Boronic Acid Transition State Inhibitors Active against KPC and Other Class A β-Lactamases: Structure-Activity Relationships as a Guide to Inhibitor Design

Abstract

g Boronic acid transition state inhibitors (BATSIs) are competitive, reversible ␤-lactamase inhibitors (BLIs). In this study, a series of BATSIs with selectively modified regions (R1, R2, and amide group) were strategically designed and tested against representative class A ␤-lactamases of Klebsiella pneumoniae, KPC-2 and SHV-1. Firstly, the R1 group of compounds 1a to 1c and 2a to 2e mimicked the side chain of cephalothin, whereas for compounds 3a to 3c, 4a, and 4b, the thiophene ring was replaced by a phenyl, typical of benzylpenicillin. Secondly, variations in the R2 groups which included substituted aryl side chains (compounds 1a, 1b, 1c, 3a, 3b, and 3c) and triazole groups (compounds 2a to 2e) were chosen to mimic the thiazolidine and dihydrothiazine ring of penicillins and cephalosporins, respectively. Thirdly, the amide backbone of the BATSI, which corresponds to the amide at C-6 or C-7 of ␤-lactams, was also changed to the following bioisosteric groups: urea (compound 3b), thiourea (compound 3c), and sulfonamide (compounds 4a and 4b). Among the compounds that inhibited KPC-2 and SHV-1 ␤-lactamases, nine possessed 50% inhibitory concentrations (IC 50 s) of <600 nM. The most active compounds contained the thiopheneacetyl group at R1 and for the chiral BATSIs, a carboxy-or hydroxy-substituted aryl group at R2. The most active sulfonamido derivative, compound 4b, lacked an R2 group. Compound 2b (S02030) was the most active, with acylation rates (k 2 /K) of 1.2 ؎ 0.2 ؋ 10 4 M ؊1 s ؊1 for KPC-2 and 4.7 ؎ 0.6 ؋ 10 3 M ؊1 s ؊1 for SHV-1, and demonstrated antimicrobial activity against Escherichia coli DH10B carrying bla SHV variants and bla KPC-2 or bla KPC-3 and against clinical strains of Klebsiella pneumoniae and E. coli producing different class A ␤-lactamase genes. At most, MICs decreased from 16 to 0.5 mg/liter.

Crystal Structures of KPC-2 and SHV-1 β-Lactamases in Complex with the Boronic Acid Transition State Analog S02030

“…This thiophene moiety of S02030 makes several van der Waals interactions in the active site of SHV-1, including with carbon atoms of residues N170, T167, and E240. The observation of relatively similar modes of binding ofS02030 to KPC-2 and SHV-1 is in agreement with the 50% inhibitory concentrations (IC 50 s) that were measured for KPC-2 and SHV-1, which are 0.080 Ϯ 0.002 and 0.130 Ϯ 0.002 M, respectively (18). The minor difference in IC 50 could in part be attributed to S02030's ability to have stacking interactions with large aromatic residues, e.g., W105, in KPC-2, whereas such an interaction is not observed in SHV-1.…”

“…1) was found to inhibit ADC-7 ␤-lactamase from Acinetobacter baumannii by forming a transition state boron-mediated bond with the catalytic serine (17). We have extended the structural investigations of S02030 and observed that it readily inhibits SHV-1 and KPC-2 ␤-lactamases (see also the companion article by Rojas et al [18]). We present here the 1.54-and 1.87-Å resolution crystal structures of S02030 bound to SHV-1 and KPC-2 ␤-lactamases, respectively, as well as an in-depth comparative analysis of the S02030 binding modes, including the ADC-7 S02030 complex.…”

The Road to Avibactam: The First Clinically Useful Non-β-Lactam Working Somewhat Like a β-Lactam

“…Further, there is clearly scope for the development of new types of antibacterial-forming acyl-enzyme type complexes, perhaps based on natural products/inhibitors of nucleophilic serine (or nucleophilic cysteine) enzymes, such as lactivicins [111], trans-lactams [101] or compounds operating via an analogous mechanism of action, but which have been developed in other fields, for example, agrochemistry such as strigolactones [157] ( Figure 10). Other types of covalent inhibitors also future science group Review Wang, Abboud, Markoulides, Brem & Schofield show promise including transition state analogues such as boronates and phosphonates, which have the potential to target β-lactamases and PBPs [115,[118][119][120][121][122][123]. In this regard, patent applications containing cyclic boronates, which potently inhibits both serine β-lactamases and metallo-β-lactamases, are of particular note [181].…”

“…It is also notable that nonacylating inhibitors of PBPs/serine β-lactamases have been developed, including 'transition state analogue' based inhibitors, such as boronic acids, some of which show activity in cells [104,[115][116][117][118][119][120][121][122][123] (Figure 10). However, these have not yet reached clinical utility, though some display promise, and are beyond the scope of this article which focuses on mechanistic aspects of acylating inhibitors (see [124][125][126] for relevant work on boronic acids and related compounds).…”

New β-Lactamase Inhibitors in the Clinic

“…4 and Table 2). 48 TheraBor Pharmaceuticals and the Regents of the University of California developed and patented (patent WO2013/056079) several sulfonamide boronates (eg, CR161) that were shown to reduce ceftazidime MICs against Enterobacteriaceae and P aeruginosa (see Fig. 4 and Table 2).…”