The pH-dependence of efflux ratios determined with bidirectional transport assays across cellular monolayers.

MDCK/Caco-2 assays serve as essential in vitro tools for evaluating membrane permeability and active transport, especially mediated by P-glycoprotein (P-gp). Despite their utility, challenges remain in quantifying active transport and using the efflux ratio (ER) to determine intrinsic values for active efflux. Such an intrinsic value for P-gp facilitated efflux necessitates knowing whether this transporter transports the neutral or ionic species of a compound.

Predicting the intrinsic membrane permeability of Caco-2/MDCK cells by the solubility-diffusion model.

Membrane permeability is one of the main determinants for the absorption, distribution, metabolism and excretion of compounds and is therefore of crucial importance for successful drug development. Experiments with artificial phospholipid membranes have shown that the intrinsic membrane permeability (P) of compounds is well-predicted by the solubility-diffusion model (SDM). However, using the solubility-diffusion model to predict the P of biological Caco-2 and MDCK cell membranes has proven unreliable so far.

Effects of Aqueous Boundary Layers and Paracellular Transport on the Efflux Ratio as a Measure of Active Transport Across Cell Layers.

The efflux ratio (ER), determined by Caco-2/MDCK assays, is the standard in vitro metric to establish qualitatively whether a compound is a substrate of an efflux transporter. However, others have also enabled the utilisation of this metric quantitatively by deriving a relationship that expresses the ER as a function of the intrinsic membrane permeability of the membrane (P0) as well as the permeability of carrier-mediated efflux (Ppgp). As of yet, Ppgp cannot be measured directly from transport experiments or otherwise, but the ER relationship provides easy access to this value if P0 is known.

Pitfalls in evaluating permeability experiments with Caco-2/MDCK cell monolayers.

When studying the transport of molecules across biological membranes, intrinsic membrane permeability (P) is more informative than apparent permeability (P), because it eliminates external (setup-specific) factors, provides consistency across experiments and mechanistic insight. It is thus an important building block for modeling the total permeability in any given scenario. However, extracting P is often difficult, if not impossible, when the membrane is not the dominant transport resistance.

Revisiting the pK-Flux method for determining intrinsic membrane permeability.

Intrinsic membrane permeability is one of several factors that critically determine the intestinal absorption of a chemical. The intrinsic membrane permeability of a chemical is usually extracted from transwell experiments with Caco-2 or MDCK cells, preferably by the pK-Flux method, which is considered the method of choice when aqueous boundary layer effects need to be excluded. The pK-Flux method has two variants, the iso-pH method, where apical and basolateral pH are equal, and the gradient-pH method, where apical and basolateral pH are different.

Mechanistic modeling of the bioconcentration of (super)hydrophobic compounds in Hyalella azteca.

Bioconcentration tests using the freshwater amphipod Hyalella azteca as an alternative to conventional fish tests have recently received much attention. An appropriate computational model of H. azteca could help in understanding the mechanisms behind bioconcentration, in comparison to the fish as test organism.

Impact of cholesterol and sphingomyelin on intrinsic membrane permeability.

Transwell experiments with Caco-2 or MDCK cells are the gold standard for determining the intestinal permeability of chemicals. The intrinsic membrane permeability (P), that can be extracted from these experiments, might be comparable to P measured in black lipid membrane (BLM) experiments and P predicted by the solubility-diffusion model. Unfortunately, the overlap between experimental P and P data is very small.

Screening of 6000 Compounds for Uncoupling Activity: A Comparison Between a Mechanistic Biophysical Model and the Structural Alert Profiler Mitotox.

Protonophoric uncoupling of phosphorylation is an important factor when assessing chemicals for their toxicity, and has recently moved into focus in pharmaceutical research with respect to the treatment of diseases such as cancer, diabetes, or obesity. Reliably identifying uncoupling activity is thus a valuable goal. To that end, we screened more than 6000 anionic compounds for in vitro uncoupling activity, using a biophysical model based on ab initio COSMO-RS input parameters with the molecular structure as the only external input.

Exploring the octanol-water partition coefficient dataset using deep learning techniques and data augmentation.

Today more and more data are freely available. Based on these big datasets deep neural networks (DNNs) rapidly gain relevance in computational chemistry. Here, we explore the potential of DNNs to predict chemical properties from chemical structures.

Could chemical exposure and bioconcentration in fish be affected by slow binding kinetics in blood?

The possible implications of slow binding kinetics on respiratory uptake, bioconcentration and exposure of chemicals were evaluated in the present study. Most physiological and chemical information needed for such an evaluation is already known from the literature or can be estimated. However, data for binding kinetics of chemicals in fish plasma have not been reported in the literature yet.

Relevance of desorption kinetics and permeability for in vitro-based predictions of hepatic clearance in fish.

The impact of desorption kinetics and permeation kinetics on in vitro-based predictions of in vivo hepatic blood clearances is investigated in the present study. Most commonly, possible limitations due to slow desorption of chemicals from albumin or slow permeation of chemicals through cellular membranes are not considered when in vivo clearances are predicted from in vitro biotransformation rate constants. To evaluate whether the most commonly used extrapolation models might thus overlook important kinetic limitations, we compare predictions of in vivo clearance that explicitly consider desorption and permeation kinetics with predictions of in vivo clearance that neglect these aspects.

Prediction of Unbound Fractions for - Extrapolation of Biotransformation Data.

For - extrapolation of biotransformation data, the different sorptive environments and need to be considered. The most common approach for doing so is using the ratio of unbound fractions and . In the literature, several algorithms for prediction of these unbound fractions are available.

Yolk Sac of Zebrafish Embryos as Backpack for Chemicals?

The zebrafish embryo () has developed into one of the most important nonsentient animal models for the hazard assessments of chemicals, but the processes governing its toxicokinetics (TK) are poorly understood. This study compares the uptake of seven test compounds into the embryonic body and the yolk sac of the zebrafish embryo using TK experiments, a dialysis approach, thermodynamic calculations, and kinetic modeling. Experimental data show that between 95% (4-iodophenol) and 67% (carbamazepine) of the total internal amount in 26 h post fertilization (hpf) embryos and between 80 and 49% in 74 hpf embryos were found in the yolk.

Predicting Uncoupling Toxicity of Organic Acids Based on Their Molecular Structure Using a Biophysical Model.

We present a purely mechanistic model to predict protonophoric uncoupling activity EC of organic acids. All required input information can be derived from their chemical structure. This makes it a convenient predictive model to gain valuable information on the toxicity of organic chemicals already at an early stage of development of new commercial chemicals (e.

Comparison of a simple and a complex model for BCF prediction using in vitro biotransformation data.

A promising approach for bioaccumulation assessment with reduced animal use is the prediction of bioconcentration factors (BCFs) using in vitro biotransformation data. However, it has been recognized that the BCFs predicted using current models often are in poor agreement with experimental BCFs. Furthermore, extrahepatic biotransformation (e.

Yolk-Water Partitioning of Neutral Organic Compounds in the Model Organism Danio rerio.

Yolk is the most important temporary biological compartment of the early life stages of fish embryos. The sorption strength of a chemical to yolk components may significantly influence the distribution of that chemical in the fish embryo. We determined yolk-water partition coefficients (K , in liters of water per kilogram of yolk, normalized to dry wt) for 70 neutral organic chemicals.

COSMO Mechanistic Prediction of Passive Membrane Permeability for Neutral Compounds and Ions and Its pH Dependence.

We present a new and entirely mechanistic COSMO method to predict passive membrane permeabilities for neutral compounds, as well as anions and cations. The COSMO approach is based on compound-specific free energy profiles within a membrane of interest from COSMO-RS (conductor-like screening model for realistic solvation) calculations. These are combined with membrane layer-specific diffusion coefficients, for example, in the water phase, the polar head groups, and the alkyl tails of biochemical phospholipid bilayers.

Environmental Sorption Behavior of Ionic and Ionizable Organic Chemicals.

Traditionally our tools for environmental risk assessment of organic chemicals have been developed for neutral chemicals. However, many commercial chemicals are ionic or ionizable and require different tools and approaches for their assessment. In recent years this task starts to obtain increasing attention but our understanding for their environmental fate is still far behind that for neutral chemicals.

The physical chemistry of odors - Consequences for the work with detection dogs.

Search dogs are used throughout the world in the search for illicit compounds or human individuals and similar tasks. Such search work is complex and not well understood in all its details which makes training of the dogs difficult. One important component for a successful education and deployment of search dogs is a good understanding of the behavior of scents under typical environmental conditions.

Predicting the Gas/Particle Distribution of SVOCs in the Indoor Environment Using Poly Parameter Linear Free Energy Relationships.

Understanding the partitioning of semi volatile organic compounds (SVOCs) between gas phase and particle phase is essential for exposure analysis and risk assessment in the indoor environment. Numerous attempts have been made to calculate gas/particle partitioning coefficients K. Single-parameter adsorption and absorption models, which relate K to the vapor pressure P or the octanol/air distribution coefficient K are usually applied.