Small molecule fluorochromes (synonyms: biosensors, chemosensors, fluorescent probes, vital stains) are widely used to investigate the structure, composition, physicochemical properties and biological functions of living cells, tissues and organisms. Selective entry and accumulation within particular cells and cellular structures are key processes for achieving these diverse objectives. Despite the complexities, probes routinely are applied using standard protocols, often without experimenter awareness of what factors that control accumulation and localization. The mechanisms of many such selective accumulations, however, now are known. Moreover, the influence of physicochemical properties of probes on their uptake and localization often can be defined numerically, hence predicted, using quantitative structure activity relations (QSAR) models with its required numerical structure parameters (or “descriptors”). The state of the art of this approach is described. Available QSAR models are summarized for uptake into cells and localization in the cytosol, endoplasmic reticulum, generic biomembranes, Golgi apparatus, lipid droplets, lysosomes/endosomes, mitochondria, eukaryotic nuclei (histones and DNA), plasma membrane, and ribosomal RNA (cytoplasmic and nucleolar). Integration of such core models to both aid understanding and troubleshooting of current fluorescent probes and to assist the design of novel probes is outlined and illustrated using case examples. Limitations and generic problems arising with this approach and comments on application of such approaches to xenobiotics other than probes, e.g., drugs and herbicides, together with a brief note about an alternative approach to prediction, are given.

The basis of the selectivity of fluorochromes routinely used to visualize the endoplasmic reticulum (ER) in live cells remains obscure. To clarify this, interactions of living cells with fluorochromes of varied physicochemical properties were analyzed experimentally and numerically using a quantitative structure activity relationship analysis (QSAR). Routine selective ER probes were found to be amphipathic, lipophilic cations with moderate-sized conjugated systems. The moderately lipophilic character permits probe uptake by passive diffusion without nonspecific accumulation in biomembranes. The moderately amphipathic character favors uptake into the ER, perhaps owing to its high concentration of zwitterionic lipid head-groups. The QSAR model rationalizes the impractical character of some ER probes mentioned in the literature, and could permit design of novel ER probes with different emission colors. The possibility of using the QSAR model as a tool to predict the accumulation of xenobiotics in the ER of living cells is illustrated by the localization of certain antipsychotic drugs in cultured cells.