Potential inhibitors designed against NDM-1 type metallo-β-actamases: an attempt to enhance efficacies of antibiotics against multi-drug-resistant bacteria

NDM-1 and its variants are the most prevalent types of metallo-beta-lactamases, hydrolyze almost all antibiotics of beta-lactam group leading to multiple-drug resistance in bacteria. No inhibitor has yet been obtained for NDM-1 or other class of metallo-beta-lactamases. Therefore, strategies to identify novel anti-beta-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we have reported the discovery of novel non-beta-lactam inhibitors against NDM-1 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Five chemical compounds were finally purchased and evaluated experimentally for their efficacies to inhibit NDM-1 producing bacterial cells, in vitro. The dissociation constants (Kd), association constant (Ka), stoichiometry (n) and binding energies (Delta G) of compounds with the respective targets were determined using isothermal titration calorimetry (ITC). Molecular dynamic simulation carried out for 25 ns revealed that these complexes were stable throughout the simulation with relative RMSD in acceptable range. Moreover, Microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by beta-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as lead molecules for future drug candidates.