Active site electrostatic effects modulate DBO inhibitor potency against OXA-48 variants
The OXA-48 class D {beta}-lactamase and its variants are clinically concerning through their carbapenemase and cephalosporinase activity. Effective inhibitors are therefore urgently needed. Diazabicyclooctanes (DBOs) are newly introduced non {beta}-lactam based inhibitors, but their potency is affected by mutations, with the more recently developed nacubactam consistently less potent than…
OXA-48 class D{beta}-lactamases and their variants pose a significant threat due to their carbapenemase and cephalosporinase activity. New inhibitors, Diazabicyclooctanes (DBOs), are being developed to tackle these enzymes, but their potency varies depending on mutations. Specifically, nacubactam, a newer DBO, shows lower potency compared to avibactam against OXA-48 variants.
This disparity is particularly notable when comparing OXA-48 to its variants OXA-163 and -405, which have mutations in the {beta}5-{beta}6 loop and prioritize cephalosporin degradation over carbapenems.
Multiscale simulations reveal that the second step of DBO acylation is the rate-limiting process. QM/MM MD simulations demonstrate that nacubactam experiences a significantly higher energy barrier for covalent inhibition of OXA-48-like enzymes compared to avibactam. This difference is directly linked to variations in the active site's electric field due to DBO-specific changes.
Additionally, simulations of non-covalent complexes suggest that nacubactam's lower potency towards OXA-48, as opposed to OXA-163 and -405, can be partly attributed to weaker binding. This is a result of electrostatic repulsion between the positively charged nacubactam tail and Arg214 in the {beta}5-{beta}6 loop.
By integrating computational predictions of covalent reaction rates and non-covalent binding affinities, the study accurately mirrors the experimental IC50 values and predicts potency against OXA-517, a newly identified OXA-48 variant with the capability to hydrolyze various antibiotics. This research not only offers insights into the mechanism of class D{beta}-lactamase inhibition but also uncovers the factors contributing to the differential potency of DBOs against OXA-48 variants, emphasizing the impact of subtle enzyme differences on inhibitory effects.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
