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Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile.
Interdiscip Sci. 2018 Sep; 10(3):583-604.IS

Abstract

This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase. The three-dimensional structures of these targets were predicted by molecular modelling. The herbal bioactive compounds were screened by computer-aided virtual screening and binding potentials against the drug targets were predicted by molecular docking. Quercetin present in Psidium guajava (binding energy of -9.1 kcal/mol), Ellagic acid found in Punica granatum and Psidium guajava (binding energy -9.0 kcal/mol) and Curcumin, present in Curcuma longa (binding energy -7.8 kcal/mol) demonstrated minimum binding energy and more number of interacting residues with the drug targets. Further, comparative study revealed that phytoligands demonstrated better binding affinities to the drug targets in comparison with usual ligands. Thus, this investigation explores the therapeutic probabilities of selected phytoligands against the putative drug targets of C. difficile.

Authors+Show Affiliations

Department of Biotechnology Engineering, R & D Centre, Dayananda Sagar Institutions, Bangalore, 560 078, India. Visvesvaraya Technological University, Belagavi, Karnataka, India.Department of Biotechnology Engineering, R & D Centre, Dayananda Sagar Institutions, Bangalore, 560 078, India. sinoshskariya@gmail.com. Visvesvaraya Technological University, Belagavi, Karnataka, India. sinoshskariya@gmail.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28217823

Citation

Kamath, Suman, and Sinosh Skariyachan. "Novel Insight From Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium Difficile." Interdisciplinary Sciences, Computational Life Sciences, vol. 10, no. 3, 2018, pp. 583-604.
Kamath S, Skariyachan S. Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile. Interdiscip Sci. 2018;10(3):583-604.
Kamath, S., & Skariyachan, S. (2018). Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile. Interdisciplinary Sciences, Computational Life Sciences, 10(3), 583-604. https://doi.org/10.1007/s12539-017-0215-x
Kamath S, Skariyachan S. Novel Insight From Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium Difficile. Interdiscip Sci. 2018;10(3):583-604. PubMed PMID: 28217823.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile. AU - Kamath,Suman, AU - Skariyachan,Sinosh, Y1 - 2017/02/20/ PY - 2016/05/15/received PY - 2017/01/03/accepted PY - 2016/12/28/revised PY - 2017/2/22/pubmed PY - 2018/11/6/medline PY - 2017/2/21/entrez KW - Clostridium difficile KW - Essential genes KW - Metabolic pathways KW - Molecular docking KW - Molecular modelling KW - Phytoligands KW - Putative drug targets SP - 583 EP - 604 JF - Interdisciplinary sciences, computational life sciences JO - Interdiscip Sci VL - 10 IS - 3 N2 - This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase. The three-dimensional structures of these targets were predicted by molecular modelling. The herbal bioactive compounds were screened by computer-aided virtual screening and binding potentials against the drug targets were predicted by molecular docking. Quercetin present in Psidium guajava (binding energy of -9.1 kcal/mol), Ellagic acid found in Punica granatum and Psidium guajava (binding energy -9.0 kcal/mol) and Curcumin, present in Curcuma longa (binding energy -7.8 kcal/mol) demonstrated minimum binding energy and more number of interacting residues with the drug targets. Further, comparative study revealed that phytoligands demonstrated better binding affinities to the drug targets in comparison with usual ligands. Thus, this investigation explores the therapeutic probabilities of selected phytoligands against the putative drug targets of C. difficile. SN - 1867-1462 UR - https://www.unboundmedicine.com/medline/citation/28217823/Novel_Insight_from_Computational_Virtual_Screening_Depict_the_Binding_Potential_of_Selected_Phytotherapeutics_Against_Probable_Drug_Targets_of_Clostridium_difficile_ L2 - https://dx.doi.org/10.1007/s12539-017-0215-x DB - PRIME DP - Unbound Medicine ER -