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Being a part of dormancy survival regulator (DosR) regulon, Rv2004c (rough morphology and virulent strain gene) has been identified in earlier experimental studies as an indispensable protein required for the growth and survival of Mycobacterium tuberculosis . This protein was predicted to have a role in inhibition of phospholipase A2 activity related to immuno-defence and other membrane-related events. Thus, considering significance of Rv2004c protein, a structure-based drug designing strategy was followed to identify potential inhibitors to this novel target. Initially, to validate the target, absence of homologous proteins in the host was verified through sequence and structure similarity search against human proteome. Then, a potential ligand binding site on the target was identified and virtual screening against Zinc database molecules was carried out. The top scoring hits along with their analogs were taken for docking studies with Glide. The binding free energy of the docked complexes of the Glide hits were predicted by Prime program from Schrodinger and molecules ZINC57990006, ZINC33605742, ZINC71773467 and ZINC34198774 were recognized as potential hits against this target. Analyzing the predicted pharmacokinetic properties of the molecules from QikProp and admetSAR tool, ZINC34198774 was identified as a valid molecule. Molecular dynamics simulation studies ascertained that ZINC34198774 could be a potential inhibitor against Rv2004c. Thus, results acquired from this study could be of use to design new therapeutics against tuberculosis.Communicated by Ramaswamy H. Sarma.

Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. UvrC protein is a part of this complex and thus helps to repair the damaged DNA of M. tuberculosis. Hence, structural bioinformatics study of UvrC protein from M. tuberculosis was carried out using homology modeling and molecular docking techniques. Assessment of the reliability of the homology model was carried out by predicting its secondary structure along with its model validation. The predicted structure was docked with the ATP and the interacting amino acid residues of UvrC protein with the ATP were found to be TRP539, PHE89, GLU536, ILE402 and ARG575. The binding of UvrC protein with the DNA showed two different domains. The residues from domain I of the protein VAL526, THR524 and LEU521 interact with the DNA whereas, amino acids interacting from the domain II of the UvrC protein included ARG597, GLU595, GLY594 and GLY592 residues. This predicted model could be useful to design new inhibitors of UvrC enzyme to prevent pathogenesis of Mycobacterium and so the tuberculosis.