Computational Analysis of <i>Psidium guajava</i> Metabolites Targeting Critical Proteins of <i>Staphylococcus aureus</i> : Insights from Pharmacokinetics, Docking and Dynamics

Staphylococcus aureus remains a critical ESKAPE pathogen due to its multidrug resistance and reliance on virulence-associated enzymes. In this study, an integrative in silico pipeline combining molecular docking, redocking-based validation, molecular dynamics (MD) simulations and pharmacokinetic profiling was applied to prioritize Psidium guajava metabolites targeting two functionally distinct proteins: the essential peptidoglycan biosynthesis enzyme MurE and the antivirulence factor sortase A (SrtA). Twenty-one metabolites were docked against both targets, and reference redocking experiments were performed using the co-crystallized ligand for MurE and quercetin for SrtA to validate the docking protocol. Flavonoids quercetin and myricetin exhibited the strongest binding affinities toward MurE ([Formula: see text]9.8 to −9.9 kcal ⋅ mol[Formula: see text] and displayed stable MD behavior over 100 ns, characterized by low backbone RMSD values (0.25–0.40[Formula: see text]nm), limited RMSF fluctuations confined to terminal regions, a stable radius of gyration and consistent potential energy profiles, indicating persistent interactions within the MurE catalytic site. In contrast, SrtA complexes with rutin and oleanolic acid showed pronounced conformational rearrangements during MD simulations, with large backbone RMSD excursions ([Formula: see text]2–9[Formula: see text]nm) and fluctuating compactness, with partial stabilization emerging toward the end of the 100 ns trajectory (after [Formula: see text]60–80[Formula: see text]ns), consistent with dynamic or transient binding rather than stable inhibition. Pharmacokinetic analyses highlighted quercetin and myricetin as the most drug-like candidates among the evaluated metabolites. Overall, the results support a complementary, target-selective strategy, identifying MurE as a robust enzymatic target for P. guajava flavonoids, while SrtA interactions are better interpreted as potential antivirulence modulation rather than strong dual-target inhibition. This refined framework provides a realistic and mechanistically grounded basis for prioritizing plant-derived scaffolds against S. aureus.