Proximity labelling-based identification of vascular homing peptide receptors

Identifying the receptors of vascular homing peptides (VHPs) is critical for mechanistic understanding and development of peptide-guided precision therapeutics. Conventional receptor discovery methods, such as affinity chromatography, require cell disruption and often expose intracellular proteins, resulting in high background and low specificity. To overcome these limitations, we developed a proximity labelling approach that tags proteins near VHP receptors on intact live cells. Cells were incubated with VHP–horseradish peroxidase (HRP) complexes, which, upon hydrogen peroxide treatment, activate biotin-tyramide to produce short-lived radicals that covalently label nearby membrane proteins. Using the prototypic C-end Rule peptide RPARPAR and its known receptor neuropilin-1 (NRP-1), we validated this method by successful receptor tagging and mass spectrometric identification. Using RPARPAR–HRP conjugates, we achieved selective proximity labeling of membrane proteins in NRP-1–positive PPC1 cells, with a 3- to 5-fold increase in fluorescence intensity over controls by flow cytometry. Affinity purification and Western blotting identified a strong ∼130 kDa band corresponding to NRP-1 exclusively in labeled PPC1 cells. Mass spectrometry analysis revealed a ∼20-fold enrichment of NRP-1 and significant enrichment of integrins (ITGAV, ITGB1, ITGA3), ALCAM, EPHA2, CD109, and PLXNB2 in RPARPAR-labeled samples compared to controls. This approach could be broadly used for molecular mapping of the homing peptide interactome and its spatial proximity in live cells, streamlining the discovery of homing peptide receptors and their associated partners.