, pyrazinyl, pyrimidinyl, thiazolyl, and thiadiazolyl.

[0073] A bioisostere in reference to a group or moiety, refers to structural motifs that express similar biological properties without the fundamental stipulation that they present a similar shape and size or express close physicochemical attributes, as would be expected of functionalities that share an isosteric relationship. Phenyl bioisosteres represent common isosteric substitutions in medicinal chemistry. Exemplary potential bioisosteres of monosubstituted (terminal) and disubstituted (para-, meta-, ortho-) benzene rings, as they are understood in the medicinal chemistry arts are described in detail in (Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem.2021 Oct 14;64(19):14046-14128, see, e.g., Figure 38 thereof). As with phenyl bioisosteres, suitable bioisosteric substitutions of other groups are broadly-known to those of ordinary skill in the medicinal chemistry arts.

[0074] As used herein, the term “patient” or “subject” refers to members of the animal kingdom including but not limited to human beings and “mammal” refers to all mammals, including, but not limited to human beings.

[0075] As used herein, the “treatment” or “treating” of a patient means administration to a patient by any suitable dosage regimen, procedure and / or administration route of a composition, device, or structure with the object of achieving a beneficial or desirable clinical / medical end-point, including but not limited to, preventing, reducing, and / or eliminating any symptom of acute kidney injury or fibrosis. An amount of any agent, administered by any suitable route, effective to treat a patient is an amount capable of preventing, reducing, and / or eliminating any symptom of acute kidney injury or fibrosis. Any suitable clinical marker may be used to determine efficacy of treatment, including, without limitation, improved survival, improved kidney function, or reduced fibrosis or a biological marker of any of the preceding. Clinical assay results can be said to “normalize” when such clinical markers approach or enter a normal or healthy range for a patient.

[0076] The compositions described herein can be administered by any effective route, such as parenteral, e.g., intravenous, intramuscular, subcutaneous, intradermal, perfusion of organ or tissue, application to organ or tissue, etc., 15 61R3271.DOCXAttorney Docket No.06527-2409107 formulations of which are described below and in the below-referenced publications, as well as are broadly-known to those of ordinary skill in the art.

[0077] Suitable dosage forms may include single-dose, or multiple-dose vials or other containers, such as medical syringes, containing a composition comprising an active ingredient, such as a compound as described herein.

[0078] Drug products, or pharmaceutical compositions comprising an active agent (e.g., drug), for example, a compound as described herein, may be prepared by any method known in the art of pharmacy, for example, by bringing into association the active ingredient with the carrier(s) or excipient(s). As used herein, a “pharmaceutically acceptable excipient”, “carrier” or “pharmaceutically acceptable carrier” includes any solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. Examples of pharmaceutically acceptable excipients include one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol, and the like, as well as combinations thereof. In many cases, it may be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition. Pharmaceutically acceptable carriers may further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives, or buffers, which enhance the shelf life or effectiveness of the active agent. The active agent may be prepared with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used in delivery systems, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Further to the above, non-limiting examples of useful excipients include: antiadherents, binders, rheology modifiers, coatings, disintegrants, emulsifiers, oils, buffers, salts, acids, bases, fillers, diluents, solvents, flavors, colorants, glidants, lubricants, preservatives, antioxidants, sorbents, vitamins, sweeteners, etc., as are available in the pharmaceutical / compounding arts. Methods for the preparation of such formulations are broadly-known to those skilled in the art.

[0079] Additionally, active agent-containing compositions may be in a variety of forms. The preferred form depends on the intended mode of administration and therapeutic application, which will in turn dictate the types of carriers / excipients. Suitable forms include, but are not limited to, liquid, semi-solid and solid dosage forms. 16 61R3271.DOCXAttorney Docket No.06527-2409107

[0080] Pharmaceutical formulations adapted for oral administration may be presented, for example and without limitation, as discrete units such as capsules or tablets; powders or granules; solutions or suspensions in aqueous or non-aqueous liquids; edible foams or whips; or oil-in-water liquid emulsions or water-in-oil liquid emulsions. In certain embodiments, the active agent may be contained in a formulation such that it is suitable for oral administration, for example, by combining the active agent with an inert diluent or an assimilable edible carrier. The active agent (and other ingredients, if desired) may also be enclosed in a hard- or soft-shell gelatin capsule, compressed into tablets, or incorporated directly into the subject’s diet. For oral therapeutic administration, the compounds may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. To administer a compound of the invention by other than parenteral administration, it may be necessary to coat the compound with, or co-administer the compound with, a material to prevent its inactivation.

[0081] Pharmaceutical formulations adapted for topical administration may be formulated, for example and without limitation, as ointments, creams, suspensions, lotions, powders, solutions, pastes, gels, sprays, aerosols, or oils. Formulations for topical administration of nucleic acids can include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions can also contain buffers, diluents, and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.

[0082] Pharmaceutical formulations adapted for nasal administration wherein the carrier is a solid include a coarse powder having a particle size, for example, in the range 20 to 500 microns which is administered in the way snuff is taken, e.g., by rapid inhalation through the nasal passage from a container of the powder held close to the nose. Suitable formulations wherein the carrier is a liquid, for administration as a nasal spray or as nasal drops, include aqueous or oil solutions of the active ingredient.

[0083] Pharmaceutical formulations adapted for administration by inhalation include, without limitation, fine particle dusts or mists which may be generated by means of various types of metered dose pressurized aerosols, nebulizers, or insufflators. In the context of delivery of the active agents described herein by inhalation, inhalation drug products, such as metered-dose inhalers, as are broadly- 17 61R3271.DOCXAttorney Docket No.06527-2409107 known in the pharmaceutical arts, are used. Metered dose inhalers are configured to deliver a single dose of an active agent per actuation, though multiple actuations may be needed to effectively treat a given patient.

[0084] Pharmaceutical formulations adapted for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain, for example and without limitation, anti-oxidants, buffers, bacteriostats, lipids, liposomes, emulsifiers, also suspending agents and rheology modifiers. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules, and tablets.

[0085] Other than living, cellular therapies, therapeutic compositions may be sterile and stable under the conditions of manufacture and storage. For example, sterile injectable solutions may be prepared by incorporating the active agent in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, typical methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The proper fluidity of a solution can be maintained, for example, using a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and using surfactants. Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin.

[0086] The compounds described herein may be complexed with a cyclodextrin. Cyclodextrins are compounds that have found substantial recognition as excipients (e.g., as carriers, vehicles, etc.) in the pharmaceutical field, for example, in oral and intravenous dosage forms. Cyclodextrins are able form non-covalent inclusion complexes and / or aggregates in solution with poorly soluble drugs, for example, BCS Class II and IV drugs (high or low intestinal permeability, respectively, but low solubility in both instances). Cyclodextrins are cyclic oligosaccharides having a hydrophilic 18 61R3271.DOCXAttorney Docket No.06527-2409107 outer surface and a lipophilic central cavity. They consist of α-1,4-linked α-D- glucopyranose units. Naturally-occurring cyclodextrins include α-, β- and γ- cyclodextrins, with 6, 7, and 8 glucopyranose units, respectively. The natural cyclodextrins can be used orally or topically, but natural β-cyclodextrin and γ- cyclodextrin cannot be used parenterally. A number of cyclodextrin derivatives have been formulated with various usefulness in different administrative routes. Common, non-limiting examples of cyclodextrin derivatives include hydroxypropyl-β-cyclodextrin (e.g., 2-hydroxypropyl-β-cyclodextrin), hydroxypropyl-γ-cyclodextrin (e.g., 2- hydroxypropyl-γ-cyclodextrin), hydroxyethyl-β-cyclodextrin, randomly methylated β- cyclodextrin, methyl-β-cyclodextrin, dimethyl-β-cyclodextrin, permethylated β- cyclodextrin, sulfobutylether β-cyclodextrin (e.g., sodium salt), sulfobutyl-γ- cyclodextrin, branched cyclodextrin (e.g., glucosyl-β-cyclodextrin or maltosyl-β- cyclodextrin, e.g., 6-O-maltosyl-β-cyclodextrin or glucosyl-β-cyclodextrin) and randomly-acetylated amorphous-β-cyclodextrin. Cyclodextrins may be complexed with a drug as inclusion complexes (included) in a solution in a 1:1 molar ratio, though increased or decreases relative amounts of the drug or cyclodextrin may be used during formulation in order to drive the reaction. Where the drug is aggregated instead of included within the cyclodextrin, an excess of cyclodextrin may be utilized. It should be recognized that the inclusion or aggregation process can be optimized, including manipulation of relative cyclodextrin-to-active ingredient ratios to obtain optimal solubility and bioavailability or other desirable features of the end-product. See, e.g., Loftsson et al. “Self-Association of Cyclodextrins and Cyclodextrin Complexes” J. Pharm. Sci.93(5):1091-1099 (2004); Loftsson et al. “Cyclodextrins in Drug Delivery” Expert. Opin. Drug Deliv. 2:335-351 (2005); Brewster et al. “Cyclodextrins as Pharmaceutical Solubilizers” Advanced Drug Delivery Reviews 59:645-666 (2007); and Rasheed et al., “Cyclodextrins as Drug Carrier Molecule: A review” Sci. Pharm. 76:567-598 (2008) for their description of cyclodextrins and uses thereof in the pharmaceutical arts. As used herein, “a cyclodextrin” or “cyclodextrins” refer not only to naturally-occurring α-, β- and γ-cyclodextrins, but to cyclodextrin derivatives, including, but not limited to those mentioned above. Likewise “α-cyclodextrin(s)”, “β- cyclodextrin(s)” and “γ-cyclodextrins” refer both to the naturally-occuring cyclodextrin and to cyclodextrin derivatives (e.g., “a β-cyclodextrin” includes both β-cyclodextrin and β-cyclodextrin derivatives, such as, without limitation, hydroxypropyl-β- cyclodextrin, hydroxyethyl-β-cyclodextrin, randomly methylated β-cyclodextrin, 19 61R3271.DOCXAttorney Docket No.06527-2409107 methyl-β-cyclodextrin, dimethyl-β-cyclodextrin, permethylated β-cyclodextrin, sulfobutylether β-cyclodextrin, branched β-cyclodextrin, etc.).

[0087] The formulation may be a liposome, lipid nanoparticle, drug-loaded extracellular vesicle, or multiphase (a liquid comprising more than one phase, such as oil in water, water in oil, liposomes or multi-lamellar structures) composition. Multi- phase systems, including liposomes, are prevalent in the pharmaceutical arts. In the case of a liposome, the drug product might comprise a phospholipid, a non-ionic detergent, and a cationic lipid, such as a composition comprising a phosphatidyl choline, a non-ionic surfactant, and a quaternary ammonium salt of a lipid-substituted D or L glutamic acid or aspartic acid, and an aqueous solvent. The liposomes or multiphase liquids and the ingredients thereof are pharmaceutically acceptable. They are typically formulated using an aqueous solvent, such as water, normal saline or PBS.

[0088] Phospholipids include any natural or synthetic diacylglyceryl phospholipid (such as phosphatidyl choline, phosphotidylethanolamine, phosphotidylserine, phosphatidylinositol, phosphatidylinositol phosphate, etc.) and phosphosphingolipid that can form self-assembling liposomes. In one example, the phospolipid is a phosphatidyl choline, a compound that comprises a choline head group, glycerophosphoric acid and fatty acid. Phosphatidyl choline can be obtained from eggs, soy, or any suitable source and can be synthesized.

[0089] A nonionic surfactant is a surfactant containing no charged groups. Nonionic surfactants comprise a hydrophilic head group and a lipophilic tail group, such as a single- or double-lipophilic chain surfactant. Examples of lipophilic tail groups include lipophilic saturated or unsaturated alkyl groups (fatty acid groups), steroidal groups, such as cholesteryl, and vitamin E (e.g., tocopheryl) groups, such as a polysorbate (a polyoxyethylene sorbitan), for example, Tween 20, 40, 60, or 80. More broadly, non- ionic surfactants include: glyceryl esters, including mono-, di- and tri-glycerides; fatty alcohols; and fatty acid esters of fatty alcohols or other alcohols, such as propylene glycol, polyethylene glycol, sorbitan, sucrose and cholesterol.

[0090] A cationic lipid is a compound having a cationic head and a lipophilic tail. Included are cationic lipids that are quaternary ammonium salts, such as quaternary ammonium salts of lipid-substituted D and L glutamic acid or aspartic acid, such as glutamic acid dialkyl amides, including, for example, L-glutamic acid-1, 5,-dioleyl amide. Other commercially-available examples of cationic lipids (e.g., available from 20 61R3271.DOCXAttorney Docket No.06527-2409107 Avanti Polar Lipids) include DC-Cholesterol (3ß-[N-(N',N'-dimethylaminoethane)- carbamoyl]cholesterol hydrochloride), DOTAP (e.g., 1,2-dioleoyl-3- trimethylammonium-propane (chloride salt)), DODAP (e.g., 1,2-dioleoyl-3- dimethylammonium-propane), DDAB (e.g., Dimethyldioctadecylammonium (Bromide Salt)), ethyl-PC (e.g., 1,2-dilauroyl-sn-glycero-3-ethylphosphocholine (chloride salt)) and DOTMA (e.g., 1,2-di-O-octadecenyl-3-trimethylammonium propane (chloride salt)).

[0091] The ratio of ingredients (phospholipid:nonionic surfactant:cationic lipid) can vary greatly, so long as a useful multilamellar structure is obtained that is able to deliver the active agents described herein. Further, each different combination of ingredients might have different optimal ratios. The ability to determine optimal ratios does not require undue experimentation because the ability of any formulation to deliver the active agent is readily tested as described herein, and as is generally known in the pharmaceutical arts. Liposome and multilamellar structures are common delivery vehicles for active agents and their manufacture, physical testing and biological assays to determine effectiveness are well-known. Useful phospholipid:nonionic surfactant:cationic lipid ratios include, for example: from 0.1- 10:0.1-10:0.1-10 (w / w), and in certain instances the nonionic surfactant:cationic lipid (w / w) ratio is approximately the same and / or the phospholipid constituent is from 2 to 10 times (w / w) that of the nonionic surfactant and cationic lipid.

[0092] Antibody-drug conjugates, where a targeting antibody is reversibly bound to a drug, or is incorporated into a complex with the drug, such as a vesicular (e.g., lipid- mediated) drug delivery vehicle or lipid nanoparticle, may be employed to target the drug to a specific tissue or organ in a patient (see, e.g., Fu, Z, et al. Antibody drug conjugate: the "biological missile" for targeted cancer therapy. Signal Transduct Target Ther.2022 Mar 22;7(1):93; Marques AC, et al. Lipid Nanoparticles Functionalized with Antibodies for Anticancer Drug Therapy. Pharmaceutics. 2023 Jan 8;15(1):216; and Topping LM, et al. Targeting Extracellular Vesicles to the Arthritic Joint Using a Damaged Cartilage-Specific Antibody. Front Immunol.2020 Feb 14;11:10).

[0093] A "therapeutically effective amount" refers to an amount of a drug product or active agent effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result. An “amount effective” for treatment of a condition is an amount of an active agent or dosage form, such as a single or multiple injection, tablet or capsule, or metered doses from a metered-dose inhaler, effective to achieve a 21 61R3271.DOCXAttorney Docket No.06527-2409107 determinable end-point. The “amount effective” is preferably safe - at least to the extent the benefits of treatment outweighs the detriments and / or the detriments are acceptable to one of ordinary skill and / or to an appropriate regulatory agency, such as the U.S. Food and Drug Administration. A therapeutically effective amount of an active agent may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the active agent to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the active agent are outweighed by the therapeutically beneficial effects. A "prophylactically effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve a desired prophylactic result. Typically, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount may be less than the therapeutically effective amount.

[0094] Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus may be administered, several divided doses may be administered over time, or the composition may be administered continuously or in a pulsed fashion with doses or partial doses being administered at regular intervals, for example, every 10, 15, 20, 30, 45, 60, 90, or 120 minutes, every 2 through 12 hours daily, or every other day, etc. The dosage may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. In some instances, it may be especially advantageous to formulate parenteral or inhaled compositions in dosage unit form for ease of administration and uniformity of dosage. The specification for the dosage unit forms of the invention may be dictated by and directly dependent on (a) the unique characteristics of the active compound and the particular therapeutic or prophylactic effect to be achieved, and (b) the limitations inherent in the art of compounding such an active compound for the treatment of sensitivity in individuals.

[0095] The compound may be administered locally or topically at a site of wound, graft, or fibrotic lesion to prevent or treat inflammation, fibrosis, or scarring. Topical administration includes ocular delivery and dosage forms. In a patient with pulmonary fibrosis or other inflammatory conditions of the lungs and / or respiratory tract, the compound may be administered locally, e.g., by spray, nebulization, aerosolization, inhalation, or by bronchoalveolar lavage, or systemically, for example intravenously. 22 61R3271.DOCXAttorney Docket No.06527-2409107

[0096] The compound may be administered to a patient systemically for treating kidney injury, treating acute kidney injury, improving kidney function, inhibiting a histone deacetylase in a cell, expanding renal progenitor cells and / or stimulating kidney repair in cells in vitro, ex vivo or in vivo (in a patient), and / or preventing fibrosis, e.g., fibrotic activity. Compositions also are provided for delivery of the compounds to a patient. Also provided are methods for treating kidney injury, treating acute kidney injury, improving kidney function, inhibiting a histone deacetylase in a cell, expanding renal progenitor cells and / or stimulating kidney repair in cells in vitro, ex vivo or in vivo (in a patient) comprising contacting the cells with, or administering to a patient and amount of one or more of the compounds effective to improve kidney function in a patient, inhibit a histone deacetylase in a cell, expand renal progenitor cells and / or stimulate kidney repair in cells. Therefore, provided are in vitro (including ex vivo) or in vivo (in a patient) methods. Efficacy of the compounds is demonstrated below. The compound described herein may be administered in any manner that is effective for treating kidney injury, treating acute kidney injury, improving kidney function, inhibiting a histone deacetylase in a cell, expanding renal progenitor cells and / or stimulating kidney repair in cells in a patient. The compounds described herein also may be administered in any manner that is effective to treat fibrosis or to reduce or prevent fibrotic activity. Examples of delivery routes include, without limitation: topical, for example, epicutaneous, inhalational, enema, ocular, otic and intranasal delivery; enteral, for example, orally, by gastric feeding tube or swallowing, and rectally; and parenteral, such as, intravenous, intraarterial, intramuscular, intracardiac, subcutaneous, intraosseous, intradermal, intrathecal, intraperitoneal, transdermal, iontophoretic, transmucosal, epidural and intravitreal. For treatment of kidney injury, acute kidney injury, stimulating kidney repair in cells, improving kidney function, inhibiting a histone deacetylase in a cell, and / or expanding renal progenitor cells oral or intravenous approaches may be employed.

[0097] As indicated above, fibrosis can lead to permanent scarring, organ malfunction and death, as with end-stage liver disease, cirrhosis, kidney disease, idiopathic pulmonary fibrosis (IPF), and heart failure. Collagen deposition is an important and reversible part of wound healing in normal tissue repair. However, it can result in an irreversible fibrotic response if the tissue injury is severe or repetitive, or if the wound-healing response becomes dysregulated. Many chronic autoimmune diseases lead to fibrosis, such as, without limitation, scleroderma, rheumatoid arthritis, 23 61R3271.DOCXAttorney Docket No.06527-2409107 Crohn’s disease, ulcerative colitis, myelofibrosis, and systemic lupus erythematosus. Fibrosis also can influence tumor invasion and metastasis, chronic graft rejection, and the pathogenesis of many progressive myopathies. For treatment of fibrosis, the compounds described herein may be administered by any suitable route and dosage regimen. For example, in the case of wound healing and scar prevention, the compound may be formulated as a topical formulation, such as a cream, ointment, tincture, spray, or drops (e.g., for optic or otic topical use). For example, in the case of gastrointestinal wound healing, e.g., for prevention of scarring or strictures in surgical patients or patients with ulcers or inflammatory bowel disease, as in Crohn’s disease or ulcerative colitis, the composition may be administered orally or via a suppository, or systemically, such as parenterally, e.g., by subcutaneous, intramuscular, intravenous, or intraperitoneal delivery routes. Other appropriate delivery routes may be utilized for specific diseases, such as intrathecally for treatment or prevention of epidural fibrosis.

[0098] In aspects, pharmaceutically acceptable salts or hydrates of any of the compounds described herein are provided and are used in the methods described herein. Pharmaceutically acceptable salt forms or hydrates of the compounds described herein may be prepared by conventional methods known in the pharmaceutical arts, for use in human or veterinary drug products. For example and without limitation, where a compound comprises a carboxylic acid group, a suitable salt thereof may be formed by reacting the compound with an appropriate base to provide the corresponding base addition salt. Non-limiting examples include: alkali metal hydroxides, such as potassium hydroxide, sodium hydroxide and lithium hydroxide; alkaline earth metal hydroxides, such as barium hydroxide and calcium hydroxide; alkali metal alkoxides, such as potassium ethanolate and sodium propanolate; and various organic bases such as piperidine, diethanolamine, and N- methylglutamine.

[0099] Acid and base addition salts may be prepared by contacting the free base form with a sufficient amount of a desired acid or base to produce the salt in a manner known in the art. The free base may be regenerated by contacting the salt form with a base or acid (depending on the nature of the salt) and isolating the free base. The free base forms differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents, but otherwise the salts are equivalent to their respective free base forms for purposes described herein. 24 61R3271.DOCXAttorney Docket No.06527-2409107

[0100] Compounds comprising basic nitrogen-containing groups may be quaternized with such agents as C1-4 alkyl halides, such as methyl, ethyl, iso-propyl and tert-butyl chlorides, bromides and iodides; C1-4 alkyl sulfate such as dimethyl, diethyl and diamyl sulfates; C10-18 alkyl halides, such as decyl, dodecyl, lauryl, myristyl and stearyl chlorides, bromides and iodides; and aryl- C1-4 alkyl halides, such as benzyl chloride and phenethyl bromide. Such salts permit the preparation of both water-soluble and oil-soluble compounds.

[0101] Non-limiting examples of pharmaceutically-acceptable base salts include: aluminum, ammonium, calcium, copper, ferric, ferrous, lithium, magnesium, manganic, manganous, potassium, sodium, and zinc salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include, without limitation: salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, and basic ion exchange resins, such as arginine, betaine, caffeine, chloroprocaine, choline, N,N'-dibenzylethylenediamine (benzathine), dicyclohexylamine, diethanolamine, diethylamine, 2- diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine, ethylenediamine, N- ethylmorpholine, N-ethylpiperidine, glucamine, glucosamine, histidine, hydrabamine, iso-propylamine, lidocaine, lysine, meglumine, N-methyl-D-glucamine, morpholine, piperazine, piperidine, polyamine resins, procaine, purines, theobromine, triethanolamine, triethylamine, trimethylamine, tripropylamine, and tris- (hydroxymethyl)-methylamine (tromethamine).

[0102] Acid addition salts may be prepared by treating a compound with pharmaceutically acceptable organic and inorganic acids, including, without limitation: hydrohalides, such as hydrochloride, hydrobromide, hydroiodide; other mineral acids and their corresponding salts such as sulfates, nitrates, and phosphates; alkyl- and mono-arylsulfonates, such as ethanesulfonate, toluenesulfonate, and benzenesulfonate; and other organic acids and their corresponding salts, such as acetate, tartrate, maleate, succinate, citrate, benzoate, salicylate, and ascorbate.

[0103] Non-limiting examples of pharmaceutically-acceptable acid salts include: acetate, adipate, alginate, arginate, aspartate, benzoate, besylate (benzenesulfonate), bisulfate, bisulfite, bromide, butyrate, camphorate, camphorsulfonate, caprylate, chloride, chlorobenzoate, citrate, cyclopentanepropionate, digluconate, dihydrogenphosphate, dinitrobenzoate, dodecylsulfate, ethanesulfonate, fumarate, galacterate, galacturonate, 25 61R3271.DOCXAttorney Docket No.06527-2409107 glucoheptanoate, gluconate, glutamate, glycerophosphate, hemisuccinate, hemisulfate, heptanoate, hexanoate, hippurate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, iodide, isethionate, iso-butyrate, lactate, lactobionate, malate, maleate, malonate, mandelate, metaphosphate, methanesulfonate, methylbenzoate, monohydrogenphosphate, 2- naphthalenesulfonate, nicotinate, nitrate, oxalate, oleate, pamoate, pectinate, persulfate, phenylacetate, 3-phenylpropionate, phosphate, phosphonate, and phthalate.

[0104] Multiple salts forms are also considered to be pharmaceutically-acceptable salts. Common, non-limiting examples of multiple salt forms include: bitartrate, diacetate, difumarate, dimeglumine, diphosphate, disodium, and trihydrochloride. Hydrates and esters of the described compounds also may be produced by known methods.

[0105] As used herein, unless indicated otherwise, for instance in a structure, all compounds and / or structures described herein comprise all possible stereoisomers, individually or mixtures thereof. The compound and / or structure may be an enantiopure preparation consisting essentially of an (-) or (+) enantiomer of the compound, or may be a mixture of enantiomers in either equal (racemic) or unequal proportions.

[0106] Certain compounds described here may have asymmetric centers and therefore exist in different enantiomeric and diastereomeric forms. A compound can be in the form of an optical isomer or a diastereomer. Accordingly, compounds described herein include their optical isomers, diastereoisomers and mixtures thereof, including a racemic mixture unless otherwise specified. Optical isomers of the compounds of the invention can be obtained by known techniques such as asymmetric synthesis, chiral chromatography, simulated moving bed technology, or via chemical separation of stereoisomers through the employment of optically active resolving agents.

[0107] Unless otherwise indicated, “stereoisomer” means one stereoisomer of a compound that is substantially free of other stereoisomers of that compound. Thus, a stereomerically pure compound having one chiral center will be substantially free of the opposite enantiomer of the compound. A stereomerically pure compound having two chiral centers will be substantially free of other diastereomers of the compound. A typical stereomerically pure compound comprises greater than about 80% by weight 26 61R3271.DOCXAttorney Docket No.06527-2409107 of one stereoisomer of the compound and less than about 20% by weight of other stereoisomers of the compound, for example greater than about 90% by weight of one stereoisomer of the compound and less than about 10% by weight of the other stereoisomers of the compound, or greater than about 95% by weight of one stereoisomer of the compound and less than about 5% by weight of the other stereoisomers of the compound, or greater than about 97% by weight of one stereoisomer of the compound and less than about 3% by weight of the other stereoisomers of the compound.

[0108] Therapeutic / pharmaceutical compositions are prepared in accordance with acceptable pharmaceutical procedures. Any of the compounds described herein may be compounded or otherwise manufactured into a suitable composition for use, such as a pharmaceutical dosage form or drug product in which the compound is an active ingredient. According to one example, the drug product described herein is an oral tablet, capsule, caplet, liquid-filled or gel-filled capsule, etc. Compositions may comprise a pharmaceutically acceptable carrier, or excipient. An excipient is an inactive substance used as a carrier for the active ingredients of a medication. Although “inactive” excipients may facilitate and aid in increasing the delivery, stability, or bioavailability of an active ingredient in a drug product. Non-limiting examples of useful excipients include: antiadherents, binders, rheology modifiers, coatings, disintegrants, emulsifiers, oils, buffers, salts, acids, bases, fillers, diluents, solvents, flavors, colorants, glidants, lubricants, preservatives, antioxidants, sorbents, vitamins, sweeteners, etc., as are available in the pharmaceutical / compounding arts.

[0109] Provided herein are histone deacetylase (HDAC) inhibitors and methods of using the same for treating kidney injury. In non-limiting embodiments, the HDAC inhibitor is an HDAC8-specific inhibitor. In non-limiting embodiments, the HDAC inhibitor is and / or includes a compound of Formula (1):(1)

[0110] With reference to Formula (1), in non-limiting embodiments, A may be a cyclohexyl, aryl, heterocyclohexyl, or heteroaryl (e.g., hetero meaning that the ring comprises one or more of N, S, or O replacing a C of the ring, with appropriate single 27 61R3271.DOCXAttorney Docket No.06527-2409107 or double bonds and H atoms), which is optionally substituted, for example with a group of up to 3, 4, 56, 7, 8, 9, 10, 15, or 20 atoms (excluding H atoms), such as saturated or unsaturated hydrocarbyl (e.g., C1-3, C1-4, C1-6, C1-10 alkyl, such as methyl, ethyl, or propyl), saturated or unsaturated alkoxyl (e.g., C1-3, C1-4, C1-6, C1-10 alkoxyl, such as methoxyl or ethoxyl), saturated or unsaturated halo-substituted hydrocarbyl (e.g., halo-substituted C1-3, C1-4, C1-6, C1-10 alkyl), optionally substituted (e.g., halo- substituted) (hetero)alkyl, optionally substituted (e.g., halo-substituted) (hetero)alkyl- aryl, poly(ethylene glycol), or a halogen (including one or more halogen atoms), such as F, Cl, Br, or I (halo-substituted). In non-limiting embodiments A may be aryl or heteroaryl. In non-limiting embodiments, B may be a five-membered ring, for example a heterocyclic 5-membered ring, with one or more additional heteroatoms, such as S, N, or O, with appropriate single or double bonds and H atoms.

[0111] In non-limiting embodiments, R1 and R2 may be, independently -X-R3, where X is an alkyl or and alkyl ether moiety, e.g., -CH2-, -CH2-CH2-, -CH2-CH2-CH2-, -O-CH2-, -O-CH2-CH2-, -O-CH2-CH2-CH2-, -CH2-O-, -CH2-CH2-O-, -CH2-CH2-CH2-O-, and R3 is aryl, heteroaryl, phenyl, cyclohexyl, or naphthyl, either of which may be halo- substituted (including one or more halogen atoms, for example Cl and / or F), (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or R3 may be benzo[d][1,3]dioxol-yl.

[0112] In non-limiting embodiments, the compound of Formula (1) may be a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically- acceptable salt thereof.

[0113] In non-limiting embodiments, the HDAC inhibitor is and / or includes A compound of Formula (2):

[0114] With reference to Formula (2), in non-limiting embodiments, R1 may be an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group. 28 61R3271.DOCXAttorney Docket No.06527-2409107

[0115] In non-limiting embodiments, R1 and / or R2 may be (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl. X may be 0-5 and Y may be -O, -N, or -S. In non-limiting embodiments, R1 and / or R2 may be -X-R4, where X is an alkyl or ether moiety, e.g., -CH2-, -CH2-CH2-, -CH2-CH2-CH2-, -O-CH2-, -O-CH2- CH2-, -O-CH2-CH2-CH2-, -CH2-O-, -CH2-CH2-O-, -CH2-CH2-CH2-O-, and R4 is aryl, heteroaryl, phenyl, cyclohexyl, or naphthyl, either of which may be halo-substituted (including one or more halogen atoms, for example Cl and / or F), (C1-3)alkoxyl- substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido-substituted, or benzo[d][1,3]dioxol-yl.

[0116] In non-limiting embodiments, A, B, C, D, E, and F may be, independently, N, CH, O, or S. In non-limiting embodiments, A, C, D, and E may be N or CH. In non- limiting embodiments, B may be a carbon, and F may be CH or N. In non-limiting embodiments, R3 may be an optionally-substituted alkyl, aryl, or heteroatom.

[0117] In non-limiting embodiments, the compound of Formula (2) may be a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically- acceptable salt thereof.

[0118] In non-limiting embodiments, the compound of Formula (1) has the structure:or a stereoisomer or enantiomer thereof.

[0119] In non-limiting embodiments, the compound of Formula (2) has the structure:or a stereoisomer or enantiomer thereof.

[0120] In non-limiting embodiments, a compound as described herein is one or more of the compounds shown in FIGS.2-4J, and should be understood to include stereoisomers, enantiomers, racemic mixtures, and combinations thereof. In non- 29 61R3271.DOCXAttorney Docket No.06527-2409107 limiting embodiments, the compound is one or more of UPHH-274 and / or UPHH-276, as shown in FIG.3 and having NMR spectra as shown in FIGS.9A-9B.

[0121] In non-limiting embodiments, a compound as described herein may be synthesized as described herein. In non-limiting embodiments, the synthesis may be a multi-step process. In non-limiting embodiments, in a first step, an amino carboxylic acid, for example having the general formula below:, where R1 may be any suitable group to provide a compound as described herein, including, without limitation, L-PhCH2, D-PhCH2, 4-f- PhCH2, 2,4,-F2-PhCH2, 2-F-PhCH2, c-Hex-CH2, 4-Cl-PhCH2, 2-NapCH2, and / or c- Hex-CH2. The amino acid may be combined with di-tert-butyl decarbonate, and sodium bicarbonate are added to a solution. The amino carboxylic acid may be a natural and / or unnatural amino acid.

[0122] In non-limiting embodiments, in a second step the amino acid may be subjected to a protection reaction to produce Compound (1):.

[0123] Suitable protection reactions are known to those of skill in the art and may include use of tert-Butyloxycarbonyl (t-Boc).

[0124] In non-limiting embodiments, in a third step, Compound (1) may be subjected to Weinreb amide coupling, under known conditions, to produce Compound (2): 30 61R3271.DOCXAttorney Docket No.06527-2409107.

[0125] In non-limiting embodiments, in a fourth step, Compound (3):may be subjected to a metal halogen exchange followed by addition of Compound (2) to produce Compound (4):.

[0126] In non-limiting embodiments, in a fifth step Compound (4) may be subjected to a deprotection reaction to produce Compound (5), the compound of interest as described herein:.

[0127] Also provided herein is a method of treating a kidney injury in a patient, where the kidney injury results from any disease or injury, by administering to a patient an effective amount of a compound as described herein, administered in an amount effective to treat kidney injury in the patient. The injury may be acute kidney injury, and may be related to trauma or may be associated with any form of kidney disease 31 61R3271.DOCXAttorney Docket No.06527-2409107 or damage, such as, without limitation, associated with chronic kidney disease; decreased blood flow to the kidneys (e.g., due to blood or drug-induced kidney damage); blood or fluid loss; use of blood pressure medications; heart attack; heart disease; infection; liver failure; sepsis; use of NSAIDs (non-steroidal anti-inflammatory drugs) such as aspirin, ibuprofen, or naproxen sodium; severe allergic reaction (e.g., anaphylaxis); burns; dehydration; blood clots in the veins and arteries in and around the kidneys; cholesterol deposits that block blood flow in the kidneys; glomerulonephritis; inflammation of the glomeruli; hemolytic uremic syndrome; lupus; use of medications such as chemotherapy drugs, antibiotics, or dyes used during imaging tests; scleroderma; thrombotic thrombocytopenic purpura; toxins including, for example, alcohol, heavy metals or cocaine; rhabdomyolysis; tumor lysis syndrome; bladder cancer; blood clots in the urinary tract; cervical cancer; colon cancer; enlarged prostate (e.g., benign prostatic hyperplasia); kidney stones; nerve damage involving the nerves that control the bladder; or prostate cancer.

[0128] Also provided herein is a method of treating fibrosis in a patient, such as administering to a patient an effective amount of a compound as described herein, administered in an amount effective to treat fibrosis in the patient. The fibrosis may result from trauma, as in wound healing, or as part of a disease or condition. The fibrosis may be pulmonary fibrosis, such as idiopathic pulmonary fibrosis. The fibrosis may be associated with, for example and without limitation, scleroderma; rheumatoid arthritis; Crohn's disease; ulcerative colitis; myelofibrosis; systemic lupus erythematosus; liver cirrhosis; non-alcoholic steatohepatitis; interstitial lung disease; kidney-, pancreas-, and heart-fibrosis; acne; and / or rosacea.

[0129] In non-limiting embodiments, treatments as described herein may be administered beginning within a certain period of time, e.g., 1-96 hours, e.g., 1 hour, 2 hours, 4 hours, 8 hours, 12 hours, 24 hours, 48 hours, 72 hours, and / or 96 hours, all values and subranges therebetween inclusive, of the injury and / or the onset of symptoms of the injury (e.g., an acute kidney injury, AKI). In non-limiting embodiments, treatments may be administered beginning within a certain period of time, e.g., 1 day, 1 week, 1 month, all values and subranges therebetween inclusive, of a diagnosis and / or onset of symptoms of the kidney injury or fibrosis. In non-limiting embodiments, treatment may continue on any suitable dosing regimen, e.g., a static dosage and / or titrating up to or down from a maximum dosage, over any suitable time course (e.g., days, months, and / or years). Treatments as described herein may also 32 61R3271.DOCXAttorney Docket No.06527-2409107 be combine (e.g., administered concurrently with and / or in an alternating fashion) with other therapeutic compositions that may be known to those of skill in the art. Example 1

[0130] A library of compounds was prepared as shown in FIG.1.

[0131] General Synthesis of (1): The amino carboxylic acid (1.0eq) was dissolved in dioxanes / water 2:1 at RT. Then di-tert-butyl dicarbonate (Boc2O) (1.2eq) and sodium bicarbonate (NaHCO3) (2.5 eq) was added to the solution and stirred at RT overnight. After removing the dioxanes by reduced pressure, the aqueous solution was washed by diethyl ether (DE). Then 1M hydrochloric acid (HCl) was used to adjust the pH of the solution to around 4. The suspension was extracted with ethyl acetate (EtOAc). The combined organic phase was washed with water and brine and dried over sodium sulfate (Na2SO4). The desired product, (1), was obtained by reduced pressure and used for the next step without further purification.

[0132] General Synthesis of (2): To a solution of 1-(3-Dimethylaminopropyl)-3- ethylcarbodimide hydrochloride (EDC HCl) (1.6 eq) in dichloromethane (DCM) was added 4-dimethylaminopyridine (DMAP) (0.1 eq). The mixture was stirred on ice for 10 minutes. To this mixture 1.3 eq of N,O-Dimethyl hydroxylamine hydrochloride is added and stirred for 10 minutes. To this mixture 1.0 eq of respected boc protected carboxylic acid was added and stirred for 20 minutes. Lastly, 1.3 eq of triethylamine (Et3N) was added and the reaction mixture was stirred overnight. The reaction was monitored by thin layer chromatography (TLC) for disappearance of carboxylic acid starting material. The reaction was quenched with 1M HCl and then diluted with DCM. The organic phase was washed with saturated brine solution. The organic phase was dried over Na2SO4, filtered and concentrated under reduced pressure to provide crude product. The crude product was purified on silica gel column (0-50% EtOAc in hexanes) to give (2).

[0133] General Synthesis of (3): Sodium hydride (NaH) (2.0 eq.) (60% w / w) was washed 3x with hexanes and dried on high vac for 3 hours. A solution of 1.0 eq of 6- bromoindole in dimethylformamide (DMF) was added dropwise to dry NaH, the mixture was stirred in an ice bath for 30 minutes.1.5 eq of 4-methoxybenzyl chloride (PMBCl) was added to the mixture dropwise and the reaction was stirred overnight. The reaction was monitored by TLC for disappearance of 6-bromoindole starting material. The reaction was quenched with saturated ammonium chloride (NH4Cl) and diluted with DCM. The organic phase was washed with saturated brine solution. The 33 61R3271.DOCXAttorney Docket No.06527-2409107 combined organic phases were dried Na2SO4, filtered and concentrated under reduced pressure to provide crude product. The crude product was purified on silica gel column (0-50% EtOAc in hexanes) to give (3).

[0134] General Synthesis of (4): To hexanes washed potassium hydride (KH) 1.0eq suspended in anhydrous diethyl ether at 0°C was added 6-bromoindole 1eq in DE. After 15 mins the solution was cooled to -78°C, 2.0eq of tert-butyllithium (t-BuLi) was added through gas tight syringe. A precipitate formed and after 10 mins the (0.33 eq) Weinreb amide (2) is dissolved in DE and is added to the reaction mixture. The reaction mixture was allowed to slowly warm to room temperature and product formation was monitored through TLC. To quenched, to the solution ice cold 1M phosphoric acid (H3PO4) and extracted with ethyl EtOAc. The combined organic phase was washed with saturated NaHCO3 dried over Na2SO4, filtered and concentrated under reduced pressure to provide crude product. The crude product was purified on silica gel column (0-70% EtOAc in hexanes) to give (4).

[0135] General Synthesis of (5) from 1A: A 2-dram vial was equipped with a magnetic stir bar. D (1.0eq) was added to 0.5mL of methanol (MeOH). Followed by adding (30 eq) of 4M HCl / dioxanes to the reaction mixture. The reaction was stirred overnight and monitored through TLC for completion. The mixture was dried with nitrogen to give (5). Example 2 HDAC8 Biochemical Fluorogenic Enzyme Assay.

[0136] HDAC8 biochemical assays were conducted according to the manufacturer’s instructions using the BPS Bioscience (San Diego, CA) HDAC8 Fluorogenic Assay Kit #50068 which contains HDAC8 enzyme, HDAC fluorogenic substrate, 2x HDAC developer, and HDAC assay buffer. The reactions were conducted in 384-Well polystyrene non-binding flat bottom microplates (Cat. # 781900) obtained from Greiner Bio-One (Monroe, NC). A master mix of 15µL containing HDAC substrate, bovine serum albumin (BSA) and HDAC assay buffer was dispensed into the wells of the microtiter assay plates. Compound wells received 5µL of a 5x compound mixture diluted in HDAC assay buffer + 5% DMSO. Maximum (MAX) and no enzyme blank control wells received 5µL of HDAC assay buffer + 5% DMSO. Minimum (MIN) control wells received 5µL of 5x UPHH-00123 (10µM final) control inhibitor in HADC assay buffer + 5% DMSO. Assay plates were pre-read for relative fluorescence intensity units (RFU’s) at Excitation 350 nm and Emission 455 34 61R3271.DOCXAttorney Docket No.06527-2409107 nm (Ex350 / Em455) using a SpectraMax M5e (Molecular Devices, LLC, Sunnyvale, CA) multi-mode plate reader prior to the addition of HDAC8 enzyme to detect auto fluorescent compounds which may interfere with the assay detection format. Reactions were initiated with the addition of 5µL of 5x HDAC8 enzyme. Blank no enzyme control wells received 5µL of HDAC assay buffer. The final reaction volume was 25 µL. Reactions were incubated at 37 °C for 30 minutes, then 25µL of 2x HDAC developer were added to each well and assay plates were incubated at room temperature for 15 minutes before the RFU’s (Ex350 / Em455) were measured using a SpectraMax M5e multi-mode plate reader.

[0137] Final HDAC8 assay conditions: HDAC8 enzyme 10ng / well, HDAC substrate 2 µM; BSA 0.1 mg / mL, DMSO 1%, MIN control compound UPHH-00123 10µM, test compounds 2nM – 40µM.

[0138] To analyze the data, the mean RFU’s of the blank no enzyme control wells were subtracted from the RFU’s for the maximum and minimum control and test compound wells. The normalized percent inhibition (% inhibition) of each well was then calculated using the equation:

[0139] % Inhibition = (Mean MAX RFU’s – test sample RFU’s) / (Mean MAX – Mean MIN RFU’s) x 100.

[0140] MAX, MIN, & no-enzyme BLANK control wells, n= 12-16

[0141] Test compounds, n=2 for each concentration

[0142] Results of the inhibition assays are shown in Table 1, below: Table 135 61R3271.DOCXAttorney Docket No.06527-2409107

[0143] As can be appreciated, each of UPHH-234, -274, -276, and -284 preferentially inhibits HDAC8 activity over other HDACs. Inhibition for two of the compounds, UPHH-276 and UPHH-274 is shown in Results are shown in FIGS.5A- 5B, respectively.

[0144] Mass spectrometry was performed on two of the generated compounds, UPHH-274 and UPHH-276, using the method described in Gurard et al. High- throughput screening of small molecule libraries using SAMDI mass spectrometry, ACS Comb. Sci.2011, 13(4): 347-350.

[0145] A zebrafish acute kidney injury (AKI) experiment was performed according to the process described in Long et al., Validation of HDAC8 inhibitors as drug discovery starting points to treat acute kidney injury, ACS Pharmacol. Transl. Sci. 2022, 5(4): 207-215. Briefly, Zebrafish larvae were injected with a single dose of gentamicin at 3 days post fertilization (dpf) with 7 ng of gentamicin as previously described. Prior to the gentamicin injection, 3 dpf zebrafish larvae were anesthetized in 0.2% tricaine / E3 medium (5 mM NaCl, 0.33 mM CaCl2, 0.33 mM MgSO4, and 0.17 mM KCl). Glass capillaries were pulled to produce microneedles and were aspirated with 10 μL of 7 ng / nL gentamicin solution diluted with filtered saline solution (Aspen Veterinary Resources, Cat No. 17861615). The larvae were injected with 1 nL of gentamicin solution, delivered via the common cardinal vein. After injection, larvae were incubated in 50 μg / mL penicillin / streptomycin diluted in E3 medium. Test compounds (UPHH-276 and UPHH-274) were diluted in E3 medium containing 0.5% DMSO, except for [rac]-2, (+)-2, and (−)-2, which were diluted in Danieau’s solution instead of E3. Larvae were treated with either DMSO, UPHD25, or test compounds (4 μM) from 2 days postinjection. Results are shown in FIG.6, where a hazard ratio of 1 is set to untreated and injured and below 1 means an increased chance of survival. As can be appreciated, UPHH-276 provides an increased chance of survival. 36 61R3271.DOCXAttorney Docket No.06527-2409107

[0146] A human kidney organoid hemin injury experiment was performed according to the process described in Long et al., Validation of HDAC8 inhibitors as drug discovery starting points to treat acute kidney injury, ACS Pharmacol. Transl. Sci. 2022, 5(4): 207-215. Briefly, after Dispase treatment iPSC clusters were suspended in medium composed of TeSR-E5 (Stemcell Technologies), 0.1% ITS-X, 1% CD lipid concentrate (Gibco), 0.25% polyvinyl alcohol, 1% penicillin / streptomycin (Gibco), and 2.5 μg / mL Plasmocin. On day 3 of the assay, embryoid bodies were transferred to the Stage II medium consisting of DMEM-low glucose, 10% KOSR (Thermo Fisher), 1% nonessential amino acids, 1% penicillin / streptomycin, 1% HEPES, 1% GlutaMAX, 0.25% polyvinyl alcohol, and 2.5 mg / mL Plasmocin. Hemin was made up in 0.1 M NaOH. Day 14 organoids were washed thrice with DMEM-low glucose before being placed into protein-free medium (1:1 ratio of DMEM-low glucose and Hams F-12 nurtrient mixture), 1% HEPES, 1% penicillin / streptomycin (Gibco), and 2.5 μg / mL Plasmocin containing Hemin in a 6-well ultralow attachment plate. The hemin concentration was at 12.5 μM. The control well contained an equivalent volume of 0.1 M NaOH as a vehicle control. All treatments were maintained for 48 h.

[0147] Kidney organoids at day 16 post hemin treatment were washed 3× with Stage II medium. For compound treatment Stage II medium was supplemented with 0.3% DMSO. A 2× solution of compound (UPHH-276) was prepared in Stage II- DMSO, and a calculated amount was added to each well to make up 1× stock in a 3 mL volume, per well of a 6-well ULA plate. The plates were maintained on the magnetic stirrer at 25% power and 120 revolutions until day 23. Deparaffinized sections of kidney organoids were washed with DPBS. A working solution of CHP was first heated for 5 min at 80°C, cooled on ice immediately, and distributed onto each section. Sections were stained overnight at 4°C in a humidified chamber. The next day, sections were washed twice, and nuclei were stained with DAPI and mounted before imaging on a Zeiss LSM700 instrument. Results are shown in FIG.7.

[0148] A human kidney organoid doxorubicin injury experiment was performed as described below. Briefly, organoids were treated for 2 days with doxorubicin, followed by 2 days with test compound (UPHH-274 or UPHH-276). Results are shown in FIGS. 8A-8D (UPHH-276). RNA from organoids collected and assayed by qPCR for (1) Podocytes (NPHS2) which should go away as podocytes are killed and any restoration of signal means recovery of podocytes; (2) Blood vessels (PECAM1), which again an increase means possibly more vessels; (3) HAVCR1 which is Kim1 and show tubule 37 61R3271.DOCXAttorney Docket No.06527-2409107 injury, so reduction is good; (4) MMP9 is a marker of epithelial cell injury and again reduction is good. UN = untreated, DOXO is Doxorubicin injury alone, PCI = PCI- 34051 treated at 0.5uM, Test compound tested at 0.2uM, 1uM and 5uM.

[0149] While the present invention has been described in terms of the above examples and detailed description, those of ordinary skill will understand that alterations may be made within the spirit of the invention. Accordingly, the above should not be considered limiting, and the scope of the invention is defined by the appended claims. 38 61R3271.DOCX

Claims

Attorney Docket No.06527-2409107 THE INVENTION CLAIMED IS 1. A method of treating a kidney injury in a patient comprising administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury, the HDAC inhibitor comprising a compound as set forth in Formula (1):wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; and R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

2. The method of claim 1, the compound having the structure:, or a pharmaceutically-acceptable salt thereof.

3. The method of claim 1, the compound having the structure: 39 61R3271.DOCXAttorney Docket No.06527-2409107, or a pharmaceutically-acceptable salt thereof.

4. The method of claim 1, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

5. The method of claim 1, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

6. The method of claim 1, wherein the HDAC inhibitor is selective for HDAC8.

7. The method of claim 1, wherein the HDAC inhibitor is administered to the patient orally, intravenously, subcutaneously, intramuscularly, intradermally, via inhalation, and / or via insufflation.

8. The method of claim 1, wherein the kidney injury is acute kidney injury (AKI). 40 61R3271.DOCXAttorney Docket No.06527-2409107 9. The method of claim 8, wherein the HDAC inhibitor is administered within 1-24 hours of the AKI.

10. The method of claim 1, wherein the kidney injury is associated with trauma in the patient.

11. The method of claim 1, wherein the kidney injury is associated with: chronic kidney disease; decreased blood flow to the kidneys; blood or fluid loss; use medications; heart attack; heart disease; infection; liver failure; sepsis; severe allergic reaction; burns; dehydration; blood clots in the veins and arteries in and around the kidneys; cholesterol deposits that block blood flow in the kidneys; glomerulonephritis; inflammation of the glomeruli; hemolytic uremic syndrome; lupus; use of dyes used during imaging tests; scleroderma; thrombotic thrombocytopenic purpura; toxins; rhabdomyolysis; tumor lysis syndrome; bladder cancer; blood clots in the urinary tract; cervical cancer; colon cancer; enlarged prostate; kidney stones; nerve damage involving the nerves that control the bladder; and / or prostate cancer.

12. A method of treating a kidney injury in a patient comprising administering to the patient an amount of a histone deacetylase (HDAC) inhibitor effective to treat the kidney injury, the HDAC inhibitor comprising a compound as set forth in Formula (2):(2), wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl, heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; 41 61R3271.DOCXAttorney Docket No.06527-2409107 A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

13. The method of claim 12, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

14. The method of claim 12, the compound having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

15. The method of claim 12, wherein the HDAC inhibitor is a selective HDAC8 inhibitor.

16. The method of claim 12, wherein the HDAC inhibitor is administered to the patient orally, intravenously, subcutaneously, intramuscularly, intradermally, via inhalation, and / or via insufflation.

17. The method of claim 12, wherein the injury is an acute kidney injury (AKI). 42 61R3271.DOCXAttorney Docket No.06527-2409107 18. The method of claim 17, wherein the HDAC inhibitor is administered within 1-24 hours of the AKI.

19. The method of claim 12, wherein the injury is associated with trauma in the patient.

20. The method of claim 12, wherein the kidney injury is associated with: chronic kidney disease; decreased blood flow to the kidneys; blood or fluid loss; use medications; heart attack; heart disease; infection; liver failure; sepsis; severe allergic reaction; burns; dehydration; blood clots in the veins and arteries in and around the kidneys; cholesterol deposits that block blood flow in the kidneys; glomerulonephritis; inflammation of the glomeruli; hemolytic uremic syndrome; lupus; use of dyes used during imaging tests; scleroderma; thrombotic thrombocytopenic purpura; toxins; rhabdomyolysis; tumor lysis syndrome; bladder cancer; blood clots in the urinary tract; cervical cancer; colon cancer; enlarged prostate; kidney stones; nerve damage involving the nerves that control the bladder; and / or prostate cancer.

21. A method of treating fibrosis in a patient comprising: administering an amount of a histone deacetylase (HDAC) inhibitor effective to treat the fibrosis in the patient, the HDAC inhibitor comprising a compound as set forth in Formula (1):wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and 43 61R3271.DOCXAttorney Docket No.06527-2409107 R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof; or a compound as set forth in Formula (2):wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

22. A compound of Formula (1):wherein: A is an optionally-substituted cyclohexyl, aryl, heterocyclohexyl, or heteroaryl; 44 61R3271.DOCXAttorney Docket No.06527-2409107 B is a heterocyclic 5-membered ring optionally substituted with one or more of S, N, or O; and R1 and R2 are, independently -X-R3, where X is a divalent alkyl or ether moiety; and R3 is aryl, heteroaryl, or naphthyl, optionally halo-substituted, (C1- 3)alkoxyl-substituted, (C1-3)alkoxy-(C1-3)alkoxyl-substituted, or phenylsulfonamido- substituted, or benzo[d][1,3]dioxol-yl, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

23. The compound of claim 22, having the structure:, or a pharmaceutically-acceptable salt thereof.

24. The compound of claim 22, having the structure:, or a pharmaceutically-acceptable salt thereof.

25. The compound of claim 22, having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof. 45 61R3271.DOCXAttorney Docket No.06527-2409107 26. The compound of claim 22, having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

27. A composition comprising the compound of claim 22 and a pharmaceutically-acceptable excipient.

28. A compound of Formula (2):wherein: R1 is an aryl group, a substituted aryl group, a heteroaryl group, a substituted heteroaryl group, an alkyl group, or a cycloalkyl group; R2 is (CH2)x-Y – aryl or heteroaryl, (CH2)x-Y – substituted aryl or substituted heteroaryl, or (CH2)x-Y – optionally substituted cycloalkyl heteroalkyl, or heterocyclyl, where X is 0-5 and Y is -O, -N, or -S; A, C, D, and E may be, independently, N or CH; B is a carbon atom; F may be CH or N; and R3 is a substituted alkyl, aryl, or heteroatom, or a stereoisomer, enantiomer, or racemic mixture thereof, or a pharmaceutically-acceptable salt thereof.

29. The compound of claim 28, having the structure: 46 61R3271.DOCXAttorney Docket No.06527-2409107, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

30. The compound of claim 28, having the structure:, or a stereoisomer, enantiomer, and / or pharmaceutically-acceptable salt thereof.

31. A composition comprising the compound of claim 28 and a pharmaceutically-acceptable excipient. 47 61R3271.DOCX

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