Characterization of the putative active site of mycobacterium tuberculosis pyrazinamidase: An application of bioinformatics software for modeling, docking and testing of drug analogues

• Main Authors: Pastor, Crist John M., Heralde, Francisco M., III
• Format: text
• Published: Animo Repository 2014
• Subjects: Pyrazinamide; Drugs—Analysis; Bioinformatics; Medicinal-Pharmaceutical Chemistry
• Online Access: https://animorepository.dlsu.edu.ph/faculty_research/6096
• Institution: De La Salle University

Pyrazinamide (PZA), a first-line pro-drug targeting Mycobacterium tuberculosis (Mtb), is a cornerstone in tuberculosis combined therapeutic management. It is converted to Pyrazinoic acid by Pyrazinamidase (PZAse), a 2kD enzyme encoded by pncA gene. Ongoing search for drug analogues of Pyrazinamide entails costly and labor-intensive in-vitro and in-vivo studies. This study presented a process to predict and characterize a putative active site of enzymes using free online softwares and databases. The developed platform was applied to Mycobacterium tuberculosis Pyrazinamidase to perform in-silico experiments such docking of its natural substrate and candidate drug analogues. Briefly, a molecular model of PZAse was constructed through online submission of wild type MTb (H37Rv) PZAse protein sequence to SwissProt Database. Conserved amino acids were identified through multiple sequence alignment of Mycobacterial strains 131, ten strains of Mycobacteria and five organisms expressing closely related nicotinamidase/pyrazinamidase. Conserved residues were plotted into the model supplemented by crevice and drug volume calculations coupled with mutation data from existing literature helped identify the putative active site. Drug docking using HEX software showed that amino acids D8, D49, C138, F13, W68, Y103, H71 and A134 interacted with PZA while residues F94 and Y95 stabilized PZA through non-polar interactions. Molecular docking of Nicotinamide and Morphazinamide revealed higher binding affinities to PZAse due to hydrophobic interactions at the binding site. Testing PZA analogues downloaded from PubChem database suggests Pyrazine-2,6-carboxamide fits the active site, shared similar proximity with PZA. This platform exhibits potential in exploring enzyme-substrate interactions that can be extended to other applications, such as exploring enzyme-substrate or receptor-drug interactions, putative active site identification, and testing candidate drugs in-silico as initial steps in rational drug design