Aptamer-Mediated Covalent Dual Lysosome-Targeting Chimeras Enhance Targeted Degradation of Cell Surface Proteins

Aptamer-based lysosome-targeting chimeras (Apt-LYTACs) have emerged as a promising strategy for the selective degradation of cell surface proteins by linking a target-specific aptamer to a lysosome-trafficking receptor ligand. However, their degradation efficiency is often limited by weak noncovalent interactions, heterogeneous receptor distribution, and the constraints of a 1:1 complex stoichiometry. To address these challenges, we developed aptamer-mediated covalent dual lysosome-targeting chimeras (Apt-cdLYTACs), which enable specific covalent anchoring to the protein of interest with spatiotemporal control by combining the specificity of aptamer recognition with proximity-induced photoreactive cross-linking. These chimeras incorporate two lysosomal receptor ligands to enhance the local avidity and promote multivalent complex formation. Compared to conventional noncovalent or single-ligand covalent Apt-LYTAC, Apt-cdLYTAC forms more stable degradation complexes, exhibits prolonged intracellular retention, and reduces efflux, thereby significantly improving degradation efficiency. Apt-cdLYTAC provides a modular, efficient, and user-friendly platform for the selective degradation of membrane proteins, with broad potential for applications in biochemical research and therapeutic development.