Time-resolved ligand dynamics revealed in a β-lactamase using room-temperature serial crystallography

Hinchliffe, P.; Tooke, C. L.; Beer, M.; Aller, P.; Kamps, J. J.; Parkinson, L.; Zhou, T.; Devenish, N.; Gu, D.-H.; Shilova, A.; Rodrigues, M. J.; Telfer, A.; Butryn, A.; Hanzevacki, M.; Freeman, E. I.; Park, S.; Schofield, C. J.; Park, J.; Owen, R. L.; Mulholland, A. J.; Orville, A. M.; Spencer, J.

doi:10.64898/2025.12.17.692331

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bioRxiv · 10.64898/2025.12.17.692331

Time-resolved ligand dynamics revealed in a β-lactamase using room-temperature serial crystallography

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Abstract

{beta}-Lactamases catalyze {beta}-lactam antibiotic hydrolysis and are important contributors to bacterial antimicrobial resistance; {beta}-lactamase inhibitors are widely used to overcome {beta}-lactamase-mediated antibiotic resistance. Nucleophilic serine {beta}-lactamases (SBLs) react with their substrates and clinically available inhibitors via a covalent reaction to give complexes which can undergo further reaction. Using room temperature drop on fixed target serial crystallography, where ligands are rapidly mixed with microcrystals, and classical single-crystal crystallography at cryogenic temperatures, we investigate the reversible covalent reaction of the SBL CTX-M-15 with the diazobicyclooctane inhibitor avibactam. We observe avibactam covalently reacted (ring-opened) with the nucleophilic Ser70, at timepoints from 80 ms to minutes (room temperature) and hours (100 K). These crystallographic data reveal time-dependent movement of the avibactam carbamoyl complex, from 1.3 s onwards, that has implications for the 5-exo-trig recyclization mechanism that determines inhibitor reformation. Combined with molecular dynamics simulations and quantum mechanics calculations at the density functional theory level, the results show that in the first seconds of the reaction the avibactam N-sulfate nitrogen is poorly positioned for recyclization. This subsequently equilibrates after 10 s to a stable endpoint that is in a conformation potentially primed to initiate recyclization through attack of the N-sulfate nitrogen on the carbamoyl carbon. These results further demonstrate the capacity of room-temperature serial crystallography to capture time-resolved changes in ligand conformation at an enzyme active site, complementing discrete classical cryo-crystallography. These data inform on ligand dynamics and the stereoelectronics of diazobicyclooctane inhibition, aiding drug discovery efforts to develop inhibitors of nucleophilic enzymes.

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Hinchliffe, P., Tooke, C. L., Beer, M., Aller, P., Kamps, J. J., Parkinson, L., Zhou, T., Devenish, N., Gu, D.-H., Shilova, A., Rodrigues, M. J., Telfer, A., Butryn, A., Hanzevacki, M., Freeman, E. I., Park, S., Schofield, C. J., Park, J., Owen, R. L., Mulholland, A. J., Orville, A. M., Spencer, J.. 2025-12-19. Time-resolved ligand dynamics revealed in a β-lactamase using room-temperature serial crystallography. https://doi.org/10.64898/2025.12.17.692331

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