Computational Identification of Novel Inhibitors Targeting Multiple Proteins of Tomato Brown Rugose Fruit Virus (ToBRFV) Through AlphaFold-Based Protein Modeling, Molecular Docking, MM/GBSA Binding Free Energy Analysis, and Molecular Dynamics Simulation

Tomato brown rugose fruit virus (ToBRFV), a tobamovirus, poses a significant threat to global tomato production due to its high infectivity, seed-borne transmission, and severe fruit symptoms. In this study, an integrative computational approach was employed to identify plant-derived phytochemicals capable of inhibiting essential viral proteins such as movement protein (MP), coat protein (CP), helicase domain, and RNA-dependent RNA polymerase (RdRP) domain. The three-dimensional structures of these viral targets were predicted using AlphaFold and subsequently validated using Ramachandran plots. A library of 2,847 phytochemicals was subjected to molecular docking, followed by MM-GBSA binding free energy calculations to evaluate binding affinity and interaction strength. Top-ranked compounds were further validated through 100-ns molecular dynamics (MD) simulations to assess complex stability and conformational behavior. Panasenoside, Kaempferol 3-sophorotrioside, Violanin, and Albireodelphin A exhibited the strongest binding affinities toward MP, CP, Helicase, and RdRP, respectively. RMSD and RMSF analyses confirmed the stability of these complexes, highlighting persistent hydrogen-bonding interactions within the active sites. The findings underscore the potential of flavonoids as effective antiviral agents against ToBRFV and provide a foundation for future in vitro and in vivo validation studies to develop flavonoid-based antiviral formulations for sustainable tomato crop protection.