Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients

Aquatic toxicity, bioaccumulation potential, and human estrogen/androgen activity of three oxo-Liquid Organic Hydrogen Carrier (oxo-LOHC) systems

The Liquid Organic Hydrogen Carrier (LOHC) technology offers a technically attractive way for hydrogen storage. If LOHC systems were to fully replace liquid fossil fuels, they would need to be handled at the multi-million tonne scale. To date, LOHC systems on the market based on toluene or benzyltoluene still offer potential for improvements. Thus, it is of great interest to investigate potential LOHCs that promise better performance and environmental/human hazard profiles. In this context, we investigated the acute aquatic toxicity of oxygen-containing LOHC (oxo-LOHC) systems. Toxic Ratio (TR) values of oxo-LOHC compounds classify them baseline toxicants (0.1 < TR < 10). Additionally, the mixture toxicity test conducted with D. magna suggests that the overall toxicity of a benzophenone-based system can be accurately predicted using a concentration addition model. The estimation of bioconcentration factors (BCF) through the use of the membrane-water partition coefficient indicates that oxo-LOHCs are unlikely to be bioaccumulative (BCF < 2000). None of the oxo-LOHC compounds exhibited hormonal disrupting activities at the tested concentration of 2 mg/L in yeast-based reporter gene assays. Therefore, the oxo-LOHC systems seem to pose a low level of hazard and deserve more attention in ongoing studies searching for the best hydrogen storage technologies.

Building Chemical Intuition about Physicochemical Properties of C8-Per-/Polyfluoroalkyl Carboxylic Acids through Computational Means

We have predicted acid dissociation constants (pK a), octanol-water partition coefficients (K OW), and DMPC lipid membrane-water partition coefficients (K lipid-w) of 150 different eight-carbon-containing poly-/perfluoroalkyl carboxylic acids (C8-PFCAs) utilizing the COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) theory. Different trends associated with functionalization, degree of fluorination, degree of saturation, degree of chlorination, and branching are discussed on the basis of the predicted values for the partition coefficients. In general, functionalization closest to the carboxylic headgroup had the greatest impact on the value of the predicted physicochemical properties.

Partitioning into phosphatidylcholine-cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation

Membrane-water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field. The methodology is general and can also be used for other applications where coarse-grained simulations are appropriate. This article addresses the effect on membrane-water partitioning of adding cholesterol to POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Nine contrasting neutral, zwitterionic and charged solutes are tested. Agreement between experiment and simulation is generally good, with the most challenging cases being permanently charged solutes. For all solutes, partitioning is found to be insensitive to membrane cholesterol concentration up to 25% mole fraction. Hence, for assessment of bioaccumulation into a range of membranes (such as those found in fish), partitioning data measured in pure lipid membranes are still informative.

In Silico Prediction of Stratum Corneum Partition Coefficients via COSMOmic and Molecular Dynamics Simulations

Stratum corneum (SC) is the main barrier of human skin where the inter-corneocytes lipids provide the main pathway for transdermal permeation of functional actives of skin care and health. Molecular dynamics (MD) has been increasingly used to simulate the SC lipid bilayer structure so that the barrier property and its affecting factors can be elucidated. Among reported MD simulation studies, solute partition in the SC lipids, an important parameter affecting SC permeability, has received limited attention. In this work, we combine MD simulation with COSMOmic to predict the partition coefficients of dermatologically relevant solutes in SC lipid bilayer. Firstly, we run MD simulations to obtain equilibrated SC lipid bilayers with different lipid types, compositions, and structures. Then, the simulated SC lipid bilayer structures are fed to COSMOmic to calculate the partition coefficients of the solutes. The results show that lipid types and bilayer geometries play a minor role in the predicted partition coefficients. For the more lipophilic solutes, the predicted results of solute partition in SC lipid bilayers agree well with reported experimental values of solute partition in extracted SC lipids. For the more hydrophilic molecules, there is a systematical underprediction. Nevertheless, the MD/COSMOmic approach correctly reproduces the phenomenological correlation between the SC lipid/water partition coefficients and the octanol/water partition coefficients. Overall, the results show that the MD/COSMOmic approach is a fast and valid method for predicting solute partitioning into SC lipids and hence supporting the assessment of percutaneous absorption of skin care ingredients, dermatological drugs as well as environmental pollutants.

Penetration of Perfluorooctanesulfonate Isomers and Their Alternatives from Maternal Blood to Milk and Its Associations with Chemical Properties and Milk Primary Components

Perfluorooctanesulfonate (PFOS) and its alternatives, including chlorinated polyfluorinated ether sulfonates (Cl-PFESAs), are mainly detected per- and polyfluoroalkyl substances (PFAS) in human samples such as milk. However, the mechanism of their blood to milk transfer was not well studied. Here, 145 paired maternal serum and human milk samples were analyzed for six PFOS isomers and Cl-PFESAs to evaluate the transfer efficiency from maternal serum to human milk (TE_HM/MS). Besides physicochemical properties, this study for the first time evaluated the influencing effects of the primary components in human milk (carbohydrate, lipid, and protein) on TE_HM/MS of PFAS. No significant association was observed between TE_HM/MS and the albumin binding affinity of the compounds (p = 0.601), but TE_HM/MS was significantly negatively correlated with the logarithmic octanol-water partition coefficients (r² = 0.853, p = 0.001), the logarithmic membrane-water partition coefficients (r² = 0.679, p = 0.012), and the carbohydrate contents in human milk. The effect of carbohydrate was further confirmed using in vitro tests. The negative associations between TE_HM/MS and hydrophobicity, membrane passive permeability, and the carbohydrate content in human milk consistently indicated that passive diffusion through the paracellular route might be the main transfer pathway for PFOS and Cl-PFESAs from blood to milk in humans.

Partition of the Reactive Species of the Suzuki-Miyaura Reaction between Aqueous and Micellar Environments

The Suzuki-Miyaura reaction between the aryl halide (1) and the phenyl boronic acid (2), in the presence of the palladium(0) complex (3) as catalyst, gives the cross-coupling product (4) in quantitative yield when performed in basic aqueous solution of the nonionic surfactant Kolliphor-EL (K-EL). The partition between the aqueous and micellar environments of the species of this reaction has been investigated by means of Molecular Dynamics (MD) simulations. Starting from the K-EL molecules dispersed in water, a micelle model has been generated by MD simulations, adopting the 2016H66 force field. Reagent and product species have been described with the same force field, once the reliability of this force field has been tested comparing the n-octanol/water partition free energies calculated from the MD and Free Energy Perturbation (FEP) method with those obtained from the quantum-mechanical SMD method. The potential of mean force for the transfer process between water and the micellar phase of the different species has been calculated by the MD simulations and the Umbrella Sampling (US) method. The overall picture that emerges from these results confirms that the molecular species involved in this reaction prefers the micellar environment and concentrates in different but close zones of the micelle. This supports the experimental evidence that the use of suitable surfactant agents promotes reactivity, allowing micelles to behave as nanoreactors in which reactive species are solubilized and enhance their local concentration.

Quantum chemical calculation of the vapor pressure of volatile and semi volatile organic compounds

The vapor pressure is a specific and temperature-dependent parameter that describes the volatility of a substance and thus its driving force for evaporation or sublimation into the gas phase. Depending on the magnitude of the vapor pressure, there are different methods for experimental determination. However, these are usually associated with a corresponding amount of effort and become less accurate as the vapor pressure decreases. For purposes of vapor pressure prediction, algorithms were developed that are usually based on quantitative structure-activity relationships (QSAR). The quantum mechanical (QM) approach followed here applies an alternative, much less empirical strategy, where the change in Gibbs free energy for the transition from the condensed to the gas phase is obtained from conformer ensembles computed for each phase separately. The results of this automatic, so-called CRENSO workflow are compared with experimentally determined vapor pressures for a large set of environmentally relevant compounds. In addition, comparisons are made with the single structure-based COSMO-RS QM approach, linear-free-energy relationships (LFER) as well as results from the SPARC program. We show that our CRENSO workflow is superior to conventional prediction models and provides reliable vapor pressures for liquids and sub-cooled liquids over a wide pressure range.

Evaluation of Constrained and Restrained Molecular Dynamics Simulation Methods for Predicting Skin Lipid Permeability

Recently, molecular dynamics (MD) simulations have been utilized to investigate the barrier properties of human skin stratum corneum (SC) lipid bilayers. Different MD methods and force fields have been utilized, with predicted permeabilities varying by few orders of magnitude. In this work, we compare constrained MD simulations with restrained MD simulations to obtain the potential of the mean force and the diffusion coefficient profile for the case of a water molecule permeating across an SC lipid bilayer. Corresponding permeabilities of the simulated lipid bilayer are calculated via the inhomogeneous solubility diffusion model. Results show that both methods perform similarly, but restrained MD simulations have proven to be the more robust approach for predicting the potential of the mean force profile. Critical to both methods are the sampling of the whole trans-bilayer axis and the following symmetrization process. Re-analysis of the previously reported free energy profiles showed that some of the discrepancies in the reported permeability values is due to misquotation of units, while some are due to the inaccurately obtained potential of the mean force. By using the existing microscopic geometrical models via the intercellular lipid pathway, the permeation through the whole SC is predicted from the MD simulation results, and the predicted barrier properties have been compared to experimental data from the literature with good agreement.

Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca

Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$d_{3}$$\end{document}d3 mixture. The structure is defined by an \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\alpha$$\end{document}α-helix that spans between Ile\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{6}$$\end{document}6-Ala\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{26}$$\end{document}26, and a cyclic disulfide-bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide’s interactions with sodium dodecyl sulfate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\alpha$$\end{document}α-helical conformation between residues Ile\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{6}$$\end{document}6-Ala\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{26}$$\end{document}26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.

Biophysical study of the structure and dynamics of the antimicrobial peptide maximin 1

Maximin 1 is a cationic, amphipathic antimicrobial peptide found in the skin secretions and brains of the Chinese red belly toad Bombina maxima. The 27 amino acid residue-long peptide is biologically interesting as it possesses a variety of biological activities, including antibacterial, antifungal, antiviral, antitumour and spermicidal activities. Its three-dimensional structural model was obtained in a 50/50% water/2,2,2-trifluoroethanol-d₃ mixture using two-dimensional NMR spectroscopy. Maximin 1 was found to adopt an α-helical structure from residue Ile² to Ala²⁶ . The peptide is amphipathic, showing a clear separation between polar and non-polar residues. The interactions with sodium dodecyl sulfate micelles, a widely-used bacterial membrane-mimicking environment, were modelled using molecular dynamics simulations. The peptide maintains an α-helical conformation, occasionally displaying a flexibility around the Gly⁹ and Gly¹⁶ residues, which is likely responsible for the peptide's low haemolytic activity. It is found to preferentially adopt a position parallel to the micellar surface, establishing a number of hydrophobic and electrostatic interactions with the micelle.

Chemical computational approaches for optimization of effective surfactants in enhanced oil recovery

The surfactant flooding becomes an attractive method among several Enhanced Oil Recovery (EOR) processes to improve the recovery of residual oil left behind in the reservoir after secondary oil recovery process. The designing of a new effective surfactant is a comparatively complex and often time consuming process as well as cost-effective due to its dependency on the crude oil and reservoir properties. An alternative chemical computational approach is focused in this article to optimize the performance of effective surfactant system for EOR. The molecular dynamics (MD), dissipative particle dynamics (DPD) and density functional theory (DFT) simulations are mostly used chemical computational approaches to study the behaviour in multiple phase systems like surfactant/oil/brine. This article highlighted a review on the impact of surfactant head group structure on oil/water interfacial property like interfacial tensions, interface formation energy, interfacial thickness by MD simulation. The effect of entropy in micelle formation has also discussed through MD simulation. The polarity, dipole moment, charge distribution and molecular structure optimization have been illustrated by DFT. A relatively new coarse-grained method, DPD is also emphasized the phase behaviour of surfactant/oil/brine as well as polymer-surfactant complex system.

Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators

Quorum sensing (QS) is a bacterial communication process mediated by both native and non-native small-molecule quorum sensing modulators (QSMs), many of which have been synthesized to disrupt QS pathways. While structure-activity relationships have been developed to relate QSM structure to the activation or inhibition of QS receptors, less is known about the transport mechanisms that enable QSMs to cross the lipid membrane and access intracellular receptors. In this study, we used atomistic MD simulations and an implicit solvent model, called COSMOmic, to analyze the partitioning and translocation of QSMs across lipid bilayers. We performed umbrella sampling at atomistic resolution to calculate partitioning and translocation free energies for a set of naturally occurring QSMs, then used COSMOmic to screen the water-membrane partition and translocation free energies for 50 native and non-native QSMs that target LasR, one of the LuxR family of quorum-sensing receptors. This screening procedure revealed the influence of systematic changes to head and tail group structures on membrane partitioning and translocation free energies at a significantly reduced computational cost compared to atomistic MD simulations. Comparisons with previously determined QSM activities suggest that QSMs that are least likely to partition into the bilayer are also less active. This work thus demonstrates the ability of the computational protocol to interrogate QSM-bilayer interactions which may help guide the design of new QSMs with engineered membrane interactions.

Synergistic Computational Modeling Approaches as Team Players in the Game of Solubility Predictions

Several approaches to predict and model drug solubility have been used in the drug discovery and development processes during the last decades. Each of these approaches have their own benefits and place, and are typically used as standalone approaches rather than in concert. The synergistic effects of these are often overlooked, partly due to the need of computational experts to perform the modeling and simulations as well as analyzing the data obtained. Here we provide our views on how these different approaches can be used to retrieve more information on drug solubility, ranging from multivariate data analysis over thermodynamic cycle modeling to molecular dynamics simulations. We are discussing aqueous solubility as well as solubility in more complex mixed solvents and media with colloidal structures present. We conclude that the field of computational pharmaceutics is in its early days but with a bright future ahead. However, education of computational formulators with broad knowledge of modeling and simulation approaches is imperative if computational pharmaceutics is to reach its full potential.

Hg-supported phospholipid monolayer as rapid screening device for low molecular weight narcotic compounds in water

This study positions the fabricated Pt/Hg-supported phospholipid sensor element in the context of more conventional biomembrane-based screening platforms. The technology has been used together with immobilised artificial membrane (IAM) chromatography and COSMOmic simulation methods to screen the interaction of a series of low molecular weight narcotic organic compounds in water with phosphatidylcholine (PC) membranes. For these chemicals it is shown that toxicity to aquatic species is related to compound hydrophobicity which is associated with compound accumulation in the phospholipid membrane as modelled by IAM chromatography measurements and COSMOmic simulations. In contrast, the Hg-supported dioleoyl phosphatidylcholine (DOPC) sensor element records membrane damage/modification which is indirectly related to general toxicity and directly related to compound structure. Electrochemical limit of detection (LoD) values depend on molecular structure and range from 20 μmolL^-1 for substituted phenols to 23 mmolL^-1 for aliphatics. Rapid cyclic voltammetry (RCV) "fingerprints" showed that the major structural classes of compounds: alkyl/chlorobenzenes, substituted phenols, quaternary ammonium compounds and neutral amines interacted distinctively with the DOPC on Hg and that these observations correlated with and supported those predicted by the COSMOmic simulations of the compound/DMPC association. In addition, the compatibility of the electrochemical and COSMOmic methods validates the electrochemical device as a meaningful high throughput technology to screen compounds in water and report on the mechanistic details of their interaction with phospholipid layers.

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.

Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning

In this review we will discuss how computational methods, and in particular classical molecular dynamics simulations, can be used to calculate solubility of pharmaceutically relevant molecules and systems. To the extent possible, we focus on the non-technical details of these calculations, and try to show also the added value of a more thorough and detailed understanding of the solubilization process obtained by using computational simulations. Although the main focus is on classical molecular dynamics simulations, we also provide the reader with some insights into other computational techniques, such as the COSMO-method, and also discuss Flory-Huggins theory and solubility parameters. We hope that this review will serve as a valuable starting point for any pharmaceutical researcher, who has not yet fully explored the possibilities offered by computational approaches to solubility calculations.

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.

COSMOplex: self-consistent simulation of self-organizing inhomogeneous systems based on COSMO-RS

During the past 20 years, the efficient combination of quantum chemical calculations with statistical thermodynamics by the COSMO-RS method has become an important alternative to force-field based simulations for the accurate prediction of free energies of molecules in liquid systems. While it was originally restricted to homogeneous liquids, it later has been extended to the prediction of the free energy of molecules in inhomogeneous systems such as micelles, biomembranes, or liquid interfaces, but these calculations were based on external input about the structure of the inhomogeneous system. Here we report the rigorous extension of COSMO-RS to a self-consistent prediction of the structure and the free energies of molecules in self-organizing inhomogeneous systems. This extends the application range to many new areas, such as the prediction of micellar structures and critical micelle concentrations, finite loading effects in micelles and biomembranes, the free energies and structure of liquid interfaces, microemulsions, and many more related topics, which often are of great practical importance.

Accessing lipophilicity of drugs with biomimetic models: A comparative study using liposomes and micelles

Lipophilicity is a physicochemical property of crucial importance in drug discovery and drug design. Biomimetic models, such as liposomes and micelles, constitute a valuable tool for the assessment of lipophilicity through the determination of partition coefficients (log K_p). However, the lack of standardization hampers the judgment about which model or method has the best and broadest passive drug permeation predictive capacity. This work provides a comparative analysis between the methodologies based on biomimetic models to determine the partition coefficient (log K_p). For that purpose, a set of reference substances preconized by the Organization for Economic Cooperation and Development (OECD) guidelines was used. The biomimetic models employed were liposomes and micelles composed by 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) and hexadecylphosphocholine (HePC), respectively. Both lipids were used as representative phospholipids of natural membranes. The partition coefficients between biomimetic models and aqueous phases were determined by derivative spectroscopy at physiological conditions (37 °C and pH 7.4). The partition coefficients obtained using biomimetic models are quite different and more reliable than the ones obtained using an octanol/water system. Comparing the performance of the two biomimetic models, micelles revealed to be suitable only for substances with high molar absorption coefficient and log K_p > 3, but in general liposomes are the best model for accessing lipophilicity of drugs. Furthermore, a comparison between experimental data and the partition coefficients determined by the computational method COSMOmic is also provided and discussed. As a final summarizing result, a decision tree is provided in order to guide the selection of a tool for assessing the lipophilicity of drugs.

Diffusion of energetic compounds through biological membrane: Application of classical MD and COSMOmic approximations

Computational studies of the potential biological impact of several energetic compounds were performed. The most commonly used explosives were considered in the present studies: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,4-dinitroanisole (DNAN), and 5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The effect of such factors as ionic strength and presence of DMSO in the water solution on the structure of the membrane were considered using the POPC lipid bilayer as an example. Molecular dynamics (MD) simulations revealed that, even on a short-time scale, the influence of those additives is noticeable, and therefore those factors should always be taken into account. The MD and the COSMOmic approaches were used to elucidate the ability of the energetic compounds to penetrate the living cell. Calculated free energy profiles and partitioning coefficients revealed distributions of the compounds in the lipid bilayer as well as an overall ability to enter the cell. MD in this case provides a better representation of the free energy profile, while the COSMOmic approach works better to predict log(K_lipw) values. The effect of the functional group was observed for the profiles that were obtained using the MD method.

Micellization and Partition Equilibria in Mixed Nonionic/Ionic Micellar Systems: Predictions with Molecular Models

In practical applications, surfactant solutions are mostly used in mixtures of nonionic and ionic surfactants because they have improved characteristics compared to those of single surfactant solutions. By adjusting the composition of the micelles and the pH value, the solubilization of solutes can be enhanced. Nevertheless, the partitioning of solutes between nonionic/ionic mixed micelles and the aqueous phase is studied to a much lesser extent than for single surfactant solutions. Theoretical methods to predict partition equilibria in mixed micelles are of interest for screening studies. For those, the composition of the mixed micelle has to be known. Here we investigate mixtures of TX-114 (Triton X-114), Brij35 (C12E23), SDS (sodium dodecyl sulfate), and CTAB (cetyltrimethylammonium bromide). First, to investigate the surfactant compositions in the micelles, molecular dynamics (MD) self-assembly simulations were applied. Thereafter, the predictive COSMO-RS model, which applies the pseudophase approach, and its extension to anisotropic systems termed COSMOmic were compared for the prediction of partition equilibria in mixed micelles, where various molar ratios of the surfactants were considered. It could be demonstrated that both methods are applicable and lead to reasonable predictions for neutral molecules. However, taking into account the three-dimensional structure of the micelle is beneficial because the calculations with COSMOmic are in better agreement with experimental results. Because the partitioning behavior of ionizable molecules in mixed micelles is of particular interest, the partitioning of ionized isovanillin in mixed Brij35/CTAB micelles at different micelle compositions was calculated with COSMOmic. Using a thermodynamic cycle, the position-dependent pK_a of isovanillin within the micelle is calculated on the basis of COSMOmic free energy profiles. As a result, the protolytic equilibrium of isovanillin within the micelles can be taken into account, which is crucial for the reliable prediction of partition coefficients.

Predicting the phospholipophilicity of monoprotic positively charged amines

The sorption affinity of eighty-six charged amine structures to phospholipid monolayers (log K_IAM) was determined using immobilized artificial membrane high-performance liquid chromatography (IAM-HPLC). The amine compounds covered the most prevalent types of polar groups, widely ranged in structural complexity, and included forty-seven pharmaceuticals, as well as several narcotics and pesticides. Amine type specific corrective increments were used to align log K_IAM data with bilayer membrane sorption coefficients (K_MW(IAM)). Using predicted sorption affinities of neutral amines, we evaluated the difference (scaling factor Δ_MW) with the measured log K_MW(IAM) for cationic amines. The Δ_MW values were highly variable, ranging from -2.37 to +2.3 log units. For each amine type, polar amines showed lower Δ_MW values than hydrocarbon based amines (C_xH_yN⁺). COSMOmic software was used to directly calculate the partitioning coefficient of ionic structures into a phospholipid bilayer (K_{DMPC-W,cation}), including quaternary ammonium compounds. The resulting root mean square error (RMSE) between log K_{DMPC-W,cation} and log K_MW(IAM) was 0.83 for all eighty-six polar amines, and 0.47 for sixty-eight C_xH_yN⁺ amines. The polar amines were then split into five groups depending on polarity and structural complexity, and corrective increments for each group were defined to improve COSMOmic predictions. Excluding only the group with sixteen complex amine structures (≥4 polar groups, M_w > 400, including several macrolide antibiotics), the resulting RMSE for corrected K_{DMPC-W,cation} values improved to 0.45 log units for the remaining set of 138 polar and C_xH_yN⁺ amines.

Phospholipophilicity of CxHyN(+) amines: chromatographic descriptors and molecular simulations for understanding partitioning into membranes

Using immobilized artificial membrane high-performance liquid chromatography (IAM-HPLC) the sorption affinity of 70 charged amine structures to phospholipids was determined. The amines contained only 1 charged moiety and no other polar groups, the rest of the molecule being aliphatic and/or aromatic hydrocarbon groups. We systematically evaluated the influence of the amine type (1°, 2°, 3° amines and quaternary ammonium), alkyl chain branching, phenyl ring positioning, charge positioning (terminal vs. central in the molecule) on the phospholipid-water partitioning coefficient (KPLIPW). These experimental results were compared with quantum-chemistry based three-dimensional (3D) molecular simulations of the partitioning of charged amines, including the most likely solute conformers, using a hydrated phospholipid bilayer in the COSMOmic module of COSMOtherm software. Both IAM-HPLC retention data and the simulations suggest that the molecular orientation of charged amines at the location in the bilayer with the lowest calculated Gibbs free energy exerts a strong influence over the partitioning within the membrane. The most favourable position of charged amines coincides with the region where the phosphate anions in the phospholipid bilayer are most abundant. Hydrocarbon units oriented in this layer are located more towards the aqueous phase and contribute less to the overall membrane affinity than hydrocarbon units extending into the more hydrophobic core of the bilayer. COSMOmic simulations explain most of the trends between the structural differences observed in IAM-HPLC based KPLIPW. For this set of cationic structures, the mean absolute difference between COSMOmic simulations and IAM-HPLC data, accounting only for amine type corrective increments, is 0.31 log units.

Experimental and computational study of membrane affinity for selected energetic compounds

The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanol-water (log(Kow)) and liposome-water (log(Klipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(Klipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(Kow) value were predicted with several program packages including the COSMOthermX software. Log(Klipw) were estimated with COSMOmic as implemented in the COSMOthermX program package. In order to verify accuracy of our experimentally obtained results, we performed basic statistical analysis of data taken from the literature. We concluded that compounds considered in this study possess a moderate ability to penetrate into membranes. Comparison of both coefficients has shown that in general, the log(Kow) values are slightly smaller than log(Klipw).

Comparison of different models predicting the phospholipid-membrane water partition coefficients of charged compounds

A large fraction of commercially used chemicals is ionizable. This results in the need for mechanistic models to describe the physicochemical properties of ions, like the membrane-water partition coefficient (K(mw)), which is related to toxicity and bioaccumulation. In this work we compare 3 different and already existing modelling approaches to describe the liposome-water partition coefficient (K(lipw)) of organic ions, including 36 cations, 56 anions, 2 divalent cations and 2 zwitterions (plus 207 neutral compounds for ensuring model consistency). 1) The empirical correlation with the octanol-water partition coefficient of the corresponding neutral species yielded better results for the prediction of anions (RMSE = 0.79) than for cations (RMSE = 1.14). Though describing most anions reasonably well, the lack of mechanistic basis and the poor performance for cations constrain the usage of this model. 2) The polyparameter linear free energy relationship (pp-LFER) model performs worse (RMSE = 1.26/1.12 for anions/cations). The different physicochemical environments, due to different sorption depths into the membrane of the different species, cannot be described with a single pp-LFER model. 3) COSMOmic is based on quantum chemistry and fluid phase thermodynamics and has the widest applicability domain. It was the only model applicable for multiply charged ions and gave the best results for anions (RMSE = 0.66) and cations (RMSE = 0.71). We expect COSMOmic to contribute to a better estimation of the environmental risk of ionizable emerging pollutants.

A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes

We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.

Rationalization of reduced penetration of drugs through ceramide gel phase membrane

Since computing resources have advanced enough to allow routine molecular simulation studies of drug molecules interacting with biologically relevant membranes, a considerable amount of work has been carried out with fluid phospholipid systems. However, there is very little work in the literature on drug interactions with gel phase lipids. This poses a significant limitation for understanding permeation through the stratum corneum where the primary pathway is expected to be through a highly ordered lipid matrix. To address this point, we analyzed the interactions of p-aminobenzoic acid (PABA) and its ethyl (benzocaine) and butyl (butamben) esters with two membrane bilayers, which differ in their fluidity at ambient conditions. We considered a dioleoylphosphatidylcholine (DOPC) bilayer in a fluid state and a ceramide 2 (CER2, ceramide NS) bilayer in a gel phase. We carried out unbiased (100 ns long) and biased z-constraint molecular dynamics simulations and calculated the free energy profiles of all molecules along the bilayer normal. The free energy profiles converged significantly slower for the gel phase. While the compounds have comparable affinities for both membranes, they exhibit penetration barriers almost 3 times higher in the gel phase CER2 bilayer. This elevated barrier and slower diffusion in the CER2 bilayer, which are caused by the high ordering of CER2 lipid chains, explain the low permeability of the gel phase membranes. We also compared the free energy profiles from MD simulations with those obtained from COSMOmic. This method provided the same trends in behavior for the guest molecules in both bilayers; however, the penetration barriers calculated by COSMOmic did not differ between membranes. In conclusion, we show how membrane fluid properties affect the interaction of drug-like molecules with membranes.

Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases

Solvation of drugs in the core (C) and headgroup (H) strata of phospholipid bilayers affects their physiological transport rates and accumulation. These characteristics, especially a complete drug distribution profile across the bilayer strata, are tedious to obtain experimentally, to the point that even simplified preferred locations are only available for a few dozen compounds. Recently, we showed that the partition coefficient (P) values in the system of hydrated diacetyl phosphatidylcholine (DAcPC) and n-hexadecane (C16), as surrogates of the H- and C-strata of the bilayer composed of the most abundant mammalian phospholipid, PC, agree well with the preferred bilayer location of compounds. High P values are typical for lipophiles accumulating in the core, and low P values are characteristic of cephalophiles preferring the headgroups. This simple pattern does not hold for most compounds, which usually have more even distribution and may also accumulate at the H/C interface. To model complete distribution, the correlates of solvation energies are needed for each drug state in the bilayer: (1) for the H-stratum it is the DAcPC/W P value, calculated as the ratio of the C16/W and C16/DAcPC (W for water) P values; (2) for the C-stratum, the C16/W P value; (3) for the H/C interface, the P values for all plausible molecular poses are characterized using the fragment DAcPC/W and C16/W solvation parameters for the parts of the molecule embedded in the H- and C-strata, respectively. The correlates, each scaled by two Collander coefficients, were used in a nonlinear, mass-balance based model of intrabilayer distribution, which was applied to the easily measurable overall P values of compounds in the DMPC (M = myristoyl) bilayers and monolayers as the dependent variables. The calibrated model for 107 neutral compounds explains 94% of experimental variance, achieves similar cross-validation levels, and agrees well with the nontrivial, experimentally determined bilayer locations for 27 compounds. The resulting structure-based prediction system for intrabilayer distribution will facilitate more realistic modeling of passive transport and drug interactions with those integral membrane proteins, which have the binding sites located in the bilayer, such as some enzymes, influx and efflux transporters, and receptors. If only overall bilayer accumulation is of interest, the 1-octanol/W P values suffice to model the studied set.

Molecular dynamics simulation of SDS and CTAB micellization and prediction of partition equilibria with COSMOmic

Molecular dynamics (MD) simulations of the self-assembly of different ionic surfactants have been performed in order to obtain representative micellar structures. Subsequently, these structures were used to predict the partition behavior of various solutes in these micelles with COSMOmic, an extension of COSMO-RS. This paper includes multiple self-assembled micelles of SDS (sodium dodecyl sulfate, anionic surfactant) and CTAB (cetyltrimethylammoniumbromide, cationic surfactant) at different concentrations. Micellar size, density profiles, and shape (eccentricity) have been investigated. However, the size strongly depends on the functional definition of a micelle. For this reason, we present a method based on the free monomer concentration in aqueous solution as an optimization criterion for the micelle definition. The combination of MD with COSMOmic has the benefit of combining detailed atomistic information from MD with fast calculations of COSMOmic. For the first time the influence of micelle structure on pratition equilibria, predicted with COSMOmic, were investigated. In case of SDS more than 4600 and for CTAB more than 800 single micelles have been studied. The predictions of the partition coefficients with COSMOmic are in good agreement with experimental data. Additionally, the most favorable locations of selected molecules in the micelles as well as probable energy barriers are determined even for complex solutes such as toluene, propanolol, ephedrine, acetone, phenol, lidocaine, syringic acid, coumarin, isovanillin, ferulic acid, and vanillic acid. This method can therefore be applied as a potential screening tool for solutes (e.g., drugs) to find the optimal solute-surfactant combination.

Prediction of micelle/water and liposome/water partition coefficients based on molecular dynamics simulations, COSMO-RS, and COSMOmic

Liposomes and micelles find various applications as potential solubilizers in extraction processes or in drug delivery systems. Thermodynamic and transport processes governing the interactions of different kinds of solutes in liposomes or micelles can be analyzed regarding the free energy profiles of the solutes in the system. However, free energy profiles in heterogeneous systems such as micelles are experimentally almost not accessible. Therefore, the development of predictive methods is desirable. Molecular dynamics (MD) simulations reliably simulate the structure and dynamics of lipid membranes and micelles, whereas COSMO-RS accurately reproduces solvation free energies in different solvents. For the first time, free energy profiles in micellar systems, as well as mixed lipid bilayers, are investigated, taking advantage of both methods: MD simulations and COSMO-RS, referred to as COSMOmic (Klamt, A.; Huniar, U.; Spycher, S.; Keldenich, J. COSMOmic: A Mechanistic Approach to the Calculation of Membrane-Water Partition Coefficients and Internal Distributions within Membranes and Micelles. J. Phys. Chem. B 2008, 112, 12148-12157). All-atom molecular dynamics simulations of the system SDS/water and CTAB/water have been applied in order to retrieve representative micelle structures for further analysis with COSMOmic. For the system CTAB/water, different surfactant concentrations were considered, which results in different micelle sizes. Free energy profiles of more than 200 solutes were predicted and validated by means of experimental partition coefficients. To our knowledge, these are the first quantitative predictions of micelle/water partition coefficients, which are based on whole free energy profiles from molecular methods. Further, the partitioning in lipid bilayer systems containing different hydrophobic tail groups (DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), SOPC (stearoyl-oleoylphosphatidylcholine), DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine), and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine)) as well as mixed bilayers was calculated. Experimental partition coefficients (log P) were reproduced with a root-mean-square error (RMSE) of 0.62. To determine the influence of cholesterol as an important component of cellular membranes, free energy profiles in the presence of cholesterol were calculated and shown to be in good agreement with experimental data.