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Inhibition of RagB gene using herbal compounds in the treatment of primary endodontic pathogenesis caused by Porphyromonas species - An in silico study

T. Vigneshwar , Sindhu Ramesh , Vishnu Priya


Herbal compounds taken from plant extracts are identified having numerous medicinal values and put into use for various treatments. Such compounds are also pave way and helpful in manufacturing such synthetic compounds for commercial use. In this article, about five herbal compounds, namely, allicin, nimbin, mangiferin, punicalin, and alpha-pinene were taken and studied for their efficacy in the treatment of primary endodontic pathogenesis. Almost all of them have antibacterial efficacy and alpha-pinene, outstands having varied application in the field of disease control. The aim of the study was to evaluate the efficacy of different herbal compounds on inhibition of RagB gene in the treatment of primary endodontic pathogenesis caused by Porphyromonas species. The three-dimensional (3D) structure of RagB gene protein was downloaded from the RCSB Protein Data Bank and was corrected using “what if ” server. Then, the 3D chemical structures of allicin, nimbin, mangiferin, punicalin, and alpha-pinene were downloaded from PubChem compound database which was followed by analysis of target active binding site; the active binding sites of targets proteins were analyzed using the Bravio Discovery Studio version 2016. Finally, molecular docking analysis was carried out by computerized ligand-target docking approach was used to analyze structural complex of the adhesion protein with allicin, nimbin, mangiferin, punicalin, and alpha-pinene to understand the structural basis of this protein target specificity. Docking was carried out with the help of iGEMDOCK software 2.1 based version. The binding energy indicated the affinity of adhesion protein docked with herbal components. Among the five compounds, alpha-pinene showed the highest negative value which indicates active binding to the target site and also showed the best interaction with target protein based on the root-mean-square deviation values as compared to standards. Porphyromonas gingivalis, an anaerobic, Gram-negative pathogen and the bacterium most associated with chronic periodontitis, demonstrated highest sensitivity to alpha-pinene among the five herbal compounds. Further investigation should be done on more herbal compounds for the prevention and treatment of various endodontic diseases.


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