IP Library Granted Patent US 12662464
Granted Patent B2
US 12662464 · App. 17/604,852 · Granted Jun 23, 2026

Degraders of cyclin-dependent kinase 12 (CDK12) and uses thereof

Inventors: Jianwei Che (Sharon, MA); Nathanael S. Gray (Stanford, CA); Tinghu Zhang (Brookline, MA); Baishan Jiang (Brookline, MA); Yang Gao (Boston, MA); Nicholas Paul Kwiatkowski (Brookline, MA)
Assignee: DANA-FARBER CANCER INSTITUTE, INC.
C07D401/14A61K45/06A61K47/555C07D417/14A61K38/00
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Quick Facts
Patent No.
US 12662464
App. No.
17/604,852
Granted
Jun 23, 2026
Kind
B2
Abstract

Provided herein are bifunctional compounds with a moiety (e.g., lenalidomide, thalidomide) that is a binder of an E3 ubiquitin ligase (e.g., Cereblon) and another moiety that is a binder of a target protein (e.g., kinase (e.g., CDK (e.g., CDK9 and/or CDK12))) to induce degradation of the target protein CDK9 and/or CDK12. Also provided are pharmaceutical compositions comprising the bifunctional compounds, and methods of treating and/or preventing diseases (e.g., proliferative diseases, such as cancers (e.g., ovarian cancer, breast cancer, or prostate cancer))). Provided also are methods of inducing the degradation of the target protein (e.g., kinase (e.g., CDK (e.g., CDK9 and/or CDK12))), and methods of inducing apoptosis in a cell in a biological sample or subject by administering the bifunctional compound or composition described herein.

Claims (75)

1 . A compound of Formula (I):

or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein:

each instance of R 1 is independently halogen, acyl, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, heteroaryl, —CN, —OR D1 , —N(R D1a ) 2 , or —SR D1 , wherein R D1 is hydrogen, acyl, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl;

wherein each occurrence of R D1a is hydrogen, acyl, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl; or two instances of R D1a are taken together with their intervening atoms to form a heteroaryl ring;

each instance of R 2 is independently halogen, acyl, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, heteroaryl, —CN, —OR D1 , —N(R D1a ) 2 , or —SR D1 ;

R 3 is hydrogen, acyl, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, or heteroaryl;

Ring A is of formula:

R Y is —SO 2 R Y1 , —P(═O)(R Y2 ) 2 , or —C(═O)N(R y3 )= 2 ;

R Y1 is C 1 -C 6 alkyl;

each instance of R Y2 is C 1 -C 6 alkyl;

each instance of R y3 is independently hydrogen or alkyl;

w1 is 1;

x is 0 or 1;

y is 0 or 1;

L1 is —NR A —; wherein R A is hydrogen;

L2 is an unsubstituted C 1-24 hydrocarbon chain, optionally wherein one or more chain atoms of the hydrocarbon chain are independently replaced with —C(═O)—, —O—, or —NR b —, wherein R b is hydrogen, or

l 4 indicates the point of attachment to D, and l R indicates the point of attachment to the moiety of formula

n1 is 1, 2, 3, 4, 5, or 6;

n2 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

and

D is of the formula:

wherein:

X A is C(O) or C(R 3A ) 2 ;

R 1A is halogen, —OH, C 1 -C 6 alkyl, or C 1 -C 6 alkoxy;

each R 3A is independently H or C 1 -C 3 alkyl;

R 3 ′ is C 1 -C 3 alkyl;

each R 4A is independently H or C 1 -C 3 alkyl; or two R 4A , together with the carbon atom to which they are attached, form C(O);

R 5A is H, C 1 -C 3 alkyl, or halogen;

m is 0 or 1;

n is 0 or 1; and

a1 is 0 or 1,

or

wherein:

R 2 ′ is halogen, —OH, C 1 -C 6 alkyl, or C 1 -C 6 alkoxy;

R 4 ′ is halogen, —OH, C 1 -C 6 alkyl, or C 1 -C 6 alkoxy;

R 5 ′ is halogen, —OH, C 1 -C 6 alkyl, or C 1 -C 6 alkoxy;

n1 is 0 or 1;

n2 is 0 or 1; and

n3 is 0 or 1.

2 . The compound of claim 1 , wherein the compound is of formula:

or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein at least one instance of R Y is —SO 2 R Y1 wherein R Y1 is C 1 -C 6 alkyl, —C(═O)N(R y3 ) 2 wherein each instance of R y3 is independently hydrogen or alkyl, or —P(═O)(R Y2 ) 2 wherein each instance of R Y2 is C 1 -C 6 alkyl.

3 . The compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein D is of the formula:

wherein:

X A is C(O) or C(R 3A ) 2 ;

each R 3A is H;

two R 4A , together with the carbon atom to which they are attached, form C(O);

R 5A is H;

m is 0;

n is 0; and

a1 is 1.

4 . The compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein D is of the formula:

5 . The compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein D is of the formula:

wherein:

R 2 ′ is —OH;

R 5 ′ is C 1 -C 6 alkyl;

n1 is 1;

n2 is 0; and

n3 is 1.

6 . The compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein D is of the formula:

7 . The compound of claim 1 , wherein the compound is of formula:

or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein at least one instance of R 1 is halogen, optionally substituted C 1-6 alkyl, —CF 3 , or —CN.

8 . The compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein L2 is:

l A indicates the point of attachment to D, and/R indicates the point of attachment to the moiety of formula

n1 is 1, 2, 3, 4, 5, or 6;

n2 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

n3 is 1, 2, 3, 4, 5, or 6; and

g is 1, 2, 3, 4, 5, or 6.

9 . The compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, wherein L2 is of the formula:

10 . The compound of claim 1 , wherein the compound is of the formula:

or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof.

11 . A pharmaceutical composition comprising a compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof, and optionally a pharmaceutically acceptable excipient,

wherein R 3A is H when D is of formula IA.

12 . A method of inducing the degradation of CDK9 and/or CDK12 in a cell, tissue, or biological sample, the method comprising:

contacting the cell, tissue, or biological sample with a therapeutically effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt, co-crystal, tautomer, stereoisomer, solvate, hydrate, polymorph, isotopically enriched derivative, or prodrug thereof,

wherein R 3A is H when D is of formula IA.