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<p>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.</p>

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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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月18日

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  • Nikeshun Vivekananthan,
  • Niranjana Prem Minipreman,
  • Chinnakaruppan Marimuthu,
  • Gnanaprakash Jeyaraj,
  • Abhilasha Singh,
  • Swati Bhuria,
  • Susheel Kumar,
  • Chandana Venkateshwara Rao,
  • Vijayanandraj Selvaraj

摘要

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.