Multiscale simulations identify origins of differential carbapenem hydrolysis by the OXA-48 β-lactamase

Viivi H A Hirvonen, Tal Weizmann, Adrian J Mulholland, James Spencer, Marc W Van der Kamp*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

9 Citations (Scopus)
40 Downloads (Pure)

Abstract

OXA-48 β-lactamases are frequently encountered in bacterial infections caused by carbapenem-resistant Gram-negative bacteria. Due to the importance of carbapenems in treatment of healthcare-associated infections, and the increasingly wide dissemination of OXA-48-like enzymes on plasmids, these βlactamases are of high clinical significance. Notably, OXA-48 hydrolyses imipenem more efficiently than other commonly used carbapenems, such as meropenem. Here, we use extensive multiscale simulations of imipenem and meropenem hydrolysis by OXA-48 to dissect the dynamics and to explore differences in reactivity of the possible conformational substates of the respective acylenzymes. QM/MM simulations of the deacylation reaction for both substrates demonstrate that deacylation is favoured when the 6αhydroxyethyl group is able to hydrogen bond to the water molecule responsible for deacylation, but
disfavoured by increasing hydration of either oxygen of the carboxylated Lys73 general base. Differences in free energy barriers calculated from the QM/MM simulations correlate well with the experimentally observed differences in hydrolytic efficiency between meropenem and imipenem. We conclude that the
impaired breakdown of meropenem, compared to imipenem, which arises from a subtle change in the hydrogen bonding pattern between the deacylating water molecule and the antibiotic, is most likely induced by the meropenem 1β-methyl group. In addition to increased insights into carbapenem breakdown by OXA
β-lactamases, which may aid in future efforts to design of antibiotics or inhibitors, our approach exemplifies the combined use of atomistic simulations in determining the possible different enzyme-substrate substates, and their influence on enzyme reaction kinetics.
Original languageEnglish
Pages (from-to)4534–4544
Number of pages11
JournalACS Catalysis
Volume12
Issue number8
DOIs
Publication statusPublished - 3 Apr 2022

Bibliographical note

Funding Information:
V.H.A.H. and this research were supported by the UK Medical Research Council (MR/N0137941/1 for the GW4 Biomed DTP awarded to the universities of Bath, Bristol Cardiff, and Exeter). M.W.K. further thanks BBSRC for support (BB/M0626280/1). A.J.M. thanks EPSRC for support (EP/M013219/1, EP/M022609/1, and EP/R026939/1). A.J.M. and J.S. thank MRC for funding (MR/T016035). This work was conducted using the computational facilities of the Advanced Computing Research Centre, University of Bristol.

Funding Information:
V.H.A.H. and this research were supported by the UK Medical Research Council (MR/N0137941/1 for the GW4 Biomed DTP awarded to the universities of Bath, Bristol, Cardiff, and Exeter). M.W.K. further thanks BBSRC for support (BB/M0626280/1). A.J.M. thanks EPSRC for support (EP/M013219/1, EP/M022609/1, and EP/R026939/1). A.J.M. and J.S. thank MRC for funding (MR/T016035). This work was conducted using the computational facilities of the Advanced Computing Research Centre, University of Bristol.

Publisher Copyright:
© 2022 American Chemical Society. All rights reserved.

Keywords

  • carbapenem hydrolysis
  • OXA-48 β-lactamase
  • meropenem
  • imipenem
  • hydrogen bonding
  • QM/MM simulations

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