Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosisDNA Gyrase ATPase Activity

Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosisinfections. Identification of new agents that inhibit M. tuberculosisDNA gyrase ATPase activity is one strategy to overcome this. Here, bioisosteric designs using known inhibitors as templates were employed to define novel inhibitors of M. tuberculosisDNA gyrase ATPase activity. This yielded the modified compound R3-13with improved drug-likeness compared to the template inhibitor that acted as a promising ATPase inhibitor against M. tuberculosisDNA gyrase. Utilization of compound R3-13as a virtual screening template, supported by subsequent biological assays, identified seven further M. tuberculosisDNA gyrase ATPase inhibitors with IC50values in the range of 0.42–3.59 μM. The most active compound 1showed an IC50value of 0.42 μM, 3-fold better than the comparator ATPase inhibitor novobiocin (1.27 μM). Compound 1showed noncytotoxicity to Caco-2 cells at concentrations up to 76-fold higher than its IC50value. Molecular dynamics simulations followed by decomposition energy calculations identified that compound 1occupies the binding pocket utilized by the adenosine group of the ATP analogue AMPPNP in the M. tuberculosisDNA gyrase GyrB subunit. The most prominent contribution to the binding of compound 1to M. tuberculosisGyrB subunit is made by residue Asp79, which forms two hydrogen bonds with the OH group of this compound and also participates in the binding of AMPPNP. Compound 1represents a potential new scaffold for further exploration and optimization as a M. tuberculosisDNA gyrase ATPase inhibitor and candidate anti-tuberculosis agent.