Boronic Acid Transition State Inhibitors as Potent Inactivators of KPC and CTX-M beta-Lactamases: Biochemical and Structural Analyses

• Type of Material: Article
• Authors: Tahani AA Alsenani, Case Western Reserve University; María Margarita Rodríguez, University of Buenos Aires; Barbara Ghiglione, University of Buenos Aires; Magdalena A Taracila, Case Western Reserve University; Maria F Mojica, Veterans Affairs Medical Center; Laura J Rojas, Veterans Affairs Medical Center; Andrea M Hujer, Case Western Reserve University; Gabriel Gutkind, University of Buenos Aires; Christopher R Bethel, Veterans Affairs Medical Center; Philip Rather, Emory University; Maria Luisa Introvigne, University of Modena and Reggio Emilia; Fabio Prati, University of Modena and Reggio Emilia; Emilia Caselli, University of Modena and Reggio Emilia; Pablo Power, University of Buenos Aires; Focco van den Akker, Case Western Reserve University; Robert A Bonomo, Case Western Reserve University
• Language: English
• Date: 2023-01-05
• Publisher: AMER SOC MICROBIOLOGY
• Publication Version: Final Published Version
• Copyright Statement: © 2023 Alsenani et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1128/aac.00930-22
• Title of Journal or Parent Work: ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
• Volume: 67
• Issue: 1
• Start Page: e0093022
• End Page: e0093022
• Grant/Funding Information: This study was supported in part by funds provided by the Harrington Foundation and funds and/or facilities provided by the Cleveland Department of Veterans Affairs, award number 1I01BX001974 to R.A.B. from the Biomedical Laboratory Research & Development Service of the VA Office of Research and Development and the Geriatric Research Education and Clinical Center VISN 10. P.N.R. is supported by Department of Veterans Affairs, award numbers I01BX001725 and IK6BX004470. This work was partially supported by UBACyT 2018 from the University of Buenos Aires and PICT 2018-01550 granted to P.P. P.P., M.M.R., B.G., and G.G. are researchers at the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) from Argentina.
• Keywords: OPTIMIZATION; CRYSTAL-STRUCTURES; KPC-2; INSIGHTS; boronate; Life Sciences & Biomedicine; beta-lactamases; MB_076; CTX-M; Microbiology; KPC; ESBL; Science & Technology; Pharmacology & Pharmacy; CTX-M-96; CLICK CHEMISTRY; COMPLEX; S02030; carbapenemase
• Research Categories: Biology, Microbiology; Health Sciences, Pharmacology

Abstract

Design of novel β-lactamase inhibitors (BLIs) is one of the currently accepted strategies to combat the threat of cephalosporin and carbapenem resistance in Gram-negative bacteria. Boronic acid transition state inhibitors (BATSIs) are competitive, reversible BLIs that offer promise as novel therapeutic agents. In this study, the activities of two α-amido-β-triazolylethaneboronic acid transition state inhibitors (S02030 and MB_076) targeting representative KPC (KPC-2) and CTX-M (CTX-M-96, a CTX-M-15-type extended-spectrum β-lactamase [ESBL]) β-lactamases were evaluated. The 50% inhibitory concentrations (IC50s) for both inhibitors were measured in the nanomolar range (2 to 135 nM). For S02030, the k2/K for CTX-M-96 (24,000 M21 s21) was twice the reported value for KPC-2 (12,000 M21 s21); for MB_076, the k2/K values ranged from 1,200 M21 s21 (KPC-2) to 3,900 M21 s21 (CTX-M-96). Crystal structures of KPC-2 with MB_076 (1.38-Å resolution) and S02030 and the in silico models of CTX-M-96 with these two BATSIs show that interaction in the CTX-M-96–S02030 and CTX-M-96–MB_076 complexes were overall equivalent to that observed for the crystallographic structure of KPC-2–S02030 and KPC-2–MB_076. The tetrahedral interaction surrounding the boron atom from S02030 and MB_076 creates a favorable hydrogen bonding network with S70, S130, N132, N170, and S237. However, the changes from W105 in KPC-2 to Y105 in CTX-M-96 and the missing residue R220 in CTX-M-96 alter the arrangement of the inhibitors in the active site of CTX-M-96, partially explaining the difference in kinetic parameters. The novel BATSI scaffolds studied here advance our understanding of structure-activity relationships (SARs) and illustrate the importance of new approaches to β-lactamase inhibitor design.