Methods and reagents for analyzing protein-protein interfaces

Patent metadata

Field	Value
Publication number	US-10466249-B2
Application number	US-201815974923-A
Country	US
Kind code	B2
Filing date	May 9, 2018
Priority date	Oct 1, 2015
Publication date	Nov 5, 2019
Grant date	Nov 5, 2019

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 having the structure:
A-L-B
wherein A has the structure of Formula Ila:

wherein Z 1 and Z 2 are each, independently, optionally substituted C 1 -C 6 alkyl, optionally substituted C 1 -C 6 heteroalkyl; and Z 2 includes a point of attachment to the L;
X 2 is absent, CH 2 , O, S, SO, SO 2 , or NR 4 ;
each R 4 is, independently, hydrogen, optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, optionally substituted aryl, C 3 -C 7 carbocyclyl, optionally substituted C 6 -C 10 aryl C 1 -C 6 alkyl, and optionally substituted C 3 -C 7 carbocyclyl 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 -C 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, i, 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 13 (C 1 ) g —(B 2 ) h — to —(B 3 ) i —(C 2 ) j —(B 4 ) k -A 2 ; and
B comprises a cross-linking group, wherein the cross-linking group is a maleimide, vinyl sulfone, isocyanate, isothiocyanate, sulfonyl chloride, acid anhydride, acylazide, imidoester, haloheteroaryl, diazo, carbodiimide, hydrazide, or alkoxyamine,
or a salt thereof.

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

Assignees

• Warp Drive Bio Inc
• 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

• A61P37/06

  Immunosuppressants, e.g. drugs for graft rejection · CPC title

• G01N2500/02

  Screening involving studying the effect of compounds C on the interaction between interacting molecules A and B (e.g. A = enzyme and B = substrate for A, or A = receptor and B = ligand for the receptor) · CPC title

• G01N33/6845 Primary

  Methods of identifying protein-protein interactions in protein mixtures · CPC title

• C07K1/13

  Labelling of peptides · CPC title

• C07K1/086

  containing sulfur · CPC title