Study of mechanism of interaction of truncated isoniazid-nicotinamide adenine dinucleotide adduct against multiple enzymes of Mycobacterium tuberculosis by a computational approach

Objective/Background: Isoniazid [INH] is one of the effective antituberculosis [TB] drugs used for TB treatment. However, most of the drug-resistant Mycobacterium tuberculosis [MTB] clinical strains are resistant to INH, a first-line antituberculous drug. Certain metabolic enzymes such as adenosylhomocysteinase [Rv3248c], universal stress protein [Rv2623], nicotinamide adenine dinucleotide [reduced]-dependent enoyl-acyl carrier protein reductase [Rv1484], oxidoreductase [Rv2971], dihydrofolate reductase [Rv2763c], pyrroline- 5-carboxylate dehydrogenase [Rv1187] have been identified to bind INH-nicotinamide adenine dinucleotide [INH-NAD] and INH-nicotinamide adenine dinucleotide phosphate adducts coupled to Sepharose resin. These enzymes are reported to be involved in many important biochemical processes of MTB, including cysteine and methionine metabolism, mycobacterial growth regulation, mycolic acid biosynthesis, detoxification of toxic metabolites, folate biosynthesis, etc. The truncated INH-nicotinamide adenine dinucleotide [oxidized] adduct, 4-isonicotinoylnicotinamide, isolated from urine samples of human TB patients treated with INH therapy is proposed to have antimycobacterial activity

Methods: To understand the mechanism of interaction of the truncated INH-NAD adduct, binding energy studies were carried out on the aforementioned six enzymes with known three-dimensional structures using AutoDock4.2

Results: In silico docking analysis of these MTB enzymes with the truncated INH-NAD adduct showed favorable binding interactions with docking energies ranging from -5.29 to -7.07 kcal/mol

Conclusion: Thus, in silico docking study revealed that the INH-NAD adduct, which is generated in vivo after INH activation, may undergo spontaneous hydrolysis to form the truncated INH-NAD adduct and further binds and inhibits multiple enzymes of MTB, in addition to InhA, confirming that INH is an effective anti-TB drug acting at multiple enzymes. Further analysis of amino acid residues in the active site of INH-NAD-binding proteins showed the probable presence of catalytic triad in four enzymes possibly involved in INH binding to the enzyme

Comparative proteomic analysis of Mycobacterium tuberculosis strain H[37]Rv versus H[37]Ra

Mycobacterium tuberculosis [MTB] H[37]Ra is an attenuated tubercle bacillus closely related to the virulent type strain MTB H[37]Rv. In spite of extensive study, variation in virulence between the MTB H[37]Rv and MTB H[37]Ra strains is still to be understood. The difference in protein expression or structure due to mutation may probably be an important factor for the virulence property of MTB H[37]Rv strain. In this study, a whole proteome comparison between these two strains was carried out using bioinformatics approaches to elucidate differences in their protein sequences. On comparison of whole proteome using NCBI standalone BLAST program between these two strains, 3759 identical proteins in both the strains out of 4003 proteins were revealed in MTB H[37]Rv and 4034 proteins were revealed in MTB H[37]Ra; 244 proteins of MTB H[37]Rv and 260 proteins of MTB H[37]Ra were found to be non-identical. A total of 172 proteins were identified with mutations [Insertions/deletions/substitutions] in MTB H[37]Ra while 53 proteins of MTB H[37]Rv and 85 proteins of MTB H[37]Ra were found to be distinct. Among 244 non-identical proteins, 19 proteins were reported to have an important biological function; In this study, mutation was shown in these proteins of MTB H[37]Ra. This study reports the protein differences with mutations between MTB H[37]Rv and H[37]Ra, which may help in better understanding the pathogenesis and virulence properties of MTB H[37]Rv