Why fluorescent probes for endoplasmic reticulum are selective: an experimental and QSAR-modelling study

Abstract

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.

Fluorescent cationic probes for nuclei of living cells: why are they selective? A quantitative structure–activity relations analysis

“…Expressed quantitatively, all cationic probes staining nuclei had log P cation values in the range À5 to 0. This contrasts markedly with cationic probes for endoplasmic reticulum (Colston et al 2003), and also probes for mitochondria (Rashid and Horobin 1990;Trapp and Horobin 2005), which are lipophilic cations with log P cation values falling in the range 0 to +5, with the former group also being amphipathic. Cationic probes of the plasma membrane may also be distinguished from nuclear probes using the log P cation parameter, as the former are superlipophilic with log P cation values>+8 (Rashid et al 1991;Ormerod 1994).…”

“…We will now use the above discussion-with the important conclusion that probe selectivity is controlled both by competition between accumulation sites and by high affinity binding to DNA-plus models for uptake and intracellular distribution of probes summarized or reported in Colston et al (2003), Horobin (2001) and Stockert et al (2004), to provide an overall QSAR model for specifying the physicochemical properties of selective nuclear probes. This will address the properties required for entry (or non-entry) into the cell, as well as the subsequent competition between organelles for the probe.…”

A Cheminformatic Toolkit for Mining Biomedical Knowledge

“…Quantitative structure-property relationships and mechanistic models have been developed for studying the intracellular distribution of molecules in different organelles inside cells (117,126,127,(140)(141)(142)(143)(144)(145), and for predicting the ability of small molecules to traverse cell monolayers and intracellular membranes (42,64,(118)(119)(120)(121)(122)(123)(124)(125)(146)(147)(148)(149). Many QSAR models for predicting membrane passage, intracellular accumulation and absorption have been published over the years, and can be compiled into a comprehensive database (73).…”

A QSAR‐modeling perspective on cationic transfection lipids. 1. Predicting efficiency and understanding mechanisms

“…Again these values imply that the compounds insert into membranes. The precise values are also of interest, since data derived from fluorescent probes (many of which are cationic) suggest that, although accumulation in most biomembranes increases substantially at AI >+5, strong binding requires an AI >+8 [32,57]. Confirmation of the importance of the mixing of the effective cationic lipids into membranes is provided by modeling cationic lipid headgroup size, using the HGS parameter.…”