in silico screening and molecular dynamics simulations study to identify novel potent inhibitors against Mycobacterium tuberculosis DnaG primase.

Tuberculosis remains a major global health threat killing millions of people. Due to existing multiple drug resistance (MDR) and prolonged treatment it becomes necessary to explore novel drug targets in Mycobacterium tuberculosis (Mtb). DnaG primase, having a significant role in primer synthesis during initiation of DNA replication, has emerged as a promising drug target. The three dimensional (3D) model of its catalytic domain (Toprim) was constructed. Further, in silico screening of the three diverse chemical compound libraries against the modeled domain was carried out. Four top screened compounds were identified and evaluated by ADMET analysis. The stability of these compounds in complex with the Toprim domain was validated through 50 ns molecular dynamics simulations. Lys 101, Glu 137 and Asp 188 in the active site predominantly formed the hydrogen bonds with the top screened compounds. Hence, the drug-like compounds identified can be taken up for the further experimental investigation as anti-tubercular agents.

Molecular dynamics analysis of the effects of GTP, GDP and benzimidazole derivative on structural dynamics of a cell division protein FtsZ from Mycobacterium tuberculosis.

The prevailing multi-drug resistance in Mycobacterium tuberculosis continues to remain one of the main challenges to combat tuberculosis. Hence, it becomes imperative to focus on novel drug targets. Filamenting temperature-sensitive mutant Z (FtsZ) is an essential cell division protein, a eukaryotic tubulin homologue and a promising drug target. During cytokinesis, FtsZ polymerises in the presence of GTP to form Z-ring and recruits other proteins at this site that eventually lead to the formation of daughter cells. Benzimidazoles were experimentally shown to inhibit Mtb-FtsZ, with one of the benzimidazole derivatives, M1, being reported to have the minimum inhibitory concentration (MIC) value of 3.13 µg/mL. In the present study, mechanism of destabilisation of FtsZ in the presence of M1 was computationally investigated in the presence of its substrate GTP/GDP employing molecular dynamics (MD) simulation analysis, principal component analysis (PCA), molecular mechanics combined with the generalised Born and surface area continuum salvation (MM-GBSA) and density functional theory (DFT). From the analyses, it is proposed that binding of M1 in the inter-domain cleft induces structural changes in the GTP-binding region that affect GTP binding, thus switching the preference of this protein towards depolymerised state and eventually inhibiting the cell division. Hence, this study provides mechanistic insights into the design of novel benzimidazole inhibitors against Mtb-FtsZ. Communicated by Ramaswamy H. Sarma.