Cyclic Boronates Inhibit All Classes of β-Lactamases

Abstract

ABSTRACTβ-Lactamase-mediated resistance is a growing threat to the continued use of β-lactam antibiotics. The use of the β-lactam-based serine-β-lactamase (SBL) inhibitors clavulanic acid, sulbactam, and tazobactam and, more recently, the non-β-lactam inhibitor avibactam has extended the utility of β-lactams against bacterial infections demonstrating resistance via these enzymes. These molecules are, however, ineffective against the metallo-β-lactamases (MBLs), which catalyze their hydrolysis. To date, there are no clinically available metallo-β-lactamase inhibitors. Coproduction of MBLs and SBLs in resistant infections is thus of major clinical concern. The development of “dual-action” inhibitors, targeting both SBLs and MBLs, is of interest, but this is considered difficult to achieve due to the structural and mechanistic differences between the two enzyme classes. We recently reported evidence that cyclic boronates can inhibit both serine- and metallo-β-lactamases. Here we report that cyclic boronates are able to inhibit all four classes of β-lactamase, including the class A extended spectrum β-lactamase CTX-M-15, the class C enzyme AmpC from Pseudomonas aeruginosa, and class D OXA enzymes with carbapenem-hydrolyzing capabilities. We demonstrate that cyclic boronates can potentiate the use of β-lactams against Gram-negative clinical isolates expressing a variety of β-lactamases. Comparison of a crystal structure of a CTX-M-15:cyclic boronate complex with structures of cyclic boronates complexed with other β-lactamases reveals remarkable conservation of the small-molecule binding mode, supporting our proposal that these molecules work by mimicking the common tetrahedral anionic intermediate present in both serine- and metallo-β-lactamase catalysis.

Structural/mechanistic insights into the efficacy of nonclassical β‐lactamase inhibitors against extensively drug resistant Stenotrophomonas maltophilia clinical isolates

“…Our structural data reveal that the bicyclic boronate 2 binds to the ESBL L2 in a manner similar to that previously observed for the closely related bicyclic boronate 1 binding to the ESBL CTX‐M‐15. For the bicyclic boronate 2 , binding of the tetrahedral boron atom to L2 and conformation of the bicyclic fused core are all consistent with the CTX‐M‐15:bicyclic boronate 1 structure (Cahill et al ., ); there is only slight variation in the amide/benzamide side chain conformations (Fig. A).…”

“…B) with the boron atom clearly in a tetrahedral geometry. This is also observed previously on binding of the closely related bicyclic boronate 1 to CTX‐M‐15 (another class A ESBL) (Cahill et al ., ) and OXA‐10 (a class D SBL) (Brem et al ., ). Hence, bicyclic boronates bind SBLs in a form that mimics the first tetrahedral intermediate formed during β‐lactam hydrolysis, which is involved in acyl‐enzyme formation, rather than mimicking the acyl‐enzyme itself, that is, these inhibitors are ‘transition state analogues’.…”

“…Accordingly, one method of overcoming the poor activity of ceftazidime/ avibactam against MBL producing bacteria would be to combine ceftazidime with a bicyclic boronate inhibitor, such as 2 (Fig. 1, bottom right), or 1, which is derived from the same scaffold (Cahill et al, 2017). Together, 1 and 2 represent the closest approach to a pan-blactamase inhibitor that has, to-date, been reported in the literature (Cahill et al, 2017).…”

19F NMR Monitoring of Reversible Protein Post‐Translational Modifications: Class D β‐Lactamase Carbamylation and Inhibition

“…(B) Proposed interaction of vaborbactam with a class D serine β‐lactamase to form a tetrahedral complex. Based on 13 C NMR studies, the lysine residue in this complex is expected to be carbamylated (Figure S14) . (C) 19 F NMR spectra showing the titration of OXA‐48 T213C* (160 μ m ) with vaborbactam, resulting in a new 19 F signal (7).…”

“…Cyclic boronates are currently of considerable interest as inhibitors of SBLs, metallo‐β‐lactamases (MBLs), and possibly of penicillin‐binding proteins (PBPs; the bacterial target of the β‐lactam antibiotics) (Figure B) Vaborbactam (formerly RPX‐7009), a (predominantly) monocyclic boronate β‐lactamase inhibitor, was recently FDA approved for use in combination with the carbapenem meropenem . Boronates form covalent complexes with SBLs in which the nucleophilic serine is bonded to the tetrahedral boron, mimicking the tetrahedral complex formed during β‐lactamase catalysis …”