Design and molecular docking studies of novel antimicrobial peptides using autodock molecular docking software

Abstract

Objective: Design of novel antimicrobial peptides (AMPs) and study through the molecular docking. Methods: The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by the MM2 method and converted to pdb extension file which is readable at the AutoDock Vina (ADT) interface. The ADT 1.5.6 software is used for molecular docking purposes. Results: Eight AMPs were designed based on the MP196 AMP. Among these KP_03R (FWRWRW-NH2) showed good binding affinity. These peptides also showed the stereochemical influence on affinity toward the 3vma protein of Escherichia coli, where AMP with R stereochemistry showed better activity than its opposite stereochemistry. Conclusion: Novel AMPs were designed by modifications on the MP196 a short chain of amino acids AMPs. Molecular docking software was used to determine the binding affinity between drug and receptor protein. Among all the designed peptides KP_03R (FWRWRW-NH2) showed the maximum binding affinity against the penicillin-binding protein of E. coli and also exhibited stereoselective activity.