Endobody: Genetically Encodable Nanobody-CPP Chimeras for Degradation of Membrane and Extracellular Proteins

Membrane protein degraders (MPDs) like LYTACs are emerging tools for targeting disease-relevant membrane proteins, but their reliance on specific endocytic receptors limits their applicability across diverse cell types. Here, we present a structurally concise and genetically encodable class of degraders, nanobody-cell-penetrating peptide (CPP) chimeras, termed endobodies. We demonstrated that a genetically fused CPP is sufficient to mediate the internalization and subsequent degradation of membrane or extracellular proteins recognized by the nanobody. Using this platform, we achieved targeted degradation of membrane proteins including EGFR, PD-L1, and HER2 in cancer cells. Importantly, the undruggable serum HE4, an ovarian cancer marker which could not be addressed by small-molecule degraders, was also effectively depleted. Additionally, we first showcased the possibility to simultaneously degrade both extracellular and membrane proteins using a bispecific endobody. To further eliminate endosomal escapees, we engineered a panel of enhanced endobodies incorporating an additional proteasome-targeting domain (PTD), resulting in more robust degradation. Notably, EGFR depletion by an enhanced endobody suppressed lung cancer cell proliferation and tumor growth in vivo. Collectively, endobody is an innovative class of MPDs, offering promising therapeutic potential.