Optimizing PepTAC structure and amphiphilicity for enhanced target protein degradation

Project Summary This study seeks to advance heterobifunctional degraders that induce targeted protein degradation through the ubiquitin proteasome pathway. Typically, molecular degraders involve a ligand that recruits an E3 ubiquitin ligase and another that targets a protein of interest (POI), forming an E3:Degrader:POI ternary complex, leading to POI ubiquitination and subsequent degradation by the 26S proteasome. Peptide-based proteolysis targeting chimeras (PepTACs) offer distinct advantages over small molecule degraders for targeting protein-protein interactions due to their specificity, manufacturability, ease of design, and expansive binding surface area. However, due to challenges related to their limited cellular permeability and stability, which is evident in the modest potencies (micromolar range) of recently reported PepTACs, structure-function studies to improve their catalytic activity have not been investigated. We highlight a recent breakthrough where we facilitate PepTAC transport at nanomolar concentrations into cells via lipid nanoparticles (LNPs), establishing a robust platform for our proposed studies. We aim to explore the structural attributes of PepTACs to improve their catalytic activity and enhance target protein degradation. Our hypothesis revolves around modifying PepTAC structure and amphipathicity to improve degradation efficiency, leveraging prior literature showing that small molecule degraders with enhanced ternary complex stability drive greater target protein degradation rates. Our study comprises three key aims: the first focuses on identifying the optimal location of the E3 ligand to create a PepTAC that promotes enhanced positive cooperativity and rapid ubiquitination. The second aim investigates how PepTAC structure impacts LNP loading, stability, and intracellular transport. Finally, our third aim proposes a universal strategy for LNP loading based on tuning PepTAC lipophilicity to enhance LNP encapsulation and systemic stability. Achieving these aims would unlock the potential of PepTACs as valuable tools for cell-specific targeted protein degradation and broadening access to a valuable class of peptide-based protein degraders.