Engineering Covalent Aptamer Chimeras for Enhanced Autophagic Degradation of Membrane Proteins

Targeted degradation of membrane proteins represents an attractive strategy for eliminating pathogenesis‐related proteins. Aptamer‐based chimeras hold great promise as membrane protein degraders, however, their degradation efficacy is often hindered by the limited structural stability and the risk of off‐target effects due to the non‐covalent interaction with target proteins. We here report the first design of a covalent aptamer‐based autophagosome‐tethering chimera (CApTEC) for the enhanced autophagic degradation of cell‐surface proteins, including transferrin receptor 1 (TfR1) and nucleolin (NCL). This strategy relies on the site‐specific incorporation of sulfonyl fluoride groups onto aptamers to enable the cross‐linking with target proteins, coupled with the conjugation of an LC3 ligand to hijack the autophagy‐lysosomal pathway for targeted protein degradation. The chemically engineered CApTECs exhibit enhanced on‐target retention and improved structural stability. Our results also demonstrate that CApTECs achieve remarkably enhanced and prolonged degradation of membrane proteins compared to the non‐covalent designs. Furthermore, the CApTEC targeting TfR1 is combined with 5‐fluorouracil (5‐FU) for synergistic tumor therapy in a mouse model, leading to substantial suppression of tumor growth. Our strategy may provide deep insights into the LC3‐mdiated autophagic degradation, affording a modular and effective strategy for membrane protein degradation and precise therapeutic applications.