(BIO06) Interaction of isoniazid with Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA): from bioinformatics perspective.

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis is a leading killer that has plagued mankind for centuries. The disease is estimated to infect 8 million and kill 2 3 million people each year (Rouse et al., 1995; Manca et al., 1997). A frequently used drug to treat TB is isonicotinic acid hydrazide (INH/ isoniazid) but unfortunately, INHresistant M. tuberculosis organisms are becoming quite common now. In a recent survey of 35 countries, 12.6 % of M. tuberculosis isolates were found to be resistant to at least one drug, including INH (Ahmad & Mustafa, 2001). Studies strongly implicated an enzymatic step(s) in the elongation of fatty acids, and the biosynthesis of the very long fatty acyl chains of mycolic acids as the site of action of INH (Winder & Collins, 1970; Davidson & Takayama, 1979; Quemard, 1991). The inhA gene product, InhA, was proposed involved in the synthesis of fatty acids, presumably the unique mycolic acid components of the outer mycobacterial cell and has been suggested to be the site of action of INH (Banerjee et al., 1994; Wang et al., 1998; Vilcheze et al., 2000). The deletions and missense mutations within the katG gene are common in INHresistant clinical isolates of M. tuberculosis added evidences in support of the role of katG-encoded catalase-peroxidase (Stoekle et al., 1993; Heym et al., 1995). These strongly suggest that INH is a prodrug which requires the katG gene product, KatG, to be activated as an antitubercular (Zhang et al., 1996; Manca et al., 1999; Lei et al., 2000). Once metabolized by KatG, the activated INH metabolite reacts with nicotinamide adenine dinucleotide (NAD) to form isonicotinic acyl-NADH (INADH), which is the inhibitor of InhA. Zhang et al. (1992) confirmed that the resistance towards INH is related to the loss of KatG catalase activity. Besides katG mutations, mutations in several genes such as inhA, ahpC, kasA and ndh (Vilcheze et al., 2000; Torres et al., 2000) and genomic regions of M. tuberculosis are involved in the occurrence of resistance to INH (Piatek et al., 2000; Slayden & Barry, 2000). Banerjee et al. (1994) have shown that low-level resistance to INH in some mycobacterial strains is associated with mutations in the inhA gene. Mutations occurring in both katG and inhA genes may account up to 80% of all organisms resistant to this critical antituberculosis agent (Morris et al., 1995; Musser et al., 1996) with the mutations in katG account for the majority of INH-resistant clinical isolates (Cynamon et al., 1999; Torres et al., 2000). Reports (Rouse et al., 1995; Miesel et al., 1998; Rozwarski et al., 1998) have shown that some INH resistant tuberculosis isolates had a single base change, from thymine to guanine at nucleotide 280 resulting in a serine to alanine replacement in codon 94 (S94A) in inhA gene. Basso et al. (1998) have proposed that INH-resistance in this S94A mutation strain is related to the reduced NADH binding affinity for enoyl reductase. This is supported by an X-ray crystallographic study which showed that there is a reduction in the hydrogen bonding network between NADH and InhA enzyme. Molecular modeling techniques have been used to understand the mechanism of interaction between a protein and a ligand, substrate or inhibitor, at the atomic level. Molecular docking is one of the most widely used methods to predict the binding mechanism of ligand binding. While molecular dynamics simulations is able to give insights into the natural dynamics on different timescales of biomolecules. Here, we report a study utilizing molecular docking and molecular dynamics simulations in our effort to understand the interactions of INH and also to address the mechanism of resistance by M. tuberculosis towards it at the atomic level. The 4th Annual Seminar of National Science Fellowship 2004