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

Allah Nawaz Safi; Mohammad Sayed Behrad; Sayed Hussain Mosawi; Abdul Musawer Bayan

doi:10.60141/AJID/V.2.I.1.3

Authors

Allah Nawaz Safi Ghalib University https://orcid.org/0009-0008-1734-7832
Mohammad Sayed Behrad Kabul University
Sayed Hussain Mosawi Ghalib University https://orcid.org/0000-0001-6516-9542
Abdul Musawer Bayan Ghalib University https://orcid.org/0009-0004-1537-677X

DOI:

https://doi.org/10.60141/AJID/V.2.I.1.3

Keywords:

Molecular docking Molecular dynamics simulation, Berberine, Class C β-Lactamase

Abstract

Background: Antibiotic resistance is a significant health concern, as bacteria produce enzymes that inhibit antimicrobial drug activity, increasing disease generation. This study investigates the inhibitory effect of berberine on β-lactamase enzyme activity and antibiotic effectiveness.

Methods: Molecular docking was utilized to find the binding pose and binding affinity of a new inhibitory ligand with the AmpC enzyme using Autodock software version 4.2.2. MD simulations were performed in free form and complicated to understand the stability of the protein-ligand docked complex.

Results: The molecular docking result indicated the proper interaction between berberine and the AmpC β-lactamase enzyme with a suitable binding pose and binding energy of -6.55 kcal/mol. The MD simulation of systems verifies the docking result, which shows stable hydrogen bonds of berberine with AmpC and good equivalence between RMSD, RMSF, SASA, etc.

Conclusion: This paper reveals that berberine, which is a natural ingredient with multiple medicinal characteristics, can be applied as a potential inhibitor of class C β-lactamase AmpC. Hence, the outcome of the calculations performed provides valuable data to design new inhibitors with therapeutic potential to control the β-lactamase activity.

Author Biographies

Allah Nawaz Safi, Ghalib University

Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan.

Mohammad Sayed Behrad, Kabul University

Thoracic and Cardiovascular Surgery Department, Kabul University of Medical Science, Kabul, Afghanistan.

Sayed Hussain Mosawi, Ghalib University

Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan.

Abdul Musawer Bayan, Ghalib University

Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan.

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