Noncovalent (reversible) drug–protein binding interactions are an integral part of intermolecular recognition processes taking place in a cell or organ environment. Characterization of basic constraints of target protein binding site(s) (affinity, stoichiometry, specificity, saturability and stereoselectivity) for particular ligand(s) is an essential output of many different drug–protein binding studies. Nonlinear and stereoselective binding phenomena, including drug–drug (or enantiomer–enantiomer) interactions and their e.g. genetically or pathophysiologically determined variability, can be predicted in this way. In general, the methods used for drug–protein binding studies can be divided into separation (nonspectroscopic) and spectroscopic methods. Separation methods are particularly suitable for the quantitative determination of drug binding, whereas spectroscopic techniques are able to characterize the qualitative features of drug–protein complexes (e.g. conformational status/changes). The primary objective was to summarize the most relevant trends in separation techniques [affinity high‐performance liquid chromatography (HPLC) and affinity capillary electrophoresis (ACE)] employed in the framework of drug–protein/biopolymer binding assays and to compare them with so‐called conventional approaches (equilibrium dialysis (ED), ultrafiltration). Focused attention has been paid particularly to HPLC and capillary electrophoresis (CE) methods designed for drug–protein studies when so‐called “dynamic” and “secondary” equilibria are involved and created. A common feature of this strategy is to use binding protein(s) or interacting drug(s) without their covalent immobilization as mobile phase or background electrolyte (BGE) (buffer) additives. This offered a new, elegant tool for the separation of “bound” and “free” forms of interacting species in a “miniaturized free solution system” operating under nearly physiological conditions. Undoubtedly, it permits simplification of the experimental protocols where it is crucial to perform repetitive analyses under “the same starting conditions”, as e.g. the occupancy of binding sites is concerned.
