Ligand‐Directed Chemistry for Protein Labeling for Affinity‐Based Protein Analysis

Abstract Structural and functional analyses of proteins‐of‐interest (POI) in multimolecular crowding conditions (mMCC) such as live cells and tissues are regarded as inevitable challenges for in depth understanding of the real shapes of POIs in their existing natural environments. Activity‐based protein profiling (ABPP) is a definitely powerful tool capable of analyzing a proteome possessing a particular activity under mMCC. While ABPP usually targets a proteome of interest, study of a particular protein in mMCC is also valuable. Although activity‐based probes (ABPs) are often used for this aim, most of conventional ABPs cause the loss of original activities, and therefore are not perfectly suitable for functional analysis of labeled proteins. Ligand‐directed chemistry (LDchem) developed by our group is an alternative approach of ABPs, that can modify a surface of POI rather than its active site using a cleavable electrophile in a traceless manner. LDchem thus enables the POI labeling with a synthetic fluorophore with no or minimal effects on the original functions of POIs even in mMCC. In this review, we briefly describe a principle of LDchem for native protein labeling and summarize its recent chemical biology applications such as the imaging‐based biological analysis of POI functions and construction of POI‐based biosensors.