Nanoinformatics-Guided Inhibition of blaOXA in Staphylococcus nepalensis using Cysteine-Conjugated Silver Nanoparticles

Urinary tract infections, particularly cystitis, are increasingly associated with multidrug-resistant pathogens, including Escherichia coli, Klebsiella pneumoniae, and Staphylococcus species. This study investigated the molecular characterization of the blaOXA gene encoding oxacillinase type beta-lactamase in Staphylococcus nepalensis and evaluated its inhibition using nanoinformatics-guided silver nanoparticles and cysteine-conjugated silver nanoparticles. The blaOXA gene was amplified by PCR and confirmed by Sanger sequencing. The protein structure was predicted using AlphaFold3 and validated through Ramachandran plot analysis. Silver nanoparticle models were designed using Materials Studio, followed by molecular docking and molecular dynamics simulations to assess enzyme nanoparticle interactions. Docking analysis revealed stronger binding of cysteine-conjugated silver nanoparticles to BlaOXA, with a binding energy of -203.30 compared to -183.03 for silver nanoparticles. Molecular dynamics simulations confirmed enhanced stability of the BlaOXA–Cys AgNP complex, as indicated by lower RMSD values, reduced radius of gyration, and decreased residue flexibility. This study integrates molecular characterization of blaOXA in Staphylococcus nepalensis with nanoinformatics-based evaluation of cysteine-conjugated silver nanoparticles. The findings suggest that targeted inhibition of BlaOXA may help restore beta-lactam antibiotic activity and support alternative therapeutic strategies for multidrug-resistant cystitis.