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Fragment ligands of the m6A-RNA reader YTHDF2

Authors:
F. Nai; R. Nachawati; F. Zálešák; X. Wang; Y. Li; A. Caflisch

Journal: ACS Med. Chem. Lett.
Year: 2022
Volume: 13
Issue: 9
Pages: 1500-1509
DOI: https://doi.org/10.1021/acsmedchemlett.2c00303
Type of Publication: Journal Article

Abstract:

We report 17 small-molecule ligands that compete with N6-methyladenosine (m6A) for binding to the m6A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol–1 per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.We report 17 small-molecule ligands that compete with N6-methyladenosine (m6A) for binding to the m6A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol–1 per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.