Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance

Aamir Mehmood; Muhammad Tahir Khan; Aman Chandra Kaushik; Anwar Sheed Khan; Muhammad Irfan; Dong-Qing Wei

doi:10.3389/fbioe.2019.00404

Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance

Front Bioeng Biotechnol. 2019 Dec 10:7:404. doi: 10.3389/fbioe.2019.00404. eCollection 2019.

Authors

Aamir Mehmood¹, Muhammad Tahir Khan², Aman Chandra Kaushik³, Anwar Sheed Khan⁴, Muhammad Irfan⁵, Dong-Qing Wei¹

Affiliations

¹ The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
² Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.
³ Wuxi School of Medicine, Jiangnan University, Wuxi, China.
⁴ Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan.
⁵ Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.

Abstract

Pyrazinamide (PZA) is one of the main FDA approved drugs to be used as the first line of defense against Mycobacterium Tuberculosis (MTB). It is activated into pyrazinoic acid (POA) via MTB's pncA gene-encoded pyrazinamidase (PZase). Mutations are most commonly responsible for PZA-resistance in nearly 70% of the resistant samples. In the present work, MTB positive samples were chosen for PZA drug susceptibility testing (DST) against critical concentration (100 ug/ml) of PZA. The resistant samples were subjected to pncA sequencing. As a result, 36 various mutations have been observed in the PZA resistant samples, uploaded to the NCBI (GeneBank accession no. MH461111). Here we report the mechanism of PZA resistance behind the three mutants (MTs), Asp12Ala, Pro54Leu, and His57Pro in comparison with the wild type (WT) through molecular dynamics simulation to unveil how these mutations affect the overall conformational stability. The post-simulation analyses revealed notable deviations as compared to the WT structure. Molecular docking studies of PZA with MTs and WT, pocket volume inspection and overall shape complementarity analysis confirmed the deleterious nature of these mutations and gave an insight into the mechanism behind PZA-resistance. These analyses provide vital information regarding MTB drug resistance and could be extremely useful in therapy management and overcoming its global burden.

Keywords: MTB; PZA; drug resistance; mutations; simulation.