Molecular dynamics simulation study of translocation of fullerene C60 through skin bilayer: effect of concentration on barrier properties

The effects of size and surface functionalization of polystyrene nanoplastics on stratum corneum model membranes: An experimental and computational study

Nanoplastics are mainly generated from the decomposition of plastic waste and artificial production and have attracted much attention due to their wide distribution in the environment and the potential risk for humans. As the largest organ of the human body, the skin is inevitably in contact with nanoplastics. Stratum corneum is the first barrier when the skin is exposed to nanoplastics. However, little is known about the interactions between nanoplastics and stratum corneum. Here, the effects of particle size and surface functionalization (amino-modified and carboxy-modified) of polystyrene nanoplastics on the stratum corneum models were studied by Langmuir monolayer and molecular dynamics simulations. An equimolar mixture of ceramide/cholesterol/free fatty acid was used to mimic stratum corneum intercellular lipids. The Langmuir monolayer studies demonstrated that the larger size and surface functionalization of polystyrene nanoplastics significantly reduced the stability of stratum corneum lipid monolayer in a concentration-dependent fashion. Simulation results elucidated that functionalized polystyrene oligomers had a stronger interaction with lipid components of the stratum corneum model membrane. The cell experiments also indicated that functionalized polystyrene nanoplastics, especially for amino-modified polystyrene nanoplastics, had significant cytotoxicity on normal human dermal fibroblast cells. Our results provide fundamental information and the basis for a deeper understanding of the health risks of nanoplastics to humans.

Formulation and Skin Permeation of Active-Loaded Lipid Nanoparticles: Evaluation and Screening by Synergizing Molecular Dynamics Simulations and Experiments

Encapsulation into nanoparticles (NPs) is a potential method to deliver pharmaceutical/cosmetic actives deep into the skin. However, understanding the NP formulations and underlying mechanism of active delivery to skin has scarcely been studied. We report a simulation platform that screens, evaluates, formulates, and provides atomic-resolution interpretation of NP-based formulations, and reveals the active permeation mechanism from NPs to skin. First, three actives, namely, ferulic acid (FA), clotrimazole (CZE), and tretinoin (TTN), and five lipid excipients' (Compritol, Precirol, Geleol, Gelot, Gelucire) combinations were screened by MD simulations for the best pairs. For each suggested pair, the actual active and lipid compositions for the synthesis of stable NP formulations were then obtained by experiments. MD simulations demonstrate that in NP formulations, FA and CZE actives are present at the surface of the NPs, whereas TTN actives are present at both the surface and interior of the NP core. The NP shapes obtained by simulation perfectly match with experiments. For each NP, separate MD simulations illustrate that active-loaded NPs approach the skin surface quickly, and then actives translocate from NP surface to skin surface followed by penetration of NPs through skin. The driving force for the translocation which initiates during the penetration process, is the stronger active-skin interaction compared to active-NP interaction. Permeation free energy indicates spontaneous transfer of actives from solution phase to the surface of the skin bilayer. The free energy barriers are increased in the order of FA < TTN < CZE. Significantly lower diffusions of actives are obtained in the main barrier region compared to bulk, and the average diffusion coefficients of actives are in the same order of magnitude (∼10^-6 cm²/s). The estimated permeability coefficients (log P) of actives are mainly governed by free energy barriers. The study would facilitate the development of novel lipid-based NP formulations for personal-care/pharmaceutical applications.

Using molecular simulation to understand the skin barrier

Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.

Investigating the Permeation Mechanism of Typical Phthalic Acid Esters (PAEs) and Membrane Response Using Molecular Dynamics Simulations

Phthalic acid esters (PAEs) are typical environmental endocrine disrupters, interfering with the endocrine system of organisms at very low concentrations. The plasma membrane is the first barrier for organic pollutants to enter the organism, so membrane permeability is a key factor affecting their biological toxicity. In this study, based on computational approaches, we investigated the permeation and intramembrane aggregation of typical PAEs (dimethyl phthalate, DMP; dibutyl phthalate, DBP; di-2-ethyl hexyl phthalate, DEHP), as well as their effects on membrane properties, and related molecular mechanisms were uncovered. Our results suggested that PAEs could enter the membrane spontaneously, preferring the headgroup-acyl chain interface of the bilayer, and the longer the side chain (DEHP > DBP > DMP), the deeper the insertion. Compared with the shortest DMP, DEHP apparently increased membrane thickness, order, and rigidity, which might be due to its stronger hydrophobicity. Potential of means force (PMF) analysis revealed the presence of an energy barrier located at the water-membrane interface, with a maximum value of 2.14 kcal mol−1 obtained in the DEHP-system. Therefore, the difficulty of membrane insertion is also positively correlated with the side-chain length or hydrophobicity of PAE molecules. These findings will inspire our understanding of structure-activity relationship between PAEs and their effects on membrane properties, and provide a scientific basis for the formulation of environmental pollution standards and the prevention and control of small molecule pollutants.

Fullerenes’ Interactions with Plasma Membranes: Insight from the MD Simulations

Understanding the interactions between carbon nanoparticles (CNPs) and biological membranes is critically important for applications of CNPs in biomedicine and toxicology. Due to the complexity and diversity of the systems, most molecular simulation studies have focused on the interactions of CNPs and single component bilayers. In this work, we performed coarse-grained molecular dynamic (CGMD) simulations to investigate the behaviors of fullerenes in the presence of multiple lipid components in the plasma membranes with varying fullerene concentrations. Our results reveal that fullerenes can spontaneously penetrate the plasma membrane. Interestingly, fullerenes prefer to locate themselves in the region of the highly unsaturated lipids that are enriched in the inner leaflet of the plasma membrane. This causes fullerene aggregation even at low concentrations. When increasing fullerene concentrations, the fullerene clusters grow, and budding may emerge at the inner leaflet of the plasma membrane. Our findings suggest by tuning the lipid composition, fullerenes can be loaded deeply inside the plasma membrane, which can be useful for designing drug carrier liposomes. Moreover, the mechanisms of how fullerenes perturb multicomponent cell membranes and how they directly enter the cell are proposed. These insights can help to determine fullerene toxicity in living cells.

Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes

Lipid nanoemulsions are promising nanomaterials for drug delivery applications in food, pharmaceutical and cosmetic industries. Despite the noteworthy commercial interest, little is known about their supramolecular organization, especially about how such multicomponent formulations interact with cell membranes. In the present work, coarse-grained molecular dynamics simulations have been employed to study the self-assembly of a 15-component lipid nanoemulsion droplet containing vitamins A and E for skin delivery. Our results display aspects of the unique "onion-like" agglomeration between the chemical constituents in the different layers of the lipid nanodroplet. Vitamin E molecules are more concentrated in the center of the droplet together with other hydrophobic constituents such as the triglycerides with long tails. On the other hand, vitamin A occupies an intermediate layer between the core and the co-emulsifier surface of the nanodroplet, together with lecithin phospholipids. Coarse-grained molecular dynamics simulations were also performed to provide insight into the first steps involved in absorption and penetration of the nanodroplet through skin membrane models, representing an intracellular (hair follicle infundibulum) and intercellular pathway (stratum corneum) through the skin. Our data provide a first view on the complex organization of commercial nanoemulsion and its interaction with skin membranes. We expect our results to open the way towards the rational design of such nanomaterials.

Studies on Aggregated Nanoparticles Steering during Deep Brain Membrane Crossing

Many central nervous system (CNS) diseases, such as Alzheimer's disease (AD), affect the deep brain region, which hinders their effective treatment. The hippocampus, a deep brain area critical for learning and memory, is especially vulnerable to damage during early stages of AD. Magnetic drug targeting has shown high potential in delivering drugs to a targeted disease site effectively by applying a strong electromagnetic force. This study illustrates a nanotechnology-based scheme for delivering magnetic nanoparticles (MNP) to the deep brain region. First, we developed a mathematical model and a molecular dynamic simulation to analyze membrane crossing, and to study the effects of particle size, aggregation, and crossing velocities. Then, using in vitro experiments, we studied effective parameters in aggregation. We have also studied the process and environmental parameters. We have demonstrated that aggregation size can be controlled when particles are subjected to external electromagnetic fields. Our simulations and experimental studies can be used for capturing MNPs in brain, the transport of particles across the intact BBB and deep region targeting. These results are in line with previous in vivo studies and establish an effective strategy for deep brain region targeting with drug loaded MNPs through the application of an external electromagnetic field.

Molecular dynamics simulations to elucidate translocation and permeation of active from lipid nanoparticle to skin: complemented by experiments

One of the most realistic approaches for delivering actives (pharmaceuticals/cosmetics) deep into skin layers is encapsulation into nanoparticles (NPs). Nonetheless, molecular-level mechanisms related to active delivery from NPs to the skin have scarcely been studied despite the large number of synthesis and characterization studies. We herein report the underlying mechanism of active translocation and permeation through the outermost layer of skin, the stratum corneum (SC), via molecular dynamics (MD) simulations complemented by experimental studies. A SC molecular model is constructed using current state-of-the-art methodology via incorporating the three most abundant skin lipids: ceramides, free fatty acids, and cholesterol. As a potent antioxidant, ferulic acid (FA) is used as the model active, and it is loaded into Gelucire 50/13 NP. MD simulations elucidate that, first, FA-loaded NP approaches the skin surface quickly, followed by slight penetration and adsorption onto the upper skin surface; FA then translocates from the NP surface to the skin surface due to stronger NP-skin interactions compared to the FA-NP interactions; then, once FA is released onto the skin surface, it slowly permeates deep into the skin bilayer. Both the free energy and resistance to permeation not only indicate the spontaneous transfer of FA from the bulk to the skin surface, but they also reveal that the main barrier against permeation exists in the middle of the lipid hydrophobic tails. Significantly lower diffusion of FA is obtained in the main barrier region compared to the bulk. The estimated permeability coefficient (log P) values are found to be higher than the experimental values. Importantly, the permeation process evaluated via MD simulations perfectly matches with experiments. The study suggests a molecular simulation platform that provides various crucial insights relating to active delivery from loaded NP to skin, and it could facilitate the design and development of novel NP-based formulations for transdermal delivery and the topical application of drugs/cosmetics.

A review on the cytotoxicity of graphene quantum dots: from experiment to simulation

Graphene quantum dots (GQDs) generate intrinsic fluorescence and improve the aqueous stability of graphene oxide (GO) while maintaining wide chemical adaptability and high adsorption capacity. Despite GO's remarkable advantages in bio-imaging, bio-sensing, and other biomedical applications, many experiments and simulations have focused on the biosafety of GQDs. Here, we review the findings on the biosafety of GQDs from experiments; then, we review the results from simulated interactions with biological membranes, DNA molecules, and proteins; finally, we examine the intersection between experiments and simulations. The biosafety results from simulations are explained in detail. Based on the literature and our experiments, we also discuss the trends toward GQDs with better biosafety.

Mechanisms of skin moisturization with hyperharmonized hydroxyl modified fullerene substance

BACKGROUND

Hyper Harmonized Hydroxyl Modified Fullerene Substance (3HFWC⁺ ) establishes hydrogen bonds with the surrounding water molecules and organizes them in clusters with the liquid crystalline state, similar to the properties of water surrounding the biomolecules.

AIMS

To investigate the moisturizing properties of hyperharmonized fullerenol-3HFWC⁺ as an emulsion O/W ingredient on the skin.

PATIENTS/METHODS

We have analyzed the reflexion of the blue light from the skin, in vivo, with different levels of moisturization and compared the influence of three groups of cosmetic products (with various active ingredients, 3HFWC⁺ or water in same percentage in the "vehiculum") on skin moisturization by measuring paramagnetic/diamagnetic properties by Optomagnetic Imaging Spectroscopy.

RESULTS

Regenerating Cream and Body Lotion have shown statistically significant increase of diamagnetic features predominantly in all 3 types of creams, while the Hand Cream formulations have not shown statistically significant results after 4 weeks of treatment. Anti-aging cream with 3HFWC⁺ demonstrated statistically significant increase of paramagnetic properties of the skin (p⁺ /p^- from 0.90 to 0.62) and showed beneficial effects on information transfer and water content in stratum corneum.

CONCLUSION

Although it does not act as a classical moisturizing agent on the skin, 3HFWC⁺ can increase moisturization as a result of hydrogen bonds established among 3HFWC⁺ and water or biomolecules, liquid crystalline state of water in 3HFWC⁺ resembling the properties of water surrounding the biomolecules, and finally, liquid crystalline state of water in the products.

Influence of Bile Composition on Membrane Incorporation of Transient Permeability Enhancers

Transient permeability enhancers (PEs), such as caprylate, caprate, and salcaprozate sodium (SNAC), improve the bioavailability of poorly permeable macromolecular drugs. However, the effects are variable across individuals and classes of macromolecular drugs and biologics. Here, we examined the influence of bile compositions on the ability of membrane incorporation of three transient PEs—caprylate, caprate, and SNAC—using coarse-grained molecular dynamics (CG-MD). The availability of free PE monomers, which are important near the absorption site, to become incorporated into the membrane was higher in fasted-state fluids than that in fed-state fluids. The simulations also showed that transmembrane perturbation, i.e., insertion of PEs into the membrane, is a key mechanism by which caprylate and caprate increase permeability. In contrast, SNAC was mainly adsorbed onto the membrane surface, indicating a different mode of action. Membrane incorporation of caprylate and caprate was also influenced by bile composition, with more incorporation into fasted- than fed-state fluids. The simulations of transient PE interaction with membranes were further evaluated using two experimental techniques: the quartz crystal microbalance with dissipation technique and total internal reflection fluorescence microscopy. The experimental results were in good agreement with the computational simulations. Finally, the kinetics of membrane insertion was studied with CG-MD. Variation in micelle composition affected the insertion rates of caprate monomer insertion and expulsion from the micelle surface. In conclusion, this study suggests that the bile composition and the luminal composition of the intestinal fluid are important factors contributing to the interindividual variability in the absorption of macromolecular drugs administered with transient PEs.

Formation of aggregates, icosahedral structures and percolation clusters of fullerenes in lipids bilayers: The key role of lipid saturation

Carbon nanoparticles (CNPs) are attractive materials for a great number of applications but there are serious concerns regarding their influence on health and environment. Here, our focus is on the behavior of fullerenes in lipid bilayers with varying lipid saturations, chain lengths and fullerene concentrations using coarse-grained molecular dynamics (CG-MD) simulations. Our findings show that the lipid saturation level is a key factor in determining how fullerenes behave and where the fullerenes are located inside a lipid bilayer. In saturated and monounsaturated bilayers fullerenes aggregated and formed clusters with some of them showing icosahedral structures. In polyunsaturated lipid bilayers, no such structures were observed: In polyunsaturated lipid bilayers at high fullerene concentrations, connected percolation-like networks of fullerenes spanning the whole lateral area emerged at the bilayer center. In other systems only separate isolated aggregates were observed. The effects of fullerenes on lipid bilayers depend strongly on fullerene aggregation. When fullerenes aggregate, their interactions with the lipid tails change.

Development and application of coarse-grained MARTINI model of skin lipid ceramide [AP]

Stratum corneum (SC), the outermost layer of the skin, contains large variety of lipids, endowing them with the amphiphilic properties, needed to fulfil their key role in skin's barrier function. The individual role of lipid types in the barrier function is difficult to understand due to the immense heterogeneity and complexity of the lipid's organization within the SC. The lipid organization is being explored using both computational (molecular dynamics simulations) and experimental (neutron diffraction) techniques. Even though atomistic simulations provide unprecedented atomic level details, the major limitation is time and length scale that can be achieved with decent computational facility. Alternatively, coarse-grain (CG) models are currently being used to capture physics at bigger time and length scale without losing essential underlined structural information. In this study, a CG model of α-hydroxy phytosphingosines (CER[AP]) is developed based on philosophy of MARTINI force field. At first, the model is validated with various atomistic simulations and available experimental data. Later on, the model's compatibility with other major skin lipids, cholesterol, and free fatty acid (palmitic acid) is checked by simulating a mixture of lipid multilayer in presence and absence of water. The developed model of CER[AP] is able to predict key structural properties within the acceptable error limits. The phenomena of ceramide conformation transformation, cholesterol flip-flop, and specificity of lipid arrangement within the multilayered systems is observed during the simulation. This signifies the importance of model in capturing higher order structural transformations.

Multiscale Modeling of Skin Electroporation

Human skin, the largest external organ of the body, provides a selective barrier to therapeutics applied topically. The molecules having specific chemical and physical properties can only penetrate the deeper layer of the skin. However, the lag time for reaching a steady state in the deeper layer is generally of the order of hours. In order to deliver higher-molecular-weight, charged, and hydrophilic therapeutics in the deeper layer, the skin barrier must be breached. Electroporation is one of the methods used to breach the skin barrier for enhancement of drug permeation and reduction of lag time. However, the underlying mechanism responsible for the enhancement of drug permeation is not well understood. In this study, a multiscale model of skin electroporation is developed by connecting molecular phenomena to a macroscopic model. At the atomic scale, molecular dynamics simulations of the lipid matrix of the human stratum corneum (SC) were performed under the influence of an external electric field. The pores get formed during the electroporation process and the transport properties (diffusivity) of drug molecules are computed. The diffusion coefficient obtained during electroporation was found to be higher than passive diffusion. However, this alone could not explain the multifold increase in the drug flux on application of an electric field as observed in the experiments. Hence, a finite element method (FEM) model of the skin SC is also developed. The release of fentanyl through this model is compared with the available experimental results. Both experimental and simulated results of pore formation on application of an electric field and many folds' increase in drug flux are comparable. Once validated, the framework was used for the design of skin electroporation experiments (in silico) by changing the electric pulse parameters such as voltage, pulse duration, and number of pulses. This multiscale modeling framework provides valuable insight at the molecular and macroscopic levels to design the electroporation experiments. The framework can be utilized as a design tool for skin electroporation applications.

Superlubricity of Fullerene Derivatives Induced by Host-Guest Assembly

Fullerenes have been recognized as good candidates for solid lubricants. In this study, the microscale superlubricity of fullerene derivatives was accomplished by the construction of regular host-guest assembly structures. Herein, the host-guest assembly structures of fullerene derivatives were successfully constructed on a highly oriented pyrolytic graphite (HOPG) surface by introducing the macrocycles as the templates and were explicitly revealed by scanning tunneling microscopy (STM). Meanwhile, the nanotribological properties of the host-guest assemblies were measured using atomic force microscopy (AFM), revealing ultralow friction coefficients of 0.003-0.008, which could be attributed to the restriction on removal of fullerene molecules after introducing the templates. The interaction energies were calculated by density functional theory (DFT) method, which indicates the correlation between friction coefficients and interaction strength in the host-guest assemblies. The effort on fullerene-related superlubricity could extend the solid superlubrication systems and provide a novel pathway to explore the friction mechanisms at the molecular level.

Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations

Nanoparticles are being explored for topical and oral drug delivery applications as they can cross various biological barriers, for example, the intestinal epithelium. The ability of nanoparticles to cross barriers depends on their morphological and surface properties such as size, surface chemistry and shape, among others. The effect of nanoparticle size on their membrane permeability has been well studied both experimentally and theoretically. However, less attention has been given to understand the role of nanoparticle shape in their translocation across biological barrier membranes. Here, we report on the influence of the nanoparticle's shape, surface chemistry and concentration on their permeation across a human intestinal apical cell membrane model. A representative multicomponent lipid bilayer model of the human intestinal apical membrane was built. The free energy of permeation of nanoparticles across the model lipid bilayer was calculated using multiple umbrella sampling simulations. The interaction of these nanoparticles with the model lipid bilayer was captured using extensive microsecond unrestrained molecular dynamics simulations. We observed that: (a) irrespective of the surface chemistry, the efficacy of nanoparticle penetration across the lipid layer was in the order of rod > disc > sphere; (b) irrespective of the shape, apolar and nonpolar nanoparticles were found to locate in the interior of the lipid bilayer, whereas charged and polar nanoparticles were either adsorbed on the lipid headgroups or remained in the water layer; (c) apolar and nonpolar disc shaped nanoparticles had higher efficacy in permeation across the lipid bilayer as compared to disc and sphere shaped nanoparticles; and (d) at a higher concentration of nanoparticles, sphere and disc shaped nanoparticles exhibited more agglomeration as compared to rod shaped nanoparticles. Based on these outcomes, a few nanoparticles were designed which penetrated readily into the lipid layer and these nanoparticles were also able to co-deliver a therapeutic protein inside the lipid layer. The apical model lipid membrane and protocols used in this study can thus be utilized for the in silico design of nanoparticles for the oral delivery of therapeutics.

Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study

Passive permeation of CD across lipid bilayer is almost impossible. Forced permeation results membrane rupture.

Collective absorption of 2,4,6-trinitrotoluene into lipid membranes and its effects on bilayer properties. A computational study

The widely used explosive, 2,4,6-trinitrotoluene (TNT), is a highly toxic chemical, which can cause hepatitis, cataracts, jaundice and so on, in humans. The interaction between TNT and biological membranes is crucial for understanding its toxic effects. Here, we mainly focused on molecular-level mechanisms for the collective adsorption of TNT into lipid membranes and the corresponding effects on bilayer properties by all-atom molecular dynamics simulations. We revealed that TNT can readily form an aggregate in the aqueous phase and quickly approach the surface of the membrane. At low concentrations of TNT (7 mol%), the aggregate is unstable and breaks up after several nanoseconds, and then the dispersed TNT molecules enter the membrane alone. At high concentrations (14 mol%), the aggregate is adsorbed as a whole and remains stable inside the membrane. After some of the TNT is absorbed by the membrane, the remaining TNT across the membrane would have greater permeability, i.e., the calculated permeability coefficient (P) is increased from 1.7 × 10^-2 to 18.3 cm s^-1. Correspondingly, a higher bioconcentration factor (BCF) was also observed. The increased level is more pronounced in the presence of TNT aggregates (i.e., high concentrations). This phenomenon is closely related to the strong interaction between TNT molecules. The results suggested that TNT molecules that have entered into the membrane can facilitate the membrane uptake, permeation and bioaccumulation of subsequent TNT molecules, exhibiting a synergistic effect. This work has a certain significance for understanding the toxicity of TNT.

Drug/Vehicle Impacts and Formulation Centered Stratagems for Enhanced Transdermal Drug Permeation, Controlled Release and Safety: Unparalleled Past and Recent Innovations-An Overview

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Transdermal drug delivery systems (TDDS) are one of the fascinating unconventional drug delivery systems offering plentiful advantages of which patient compliance is of paramount importance. However, as a matter of fact, the transdermal delivery of drug molecules is absolutely a tedious job which is precisely influenced by a number of factors including penetration barrier properties of the skin, drug characteristics formulation allied issues, etc. Over the years, innumerable tremendous efforts have been made in transporting the drugs through the skin into the systemic circulation by noteworthy tactics. This paper discusses such revolutionary formulation based techniques that have been endeavored in achieving the enhanced skin permeation of drugs, controlled release, and safety.

Computer-Aided Design of Nanoparticles for Transdermal Drug Delivery

Human skin provides an excellent opportunity for drug delivery application. However, the delivery of hydrophilic drug and big protein molecules is challenging due to barrier provided by the top layer of skin known as stratum corneum (SC). The chemical permeation enhancers or specialized carriers such as nanoparticles (NPs) are needed which can deliver drug molecules into the deeper layer.Here, we describe the in silico design of nanoparticle carriers using molecular dynamics (MD) simulations for the transdermal drug delivery application. At first, setup of a skin lipid bilayer model is demonstrated. Further, nanoparticles are designed based on the Monte Carlo simulation technique. These nanoparticles are then tested on skin model using various MD simulation techniques.

Response of microbial membranes to butanol: interdigitation vs. disorder

Biobutanol production by fermentation is potentially a sustainable alternative to butanol production from fossil fuels. However, the toxicity of butanol to fermentative bacteria, resulting largely from cell membrane fluidization, limits production titers and is a major factor limiting the uptake of the technology. Here, studies were undertaken, in vitro and in silico, on the butanol effects on a representative bacterial (i.e. Escherichia coli) inner cell membrane. A critical butanol : lipid ratio for stability of 2 : 1 was observed, computationally, consistent with complete interdigitation. However, at this ratio the bilayer was ∼20% thicker than for full interdigitation. Furthermore, butanol intercalation induced acyl chain bending and increased disorder, measured as a 27% lateral diffusivity increase experimentally in a supported lipid bilayer. There was also a monophasic Tm reduction in butanol-treated large unilamellar vesicles. Both behaviours are inconsistent with an interdigitated gel. Butanol thus causes only partial interdigitation at physiological temperatures, due to butanol accumulating at the phospholipid headgroups. Acyl tail disordering (i.e. splaying and bending) fills the subsequent voids. Finally, butanol short-circuits the bilayer and creates a coupled system where interdigitated and splayed phospholipids coexist. These findings will inform the design of strategies targeting bilayer stability for increasing biobutanol production titers.

Computational Modeling of Realistic Cell Membranes

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

Molecular Dynamics Simulations of Membrane Permeability

This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.

Structural and barrier properties of the skin ceramide lipid bilayer: a molecular dynamics simulation study

Skin provides excellent protection against the harsh external environment and foreign substances. The lipid matrix of the stratum corneum, which contains various kinds of ceramides, plays a major role in the barrier function of the skin. Here we report a study of the effects of ceramide type on the structural and transport properties of ceramide bilayers using molecular dynamics (MD) simulations. Specifically, the effects of headgroup chemistry (number and positions of hydroxyl groups) and tail structure (unsaturation of the sphingoid moiety) on the structural and transport properties of various ceramide bilayers at 310 K were analyzed. Theoretical results for structural properties such as area per lipid, bilayer thickness, lateral arrangement, order parameter, and hydrogen bonding are reported here and compared with corresponding experimental data. Our study revealed that the presence of a double bond disrupts the bilayer packing, which leads to a low area compressibility modulus, a large area per lipid, and low bilayer thickness. Furthermore, the effect of structural changes on water permeation was studied using steered MD simulations. Water permeation was found to be influenced by headgroup polarity, chain packing, and the ability of the water to hydrogen bond with the ceramides. The molecular-level information obtained from the current study should aid the design of mixed bilayer systems with desired properties and provide the basis for the development of higher order coarse-grained models.

Effect of Chemical Permeation Enhancers on Skin Permeability: In silico screening using Molecular Dynamics simulations

Breaching of the skin barrier is essential for delivering active pharmaceutical ingredients (APIs) for pharmaceutical, dermatological and aesthetic applications. Chemical permeation enhancers (CPEs) are molecules that interact with the constituents of skin’s outermost and rate limiting layer stratum corneum (SC), and increase its permeability. Designing and testing of new CPEs is a resource intensive task, thus limiting the rate of discovery of new CPEs. In-silico screening of CPEs in a rigorous skin model could speed up the design of CPEs. In this study, we performed coarse grained (CG) molecule dynamics (MD) simulations of a multilayer skin lipid matrix in the presence of CPEs. The CPEs are chosen from different chemical functionalities including fatty acids, esters, and alcohols. A multi-layer in-silico skin model was developed. The CG parameters of permeation enhancers were also developed. Interactions of CPEs with SC lipids was studied in silico at three different CPE concentrations namely, 1% w/v, 3% w/v and 5% w/v. The partitioning and diffusion coefficients of CPEs in the SC lipids were found to be highly size- and structure-dependent and these dependencies are explained in terms of structural properties such as radial distribution function, area per lipid and order parameter. Finally, experimentally reported effects of CPEs on skin from the literature are compared with the simulation results. The trends obtained using simulations are in good agreement with the experimental measurements. The studies presented here validate the utility of in-silico models for designing, screening and testing of novel and effective CPEs.

Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy

It is well-known that fullerenes aggregate inside lipid membranes and that increasing the concentration may lead to (lethal) membrane rupture. It is not known, however, how aggregation and rupture depend on the lipid type, what physical mechanisms control this behavior and what experimental signatures detect such changes in membranes. In this paper, we attempt to answer these questions with molecular simulations, and we show that aggregation and membrane damage depend critically on the degree of saturation of the lipid acyl chains: unsaturated bonds, or "kinks", impose a subtle but crucial compartmentalization of the bilayer into core and surface regions leading to three distinct fullerene density maxima. In contrast, when the membrane has only fully saturated lipids, fullerenes prefer to be located close to the surface under the head groups until the concentration becomes too large and the fullerenes begin clustering. No clustering is observed in membranes with unsaturated lipids. The presence of "kinks" reverses the free energy balance; although the overall free energy profiles are similar, entropy is the dominant component in unsaturated bilayers whereas enthalpy controls the fully saturated ones. Fully saturated systems show two unique signatures: 1) membrane thickness behaves non-monotonously while the area per lipid increases monotonously. We propose this as a potential reason for the observations of low fullerene concentrations being effective against bacteria. 2) The fullerene-fullerene radial distribution function (RDF) shows splitting of the second peak indicating the emergence short-range order and the importance of the second-nearest neighbor interactions. Similar second peak splitting has been reported in metal glasses.

Fullerene-based delivery systems

With the development of new drugs, there have been many attempts to explore innovative delivery routes. Targeted delivery systems are a desired solution designed to overcome the deficiency of routine methods. To transform this idea into reality, a wide range of nanoparticles has been proposed and studied. These nanoparticles should interact well with biological environments and pass through cell membranes to deliver therapeutic molecules. One of the pioneer classes of carbon-based nanoparticles for targeted delivery is the fullerenes. Fullerenes have a unique structure and possess suitable properties for interaction with the cellular environment. This short review concentrates on newly developed fullerene derivatives and their potential as advanced delivery systems for pharmaceutical applications.

Coarse-Grained Simulations Using a Multipolar Force Field Model

This paper presents a coarse-grained molecular simulation for fullerenes based on a multipolar expansion method developed previously. The method is enabled by the construction of transferable united atoms potentials that approximate the full atomistic intermolecular interactions, as obtained from ab initio electronic structure calculations supplemented by empirical force fields and experimental data, or any combination of the above. The resultant series contains controllable moment tensors that allow to estimate the errors, and approaches the all-atom intermolecular potential as the expansion order increases. We can compute the united atoms potentials very efficiently with a few interaction moment tensors, in order to implement a parallel algorithm on molecular interactions. Our simulations describe the mechanism for the condensation of fullerenes, and they produce excellent agreement with benchmark fully atomistic molecular dynamics simulations.

Electroporation of Skin Stratum Corneum Lipid Bilayer and Molecular Mechanism of Drug Transport: A Molecular Dynamics Study

The electroporation technique has been used significantly to increase drug permeation through the skin. This technique relies on the application of short-timed (microseconds to millisecond) electric fields (generally, order of 50--300 V) on the skin to create microscopic pores. However, the molecular mechanism of pore formation, resulting in an enhanced flux of active molecules through the skin, remains poorly understood. In this study, extensive atomistic molecular dynamics simulation of skin lipids [made up of ceramide (CER), cholesterol (CHOL), and free fatty acid (FFA)] has been performed at various external electric fields. We show for the first time the pore formation in the skin lipid bilayer during electroporation. We show the effect of the applied external electrical field (0.6-1.0 V/nm) on the pore formation dynamics in the lipid bilayer of different sizes (154, 616, and 2464 lipids) and compositions (CER/CHOL/FFA, 1:0:0, 1:0:1, 1:1:0, 1:1:1). The pore formation and resealing kinetics were different and were found to be highly dependent on the composition of the skin lipid bilayer. The pore formation time decreased with increase in the bilayer size. The pore sustaining electric field was found to be in the range of 0.20-0.25 V/nm for equimolar CER, CHOL, and FFA lipid bilayers. The skin lipid bilayer (1:1:1) sealed itself within 20 ns after the removal of the external electric field. We also present the molecular mechanism of enhancement of drug permeation in the presence of external field as compared to the passive diffusion. The molecular-level understanding obtained here could help in optimizing/designing the electroporation experiments for effective drug delivery. For a given skin composition and size of the drug molecule, the combination of pore formation time and pore growth model can be used to know a priori the desired electric field and time for the application of the electric field.

Nanoparticle wrapping at small non-spherical vesicles: curvatures at play

Nanoparticles in biological systems encounter lipid-bilayer membranes as barriers. They interact with plasma membranes, membranous organelles, such as the endoplasmic reticulum and the Golgi apparatus, the nucleus, and intracellular and extracellular vesicles, such as autophagosomes, lysosomes, and exosomes. Extracellular vesicles have recently attracted particular attention, as they are involved in the transmission of biological signals and as regulators for biological processes. For example, exosomes, small vesicles containing proteins, mRNA, and miRNA, that are released by cells into the extracellular environment, have been suggested to participate in tumor metastasis. Furthermore, vesicles can be applied as targeted-drug-delivery systems. We systematically characterize wrapping of spherical nanoparticles that enter and exit vesicles, depending on particle size, vesicle size, vesicle reduced volume, and membrane spontaneous curvature. We predict the complex wrapping behavior, in particular for large particle-to-vesicle size ratios, where the shape changes of the free membrane contribute significantly to the deformation energy and where nanoparticle wrapping transitions and vesicle shape transitions are coupled. Partial-wrapped membrane-bound particles impose boundary conditions on the membrane that stabilise oblates and stomatocytes for particle entry, and prolates and stomatocytes for particle exit. Our results suggest that nanoparticles may stimulate autophagocytic engulfment, which would facilitate transport of the nanoparticles into lysosomes and would lead to subsequent degradation of nanoparticle-attached proteins.

In-silico design of nanoparticles for transdermal drug delivery application

Nanoparticles are used in the medical field for various applications like cell imaging, drug delivery, gene and si-RNA delivery, to name a few. Designing nanoparticles for a given application, purely based on the trial and error experimentation, requires a lot of time and effort. In this study we show that computer simulations could help in designing nanoparticles for drug delivery thus reducing the time and cost associated with their design, development and deployment. The permeation of nanoparticles, having various surface chemistries and patterns, through the skin lipid bilayer was studied using constrained and unconstrained molecular dynamics simulations. Interestingly, the permeation mechanism of nanoparticles having the same surface chemistry but different patterns was found to be completely different. Nanoparticles (NPs) were screened based on the free energy of permeation through the skin lipid bilayer. The behavior of the screened NPs was further validated with unconstrained simulations using the skin lipid bilayer. Nanoparticles thus screened through both of the techniques were further used for the co-delivery of a model protein into the skin lipid bilayer. It was observed that the nanoparticles having a 2 : 1 homogeneous ratio of hydrophobic to hydrophilic regions were the most promising in transdermal delivery of proteins. The obtained results are in line with the results of recent permeation experiments on cell and plasma membrane. Our study could help in in-silico design of nanoparticles for delivery of actives through skin. These in-silico experiments thus could help speed up the development process by guiding formulation chemists.

In-Silico Skin Model: A Multiscale Simulation Study of Drug Transport

Accurate in-silico models are required to predict the release of drug molecules through skin in order to supplement the in-vivo experiments for faster development/testing of drugs. The upper most layer of the skin, stratum corneum (SC), offers the main resistance for permeation of actives. Most of the SC's molecular level models comprise cholesterol and phospholipids only, which is far from reality. In this study we have implemented a multiscale modeling framework to obtain the release profile of three drugs, namely, caffeine, fentanyl, and naphthol, through skin SC. We report for the first time diffusion of drugs through a realistic skin molecular model comprised of ceramides, cholesterol, and free fatty acid. The diffusion coefficients of drugs in the SC lipid matrix were determined from multiple constrained molecular dynamics simulations. The calculated diffusion coefficients were then used in the macroscopic models to predict the release profiles of drugs through the SC. The obtained release profiles were in good agreement with available experimental data. The partition coefficient exhibits a greater effect on the release profiles. The reported multiscale modeling framework would provide insight into the delivery mechanisms of the drugs through the skin and shall act as a guiding tool in performing targeted experiments to come up with a suitable delivery system.