molecular docking (mdp) and molecular dynamics simulation (mds) approaches to investigate the relationship and interactions of berberin natural with class d β-lactamase oxa-10 (pdb code: 4s2o)

Introduction: researchers are focusing on bacterial survival against antibiotics due to their hydrolyzing activity, which allows them to bypass the antibiotic's effect, leading to high fatalities due to their lack of effect. the study investigated the inhibitory effect of berberin, an isoquinoline alkaloid, on the β-lactamase enzyme, thereby enhancing the efficacy of clinical antimicrobial drugs. materials and methods: the study utilized molecular docking to understand the binding pose and affinity of a new inhibitory ligand with the oxa-10 enzyme, using autodock software version 4.2.2 and performing md simulations in free and complexed forms under physiological conditions. results: the molecular docking result showed a suitable interaction between berberin and oxa-10 β-lactamase enzyme, with a binding energy of -6.29 kcal/mol. md simulation confirmed constant hydrogen bonds between berberin and oxa-10, indicating well-equilibrated rmsd and rmsf. conclusion: the findings of this paper suggest that berberin, which is a natural compound with several medicinal effects, can be used as a potential inhibitor of class d β-lactamase oxa-10. therefore, it is clear that this identified inhibitor will serve as a better initiating tip for further experimental studies of β-lactamase inhibitors in the drug design and discovery process.