Virtual screening of potato virus Y coat protein for discovering lead inhibitors of viral intercellular traffic.

Potato virus Y (PVY) is one of the most economically detrimental phytoviruses affecting global Solanaceae, possessing challenges in agrochemical control. The structural elucidation of PVY coat protein (CP) offers opportunities for the rational design of CP-targeted antivirals; however, the feasibility of identifying lead compounds via virtual screening remains largely unexplored. Herein, we report the successful case of structure-based virtual screening leveraging PVY CP, enabling the identification of a structurally novel lead with a unique mechanism of action. Combining quantitative analysis of complex stability and anti-PVY assay allows the determination of molecule 501990 as a promising candidate. 501990 demonstrates exceptional inactivating properties against PVY with EC50 of 68.80 μg/mL, significantly better than ribavirin (EC50 = 84.43 μg/mL). Mechanistic studies elucidate the dual interaction of 501990 between PRO126 (P126) and LYS153 (K153) residues on PVY CP. Site-directed mutagenesis along with confocal microscopy observation confirm pathogenesis disruption, as mutant strains (P126A/K153A) exhibit almost loss of intercellular movement and systemic infection capabilities. This study establishes a paradigm for phytoviral protein-based drug discovery, and the identified 501990 may serve as a lead for future virucide developments.