Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments

ACS Chem Biol. 2020 Mar 20;15(3):618-625. doi: 10.1021/acschembio.9b00894. Epub 2020 Mar 2.


We report a crystallographic analysis of small-molecule ligands of the human YTHDC1 domain that recognizes N6-methylated adenine (m6A) in RNA. The 30 binders are fragments (molecular weight < 300 g mol-1) that represent 10 different chemotypes identified by virtual screening. Despite the structural disorder of the binding site loop (residues 429-439), most of the 30 fragments emulate the two main interactions of the -NHCH3 group of m6A. These interactions are the hydrogen bond to the backbone carbonyl of Ser378 and the van der Waals contacts with the tryptophan cage. Different chemical groups are involved in the conserved binding motifs. Some of the fragments show favorable ligand efficiency for YTHDC1 and selectivity against other m6A reader domains. The structural information is useful for the design of modulators of m6A recognition by YTHDC1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amines / chemistry
  • Amino Acid Sequence
  • Binding Sites
  • Crystallization
  • Hydrogen Bonding
  • Ligands
  • Models, Molecular
  • Nerve Tissue Proteins / chemistry*
  • Peptide Fragments / chemistry*
  • Protein Binding
  • Protein Domains
  • RNA / chemistry*
  • RNA Splicing Factors / chemistry*
  • Structure-Activity Relationship


  • Amines
  • Ligands
  • Nerve Tissue Proteins
  • Peptide Fragments
  • RNA Splicing Factors
  • YTHDC1 protein, human
  • RNA