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

Cell Rep. 2019 Mar 26;26(13):3762-3771.e5. doi: 10.1016/j.celrep.2019.02.100.

Abstract

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.

Keywords: N-6-methyladenosine; N6-adenosine-methyltransferases; RNA methylation; computer-aided design; epitranscriptomics; ligand binding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Catalytic Domain*
  • Cell Cycle Proteins / metabolism*
  • HEK293 Cells
  • Humans
  • Ligands
  • Methylation
  • Methyltransferases / metabolism*
  • Protein Binding
  • RNA Processing, Post-Transcriptional / drug effects*
  • RNA Splicing Factors / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / metabolism
  • Sf9 Cells
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*
  • Spodoptera

Substances

  • Cell Cycle Proteins
  • Ligands
  • RNA Splicing Factors
  • RNA, Messenger
  • RNA, Ribosomal
  • Small Molecule Libraries
  • WTAP protein, human
  • Methyltransferases
  • METTL3 protein, human