Healthcare, Canada (Commonwealth Union) – Scientists from Sinai Health and the University of Toronto (U of T) have pioneered a groundbreaking platform for pinpointing proteins that regulate the stability of other proteins—a novel and largely untapped avenue for combating diseases.
Their method involves scrutinizing the entire human proteome to uncover “effector” proteins capable of influencing the stability of other proteins through induced proximity. Essentially, this strategy aims to repurpose cellular mechanisms for therapeutic benefits.
This study marks the inaugural attempt to systematically hunt for effector proteins on such a comprehensive scale, resulting in the identification of numerous novel effectors with potential for drug development.
Lead author Juline Poirson, a visiting scientist at U of T’s Donnelly Centre for Cellular and Biomolecular Research, stated that they discovered over 600 new effector proteins within 14,000 genes. Among these, more than 200 demonstrated proficient degradation of their target proteins, while approximately 400 effectors exhibited the ability to stabilize and increase the abundance of an artificial target protein.
Published in the journal Nature, this collaborative study, which involved researchers from Sinai Health’s Lunenfeld-Tanenbaum Research Institute, represents a significant stride towards unlocking new therapeutic avenues.
“Targeting proteins through induced proximity is a new and promising area of biomedical research,” added Mikko Taipale, who is the principal investigator on the study as well as an associate professor of molecular genetics at the Donnelly Centre and in the Temerty Faculty of Medicine. “Not only did we find new effectors worth further investigation for drug discovery, we developed a synthetic platform that can be used to conduct unbiased, proteome-wide, induced-proximity screens to continue expanding the library of effector proteins.”
Current methods for targeted protein degradation and stabilization primarily utilize E3 ubiquitin ligases (E3s) and deubiquitinases (DUBs) respectively. E3 enzymes attach ubiquitin molecules to target proteins, marking them for degradation by proteosomes. Conversely, DUB enzymes remove ubiquitin tags, thus preventing degradation.
The ubiquitin-proteasome system (UPS) is a crucial cellular pathway responsible for maintaining protein homeostasis. This system is responsible for the degradation of misfolded, damaged, or unnecessary proteins, thereby regulating various cellular processes such as cell cycle progression, transcription, and signal transduction. The E3 ubiquitin ligase, the final component of the UPS, is responsible for the selective transfer of ubiquitin to target proteins, marking them for degradation by the proteasome.
Given their central role in the UPS, E3 ubiquitin ligases have been implicated in various biological processes and disease states. Dysregulation of E3 ubiquitin ligase activity has been linked to the development of several human diseases, including cancer, neurodegenerative disorders, and immune system dysfunction.
Research findings indicate variability among E3s in their effectiveness at degrading target proteins. Additionally, the identification of “angry E3s” highlights certain enzymes that consistently degrade targets regardless of cellular location.
An unexpected discovery that was found in the study was the potency of some E2 conjugating enzymes in targeted protein degradation, surpassing certain E3s. Unlike E3s, E2s act earlier in the degradation process without directly interacting with the target protein. Despite being overlooked for drug targeting previously, E2s offer untapped potential as formidable effectors for protein degradation.
The research underscores the vast potential of exploring the entire proteome to induce proximity, opening significant avenues to be used as a therapeutic.
Among the identified effectors, KLHL40 emerges as a promising candidate for targeted protein stabilization, holding potential for the treatment of skeletal muscle disorders. Additionally, the study highlights FBXL12 and FBXL15 effectors as valuable assets for targeted protein degradation, offering potential avenues for addressing chronic myeloid leukemia.
However, despite the promise of targeted protein degradation and stabilization, these methods have faced challenges, notably the “protein pair problem.” This issue arises from the difficulty in accurately predicting the most suitable effector for a given target protein. Therefore, the precise matching of target proteins with their corresponding effectors is crucial for the effective and safe facilitation of degradation and stabilization processes within tissues.
“The synthetic screening platform developed by our team solves the protein matching issue through rapid, large-scale testing of effector and target protein interactions,” explained Poirson. “We’re confident that an unbiased induced-proximity approach can be used to find effectors for almost any target.”
The study was funded by the David Dime and Elisa Nuyten Catalyst Fund, the Mark Foundation for Cancer Research, the Charles H. Best Postdoctoral Fellowship, and the Canadian Institutes of Health Research (CIHR) Fellowship.
