Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants

The β-lactamase OXA-48 efficiently hydrolyzes carbapenem antibiotics, especially imipenem. Carbapenem resistance is a rising clinical concern and is frequently associated with OXA-48 and its variants. OXA-48 variants carrying different mutations in the β5-β6 loop differ in hydrolytic activity toward imipenem. OXA-517 has a higher KM, but a similar kcat for imipenem hydrolysis, compared to that of OXA-48, whereas those of OXA-163 and -405, which have similar mutations in the β5-β6 loop, are less active. Multiscale simulations (using quantum mechanics/molecular mechanics, QM/MM) of deacylation of the respective imipenem acylenzymes show this to be most efficient when the deacylating water (DW) acts as a hydrogen bond (H-bond) donor to imipenem, and the carboxylated Lys73 base is less hydrated. Calculated barriers for deacylation correlate very well with experimental data but, for OXA-163 and -405, only when DW acts as an H-bond acceptor. Molecular dynamics simulations of imipenem acylenzyme complexes show that mutations in the β5-β6 loop change the active site H-bond network. In OXA-48, the DW H-bonding pattern linked to high activity is more frequently sampled, and in OXA-517, it is stabilized through H-bonding to Thr213, explaining the higher kcat values compared to those of OXA-163 and -405, where this is not the case. Furthermore, simulations of noncovalent imipenem complexes indicate that increased KM for OXA-517 is linked to lower binding affinity caused by the repositioning of bound imipenem. Our work identified the molecular basis for differences in imipenem hydrolytic activity between OXA-48 variants, offering detailed insights into how active site interactions alter the dynamics and reaction efficiencies related to antibiotic resistance.