Proteolysis Targeting Chimera Degraders of the METTL3–14 m⁶A-RNA Methyltransferase

Abstract

Methylation of adenine N6 (m 6 A) is the most frequent RNA modification. On mRNA, it is catalyzed by the METTL3−14 heterodimer complex, which plays a key role in acute myeloid leukemia (AML) and other types of blood cancers and solid tumors. Here, we disclose the first proteolysis targeting chimeras (PROTACs) for an epitranscriptomics protein. For designing the PROTACs, we made use of the crystal structure of the complex of METTL3−14 with a potent and selective smallmolecule inhibitor (called UZH2). The optimization of the linker started from a desfluoro precursor of UZH2 whose synthesis is more efficient than that of UZH2. The first nine PROTAC molecules featured PEG-or alkyl-based linkers, but only the latter showed cell penetration. With this information in hand, we synthesized 26 PROTACs based on UZH2 and alkyl linkers of different lengths and rigidity. The formation of the ternary complex was validated by a FRET-based biochemical assay and an in vitro ubiquitination assay. The PROTACs 14, 20, 22, 24, and 30, featuring different linker types and lengths, showed 50% or higher degradation of METTL3 and/or METTL14 measured by Western blot in MOLM-13 cells. They also showed substantial degradation on three other AML cell lines and prostate cancer cell line PC3.

Small molecule inhibitors targeting m6A regulators

“…Moreover, the application of emerging technologies offers avenues for refining the selectivity and efficacy of these small molecules. Employing ABPP technology to pinpoint more efficient enzyme targets, utilizing TPP to identify targets with robust cellular activity, harnessing PROTAC [ 243 , 244 ] or molecular glues to directly degrade m 6 A regulator proteins, alongside exploring small molecules that interfere with MTC complex interactions, thus strategically influencing the dynamic equilibrium of m 6 A modification. Moreover, the application of AI and ML technologies in biological activity and target identification, through tools like DEEP Picker for NMR spectroscopy analysis, accelerates the discovery of potential drugs, allowing for the early prediction of the biological effects of compounds, providing key support for drug development [ 240 ].…”