Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of <i>Mycobacterium tuberculosis</i>

Tuberculosis, caused by Mycobacterium tuberculosis ( M. tuberculosis ), kills 1.6 million people annually. To bridge the gap between structure- and cell-based drug discovery strategies, we are pioneering a computer-aided discovery paradigm that merges structure-based virtual screening with ligand-based, machine learning methods trained with cell-based data. This approach successfully identified N -(3-methoxyphenyl)-7-nitrobenzo[ c ][1,2,5]oxadiazol-4-amine (JSF-2164) as an inhibitor of purified InhA with whole-cell efficacy versus in vitro cultured M. tuberculosis . When the intrabacterial drug metabolism (IBDM) platform was leveraged, mechanistic studies demonstrated that JSF-2164 underwent a rapid F 420 H 2 -dependent biotransformation within M. tuberculosis to afford intrabacterial nitric oxide and two amines, identified as JSF-3616 and JSF-3617. Thus, metabolism of JSF-2164 obscured the InhA inhibition phenotype within cultured M. tuberculosis . This study demonstrates a new docking/Bayesian computational strategy to combine cell- and target-based drug screening and the need to probe intrabacterial metabolism when clarifying the antitubercular mechanism of action.