Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of the piperine with Class D β-Lactamase

Abstract

Introduction: The study explores the potential of piperine, a natural compound with diverse medicinal effects, as a potential inhibitor targeting OXA-10 class D β-lactamase enzymes, as a potential solution to the drug resistance caused by β-lactamase-producing organisms, which contributes to millions of deaths and morbidity cases worldwide each year. Materials and Methods: Through the utilization of molecular approaches such as molecular docking and molecular dynamics simulation, this study investigated the binding sites and binding energy of class D β-lactamase in the presence of piperine. These analyses were conducted using Autodock 4.2.2 software and the GROMACS 2019.6 program, applying the AMBER99SB force field. Results: Molecular docking findings and interactional analysis studies of molecular dynamics simulations indicated suitable hydrogen bonds and van der Waals interactions of piperine with OXA-10. These findings suggest that targeting β-lactamase using piperine as an inhibitor analog could provide a good pathway to deal with multi-drug resistance. Conclusion: By applying calculation-based methodology, including molecular docking and molecular dynamics simulation, this study suggested that piperine, renowned for its various medicinal properties, can serve as an inhibitor or has the potential to act as an inhibitor targeting the OXA-10 class D β-lactamase enzyme.