Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity

Mutations in DNA gyrase confer resistance to fluoroquinolones,
second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA 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. tuberculosis DNA gyrase ATPase activity. This
yielded the modified compound R3-13 with improved drug-likeness
compared to the template inhibitor that acted as a promising ATPase
inhibitor against M. tuberculosis DNA
gyrase. Utilization of compound R3-13 as a virtual screening
template, supported by subsequent biological assays, identified seven
further M. tuberculosis DNA gyrase
ATPase inhibitors with IC50 values in the range of 0.42–3.59
μM. The most active compound 1 showed an IC50 value of 0.42 μM, 3-fold better than the comparator
ATPase inhibitor novobiocin (1.27 μM). Compound 1 showed noncytotoxicity to Caco-2 cells at concentrations up to 76-fold
higher than its IC50 value. Molecular dynamics simulations
followed by decomposition energy calculations identified that compound 1 occupies the binding pocket utilized by the adenosine group
of the ATP analogue AMPPNP in the M. tuberculosis DNA gyrase GyrB subunit. The most prominent contribution to the
binding of compound 1 to M. tuberculosis GyrB 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 1 represents a potential
new scaffold for further exploration and optimization as a M. tuberculosis DNA gyrase ATPase inhibitor and candidate
anti-tuberculosis agent.