Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins

• Published in: Nature communications Vol. 15; no. 1; pp. 5808 - 21
• Main Authors: Chan, Alexander, Haley, Rebecca M., Najar, Mohd Altaf, Gonzalez-Martinez, David, Bugaj, Lukasz J., Burslem, George M., Mitchell, Michael J., Tsourkas, Andrew
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.07.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 13/106; 13/109; 13/31; 14/1; 14/35; 631/1647/338; 631/45/474; 631/61/2297; 82/16; 82/29; 82/58; 82/80; 82/83; Animals; Biocompatibility; Biodegradation; Chimeras; Cytosol; Cytosol - metabolism; Degradation; Drug Delivery Systems; Electrostatic properties; Humanities and Social Sciences; Humans; Intracellular; Lipids; Lipids - chemistry; Liposomes; Membranes; Mice; Modular design; multidisciplinary; Nanoparticles; Nanoparticles - chemistry; Permeability; Pharmacology; Proteins; Proteolysis; Proteolysis - drug effects; Recombinant Proteins - metabolism; Science; Science (multidisciplinary); Substrate specificity; Substrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50235-x

Recently, targeted degradation has emerged as a powerful therapeutic modality. Relying on “event-driven” pharmacology, proteolysis targeting chimeras (PROTACs) can degrade targets and are superior to conventional inhibitors against undruggable proteins. Unfortunately, PROTAC discovery is limited by warhead scarcity and laborious optimization campaigns. To address these shortcomings, analogous protein-based heterobifunctional degraders, known as bioPROTACs, have been developed. Compared to small-molecule PROTACs, bioPROTACs have higher success rates and are subject to fewer design constraints. However, the membrane impermeability of proteins severely restricts bioPROTAC deployment as a generalized therapeutic modality. Here, we present an engineered bioPROTAC template able to complex with cationic and ionizable lipids via electrostatic interactions for cytosolic delivery. When delivered by biocompatible lipid nanoparticles, these modified bioPROTACs can rapidly degrade intracellular proteins, exhibiting near-complete elimination (up to 95% clearance) of targets within hours of treatment. Our bioPROTAC format can degrade proteins localized to various subcellular compartments including the mitochondria, nucleus, cytosol, and membrane. Moreover, substrate specificity can be easily reprogrammed, allowing modular design and targeting of clinically-relevant proteins such as Ras, Jnk, and Erk. In summary, this work introduces an inexpensive, flexible, and scalable platform for efficient intracellular degradation of proteins that may elude chemical inhibition. Targeted degradation has emerged as a powerful therapeutic modality. In this study, the authors develop a lipid-based platform to deliver recombinant bioPROTACs into cells for targeted protein degradation, providing a platform for efficient intracellular degradation of proteins that may elude chemical inhibition.