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  4. SCREENING THE E3 LIGASE LANDSCAPE FOR RATIONAL DESIGN IN UBIQUIBODY-MEDIATED TARGETED PROTEIN DEGRADATION

SCREENING THE E3 LIGASE LANDSCAPE FOR RATIONAL DESIGN IN UBIQUIBODY-MEDIATED TARGETED PROTEIN DEGRADATION

File(s)
Monticello_cornellgrad_0058F_15403.pdf (6.38 MB)
Ubiquibody_Sequences.xlsx (532.21 KB)
Permanent Link(s)
https://doi.org/10.7298/3093-my46
https://hdl.handle.net/1813/121089
Collections
Cornell Theses and Dissertations
Author
Monticello, Connor
Abstract

Targeting the proteome for protein degradation has been a long sought after issue, generating such innovations as Proteolysis Targeting Chimeras, or PROTACS. Simply put, these are heterobifunctional molecules that leverage the extant ubiquitin proteasome system (UPS) by bridging the gap between UPS E3 ligases and a Protein of Interest (POI), leading to its degradation. Our lab has similarly developed protein chimeras, dubbed ubiquibodies (uAbs), that fuse a protein binding domain to the E3 ligase, to target a POI directly. Besides allowing for more modularity in the binding domain towards a POI, uAbs also provide a distinct advantage in testing E3 ligases, as previously they’ve been limited to those that have small molecule interactions. Given the overall number of E3 ligases that have been tested is low, and that there are over 600 potential human E3 ligases, this work aims to provide a first step in cataloguing and organizing the efficacy and robustness of the E3 ligase superfamily, in the context of targeted protein degradation. Leveraging both the ubiquibody’s inherent modularity and previous work targeting β-catenin, a clinically relevant POI, we have developed a screen to find novel degraders. To wit the top five E3 ligases from the screening are BFAR, E4F1, G2E3, HACE1, and HERC6, and are all novel for use in targeted protein degradation. Besides successful hits, data collected from the screen allows for predictions for new ubiquibody designs and a good framework for testing new designs.

Description
79 pages
Supplemental file(s) description: None.
Date Issued
2025-12
Keywords
bioPROTACs
•
E3 ubiquitin ligase
•
proteome editing
•
targeted protein degradation
•
ubiquibodies
•
ubiquitination
Committee Chair
DeLisa, Matthew
Committee Member
Mao, Yuxin
Putnam, David
Degree Discipline
Biomedical Engineering
Degree Name
Ph. D., Biomedical Engineering
Degree Level
Doctor of Philosophy
Type
dissertation or thesis

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