Targeting the conserved active site of splicing machines with specific and selective small molecule modulators

• Published in: Nature communications Vol. 15; no. 1; pp. 4980 - 15
• Main Authors: Silvestri, Ilaria, Manigrasso, Jacopo, Andreani, Alessandro, Brindani, Nicoletta, Mas, Caroline, Reiser, Jean-Baptiste, Vidossich, Pietro, Martino, Gianfranco, McCarthy, Andrew A., De Vivo, Marco, Marcia, Marco
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.06.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/500; 631/535/1266; Binders; Biotechnology; Cancer; Catalysis; Catalytic Domain; Congenital diseases; Crystallography; Genetic disorders; Humanities and Social Sciences; Humans; Introns; Introns - genetics; Life Sciences; Ligands; Modulators; multidisciplinary; Ribonucleic acid; RNA; RNA probes; RNA Splicing; RNA Splicing - drug effects; Science; Science (multidisciplinary); Small Molecule Libraries; Small Molecule Libraries - chemistry; Small Molecule Libraries - pharmacology; Spliceosomes; Spliceosomes - drug effects; Spliceosomes - metabolism; Splicing; Therapeutic targets
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-48697-0

The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers. Splicing is a vital biological reaction and a druggable pathway to treat infection, genetic diseases and cancer. Here, the authors describe how splicing is modulated by small molecules that target the conserved splicing active site in the group II introns.