Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain

  • Commun Chem. 2025 Jun 13;8(1):185. doi: 10.1038/s42004-025-01574-3.
Yeojin Kim  #  1  2 ,  Aleksandar Lučić  #  1  2 ,  Christopher Lenz  1  2 ,  Frederic Farges  1  2 ,  Martin P Schwalm  1  2  3 ,  Krishna Saxena  1  2 ,  Thomas Hanke  1  2 ,  Peter G Marples  4  5 ,  Jasmin C Aschenbrenner  4  5 ,  Daren Fearon  4  5 ,  Frank von Delft  4  5  6 ,  Andreas Krämer  7  8  9 ,  Stefan Knapp  10  11  12  13
Affiliations
  • 1. Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany.
  • 2. Structural Genomics Consortium, Buchmann Institute of Molecular Life Sciences (BMLS), Frankfurt am Main, Germany.
  • 3. German Translational Cancer Consortium (DKTK), Frankfurt am Main, Germany.
  • 4. Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK.
  • 5. Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK.
  • 6. Centre for Medicines Discovery, NDM Research Building, University of Oxford, Oxford, UK.
  • 7. Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany. [email protected].
  • 8. Structural Genomics Consortium, Buchmann Institute of Molecular Life Sciences (BMLS), Frankfurt am Main, Germany. [email protected].
  • 9. Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany. [email protected].
  • 10. Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany. [email protected].
  • 11. Structural Genomics Consortium, Buchmann Institute of Molecular Life Sciences (BMLS), Frankfurt am Main, Germany. [email protected].
  • 12. German Translational Cancer Consortium (DKTK), Frankfurt am Main, Germany. [email protected].
  • 13. Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany. [email protected].
  • # Contributed equally.
PMID: 40514378 DOI: 10.1038/s42004-025-01574-3
Abstract

Tripartite motif-containing protein 21 (TRIM21), and particularly its PRY-SPRY protein interaction domain, plays a critical role in the immune response by recognizing intracellular antibodies targeting them for degradation. In this study, we performed a crystallographic fragment screening (CFS) campaign to identify potential small molecule Binders targeting the PRY-SPRY domain of TRIM21. Our screen identified a total of 109 fragments binding to TRIM21 that were distributed across five distinct binding sites. These fragments have been designed to facilitate straightforward follow-up chemistry, making them ideal starting points for further chemical optimization. A subsequent fragment merging approach demonstrated improved activity. To enable functional validation of compounds with full length human TRIM21, we established a NanoBRET assay suitable for measuring target engagement to the main Fc binding site in life cells. The high-resolution structural data and observed binding modes across the different sites highlight the versatility of the PRY-SPRY domain as a target for small-molecule intervention. The presented data provide a solid foundation for structure-guided ligand design, enabling the rational design of more potent and selective compounds, with the goal to develop bivalent molecules such as Proteolysis Targeting Chimeras (PROTACs).

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