Chemical reactions for the ligand-directed modification of native proteins

Selective modifications of native proteins provide powerful opportunities to study and manipulate biological systems, yet achieving site-selective functionalization remains challenging due to the surfeit of competing amino acids, often addressed by genetic engineering of target proteins. Ligand-directed protein modification addresses these limitations by exploiting reversible molecular recognition to position reactive groups in proximity to a defined protein site, thereby enabling selective covalent modification of native proteins under physiological conditions. Importantly, ligand-directed protein modification is evolving from a specialized labeling methodology into a versatile platform for the selective manipulation of protein function in native biological environments. In this review, we discuss recent advances in ligand-directed strategies that employ synthetically accessible small molecules and peptides as recognition elements. Current approaches are categorized into (i) ligation reactions, in which the ligand remains attached to the protein, (ii) transfer reactions, which install a functional moiety while releasing the ligand, and (iii) ligand-directed catalysis, where ligand-tethered catalysts promote protein-substrate reactions with catalytic turnover. For each strategy, employed chemical reactions, amino acid selectivities, and applications in chemical biology and biotechnology are described. We further compare the strengths and limitations of these approaches considering the balance between reactivity, selectivity, and biocompatibility.