Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?

Abstract

β-lactamases (BLs) represent the most frequent cause of antimicrobial resistance in Gram-negative bacteria. Despite the continuous efforts in the development of BL inhibitors (BLIs), new BLs able to hydrolyze the last developed antibiotics rapidly emerge. Moreover, the insurgence rate of effective mutations is far higher than the release of BLIs able to counteract them. This results in a shortage of antibiotics that is menacing the effective treating of infectious diseases. The situation is made even worse by the co-expression in bacteria of BLs with different mechanisms and hydrolysis spectra, and by the lack of inhibitors able to hit them all. Differently from other targets, BL flexibility has not been deeply exploited for drug design, possibly because of the small protein size, for their apparent rigidity and their high fold conservation. In this mini-review, we discuss the evidence for BL binding site dynamics being crucial for catalytic efficiency, mutation effect, and for the design of new inhibitors. Then, we report on identified allosteric sites in BLs and on possible allosteric inhibitors, as a strategy to overcome the frequent occurrence of mutations in BLs and the difficulty of competing efficaciously with substrates. Nevertheless, allosteric inhibitors could work synergistically with traditional inhibitors, increasing the chances of restoring bacterial susceptibility towards available antibiotics.

Discovery of an Effective Small-Molecule Allosteric Inhibitor of New Delhi Metallo-β-lactamase (NDM)

“…Specifically for NDM, inhibitors that do not anchor at the zinc ion cluster could avoid some pitfalls, including the use of promiscuous metal-ion binding groups or highly charged anionic species that may limit membrane permeability. Allosteric inhibitors also hold the potential to synergize with active-site directed inhibitors and could be used in tandem to achieve more effective NDM inhibition …”

“…pneumoniae isolates. The sequence diversity in this family of enzymes suggests that QDP-1 may not be a wide-spectrum inhibitor . However, infectious bacteria typically only carry one MBL at a time (e.g., ref ), and >60% of MBL-positive isolates carry NDM, making a narrow-spectrum NDM-targeted therapeutic a clinically valuable advance.…”

“…Allosteric inhibitors also hold the potential to synergize with active-site directed inhibitors and could be used in tandem to achieve more effective NDM inhibition. 54 Some information is available about three small-molecule NDM-1 inhibitors previously reported as possible allosteric inhibitors. Azolylthioacetamide inhibitors were determined to use a mixture of competitive and uncompetitive inhibition modes.…”

“…enzymes suggests that QDP-1 may not be a wide-spectrum inhibitor. 54 However, infectious bacteria typically only carry one MBL at a time (e.g., ref 50), and >60% of MBL-positive isolates carry NDM, 63 making a narrow-spectrum NDMtargeted therapeutic a clinically valuable advance. Discovery and characterization of the inhibitor QDP-1 provides an example of a promising parallel strategy for NDM drug development with the potential to be used alone or in tandem with active-site directed NDM inhibitors to address antimicrobial resistance in carbapenem-resistant enterobacterales.…”

Novel Targets and Mechanisms in Antimicrobial Drug Discovery

“…Gianquinto and coworkers [ 10 ] propose a review of β-lactamase (BL), the bacterial enzymes representing a major resistance mechanism to β-lactam antibiotics in Gram-negative bacteria. The interest in discovering novel BL inhibitors is high as the more newly emerged BLs are not inhibited by the available inhibitors.…”