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WD repeat-containing protein 5 (WDR5) is a scaffolding protein involved in critical protein-protein interactions and a promising target for therapeutic development. Novel small-molecule ligands targeting WDR5 were identified using the DELopen platform, a free-access DNA-encoded chemical library (DEL) for academic research. Through off-DNA structure-activity relationship studies and photoaffinity labeling, two promising initial leads, DBL-6-13 and DBL-6-33, were identified as new binders of WDR5. These compounds exhibited moderate to good binding affinities and were confirmed to bind the WIN-site through co-crystal structure analysis. Our findings demonstrate the utility of DEL technology in identifying ligands for challenging targets like WDR5, particularly within an academic research setting using the DELopen platform. The identified WDR5 ligands offer a foundation for further optimization and exploration as chemical probes for WDR5 research.
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http://dx.doi.org/10.1016/j.bioorg.2024.107948 | DOI Listing |
RSC Chem Biol
July 2025
Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University Max-von-Laue-Str. 9 D-60438 Frankfurt am Main Germany
Herein we present the rapid development of LH168, a potent and highly selective chemical probe for WDR5, streamlined by utilizing a DEL-ML (DNA encoded library-machine learning) hit as the chemical starting point. LH168 was comprehensively characterized in bioassays and demonstrated potent target engagement at the WIN-site pocket of WDR5, with an EC of approximately 10 nM, a long residence time, and exceptional proteome-wide selectivity for WDR5. In addition, we present the X-ray co-crystal structure and provide insights into the structure-activity relationships (SAR).
View Article and Find Full Text PDFAnal Chem
September 2025
Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
DNA-encoded libraries have become widely used in drug discovery, and several different setups to link chemical compounds to DNA have been employed in the field, including single-stranded and double-stranded DNA tags as well as a variety of linker chemistries. In our previous study, we observed distinct differences in binding affinities between ligands coupled either to single-stranded or double-stranded DNA; however, the molecular basis for these differences remained unclear. Here, we present a native ion mobility mass spectrometry approach that incorporates gas- and solution-phase activation techniques to systematically investigate these differences, specifically the impact of DNA tags on binding performance in protein-ligand interactions.
View Article and Find Full Text PDFChem Pharm Bull (Tokyo)
August 2025
Graduate School of Pharmaceutical Sciences, The University of Osaka.
Recently, oligonucleotide-based drug discovery has attracted considerable amounts of attention. As oligonucleotide therapeutics have evolved into practical use, research into the development of functional artificial nucleic acids has been vigorously conducted worldwide. However, the synthesis of artificial nucleic acids generally requires long sequences from starting materials; hence, structurally optimizing oligonucleotide therapeutics is extremely difficult.
View Article and Find Full Text PDFMedComm (2020)
September 2025
DP Technology Beijing China.
RNA-targeting small molecules represent a transformative frontier in drug discovery, offering novel therapeutic avenues for diseases traditionally deemed undruggable. This review explores the latest advancements in the development of RNA-binding small molecules, focusing on the current obstacles and promising avenues for future research. We highlight innovations in RNA structure determination, including X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy, which provide the foundation for rational drug design.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
August 2025
Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea.
Capture agents that selectively bind to biological targets are indispensable tools in diagnostics, therapeutics, and biomedical research. However, discovering such capture agents, particularly for structurally conserved or challenging targets, remains a challenge. Here, we describe a protein-templated in situ click strategy enabled by a nanoparticle-based DNA-encoded library (nanoDEL) platform.
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