EP-4734989-A2 - SYNTHESIS AND IN VITRO CHARACTERIZATION OF PROTEOLYSIS TARGETING CHIMERAS (PROTACS) FOR DEGRADATION OF DNA METHYLTRANSFERASE 1 (DNMT1)

Abstract

Disclosed are compounds (degraders) that target DNMT1 for degradation. Also disclosed are pharmaceutical compositions containing the compounds and methods of using the compounds to treat diseases and disorders characterized or mediated by aberrant DNMT1 activity.

Inventors

• QI, JUN
• LIOW, Priscilla
• WANG, Tingjian

Assignees

• Dana-Farber Cancer Institute, Inc.

Dates

Publication Date

20260506

Application Date

20240628

Claims (1)

1. What is claimed is: 1. A compound of formula (I): ( DNMTF ..1 I Targeting Ligand fTLij ' - ' (I), or a pharmaceutically acceptable salt or stereoisomer thereof, wherein: DNMT1 Targeting Ligand is of Formula TL-1 or TL-2: R 3 and R 4 , together with the nitrogen atom to which they are attached, form an optionally substituted 6-rnembered heterocyclyl, or R 3 and R 4 . together with the nitrogen atom to which they are attached, form an optionally substituted 6-membered heterocyclyl which is also bound to the linker: Rs and Ri, are independently H, optionally substituted alkyd, or 5 : wherein « is a bond between the DNMT1 Targeting Ligand and the Linker, provided that there is only one bond between the DNMT1 Targeting Ligand and the L inker; the linker represents a moiety that connects covalently the degron and the targeting ligand; and the Degron is of Formula DI, D2, or D3: wherein: Q is CH 2 or C(O); and X1 is O. NH. CH 2 or C C. R7 is H or optionally substituted C1-C 3 alkyl, or R7 and Rs, together with the carbon atom to which they are attached, form cyclopropyl; R10 and R11 are both H. or R10 and R11, together with the carbon atom to which they are atached, form cyclopropyl; R12 is H, fluoro, cyano, or NMe2: and wherein is a bond between the Degron and the Linker, provided that there is only one bond between the Degron and the Linker. 2. The compound of claim 1, wherein R 2 is NH2. 3. The compound of claim I or 2. wherein Rs is H and R 4 is . and Formula TL-1 is or IL-ra: 4. The compound of claim I or 2. wherein Rs is Me and R 4 is , and Formula TL-1 is 5. The compound of claim I or 2, wherein Rs and R 4 , together with the nitrogen atom to which they are attached, form an optionally substituted 6-membered heterocycly] which is also bound to the linker. 6. The compound of claim 5, wherein Rs and Rr, together with the nitrogen atom to which they are attached, form piperidyl, the Formula TL-1 is of TL-1 c: 7. The compound of claim 1, wherein Rs and R 4 . together with the nitrogen atom to which they are attached, form an optionally substituted 6-membered heterocycly!. 8. The compound of claim 7, wherein Rs and R 4 , together with the nitrogen atom to which they are attached, form optionally substituted piperidyl. 9 The compound of claim 8, wherein piperidyl is substituted with an amino group. 10. The compound of any one of claims 7-9, wherein R 2 is and Formula TL-1 is of TL-id: -ld). 1 1 . The compound of claim 1 , wherein the DNMT1 Targeting Ligand is of Formula TL-2 and R 6 is H, or R 5 is H or optionally substituted alkyl and R 6 is . 12. The compound of any one of claims 1-11 , wherein the Degron is of Formula DI . 13. The compound of claim 12, wherein Formula DI is of Formula Dla-Dlp: 4. The compound of any one of claims 1-11, wherein the Degron is of Formula D2 or D3. The compound of claim 14, wherein the Degron is of Formula D2a-D2o or D3a-Djg. r stereoisomer thereof 16, The compound of any one of claims 1-15, wherein the Linker is of Formula LO: or stereoisomer thereof, wherein p1 is fin integer selected from 0 to 6; p2 is an integer selected from 0 to 12; p3 is an integer selected from 0 to 12; each W is independently absent, CH 2 , O, S, NR 13 , or C(O)NH; each R13 is independently hydrogen or C 1 -C 6 alkyl; W1 and W2 are independently absent, Z 1 and Z? are independently absent, , bonded to a Targeting Ligand via the next to Wi, or the Linker is covalently bonded to a Degron via the next to W1, and covalently bonded to a Targeting Ligand via the next to W2. 17. The compound of claim 16, wherein Formula LO is of Formula LOa-LOj: 18. The compound of any one of claims 1-15, wherein the Linker is a bond or comprises an alkylene chain or a bivalent alkylene chain, either of which may be interrupted by. and/or terminates at either or both termini with at least one ( ) , ( ) C 3 -C 12 carbocy clone, 3- to 12- membered heterocyciene, 5- to 12-membered heteroarylene or any combination thereof. wherein R' is H or C 1 -C 6 alkyl, wherein the interrupting and the one or both terminating groups may be the same or different. 19. The compound of any one of claims 1-15, wherein the Linker is a polyethylene glycol (PEG) chain which may be interrupted by, and/or terminates at either or both termini with at least one of N(R')S(0)N(R’)-, C 3 -C 12 carbocyclene, 3- to 12-membered heterocyclene, 5- to 12-membered heteroarylene or any combination thereof, wherein R' is H or C 1 -C 6 alkyl, wherein the interrupting and the one or both terminating groups may be the same or different. 20. The compound of any one of claims 1-15, wherein the Linker is represented by any one of structures: or stereoisomer thereof. 22 A pharmaceutical composition, comprising a therapeutically effective amount of the compound or pharmaceutically acceptable salt or stereoisomer thereof of any one of claims 1- 21 , and a pharmaceutically acceptable carrier. 23. A method of treating a disease or disorder characterized or mediated by aberrant DNMT1 activity, comprising administering a therapeutically effective amount of the compound of any one of claims 1-21 or a pharmaceutically acceptable salt or stereoisomer thereof, to a subject in need thereof. 24. The method of claim 23, wherein the disease or disorder is cancer. 25. The method of claim 24. wherein the cancer is breast, colon, or prostate cancer.

Description

SYNTHESIS AND IN VITRO CHARACTERIZATION OF PROTEOLYSIS TARGETING CHIMERAS (PROTACS) FOR DEGRADATION OF DNA METHYLTRANSFERASE 1 (DNMT1) RELATED APPLICATIONS [0001] This app1ication claims the benefit of priority under 35 U.S.C. § 119(e) to U.S. Provisional Application No: 63/523.993, filed June 29, 2023. which is incorporated herein by reference in its entirety. BACKGROUND OF THE DISCLOSURE [0002] Deoxyribonucleic acid methyl transferase 1 (DNMT1) is an epigenetic writer protein which is responsible for the maintenance of DNA methylation during cell proliferation. DNA methylation is a well-studied mechanism of epigenetic regulation, affecting the transcription of crucial genes, and DNA hyper- or hypo-methylation has been found to be associated with a number of human diseases including cancer As such, abnormal DNMT1 activity p1ays an important role in cancer development. Existing drugs for DNMT1 dysregulation, such as decitabine and 5-azacytidine, are highly toxic, and cancer cells often develop drug resistance. SUMMARY OF THE INVENTION [0003] A first aspect of the present disclosure is directed to a compound of formula I, (I), or a pharmaceutically acceptable salt or stereoisomer thereof, wherein: DNMT1 Targeting Ligand is of Formula TL-I or TL-2: R1 is NR3R4; R3 is H or methyl , R3 and R4, together with the nitrogen atom to which they are atached, form an optionally substituted 6-rnembered heterocyclyl, or R3 and R4. together with the nitrogen atom to which they are attached, form an optionally substituted 6-membered heterocyclyl which is also bound to the linker; Rs and Rc are independently H, optionally substituted alkyd, or ; § wherein « is a bond between the DNMT1 Targeting Ligand and the Linker, provided that there is only one bond between the DNMT1 Targeting Ligand and the Linker; the linker represents a moiety that connects covalently the degron and the targeting ligand; and the Degron is of Formula DI, D2, or D3: wherein Q is CH2 or C(O); and Xi is O. NH, CH2, or C-C; R7 is H or optionally substituted C1-C6 alkyl, or R7 and R8, together with the carbon atom to which they are attached, form cyclopropyl; R10 and R11 are both H, or R10 and R11, together with the carbon atom to which they are attached, form cyclopropyl; R12 is H, fluoro, cyano, orNMe2; and wherein ' is a bond between the Degron and the Linker, provided that there is only one bond between the Degron and the Linker. [0004] Another aspect of the present disclosure is directed to a pharmaceutical composition containing a therapeutically effective amount of a compound offormulal or a pharmaceutically acceptable salt or stereoisomer thereof, and a pharmaceutically acceptable carrier. [0005] In another aspect of the present disclosure, methods of making the compounds are provided. [0006] A further aspect of the presen t disclosure is directed to a method of treating a disease or disorder involving (characterized or mediated by) aberrant DNMT1 activity, that includes administering a therapeutically effective amount of a compound of formula I or a pharmaceutically acceptable salt or stereoisomer thereof, to a subject in need thereof [0007] Without intending to be bound by any particular theory1 of operation, compounds of formula I (also referred to herein as PROTAC6 or degraders) are believed to promote the degradation of DNMT1 via cells’ Ubiquitin/Proteasome System, whose function is to routinely identify' and remove damaged proteins. After destruction of an DNMT1 protein molecule, the degrader is released and continues to be active. Therefore, by' engaging and exp1oiting the body’s own natural protein disposal system, compounds of the present disclosure may represent a potential improvement over current small molecule inhibitors of DNMT1. Therefore, effective intracellular concentrations of the degraders may' be significantly lower than for small molecule DNMT1 inhibitors. BRIEF DESCRIPTION OF THE DRAWINGS [0008] FIG. 1 is a Western Blot showing that compounds 1-4 degraded DNMT1 in HL60 cells at indicated concentrations. [0009] FIG. 2 is a Western Blot showing that compounds 5-8 degraded DNMT1 in HL60 cells at indicated concentrations. [0010] FIG. 3 is a Western Blot showing that compounds 9-12 degraded DNMTl in HL60 cells at indicated concentrations. [0011] FIG. 4 is a Western Blot showing that compounds 13-16 degraded DNMTl in HL60 cells at indicated concentrations. [0012] FIG. 5 is a Western Blot showing that compounds 17-19 degraded DNMTl in HL60 cells at indicated concentrations. [0013] FIG. 6 is a Western Blot showing that compounds 20-23 degraded DNMTl in HL60 cells at indicated concentrations. [0014] FIG. 7 is a Western Blot showing that compound 20 degraded DNMTl in HL60 cells at indicated concentrations. [0015] FIG. 8 is a Western Blot show ing that compound 20 degraded DNMT I in Jurkat cells at indicated concentrations. [0016] FIG. 9 is a Western Blot showing that compound 20 degraded DNMTl in A172 cells a