Structure-based multi-pocket virtual screening identifies FDA-approved candidate compounds targeting MPXV thymidylate kinase

Abstract

Background Mpox, caused by monkeypox virus (MPXV), has emerged as a growing global health concern, yet effective targeted antiviral therapies remain limited. Thymidylate kinase (TMK), an essential enzyme required for viral DNA replication, represents a potential therapeutic target. Methods We established a structure-based drug repurposing workflow integrating multi-pocket virtual screening and molecular dynamics (MD) simulations. A curated library of FDA-approved compounds was screened across five predicted TMK binding pockets, followed by consensus ranking based on cross-pocket recurrence and docking scores. Top candidates were further evaluated using multiple independent MD simulations to assess binding stability and conformational dynamics. Results Phylogenetic and structural analyses indicated that MPXV TMK is highly conserved among orthopoxviruses while structurally distinct from the human homolog. Virtual screening identified several prioritized candidates, among which capmatinib (DB11791), nebivolol (DB04861), and tucatinib (DB11652) consistently ranked highly across multiple pockets. MD simulations showed that all systems approached relatively stable conformational regimes after the initial phase of the simulations. Notably, DB11791 exhibited lower ligand RMSD and more stable pocket retention across independent simulations. Free energy landscape analysis further suggested that DB11791 adopted a more confined low-energy conformational state compared to other candidates. Conclusion These findings suggest that DB11791 may represent a promising TMK-targeting candidate. More broadly, the combined multi-pocket consensus screening and dynamic evaluation strategy provides a computational framework for antiviral drug repurposing. Further experimental validation is required to confirm the antiviral activity of these candidates.