Insights from the molecular mechanism of pyrazinamide to mutated pyrazinamidase linked to the pncA gene in clinical isolates of Mycobacterium tuberculosis

Abstract

This study aims to conduct a comprehensive molecular dynamics strategy to evaluate whether mutations found in pyrazinamide monoresistant (PZAMR) strains of Mycobacterium tuberculosis (MTB) can potentially reduce the effectiveness of pyrazinamide (PZA) for tuberculosis (TB) treatment. Five single point mutations of pyrazinamidase (PZAse), an enzyme which is responsible for the activation of prodrug PZA into pyrazinoic acid, found in MTB clinical isolates, namely His82Arg, Thr87Met, Ser66Pro, Ala171Val, and Pro62Leu, were analyzed by the dynamics simulations both in the apo state (unbound state) and in the PZA bound state. The results showed that the mutation of His82 to Arg, Thr87 to Met, and Ser66 to Pro in PZAse affects the coordination state of the Fe²⁺ ion, which is a cofactor required for enzyme activity. These mutations change the flexibility, stability, and fluctuation of His51, His57, and ASP49 amino acid residues around the Fe²⁺ ion, culminating in an unstable complex and dissociation of PZA from the PZAse binding site. However, mutations of Ala171 to Val and Pro62 to Leu were found to have no effect on the complex’s stability. Based on the results, PZAse mutations of His82Arg, Thr87Met, and Ser66Pro culminated in weak binding affinity for PZA and caused significant structural deformations that led to PZA resistance. Future structural and functional studies, as well as investigations into other aspects of drug resistance in PZAse, will require experimental clarification.

Communicated by Ramaswamy H. Sarma

Keywords:

• Drug resistance
• pyrazinamide monoresistant
• tuberculosis
• molecular dynamics simulations

Acknowledgments

This study was supported by Directorate of Research and Community Service Universitas Padjadjaran.

Author’s contributions

All experiments were designed by DAEP and LC. All experiments were carried out by DAEP, AA, and DSFR. Data analysis were DAEP and AA. Work was supervised by LC. Manuscript was prepared by DAEP and AA and reviewed by LC. All authors read and approved the final manuscript.

Data availability statement

All data generated or analyzed during this study are included in this published article.

Disclosure statement

The authors report there are no competing interests to declare.

Additional information

Funding

This research was funded by Universitas Padjadjaran (2203/UN6.3.1/PT.00/2022).