Unbinding pathways and energetics of papaya-derived flavonoids as dengue MTase inhibitors via SMD-US and MMGBSA methods

Dengue virus methyltransferase (DENV MTase) facilitates the methylation of the viral RNA cap and continues to be a confirmed target for antiviral development. This study examined papaya-derived flavonoids as potential MTase inhibitors through an extensive computational workflow that integrated molecular docking, molecular dynamics (MD) simulations, MM/GBSA binding energy, and steered molecular dynamics–umbrella sampling (SMD–US) to assess unbinding energetics. Neohesperidin, Quercetin, and Myricetin exhibited the highest binding affinities for DENV MTase among the analysed flavonoids, with binding free energies (ΔGUS) of −15.31, −14.67, and −13.69 kcal/mol, respectively from umbrella sampling. Potential mean force (PMF) profiles derived from umbrella sampling offer insights about the unbinding mechanisms and thermodynamic feasibility of these naturally occurring inhibitors. The results of MMGBSA binding energy and the identification of key amino acids at the active site, namely ASP131, LYS105, and ILE147, in the context of MTase-flavonoid binding through non-covalent interaction analysis further corroborated these conclusions. To evaluate Carica papaya-derived flavonoids as MTase inhibitors, this work is the first to combine SMD-US and MMGBSA analyses. The findings substantiate the promise of papaya-associated flavonoids as scaffolds for dengue MTase inhibition.