Molecular docking (MDP) and molecular dynamics simulation (MDS) approaches to investigate the relationship and interactions of Berberin natural compound with class D β -lactamase OXA-10

Abstract

Abstract: bacterial survival against antibiotics drawn attention of most researchers due their hydrolyzing activity by secretion of β-lactamase enzyme that can hydrolyze the β-lactam antibiotic, hence bacteria experience no effect of the antibiotic used against them and led to high fatality. This study targeted to find the inhibitory effect of berberin, an isoquinoline alkaloid to inhibit the activity of β-lactamase enzyme and increase the efficiency of clinical antimicrobial drugs.  

Methods: Molecular docking used to understand the binding pose and binding affinity of new inhibitory ligand with OXA-10 enzyme utilizing Autodock software version 4.2.2. MD simulations were executed in free form and complexed form at physiological condition, to study the stability of the protein–ligand docked complex and the binding pose obtained by docking.

Result: Molecular docking result indicated the suitable interaction between berberin and OXA-10 β-lactamase enzyme with proper binding pose and binding energy of -6.29kcal/mol. The MD Simulation of systems validated the docking result which show constant hydrogen bonds of berberin with OXA-10 and well equilibrated RMSD, RMSF and etc. 

Conclusion: The finding of this paper suggest that berberin which is a natural compound, with several medicinal effect, can be used as a potential inhibitor of class D β -lactamase OXA-10. Therefore, it is visualized that this identified inhibitor will serve as a better initiating tip for further experimental studies of β -lactamase inhibitor in drug design and discovery process.