Where do dyes go inside living cells? Predicting uptake, intracellular localisation, and accumulation using QSAR models

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Uptake of dyes into living cells and organisms is of concern to several diverse groups of people. These include those not wishing dyes to enter cells (e.g. manufacturers and users of textile dyes, or laboratory workers using dyes as analytical reagents) and those requiring dye entry (e.g. biologists imaging cell contents, or clinicians using photoactive dyes as antitumour drugs). This diversity results in the need to consider an extremely wide range of dyes – and indeed of cells and organisms. An overview of methods for predicting uptake and intracellular localisation is provided, followed by a more detailed account of the concepts and procedures involved in decision‐rule quantitative structure–activity relationship (QSAR) models. Some of these models permit the prediction of which dyes are likely to enter cells, and which dyes will be excluded. Other models predict where internalised dyes will localise within the live cells. Use of QSAR models to understand intracellular accumulation, redistribution, loss from the cell, and metabolic modification of dyes is also considered. In particular, the relationship of such predictions to toxicity is discussed. An extended case example is provided, describing the modelling of dye binding to nucleic acids in single‐cell systems. A further case example then illustrates dye localisation in multicellular organisms. Finally, conclusions, critiques, and probable future directions concerning the QSAR modelling approach to dye uptake and localisation are given. A summary of key QSAR decision rules in the form of decision logic tabulations is provided.