Molecular insight into multiple RpoB clinical mutants of Mycobacterium tuberculosis: An attempt to probe structural variations in rifampicin binding site underlying drug resistance

Rifampicin (RMP) resistant strains are still persisting as a threat to the global TB control program. Therefore, understanding the RMP resistant mechanism is need of the hour. The current study has investigated the role of each RMP binding site (RBS) residues, deploying computational alanine scanning mutagenesis (CASM) to unravel the critical and non-critical binding site residues. In addition, conformational shifts in RBS cavity of different RNAP beta-subunit (RpoB) systems have also been analyzed. Our initial findings showed that in addition to reported mutational sites, Q510, Q513, R529, P564 and P566 were also critical binding site residues, which upon mutation de-stabilize the RMP binding. Study also indicated that R3, R4 and R5 regions of RpoB were very significant for the functioning of RMP. The concerted interactions of these regions with RMP hold it into the centre position of RBS and restrict the entrance of elongating RNA transcript. Whereas, after mutation, due to repositioning of RMP and changes in its interactions, the overall cavity becomes significantly hollow which may confer space for phosphodiester bond formation during transcription elongation. Our findings provide valuable details to forestall RMP resistance and may help in the development of new leads against the RMP resistant strains. (C) 2018 Elsevier B.V. All rights reserved.