cIAP1-based degraders induce degradation via branched ubiquitin architectures

Area of Science:

• Biochemistry
• Molecular Biology
• Precision Medicine

Background:

• Targeted protein degradation using proteolysis-targeting chimeras (PROTACs) is a promising precision medicine strategy.
• E3 ubiquitin ligases and the resulting ubiquitin code dictate substrate fate.
• While CRL2^VHL and CRL4^CRBN are common E3s in PROTACs, the full ubiquitin code diversity for chemical degradation remains unexplored.

Purpose of the Study:

• To investigate the role of the E2 enzyme UBE2N and specific ubiquitin linkages in the efficacy of cIAP1-targeting degraders.
• To elucidate the mechanism by which UBE2N influences protein degradation and cancer cell apoptosis.
• To explore the broader implications for the ubiquitin code diversity in chemical hijacking strategies.

Main Methods:

• Utilized cIAP1-targeting degraders and ligands to induce protein degradation.
• Assessed the dependence on the E2 enzyme UBE2N for degradation and apoptosis.
• Analyzed the types of ubiquitin chains formed (K63, K48, K11) and their role in recruiting downstream degradation machinery (p97/VCP, UCH37, proteasome).

Main Results:

• The efficacy of cIAP1-targeting degraders was found to be dependent on the K63-specific E2 enzyme UBE2N.
• UBE2N promotes the degradation of cIAP1 and subsequent cancer cell apoptosis.
• UBE2N facilitates the formation of complex K48/K63 and K11/K48 branched ubiquitin chains, essential for recruiting the proteasome.
• Degradation of neo-substrates by cIAP1-recruiting PROTACs also requires UBE2N.

Conclusions:

• Revealed an unexpected critical role for K63-linked ubiquitin chains and UBE2N in degrader-induced proteasomal degradation.
• Demonstrated the significant diversity of the ubiquitin code utilized in chemical hijacking approaches.
• Highlights UBE2N as a key player in the efficacy of certain targeted protein degradation strategies.