Structure-based design of a potent and selective YTHDC1 ligand

TitleStructure-based design of a potent and selective YTHDC1 ligand
Publication TypeJournal Article
Year of Publication2024
AuthorsZálešák F., Nai F., Herok M., Bochenkova E., Bedi R.K, Li Y., Errani F., Caflisch A.
JournalJournal of Medicinal Chemistry
Volume67
Issue11
Pagination9516-9535
Date Published2024 May 24
Type of ArticleResearch Article
Abstract

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-A 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.

URLhttps://pubs.acs.org/doi/10.1021/acs.jmedchem.4c00599
DOI10.1021/acs.jmedchem.4c00599
pubindex

0297

Alternate JournalJ. Med. Chem.
Highlight Role: 
Drug Design