Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes

Molecular modelling of shockwave-mediated delivery of paclitaxel aggregates across the neuronal plasma membrane

Shock-assisted paclitaxel (PTX) transport across the blood-brain barrier offers a promising treatment strategy for brain tumors. Here, based on a realistically complex human brain plasma membrane (PM) model, we investigated the dynamic transmembrane behavior of a PTX cluster by shock induced bubble collapse, focusing on the effect of impulse (I), bubble diameter (D) and arrays. The results show that all three factors can control the transport depth (ΔDPM) of PTX. For a fixed D, the ΔDPM grows exponentially with I, ΔDPM ∼ exp (I), and eventually reaches a critical depth. But the depth, ΔDPM, can be adjusted linearly in a wider range of D. This mainly depends on the size of jets from bubble collapse. For bubble arrays, the bubbles in series can transport PTX deeper than a single bubble, while the parallel does the opposite. In addition, only PTX clusters in the range of jet action can be successfully transported. Finally, the absorption of PTX clusters was examined via recovery simulation. Not all PTX clusters across the membrane can be effectively absorbed by cells. The shallow PTX clusters are quickly attracted by the membrane and embedded into it. The critical depth at which PTX clusters can be effectively absorbed is about 20 nm. These molecular-level mechanisms and dynamic processes of PTX clusters crossing the PM membrane may be helpful in optimizing the application of shock-induced bubble collapse for the delivery of PTX to tumor cells.

Effects of Paclitaxel on Plasma Membrane Microviscosity and Lipid Composition in Cancer Cells

The cell membrane is an important regulator for the cytotoxicity of chemotherapeutic agents. However, the biochemical and biophysical effects that occur in the membrane under the action of chemotherapy drugs are not fully described. In the present study, changes in the microviscosity of membranes of living HeLa-Kyoto tumor cells were studied during chemotherapy with paclitaxel, a widely used antimicrotubule agent. To visualize the microviscosity of the membranes, fluorescence lifetime imaging microscopy (FLIM) with a BODIPY 2 fluorescent molecular rotor was used. The lipid profile of the membranes was assessed using time-of-flight secondary ion mass spectrometry ToF-SIMS. A significant, steady-state decrease in the microviscosity of membranes, both in cell monolayers and in tumor spheroids, was revealed after the treatment. Mass spectrometry showed an increase in the unsaturated fatty acid content in treated cell membranes, which may explain, at least partially, their low microviscosity. These results indicate the involvement of membrane microviscosity in the response of tumor cells to paclitaxel treatment.

Newly Synthesized Thymol Derivative and Its Effect on Colorectal Cancer Cells

Thymol affects various types of tumor cell lines, including colorectal cancer cells. However, the hydrophobic properties of thymol prevent its wider use. Therefore, new derivatives (acetic acid thymol ester, thymol β-D-glucoside) have been synthesized with respect to hydrophilic properties. The cytotoxic effect of the new derivatives on the colorectal cancer cell lines HT-29 and HCT-116 was assessed via MTT assay. The genotoxic effect was determined by comet assay and micronucleus analysis. ROS production was evaluated using ROS-Glo™ H₂O₂ Assay. We confirmed that one of the thymol derivatives (acetic acid thymol ester) has the potential to have a cyto/genotoxic effect on colorectal cancer cells, even at much lower (IC₅₀~0.08 μg/mL) concentrations than standard thymol (IC₅₀~60 μg/mL) after 24 h of treatment. On the other side, the genotoxic effect of the second studied derivative-thymol β-D-glucoside was observed at a concentration of about 1000 μg/mL. The antiproliferative effect of studied derivatives of thymol on the colorectal cancer cell lines was found to be both dose- and time-dependent at 100 h. Moreover, thymol derivative-treated cells did not show any significantly increased rate of micronuclei formation. New derivatives of thymol significantly increased ROS production too. The results confirmed that the effect of the derivative on tumor cells depends on its chemical structure, but further detailed research is needed. However, thymol and its derivatives have great potential in the prevention and treatment of colorectal cancer, which remains one of the most common cancers in the world.

Polarization Switching Method for Effective Free Energy Calculation of Membrane Translocation on the Nano-scale

Free-energy calculations are crucial for investigating biomolecular interactions on the Nano-scale level. However, in theoretical studies, the neglect of electronic polarization can jeopardize their accuracy and correct predictive capabilities, specifically...

Phase Behavior of Pure PSPC and PEGylated Multicomponent Lipid and Their Interaction with Paclitaxel: An All-Atom MD Study

Exploring structural behavior of pure 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine (PSPC) and multicomponent PSPC and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N[amino(poly(ethylene glycol))-2000] (DSPE-PEG₂₀₀₀) membranes and their interaction with pharmaceutically important drugs carry huge importance in drug delivery. Using all-atom molecular dynamics (MD) simulations, we investigated the phase behavior of pure and PEGylated membranes at the temperature range of 280-360 K. We observe a gel-to-liquid crystalline phase transition for pure PSPC between 320 and 330 K, and in the case of multicomponent membranes, at 320 K, a coexistence of order-disorder phases is observed, which gradually transform to a complete liquid crystalline to gel phase between 320 and 310 K. We further studied the interaction of Paclitaxel with pure PSPC and PEGylated bilayers and elucidated the interaction behavior of Paclitaxel at the bilayer interfaces. Understanding of structural and interaction behaviors of the PEGylated bilayers with Paclitaxel will help to explore Paclitaxel-based drug applications in the future.

Effects of cholesterol on chlorzoxazone translocation across POPC bilayer

Cholesterol plays a crucial role in modulating the physicochemical properties of membranes, thus influencing the membrane transport of drugs. In this paper, the effects caused by cholesterol on the membrane transport of chlorzoxazone (CZX), a centrally acting muscle relaxant drug, were probed through molecular dynamics simulations. POPC was selected as the model lipid, and three different cholesterol concentrations (0%, 20%, and 50% CHOL) were considered. The outcomes reveal that the area per lipid of POPC decreases and the order parameter increases with enhanced concentration of CHOL. CZX prefers to localize at the interface between the headgroup region and the hydrophobic tail region of POPC, and the main energy barrier occurs in the hydrophobic region. The impact of CHOL on the free energy profile is correlated with concentration: low concentration facilitates CZX permeation, while high concentration hinders CZX permeation. Our findings coincide with experimental results, enhancing the mechanism understanding of how drug molecules are transported through membranes in the presence of CHOL. • The effects caused by cholesterol (CHOL) on the membrane transport of chlorzoxazone (CZX) were studied. • Low CHOL concentration facilitates CZX permeation, while high concentration hinders CZX permeation. • Our findings improve the mechanism understanding of CHOL effects on CZX translocation across membrane.

Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers

Understanding the permeation of molecules through lipid membranes is fundamental for predicting the cellular uptake of solutes and drug delivery mechanisms. In molecular simulations, the usual approach is to compute the free energy (FE) profile of a molecule across a model lipid bilayer, which can then be used to estimate the permeability of the molecule. Umbrella Sampling (US), which involves carrying out a series of biased simulations along a defined reaction coordinate (usually the bilayer normal direction), is a popular method for the computation of such FE profiles. However, US can be challenging to implement because the results are dependent on the strength of the biasing potential and the spacing of windows along the reaction coordinate, which, in practice, are usually optimized by an inefficient trial and error approach. The Steered Molecular Dynamics implementation of the Jarzynski Equality (JE-SMD) has been identified as an alternative to equilibrium sampling methods for measuring the FE change across a reaction coordinate. In the JE-SMD approach, equilibrium FE values are evaluated from the average of rapid non-equilibrium trajectories, thus avoiding the practical issues that come with US. Here, we use three different corrections of the JE-SMD method to calculate the FE change for the translocation of two aromatic substrates, phenylalanine and toluene, across a lipid bilayer and compare the accuracy and computational efficiency of these approaches to the results obtained using US. We show evidence that when computing the free energy profile, the JE-SMD approach suffers from insufficient sampling convergence of the bilayer environment and is dependent on the characteristic of the aromatic substrate itself. We deduce that, despite its drawbacks, US remains the more viable approach of the two for computing the FE profile.

The Interaction of Supramolecular Anticancer Drug Amphiphiles with Phospholipid Membranes

The shape of drug delivery vehicles impacts both the circulation time and the effectiveness of the vehicle. Peptide-based drug amphiphiles (DAs) are promising new candidates as drug delivery vehicles that can self-assemble into shapes such as nanofilament and nanotube (diameter ~ 6-10 nm). The number of conjugated drugs affects the IC50 of these DAs, which is correlated to the effective cellular uptake. Characterizing and optimizing the interaction of these DAs and their assemblies with the cellular membrane is experimentally challenging. Long-time molecular dynamics can determine if the DA molecular structure affects the translocation across and interaction with the cellular membrane. Here, we report long-time atomistic simulation on Anton 2 (up to 25 μs) of these DAs with model cellular membranes. Results indicate that the interaction of these DAs with model cellular membranes is dependent on the number of conjugated drugs. We find that, with increased drug loading, the hydrophobic drug (camptothecin) builds up in the outer hydrophobic core of the membrane, pulling in positively charged peptide groups. Next, we computationally probe the interaction of differing shapes of these model drug delivery vehicles-nanofilament and nanotube-with the same model membranes, finding that the interaction of these nanostructures with the membrane is strongly repulsive. Results suggest that the hydrogen bond density between the nanostructure and the membrane may play a key role in modulating the interaction between the nanostructure and the membrane. Taken together, these results offer important insights for the rational design of peptide-based drug delivery vehicles.

Cholesterol-like Condensing Effect of Perfluoroalkyl Substances on a Phospholipid Bilayer

To understand the potential cytotoxicity of perfluoroalkyl substances (PFAS), we study their interactions with a model phospholipid bilayer membrane using molecular dynamics (MD) simulations. Four typical PFAS molecules are investigated, including perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorooctanesulfonic acid (PFOS), and perfluorohexane sulfonate (PFHxS). All of these PFAS molecules are found to spontaneously penetrate the lipid bilayer within a short simulation time (a few nanoseconds). During the penetration process, further free-energy analysis reveals that a PFAS molecule encounters an energy barrier at the bilayer/water interface. To overcome this free-energy barrier, the PFAS molecule flips itself at the interface. We further investigate the influence of embedded PFAS molecules on the membrane properties. All of the embedded PFAS molecules are found to produce a cholesterol-like condensing effect on the lipid bilayer, which includes increases of the order parameters of lipid tails and the thickness of the lipid bilayer and a decrease of area per lipid. Moreover, the PFAS molecules are found to form hydrogen bonds with oxygen atoms at three different positions of a lipid molecule. Our work reveals the penetration pathway of PFAS molecules entering into a lipid bilayer. In addition, the cholesterol-like condensing effect induced by embedded PFAS molecules on model membranes is systematically investigated and discussed. Our simulations can help understand the physical mechanisms of PFAS cytotoxicity.

Interaction of Camptothecin with Model Cellular Membranes

Accurate and efficient prediction of drug partitioning in model membranes is of significant interest to the pharmaceutical industry. Herein, we utilize advanced sampling methods, specifically, the adaptive biasing force methodology to calculate the potential of mean force for a model hydrophobic anticancer drug, camptothecin (CPT), across three model interfaces. We consider an octanol bilayer, a thick octanol/water interface, and a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/water interface. We characterize the enthalpic and entropic contributions of the drug to the potential of mean force. We show that the rotational entropy of the drug is inversely related to the probability of hydrogen bond formation of the drug with the POPC membrane. In addition, in long-time microsecond simulations of a high concentration of CPT above the POPC membrane, we show that strong drug-drug aromatic interactions shift the spatial orientation of the drug with the membrane. Stacks of hydrophobic drugs form, allowing penetration of the drug just under the POPC head groups. These results imply that inhomogeneous membrane models need to take into account the effect of drug aggregation on the membrane environment.

The aggregation of striped nanoparticles in mixed phospholipid bilayers

The unique and adjustable properties of nanoparticles present enormous opportunities for their use as targeted drug delivery vectors. For example, nanoparticles functionalized with key surface ligands have been shown to pass through phospholipid bilayers without causing localised disruption. However, the further effects nanoparticles have on multi-component phospholipid bilayers remain unclear. We use coarse-grained computational models to investigate the structural properties of mixed phospholipid bilayers in the presence of ligand-functionalized nanoparticles. Model bilayers are composed of DPPC, DUPC, DFPC and cholesterol, and the nanoparticles are striped with a hydrophobic-ligand band and charged-ligand spherical caps. Our results show that nanoparticles aggregate near unsaturated phospholipid regions, phospholipid bilayer phase-separation is promoted in the presence of nanoparticles, and the heterogeneous components of a phospholipid bilayer play a significant role in the lateral organization of nanoparticles. This study highlights the need for considering the complexity of realistic phospholipid bilayers when optimising ligand functionalized nanoparticles for efficient drug delivery vectors.

Investigating the effect of starch/Fe3O4 nanoparticles on biodesulfurization using molecular dynamic simulation

The application of dibenzothiophene (DBT) as a source of energy leads to air pollution. The key solution to overcome this drawback is desulfurization. Magnetic nanoparticles have shown an excellent performance in the desulfurization of dibenzothiophene. In this study, molecular dynamic (MD) simulation was considered for the first time to gain insight about the molecule interactions in the biodesulfurization (BDS) process of DBT using Rhodococcus erythropolis IGTS8, in the presence and absence of starch/magnetic nanoparticles. According to the MD simulation results, the density of the system in the presence of starch/Fe₃O₄ was ascending while in the absence of these nanoparticles, the density was descending. Starch/magnetic nanoparticles caused more rapid equilibrium state in the biodesulfurization process. The energy diagram showed that magnetic nanoparticles decrease the energy fluctuation and increase the difference of non-bounding energy and potential energy (8 times) compared to (BDS) without nanoparticle, which reflects higher bounded energy in the system using starch/magnetic nanoparticles. The height of RDF peak in the presence of starch/Fe₃O₄ was 4 times more than the RDF peak in the absence of nanoparticle. In addition, the nanoparticles decreased the fluctuations around optimal temperature in BDS up to 5% compared to other state.

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.

Enhanced Antitumor Efficacy Achieved Through Combination of nsPEFs and Low-Dosage Paclitaxel

Looking for a safe and effective cancer therapy for patients is becoming an important and promising research direction. Nanosecond pulsed electric field (nsPEF) has been found to be a potential non-thermal therapeutic technique with few side effects in pre-clinical studies. On the other hand, paclitaxel (PTX), as a common chemotherapeutic agent, shows full anti-tumor activities and is used to treat a wide variety of cancers. However, the delivery of PTX is challenging due to its poor aqueous solubility. Hence, high dosages of PTX have been used to achieve effective treatment, which creates some side effects. In this study, nsPEF was combined with low-level PTX, in order to validate if this combined treatment could bring about enhanced efficacy and allow reduced doses of PTX in clinical application. Cell proliferation, apoptosis, and cell cycle distribution were examined using MTT and flow cytometry assay, respectively. Results showed that combination treatments of nsPEF and PTX exhibited significant synergistic effects in vitro. The underlying mechanism might be that these two agents acted at different targets and coordinately enhanced MDA-MB-231 cell death.

Rational Design of Cholesterol Derivative for Improved Stability of Paclitaxel Cationic Liposomes

PURPOSE

This work explores synthesis of novel cholesterol derivative for the preparation of cationic liposomes and its interaction with Paclitaxel (PTX) within liposome membrane using molecular dynamic (MD) simulation and in-vitro studies.

METHODS

Cholesteryl Arginine Ethylester (CAE) was synthesized and characterized. Cationic liposomes were prepared using Soy PC (SPC) at a molar ratio of 77.5:15:7.5 of SPC/CAE/PTX. Conventional liposomes were composed of SPC/cholesterol/PTX (92:5:3 M ratio). The interaction between paclitaxel, ligand and the membrane was studied using 10 ns MD simulation. The interactions were studied using Differential Scanning Calorimetry (DSC) and Small Angle Neutron Scattering analysis. The efficacy of liposomes was evaluated by MTT assay and endothelial cell migration assay on different cell lines. The safety of the ligand was determined using the Comet Assay.

RESULTS

The cationic liposomes improved loading efficiency and stability compared to conventional liposomes. The increased PTX loading could be attributed to the hydrogen bond between CAE and PTX and deeper penetration of PTX in the bilayer. The DSC study suggested that inclusion of CAE in the DPPC bilayer eliminates T_g. SANS data showed that CAE has more pronounced membrane thickening effect as compared to cholesterol. The cationic liposomes showed slightly improved cytotoxicity in three different cell lines and improved endothelial cell migration inhibition compared to conventional liposomes. Furthermore, the COMET assay showed that CAE alone does not show any genotoxicity.

CONCLUSIONS

The novel cationic ligand (CAE) retains paclitaxel within the phospholipid bilayer and helps in improved drug loading and physical stability. Graphical Abstract ᅟ.

Three-Dimensional Microphase Separation and Synergistic Permeability in Stacked Lipid-Polymer Hybrid Membranes

We present new structures of soft-material thin films that augment the functionality of substrate-mediated delivery systems. A hybrid material composed of phospholipids and block copolymers adopts a multilayered membrane structure supported on a solid surface. The hybrid films comprise intentional intramembrane heterogeneities that register across multilayers. These stacked domains convey unprecedented enhancement and control of permeability of solutes across micrometer-thick films. Using grazing incidence X-ray scattering, phase contrast atomic force microscopy, and confocal microscopy, we observed that in each lamella, lipid and polymers partition unevenly within the membrane plane segregating into lipid- or polymer-rich domains. Interestingly, we found evidence that like-domains align in registry across multilayers, thereby making phase separation three-dimensional. Phase boundaries exist over extended length scales to compensate the height mismatch between lipid and polymer molecules. We show that microphase separation in hybrid films can be exploited to augment the capability of drug-eluting substrates. Lipid-polymer hybrid films loaded with paclitaxel show synergistic permeability of drug compared to single-component counterparts. We present a thorough structural study of stacked lipid-polymer hybrid membranes and propose that the presence of registered domains and domain boundaries impart enhanced drug release functionality. This work offers new perspectives in designing thin films for controlled delivery applications.

Naratriptan aggregation in lipid bilayers: perspectives from molecular dynamics simulations

In order to understand the interaction between naratriptan and a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC), we carried out molecular dynamics simulations. The simulations were performed considering neutral and protonated ionization states, starting from different initial conditions. At physiological pH, the protonated state of naratriptan is predominant. It is expected that neutral compounds could have larger membrane partition than charged compounds. However, for the specific case of triptans, it is difficult to study neutral species in membranes experimentally, making computer simulations an interesting tool. When the naratriptan molecules were originally placed in water, they partitioned between the bilayer/water interface and water phase, as has been described for similar compounds. From this condition, the drugs displayed low access to the hydrophobic environment, with no significant effects on bilayer organization. The molecules anchored in the interface, due mainly to the barrier function of the polar and oriented lipid heads. On the other hand, when placed inside the bilayer, both neutral and protonated naratriptan showed self-aggregation in the lipid tail environment. In particular, the protonated species exhibited a pore-like structure, dragging water through this environment. Graphical Abstract Different behaviour of Naratriptan and Sumatriptan, when the drugs were originally placed in the lipid core.

Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study

Compounds with nominally similar biological activity may exhibit differential toxicity due to differences in their interactions with cell membranes. Many pharmaceutical compounds are amphiphilic and can be taken up by phospholipid bilayers, interacting strongly with the lipid-aqueous interface whether or not subsequent permeation through the bilayer is possible. Bolaamphiphilic compounds, which possess two hydrophilic ends and a hydrophobic linker, can likewise undergo spontaneous uptake by bilayers. While membrane-spanning bolaamphiphiles can stabilize membranes, small molecules with this characteristic have the potential to create membrane defects via disruption of bilayer structure and dynamics. When compared to the amphiphilic therapeutic anticoagulant, warfarin, the bolaamphiphilic analogue, brodifacoum, exhibits heightened toxicity that goes beyond superior inhibition of the pharmacological target enzyme. We explore, herein, the consequences of anticoagulant accumulation in a dipalmitoylphosphatidylcholine (DPPC) bilayer. Coarse-grained molecular dynamics simulations reveal that permeation of phospholipid bilayers by brodifacoum causes a disruption of membrane barrier function that is driven by the bolaamphiphilic nature and size of this molecule. We find that brodifacoum partitioning into bilayers causes membrane thinning and permeabilization and promotes lipid flip-flop - phenomena that are suspected to play a role in triggering cell death. These phenomena are either absent or less pronounced in the case of the less toxic, amphiphilic compound, warfarin.

Molecular simulation of nonfacilitated membrane permeation

This is a review. Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.