Selectively Disrupting m6A-Dependent Protein–RNA Interactions with Fragments

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.