In Silico Analysis of the Binding Mode of Verteporfin, a YAP–TEAD Interaction Inhibitor

Abstract

The Hippo signaling pathway plays a central role in regulating cell growth, and dysregulation of its downstream effector Yes-associated protein (YAP) leads to tumorigenesis. Verteporfin (VP), a clinically approved drug, inhibits YAP–TEA domain (TEAD) complex formation, yet its binding mechanism remains unclear. In this study, we conducted a comprehensive in silico analysis of all 4 VP isomers within the context of the full-length YAP–TEAD complex. The complex structure was modeled using AlphaFold2 multimer, which provided sufficient accuracy for docking simulations despite incomplete experimental data on YAP. Docking calculations were performed against 2 grids, one centered on a predicted druggable pocket and the other on the YAP–TEAD interface. A total of 304 poses were generated, and the top-scoring 100 were clustered using protein–ligand interaction fingerprints. Clusters derived from the interface grid revealed strong interactions with residues critical for YAP–TEAD binding. Among the 4 isomers, Ia-2 consistently showed the most favorable binding free energies. Notably, Cluster 7 highlighted a unique Ia-2 binding mode involving simultaneous interactions with Met86 and Arg87, suggesting a competitive mechanism at the YAP–TEAD interface. These results suggest that structural chirality may influence binding stability and interaction patterns, and that the Ia-2 isomer is predicted to preferentially stabilize an inhibitory binding mode. This study provides the first systematic comparison of all VP isomers with full-length YAP and suggests that isolating Ia-2 from Visudyne may enhance anticancer efficacy. The findings further support the rational strategies for designing selective YAP–TEAD inhibitors.