Structural Basis And Binding Kinetics Of Vaborbactam In Class A Beta-Lactamase Inhibition

Class A beta-lactamases are a major cause of beta-lactam resistance in Gramnegative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A beta-lactamases, including CTX-M extended-spectrum beta-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-angstrom crystal structure of CDX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-angstrom crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the beta 3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved beta-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.