Expanding PROTACtable genome universe of E3 ligases

Yuan Liu, Jingwen Yang, Tianlu Wang, Mei Luo, Yamei Chen, Chengxuan Chen, Ze’ev Ronai, Yubin Zhou, Eytan Ruppin () and Leng Han ()
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Yuan Liu: Indiana University
Jingwen Yang: Indiana University
Tianlu Wang: Texas A&M University
Mei Luo: Indiana University
Yamei Chen: Indiana University
Chengxuan Chen: Indiana University
Ze’ev Ronai: Sanford Burnham Prebys Medical Discovery Institute
Yubin Zhou: Texas A&M University
Eytan Ruppin: Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH)
Leng Han: Indiana University

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract Proteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD) molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new opportunities to engage targets that remain challenging to be inhibited by conventional small molecules. One fundamental element in the degradation process is the E3 ligase. However, less than 2% amongst hundreds of E3 ligases in the human genome have been engaged in current studies in the TPD field, calling for the recruiting of additional ones to further enhance the therapeutic potential of TPD. To accelerate the development of PROTACs utilizing under-explored E3 ligases, we systematically characterize E3 ligases from seven different aspects, including chemical ligandability, expression patterns, protein-protein interactions (PPI), structure availability, functional essentiality, cellular location, and PPI interface by analyzing 30 large-scale data sets. Our analysis uncovers several E3 ligases as promising extant PROTACs. In total, combining confidence score, ligandability, expression pattern, and PPI, we identified 76 E3 ligases as PROTAC-interacting candidates. We develop a user-friendly and flexible web portal ( https://hanlaboratory.com/E3Atlas/ ) aimed at assisting researchers to rapidly identify E3 ligases with promising TPD activities against specifically desired targets, facilitating the development of these therapies in cancer and beyond.

Date: 2023
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DOI: 10.1038/s41467-023-42233-2

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