DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL ANTIMICROBIAL PEPTIDES USING AUTODOCK MOLECULAR DOCKING SOFTWARE

  • Kiranpreet Kaur Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Jalandhar, Phagwara - 144 411, Punjab, India
  • Paranjeet Kaur Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Jalandhar, Phagwara - 144 411, Punjab, India
  • Amit Mittal Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Jalandhar, Phagwara - 144 411, Punjab, India
  • Surendra Kumar Nayak Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Jalandhar, Phagwara - 144 411, Punjab, India
  • Gopal L Khatik Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Jalandhar, Phagwara - 144 411, Punjab, India

Abstract

Objective: Design of novel antimicrobial peptides 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 theMM2 method and converted to pdbextension file which is readable at the ADT interface. The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes.

Results: Eight antimicrobial peptides (AMPs) were designed based on theMP196antimicrobial peptide. Among these KP_03R (FWRWRW-NH2) showed good binding affinity. These peptides also showed the stereochemical influence on affinity toward the3vma protein of E. 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 antimicrobial peptides. 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 thepenicillin-binding protein of E.coli and also exhibited stereoselective activity.

Keywords: Antimicrobial peptides, MP196, AutoDock Vina, Molecular docking.

Author Biography

Kiranpreet Kaur, Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Jalandhar, Phagwara - 144 411, Punjab, India
School of Pharmaceutical Sciences, Asst. Prof

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Kaur, K., P. Kaur, A. Mittal, S. K. Nayak, and G. L. Khatik. “DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL ANTIMICROBIAL PEPTIDES USING AUTODOCK MOLECULAR DOCKING SOFTWARE”. Asian Journal of Pharmaceutical and Clinical Research, Vol. 10, no. 16, Sept. 2017, pp. 28-31, doi:10.22159/ajpcr.2017.v10s4.21332.
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