Methods and reagents for analyzing protein-protein interfaces
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.
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.