Elucidating the linagliptin and fibroblast activation protein binding mechanism through molecular dynamics and binding free energy analysis.

Fibroblast activation protein (FAP) is highly expressed in solid tumors and may be a potential diagnostic and therapeutic target in solid cancers. Linagliptin inhibits FAP; however, the interaction mechanism between linagliptin and FAP remains unclear. In this study, the binding free energy for linagliptin with human FAP was estimated at -13.66 kcal/mol, and the dissociation constant was 243 nM based on surface plasmon resonance analyses. E203, E204, and Y656 formed hydrogen bonds with ammonium. Y625 formed an unstable hydrogen bond with the carbonyl group. W623 and Y541 interacted with the quinazoline and pyrimidine-2,4-dione rings, respectively, via π-π interactions. The butyne group formed hydrophobic interactions with residues V650, Y653, Y656, and Y660. ZINC000299754517 and ZINC000299754576 were identified as potential FAP inhibitors. The R1 and R4 regions of linagliptin could be optimized to increase its FAP binding affinity. These findings can guide linagliptin structural optimization to improve its FAP binding affinity.