Investigation of Various Antibiotics in the Structure of Sars Cov-2 Mpro by Molecular Docking and Molecular Dynamics Simulation Method

Authors

Keywords:

Sars-Cov-2 Mpro, Antibiotics Coumpounds, Molecular Docking, Molecular Dynamics Simulation

Abstract

Since the development of new antiviral agents to treat Sars-Cov-2 infection takes a long time, the reusability of existing drugs made more sense to investigate. The SARS-CoV-2 Mpro construct is the most likely biological target for antiviral drugs. Our aim in this study is to target and investigate various antibiotics to N3 inhibitor, which is sars cov-2 Mpro inhibitor. The protein structure of Sars-Cov2 Mpro (PDB ID:6LU7) was retrieved from the Protein Data Bank. Antibiotic compounds were obtained from PubChem. Molecular docking work was done using AutoDock Vina program. Molecular dynamics simulation study was done in Desmond Maestro software. According to the results of molecular insertion, GPER cell modulation in immunity, inflammation and consultation, compared with the antibiotic compounds N3 inhibitor, amoxicillin has better binding affinity while sulcaktam has lower binding affinity. Other antibiotic compounds showed close binding affinity with the N3 inhibitor. According to the molecular dynamics simulation results, we found that the antibiotic compounds complexes we placed on Sars-Cov2 Mpro had good conformational stability. When we look at the MM/GBSA result, amoxicillin has the best binding energy compared to the N3 inhibitor. Sulbactam has low binding energy and has shown close results with other N3 inhibitory antibiotic compounds  As a result, our results support that amoxicillin, which shows better binding affinity than N3 inhibitor, and clavulanic acid, ampicillin, amikacin sulfate, azithromycin, and cefuroxime sodium compounds, which show close binding affinity, will be a usable inhibitor in Sars-Cov-2 Mpro target.

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Published

2023-12-24

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Medical Science