Isoniazid (INH), a frontline antitubercular drug, inhibits InhA, the enoyl reductase from Mycobacterium tuberculosis, by forming a covalent adduct with the NAD cofactor. Here, we report that the INH-NAD adduct is a slow, tight-binding competitive inhibitor of InhA. Demonstration that the adduct binds to WT InhA by a two-step enzyme inhibition mechanism, with initial, weak binding (K ؊1 ؍ 16 ؎ 11 nM) followed by slow conversion to a final inhibited complex (EI*) with overall K i ؍ 0. 75 A ttempts to treat tuberculosis, a disease that kills more than two million people every year, are hindered by the spread of multidrug-resistant strains of Mycobacterium tuberculosis (MDRTB), the causative agent, and by the increased susceptibility of HIV-positive individuals to this disease (1-4). Although isoniazid (INH; Scheme 1) has been the most effective and widely used drug for the treatment of tuberculosis since the 1950s, the mode of action of this compound is still not completely understood. INH is a prodrug that is activated by the mycobacterial catalase-peroxidase enzyme KatG (Scheme 1) (5-8) and a substantial fraction of all clinical isolates that are resistant to INH result from KatG mutations (2, 9-11). Consequently, compounds that inhibit the ultimate molecular target(s) of INH, but that do not require activation by KatG, have tremendous promise as novel drugs for combating MDRTB.Two enzymes, InhA and KasA, have been proposed as targets for INH. Both are members of the type II dissociated fatty acid biosynthesis pathway (FASII) in M. tuberculosis (Scheme 2), consistent with the observation that INH interferes with the biosynthesis of mycolic acids, very long chain fatty acid components of the mycobacterial cell wall. InhA, an enoyl reductase that catalyzes the NADH-dependent reduction of long chain trans-2-enoyl-acyl carrier proteins (ACPs), was first identified as a target by Jacobs and coworkers (6, 12) who observed mutations in the inhA gene in INH-resistant clinical isolates and identified a point mutant (S94A) that conferred resistance to INH and ethionamide in Mycobacterium smegmatis and in Mycobacterium bovis. Subsequently, Blanchard, Sacchettini, and coworkers (13-15) demonstrated that InhA was inhibited in vitro by a covalent adduct formed between activated INH and the nicotinamide head group of NAD (Scheme 1). InhA mutations observed in INH-resistant clinical isolates were found to be localized to the cofactor binding site and were shown to result in decreased affinity of the purified enzyme for NADH (12,16), consistent with the hypothesis that binding of NADH to the enzyme precedes adduct formation. In addition, Vilcheze et al. (17) used a temperature-sensitive mutation in the inhA gene to show that the phenotypic response to InhA inactivation in M. smegmatis was identical to that caused by treatment with INH, thereby validating InhA as a target for drug discovery. However, although there is convincing evidence that InhA is inhibited by INH, Barry and coworkers (18) have also proposed that KasA, on...