
In a remarkable advancement for rewiring cellular signalling, researchers from the Sapkota Lab have developed a novel approach to precisely control the levels of protein phosphorylation.
Protein phosphorylation, which involves the addition of a phosphate moiety to proteins, is essential for regulating various cellular activities and the process is tightly regulated. However, errors in this process can lead to many diseases, including cancer and neurodegeneration. Traditional methods to control phosphorylation include the inhibition of enzymes called kinases that add the phosphate moiety. Yet, kinase inhibitors have significant limitations, such as lack of specificity and broad substrate effects, potentially leading to many side-effects. Precise substrate-level phospho-control is therefore a desirable goal but one that is very challenging.
New research from the Sapkota group specifically addressed this challenge.
The new method, featuring a small molecule which the team developed and named BDPIC (bromoTAG-dTAG proximity-inducing chimera), recruited the phosphatase enzymes to the phosphorylated target proteins inside cells to effectuate removal of the phosphate moieties from the target proteins. This “targeted dephosphorylation” of the target proteins was achieved on multiple target proteins by different phosphatases and altered the function of these proteins.
In the new study, now published in iScience https://www.cell.com/iscience/fulltext/S2589-0042(24)01657-2, led by postdoctoral fellow Dr. Jin-Feng Zhao, targeted dephosphorylation of the TFEB transcription factor, which controls expression of genes involved in lysosomal function and autophagy in response to metabolic and other stressors, by recruiting the PP2A phosphatase caused its translocation to the nucleus and transcription of some target genes even in the absence of stressors.
In another new study now also published in iScience, https://www.cell.com/iscience/fulltext/S2589-0042(24)01648-1, led by PhD student Abigail Brewer, targeted dephosphorylation of the transcription factor SMAD3, which controls cellular responses to transforming growth factor β (TGFβ) ligands, resulted in the inhibition of TGFβ-induced gene transcription and epithelial to mesenchymal transition, a process that is a key step in cancer metastasis.
Professor Gopal Sapkota said, “These exciting studies establish proof-of-concept for targeted dephosphorylation at the endogenous, cellular level. Now the challenge is to develop tools that will allow us to covert these ideas into promising therapeutic approaches. To this end, we are already collaborating with leading pharmaceutical companies to develop small molecules that can achieve targeted dephosphorylation in the cellular and disease contexts.”
BDPIC, with its innovative heterobifunctional properties, also offers a transformative approach of recruiting any two proteins inside cells into proximity beyond just targeted dephosphorylation. By binding to dTAG on one end and bromoTAG on the other, BDPIC leverages induced-proximity to achieve accurate and targeted modulation of proteins of interest by any protein-modifying enzyme of interest.
Natalia Shpiro, Gajanan Sathe, Thomas J. Macartney Nicola T. Wood, Mel Wightman, Rotimi Fasimoye and Dario Alessi from Dundee and Florentina Negoita and Kei Sakamoto from Novo Nordisk Foundation Centre for Basic Metabolic Research, University of Denmark also contributed to the work. The work on TFEB was a joint collaborative endeavour between the Sapkota lab (Dundee) and Sakamoto lab (Denmark).
Professor Dario Alessi, director of the MRC PPU said, “I congratulate the Sapkota lab and his collaborators for developing this new approach to induce rapid dephosphorylation of key target proteins. This pioneering approach will enable the functional roles that protein phosphorylation play to be better assessed. This method could also be developed into a powerful therapeutic approach to modulate the phosphorylation and activity of disease modifying targets.”