Bifunctional chimeric molecules for labeling of kinases with target binding moieties and methods of use thereof

Patent metadata

Field	Value
Publication number	US-12404348-B2
Application number	US-202218057127-A
Country	US
Kind code	B2
Filing date	Nov 18, 2022
Priority date	Nov 19, 2021
Publication date	Sep 2, 2025
Grant date	Sep 2, 2025

Abstract

The present disclosure relates to chimeric small molecules, which find utility as modifiers of target substrates according to the formula A-L 1 -E-B or A-L 1 -E-L 2 -B, wherein A is a kinase binding moiety; B is a target binding moiety; L 1 and L 2 are each a linker; and E is an electrophilic reactive group. Molecules according to the present invention find use making substrate modifications such as post-translational modifications to targets that are not the natural substrate of the kinase; accordingly, diseases or disorders may be treated or prevented with molecules of the present disclosure.

First claim

What is claimed is:

1. A chimeric small molecule according to the formula A-L1-E-B or A-L1-E-L2-B,
wherein A is a kinase protein binding moiety selected from the group consisting of FKBP, PKC, AMPK, ABL, PK, IRTK, MAPK, p38a MAPK, EGFR, FGFR, NGFR, TrkA, ABL, CDK, PI3K, VEGFR, BRAF, MEK, AKT, ALK, BTK, BCKDK, FLT3, JAK2, AURKA, c-MET, DDR, INSR, JNK, IkB, IKK, Lyn, mTOR, PAK, PDK, PTK2/FAK, pyruvate kinases, RAC-a, RIPK, TYK2, SHP, aPKC, NOP, GPC family, μ opioid receptor, δ opioid receptor, UMPK, SphK, PDGFR, and GSK-3 binding moiety;
B is a target oncogenic protein binding moiety selected from the group consisting of KRAS, RAS, FKPB 12F36V , EGFR, HSP90, BTK, MDM2, BRD4, BCR-ABL, NF-kB, LDH-A, p53, GP73, MUC1, MUC16, CD44, GPCR, HMGB1, RIOK1, CHK1, UBE2F, HuR, PTEN, STAT-3, Osteopontin, AKT, DAPK1, Rho, Ubc9, FOXK2, HIC1, HER2, BRAF, BCL-2, CD117, c-KIT, ALK, PI3K, Delta, DNMT1, and SMO;
L1 and L2 are each a linker; and
E is an electrophilic reactive group and is selected from the group consisting of:

2. The chimeric small molecule of claim 1 , wherein the kinase binding moiety has a half-life shorter than the half-life of the kinase.

3. The chimeric small molecule of claim 1 , wherein the kinase binding moiety is a kinase inhibitor or kinase activator.

4. The chimeric small molecule of claim 3 , wherein the kinase inhibitor is a promiscuous kinase inhibitor.

5. The chimeric small molecule of claim 1 , wherein L selected from: alkane; alkene; alkyne; amine; ether; thiol; sulfone; carbonyl; acyl; ketone; carboxylate ester; amide; enone; anhydride; imide; PEG, or any combination thereof.

6. The chimeric small molecule of claim 1 , wherein L1 and L2 are the same or are different molecules selected from alkane; alkene; alkyne; amine; ether; thiol; sulfone; carbonyl; acyl; ketone; carboxylate ester; amide; enone; anhydride; imide; PEG, or any combination thereof.

7. The chimeric small molecule of claim 1 , wherein the kinase binding moiety further comprises a bio-orthogonal group.

8. The chimeric small molecule of claim 7 , wherein the bio-orthogonal group is selected from tetrazines, triazines, cyclooctenes, cyclopropenes and diazo.

9. The chimeric small molecule of claim 7 , wherein the bio-orthogonal group is selected from the group consisting of:

10. The chimeric small molecule of claim 1 , wherein the target is a protein.

11. The chimeric small molecule of claim 1 , wherein the chimeric small molecule is capable of covalently labeling a kinase with the kinase binding moiety.

12. The chimeric small molecule of claim 1 with the formula:

wherein m=0 or 1; n=1, 2, 3, 4 or 5; and X=CH2 or (CH2)2O.

13. The chimeric small molecule of claim 1 with the formula:

wherein X and Y are independently selected from CH2 or (CH2)2O and n and m are independently selected from 1, 2, 3, 4, 5, or 6.

14. A method of inducing modification of a target substrate comprising administering to a cell or cell population a chimeric small molecule of claim 1 .

15. A method of modifying a substrate comprising introducing a molecule of claim 1 to a cell.

16. The chimeric small molecule of claim 2 , wherein the kinase binding moiety half-life is at least 2, 3, 4, 5 times shorter than the half-life of the kinase.

17. The chimeric small molecule of claim 3 , wherein the kinase inhibitor is sorafenib, SB2035890 or Skepinone B, or an analog or derivative thereof.

18. The chimeric small molecule of claim 3 , wherein the kinase inhibitor is Gefitinib, or an analog or derivative thereof.

19. The chimeric small molecule of claim 3 , wherein the kinase inhibitor is Imatinib, or an analog or derivative thereof.

20. The chimeric small molecule of claim 3 , wherein the kinase inhibitor is Idelasilib, or an analog or derivative thereof.

21. The chimeric small molecule of claim 10 , wherein the target protein is from a pathogen.

22. The chimeric small molecule of claim 21 , wherein the pathogen is a virus, bacteria, fungi, or protozoa.

23. The chimeric small molecule of claim 3 , wherein the target protein is in an intracellular or extracellular pathogen protein.

24. The chimeric small molecule of claim 23 , wherein the intracellular pathogen is Mycobacterium tuberculosis or the extracellular pathogen is Pseudomonas aeruginosa.

25. The chimeric small molecule of claim 3 , wherein the kinase binding moiety is a phosphatase A (PtpA) binding moiety or a phosphatase B (PtpB) binding moiety.

26. The chimeric small molecule of claim 11 , wherein the labeling is of a nucleophile disposed on the kinase.

27. The method of claim 15 , wherein the electrophilic reactive group reacts with a nucleophilic group of one of Cysteine, Serine, Threonine, Tyrosine, Glutamic Acid, Aspartic Acid, Lysine, Arginine, and Histidine.

Assignees

• Brigham & Womens Hospital Inc
• Broad Inst Inc

Inventors

• Choudhary Amit
• Anokhina Vika
• Chaudhary Santosh
• Singh Prashant
• Singh Sameek
• Shoba Veronika
• Dhawa Uttam
• Modell Ashley
• Tiwari Praveen

Classifications

• C07D233/58

  with only hydrogen atoms or radicals containing only hydrogen and carbon atoms, attached to ring nitrogen atoms · CPC title

• C07K16/40

  against enzymes · CPC title

• A61K49/0017

  Fluorescence in vivo · CPC title

• C12R2001/32

  Mycobacterium · CPC title

• C12R2001/385

  Pseudomonas aeruginosa · CPC title