Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of quercetin with Class D beta-lactamase, OXA-10
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Abstract
Introduction: The misuse of β-lactam antibiotics has led to the development of β-lactamase-producing organisms, which inhibit β-lactam activity by hydrolyzing the peptide bond. This study aims to investigate the inhibitory effect of quercetin, a natural composite and isoquinoline alkaloid, on β-lactamase enzyme action, potentially increasing antibiotic effectiveness.
Materials and Methods: This study utilized computational techniques like molecular docking and MD simulation to predict the binding mode and possible conformation poses of quercetin with the OXA-10 β-lactamase enzyme. Autodock software was used for docking, while Gromacs 2019.6 package was used for MD simulations to study molecular complex behavior over time.
Results: The outcomes of the molecular docking analysis revealed a favorable interaction between quercetin and the OXA-10 β-lactamase enzyme, as evidenced by a binding energy of -5.95 kcal/mol and a suitable binding mode. MD simulations confirmed the docking results, showing stable hydrogen bonds between Quercetin and OXA-10, as well as comparable RMSD, RMSF, SASA values, and other parameters.
Discussion: This research shows the potential of quercetin, a natural compound with multiple medicinal effects, as a possible inhibitor of the class D type β-lactamase OXA-10. Therefore, this study maintains valuable intuition for designing new inhibitors of antimicrobial resistance to combat β-lactamase activity.
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