Electrostatic interactions define nacubactam potency against OXA-48-like β-lactamases

Hoff, J. F.; Goudar, K. E.; Beer, M.; Hinchliffe, P.; Shaw, J. M.; Tooke, C. L.; Takebayashi, Y.; Mulholland, A. J.; Schofield, C. J.; Spencer, J.

doi:10.1101/2024.10.30.621041

bioRxiv · 10.1101/2024.10.30.621041

Electrostatic interactions define nacubactam potency against OXA-48-like β-lactamases

Hoff, J. F.·Goudar, K. E.·Beer, M.·Hinchliffe, P.·Shaw, J. M.·Tooke, C. L.·Takebayashi, Y.·Mulholland, A. J.·Schofield, C. J.·Spencer, J.

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Abstract

Carbapenemases, {beta}-lactamases hydrolysing carbapenem antibiotics, severely challenge treatment of multi-drug resistant bacterial infections. OXA-48 is among the most widely disseminated carbapenemases in Enterobacterales, consequently new treatment options for OXA-48 producers are urgently required. Development of diazabicyclooctane (DBO) inhibitors to overcome {beta}-lactamase-mediated resistance is one attractive option, due to their efficacy against a wide range of {beta}-lactamases. The DBO avibactam is already licensed for clinical use, with the related compound nacubactam currently in phase III trials for carbapenem-resistant infections. Here we investigate the activities of avibactam and nacubactam towards OXA-48 and two variants, OXA-163 and OXA-405, that contain deletions in the {beta}5 - {beta}6 loop adjacent to the active site and show modified activity towards different {beta}-lactam classes. Compared to avibactam, nacubactam is c. 80-fold less potent towards OXA-48, but this difference is reduced in OXA-163 and OXA-405. Crystal structures of the respective avibactam and nacubactam complexes, and molecular dynamics simulations based upon these, reveal residue Arg214 on the OXA-48 {beta}5 - {beta}6 active-site loop to be electrostatically repelled by nacubactam, but not avibactam, binding. This increases flexibility of the OXA-48 {beta}5 - {beta}6 loop, as well as neighbouring active site loops, in simulations of the OXA-48:nacubactam, compared to the avibactam, complex. Such effects are not observed in simulations of the respective complexes of OXA-163 and OXA-405, which lack Arg214. These data indicate that interactions with Arg214 can determine DBO potency towards OXA-48-like enzymes, and suggest that sequence variation in this {beta}-lactamase family affects reactivity towards inhibitors as well as {beta}-lactam substrates.

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Hoff, J. F., Goudar, K. E., Beer, M., Hinchliffe, P., Shaw, J. M., Tooke, C. L., Takebayashi, Y., Mulholland, A. J., Schofield, C. J., Spencer, J.. 2024-10-30. Electrostatic interactions define nacubactam potency against OXA-48-like β-lactamases. https://doi.org/10.1101/2024.10.30.621041

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