IP Library › Granted Patent US 10,342,798

Granted Patent B2

US 10,342,798 · App. 15/737,683 · Granted Jul 9, 2019

Fused bicyclic pyrimidine derivatives and uses thereof

Inventors: Nathanael S. Gray (Boston, MA); Tinghu Zhang (Brookline, MA)

Assignee: Dana-Farber Cancer Institute, Inc.

A61K31/519 A61K31/166 A61K31/167 A61K31/34 A61K31/381 A61K31/437 A61K45/06 A61P35/02 C07D491/048 C07D495/04 C07D519/00

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Quick Facts

Patent No.: US 10,342,798
App. No.: 15/737,683
Granted: Jul 9, 2019
Kind: B2

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Abstract

The present invention provides novel compounds of Formula (I), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeled derivatives, prodrugs, and compositions thereof. Also provided are methods and kits involving the inventive compounds or compositions for treating or preventing proliferative diseases (e.g., cancers (e.g., lung cancer, breast cancer, leukemia, lymphoma, melanoma, multiple myeloma, Ewing's sarcoma, osteosarcoma, brain cancer, neuroblastoma), benign neoplasms, angiogenesis, inflammatory diseases, autoinflammatory diseases, and autoimmune diseases) in a subject. Treatment of a subject with a proliferative disease using a compound or composition of the invention may inhibit the aberrant activity of a kinase (e.g. a protein kinase (e.g. a cyclin-dependent kinase (CDK) (e.g. CDK7, CDK12, or CDK13) or a lipid kinase such as a phosphatidylinositol-5-phosphate 4-kinase (PIP4K) (e.g., PI5P4Kα, PI5P4Kβ, or PI5P4Kγ)) in the subject.

Claims (102)

1. A compound of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein:

Ring A is a substituted or unsubstituted, monocyclic or bicyclic heteroaryl ring or a substituted or unsubstituted, monocyclic heterocyclic ring;

each instance of R A is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C(═NR a )R a , —C(═NR a )OR a , —C(═NR a )N(R a ) 2 , —C(═O)R a , —C(═O)OR a , —C(═O)N(R a ) 2 , —NO 2 , —NR a C(═O)R a , —NR a C(═O)OR a , —NR a C(═O)N(R a ) 2 , —OC(═O)R a , —OC(═O)OR a , or —OC(═O)N(R a ) 2 ;

each instance of R a is independently hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two instances of R a are joined to form a substituted or unsubstituted, heterocyclic ring, or substituted or unsubstituted, heteroaryl ring;

k is 0, 1, 2, 3, 4, 5, or 6;

M is NR M , O, or S;

R M is hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, or a nitrogen protecting group;

L 1 is a bond, —C(R b ) 2 —, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O) 2 —, or —NR c —;

each instance of R b is independently hydrogen, halogen, or substituted or unsubstituted C 1-6 alkyl;

each instance of R c is independently hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group;

R B1 is hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C(═NR a )R a , —C(═NR a )OR a , —C(═NR a )N(R a ) 2 , —C(═O)R a , —C(═O)OR a , —C(═O)N(R a ) 2 , —NO 2 , —NR a C(═O)R a , —NR a C(═O)OR a , —NR a C(═O)N(R a ) 2 , —OC(═O)R a , —OC(═O)OR a , or —OC(═O)N(R a ) 2 ;

R B2 is hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C(═NR a )R a , —C(═NR a )OR a , —C(═NR a )N(R a ) 2 , —C(═O)R a , —C(═O)OR a , —C(═O)N(R a ) 2 , —NO 2 , —NR a C(═O)R a , —NR a C(═O)OR a , —NR a C(═O)N(R a ) 2 , —OC(═O)R a , —OC(═O)OR a , or —OC(═O)N(R a ) 2 ;

X is —C(R b ) 2 —, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O) 2 —, —NR c —, —C(R b ) 2 C(R) 2 —, —C(R b ) 2 C(═O)—, —C(═O)C(R b ) 2 —, (E)-CR b ═CR b —, (Z)—CR b ═CR b- , —C≡C—, —OC(═O)—, —C(═O)O—, —SC(═O)—, —C(═O)S—, —NR c C(═O)—, —C(═O)NR c —, —OC(R b ) 2 —, —C(R b ) 2 O—, —SC(R b ) 2 —, —C(R b ) 2 S—, —NR c C(R b ) 2 —, —C(R b ) 2 NR c , —S(═O)O—, —OS(═O)—, —S(═O)NR c —, —NR c S(═O)—, —S(═O) 2 O—, —OS(═O) 2 —, —S(═O) 2 NR c —, or —NR c S(═O) 2 —;

Ring C is a substituted or unsubstituted phenyl ring;

Ring D is a substituted or unsubstituted phenyl ring;

each instance of R C is independently halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C(═NR a )R a , —C(═NR a )OR a , —C(═NR a )N(R a ) 2 , —C(═O)R a , —C(═O)OR a , —C(═O)N(R a ) 2 , —NO 2 , —NR a C(═O)R a , —NR a C(═O)OR a , —NR a C(═O)N(R a ) 2 , —OC(═O)R a , —OC(═O)OR a , or —OC(═O)N(R a ) 2 ;

n is 0, 1, 2, 3, or 4;

L 2 is —C(R b ) 2 —, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O) 2 —, —NR c —, —C(R b ) 2 C(R b ) 2 —, —C(R b ) 2 C(═O)—, —C(═O)C(R b ) 2 —, (E)-CR b ═CR b —, (Z)—CR b ═CR b —, —C≡C—, —OC(═O)—, —C(═O)O—, —SC(═O)—, —C(═O)S—, —NR c C(═O)—, —C(═O)NR c —, —OC(R b ) 2 —, —C(R b ) 2 O—, —SC(R b ) 2 —, —C(R b ) 2 S—, —NR c C(R b ) 2 —, —C(R b ) 2 NR c —, —S(═O)O—, —OS(═O)—, —S(═O)NR c —, —NR c s(═O)—, —S(═O) 2 O—, —OS(═O) 2 —, —S(═O) 2 NR c —, —NR c (═O) 2 —, —OC(═O)O—, —NR c C(═O)O—, —OC(═O)NR c —, NR c C(═O)NR c —, —C(R b ) 2 C(═O)C(R b ) 2 —, —OC(═O)C(R b ) 2 —, —C(R b ) 2 C(═O)O—, —NR c C(═O)C(R b ) 2 —, —C(R b ) 2 C(═O)NR c —, or a substituted or unsubstituted C 1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C(═O)—, —O—, —S—, —S(═O)—, —S(═O) 2 —, or —NR c —;

each instance of R D is independently halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C(═NR a )R a , —C(═NR a )OR a , —C(═NR a )N(R a ) 2 , —C(═O)R a , —C(═O)OR a , —C(═O)N(R a ) 2 , —NO 2 , —NR a C(═O)R a , —NR a C(═O)OR a , —NR a C(═O)N(R a ) 2 , —OC(═O)R a , —OC(═O)OR a , or —OC(═O)N(R a ) 2 ;

p is 0, 1, 2, 3, or 4;

R E is of the formula:

L 3 is —C(R b ) 2 —, —C(═O)—, —O—, —S—, —S(═O)—, —S(═O) 2 —, —NR c —, —C(R b ) 2 C(R b ) 2 —, —C(R b ) 2 C(═O)—, —C(═O)C(R b ) 2 —, (E)-CR b ═CR b —, (Z)—CR b ═CR b —, —C≡C—, —OC(═O)—, —C(═O)O—, —SC(═O)—, —C(═O)S—, —NR c C(═O)—, —C(═O)NR c —, —OC(R b ) 2 —, —C(R b ) 2 O—, —SC(R b ) 2 —, —C(R b ) 2 S—, —NR c C(R b ) 2 —, —C(R b ) 2 NR c —, —S(═O)O—, —OS(═O)—, —S(═O)NR c —, —NR c S(═O)—, —S(═O) 2 O—, —OS(═O) 2 —, —S(═O) 2 NR c —, —NR c S(═O) 2 —, —OC(═O)O—, —NR c C(═O)O—, —OC(═O)NR c —, —NR c C(═O)NR c —, —C(R b ) 2 C(═O)C(R b ) 2 —, —OC(═O)C(R b ) 2 —, —C(R b ) 2 C(═O)O—, —NR c C(═O)C(R b ) 2 —, —C(R b ) 2 C(═O)NR c —, or a substituted or unsubstituted C 1-4 hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain are independently replaced with —C(═O)—, —O—, —S—, —S(═O)—, —S(═O) 2 —, or —NR c —;

L 4 is a bond or substituted or unsubstituted C 1-6 hydrocarbon chain;

each of R E1 , R E2 , and R E3 is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —CN, —CH 2 OR a , —CH 2 N(R a ) 2 , —CH 2 SR a , —OR a , —N(R a ) 2 , —SR a , or —Si(R a ) 3 ; or R E1 and R E3 , or R E2 and R E3 , or R E1 and R E2 are joined to form a substituted or unsubstituted, carbocyclic ring, or substituted or unsubstituted, heterocyclic ring;

R E4 is a leaving group;

R E5 is halogen;

R E6 is hydrogen, substituted or unsubstituted C 1-6 alkyl, or a nitrogen protecting group;

each instance of Y is independently O, S, or NR c ;

a is 1 or 2; and

each instance of z is independently 0, 1, 2, 3, 4, 5, or 6.

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

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

4. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein Ring A is a substituted or unsubstituted, bicyclic heteroaryl ring.

5. The compound of claim 4 , or a pharmaceutically acceptable salt thereof, wherein Ring A is of Formula (A-i):

wherein:

R A1 is hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, or a nitrogen protecting group; and

each instance of R A2 is independently hydrogen, halogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —CN, —OR A2a , —N(R A2a ) 2 , or —SR A2a , wherein each occurrence of R A2a is independently hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two R A2a groups are joined to form a substituted or unsubstituted heterocyclic ring.

6. The compound of claim 4 , or a pharmaceutically acceptable salt thereof, wherein Ring A is of Formula (A-ii):

wherein:

each instance of R A2 is independently hydrogen, halogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —CN, —OR A2a , —N(R A2a ) 2 , or —SR A2a , wherein each occurrence of R A2 a is independently hydrogen, substituted or unsubstituted acyl, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogen protecting group when attached to a nitrogen atom, an oxygen protecting group when attached to an oxygen atom, or a sulfur protecting group when attached to a sulfur atom, or two R A2a groups are joined to form a substituted or unsubstituted heterocyclic ring.

7. The compound of claim 4 , or a pharmaceutically acceptable salt thereof, wherein Ring A is of Formula (A-iii):

wherein:

8. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein Ring A is a substituted or unsubstituted, monocyclic heteroaryl ring.

9. The compound of claim 8 , or a pharmaceutically acceptable salt thereof, wherein Ring A is of Formula (A-v):

wherein:

10. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein Ring A is a substituted or unsubstituted, monocyclic heterocyclic ring.

11. The compound of claim 10 , or a pharmaceutically acceptable salt thereof, wherein Ring A is of Formula (A-vi):

wherein:

J is C(R CJ ) 2 or NR NJ ;

each instance of R CJ is independently hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, —OR a , —N(R a ) 2 , —SR a , —CN, —SCN, —C(═NR a )R a , —C(═NR a )OR a , —C(═NR a )N(R a ) 2 , —C(═O)R a , —C(═O)OR a , —C(═O)N(R a ) 2 , —NO 2 , —NR a C(═O)R a , —NR a C(═O)OR a , —NR a C(═O)N(R a ) 2 , —OC(═O)R a , —OC(═O)OR a , or —OC(═O)N(R a ) 2 ; and

R NJ is hydrogen, halogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, optionally substituted acyl, or a nitrogen protecting group; and

12. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 1 is a bond.

13. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 1 is —O—.

14. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 1 is —NR c —.

15. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein X is —NR c —.

16. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 2 is —NR c C(═O)— or —C(═O)NR c —.

17. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein R E is of Formula (i-18):

18. The compound of claim 17 , or a pharmaceutically acceptable salt thereof, wherein R E is of the formula:

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

or a pharmaceutically acceptable salt thereof.

20. A pharmaceutical composition comprising a compound of claim 1 , or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.

21. A method of treating a proliferative disease in a subject in need thereof, the method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

22. A method of modulating the activity of a kinase in a biological sample or subject, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

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

or a pharmaceutically acceptable salt thereof.

26. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein X is —NH—.

27. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein L 2 is —NHC(═O)—.

28. The compound of claim 1 , or a pharmaceutically acceptable salt thereof, wherein R E is of the formula:

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

or a pharmaceutically acceptable salt thereof.

30. The method of claim 21 , wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof.

31. The method of claim 21 , wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof.

32. The method of claim 21 , wherein the proliferative disease is cancer.

33. The method of claim 21 , wherein the proliferative disease is breast cancer.

34. The method of claim 21 , wherein the proliferative disease is lung cancer.

35. A kit comprising:

a compound of claim 1 , or a pharmaceutically acceptable salt thereof; and

instructions for administering to a subject or contacting a biological sample with the compound, or a pharmaceutically acceptable salt thereof.

36. A method of inhibiting the growth of an abnormally proliferative cell in a subject or biological sample, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

37. A method of inhibiting transcription in a biological sample or subject, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of claim 1 , or a pharmaceutically acceptable salt thereof.

38. A compound of the formula:

or a pharmaceutically acceptable salt thereof.

39. A pharmaceutical composition comprising a compound of claim 38 , or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.

40. A kit comprising:

a compound of claim 38 , or a pharmaceutically acceptable salt thereof; and

instructions for administering to a subject or contacting a biological sample with the compound, or a pharmaceutically acceptable salt thereof.

41. A method of treating a proliferative disease in a subject in need thereof, the method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of claim 38 , or a pharmaceutically acceptable salt thereof.

42. A method of modulating the activity of a kinase in a biological sample or subject, inhibiting the growth of an abnormally proliferative cell in a biological sample or subject, or inhibiting transcription in a biological sample or subject, the method comprising administering to the subject or contacting the biological sample with an effective amount of a compound of claim 38 , or a pharmaceutically acceptable salt thereof.

Assignments (2)

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 7, 2018

From: GRAY, NATHANAEL S.; ZHANG, TINGHU

To: DANA-FARBER CANCER INSTITUTE, INC.

Reel/Frame 046814/0677 →

CONFIRMATORY LICENSE Recorded Mar 6, 2018

From: DANA-FARBER CANCER INST

To: NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT

Reel/Frame 045505/0989 →

Continuity (3)

Provisional Application 62185366 · Jun 26, 2015

Related Publication 20180153894A1 · Jun 7, 2018

Related Publication 20180369243A9 · Dec 27, 2018

Cited By (4)

US 50,776 US 12,187,701 US 12,281,126 US 12,637,453