Ligand-Based Virtual Screening for Discovery of Indole Derivatives as Potent DNA Gyrase ATPase Inhibitors Active against and Hit Validation by Biological Assays.

is the single most important global infectious disease killer and a World Health Organization critical priority pathogen for development of new antimicrobials. DNA gyrase is a validated target for anti-TB agents, but those in current use target DNA breakage-reunion, rather than the ATPase activity of the GyrB subunit. Here, virtual screening, subsequently validated by whole-cell and enzyme inhibition assays, was applied to identify candidate compounds that inhibit GyrB ATPase activity from the Specs compound library. This approach yielded six compounds: four carbazole derivatives (, , , and ), the benzoindole derivative , and the indole derivative . Carbazole derivatives can be considered a new scaffold for DNA gyrase ATPase inhibitors. IC values of compounds , , and (0.26, 0.56, and 0.08 μM, respectively) for inhibition of DNA gyrase ATPase activity are 5-fold, 2-fold, and 16-fold better than the known DNA gyrase ATPase inhibitor novobiocin. MIC values of these compounds against growth of H37Ra are 25.0, 3.1, and 6.2 μg/mL, respectively, superior to novobiocin (MIC > 100.0 μg/mL). Molecular dynamics simulations of models of docked GyrB:inhibitor complexes suggest that hydrogen bond interactions with GyrB Asp79 are crucial for high-affinity binding of compounds , , and to GyrB for inhibition of ATPase activity. These data demonstrate that virtual screening can identify known and new scaffolds that inhibit both DNA gyrase ATPase activity in vitro and growth of bacteria.