Drug repurposing approach to identify novel inhibitors for targeting DNA gyrase in Mycobacterium tuberculosis: Insights from Biophysical and Biochemical Studies

Drug repurposing has gained momentum globally and become an alternative avenue for identifying new drugs against tuberculosis (TB). TB can be cured with the use of currently available anti-tubercular drugs, emergence of drug resistant strains of Mycobacterium tuberculosis H37Rv (Mtb) and the huge death toll globally, together necessitate urgently newer and effective drugs for TB. To address this problem, we have employed drug repurposing approach to screen FDA-approved drugs by virtual screening and binding free energy calculations to identify novel inhibitors against Mtb target enzyme, DNA gyrase. Screening of compounds was done against the active site of Mtb DNA gyrase, the region of ATP binding (N-terminal domain) pocket on gyrase B subunit. Here, we identified total of four compounds (Drug97, Drug45, Drug77, Drug38) tightly binds to ATPase binding pocket of gyrase B (MtbGyrB). These compounds were simulated using GROMACS; the results generated were subjected to molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) calculation. Docked results shows binding energy for drugs (Drug97, Drug45, Drug77, Drug38) as -9.94, -9.93, -9.69 and -8.87 kcal/mol. MM-PBSA predicted the binding free energy of the drug97, drug45, drug77 and drug38 to be -1123.18, -1025.211, -1016.250 and -339.745 kcal/mol, respectively. These four compounds showed equilibrium dissociation constant, kD values of 2.1-53.0 µM. Among them, drug97 shows kD values of 2.1±0.17 µM. Our results suggests that the screened compounds binds to the ATPase domain of gyrase B subunit and inhibits gyrase catalytic cycle. This finding indicates all the identified compounds represents potential scaffolds for further optimization of novel antibacterial agents that can act on drug-resistant strains.