Structure-based design of a potent and selective YTHDC1 ligand

N6-Adenosine methylation (m6A) is a prevalent post-transcriptional modification of mRNA, with YTHDC1 being the reader protein responsible for recognizing this modification in the nucleus of the cell. Here we present a protein structure-based medicinal chemistry campaign that resulted in the YTHDC1 inhibitor 40 which shows an equilibrium dissociation constant (Kd) of 49 nM. The crystal structure of the complex (1.6-Å resolution) validated the design. Compound 40 is selective against the cytoplasmic m6A-RNA readers YTHDF1-3 and YTHDC2 and shows antiproliferative activity against the acute myeloid leukemia (AML) cell lines THP-1, MOLM-13, and NOMO1. For the series of compounds that culminated into ligand 40, the good correlation between the affinity in the biochemical assay and antiproliferative activity in the cellular assay (THP-1) provides evidence of YTHDC1 target engagement in the cell. Thus compound 40 meets chemical probe properties for studying the role of YTHDC1 in AML.