Even in the first-generation labeling systems, organocatalytic acylation reactions through protein-ligand interaction demonstrated their usefulness for site-specific modification of target proteins for live cells and tissue samples (Scheme 15A). The seminal work of the organocatalytic bioconjugation was by Hamachi and co-workers, which demonstrated acylation of a glycoprotein-binding protein, lectin with a dialkylaminopyridinebased catalyst (i.e., dimethylaminopyridine or DMAP-type catalyst, Scheme 15B). The DMAP catalyst was tethered with saccharide-ligand, and thiophenyl esters were employed as acyl donors for the site-specific labeling of lectins. By the virtue of proximity-driven effects, target proteins can be selectively modified even in the presence of other proteins (e.g., in cell and tissue lysates). In addition to saccharide ligands, the DMAPbased catalyst can be conjugated to proteins that bind to protein targets; for instance, DMAP-tethered lectin was utilized for the labeling of glycoproteins on live cell surfaces. As a similar approach, a DMAP-tethered antibody fragment was developed to selectively modify receptors on cell membranes, which enabled epitope mapping of antibodies. Another early example of ligand-directed catalysts is an organocatalyst based on dimethylalkylamine tethered with biotin, which was used for modification of carboxyl groups of aspartate and glutamate residues of avidin. More efficient catalysis at physiological pH than the firstgeneration DMAP-based catalysis was demonstrated with anionic catalysts and thiol-based catalysts with milder acyl donors (Scheme 15B). One of the challenges in the DMAP catalysis is that pKa of the conjugate acid of the DMAP-based moiety is 8.6, 228 and substantial portions of the catalyst could be protonated at physiological pH ranges. To this end, pyrydinium oximes and hydroxamic acids were proposed as alternatives because of their lower pKas (6.6 230 and 6.5 , respectively) that could allow faster protein labeling than DMAP at physiological pH. Thiol-based catalysts possess additional benefits, compared to DMAP-based catalysts, that are kinetically favorable thiol-thioester exchange between the catalyst and the acyl donor. As an independent approach from the thiol-based catalysis, Kanai and co-workers developed a unique proximity-driven approach through reversible boronate formation to facilitate the organocatalytic modification for site-specific modification of target within live cells (Scheme 15B). 229 Such a range of the second-generation catalysts allowed the use of moderate electrophilic acyl donors (e.g., acetyl-CoA) compared to the one used with DMAP-based catalysts (thioesters derived from thiophenol), attenuating off-target labeling. For example, in the DMAP-based catalysis, the reaction usually requires a low temperature (e.g., 4 °C) to minimize the nonspecific labeling arising from the high electrophilicity of the thioester acyl donor. Therefore, the use of milder acyl donors such as N-acyl-N-alkyl sulfonamides, 227 alkyl thioesters, and acyl imidazoles 236 can be beneficial through suppression of the labeling agents' off-target reactivities. A notable application of the second-generation approach is that a hydroxamic acid-thiolbased catalyst conjugated with histone-ligand has been used for acylation of lysine-120 (K120) of histone H2B with endogenous acyl-CoA as an acyl donor. Since acetylation of lysine residues of histone proteins is a naturally occurring post-translational modification that regulates gene expression (epigenetic regulation), 237 this approach could be useful for the chemical manipulation of the epigenetic regulation of gene expression.