Predicting small molecule fluorescent probe localization in living cells using QSAR modeling. 2. Specifying probe, protocol and cell factors; selecting QSAR models; predicting entry and localization

Abstract

We describe the practical issues and the methodological procedures that must be carried out to construct and use QSAR models for predicting localization of probes in single cells. We address first the determination of probe factors starting with a consideration of the chemical nature of probe molecules present. What is their identity? Do new compounds arise in incubation media or intracellularly? For each probe, how many distinct chemical species are present? For each probe species, the derivation of the following numerical structure parameters, or descriptors, is set out with worked examples of electric charge and acid/base strength (Z and pKa); hydrophilicity/lipophilicity (log P); amphiphilicity (AI and HGH); conjugated bond number and largest conjugated fragment (CBN and LCF); width and length (W and L); and molecular and ionic weights, head group size and substituent bulk (MW, IW, HGS and SB). Next, protocol factors are specified by focusing separately on the mode of introduction of the probe to the cells, other application phenomena, and factors that influence directly observations of outcomes. Cell factors then are specified by considering separately structural and functional aspects. The next step is to select appropriate QSAR models and to integrate probe, protocol and cell factors to predict the interactions of the probe with the cell. Finally, we use an extended case example to explore the intracellular localization of certain photodynamic therapy dyes to illustrate these procedures.

Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe

“…Through cell imaging experiments, we confirmed that only IMT could stain DNA G-quadruplexes in the nucleus, while other probes mainly stain nucleoli. Differences in the localization of these probes within the cells may involve a variety of factors (58,59), such as the water/octanol partition coefficient (log P ), substituent bulk parameter and differential fluorescence identification of DNA and RNA G-quadruplexes. IMT is almost non-fluorescent before binding to a target molecule or after binding to single/double-stranded nucleic acids, but exhibits over 200-fold fluorescence enhancement after binding with G-quadruplexes.…”

“…Since IMT does not show a significant difference in fluorescence after binding to the G-quadruplex structures of DNA and RNA, theoretically the fluorescence foci derived from the labeling of RNA G-quadruplexes should be observed in the cytoplasm. According to the quantitative structure activity relations (QSAR) models (58,59), the physicochemical characteristics of a probe molecule determine its localization within the cells. As a permanent cationic species, the physicochemical characteristics of IMT make it more likely to localize to the nuclear chromatin rather than the cytoplasm.…”

Massive Bioaccumulation and Self‐Assembly of Phenazine Compounds in Live Cells

“…For each species, structure parameter values, as estimated above, were inserted into published QSAR models predicting cell uptake and intracellular localizations. [22] The poor-moderate-good predictions in Tables S1, S3 and S5 in the supporting information relate to the log P of the major species present, usually the free base, as follows:…”

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

“…Thus, when the values of certain physicochemical properties of a dye are available (see [98] for procedures), and are expressed as numerical structure parameters (AI, CBN, HGH, HGS, LCF, log P, pK a , SB, W/L, Z), then insertion of these values into simple QSAR models (see [40] for a summary) allows the prediction of dye exclusion from, or uptake into, living eukaryotic cells. Similarly, if dye uptake into live cells occurs, then additional simple QSAR models, summarised in [40], can predict many subcellular dye accumulation sites (e.g.…”