Computational discovery of potent Escherichia coli DNA gyrase inhibitor: Selective and safer novobiocin analogues

Bacterial infections caused by resistant strains, especially those conferring multi-drug resistance (MDR), have become a severe health problem worldwide. Novobiocin (NB) is a widely used antibiotic that inhibits the action of DNA gyrase in Escherichia coli (E. coli). The drug's efficiency is hindered by its strong binding with the resistance causing efflux pump AcrAB-TolC on recurrent exposure. Consequently, the discovery of alternate/substitute analogue compounds for the parent drug with higher selectivity could counter drug resistance. In this work, we identified potent analogues of drug NB against the gyrase B enzyme by performing high throughput virtual screening of forty analogues that includes drug-likeness properties, pharmacokinetic parameters analysis, molecular docking, and molecular dynamics (MD) simulations. Our comprehensive pharmacological profiling with intrinsic analysis of selectivity and safety resulted in the identification of four potential compounds, C4 (ZINC218812366), C6 (ZINC221968665), C8 (ZINC49783724) and C10 (ZINC49783727), have better inhibitory and binding capacity against the primary target gyrase B subunit and reduced interaction with the counterpart of resistant target AcrB. These findings provide proof of concept for developing lead compounds targeting gyrase B and help in combatting AcrB-mediated drug resistance.