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Inhibition of superoxide dismutase using herbal compounds to treat oral diseases caused by Streptococcus mutans - An in silico study


M. Karthick Auswin , Sindhu Ramesh , R. Gayathri , V. Vishnu Priya

Abstract

The aim of this study is to evaluate the efficiency of different herbal compounds in inhibition of superoxide dismutase to treat oral diseases caused by Streptococcus mutans. The three-dimensional crystallographic structure of superoxide dismutase was downloaded from RCSB protein data bank, and then, the protein structure was corrected using “What if ”server. The three-dimensional chemical structures of compounds cianidanol, punicalagins, quercetin, rutin, and epigallocatechin gallate (EGCG) were obtained from the PubChem compound database. It was prepared using Biovia discovery studio 2016, where the standard delay format of this ligand was converted to PDB file using Pymol version 1.7.4.5 tool to generate atomic coordinate. The active binding sites of target protein were analyzed using the Biovia discovery studio 2016. Docking was carried out by iGemdoc software version 2.1 based on scoring functions. The energy of interaction of herbal components with the adhesion protein is assigned. The binding energy indicates the affinity of the adhesion of protein structure docked with the herbal compounds of which EGCG showed best docking with the superoxide dismutase of which EGCG had a better interaction with target protein based on root-mean-square deviation values compared to standards. EGCG suppresses S. mutans at transcriptional level disrupting the initial attachment of S. mutans and the formation of mature biofilm. The probable mechanism of EGCG is its interaction with the cell membranes of bacteria causing the disruption of the bacterial cell morphology membrane integrity and permeability. Thus, EGCG has been used in inhibition of superoxide dismutase to treat the oral diseases caused. The docking analysis revealed that EGCG has the maximum binding energy of −90.0926 of all the five herbal compounds.



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