Structure-Based Design of a Potent and Selective YTHDC1 Ligand

Area of Science:

• Biochemistry
• Molecular Biology
• Medicinal Chemistry

Background:

• N6-Adenosine methylation (m6A) is a crucial mRNA modification regulating gene expression.
• YTHDC1 is the nuclear reader protein that specifically recognizes m6A modifications.

Purpose of the Study:

• To design and synthesize novel inhibitors of YTHDC1 using a structure-based medicinal chemistry approach.
• To evaluate the biochemical and cellular activity of the developed inhibitors, particularly compound 40, in the context of acute myeloid leukemia (AML).

Main Methods:

• Protein structure-based drug design and medicinal chemistry campaign.
• Biochemical assays to determine inhibitor affinity (Kd) and selectivity against m6A readers.
• Cellular assays including antiproliferative activity and cellular thermal shift assay (CETSA) for target engagement.

Main Results:

• Compound 40 was identified as a potent YTHDC1 inhibitor with a Kd of 49 nM.
• Crystal structure at 1.6 Å resolution confirmed the binding mode and validated the design.
• Compound 40 exhibited selectivity against cytoplasmic YTHDF1-3 and YTHDC2 readers.
• Significant antiproliferative activity was observed against AML cell lines (THP-1, MOLM-13, NOMO-1).
• Correlation between biochemical affinity and cellular antiproliferative activity confirmed YTHDC1 target engagement in cells.

Conclusions:

• Compound 40 is a selective and potent YTHDC1 inhibitor with demonstrated antiproliferative effects in AML cells.
• The study provides strong evidence for YTHDC1's role in AML.
• Compound 40 serves as a valuable chemical probe for investigating YTHDC1 function in AML pathogenesis.