Exploration of novel β-lactamase inhibitors against Klebsiella pneumoniae using fragment-based drug discovery approach.

The rise of multidrug-resistant Klebsiella pneumoniae is largely driven by β-lactamases, posing a critical health threat worldwide. The conventional inhibitors are not broad-spectrum and have limited efficacy against the evolving β-lactamase variants. Therefore, identification of novel inhibitors targeting β-lactamases is crucial. Fragment-based drug discovery (FBDD) offers a promising strategy to identify novel molecules with the potential to bind selectively to the active site of resistant enzymes. In this study, a library of fragments was generated and combined using the FDA-approved, clinical and preclinical β-lactamase inhibitors. The obtained novel molecules targeted five clinically important β-lactamases, including SHV-1, TEM, CTX-M-15, OXA-48, and NDM-1. The top-scoring molecules, such as ETXLN28, GTMK4, GTMK30, and ETXLN1, were obtained for each β-lactamase and subjected to further analysis. The dynamic stability of the native and ligand-bound enzyme complexes was confirmed through molecular dynamics simulation for 200 ns. Free energy landscape analysis supported the conformational stability and ADME profiling revealed the drug-likeness and pharmacokinetic properties of the top hit molecules. This integrated computational approach highlights the potential of FBDD to unravel the promising β-lactamase inhibitors that potentiate the β-lactams against K. pneumoniae. The future work will involve hit to lead development and in vitro/in vivo validation of inhibitory activity for clinical application.