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

Alexander Chan, Rebecca M. Haley, Mohd Altaf Najar, David Gonzalez-Martinez, Lukasz J. Bugaj, George M. Burslem, Michael J. Mitchell and Andrew Tsourkas ()
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Alexander Chan: University of Pennsylvania
Rebecca M. Haley: University of Pennsylvania
Mohd Altaf Najar: University of Pennsylvania
David Gonzalez-Martinez: University of Pennsylvania
Lukasz J. Bugaj: University of Pennsylvania
George M. Burslem: University of Pennsylvania
Michael J. Mitchell: University of Pennsylvania
Andrew Tsourkas: University of Pennsylvania

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-50235-x

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