Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2
PROTAC® (proteolysis-targeting chimera) molecules induce proximity between an E3 ligase and protein-of-interest (POI) to target the POI for ubiquitin-mediated degradation. Cooperative E3-PROTAC-POI complexes have potential to achieve neo-substrate selectivity beyond that established by POI binding to the ligand alone. Here, we extend the collection of ubiquitin ligases employable for cooperative ternary complex formation to include the C-degron E3 KLHDC2. Ligands were identified that engage the C-degron binding site in KLHDC2, subjected to structure-based improvement, and linked to JQ1 for BET-family neo-substrate recruitment. Consideration of the exit vector emanating from the ligand engaged in KLHDC2's U-shaped degron-binding pocket enabled generation of SJ46421, which drives formation of a remarkably cooperative, paralog-selective ternary complex with BRD3<sup>BD2</sup>. Meanwhile, screening pro-drug variants enabled surmounting cell permeability limitations imposed by acidic moieties resembling the KLHDC2-binding C-degron. Selectivity for BRD3 compared to other BET-family members is further manifested in ubiquitylation in vitro, and prodrug version SJ46420-mediated degradation in cells. Selectivity is also achieved for the ubiquitin ligase, overcoming E3 auto-inhibition to engage KLHDC2, but not the related KLHDC1, KLHDC3, or KLHDC10 E3s. In sum, our study establishes neo-substrate-specific targeted protein degradation via KLHDC2, and provides a framework for developing selective PROTAC protein degraders employing C-degron E3 ligases.
Authors
- Taosheng Chen (ORCID: https://orcid.org/0000-0001-6420-3809)
- Darcie J. Miller (ORCID: https://orcid.org/0000-0003-1202-511X)
- Brenda Arlene Schulman (ORCID: https://orcid.org/0000-0002-3083-1126)
- Ha Won Lee (ORCID: https://orcid.org/0000-0001-5382-9646)
- Daniel C. Scott (ORCID: https://orcid.org/0000-0002-7688-5568)
- Stephen J. Elledge (ORCID: https://orcid.org/0000-0001-7923-6283)
- João A. Paulo (ORCID: https://orcid.org/0000-0002-4291-413X)
- Lei Yang (ORCID: https://orcid.org/0000-0002-3060-0790)
- Rajendra Tangallapally (ORCID: https://orcid.org/0000-0002-8727-2310)
- Jason Ochoada
- J. Wade Harper (ORCID: https://orcid.org/0000-0002-6944-7236)
- Thilina D. Jayasinghe (ORCID: https://orcid.org/0000-0003-3436-0795)
- Sergio C. Chai (ORCID: https://orcid.org/0000-0002-8257-8599)
- Clifford T. Gee (ORCID: https://orcid.org/0000-0001-7181-603X)
- Moeko T. King (ORCID: https://orcid.org/0000-0002-4192-8337)
- Richard Lee (ORCID: https://orcid.org/0000-0002-2397-0443)
- Chan Lee (ORCID: https://orcid.org/0000-0002-5512-8146)
- Suresh Dharuman (ORCID: https://orcid.org/0000-0002-5491-6677)
- Elizabeth C. Griffith
- Victoria C. Loudon
- Jarrid Ronnebaum
- Yong Li
Institutions
- Brigham and Women's Hospital (US)
- St. Jude Children's Research Hospital (US)
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Max Planck Institute of Biochemistry (DE)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-10-12
- DOI
- https://doi.org/10.1038/s41467-024-52966-3
- Citations
- 21
- Primary Topic
- Protein Degradation and Inhibitors
- Type
- article
- Field-Weighted Citation Impact
- 4.91
Funders
- Howard Hughes Medical Institute
- U.S. Department of Energy
- St. Jude Children's Research Hospital
- American Lebanese Syrian Associated Charities
- Max-Planck-Gesellschaft
- National Institutes of Health
- Office of Science
- National Institute on Aging
- National Cancer Institute
- National Institute of General Medical Sciences
- Biological and Environmental Research
- Argonne National Laboratory
- Division of Cancer Epidemiology and Genetics, National Cancer Institute