Molecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from Mycobacterium tuberculosis.

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.