Developing open access protein degradation tools for drug discovery

Challenge: PROTACs (PROteolysis TArgeting Chimeras) are bifunctional drugs that recruit a ubiquitin E3 ligase to a targeted protein, thereby catalyzing poly-ubiquitylation of the target and its subsequent degradation by the proteasome. PROTAC induced protein degradation offers advantages over classical enzyme inhibition: it acts via a catalytic instead of occupancy-based mechanism and shows superior efficacy with fewer off-target side effects and prolonged pharmacodynamic effects beyond drug exposure. Although humans have hundreds of E3 ligases only six E3s have been utilized to develop PROTACs to date. Furthermore, predicting the ability of PROTACs to degrade proteins of interest remains elusive because of the lack of chemical tools and assays to characterize them.

Solution: To overcome these issues and to double the set of E3 ligases that can be harnessed for future PROTAC discovery, the research team aims to develop know-how, protocols and research tools allowing the identification and characterization of small-molecule ligands to new E3 ligases. These Target Enabling Packages for each selected E3 ligase will include a combination of protein expression constructs and protocols, crystallization protocols and X-ray crystal structures of proteins, screening assays suitable for hit-finding of small molecule binders, in vitro orthogonal assays for hit confirmation, and preliminary screening results for drug-like small molecules that bind to new E3 ligases.

Expected Achievements/Impact: Thanks to the expertise of the Structural Genomic Consortium scientists in protein expression, protein crystallization, and X-ray crystallography, this project is expected to generate Target Enabling Packages containing know-how and reagents for 6-8 new E3 ligases that will be specifically chosen in collaboration with Takeda and Pfizer. These data packages will be made available to the wider scientific community to facilitate the development of new chemical tools to understand the biology of new E3 ligases and develop PROTACs molecules utilizing the novel E3 ligases.







Principal Investigator:

Cheryl Arrowsmith
Structural Genomics Consortium,
University of Toronto


Masoud Vedadi
University of Toronto

Jinrong Min
University of Toronto

Matthieu Schapira
University of Toronto

Ongoing Project
$1,280,000 / 3 years
Supported by CQDM through:
• Pfizer
• Takeda
And by a co-funding partner: