Class D β-lactamases: a reappraisal after five decades

Abstract

Despite 70 years of clinical use, β-lactam antibiotics still remain at the forefront of antimicrobial chemotherapy. The major challenge to these life-saving therapeutics is the presence of bacterial enzymes (i.e., β-lactamases) that can hydrolyze the β-lactam bond and inactivate the antibiotic. These enzymes can be grouped into four classes (A-D). Among the most genetically diverse are the class D β-lactamases. In this class are β-lactamases that can inactivate the entire spectrum of β-lactam antibiotics (penicillins, cephalosporins, and carbapenems). Class D β-lactamases are mostly found in Gram-negative bacteria such as Pseudomonas aeruginosa , Escherichia coli , Proteus mirabilis , and Acinetobacter baumannii . The active-sites of class D β-lactamases contain an unusual N-carboxylated lysine post-translational modification. A strongly hydrophobic active-site helps create the conditions that allow the lysine to combine with CO2, and the resulting carbamate is stabilized by a number of hydrogen bonds. The carboxy-lysine plays a symmetric role in the reaction, serving as a general base to activate the serine nucleophile in the acylation reaction, and the deacylating water in the second step. There are more than 250 class D β-lactamases described, and the full set of variants shows remarkable diversity with regard to substrate binding and turnover. Narrow-spectrum variants are most effective against the earliest generation penicillins and cephalosporins such as ampicillin and cephalothin. Extended-spectrum variants (also known as extended-spectrum β-lactamases, ESBLs) pose a more dangerous clinical threat as they possess a small number of substitutions that allow them to bind and hydrolyze later generation cephalosporins that contain bulkier side-chain constituents (e.g., cefotaxime, ceftazidime, and cefepime). Mutations that permit this versatility seem to cluster in the area surrounding an active-site tryptophan resulting in a widened active-site to accommodate the oxyimino side-chains of these cephalosporins. More concerning are the class D β-lactamases that hydrolyze clinically important carbapenem β-lactam drugs (e.g., imipenem). Whereas carbapenems irreversibly acylate and inhibit narrow-spectrum β-lactamases, class D carbapenemases are able to recruit and activate a deacylating water. The rotational orientation of the C6 hydroxyethyl group found on all carbapenem antibiotics likely plays a role in whether the deacylating water is effective or not. Inhibition of class D β-lactamases is a current challenge. Commercially available inhibitors that are active against other classes of β-lactamases are ineffective against class D enzymes. On the horizon are several compounds, consisting of both β-lactam derivatives and non-β-lactams, that have the potential of providing novel leads to design new mechanism-based inactivators that are effective against the class D enzymes. Several act synergistically when given in combination with a β-lactam antibiotic, and others show a unique mechanism of inhibition that is distinct from the traditional β-lactamase inhibitors. These studies will bolster structure-based inhibitor design efforts to facilitate the optimization and development of these compounds as class D inactivators.

Figure 1

Comparison of the overall topology of a narrow spectrum class D β-lactamase (OXA-10) with the penicillin ampicillin forming an acyl-enzyme intermediate (cyan; PDB 2WKH), a class D carbapenemase (OXA-24/40) acylated with the carbapenem doripenem (green; PDB 3PAE) and one of the related β-lactamase sensors (BlaR1) acylated with the cephalosporin ceftazidime (magenta; PDB 1HKZ). In each case, the drug is found near the interface of an all helical domain (left) and a mixed α/β domain (right).

Figure 2

An expanded view of the active-site of OXA-10 (PDB 1E4D).

Figure 3

A proposed mechanism for class D β-lactamases. The initial acylation step is aided by carboxy-lysine-mediated deprotonation of S67. The carbamate also activates the deacylating water in the second step.

Figure 4

Inhibitors with activity against class D β-lactamases. Methylidine penem, BRL 42715 (1). Bicyclic penem derivative, BLI-489 (2). Penicillin sulfone, LN-1-255 (3).Avibactam (4). 4-phenylphosphonate (5). 4,7-dichloro-1-benzothien-2-yl sulfonylaminomethyl boronic acid (DSABA) (6).

Figure 5

Overlay of the X-ray crystal structures of OXA-24/40 with the final products obtained following rearrangement of the acyl-enzyme intermediate derived from the reaction with several penicillin sulfone inhibitors (PDB 3FYZ, carbon atoms green; 3FV7, carbon atoms magenta; and 3FZC, carbon atoms cyan). Residues in this figure are labeled with OXA-24/40 numbering.