Drug Discovery in the Field of β-Lactams: An Academic Perspective

Abstract

β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.

Keywords: cell wall transpeptidase; peptidoglycan; resistance mechanisms; β-lactam; β-lactamase; β-lactamase inhibitor.

Figure 1

Bacterial cell wall biosynthesis. The polymerization of a bacterial cell wall peptidoglycan layer consists of transglycosylation (1), transpeptidation (2,3). _D,D-Carboxypeptidases cleave between the last two D-alanines of the pentapeptide (4), shortening it to a tetrapeptide. _D,D-Transpeptidases and _L,D-transpeptidases create the 4→3 and 3→3 transpeptide linkages, respectively, cleaving the terminal D-alanine in the pentapeptide or tetrapeptide. The box on the right shows the peptide composition of NAM in Gram-negative bacteria and Gram-positive bacilli.

Figure 2

Different mechanisms of serine β-lactamases and metallo-β-lactamases. (a) Catalytic mechanism of SBLs, where the catalytic serine forms an acyl-enzyme intermediate with H⁺ provided by a general acid, followed by a deacylation step to release a hydrolyzed β-lactam; (b) Catalytic mechanism of MBLs, which rely on coordinated zinc ions for the activation of a nucleophilic water to hydrolyze substrate. H⁺ is from the solution.

Figure 3

Clinically available β-lactamase inhibitors and select β-lactamase inhibitors. The compound numbers/names for the new inhibitors are shown in bold in the figure and main text. The compound name in the original publication is provided in parenthesis. (1 [105], 2 [106], 3 [107], 4 [108], Ixazomib [109], 5 [110], 6 [111], 7 [112], ZINC549719643 [89], 8 [113], 9 [114], 10 [115], 11 [116], 12 [117], 13 [118], 14 [119], 15 [120], 16 [121], QPX7728 [122,123], 17 [124], 18 [125], 19 [126], 20 [127]).

Figure 4

Active sites of representative β-lactamases and transpeptidases. The catalytic serine and cysteine are labeled in red, highlighting the similarities between SBLs and PBPs. (a) Class A SBL KPC-2 in complex with avibactam (PDB 4ZBE); (b) Class B MBL NDM-1 in complex with imipenem (PDB 5YPL); (c) Class C SBL AmpC in complex with avibactam (PDB 6LC8); (d) Class D SBL OXA-48 in complex with avibactam (PDB 4WMC); (e) P. aeruginosa PBP3 in complex with avibactam (PDB 7KIV); (f) Enterococcus faecium Ldt_fm in complex with avibactam (PDB 6FJ1).

Figure 5

Four classes of β-lactam antibiotics and recently developed novel cell wall transpeptidase inhibitors. The compound name in the original publication is provided in parenthesis. (21 [211], 22 [196], 23 [212], LYS228 [213], 24 [217], 25 [218], 26 [219], 27 [152], 28 [220], ETX0462 [221], 29 [222], 30 [223]).