Biochemical Characterization and Computational Identification of Mycobacterium tuberculosis Pyrazinamidase in Some Pyrazinamide-Resistant Isolates of Iran

Farahnoosh Doustdar, Mohammad Pazhang, Faramarz Mehrnejad, Mehrnoosh Safarzadeh, Davod Rabiei, Nader Chaparzadeh, Hanieh Falahati, Mohammad Mir-Derikvand

Pyrazinamide (PZA) is one the first line anti-tuberculosis drugs that require activation by the pyrazinamidase (PZase). Most PZA-resistant Mycobacterium tuberculosis strains have mutations in the pncA gene which encoding PZase that result in the reduction or loss of the enzyme activity. Herein, we have examined how various mutations, which have been found from the PZA-resistant M. t uberculosis strains in Iran, modify the PZase activity. To elucidate the possible role of these mutations, namely A143T (MUT1), L151S (MUT2), A143T/T168A/E173K (MUT3), in the bioactivity of the enzyme, the PZase and mutant genes were cloned, functionally expressed and biochemically and computationally characterized. In comparison to the PZase enzyme, the enzymatic efficiency of mutant enzymes was decreased, with MUT2 indicating the largest enzymatic efficiency reduction. Homology models of mutants were constructed based on the PZase X-ray crystal structure. Molecular modeling and substrate docking revealed that the wild-type has much stronger binding affinity to PZA than the mutants whereas MUT2 has the weakest binding affinity. In addition, the molecular dynamics simulations and the essential dynamics results illustrated that the positions of the 51st to 71st residues were more dynamics in MUT2 as compared to the other atoms in PZase, MUT1 and MUT3 which could decrease the K m and k cat values of the enzymes.