Indole-containing inhibitors with improved efficacy targeting the gyrase of Mycobacterium tuberculosis

Tuberculosis is a major cause of mortality worldwide, with drug-resistant strains complicating its treatment. We report the discovery of small-molecule inhibitors targeting the gyrase of Mycobacterium tuberculosis, the bacterium responsible for tuberculosis. Gyrase, a type II topoisomerase, consists of two subunits: GyrA, which breaks and rejoins DNA, and GyrB, which contains the ATPase domain responsible for ATP binding and hydrolysis. An indole scaffold identified by nuclear magnetic resonance fragment screening was grown into drug-sized candidates through computational optimization, chemical synthesis and functional selection. Several indole-containing gyrase inhibitors were found to be specific for the GyrB subunit of M. tuberculosis. Structural studies using double electron-electron resonance spectroscopy between the Mn(II) ion in the catalytic site of GyrB and a nitroxide-labeled inhibitor provided insights into the potential docking sites of the protein target. Key chemical descriptors essential for gyrase binding were identified for the small-molecule inhibitors using data-driven algorithms. Our results demonstrate the effectiveness of fragment screening and computational optimization in drug discovery. The inhibitors presented in this study are promising candidates for further pharmacological studies in vivo.