Splicing is a cellular process involving nearly all of our genes, and consisting in the removal of RNA sequences (introns) from precursor transcripts, while other regions (exons) are joined together to form mature coding or non-coding RNAs. Considering the central role that splicing plays in regulating gene expression, it has recently emerged that targeting splicing could be a new viable therapeutic strategy to treat human diseases, such as cancer and genetic disorders [1-3].
In eukaryotic nuclei, splicing is catalyzed by a large ribonucleoprotein complex called the spliceosome. The evolutionary ancestors of this machinery in prokaryotes and eukaryotic organelles are so-called self-splicing group II introns. Both these splicing machines share a similar architecture of the active site, which is complemented by an essential cluster of mono- and di-valent metal ions.
A recent study published in Nature Communications describes for the first time how such a conserved splicing active site can be selectively and specifically targeted with small molecules [4] and (Figure). This study is the result of a collaboration between Dr. Marco Marcia’s laboratory at EMBL Grenoble and Dr. Marco De Vivo’s laboratory at the Italian Institute of Technology in Genoa (Italy) that has been crucially supported by the PSB biophysics facilities and EMBL-ESRF Joint Structural Biology Group beamlines at the ESRF.
Through an interdisciplinary approach, combining medicinal and computational chemistry with biochemistry, biophysics and enzymatic experiments, the study has elucidated the binding mode and molecular mechanism of a potent splicing inhibitor. X-ray crystallography was used to visualized the inhibitor interactions with the splicing site of a bacterial group II intron at near-atomic resolution. As such, this study paves the way for the rational design of novel species-specific splicing modulators, some of which have already been patented by the EMBL and IIT research groups.
These results mark a significant advance in the context of RNA-directed structure-based drug design, an area notoriously challenging due to the dynamic and complex nature of RNA structures. Moreover, this achievement not only highlights the potential for designing specific splicing modulators but also underscores the catalytic role that the PSB plays in seeding productive collaborative research, which helps overcome the scientific challenges associated with RNA-targeted drug design.
I. Silvestri (EMBL, IIT) and M. Marcia(EMBL)
[1] Fedorova O, Jagdmann GE, Adams RL, Yuan L et al. (2018) Nat. Chem. Biol., 14, 1073-1078
[2] Manigrasso J, Chillón I, Genna V, Vidossich P et al. (2020) Nat. Commun., 11, 2837
[3] Marcia M and Pyle AM (2012) Cell, 151, 497-507
[4] Silvestri I, Manigrasso J, Andreani A, Brindani N et al. (2024) Nat. Commun., 15, 4980
Figure: Group II intron inhibitor adopts two distinct poses at different catalytic steps to prevent splicing progression.
