Peptide substrate profiling defines fibroblast activation protein as an endopeptidase of strict Gly2-Pro1-cleaving specificity

Fibroblast activation protein (FAP) is a serine protease of undefined endopeptidase specificity implicated in tumorigenesis. To characterize FAP's P-4-P'(2) specificity, we synthesized intramolecularly quenched fluorescent substrate sets based on the FAP cleavage site in alpha(2)-antiplasmin (TSGP-NQ). FAP required substrates with Pro at P-1 and Gly or D-amino acids at P-2 and preferred small, uncharged amino acids at P-3, but tolerated most amino acids at P-4, P'(1) and P'(2). These substrate preferences allowed design of peptidyl-chloromethyl ketones that inhibited FAP, but not the related protease, dipeptidyl peptidase-4. Thus, FAP is a narrow specificity endopeptidase and this can be exploited for inhibitor design. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.