Molecular Docking of Some Phytochemicals Against DNA Gyrase of Gram-Negative and Gram-positive Bacteria
Keywords:
Phytochemicals, DNA Gyrase, Molecular DockingAbstract
Molecular docking is a computational technique that predicts the binding orientation and affinity of a small molecule (ligand) to a target macromolecule (receptor). It involves the calculation of the intermolecular interactions between the ligand and receptor to estimate the binding energy and to identify the most stable and favorable binding conformation. Molecular docking can be used for drug discovery and design, as it can help identify potential drug candidates that bind to a specific target with high affinity and selectivity. It is also widely usedin structural biology, as it can provide insights into the structural basis of ligand- receptor interactions. The objective of this study was to investigate the potential activity of various phytochemicals against DNA gyrase of Escherichia coli and Staphylococcus aureus, using molecular docking technique. The study involved 43 phytochemical compounds, along with Ciprofloxacin and Nalidixic acid. The 3D structures of these compounds were obtained from PubChem database and prepared using PyRx-Vina Program 0.8 and OpenBabel software version 3.1.1. DNA gyrase of E. coli (ID 7P2M) and S. aureus (ID 3U2D) were obtained from the RCSB PDB database and refined through energy minimization using the PyRx-Vina Program 0.8. According to the binding affinity values, the results indicated that Diospyrinwas the most active compound against DNA gyrase of E. coli (-8.7) and S. aureus (-9.1), while Imidazoline was the least active against DNA gyrase of E. coli (-3) and Allyl methyl disulfide was the least active against DNA gyrase of S. aureus (-3) when compared with Ciprofloxacin and Nalidixic acid. The study also revealed that the number of amino acids that interacted with each compound varied. The findings suggest that phytochemical compounds could beused as potential antibacterial agents, and further in-vitro and in-vivo studies are recommended using the most active compounds.
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