Structural insights of catalytic mechanism in mutant pyrazinamidase of Mycobacterium tuberculosis

Abstract

Pyrazinamidase (PZase) is a member of Fe-dependent amidohydrolases that activates pyrazinamide (PZA) into active pyrazinoic acid (POA). PZA, a nicotinamide analogue, is an essential first-line drug used in Mycobacterium tuberculosis (Mtb) treatment. The active form of PZA, POA, is toxic and potently inhibits the growth of latent Mtb, which makes it possible to shorten the conventional 9-month tuberculosis treatment to 6 months. In this study, an extensive molecular dynamics simulation was carried out to the study the resistance mechanism offered by the three mutations Q10P and D12A and G97D. Our results showed that two regions Gln10-His43, Phe50-Gly75 are profoundly affected by these mutations. Among the three mutations, Q10P and D12A mutations strongly disturb the communication among the catalytic triad (Asp8, Lys98 and Cys138). The oxyanion hole is formed between the backbone nitrogen atoms of A134 and C138 which stabilizes the hydroxyl anion of nicotinamide. The D12A mutation greatly disturbs the oxyanion hole formation followed by the Q10P and G97D. Our results also showed that these mutations destabilize the interaction between Fe²⁺ ion and Asp49, His51, His57 and His71. The binding pocket analysis showed that these mutations increase the cavity volume, which results in loose binding of PZA. MMGBSA analyzes have shown that these mutations reduce the binding affinity to the PZA drug. Our results may provide useful information for the design of new and effective PZase inhibitors based on structural information of WT and mutant PZases.

Communicated by Ramaswamy H. Sarma

Keywords:

• PZase
• PZA
• pyrazinoic acid
• Mycobacterium tuberculosis
• oxyanion hole

Disclosure statement

No potential conflict of interest was reported by the author(s).

Acknowledgements

The computations were partially performed at the Center for High Performance Computing, Shanghai Jiao Tong University.

Additional information

Funding

This work is supported by the grants from the Key Research Area (Grant no. 2016YFA0501703) of the Ministry of Science and Technology of China, the National Natural Science Foundation of China (Contract nos. 61832019 and 61503244), the State Key Lab of Microbial Metabolism and Joint Research Funds for Medical and Engineering and Scientific Research at Shanghai Jiao Tong University (grant no. YG2017ZD14).