The emergence of multi-drug-resistant Mycobacterium tuberculosis (Mtb) strains has rendered many of the currently available anti-TB drugs ineffective. Hence, there is a pressing need to discover new potential drug targets/candidates. In this study, attempts have been made to identify novel inhibitors of the ribonuclease VapC2 of Mtb H37Rv using various computational techniques. Ribonuclease VapC2 Mtb H37Rv’s protein structure was retrieved from the PDB databank, 22 currently used anti-TB drugs were retrieved from the PubChem database, and protein–ligand interactions were analyzed by docking studies. Out of the 22 drugs, rifampicin (RIF), being a first-line drug, showed the best binding energy (−8.8 Kcal/mol) with Mtb H37Rv VapC2; hence, it was selected as a parent molecule for the design of its derivatives. Based on shape score and radial plot criteria, out of 500 derivatives designed through SPARK (Cresset®, Royston, UK) program, the 10 best RIF derivatives were selected for further studies. All the selected derivatives followed the ADME criteria concerning drug-likeness. The docking of ribonuclease VapC2 with RIF derivatives revealed the best binding energy of −8.1 Kcal/mol with derivative 1 (i.e., RIF-155841). A quantitative structure–activity relationship study revealed that derivative 1’s activity assists in the inhibition of ribonuclease VapC2. The stability of the VapC2–RIF155841 complex was evaluated using molecular dynamics simulations for 50 ns and the complex was found to be stable after 10 nsec. Further, a chemical synthesis scheme was designed for the newly identified RIF derivative (RIF-155841), which verified that its chemical synthesis is possible for future in vitro/in vivo experimental validation. Overall, this study evaluated the potential of the newly designed RIF derivatives with respect to the Mtb VapC2 protein, which is predicted to be involved in some indispensable processes of the related pathogen. Future experimental studies regarding RIF-155841, including the exploration of the remaining RIF derivatives, are warranted to verify our current findings.
New treatment regimens against tuberculosis (TB), which is still a serious social problem, are urgently needed. Herein, the anti‐TB potential of methanolic extract of Saraca asoca (S. asoca) was evaluated against Mycobacterium tuberculosis (Mtb) H37Rv strain and ∼88 % inhibition was achieved. To explore the interaction of phytochemicals with the targets of mycobacteria, 13 phytochemicals of S. asoca were docked with 3 receptors of Mtb H37Rv viz VapC2, PPE41, and CarD. Among these phytochemicals, Epicatechol, Leucocynadin and Procynidin were found most effective against Mtb H37Rv VapC2 protein with docking energy of −9.92110, −9.77605 and −10.62900 kcal/mol, respectively. Isolariciresinol and Procynidin were effective against CarD (−8.18264 and −9.97703 kcal/mol, respectively) and PPE41 (docking energy −9.16713 and −11.59770 kcal/mol, respectively). ADMET properties suggested good bioavailability of the active compounds. Molecular dynamics simulation studies revealed that Epicatechol complex with VapC2 protein stabilized after 20 ns and can be further explored for its anti‐TB potential via cell‐based co‐culture assays and animal studies.
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