Atomistic and thermodynamic analysis of the N6-methyladenosine (m6A) recognition by the reader YTHDC1 and the chemical probe development
RNA epigenetics has been a rapidly growing field in recent years. This field studies the impacts of post transcriptional RNA modification on many biological functions, including brain development, chromatin accessibility, heat shock response, oocyte maturation, the immune response to infection. As a representative RNA modification, N6-methyladenosin (m6A) is best studied in the field. The m6A modification is installed on mRNA by a methyltransferase complex. It is reversibly removed by corresponding demethylases. The methylated RNA exerts its effects on the downstream cellular functions by binding m6A-reader proteins. Recently, the modification is associated with tumorigenesis in many cancers and thus attracts much attention from the pharmaceutical industry. Despite the increasing interests, studies in the biophysical aspect are surprisingly scarce, i.e., on molecular recognition mechanisms. This knowledge deficit impedes turning the field’s focus into unlocking new therapeutic targets, editing tools of RNA modification, and medicinal chemistry. In this talk, I will introduce our recent progress in elucidating the recognition mechanism between m6A-containing RNA and its reader proteins (here, I use the YTHDC1 as the study model). By combining atomistic simulations, site-directed mutagenesis, and several biophysical experiments, we have 1) elucidated how the reader protein recognizes its preferred RNA sequence; 2) decomposed the thermodynamic parameters, i.e., enthalpic and entropic contributions to the molecular recognition; 3) unclosed multiple (meta)stable conformations by crystallization and molecular dynamics simulations; 4) discovered the first class of chemical probes. Our contributions may accelerate the discovery of better chemical probes, m6A-editing tools, and drug candidates against reader proteins.