Discovery of Small Molecules that Activate RNA Methylation through Cooperative Binding to the METTL3-14-WTAP Complex Active Site

Abstract

Summary: Chemical modifications of RNA provide an additional, epitranscriptomic, level of control over cellular functions. N-6-methylated adenosines (m6As) are found in several types of RNA, and their amounts are regulated by methyltransferases and demethylases. One of the most important enzymes catalyzing generation of m6A on mRNA is the trimer N-6-methyltransferase METTL3-14-WTAP complex. Its activity has been linked to such critical biological processes as cell differentiation, proliferation, and death.We used in silico-based discovery to identify small-molecule ligands that bind to METTL3-14-WTAP and determined experimentally their binding affinity and kinetics, as well as their effect on enzymatic function. We show that these ligands serve as activators of the METTL3-14-WTAP complex. : The methyltransferase complex METTL3-14-WTAP catalyzes generation of m6A on mRNA. Selberg et al. report the in silico discovery and experimental characterization of small-molecule compounds with exceptionally high binding efficiencies to METTL3-14-WTAP. Remarkably, these compounds act as enzyme activators and lead to increased m6A levels in RNA. Keywords: RNA methylation, N6-adenosine-methyltransferases, N-6-methyladenosine, ligand binding, computer-aided design, epitranscriptomics