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In silico identification of potential drug targets in Clostridium difficile R20291: modeling and virtual screening analysis of a candidate enzyme MurG

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Abstract

Clostridium difficile is an etiologic agent of a variety of gastrointestinal diseases in human including mild sporadic diarrhea and severe life-threatening pseudomembranous colitis. The continuous rise of C. difficile infection worldwide accompanied by rapid emergence of multidrug-resistant and hypervirulent strains has necessitated the search for novel drug targets. The present study is aimed at identifying putative therapeutic targets in this pathogen by in silico approach which encompassed four steps, viz, similarity search between pathogen and host, essentiality study using the database of essential genes, metabolic functional association study using Kyoto Encyclopedia of Genes and Genomes database, and choke point analysis. The study identified 19 promising drug targets which are non-homologous to host proteins, potentially essential for the pathogen, choke point enzymes, and participate in four pathogen-specific pathways, namely peptidoglycan biosynthesis, phosphotransferase system, two component system, and d-alanine metabolism pathways. The peptidoglycan biosynthesis pathway is the highest donor to the list of candidate target proteins. Furthermore, a three-dimensional model of one of the identified potential targets, MurG from peptidoglycan biosynthesis pathway, was constructed by homology modeling. Subsequently, by means of a virtual screening approach, the study identified eight potential inhibitors from small molecules databases, which have better docking scores, varying from −7.9 to −10.3 kcal/mol, and stronger binding affinity with target compared to known inhibitors and natural substrate of MurG. The docking analysis revealed that the active site residue Gln298 plays a critical role in ligand–target interactions which was validated through in silico mutational study. Other active site residues like Arg168, Ser198, Arg202, Ser269, and His297 were also found to play a role in binding interactions. The identified compounds may facilitate the development of new drugs to combat C. difficile-associated diseases.

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Acknowledgments

Vijayalakshmi is grateful to Pondicherry University, India, for the pre-doctoral fellowship. We thank Dr. Mohane Coumar, Pondicherry University, Pondicherry, for providing valuable suggestions. Research carried on at the Laboratory of the Centre for Excellence in Bioinformatics, Pondicherry University, India, is funded by the Department of Information Technology (DIT) and the Department of Biotechnology (DBT), Government of India, New Delhi, India.

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  1. Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, 605014, Pondicherry, India

    Vijayalakshmi Ezhilarasan, Om Prakash Sharma & Archana Pan

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  1. Vijayalakshmi Ezhilarasan
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  2. Om Prakash Sharma
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Correspondence to Archana Pan.

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44_2012_262_MOESM6_ESM.doc

Supplementary Fig. 1. 2D interaction maps for dock complexes: a–l 12 lead compounds, m known inhibitor 13b, n known inhibitor 14b and o natural substrate with target protein MurG (DOC 1121 kb)

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Ezhilarasan, V., Sharma, O.P. & Pan, A. In silico identification of potential drug targets in Clostridium difficile R20291: modeling and virtual screening analysis of a candidate enzyme MurG. Med Chem Res 22, 2692–2705 (2013). https://doi.org/10.1007/s00044-012-0262-0

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