Rational Design and Screening of Inhibitors Using Recombinant Metallo-β-Lactamases

Abstract Objective: A comparative study of the affinity and inhibitory activity of derivatives of three groups of heterocyclic carboxylic acids against metallo-β-lactamases (MBLs) of the NDM and VIM families was performed. Methods: The study utilized recombinant enzymes, differential scanning fluorimetry, and enzyme kinetics. Results and Discussion: The structure of the heterocyclic ring, the nature of the substituents, and the presence of a carboxyl group were shown to significantly influence both the inhibition efficiency and the spectrum of inhibitory activity of the compounds against different types of MBLs. Dipicolinic acid derivatives were found to exhibit activity primarily against NDM-1, acting via a chelating mechanism based on the stripping of zinc ions from the active site of the enzyme. In contrast, inhibition of MBLs by indole-2- and pyrrole-2-carboxylic acid derivatives is not associated with nonspecific chelation of metal ions. Indole-2-carboxylic acid derivatives, which are capable of effectively inhibiting both NDM-1 and VIM-2, hold the greatest promise for further research toward the development of a universal pan-inhibitor of clinically significant MBLs. At the same time, structural optimization of their pyrrole analogues yielded compounds that inhibit NDM-1 with IC50 values in the nanomolar range, confirming the high potential of this scaffold for the development of selective NDM inhibitors. Conclusions: These results advance our understanding of the structure–activity relationships among MBL inhibitors and form the basis for the further rational design and optimization of lead compounds.