Methods and reagents for analyzing protein-protein interfaces

Patent metadata

Field	Value
Publication number	US-10948495-B2
Application number	US-201815974921-A
Country	US
Kind code	B2
Filing date	May 9, 2018
Priority date	Oct 1, 2015
Publication date	Mar 16, 2021
Grant date	Mar 16, 2021

Abstract

The present disclosure provides methods and reagents useful for analyzing protein-protein interfaces such as interfaces between a presenter protein (e.g., a member of the FKBP family, a member of the cyclophilin family, or PIN1) and a target protein. In some embodiments, the target and/or presenter proteins are intracellular proteins. In some embodiments, the target and/or presenter proteins are mammalian proteins.

First claim

What is claimed is:

1. A compound, or salt thereof, which binds to cyclophilin and which has the structure:
A-L-B,
wherein A is a cyclophilin binding moiety having the structure of Formula III:

wherein Z 3 and Z 4 are each, independently, hydroxyl, optionally substituted C 1 -C 6 alkyl, optionally substituted C 1 -C 6 heteroalkyl, or Z 3 and Z 4 combine to form, with the atoms to which they are attached, an optionally substituted 13 to 40 member macrocycle;
Z 4 comprises a point of attachment to L;
R 5 is optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, optionally substituted C 1 -C 6 heteroalkyl, optionally substituted C 2 -C 6 heteroalkenyl, optionally substituted C 2 -C 6 heteroalkynyl, optionally substituted C 3 -C 10 carbocyclyl, optionally substituted C 6 -C 10 optionally substituted C 6 -C 10 aryl C 1 -C 6 alkyl, optionally substituted C 2 -C 9 heterocyclyl, or optionally substituted C 2 -C 9 heterocyclyl C 1 -C 6 alkyl;
R 6 is optionally substituted C 1 -C 6 alkyl;
L is a linker having the structure:
A 1 -(B 1 ) f —(C 1 ) g —(B 2 ) h -(D)-(B 3 ) i —(C 2 ) j —(B 4 ) k -A 2

wherein A 1 is a bond between the linker and A; A 2 is a bond between B and the linker; B 1 , B 2 , B 3 , and B 4 each, independently, is selected from optionally substituted C 1 -C 2 alkyl, optionally substituted C 1 -C 3 heteroalkyl, O, S, and NR N ; R N is hydrogen, optionally substituted C 1-4 alkyl, optionally substituted C 2-4 alkenyl, optionally substituted C 2-4 alkynyl, optionally substituted C 2-6 heterocyclyl, optionally substituted C 6-12 aryl, or optionally substituted C 1-7 heteroalkyl; C 1 and C 2 are each, independently, selected from carbonyl, thiocarbonyl, sulphonyl, or phosphoryl; f, g, h, l, j, and k are each, independently, 0 or 1; and D is optionally substituted C 1-10 alkyl, optionally substituted C 2-10 alkenyl, optionally substituted C 2-10 alkynyl, optionally substituted C 2-6 heterocyclyl, optionally substituted C 6-12 aryl, optionally substituted C 2 -C 10 polyethylene glycol, or optionally substituted C 1-10 heteroalkyl, or a chemical bond linking A 1 -(B 1 ) f —(C 1 ) g —(B 2 ) h — to —(B 3 ) i —(C 2 ) j —(B 4 ) k -A 2 ; and
B is a cross-linking group, wherein the cross-linking group is a maleimide, vinyl sulfone having the structure

isocyanate, isothiocyanate, or haloheteroaryl.

2. The compound, or salt thereof, of claim 1 , wherein the cross-linking group is a maleimide.

3. The compound, or salt thereof, of claim 1 , wherein the interaction between the cyclophilin binding moiety and cyclophilin is non-covalent.

4. The compound, or salt thereof, of claim 1 , wherein the cyclophilin binding moiety is a cyclophilin binding moiety capable of binding PP1A, CYPB, CYPC, CYP40, CYPE, CYPD, NKTR, SRCyp, CYPH, CWC27, CYPL1, CYP60, CYPJ, PPIL4, PPIL6, RANBP2, or PPWD1.

Assignees

• Revolution Medicines Inc

Inventors

• Verdine Gregory L
• Nichols M James
• Townson Sharon A
• Shigdel Uddhav Kumar
• Lee Seung-Joo
• Stiles Dylan T
• Anthony Neville J

Classifications

• C12Q1/533

  involving isomerase · CPC title

• C07K5/06034

  the side chain containing 2 to 4 carbon atoms · CPC title

• G01N33/566

  using specific carrier or receptor proteins as ligand binding reagents {where possible specific carrier or receptor proteins are classified with their target compounds} · CPC title

• G01N2410/08

  Cyclosporins and related peptides · CPC title

• C07K5/0215

  containing natural amino acids, forming a peptide bond via their side chain functional group, e.g. epsilon-Lys, gamma-Glu · CPC title