Fibroblast activation protein (FAP) is a transmembrane serine peptidase that belongs to the prolyl peptidase family. FAP has been implicated in cancer; however, its specific role remains elusive because inhibitors that distinguish FAP from other prolyl peptidases like dipeptidyl peptidase-4 (DPP-4) have not been developed. To identify peptide motifs for FAP-selective inhibitor design, we used P 2 -Pro 1 and acetyl (Ac)-P 2 -Pro 1 dipeptide substrate libraries, where P 2 was varied and substrate hydrolysis occurs between Pro 1 and a fluorescent leaving group. With the P 2 -Pro 1 library, FAP preferred Ile, Pro, or Arg at the P 2 residue; however, DPP-4 showed broad reactivity against this library, precluding selectivity. By contrast, with the Ac-P 2 -Pro 1 library, FAP cleaved only Ac-Gly-Pro, whereas DPP-4 showed little reactivity with all substrates. FAP also cleaved formyl-, benzyloxycarbonyl-, biotinyl-, and peptidyl-GlyPro substrates, which DPP-4 cleaved poorly, suggesting an N-acylGly-Pro motif for inhibitor design. Therefore, we synthesized and tested the compound Ac-Gly-prolineboronic acid, which inhibited FAP with a K i of 23 ؎ 3 nM. This was ϳ9-to ϳ5400-fold lower than the K i values for other prolyl peptidases, including DPP-4, DPP-7, DPP-8, DPP-9, prolyl oligopeptidase, and acylpeptide hydrolase. These results identify Ac-Gly-BoroPro as a FAP-selective inhibitor and suggest that N-acyl-Gly-Pro-based inhibitors will allow testing of FAP as a therapeutic target.Tumor-associated stromal cells can promote epithelial tumorigenesis (1, 2), suggesting that stromal proteins may represent novel therapeutic targets. Fibroblast activation protein (FAP), 2 a transmembrane serine peptidase, is one potential target because it is highly expressed by stromal fibroblasts in most epithelial cancers (3-7). Increased FAP expression in tumors correlates with increased FAP activity relative to normal tissues (8, 9), and FAP overexpression promotes tumorigenesis in xenograft models (10 -12). This effect requires catalytically active FAP (12), suggesting that FAP activity promotes tumor growth and that FAP inhibition may have therapeutic value.FAP belongs to the prolyl peptidase family, which comprises serine proteases that typically cleave peptide substrates after a proline residue. This family has been implicated in several diseases, including diabetes, cancer, and mood disorders (13,14), and includes dipeptidyl peptidase-4 (DPP-4), DPP-7, DPP-8, DPP-9, prolyl oligopeptidase, acylpeptide hydrolase, and prolyl carboxypeptidase. These proteases differ in structure at the N terminus, but each has a C-terminal ␣-hydrolase domain that contains the catalytic Ser, Asp, and His residues. FAP, like its most closely related family member, DPP-4, is a type II transmembrane protein; both have a short cytoplasmic tail, a transmembrane domain, and a -propeller domain containing several sites of N-linked glycosylation (5,(15)(16)(17)(18)(19)(20). Crystallographic data for FAP and DPP-4 show that the -propeller has important substrate ...