Will morphing boron-based inhibitors beat the β-lactamases?

Abstract

The β-lactams remain the most important antibacterials, but their use is increasingly compromised by resistance, importantly by β-lactamases. Although β-lactam and non-β-lactam inhibitors forming stable acyl-enzyme complexes with nucleophilic serine β-lactamases (SBLs) are widely used, these are increasingly susceptible to evolved SBLs and do not inhibit metallo-β-lactamases (MBLs). Boronic acids and boronate esters, especially cyclic ones, can potently inhibit both SBLs and MBLs. Vaborbactam, a monocyclic boronate, is approved for clinical use, but its β-lactamase coverage is limited. Bicyclic boronates rapidly react with SBLs and MBLs forming stable enzyme-inhibitor complexes that mimic the common anionic high-energy tetrahedral intermediates in SBL/MBL catalysis, as revealed by crystallography. The ability of boronic acids to 'morph' between sp² and sp³ hybridisation states may help enable potent inhibition. There is limited structure-activity relationship information on the (bi)cyclic boronate inhibitors compared to β-lactams, hence scope for creativity towards new boron-based β-lactamase inhibitors/antibacterials.

Figure 1

β-Lactam antibacterials, β-lactamase inhibitors and selected boron-containing natural products. (a) Major classes of β-lactam antibacterials; (b) clinically relevant SBL inhibitors (Clavulanic acid, Sulbactam, Tazobactam); the recently introduced non-β-lactam β-lactamase inhibitors Avibactam (a diazabicyclooctanone) and Vaborbactam (the first boron-containing β-lactamase inhibitor), and the candidate VNRX-5133 (Phase 3 compound). (c) Outline role of boron in quorum sensing in bacteria via borate complexation with (2S,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (S-THMF) to produce the Autoinducer-2 (AI-2) which activates luminescence thus allowing bacteria to sense cell density [58,62]; (d) structures of two boron-containing natural products with antibacterial properties [63].

Figure 2

Modes of action of transpeptidases, serine-β-lactamases (SBLs) and metallo-β-lactamases (MBLs); potential transition state analogues and views from structures of reacted meropenem bound to representative transpeptidase, SBLs and MBLs. Outline mechanisms of (a) transpeptidase, (b) SBL and (c) MBL β-lactam (carbapenem) hydrolysis exemplified with (d) meropenem. Note the structural elements of the first anionic tetrahedral intermediate (in a red box) are common to SBLs and MBLs. (e) Selected examples of analogues of the first tetrahedral intermediate. Active site views from structures of meropenem in complex with (f) transpeptidase PBP-3 [64], (g) SBL OXA-23 [65] and (h) MBL NDM-1 [66]. Hydrogen-bond interactions are shown as dashed lines.

Figure 3

Structural analyses of boron-based enzyme inhibitors. Chemical structures of ‘boron’ inhibitors and active site views of (a) proteasome β5 subunit with Velcade [33]; (b) leucyl-tRNA synthetase (LeuRS) editing domain CP1 with Tavaborole-AMP [35]; (c) mammalian arginase with dehydro-2(S)-amino-6-boronohexanoic acid (dehydro-ABH) [67]; (d) human carbonic anhydrase II with benzoxaborole; note, two binding modes were observed. The major involves Zn(II) complexation via one of the exocyclic boronate oxygens (binding mode A, shown); in the minor (not shown) the inhibitor complexes via its endocyclic boronate oxygen and one of its exocyclic boronate oxygens [68]; (e) AmpC (E. coli) with an acyclic boronic acid [69]; (f) class A SBL CTX-M-15 with Vaborbactam [36]; (g) penicillin-binding protein 1b (PBP-1B) with an acyclic boronic acid [48]; (h) DD-transpeptidase (Actinomadura sp. R39) with an acyclic boronic acid showcasing an unusual tricovalent binding mode of the boronate [70]; (i) class D SBL OXA-10 with a benzoxaborole analogue [71].

Figure 4

Structural analyses of bicyclic boronates with serine β-lactamases (SBLs), metallo-β-lactamases (MBLs) and transpeptidases. Views from crystal structures of Bicyclic Boronate 1 in complex with (a) SBL CTX-M-15 [30] and Bicyclic Boronate 2 complexed with (b) transpeptidase PBP-5 from E. coli [38^••] and (c) MBL VIM-2 [38^••]. (d) Current evidence implicates that sp² boronic acid form may bind to the enzyme targets of the bicyclic boronate inhibitors.