Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Resistance Studies

Background:

• Pyrazinamide (PZA) is a crucial first-line anti-tuberculosis drug.
• Resistance to PZA in *Mycobacterium tuberculosis* (MTB) is often caused by mutations in the *pncA* gene, which encodes pyrazinamidase (PZase).
• Understanding the molecular mechanisms of these mutations is vital for effective TB management.

Purpose of the Study:

• To investigate the molecular mechanisms underlying PZA resistance caused by novel *pncA* mutations.
• To compare the structural and dynamic properties of wild-type (WT) and mutant PZase using molecular dynamics simulations.
• To elucidate how these mutations affect PZase's catalytic activity in converting PZA to its active form, pyrazinoic acid (POA).

Main Methods:

• Detection of novel *pncA* mutations (V131F, Q141P, R154T, A170P, V180F) in PZA-resistant MTB isolates.
• Gene sequencing of the *pncA* gene.
• Molecular dynamics (MD) simulations of WT and mutant PZase structures (apo and PZA-complexed) over 40 ns.
• Analysis of structural parameters including root mean square deviation (RMSD), root mean square fluctuations (RMSF), binding pocket volume, and total energy.

Main Results:

• Mutant PZase (MTs) exhibited higher deviation and fluctuation compared to WT PZase.
• MTs showed reduced binding pocket volumes and lower shape complementarity scores, but higher docking scores, compared to WT.
• Residual motions in MTs appeared to be dominant in anti-correlated motion, suggesting altered enzyme dynamics.
• The identified mutations (V131F, Q141P, R154T, A170P, V180F) are likely responsible for structural changes impacting PZase's catalytic function.

Conclusions:

• Novel mutations in the *pncA* gene significantly alter PZase structure and dynamics.
• These alterations potentially impair the conversion of PZA to POA, leading to drug resistance.
• The findings provide valuable insights for understanding and managing PZA-resistant tuberculosis.