Small-Molecule Ebselen Binds to YTHDF Proteins Interfering with the Recognition of <i>N</i><sup>6</sup>-Methyladenosine-Modified RNAs
Mariachiara Micaelli, Andrea Dalle Vedove, Linda Cerofolini, Jacopo Vigna, Denise Sighel, Sara Zaccara, Isabelle Bonomo, Georgios Poulentzas, Emanuele Filiberto Rosatti, Giulia Cazzanelli, Laura Alunno, Romina Belli, Daniele Peroni, Erik Dassi, Shino Murakami, Samie R. Jaffrey, Marco Fragai, Ines Mancini, Graziano Lolli, Alessandro Quattrone, Alessandro Provenzani
Abstract
orthogonal assays, cannot discriminate between the binding domains of the three YTHDF paralogs but can disrupt the interaction of the YTHDF m6A domain with the m6A-decorated mRNA targets. X-ray, mass spectrometry, and NMR studies indicate that in YTHDF1 ebselen binds close to the m6A cage, covalently to the Cys412 cysteine, or interacts reversibly depending on the reducing environment. We also showed that ebselen engages YTHDF proteins within cells, interfering with their mRNA binding. Finally, we produced a series of ebselen structural analogs that can interact with the YTHDF m6A domain, proving that ebselen expansion is amenable for developing new inhibitors. Our work demonstrates the feasibility of drugging the YTH domain in YTHDF proteins and opens new avenues for the development of disruptors of m6A recognition.