Methods and reagents for analyzing protein-protein interfaces

A compound having the structure:

• A-L-B,
• wherein A comprises a cyclophilin binding moiety having the structure of Formula IV:
• wherein Z3 and Z4 are each, independently, hydroxyl, optionally substituted C1-C6 alkyl, optionally substituted C1-C6 heteroalkyl, or Z3 and Z4 combine to form, with the atoms to which they are attached, an optionally substituted 10 to 40 member macrocycle;
• at least one of Z3, Z4, or R5 comprises a point of attachment to the cross-linking group;
• R5 is optionally substituted C1-C6 alkyl, optionally substituted C2-C6 alkenyl, optionally substituted C2-C6 alkynyl, optionally substituted C1-C6 heteroalkyl, optionally substituted C2-C6 heteroalkenyl, optionally substituted C2-C6 heteroalkynyl, optionally substituted C3-C10 carbocyclyl, optionally substituted C6-C10 aryl, optionally substituted C6-C10 aryl C1-C6 alkyl, optionally substituted C2-C9 heterocyclyl, or optionally substituted C2-C9 heterocyclyl C1-C6 alkyl;
• R6 is optionally substituted C1-C6 alkyl;
• L is a linker having the structure:
• A1-(B1)f—(C1)g—(B2)h-(D)-(B3)i—(C2)j—(B4)k-A2
• wherein A1 is a bond between the linker and the cyclophilin binding moiety;
• A2 is a bond between the cross-linking group and the linker;
• B1, B2, B3, and B4 each, independently, is selected from optionally substituted C1-C2 alkyl, optionally substituted C1-C3 heteroalkyl, O, S, and NRN;
• RN is hydrogen, optionally substituted C1-4 alkyl, optionally substituted C2-4 alkenyl, optionally substituted C2-4 alkynyl, optionally substituted C2-6 heterocyclyl, optionally substituted C6-12 aryl, or optionally substituted C1-7 heteroalkyl;
• C1 and C2 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 C1-10 alkyl, optionally substituted C2-10 alkenyl, optionally substituted C2-10 alkynyl, optionally substituted C2-6 heterocyclyl, optionally substituted C6-12 aryl, optionally substituted C2-C10 polyethylene glycol, or optionally substituted C1-10 heteroalkyl, or a chemical bond linking A-(B1)f—(C1)g—(B2)h— to —(B3)i—(C2)j—(B4)k-A2;
• and
• B comprises a cross-linking group, wherein the cross-linking group is a mixed disulfide, maleimide, vinyl sulfone, vinyl ketone, alkyl halide, isocyanate, isothiocyanate, sulfonyl chloride, acid halide, active ester, acid anhydride, acylazide, imidoester, haloheteroaryl, diazo compound, carbodiimide, hydrazide, alkoxyamine, azide, or alkyne.