First-in-class inhibitors of the protein lysine methyltransferase METTL21A

Methyltransferases (MTases) play central roles in numerous biological processes and have emerged as attractive therapeutic targets in a wide range of diseases. METTL21A is a protein lysine MTase responsible for the trimethylation of HSP70 family members. Moreover, METTL21A is overexpressed in hepatocellular carcinoma (HCC), where overexpression correlates with poor clinical outcome. Despite its biological and clinical relevance, small-molecule inhibitors of METTL21A remain largely unexplored. Here, we report the identification of 6d as a METTL21A inhibitor and the subsequent structure-activity relationship (SAR) study of analogues decorated with various fluorinated substituents, leading to metabolically stable 6n (HK262) with an IC₅₀ 1.10 μM. We solved a crystal structure of METTL21A in complex with 6m (HK474), providing structural insight into ligand recognition and supporting further structure-guided optimization. These findings establish a biochemically and structurally validated starting point for probing METTL21A function and a foundation for the development of cellularly active METTL21A-targeted chemical tools.