Ketoboronate as a Minimal Covalent-Reversible Tag for Targeted Lysosomal Degradation of Extracellular and Membrane Proteins

Extracellular and membrane-associated proteins play essential roles in nearly all our body’s biochemical processes and are implicated in cancer, autoimmune disorders, and neurodegenerative diseases. Consequently, a selective and universally applicable technique for the degradation of these proteins in disease-relevant conditions could significantly improve human health prospects. Lysosome-targeting chimeras (LYTACs) are bifunctional degraders comprising of an antibody conjugated with a cell–surface receptor ligand that enables cargo lysosome shuttling and degradation. Herein, we demonstrate that conjugation of antibodies with a small ketoboronate-based, lysine-reactive, covalent-reversible uptake tag (KB) enables the internalization of plasma membrane and extracellular proteins, directing them to lysosomal degradation via receptor-mediated endocytosis. Chemoproteomic target deconvolution revealed that reversible modification of lysine residues on the transferrin receptor protein 1 (TFRC) and HLA class I histocompatibility antigen A, B and C (HLA-ABC) enabled efficient uptake and lysosomal targeting through both clathrin-dependent and -independent mechanisms. KB-antibody conjugates (KB-TACs) efficiently degrade the epidermal growth factor receptor (EGFR), vascular endothelial growth factor A (VEGFA) and epidermal growth factor receptor 2 (HER2) in cancer cells. Furthermore, we showed KB-TTZ degrades HER2 in vivo in BT-474 tumor xenografts, with a significant reduction in tumor volumes compared to TTZ and vehicle treatments. Altogether, the KB tag represents a versatile, minimal-size chemical unit to functionalize therapeutic antibodies for targeted protein degradation through dual receptor-mediated endocytosis and lysosomal delivery.