Antimicrobial potential of C.sativum seed extract against S.aureus In vitro, ADMET, Docking and MD simulation

Articles in Press

Document Type : Research Article

Authors

Government College of Engineering, Salem-11, Tamil Nadu, India

10.24200/sci.2025.64878.9181

Abstract

In this study, seeds of C.sativum purchased from the market were extracted using Soxhlet extraction in vitro, from which 38 active components were confirmed by GC – MS and FT – IR analysis. All 38 ligands were docked using AutoDoc Vina with the four proteins (PDB ID: 4F6X, 3ACX, 2ZCQ, 2ZCS) obtained from RCSB PDB. Out of 38, two ligands from plant extract (2,4-DTBP and 3-ethyl-5-isopropyl-2-methyl phenol) showed good docking scores of more than -7.5 kcal / mol. Among those four proteins, PDB ID 4F6X has the highest docking affinity of -7.9 kcal / mol when compared to the other compounds. Well diffusion method confirmed the antimicrobial activity. In silico analysis using ADMET studies showed that the compounds have high log Kp values, high GI, BBB permeability, high HIA, and low toxicity levels. Non-violation of Lipinski’s rule of five was found in both the ligands. Also, the values of hydrogen Bond, RMSD, RMSF, SASA and Rg fall within a good range. In post-MD, MM–PBSA studies, the results showed that the total binding free energies are more contributing in 3ACX and 2ZCS complexes than in 4F6X and 2ZCQ complexes. Hence, both the in vitro and in silico studies provide the evidence that the two active components have good interaction with the four protein targets.

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Scientia Iranica

Articles in Press, Accepted Manuscript
Available Online from 11 May 2025

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History

  • Receive Date: 03 July 2024
  • Revise Date: 20 April 2025
  • Accept Date: 03 May 2025

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