Partitioning into Colloidal Structures of Fasted State Intestinal Fluid Studied by Molecular Dynamics Simulations

Protonation State of a Bioactive Compound Regulates Its Release from Lamellar Gel-Phase Bilayers

Lamellar gel networks (LGNs) in personal care or pharmaceutical lotions and creams provide an opaque cream appearance and a creamy texture to these products. Within the LGNs, the lamellar gel (Lβ) phase composed of regularly spaced bilayers of surfactants and long-chain fatty alcohols is predominately responsible for the unique rheological properties of the LGNs. To extend the shelf life of LGN-containing products, bioactive compounds with antimicrobial properties are often incorporated into the formulation. However, how the protonation state of the bioactive compounds regulates their release from the Lβ-phase bilayers is currently unknown. Using molecular dynamics simulations, we found that the protonated (neutral) form of cinnamic acid, a common antimicrobial food additive, has a retention ratio higher than that of its deprotonated (charged) counterpart in the Lβ-phase bilayer. From free energy calculations, we determined that not only is the protonated molecule more stable in the hydrophobic interior of the bilayer but also the formation of hydrogen-bonded dimers significantly enhances its stability within the bilayer. Thus, the protonation state has a profound impact on bioavailability of the compounds. Our results also highlight the importance of considering possible oligomeric states of molecules when performing calculations to estimate the permeability of molecules within various bilayers.

Molecular Dynamics Simulation Prediction of the Partitioning Constants (KH, Kiw, Kia) of 82 Legacy and Emerging Organic Contaminants at the Water-Air Interface

The tendency of organic contaminants (OCs) to partition between different phases is a key set of properties that underlie their human and ecological health impacts and the success of remediation efforts. A significant challenge associated with these efforts is the need for accurate partitioning data for an ever-expanding list of OCs and breakdown products. All-atom molecular dynamics (MD) simulations have the potential to help generate these data, but existing studies have applied these techniques only to a limited variety of OCs. Here, we use established MD simulation approaches to examine the partitioning of 82 OCs, including many compounds of critical concern, at the water-air interface. Our predictions of the Henry's law constant (K_H) and interfacial adsorption coefficients (K_iw, K_ia) correlate strongly with experimental results, indicating that MD simulations can be used to predict K_H, K_iw, and K_ia values with mean absolute deviations of 1.1, 0.3, and 0.3 logarithmic units after correcting for systematic bias, respectively. A library of MD simulation input files for the examined OCs is provided to facilitate future investigations of the partitioning of these compounds in the presence of other phases.

Intrinsic lipolysis rate for systematic design of lipid-based formulations

Lipid-based formulations (LBFs) are used by the pharmaceutical industry in oral delivery systems for both poorly water-soluble drugs and biologics. Digestibility is key for the performance of LBFs and in vitro lipolysis is commonly used to compare the digestibility of LBFs. Results from in vitro lipolysis experiments depend highly on the experimental conditions and formulation characteristics, such as droplet size (which defines the surface area available for digestion) and interfacial structure. This study introduced the intrinsic lipolysis rate (ILR) as a surface area-independent approach to compare lipid digestibility. Pure acylglycerol nanoemulsions, stabilized with polysorbate 80 at low concentration, were formulated and digested according to a standardized pH-stat lipolysis protocol. A methodology originally developed to calculate the intrinsic dissolution rate of poorly water-soluble drugs was adapted for the rapid calculation of ILR from lipolysis data. The impact of surfactant concentration on the apparent lipolysis rate and lipid structure on ILR was systematically investigated. The surfactant polysorbate 80 inhibited lipolysis of tricaprylin nanoemulsions in a concentration-dependent manner. Coarse-grained molecular dynamics simulations supported these experimental observations. In the absence of bile and phospholipids, tricaprylin was shielded from lipase at 0.25% polysorbate 80. In contrast, the inclusion of bile salt and phospholipid increased the surfactant-free area and improved the colloidal presentation of the lipids to the enzyme, especially at 0.125% polysorbate 80. At a constant and low surfactant content, acylglycerol digestibility increased with decreasing acyl chain length, decreased esterification, and increasing unsaturation. The calculated ILR of pure acylglycerols was successfully used to accurately predict the IRL of binary lipid mixtures. The ILR measurements hold great promise as an efficient method supporting pharmaceutical formulation scientists in the design of LBFs with specific digestion profiles.

In Silico Prediction of Food Properties: A Multiscale Perspective

Several open software packages have popularized modeling and simulation strategies at the food product scale. Food processing and key digestion steps can be described in 3D using the principles of continuum mechanics. However, compared to other branches of engineering, the necessary transport, mechanical, chemical, and thermodynamic properties have been insufficiently tabulated and documented. Natural variability, accented by food evolution during processing and deconstruction, requires considering composition and structure-dependent properties. This review presents practical approaches where the premises for modeling and simulation start at a so-called “microscopic” scale where constituents or phase properties are known. The concept of microscopic or ground scale is shown to be very flexible from atoms to cellular structures. Zooming in on spatial details tends to increase the overall cost of simulations and the integration over food regions or time scales. The independence of scales facilitates the reuse of calculations and makes multiscale modeling capable of meeting food manufacturing needs. On one hand, new image-modeling strategies without equations or meshes are emerging. On the other hand, complex notions such as compositional effects, multiphase organization, and non-equilibrium thermodynamics are naturally incorporated in models without linearization or simplifications. Multiscale method’s applicability to hierarchically predict food properties is discussed with comprehensive examples relevant to food science, engineering and packaging. Entropy-driven properties such as transport and sorption are emphasized to illustrate how microscopic details bring new degrees of freedom to explore food-specific concepts such as safety, bioavailability, shelf-life and food formulation. Routes for performing spatial and temporal homogenization with and without chemical details are developed. Creating a community sharing computational codes, force fields, and generic food structures is the next step and should be encouraged. This paper provides a framework for the transfer of results from other fields and the development of methods specific to the food domain.

Explicit-pH Coarse-Grained Molecular Dynamics Simulations Enable Insights into Restructuring of Intestinal Colloidal Aggregates with Permeation Enhancers

Permeation enhancers (PEs) can increase the bioavailability of drugs. The mechanisms of action of these PEs are complex, but, typically, when used for oral administration, they can transiently induce the alteration of trans- and paracellular pathways, including increased solubilization and membrane fluidity, or the opening of the tight junctions. To elucidate these mechanistic details, it is important to understand the aggregation behavior of not only the PEs themselves but also other molecules already present in the intestine. Aggregation processes depend critically on, among other factors, the charge state of ionizable chemical groups, which is affected by the pH of the system. In this study, we used explicit-pH coarse-grained molecular dynamics simulations to investigate the aggregation behavior and pH dependence of two commonly used PEs—caprate and SNAC—together with other components of fasted- and fed-state simulated intestinal fluids. We also present and validate a coarse-grained molecular topology for the bile salt taurocholate suitable for the Martini3 force-field. Our results indicate an increase in the number of free molecules as a function of the system pH and for each combination of FaSSIF/FeSSIF and PEs. In addition, there are differences between caprate and SNAC, which are rationalized based on their different molecular structures and critical micelle concentrations.

Computational and Experimental Models of Type III Lipid-Based Formulations of Loratadine Containing Complex Nonionic Surfactants

Type III lipid-based formulations (LBFs) combine poorly water-soluble drugs with oils, surfactants, and cosolvents to deliver the drugs into the systemic circulation. However, the solubility of the drug can be influenced by the colloidal phases formed in the gastrointestinal tract as the formulation is dispersed and makes contact with bile and other materials present within the GI tract. Thus, an understanding of the phase behavior of LBFs in the gut is critical for designing efficient LBFs. Molecular dynamics (MD) simulation is a powerful tool for the study of colloidal systems. In this study, we modeled the internal structures of five type III LBFs of loratadine containing poly(ethylene oxide) nonionic surfactants polysorbate 80 and polyoxyl hydrogenated castor oil (Kolliphor RH40) using long-timescale MD simulations (0.4-1.7 μs). We also conducted experimental investigations (dilution of formulations with water) including commercial Claritin liquid softgel capsules. The simulations show that LBFs form continuous phase, water-swollen reverse micelles, and bicontinuous and phase-separated systems at different dilutions, which correlate with the experimental observations. This study supports the use of MD simulation as a predictive tool to determine the fate of LBFs composed of medium-chain lipids, polyethylene oxide surfactants, and polymers.

Role of Permeability on the Biopredictive Dissolution of Amorphous Solid Dispersions

An ideal dissolution test for amorphous solid dispersions (ASDs) should reflect physicochemical, physiological, and hydrodynamic conditions which accurately represent in vivo dissolution. However, this is confounded by the evolution of different molecular and colloidal species during dissolution, generating a supersaturated state of the drug. The supersaturated state of a drug is thermodynamically unstable which drives the process of precipitation resulting in a loss of solubility advantage. Maintaining a supersaturated state of the drug with the help of precipitation inhibiting excipients is a key component in the design of ASDs. Therefore, a biopredictive dissolution test is critical for proper risk assessment during the development of an optimal ASD formulation. One of the overlooked components of biopredictive dissolution is the role of drug permeability. The kinetic changes in the phase behavior of a drug during dissolution of ASDs are influenced by drug permeability across a membrane. Conventionally, drug dissolution and permeation are analyzed separately although they occur simultaneously in vivo. The kinetic phase changes occurring during dissolution of ASDs can influence the thermodynamic activity and membrane flux of a drug. The present review evaluates the feasibility, predictability, and practicability of permeability/dissolution for the optimal development and risk assessment of ASD formulations.

Molecular Dynamics Simulations and Experimental Results Provide Insight into Clinical Performance Differences between Sandimmune® and Neoral® Lipid-Based Formulations

OBJECTIVE

Molecular dynamics (MD) simulations provide an in silico method to study the structure of lipid-based formulations (LBFs) and the incorporation of poorly water-soluble drugs within such formulations. In order to validate the ability of MD to effectively model the properties of LBFs, this work investigates the well-known cyclosporine A formulations, Sandimmune® and Neoral®. Sandimmune® exhibits poor dispersibility and its absorption from the gastrointestinal tract is enhanced when administered after food, whereas Neoral® disperses comparatively well and shows no food effect.

METHODS

MD simulations were performed of both LBFs to investigate the differences observed in fasted and fed conditions. These conditions were also tested using an in vitro experimental model of dispersion and digestion.

RESULTS

These MD simulations were able to show that the food effect observed for Sandimmune® can be explained by large changes in drug solubilization on addition of bile. In contrast, Neoral® is well dispersed in water or in simulated fasted conditions, and this dispersion is relatively unchanged on moving to fed conditions. These differences were confirmed using dispersion and digestion in vitro experimental model.

CONCLUSIONS

The current data suggests that MD simulations are a potential method to model the fate of LBFs in the gastrointestinal tract, predict their dispersion and digestion, investigate behaviour of APIs within the formulations, and provide insights into the clinical performance of LBFs.

Molecular dynamics exploring of atmosphere components interacting with lung surfactant phospholipid bilayers

Sulfur dioxide (SO₂), nitrogen oxide (NO₂) and ozone (O₃) in the atmosphere are significantly correlated with various respiratory and cardiovascular diseases. High doses of each of these gases or a mixture can change the physical and chemical properties of the lung membrane, thus leading to an increased pulmonary vascular permeability and structural failure of the alveolar cell membrane. In the present study, detailed molecular dynamic (MD) modeling was applied to investigate the effects of SO₂, NO₂, O₃ and mixtures of these gases on the dipalmitoyl phosphatidylcholine (DPPC) phospholipid bilayer. The results showed that several key physical properties, including the mass density, lipid ordering parameter, lipid diffusion, and electrostatic potential of the cell membrane, have been changed by the binding of different compounds. This resulted in significant variations and more disorder in the DPPC bilayer. The multiple analyses of membrane properties proved the toxicity of NO₂, O₃, and SO₂ to the DPPC bilayer, providing a theoretical basis for the experimental phenomenon that SO₂, NO₂ and O₃ can cause lung cell apoptosis. For the single systems, the damage to DPPC bilayer caused by O₃ was more serious than NO₂ and SO₂. More importantly, the MD simulations using the mixtures of SO₂, NO₂, and O₃ showed a much greater decline of membrane fluidity and the aggravation of membrane damage than the single systems, indicating a synergistic effect when NO₂, SO₂, and O₃ coexisted in the atmosphere, which could lead to much more severe damage and greater toxicities to the lung.

Molecular Dynamics Simulations Reveal Membrane Interactions for Poorly Water-Soluble Drugs: Impact of Bile Solubilization and Drug Aggregation

Molecular transport mechanisms of poorly soluble hydrophobic drug compounds to lipid membranes were investigated using molecular dynamics (MD) simulations. The model compound danazol was used to investigate the mechanism(s) by which bile micelles delivered it to the membrane. The interactions between lipid membrane and pure drug aggregates-in the form of amorphous aggregates and nanocrystals-were also studied. Our simulations indicate that bile micelles formed in the intestinal fluid may facilitate danazol incorporation into cellular membranes through two different mechanisms. The micelle may be acting as: i) a shuttle that presents the danazol directly to the membrane or ii) an elevator that moves the solubilized danazol with it as the colloidal structure itself becomes incorporated and solubilized within the membrane. The elevator hypothesis was supported by complementary lipid monolayer adsorption experiments. In these experiments, colloidal structures formed with simulated intestinal fluid were observed to rapidly incorporate into the monolayer. Simulations of membrane interaction with drug aggregates showed that both the amorphous aggregates and crystalline nanostructures incorporated into the membrane. However, the amorphous aggregates solubilized more quickly than the nanocrystals into the membrane, thereby improving the danazol absorption.

Molecular Dynamics Simulations on Interindividual Variability of Intestinal Fluids: Impact on Drug Solubilization

Efficient delivery of oral drugs is dependent on their solubility in human intestinal fluid, a complex and dynamic fluid that contains colloidal structures composed of small molecules. These structures solubilize poorly water-soluble compounds, increasing their apparent solubility, and possibly their bioavailability. In this study, we conducted coarse-grained molecular dynamics simulations with data from duodenal fluid samples previously acquired from five healthy volunteers. In these simulations, we observed the self-assembly of mixed micelles of bile salts, phospholipids, and free fatty acids. The micelles were ellipsoids with a size range of 4–7 nm. Next, we investigated micelle affinities of three model drugs. The affinities in our simulation showed the same trend as literature values for the solubility enhancement of drugs in human intestinal fluids. This type of simulations is useful for studies of events and interactions taking place in the small intestinal fluid.

Successful oral delivery of poorly water-soluble drugs both depends on the intraluminal behavior of drugs and of appropriate advanced drug delivery systems

Poorly water-soluble drugs continue to be a problematic, yet important class of pharmaceutical compounds for treatment of a wide range of diseases. Their prevalence in discovery is still high, and their development is usually limited by our lack of a complete understanding of how the complex chemical, physiological and biochemical processes that occur between administration and absorption individually and together impact on bioavailability. This review defines the challenge presented by these drugs, outlines contemporary strategies to solve this challenge, and consequent in silico and in vitro evaluation of the delivery technologies for poorly water-soluble drugs. The next steps and unmet needs are proposed to present a roadmap for future studies for the field to consider enabling progress in delivery of poorly water-soluble compounds.

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.

Automated assays for thermodynamic (equilibrium) solubility determination

Solubility is a crucial physicochemical property for drug candidates and is important in both drug discovery and development. Poor solubility is detrimental to absorption after oral administration and can mask compound activity in bioassays in various ways. Hence, solubility liabilities should ideally be identified as early as possible in the drug development process. With the increasing number of compounds as potential drug candidates, automated thermodynamic solubility assays for high throughput screening enabling rapid evaluation of a large number of compounds are becoming increasingly important. This review discusses the current status of the most widely used automated assays for thermodynamic solubility, followed by recent high throughput measurements of properties related to solubility (e.g. dissolution rate and supersaturation) and a brief overview of predictive computational methods for thermodynamic solubility reported in the literature.

Computational prediction of drug solubility in water-based systems: Qualitative and quantitative approaches used in the current drug discovery and development setting

In this review we will discuss recent advances in computational prediction of solubility in water-based solvents. Our focus is set on recent advances in predictions of biorelevant solubility in media mimicking the human intestinal fluids and on new methods to predict the thermodynamic cycle rather than prediction of solubility in pure water through quantitative structure property relationships (QSPR). While the literature is rich in QSPR models for both solubility and melting point, a physicochemical property strongly linked to the solubility, recent advances in the modelling of these properties make use of theory and computational simulations to better predict these properties or processes involved therein (e.g. solid state crystal lattice packing, dissociation of molecules from the lattice and solvation). This review serves to provide an update on these new approaches and how they can be used to more accurately predict solubility, and also importantly, inform us on molecular interactions and processes occurring during drug dissolution and solubilisation.

Characterization of Solubilizing Nanoaggregates Present in Different Versions of Simulated Intestinal Fluid

The absorption of hydrophobic drugs and nutrients from the intestine is principally determined by the amount that can be dissolved by the endogenous fluids present in the gut. Human intestinal fluids (HIFs) comprise a complex mixture of bile salts, phospholipids, steroids and glycerides that vary in composition in the fed and fasted state and between subjects. A number of simulated intestinal fluid (SIF) compositions have been developed to mimic fasted and fed state intestinal conditions and allow the in vitro determination of drug solubility as a proxy for the maximum dissolved concentration it is possible to reach. In particular these solvents are used during the development of lipophilic and poorly water-soluble drugs but questions remain around the differences that may arise from the source and methods of preparation of these fluids. In this work, a range of SIFs were studied using small-angle X-ray scattering (SAXS), cryogenic-transmission electron microscopy (cryo-TEM) and molecular dynamics (MD) simulations in order to analyze their structures. In-house prepared SIFs based on sodium taurodeoxycholate (NaTDC) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) formed oblate ellipsoidal micelles irrespective of lipid concentration and preparation conditions. In contrast, commercially available SIFs based on sodium taurocholate and lecithin formed prolate ellipsoidal micelles in the fed state and vesicles in the fasted state. These structural variations are the likely reason for the dramatic differences sometimes observed in the solubility enhancements for hydrophobic drugs, nutrients and digestion products when using different SIFs. However, the structural homogeneity of the NaTDC/DOPC micelles makes them ideal candidates for standardizing SIF formulations as the structures of the solubilizing nanoaggregates therein are not sensitive to the preparation method.

Self-Assembly of Lecithin and Bile Salt in the Presence of Inorganic Salt in Water: Mesoscale Computer Simulation

The influence of inorganic salt on the structure of lecithin/bile salt mixtures in aqueous solution is studied by means of dissipative particle dynamics simulations. We propose a coarse-grained model of phosphatidylcholine and two types of bile salts (sodium cholate and sodium deoxycholate) and also take into account the presence of low molecular weight salt. This model allows us to study the system on rather large time and length scales (up to about ∼20 μs and 50 nm) and to reveal mechanisms of experimentally observed increasing viscosity upon increasing the low molecular weight salt concentration in this system. We show that increasing the low molecular weight salt concentration induces the growth of cylinder-like micelles formed in lecithin/bile salt mixtures in water. These wormlike micelles can entangle into transient networks displaying perceptible viscoelastic properties. Computer simulation results are in good qualitative agreement with experimental observations.