β-Lactamases and β-Lactamase Inhibitors in the 21st Century

Abstract

The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli ) and non-fermenting organisms (e.g., Pseudomonas aeruginosa ). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.

MBLinhibitors.com, a Website Resource Offering Information and Expertise for the Continued Development of Metallo-β-Lactamase Inhibitors

“…Penicillins, cephalosporins, carbapenems, and monobactams are all members of the β-lactam class [5]. The widespread use of this class of antibiotics has led to the emergence of different resistance mechanisms, including: (a) the production of altered penicillin binding proteins (PBP) with lower binding affinities for most β-lactam antibiotics; and (b) the production of β-lactamases, which is the most common resistance mechanism in Gram-negative bacteria [6]. In 2019, there are more than 2800 identified β-lactamase genes [7].…”

“…Examples of these FDA-approved inhibitors include clavulanic acid, sulbactam, avibactam, and tazobactam [10]. However, despite considerable efforts to develop such inhibitors [6], there are no clinically-approved inhibitors that are available for MBLs, making infections from bacteria that produce MBL a serious challenge. An ideal MBL inhibitor would have good inhibition properties, low toxicity, and is broad-spectrum [11].…”

“…Another example is the bicyclic boronate VNRX-5133, which exhibits good inhibition against NDM and other subclass B1 enzymes [16]; however, this compound is not a good inhibitor of subclass B3 MBL L1 [16]. Secondly, it is imperative that any clinical MBL inhibitor be selective towards bacterial MBLs over human MBL-fold containing enzymes, some of which have important physiological roles [6]. The most common (and perhaps most obvious) way to inhibit an MBL is through the use of a chelating agent that binds to the Zn(II) ion(s) in the active site [17].…”

“…With the increasing number of compounds ( Figure 1C), it is becoming more difficult to collect and sort through the review articles or the original articles, which are not interactive or searchable. To address these issues, we have developed a website called MBLinhibitors.com (link: https://MBLinhibitors.miamioh.edu), which is the first effort, to our knowledge, to provide a searchable In the past five years, there has been significant effort to identify novel inhibitors of the MBL [6,11]. The numbers of MBL inhibitors and publications describing MBL inhibitors have increased over the last decade ( Figures 1B and 1C).…”

Mechanistic understanding enables the rational design of salicylanilide combination therapies for Gram-negative infections

“…Mechanistic understanding of synergy may reveal novel antibiotic targets and guide the rational design of superior drug combinations e.g. , the co-administration of β-lactam compounds and β-lactamase inhibitors (9). However, for the majority of combination therapies the underlying basis of synergism is unclear.…”