Evidence map›Paper›PMID 38898213›Full record

ArticleNature chemistry2024

Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria.

Alexander T Bakker, Ioli Kotsogianni, Mariana Avalos, Jeroen M Punt, Bing Liu, Diana Piermarini, Berend Gagestein, Cornelis J Slingerland, Le Zhang, Joost J Willemse and 9 more

Abstract read
In one paragraph

Article in Nature chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Deciphering competing reaction pathways in the α-C-H functionalization of unprotected alicyclic aminesOrganic chemistry frontiers : an international journal of organic chemistry · 2026
    Article
  2. Article
  3. Characterization of beddomeilactone amide as bacterial DNA gyrase inhibitor: in vitro evaluation and computational insights.Medicinal chemistry research : an international journal for rapid communications on design and mechanisms of action of biologically active agents · 2026
    Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research.Angewandte Chemie (International ed. in English) · 2025
    Review
  10. Structural basis of chiral wrap and T-segment capture byProceedings of the National Academy of Sciences of the United States of America · 2024
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Alexander T Bakker *Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Ioli Kotsogianni *Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.ORCID 0000-0003-0078-0206
Mariana AvalosDepartment of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands.ORCID 0000-0001-9891-924X
Jeroen M PuntDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.ORCID 0000-0002-0887-3557
Bing LiuDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Diana PiermariniDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Berend GagesteinDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Cornelis J SlingerlandBiological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.ORCID 0000-0003-0027-7491
Le ZhangDepartment of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands.
Joost J WillemseDepartment of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands.ORCID 0000-0001-5210-650X
Leela B GhimireDepartment of Molecular Microbiology, John Innes Centre, Norwich, UK.ORCID 0009-0006-7026-6308
Richard J H B N van den BergDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Antonius P A JanssenDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.ORCID 0000-0003-4203-261X
Tom H M OttenhoffDepartment of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands.ORCID 0000-0003-3706-3403
Constant A A van BoeckelDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Gilles P van WezelDepartment of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands.ORCID 0000-0003-0341-1561
Dmitry GhilarovDepartment of Molecular Microbiology, John Innes Centre, Norwich, UK. dmitry.ghilarov@jic.ac.uk.ORCID 0000-0001-9325-3207
Nathaniel I MartinBiological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands. n.i.martin@biology.leidenuniv.nl.ORCID 0000-0001-8246-3006
Mario van der SteltDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands. m.van.der.stelt@chem.leidenuniv.nl.ORCID 0000-0002-1029-5717

Funding

Wellcome Trust
6 · The paper itself

Abstract

Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase-LEI-800-DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.

Indexed as

Anti-Bacterial AgentsDNA GyraseDrug Resistance, BacterialEscherichia coliFluoroquinolonesIsoquinolinesSulfonamidesTopoisomerase II InhibitorsAllosteric RegulationDrug DiscoveryMicrobial Sensitivity TestsStructure-Activity RelationshipAnti-Bacterial AgentsDNA GyraseFluoroquinolonesisoquinolineIsoquinolinesSulfonamidesTopoisomerase II Inhibitors

Identifiers

PMID38898213
PMCPMC11374673

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.