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Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of Berberine with Class C β-Lactamase
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10.60141/AJID/V.2.I.1.3
Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of Berberine with Class C β-Lactamase
<p><strong>Background:</strong> 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.</p>
<p><strong>Methods:</strong> 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.</p>
<p><strong>Results:</strong> 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.</p>
<p><strong>Conclusion:</strong> 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.</p>
https://creativecommons.org/licenses/by/4.0
2024
Molecular docking Molecular dynamics simulation
Berberine
Class C β-Lactamase
Allah Nawaz
Safi
Ghalib University
AF
sayedhussain.mosawi@ghalib.edu.af
https://orcid.org/0009-0008-1734-7832
<p>Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan.</p>
Mohammad Sayed
Behrad
Kabul University
AF
sayedhussain.mosawi@ghalib.edu.af
<p>Thoracic and Cardiovascular Surgery Department, Kabul University of Medical Science, Kabul, Afghanistan.</p>
Sayed Hussain
Mosawi
Ghalib University
AF
sayedhussain.mosawi@ghalib.edu.af
https://orcid.org/0000-0001-6516-9542
<p>Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan.</p>
Abdul Musawer
Bayan
Ghalib University
AF
sayedhussain.mosawi@ghalib.edu.af
https://orcid.org/0009-0004-1537-677X
<p>Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan.</p>
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Second Volume, First issue, january 2024
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