Background:
Resistance to the critical first line anti-tubercular drug, Pyrazinamide, is a significant obstacle to
achieving the global end to tuberculosis targets. Approximately 50% of multidrug-resistant tuberculosis and over 90% of
extensively drug-resistant tuberculosis strains are also Pyrazinamide resistant. Pyrazinamide is a pro-drug that reduce the
duration of tuberculosis therapy time by 9-12 months, while used as an anti-biotic in the 1st- & 2nd-line tuberculosis treatment regimens. Pyrazinamidase is an enzyme, encoded by pncA gene, is responsible for the amide hydrolysis of Pyrazinamide into active Pyrazinoic acid. Pyrazinoic acid, could inhibit trans-translation by binding to Ribosomal protein S1
and competing with tmRNA, the natural cofactor of Ribosomal protein S1. Although pncA mutations have been commonly
associated with Pyrazinamide resistance, a small number of resistance cases have been associated with mutations in Ribosomal protein S1. Ribosomal protein S1was recently identified as a possible target of Pyrazinamide based on its binding
activity to Pyrazinoic acid and the capacity to inhibit trans-translation.
Objective:
Despite the critical role played by Pyrazinamide, its mechanisms of action are not yet fully understood. Therefore, an effort to explore the resistance mechanism toward Pyrazinamide drug in Mycobacterium (M.) tuberculosis.
Methods:
An extensive molecular dynamics simulation was performed using the AMBER software package. We mutated
residues of the binding site (i.e., F307A, F310A, and R357A) in the RpsA S1 domain to address the drug-resistant mechanism of RpsA in complex that might be responsible for Pyrazinamide resistance.
Moreover, it is challenging to collect the drug mutant combine complex of a protein by single-crystal X-ray diffraction.
Thus, the total three structures were prepared by inducing mutations in the wild-type protein using PyMol.
Results:
The dynamics results revealed that mutation in binding pocket produced Pyrazinamide resistance due to the specificity of these residues in binding pockets which result in scarcity of hydrophobic and hydrogen bonding interaction with
Pyrazinoic acid, which increases the CA-distance between the binding pocket residues as compared to wild type RpsA that
lead to structural instability.
Conclusion:
The overall dynamic results will provide useful information behind the drug resistance mechanism to manage
tuberculosis and also helps in better management for future drug resistance.
Mycobacterium tuberculosis ribosomal protein S1 (RpsA) and variants with truncated C-terminal end show absence of interaction with pyrazinoic acid
