Insights into RpoB clinical mutants in mediating rifampicin resistance in Mycobacterium tuberculosis

• Published in: Journal of molecular graphics & modelling 2016-06, Vol.67, p.20-32
• Main Authors: Nusrath Unissa, Ameeruddin, Hassan, Sameer, Indira Kumari, Venkatesan, Revathy, Ravi, Hanna, Luke Elizabeth
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Binding energy; Binding Sites; Deviation; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - genetics; Docking; Drug Resistance, Bacterial - drug effects; Drug Resistance, Bacterial - genetics; Dynamics; Hydrogen Bonding; Mean square values; Models, Molecular; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular modeling; Mutants; Mutation - genetics; Mutations; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Proteins; Reproducibility of Results; RIF resistance; Rifampin - chemistry; Rifampin - pharmacology; Roots; RpoB; Simulation; Thermodynamics; Time Factors; Tuberculosis
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2016.04.005

[Display omitted] •Rifampicin (RIF) an essential first-line anti-tuberculosis (TB) drug, resistance to RIF is a potential threat to TB control program and widely considered as surrogate marker for detection of multi-drug resistant-TB (MDR-TB).•To understand the differences in binding ability between the wild type (WT) and mutant (MT) such as D516V, L521M, H526D, H526R, H526Y, S531L and L533P-RpoB proteins associated with RIF resistance in MTB; these proteins were modelled, docked and simulated using in silico approaches in comparison to WT.•Molecular docking suggests that the high score in WT and MT- L521M may be due to the presence of favorable interactions with RIF which lacks in other MTs.•Molecular dynamics simulation suggests that the root mean square deviation (RMSD) was more and root mean square fluctuation (RMSF) was less in WT compared to MTs.•In short, these results suggest that RIF binding ability shows differences between WT and MTs, which could be because of different substitutions affecting the conformation of the MT proteins, leading to changes in binding interactions with RIF, eventually to the cause of RIF resistance. Rifampicin (RIF) an essential first-line anti-tuberculosis (TB) drug, resistance to RIF is a potential threat to TB control program and widely considered as surrogate marker for detection of multi-drug resistant-TB (MDR-TB), molecular understanding of which is the utmost need of the hour. Mutations at RIF resistance-determining region (RRDR) of 81-bp in the rpoB gene coding for β subunit or RpoB protein is the major cause of RIF resistance in Mycobacterium tuberculosis (MTB). Mutation at positions 526 and 531 are generally associated with high-level RIF resistance and at codons 516, 521 and 533 with low-level resistance. Thus, in order to understand the interactions between the clinical mutants (MTs) of RpoB and RIF which are responsible for mediating both levels of RIF resistance from MTB. In the present study, models of wild type (WT) and seven MTs (D516V, L521M, H526D, H526R, H526Y, S531L and L533P) of RpoB from MTB were generated using crystal structure of 2A68 and 4KBM as templates, for deducing 3 domains structure. Molecular docking between RpoB proteins and RIF was carried out, which showed higher values for WT compared to MTs. The high score in WT may be due to the presence of favorable interactions with RIF and MT-L521M which lacks in other MTs. Molecular dynamics (MD) simulation was performed for over 10 nanoseconds