Probing the Molecular Mechanism of Rifampin Resistance Caused by the Point Mutations S456L and D441V on Mycobacterium tuberculosis RNA Polymerase through Gaussian Accelerated Molecular Dynamics Simulation

Abstract

Rifampicin is the first line anti-tuberculosis drug with Mycobacterium tuberculosis RNA polymerase as molecular target. Unfortunately, Mycobacterium tuberculosis (Mtb) strains that are resistant to rifampicin have been identified in clinical, which limits the therapeutic effects of rifampicin. In clinical isolates, S531L and D516V (E.coli) are two common mutated codons on rpoB gene, corresponding to S456L and D441V in Mtb. However, the resistance mechanism at the molecular level is still elusive. In this work, Gaussian accelerated molecular dynamics simulations were performed to uncover the resistance mechanism of rifampicin due to S456L and D441V mutations at the atomic level. The binding free energy analysis reveals that the reduction of binding ability of two mutants to rifampicin mainly is from the decrease of electrostatic interaction, especially the decrease of energy contribution of R454 residue. R454 residue acts as an anchor and forms stable hydrogen bond interaction with rifampicin, allowing rifampicin to be stably incorporated in the center of the binding pocket. However, the disappearing of hydrogen bond between R454 and the mutated residues increases the flexibility of the side chain of R454. And then, the conformation of R454 changes and the hydrogen bond interaction between it and rifampicin is disrupted. As result, rifampicin molecule moves to the outside of the pocket and the binding affinity decreases. Overall, these findings can provide useful information for understanding the drug resistance mechanism of rifampicin and also can give some theoretical guidance for further design of novel inhibitors to overcome the drug resistance.