Next-Gen Targeted Protein Degradation: Directing Disease Proteins to the Proteasome

The ubiquitin-proteasome system (UPS) is crucial for maintaining diverse cellular functions through the selective degradation of proteins. Targeted Protein Degradation (TPD) has emerged as an innovative therapeutic strategy that harnesses the UPS to selectively degrade disease-causing proteins. A major advancement in TPD is the use of proteolysis-targeting chimeras (PROTACs), small molecules that bind both an E3 ligase (E3) and the target protein, to induce ubiquitination and subsequent degradation of the target. While PROTACs have shown promise, their reliance on E3s poses challenges, including tissue-specific expression of E3s, the requirement for accessible ubiquitination sites on target proteins, and potential resistance mechanisms due to E3 mutations. Furthermore, only a small subset of E3s has been successfully utilized for TPD.To address these challenges, this ERC PoC project explores an alternative approach: direct targeting of proteins to the proteasome for degradation, bypassing the need for ubiquitination. This strategy eliminates reliance on specific E3s and provides a broader, universal approach for proteolysis. During our ERC StG project, using cutting-edge proteomics technology, we identified short peptide motifs that when fused to target proteins, can promote their ubiquitin-independent proteasomal degradation (UbInPD). These findings present a novel opportunity to design PROTACs that directly recruit targets to the proteasome, bypassing the traditional limitations of E3-based systems.Here, we aim to develop PROTACs incorporating UbInPD short peptide motifs to enhance TPD of model disease-associated proteins, such as the androgen receptor and BRD proteins, for cancer treatment. This approach could significantly broaden the scope of targetable proteins, opening up new avenues for drug discovery. Successful outcomes could lead to groundbreaking therapeutic applications and establish novel, ubiquitin-independent TPD strategies in precision medicine.