Molecular Basis of Substrate Recognition and Product Release by the Klebsiella pneumoniae Carbapenemase (KPC-2)

Abstract

Carbapenem-resistant Enterobacteriaceae (CRE) are resistant to most β-lactam antibiotics due to production of the KPC-2 class A β-lactamase. Here we present the first product complex crystal structures of KPC-2 with β-lactam antibiotics, containing hydrolyzed cefotaxime and faropenem. They provide experimental insights into substrate recognition by KPC-2 and its unique cephalosporinase/carbapenemase activity. These structures also represent the first product complexes for a wild type serine β-lactamase, elucidating the product release mechanism of these enzymes in general.

Cyclic boronates as versatile scaffolds for KPC-2 β-lactamase inhibition

“…Notably, Trp105 is modelled in a single conformation in both the vaborbactam and taniborbactam structures ( Figure 2D). Interactions of KPC-2 Trp105 with β-lactams are suggested to be essential for hydrolysis 28 , and KPC-2 Trp105 is indeed stabilised by binding of the β-lactam substrates cefotaxime and faropenem (as observed crystallographically 29 ). Conversely, however, we have previously observed flexibility of Trp105 (as modelled in multiple conformations) in complexes with the DBO inhibitor relebactam.…”

Phenylboronic Acids Probing Molecular Recognition against Class A and Class C β-lactamases

“…Against KPC-2, instead, the ortho derivatives 2 and 4 resulted very active since the acrylic acid side-chain orients toward the highly conserved carboxylate binding site formed by Thr235, Gly236, Thr237, and Ser130 similarly to the structure of KPC-2 bound to the β-lactam cefotaxime (PDB ID:5UJ3 [33]). The existence of the interaction between Trp105 and the phenyl ring of the compound 2 in KPC-2:2 and between Trp105 and the six-membered dihydrothiazine group in KPC-2: cefotaxime is a consequence of a higher degree of freedom of the Trp105 side chain, prone to adopt the proper conformation depending on the substrate arrangement ( Figure S3).…”

4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo-β-Lactamases

“…KPC-2. X-ray resolved structure of apo-KPC-2 was retrieved from the Protein Data Bank (PDB code 5ul8), all waters were omitted in docking calculations [23].…”

“…Conversely, in KPC-2, like in all SBLs, the process involves the catalytic Ser70, which performs a nucleophilic attack on the β-lactam core. The β−lactam substrate is further stabilized in the active site by an extensive network of interactions [22][23][24]. The first inhibitor active against both SBLs and MBLs classes has, only recently, reached clinical trials [19,20].…”