IN SILICO/IN VITRO APPROACHES FOR THE IDENTIFICATION OF NEW CARBAPENEMASE INHIBITORS

The ongoing emergence of bacterial strains resistant to even third- and fourth-generation β-lactam antibiotics is one of the most pressing and challenging issues in clinical therapy. Resistance is most often mediated by beta-lactamases (BLs), and in particular by carbapenemases (i.e KPC, NDM-1, VIM), which have emerged in both Gram-positive and Gram-negative bacteria (1). Among these, NDM-1 has emerged as a global health threat, capable of easy propagation to other species. No inhibitors are available for NDM-1 so far, despite the number of reports claiming the design and development of novel inhibitors for this enzyme. To this aim we applied a multidisciplinary approach integrating in silico/in vitro analysis for the design and identification of novel non-covalent BL inhibitors. Through a structure-based in silico screening of commercially libraries we identified several promising candidates active against class A and class B carbapenemases. The binding affinities of the high scoring hits were measured in vitro revealing, for some of them, low micromolar affinity towards BLs. Experimental analyses confirmed a 30% and a 50% prediction success rate for KPC-2 and NDM-1, respectively. These results overcome the standard virtual screening success rate which, for random screens, typically range from 0.1 to 0.5%. For NDM-1 the best inhibitors efficacy against resistant bacterial strains overexpressing NDM-1 was also validated, confirming their favorable synergistic effect in combination with the carbapenem meropenem (2). At the same time, we developed a multiligand set of covalent boronic β-lactamase inhibitors using a combination of molecular modeling, synthetic chemistry, enzyme kinetics and antibacterial susceptibility testing. The analyses confirmed the possibility to discriminate between clinically-relevant β-lactamases on the basis of its inhibition profile by each compound of the set. Interestingly, this work allowed the identification of potent multi-spectrum KPC-2 and NDM-1 inhibitors able to significantly potentiate the activity of cefotaxime on resistant clinical isolates (MIC reduction, 32-fold) and opened the way to the potential use the designed compounds set as a diagnostic tool for sensitive detection of clinically-relevant β-lactamases (3).