Endobody nanobody-CPP chimeras achieve genetically encodable degradation of membrane and extracellular proteins

Targeted protein degradation (TPD) has revolutionized drug discovery, but most strategies are limited to intracellular proteins. While lysosome-targeting chimeras (LYTACs) extend TPD to membrane and extracellular proteins, their reliance on specific endocytic receptors restricts broad applicability across diverse cell types. There remains a critical need for structurally concise, broadly applicable, and genetically encodable degraders to target disease-relevant membrane and extracellular proteins, particularly those considered undruggable by small molecules, such as the ovarian cancer marker HE4.

Researchers developed a novel class of genetically encodable degraders, nanobody-cell-penetrating peptide (CPP) chimeras, termed Endobodies. They demonstrated that a genetically fused CPP was sufficient to mediate internalization and subsequent degradation of target proteins. The platform was tested for targeted degradation of membrane proteins including EGFR, PD-L1, and HER2 in various cancer cell lines. They also targeted the extracellular protein HE4. To enhance efficacy, a panel of 'enhanced endobodies' was engineered by incorporating an additional proteasome-targeting domain (PTD). The therapeutic potential was further evaluated by assessing EGFR depletion on lung cancer cell proliferation and tumor growth in an in vivo model.

Endobody nanobody-CPP chimeras successfully mediated the internalization and subsequent degradation of both membrane and extracellular proteins. Targeted degradation was achieved for membrane proteins including EGFR, PD-L1, and HER2 in cancer cells. Importantly, the previously undruggable serum HE4, a key ovarian cancer marker, was also effectively depleted. The study also showcased the ability to simultaneously degrade both extracellular and membrane proteins using a bispecific endobody. Enhanced endobodies, incorporating a proteasome-targeting domain (PTD), resulted in more robust degradation. > Notably, EGFR depletion by an enhanced endobody significantly suppressed lung cancer cell proliferation and tumor growth in vivo, demonstrating therapeutic potential.