Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors

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  • Jürgen Brem
  • Tharindi Panduwawala
  • Jon Ulf Hansen
  • Joanne Hewitt
  • Edgars Liepins
  • Pawel Donets
  • Laura Espina
  • Alistair J.M. Farley
  • Kirill Shubin
  • Gonzalo Gomez Campillos
  • Paula Kiuru
  • Shifali Shishodia
  • Daniel Krahn
  • Robert K. Leśniak
  • Juliane Schmidt (Adrian)
  • Karina Calvopiña
  • María Carmen Turrientes
  • Madeline E. Kavanagh
  • Dmitrijs Lubriks
  • Philip Hinchliffe
  • Gareth W. Langley
  • Ali F. Aboklaish
  • Anders Eneroth
  • Maria Backlund
  • Andrei G. Baran
  • Elisabet I. Nielsen
  • Michael Speake
  • Janis Kuka
  • John Robinson
  • Solveiga Grinberga
  • Lindsay Robinson
  • Michael A. McDonough
  • Anna M. Rydzik
  • Thomas M. Leissing
  • Juan Carlos Jimenez-Castellanos
  • Matthew B. Avison
  • Solange Da Silva Pinto
  • Andrew D. Pannifer
  • Marina Martjuga
  • Emma Widlake
  • Martins Priede
  • Iva Hopkins Navratilova
  • Marek Gniadkowski
  • Anna Karin Belfrage
  • Peter Brandt
  • Jari Yli-Kauhaluoma
  • Eric Bacque
  • Malcolm G.P. Page
  • Jonathan M. Tyrrell
  • James Spencer
  • Pauline A. Lang
  • Pawel Baranczewski
  • Rafael Cantón
  • Stuart P. McElroy
  • Philip S. Jones
  • Fernando Baquero
  • Edgars Suna
  • Angus Morrison
  • Timothy R. Walsh
  • Christopher J. Schofield

Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure–activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL–carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models. [Figure not available: see fulltext.]

Original languageEnglish
JournalNature Chemistry
Pages (from-to)15–24
Publication statusPublished - 2022

Bibliographical note

Funding Information:
We thank the ELF Screening partners for efforts leading to the initial hits, the current and past ENABLE Portfolio Management Committee (PMC) members and EFPIA partners for guidance, and the Diamond Light Source synchrotron for access to the IO3, IO4 and IO4-1 beamlines. J.U.H. thanks N. Sipari from the Viikki Metabolomics Unit (Helsinki Institute of Life Science, University of Helsinki and Biocenter Finland) for her expertise with the liquid chromatography–mass spectroscopy analyses. L.E. thanks Y. Zhou for help in the laboratory, and H. Saif, R. Farzana, E. Portal, K. Sands, K. Thomson and B. Hassan for providing strains for the Enterobacterales collection. The ELF work and the ENABLE project that led to these results were supported by the Innovative Medicines Initiative Joint Undertaking (grant agreements no. 115489 and no. 115583), which have financial contributions from the European Union’s Seventh Framework Programme (FP7/2007–2013), and the EFPIA companies’ in-kind contributions. The ENABLE project is financially supported by contributions from Academic and SME partners. The Oxford work was also supported by Cancer Research UK (C9047/ A24759), the Medical Research Council, the Biotechnology and Biological Research Council (BB/S50676X/1) and the Ineos Oxford Institute for Antimicrobial Research (C.J.S.). This research was funded in whole, or in part, by the Wellcome Trust (grant no. 106244/Z/14/Z and no. 099141/Z/12/Z). The Bristol work was also supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIH) grant R01AI100560 (J.S. and P.H.) (the content is the responsibility of the authors and does not necessarily represent official views of the NIH) and the BrisSynBio Biosuite (UK Biotechnology and Biological Sciences (BBSRC) and Engineering and Physical Sciences (EPSRC) Research Councils (BB/L01386X/1) and BBSRC ALERT14 initiative (BB/M012107/1).

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© 2021, The Author(s), under exclusive licence to Springer Nature Limited.

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