Carbohydrate-Directed Labeling Probes for UV-Independent Chemoproteomic Profiling of Carbohydrate-Protein Interactions.

Weak and transient carbohydrate-protein interactions hinder the detection of carbohydrate-binding proteins (CBPs) in native settings. Here, we introduce carbohydrate-directed labeling probes (CDLPs), modular ligand-directed covalent probes composed of a glycan ligand, an acyl-transfer electrophile, and a distal azide handle. Glycan binding positions the electrophile for proximity-enhanced, glycan-releasing acyl transfer, leaving an azide-bearing acyl tag on the protein. Benchmark CDLPs capture carbohydrate-protein interactions with monovalent KD values extending into the millimolar range. In Daudi B cells, a 6'-sialyllactose CDLP preferentially captures CD22 (Siglec-2), demonstrating glycan-dependent labeling in live cells. Quantitative chemoproteomics using 6'-sialyllactose- and lactose-CDLPs yields complementary competition-sensitive CDLP-capture profiles (6'SL-CDLP: 95; Lac-CDLP: 113; 21 shared), including canonical CBPs, glycan-processing proteins, and candidate proteins lacking prior glycan-related annotations. CDLPs provide an accessible, UV-independent route to durable covalent readouts for targeted validation and proteome-scale candidate discovery.