Ligand-Induced Opening of a Cryptic Pocket in METTL14

The complex of methyltransferase-like proteins 3 and 14 (METTL3–14) is the main human enzyme that deposits the most abundant internal mRNA modification, N6-methyladenosine (m6A). In the heterodimeric complex, METTL3 acts as a catalytic subunit while METTL14 is involved in mRNA binding and complex stabilization. Here, we present the discovery of small-molecule ligands that bind to a cryptic pocket in METTL14 by protein crystallography. A comparative analysis of crystal structures revealed that the METTL14 cryptic pocket is closed in the apo structure of METTL3–14, and in the structures of METTL3–14 in the complex with the cosubstrate S-adenosyl-methionine (SAM) and a large number of SAM-competitive inhibitors. We first discovered compounds 1 and 2 that bind to both the SAM pocket in METTL3 and the cryptic pocket in METTL14. With this structural information, we designed compound 3 that binds only to the METTL14 cryptic pocket. Compound 3 does not inhibit the catalytic activity of METTL3–14 but can be used as an anchor for heterobifunctional molecules. We propose a route for its further development into heterobifunctional ligands, e.g., proteolysis targeting chimeras (PROTACs).