Predicting the phospholipophilicity of monoprotic positively charged amines

Using membrane-water partition coefficients in a critical membrane burden approach to aid the identification of neutral and ionizable chemicals that induce acute toxicity below narcosis levels

The risk assessment of thousands of chemicals used in our society benefits from adequate grouping of chemicals based on the mode and mechanism of toxic action (MoA). We measure the phospholipid membrane-water distribution ratio (D_MLW) using a chromatographic assay (IAM-HPLC) for 121 neutral and ionized organic chemicals and screen other methods to derive D_MLW. We use IAM-HPLC based D_MLW as a chemical property to distinguish between baseline narcosis and specific MoA, for reported acute toxicity endpoints on two separate sets of chemicals. The first set comprised 94 chemicals of US EPA's acute fish toxicity database: 47 categorized as narcosis MoA, 27 with specific MoA, and 20 predominantly ionic chemicals with mostly unknown MoA. The narcosis MoA chemicals clustered around the median narcosis critical membrane burden (CMB_narc) of 140 mmol kg^-1 lipid, with a lower limit of 14 mmol kg^-1 lipid, including all chemicals labelled Narcosis_I and Narcosis_II. This maximum 'toxic ratio' (TR) between CMB_narc and the lower limit narcosis endpoint is thus 10. For 23/28 specific MoA chemicals a TR >10 was derived, indicative of a specific adverse effect pathway related to acute toxicity. For 10/12 cations categorized as "unsure amines", the TR <10 suggests that these affect fish via narcosis MoA. The second set comprised 29 herbicides, including 17 dissociated acids, and evaluated the TR for acute toxic effect concentrations to likely sensitive aquatic plant species (green algae and macrophytes Lemna and Myriophyllum), and non-target animal species (invertebrates and fish). For 21/29 herbicides, a TR >10 indicated a specific toxic mode of action other than narcosis for at least one of these aquatic primary producers. Fish and invertebrate TRs were mostly <10, particularly for neutral herbicides, but for acidic herbicides a TR >10 indicated specific adverse effects in non-target animals. The established critical membrane approach to derive the TR provides for useful contribution to the weight of evidence to bin a chemical as having a narcosis MoA or less likely to have acute toxicity caused by a more specific adverse effect pathway. After proper calibration, the chromatographic assay provides consistent and efficient experimental input for both neutral and ionizable chemicals to this approach.

Human Apparent Volume of Distribution Predicts Bioaccumulation of Ionizable Organic Chemicals in Zebrafish Embryos

Chemicals with elevated bioaccumulation profiles present potential hazards to public health and the environment. Ionizable organic compounds (IOCs) increasingly represent a large proportion of commercial chemicals; however, historical approaches for bioaccumulation determinations are mainly developed for neutral chemicals, which were not appropriate for IOCs. Herein, we employed the zebrafish embryo, a common vertebrate model in environmental and biomedical studies, to elucidate toxicokinetics and bioconcentration of eight IOCs with diverse physicochemical properties and pharmacokinetic parameters. At an environmentally relevant pH (7.5), most IOCs exhibited rapid uptake and depuration in zebrafish, suggesting the ionized forms of IOCs are readily bioavailable. Bioconcentration factors (BCF) of these IOCs ranged from 0.0530 to 250 L·kg^-1 wet weight. The human pharmacokinetic proportionality factor, apparent volume of distribution (V_D), better predicted the BCF of selected IOCs than more commonly used hydrophobicity-based parameters (e.g., pH-dependent octanol-water distribution ratio, D_ow). Predictive bioaccumulation models for IOCs were constructed and validated using V_D alone or with D_ow. Significant relationships between fish BCF and human V_D, which is readily available for pharmaceuticals, highlighted the utility of biologically based "read-across" approaches for predicting bioaccumulative potential of IOCs. Our novel findings thus provided an understanding of the partitioning behavior and improved predictive bioconcentration modeling for IOCs.

Concentration of Antioxidant Compounds from Calendula officinalis through Sustainable Supercritical Technologies, and Computational Study of Their Permeability in Skin for Cosmetic Use

The growing interest in the cosmetic industry in using compounds of natural and sustainable origin that are safe for humans is encouraging the development of processes that can satisfy these needs. Chlorogenic acid (CHA), caffeic acid (CAF) and ferulic acid (FA) are three compounds widely used within the cosmetic industry due to their functionalities as antioxidants, collagen modifiers or even as radiation protectors. In this work, two advanced separation techniques with supercritical CO2 are used to obtain these three compounds from Calendula officinalis, and these are then evaluated using a computational skin permeability model. This model is encompassed by the COSMO-RS model, the calculations of which make it possible to study the behaviour of the compounds in the epidermis. The results show that both CAF and FA are retained in the stratum corneum, while CHA manages to penetrate to the stratum spinosum. These compounds were concentrated by antisolvent fractionation with super-critical CO2 using a Response Surface Methodology to study the effect of pressure and CO2 flow rate. CHA, CAF and FA were completely retained in the precipitation vessel, with concentrations between 40% and 70% greater than in the original extract. The conditions predicted that the optimal overall yield and enrichment achieved would be 153 bar and 42 g/min.

Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning

With a view to high-throughput simulations, we present an automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field. The method scales to larger molecules and a broader chemical space than existing schemes. The core of the mapping process is a graph-based analysis of the molecule's bonding network, which has the advantages of being fast, general, and preserving symmetry. The parameterization process pays special attention to coarse-grained beads in aromatic rings. It also includes a method for building efficient and stable frameworks of constraints for molecules with structural rigidity. The performance of the method is tested on a diverse set of 87 neutral organic molecules and the ability of the resulting models to capture octanol-water and membrane-water partition coefficients. In the latter case, we introduce an adaptive method for extracting partition coefficients from free-energy profiles to take into account the interfacial region of the membrane. We also use the models to probe the response of membrane-water partitioning to the cholesterol content of the membrane.

Tissue Distribution of Several Series of Cationic Surfactants in Rainbow Trout (Oncorhynchus mykiss) Following Exposure via Water

Bioaccumulation assessment is important for cationic surfactants in light of their use in a wide variety of consumer products and industrial processes. Because they sorb strongly to natural surfaces and to cell membranes, their bioaccumulation behavior is expected to differ from other classes of chemicals. Divided over two mixtures, we exposed rainbow trout to water containing 10 alkyl amines and 2 quaternary alkylammonium surfactants for 7 days, analyzed different fish tissues for surfactant residues, and calculated the tissues' contribution to fish body burden. Mucus, skin, gills, liver, and muscle each contributed at least 10% of body burden for the majority of the test chemicals. This indicates that both sorption to external surfaces and systemic uptake contribute to bioaccumulation. In contrast to the analogue alkylamine bases, the permanently charged quaternary ammonium compounds accumulated mostly in the gills and were nearly absent in internal tissues, indicating that systemic uptake of the charged form of cationic surfactants is very slow. Muscle-blood distribution coefficients were close to 1 for all alkyl amines, whereas liver-blood distribution coefficients ranged from 13 to 90, suggesting that the dominant considerations for sorption in liver are different from those in blood and muscle. The significant fraction of body burden on external surfaces can have consequences for bioaccumulation assessment.

Development of liposome/water partition coefficients predictive models for neutral and ionogenic organic chemicals

Membrane/water partition coefficient (K_m/w) is a vital parameter used to characterize the membrane permeability of compounds. Considering the K_m/w value is difficult to observe experimentally for real biological membranes, liposome/water partition coefficient (K_lip/w) is employed to approximate K_m/w. Here, quantitative structure property relationship (QSPR) models for logK_lip/w of the neutral organic chemicals and the neutral form of ionogenic organic chemicals (IOCs) (logK_{lip/w-neutral}), ionic form of IOCs (logK_lip/w-ionic), the speciation-corrected liposome-water distribution ratios at a pH = 7.40 (logD_{lip/w-(pH=7.40)}) were developed. In the modeling, two modeling methods (multiple linear regressions (MLR) and k-nearest neighbor (kNN)) were used. The predictive variables employed here could be calculated from the molecular structure directly. For logK_{lip/w-neutral} and logD_{lip/w-(pH=7.40)}, the logK_OW and logD_OW-based, non-logK_OW and non-logD_OW-based kNN-QSPR and MLR-QSPR models were developed, respectively. The evaluation results implied that the predictive performance of kNN-QSPR models is better than that of MLR-QSPR models. For logK_lip/w-ionic, only one acceptable MLR-QSPR model was developed for cation and anion, respectively. The model quality of the derived models was evaluated following the OECD QSPR models validation guideline. The determination coefficient (R²), leave-one-out cross validation Q² (Q²_LOO) and bootstrapping coefficient (Q²_BOOT), the external validation coefficient (Q²_EXT) of all the models met the acceptable criteria (Q² > 0.600, R² > 0.700); while the root-mean-square error (RMSE) range from 0.351 to 0.857. All the results implied that the models had good goodness-of-fit, robustness and predictive ability. Therefore, the developed models could be used to fill the data gap for substances within the applicability domain on their missing logK_{lip/w-neutral}, logK_lip/w-ionic, logD_{lip/w-(pH=7.40)} values.

In Silico Prediction of the Thermodynamic Equilibrium of Solute Partition in Multiphase Complex Fluids: A Case Study of Oil-Water Microemulsion

Multiphase complex fluids such as micelles, microemulsions, and dispersions are ubiquitous in product formulations of foods, pharmaceuticals, cosmetics, and fine chemicals. Quantifying how active solutes partition in the microstructure of such multiphase fluids is necessary for designing formulations that can optimally deliver the benefits of functional actives. In this paper, we at first predict the structure of a heptane/butanol/sodium dodecyl sulfate droplet in water that self-assembled to form a microemulsion through the molecular dynamics (MD) simulation and subsequently investigate the thermodynamic equilibrium of solute partitioning using COSMOmic. To our knowledge, this is the first time that the MD/COSMOmic approach is used for predicting solute partitioning in a microemulsion. The predicted partition coefficients are compared to experimental values derived from retention measurements of the same microemulsion. We show that the experimental data of droplet-water partition coefficients (K_droplet/w) can be reliably predicted by the method that combines MD simulations with COSMOmic.

Does the Lipid Bilayer Orchestrate Access and Binding of Ligands to Transmembrane Orthosteric/Allosteric Sites of G Protein-Coupled Receptors?

The ligand-binding sites of many G protein-coupled receptors (GPCRs) are situated around and deeply embedded within the central pocket formed by their seven transmembrane-spanning α-helical domains. Generally, these binding sites are assumed accessible to endogenous ligands from the aqueous phase. Recent advances in the structural biology of GPCRs, along with biophysical and computational studies, suggest that amphiphilic and lipophilic molecules may gain access to these receptors by first partitioning into the membrane and then reaching the binding site via lateral diffusion through the lipid bilayer. In addition, several crystal structures of class A and class B GPCRs bound to their ligands offer unprecedented details on the existence of lipid-facing allosteric binding sites outside the transmembrane helices that can only be reached via lipid pathways. The highly organized structure of the lipid bilayer may direct lipophilic or amphiphilic drugs to a specific depth within the bilayer, changing local concentration of the drug near the binding site and affecting its binding kinetics. Additionally, the constraints of the lipid bilayer, including its composition and biophysical properties, may play a critical role in "pre-organizing" ligand molecules in an optimal orientation and conformation to facilitate receptor binding. Despite its clear involvement in molecular recognition processes, the critical role of the membrane in binding ligands to lipid-exposed transmembrane binding sites remains poorly understood and warrants comprehensive investigation. Understanding the mechanistic basis of the structure-membrane interaction relationship of drugs will not only provide useful insights about receptor binding kinetics but will also enhance our ability to take advantage of the apparent membrane contributions when designing drugs that target transmembrane proteins with improved efficacy and safety. In this minireview, we summarize recent structural and computational studies on membrane contributions to binding processes, elucidating both lipid pathways of ligand access and binding mechanisms for several orthosteric and allosteric ligands of class A and class B GPCRs.

Membrane-Water Partition Coefficients to Aid Risk Assessment of Perfluoroalkyl Anions and Alkyl Sulfates

This study determined the sorption affinity to artificial phospholipid membranes ( K_MW) for series of perfluorinated carboxylates (PFCAs), perfluorinated sulfonates (PFSAs), alkyl sulfates (C _xSO₄), and 1-alkanesulfonates (C _xSO₃). A sorbent dilution assay with solid supported lipid membranes (SSLM) showed consistent CF₂ unit increments of 0.59, and CH₂ unit increments of 0.53, for the log K_MW of perfluorinated and hydrogenated anions, respectively. PFSAs sorbed 0.90 log units stronger than analogue PFCAs; C _xSO₄ sorbed 0.75 log units stronger than analogue C _xSO₃ anions. The log K_MW values for the octyl analogues increase in the order H(CH₂)₈SO₃^- (1.74) < H(CH₂)₈SO₄^- (2.58) < F(CF₂)₈CO₂^- (PFNA, 4.04) < F(CF₂)₈SO₃^- (PFOS, 4.88). Intrinsic partition ratios determined on a phospholipid coated HPLC column (IAM-HPLC) closely aligned with SSLM K_MW values. COSMO-RS based molecular calculations of K_MW aligned with SSLM K_MW values for hydrogenated anions with C₈-C₁₄ alkyl chains but strongly underestimated CF₂ and CH₂ unit increments for C₄-C₈ based anions. Dividing the critical narcotic membrane burden of 100 mmol/kg by the experimental K_MW predicts lethal baseline toxicity concentrations (LC_50,narc). The LC_50,narc coincides with the lowest reported acute LC₅₀ values for several anionic surfactants but were on average about an order of magnitude lower.