Molecular Docking Studies of Plumbagin From Root Bark of Plumbago Indica L. Against Staphylococcus Aureus
Posted: 5 Dec 2019
Date Written: December 3, 2019
Plumbago indica L. (Family: Plumbaginaceae) is an important plant used against infectious diseases. High anti-microbial activity against Staphylococcus aureus has been reported by Saha et al. in (2014). Recent literature documented that plumbagin (5-hydroxy-2 methyl-1, 4-naphthoquinone) exerts an array of biological activities, including anti-microbial activity. Such quinone compounds have been known to express anti-bacterial properties by disrupting the function of bacterial type II topoisomerases. Hence, the current study was conducted to confirm the inhibitory activity of Plumbagin against type II topoisomerase (DNA gyrase) enzyme of Staphylococcus aureus using Schrödinger Glide docking. Initially, the protein structure of topoisomerase II DNA gyrase enzyme of S. aureus was obtained from the PDB data bank (PDB ID: 2XCT) and prepared for docking using BioLuminate protein preparation wizard, which was followed by protein optimization and energy minimization procedures. Similarly, the 3D structure of Plumbagin molecule was obtained through PubChem (PubChem CID: 10205) and the ligand was prepared using LigPrep, which also included optimization and energy minimization procedures. Since it was difficult to conduct a singular docking analysis for the entire protein due to its size, all potential active sites were mapped using the SiteMap software analysis. Finally, the docking analysis was conducted (Schrödinger Glide docking) in order to find the most feasible Glide docking score for each active site. The SiteMap software analysis revealed five potential active sites; with the most feasible docking result in the second active site (Glide score -7.651 kcal/mol). Therefore, according to molecular docking results, the anti-bacterial activity of Plumbagin could be linked with type II topoisomerase (DNA gyrase) enzyme. Future docking studies using other bacterial enzymes are warranted to confirm other inhibitory mechanisms.
Keywords: molecular docking, plumbagin, staphylococcus aureus, glide score, type ii topoisomerase
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