Staphylococcus aureus, a prevalent component of the human microbiota, is associated with skin infections to life-threatening diseases, presenting challenges in treatment options and necessitating the development of effective treatments. This study integrated computational and in vitro approaches to identify promising phytocompounds with therapeutic potential. Staphopain B emerged as a target protein for its role in immune evasion, exhibiting stability during molecular dynamic simulation (MDS) with a root mean square deviation value of 2.376 Å. Screening 115 phytocompounds with antibacterial properties from the PubChem database identified 12 with drug-like properties, nine of which showed superior binding affinity to Staphopain B compared to a commercial antibiotic, doxycycline (−7.8 kcal mol−1). Notably, epoxyazadiradione and nimbolide displayed higher estimated free energy of binding scores (−7.91 and −7.93 kcal mol−1, respectively), indicating strong protein–ligand interactions. The root mean square fluctuation values for epoxyazadiradione and nimbolide were 1.097 and 1.034 Å, respectively, which was confirmed through MDS. Crude ethanolic extracts (100% and 70%) of neem (Azadirachta indica) leaves demonstrated narrow inhibition against the bacteria in comparison to doxycycline in the disc-diffusion assay. This study underscores the potential of phytocompounds as therapeutic agents against S. aureus; however, further in vitro experiments and testing of the phytocompounds in vivo are required.

Staphylococcus aureus , a bacterial pathogen, is increasingly linked to severe healthcare-associated diseases, from mild skin infections to toxic shock syndrome. Due to limitations in conventional methods, we use computational techniques to screen potential phytocompounds for new drug development and to construct a multiepitope vaccine. Aminoacyltransferase FemA, essential for peptidoglycan formation, was chosen as the target protein for drug and vaccine development. Meanwhile, 1100 phytocompounds were retrieved from 54 plants using the NPASS database and analyzed for drug-likeness and ADMET properties. Paulownin was selected for its higher binding affinity (−7.78 Kcal/mol) than the control drug, Doxycycline (−7.5 Kcal/mol) in molecular docking. It also showed lower RMSD, RMSF, and stronger hydrogen bonding (1.11/0.8 Å, 1.594/1.613 Å, and 3/2, respectively) in molecular dynamics simulations. It demonstrated potential higher affinity, scoring −39.74 ± 6.05 Kcal/mol, outperforming Doxycycline's −28.15 ± 5.90 Kcal/mol in MM-GBSA. For the vaccine, 12 selected epitopes were compiled utilizing GPGPG, two KK peptides, and AAY linkers. The N-flanking immunogenicity of the vaccine was enhanced by adding a lipoprotein adjuvant, LprG. The vaccine alone and the vaccine with the receptor molecule TLR2 showed RMSF (4.247 Å/2.42 Å), RMSD (12.9 Å/7.52 Å), SASA (228.48 nm²/220.29 nm²), Rg (33.76 Å/28.48 Å), and hydrogen bonds (171/165), indicating the vaccine’s predicted immune response patterns. These findings computationally prioritize Paulownin and the multi-epitope construct as candidates for further experimental evaluation. As the study is entirely in silico, experimental validation is required to confirm biological activity and immunogenicity.