Inhibition of the Mycobacterium tuberculosis enoyl acyl carrier protein reductase InhA by arylamides

Abstract

InhA, the enoyl acyl carrier protein reductase (ENR) from Mycobacterium tuberculosis, is one of the key enzymes involved in the type II fatty acid biosynthesis pathway of M. tuberculosis. We report here the discovery, through high-throughput screening, of a series of arylamides as a novel class of potent InhA inhibitors. These direct InhA inhibitors require no mycobacterial enzymatic activation and thus circumvent the resistance mechanism to antitubercular prodrugs such as INH and ETA that is most commonly observed in drug-resistant clinical isolates. The crystal structure of InhA complexed with one representative inhibitor reveals the binding mode of the inhibitor within the InhA active site. Further optimization through a microtiter synthesis strategy followed by in situ activity screening led to the discovery of a potent InhA inhibitor with in vitro IC(50)=90 nM, representing a 34-fold potency improvement over the lead compound.

Figure 1. Inhibitor b3 bound to the active site of the M. tuberculosis InhA

A, Purple molecular surface shows the active site cleft in which compound b3 (in capped stick model) binds. B, Details of InhA-b3 interactions. Key residues within a 4.5 Å sphere of the b3 binding pocket are shown. The oxygen on the carbonyl group of the amide makes hydrogen-bonding interactions with the 2′-hydroxyl moiety of the nicotinamide ribose and the hydroxyl group of Tyr158 (blue line). C. A different perspective of inhibitor b3 bound in the active site of M. tuberculosis InhA further illustrating the key contacts of the inhibitor with the protein. Single molecules in the structure are denoted by an x.

Figure 2

Structures of the carboxylic acids and amines utilized in the microtiter focused library synthesis.