Identifying and hijacking tissue-restricted ubiquitin E3 ligase for targeted protein degradation

E3 ligases are diverse enzymes that catalyse the transfer of ubiquitin to substrate proteins. E3 ligases were traditionally viewed to be challenging targets to small molecules. because of their complex structural features, and the need to modulate protein-protein interactions often involving shallow and difficult-to-target binding sites (1).



Recently, the advent of the field of "targeted protein degradation" has brought E3 ligases to the forefront as target class. E3 ligases can be co-opted by small molecules called "degraders" to recruit disease-causing proteins that are not their substrates under normal conditions, leading to their ubiquitination and degradation. Such small molecules include "molecular glue" degraders, either monovalent or bi- or tri-valent chimeric molecules, also known as proteolysis targeting chimeras (PROTACs). Small molecules binders can also act as E3 modulators, inhibiting or activating the enzyme, or even stabilizing i.e. increasing its protein level - which allows to modulate directly the pathway in which the E3 ligase is itself involved.



The Ciulli lab works on developing E3 ligase targeting ligands including PROTACs and molecular glues. The Ciulli lab has pioneered the structure-guided development and understanding of E3 ligase ligands and PROTACs targeting the von Hippel-Lindau (VHL) E3 ligase (2). The Virdee lab has pioneered the development of novel chemical biology tools for studying E3 ligases. These include the development of activity-based probes that measure the hallmark trans-thiolation activity of ubiquitin conjugation enzymes, allowing insights into disease-relevant E3 regulation (3).



This project aims to study new E3 ligases and ligand them with small molecules. The project will initially focus on mining MS-proteomics databases to identify E3 ligases preferentially expressed in tissues of interest. In parallel, activity-based probes developed in the Virdee lab will be developed and applied to assess their relative activities and functionalities. Once E3 ligases meeting criteria of relative abundance and functionalities are validated, we will use degron tags e.g. our BromoTag technology, to induce proximity between the E3 ligase and tissue-required disease-causing target protein(s), to validate small-molecule induced activity. Finally, using structure-based design small-molecule E3 binders will be developed that will enable design of PROTAC molecular glues.



The project will untap novel hijackable E3 ligases for illuminating biology and improved therapies and the student will receive outstanding training in multidisciplinary areas in cutting-edge research in fundamental and translational chemical and structural biology.