Nanoscale Direct-to-Biology Optimization and Structural Insights into Selective S. aureus TrmD Inhibitors

  • J Med Chem. 2025 Dec 25;68(24):26246-26262. doi: 10.1021/acs.jmedchem.5c02323.
Ariane F Hübner  1 ,  Annabelle C Weldert  1 ,  Tessa Marciniak  2 ,  Florian Hof  3 ,  Vivien S Beck  2 ,  Samuel Carien  2 ,  Sophie N Mulartschyk  1 ,  Eva Wolf  3 ,  Wilma Ziebuhr  2 ,  Fabian Barthels  1
Affiliations
  • 1. Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany.
  • 2. Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
  • 3. Institute of Molecular Physiology, Johannes Gutenberg-University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.
PMID: 41367353 DOI: 10.1021/acs.jmedchem.5c02323
Abstract

The tRNA m1G37 methyltransferase (TrmD) is considered essential in various bacteria, including Staphylococcus aureus, a pathogen responsible for a wide range of diseases. Here, we have performed a high-throughput nanomole-scale synthesis campaign (nanoSAR) by late-stage copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC)-functionalizing a library of structurally diverse azides (N = 320) to a pyrrolopyrimidone alkyne. We have identified selective S. aureus TrmD inhibitors with inhibitory activity in the nanomolar to low micromolar range using a direct-to-biology assay read-out. A carbamate-masked guanidine intermediate of the lead structure selectively inhibited S. aureus growth at low micromolar concentrations in cell-based assays, while Gram-negative bacteria and an off-target panel of methyltransferases were not affected. Subsequent cocrystallization resulted in a crystal structure of S. aureus TrmD bound to an inhibitor, providing detailed insights into its binding mode and enabling future structure-guided optimization.

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