Computational identification of flavonoid phytochemicals as potential inhibitors of foot-and-mouth disease virus (FMDV) 3C protease

Foot-and-mouth disease (FMD) remains a persistent threat to global livestock health. The 3C protease (3Cpro) of FMD virus (FMDV) is essential for viral polyprotein processing and contributes to immune evasion, positioning 3Cpro as an attractive target for antiviral drug discovery. In this study, we applied an integrative in silico approach that combined structure-based virtual screening of the South African Natural Compounds Database (SANCDB), molecular dynamics (MD) simulations, and binding free-energy calculations to identify potential phytochemical inhibitors of FMDV 3Cpro. Virtual screening identified 6 flavonoid-based phytocompounds with high predicted binding affinities toward 3Cpro active site as compared to a reference inhibitor. Among these, Nepetin (SANC01131) and SANC00351 were prioritized as potential lead candidates, with docking scores of − 10.26 and − 9.09 kcal/mol, respectively. Detailed interaction analysis revealed that both compounds formed stable hydrogen bonds and π–π interactions with key catalytic and substrate-recognition residues, including His46, Asp144, Gly184, and Glu50, supporting their potential inhibitory activity. ADMET profiling indicated favorable oral bioavailability, low predicted toxicity, and compliance with Lipinski’s rule of five. Subsequent MD simulations demonstrated that Nepetin maintained exceptional structural stability within the 3Cpro binding pocket, characterized by low root-mean-square deviation (RMSD) values, minimal conformational drift, and sustained compactness throughout a 400 ns simulation period. Binding free-energy estimation using the MM/GBSA (Molecular Mechanics/Generalized Born Surface Area) approach further supported these findings, with Nepetin exhibiting the most favorable total binding free energy (− 34.27 ± 0.2 kcal/mol). This computational study suggests that Nepetin may act as a promising plant-derived inhibitor of the FMDV 3C protease; however, further experimental validation is necessary to confirm its antiviral efficacy and therapeutic potential. Collectively, these findings indicate that phytochemical-based antivirals could complement existing vaccination programs and support integrated strategies for foot-and-mouth disease control, particularly in regions challenged by viral persistence and recurrent outbreaks.