Structure‐Guided Development of Chemically Tailored Peptide Binders of RNF43/ZNRF3 to Enable Versatile Design of Membrane Protein‐Targeting PROTACs

Abstract Targeted membrane protein degradation using cell surface E3 ligases RNF43/ZNRF3 via proteolysis targeting chimeras (PROTACs) represents an effective strategy for treating membrane drug targets that cannot be fully inhibited using traditional inhibitors. Several ingenious chimeras have been developed to tether RNF43/ZNRF3 to target membrane proteins, resulting in the degradation of targets at sub‐nanomolar concentrations both in vitro and in vivo. However, currently available RNF43/ZNRF3 binders are genetically encoded and have poor plasticity, which limits the design and promotion of such PROTACs. Here, we exploited the AlphaFold‐predicted complex structures of ligand‐bound RNF43/ZNRF3 and developed a class of chemically tailored peptide binders for ZNRF3/RNF43. With these peptide binders that can be conveniently prepared by de novo peptide synthesis, we established a new membrane protein degradation platform that allows versatile modular design and targeted degradation of clinically relevant membrane proteins, i.e., PD‐L1 and EGFR. This study presents a new subtype within the PROTAC field to develop therapeutic peptides targeting membrane proteins.