Targeted Degradation of Intracellular Proteins using Ubiquitin Variant Induced Proximity

Eukaryotic cells rely on proteasomal degradation mechanisms to maintain protein homeostasis, quantity, and quality, essential for regulating various biological processes. A recent trend in drug development involves harnessing the ubiquitin (Ub)-mediated proteolysis pathway for the targeted degradation of disease-causing proteins. One promising approach in this domain is the use of Proteolysis Targeting Chimeras (PROTACs), which are heterobifunctional molecules that contain a module to recruit E3 ligases, a target-binding module, and a linker, thereby directing the target protein to E3 ligases for ubiquitination and subsequent proteasomal degradation. Despite the progress in chemical PROTACs, limited information is available on peptide-based degraders. Previous research in our laboratory has focused on engineered Ub variants (UbVs) as inhibitors and activators of Ub related enzymes, targeting protein-protein interaction surfaces that are often elusive to chemical inhibitors. Building upon this foundation, we hypothesized that UbVs could serve as fusion protein components to facilitate targeted protein degradation—a concept we term UbV induced proximity (UbVIP). The UbVIP approach presents several advantages over small-molecule PROTACS, primarily due to its ability to bind protein-protein interaction sites on target proteins that small molecules cannot access and the utilization of novel E3 ligases. In this PhD thesis, I explore the application of UbVIP technology for intracellular proteins. Chapter 2 of this thesis demonstrates the successful degradation of the target protein, 53BP1, by employing UbVIP to recruit the E3 ligases RFWD3 and NEDD4L. Chapter 3 investigates the effectiveness of recruiting the E2 conjugating enzyme, UBE2B, in degrading target proteins. Collectively, the findings from this research shed light on a peptide-based targeted protein degradation strategy and provide compelling evidence for the exploitation of novel E2 conjugating enzymes and E3 ligases in the ubiquitination and degradation of intracellular proteins. The UbVIP approach holds great promise as a valuable tool in drug development and therapeutic interventions for a wide range of diseases.

Grantor dc:publisher

University of Guelph

Author dc:creator

• Aminu, Bayonle

Advisor dc:contributor.advisor

• Zhang, Wei

• Targeted Protein Degradation
• Ubiquitin
• Ubiquitin Variants
• Protein Interactions

Language dc:language.iso

en

Handle dc:identifier.uri

https://hdl.handle.net/10214/28069

OAI record oai:identifier

https://atrium.lib.uoguelph.ca/server/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Aatrium.lib.uoguelph.ca%3A10214%2F28069