Coarse-grained model for PEGylated lipids: effect of PEGylation on the size and shape of self-assembled structures

Rational design of magnetoliposomes for enhanced interaction with bacterial membrane models

There is a growing need for alternatives to target and treat bacterial infection. Thus, the present work aims to develop and optimize the production of PEGylated magnetoliposomes (MLPs@PEG), by encapsulating superparamagnetic iron oxide nanoparticles (SPIONs) within fusogenic liposomes. A Box-Behnken design was applied to modulate size distribution variables, using lipid concentration, SPIONs amount and ultrasonication time as independent variables. As a result of the optimization, it was possible to obtain MLPs@PEG with a mean size of 182 nm, with polydispersity index (PDI) of 0.19, and SPIONs encapsulation efficiency (%EE) around 76%. Cytocompatibility assays showed that no toxicity was observed in fibroblasts, for iron concentrations up to 400μg/ml. Also, for safe lipid and iron concentrations, no hemolytic effect was detected. The fusogenicity of the nanosystems was first evaluated through lipid mixing assays, based on Förster resonance energy transfer (FRET), using liposomal membrane models, mimicking bacterial cytoplasmic membrane and eukaryotic plasma membrane. It was shown that the hybrid nanosystems preferentially interact with the bacterial membrane model. Confocal microscopy and fluorescence lifetime measurements, using giant unilamellar vesicles (GUVs), validated these results. Overall, the developed hybrid nanosystem may represent an efficient drug delivery system with improved targetability for bacterial membrane.

A review on microfluidic-assisted nanoparticle synthesis, and their applications using multiscale simulation methods

Recent years have witnessed an increased interest in the development of nanoparticles (NPs) owing to their potential use in a wide variety of biomedical applications, including drug delivery, imaging agents, gene therapy, and vaccines, where recently, lipid nanoparticle mRNA-based vaccines were developed to prevent SARS-CoV-2 causing COVID-19. NPs typically fall into two broad categories: organic and inorganic. Organic NPs mainly include lipid-based and polymer-based nanoparticles, such as liposomes, solid lipid nanoparticles, polymersomes, dendrimers, and polymer micelles. Gold and silver NPs, iron oxide NPs, quantum dots, and carbon and silica-based nanomaterials make up the bulk of the inorganic NPs. These NPs are prepared using a variety of top-down and bottom-up approaches. Microfluidics provide an attractive synthesis alternative and is advantageous compared to the conventional bulk methods. The microfluidic mixing-based production methods offer better control in achieving the desired size, morphology, shape, size distribution, and surface properties of the synthesized NPs. The technology also exhibits excellent process repeatability, fast handling, less sample usage, and yields greater encapsulation efficiencies. In this article, we provide a comprehensive review of the microfluidic-based passive and active mixing techniques for NP synthesis, and their latest developments. Additionally, a summary of microfluidic devices used for NP production is presented. Nonetheless, despite significant advancements in the experimental procedures, complete details of a nanoparticle-based system cannot be deduced from the experiments alone, and thus, multiscale computer simulations are utilized to perform systematic investigations. The work also details the most common multiscale simulation methods and their advancements in unveiling critical mechanisms involved in nanoparticle synthesis and the interaction of nanoparticles with other entities, especially in biomedical and therapeutic systems. Finally, an analysis is provided on the challenges in microfluidics related to nanoparticle synthesis and applications, and the future perspectives, such as large-scale NP synthesis, and hybrid formulations and devices.

Effects of Lipid Shape and Interactions on the Conformation, Dynamics, and Curvature of Ultrasound-Responsive Liposomes

We perform coarse-grained molecular dynamics simulations of bilayers composed of various lipids and cholesterol at their different ratios. Simulations show that cholesterol-lipid interactions restrict the lateral dynamics of bilayers but also promote bilayer curvature, indicating that these opposite effects simultaneously occur and thus cannot significantly influence bilayer stability. In contrast, lyso-lipids effectively pack the vacancy in the bilayer composed of cone-shaped lipids and thus reduce bilayer dynamics and curvature, showing that bilayers are more significantly stabilized by lyso-lipids than by cholesterol, in agreement with experiments. In particular, the bilayer composed of cone-shaped lipids shows higher dynamics and curvature than does the bilayer composed of cylindrical-shaped lipids. To mimic ultrasound, a high external pressure was applied in the direction of bilayer normal, showing the formation of small pores that are surrounded by hydrophilic lipid headgroups, which can allow the release of drug molecules encapsulated into the liposome. These findings help to explain experimental observations regarding that liposomes are more significantly stabilized by lyso-lipids than by cholesterol, and that the liposome with cone-shaped lipids more effectively releases drug molecules upon applying ultrasound than does the liposome with cylindrical-shaped lipids.

CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids

A lipid nanoparticle (LNP) formulation is a state-of-the-art delivery system for genetic drugs such as DNA, messenger RNA, and small interfering RNA, which is successfully applied to COVID-19 vaccines and gains tremendous interest in therapeutic applications. Despite its importance, a molecular-level understanding of the LNP structures and dynamics is still lacking, which makes rational LNP design almost impossible. In this work, we present an extension of CHARMM-GUI Membrane Builder to model and simulate all-atom LNPs with various (ionizable) cationic lipids and PEGylated lipids (PEG-lipids). These new lipid types can be mixed with any existing lipid types with or without a biomolecule of interest, and the generated systems can be simulated using various molecular dynamics engines. As a first illustration, we considered model LNP membranes with DLin-KC2-DMA (KC2) or DLin-MC3-DMA (MC3) without PEG-lipids. The results from these model membranes are consistent with those from the two previous studies, albeit with mild accumulation of neutral MC3 in the bilayer center. To demonstrate Membrane Builder's capability of building a realistic LNP patch, we generated KC2- or MC3-containing LNP membranes with high concentrations of cholesterol and ionizable cationic lipids together with 2 mol % PEG-lipids. We observe that PEG-chains are flexible, which can be more preferentially extended laterally in the presence of cationic lipids due to the attractive interactions between their head groups and PEG oxygen. The presence of PEG-lipids also relaxes the lateral packing in LNP membranes, and the area compressibility modulus (KA) of LNP membranes with cationic lipids fit into typical KA of fluid-phase membranes. Interestingly, the interactions between PEG oxygen and the head group of ionizable cationic lipids induce a negative curvature. We hope that this LNP capability in Membrane Builder can be useful to better characterize various LNPs with or without genetic drugs for rational LNP design.

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.

CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids

A lipid nanoparticle (LNP) formulation is a state-of-the-art delivery system for genetic drugs such as DNA, mRNA, and siRNA, which is successfully applied to COVID-19 vaccines and gains tremendous interest in therapeutic applications. Despite its importance, a molecular-level understanding of the LNP structures and dynamics is still lacking, which makes a rational LNP design almost impossible. In this work, we present an extension of CHARMM-GUI Membrane Builder to model and simulate all-atom LNPs with various (ionizable) cationic lipids and PEGylated lipids (PEG-lipids). These new lipid types can be mixed with any existing lipid types with or without a biomolecule of interest, and the generated systems can be simulated using various molecular dynamics engines. As a first illustration, we considered model LNP membranes with DLin-KC2-DMA (KC2) or DLin-MC3-DMA (MC3) without PEG-lipids. The results from these model membranes are consistent with those from the two previous studies albeit with mild accumulation of neutral MC3 in the bilayer center. To demonstrate Membrane Builder's capability of building a realistic LNP patch, we generated KC2- or MC3-containing LNP membranes with high concentrations of cholesterol and ionizable cationic lipids together with 2 mol% PEG-lipids. We observe that PEG-chains are flexible, which can be more preferentially extended laterally in the presence of cationic lipids due to the attractive interactions between their head groups and PEG oxygen. The presence of PEG-lipids also relaxes the lateral packing in LNP membranes, and the area compressibility modulus (KA) of LNP membranes with cationic lipids fit into typical KA of fluid-phase membranes. Interestingly, the interactions between PEG oxygen and head group of ionizable cationic lipids induce a negative curvature. We hope that this LNP capability in Membrane Builder can be useful to better characterize various LNPs with or without genetic drugs for a rational LNP design.

Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails

We carried out a series of coarse-grained molecular dynamics liposome-copolymer simulations with varying extent of copolymer concentration in an attempt to understand the effect of copolymer structure and concentration on vesicle self-assembly and stability. For one particular case molecular dynamics simulation data was successfully verified against experimental NMR results enhancing the credulity in the simulation methodology. The study focused on a new class of promising copolymers based on ethylene oxide (EO) chains and short blocks of aliphatic double chains that mimic lipid tails. The lipid mimetic units are based on 1,3-didodecyloxy-2-glycidylglycerol (DDGG) and 1,3-didodecyloxy-propane-2-ol (DDP). The conducted simulations indicate that multiple lipid anchor-bearing copolymers lead to stable hybrid liposome formations. Single lipid bearing might incur liposome-stabilizing potential for relatively small ethylene oxide chains but fails dramatically in combination with a longer EO-based moiety. The consistency of the theoretical evidence with experimental NMR observation for certain cases provides confidence for the relevance of the methodology in eliciting the factors governing liposome-polymer stability which is of fundamental and practical significance.

Hydrophilic dangling chain interfacial segregation in polyurethane networks at aqueous interfaces and its underlying mechanisms: molecular dynamics simulations

Polymer networks with hydrophilic dangling chains are ideal candidates for many submerged applications, e.g., protein non-adhesive coatings with non-fouling behavior. The dangling chains segregate from the polymer network towards the water and form a brush-like structure at the interface. Several factors such as the polymer network structure, dangling chain length, and water/dangling chain interaction may all affect the interfacial performance of the polymer. Therefore, we employed a Martini based coarse-grained (CG) molecular dynamics (MD) simulation to elucidate the influences of the abovementioned parameters on dangling chain interfacial segregation. We built up several polyurethane (PU) networks based on poly(tetra methylene glycol) (PTMG), as a macrodiol, and methoxy poly(ethylene glycol) (mPEG), as a dangling chain, with varying molecular weights. We found out that the macrodiol/dangling chain length ratio considerably smaller than one impedes the migration of dangling chains towards the water interface, while the dangling chain hydrophilicity and length determine the polymer interfacial layer density/thickness. Then, we artificially changed the dangling chain affinity to water from an intermediate to a very attractive water/dangling chain interaction. We justified that a brush-like structure forms in two consecutive steps: first, a longitudinal, and then a lateral migration of dangling chains in water. The latter step results in a uniform interfacial layer over the polymer interface that mainly occurs in the case of the attractive water/dangling chain interaction.

Controlled Solvent Removal from Antiviral Drugs and Excipients in Solution Enables the Formation of Novel Combination Multi-Drug-Motifs in Pharmaceutical Powders Composed of Lopinavir, Ritonavir and Tenofovir

Diverging physicochemical properties of HIV drug combinations are challenging to formulate as a single dosage form. We have found that 2-to-4 hydrophilic and hydrophobic HIV drugs in combination can be stabilized with lipid excipients under a controlled solvent removal process to form a novel pharmaceutical powder distinct from typical amorphous material. This discovery has enabled production of a drug combination nanoparticle (DcNP) powder composed of 3 HIV drugs-water-insoluble lopinavir (LogP = 4.7) and ritonavir (LogP = 5.6) and water-soluble tenofovir (LogP = -1.6). DcNP powder, exhibiting repeating units of multi-drug-motifs (referred to as MDM), is made by dissolving all constituents in ethanolic solution, followed by controlled solvent removal. The DcNP powder intersperses chemically diverse drug molecules with lipid excipients to form repeating MDM units. The proposed MDM structure is consistent with data collected with X-ray diffraction, differential calorimetry, and time-of-flight secondary ion mass spectrometry. The successful assembly of chemically diverse drugs in MDM structure is likely due to a novel process of making drug combination powders. The method described here has successfully extended to formulating other clinically prescribed antiviral drug combinations, and thus may serve as a platform technology for developing drug combination nanoparticles for treating a wide range of chronic diseases.

Impeded Molecular Reorganization by Polyethylene Glycol Conjugation Revealed by X-ray Reflectivity and Diffraction Measurements

Polyethylene glycol (PEG) coatings have been widely applied in pharmaceutical and biomedical systems to prevent nonspecific protein absorption, increase vesicle blood circulation time, and sustain drug release. This study systematically investigated the planar interfacial organization of phospholipid monolayers containing various amounts of PEG conjugations before and after enzyme-catalyzed degradation of the lipids using X-ray reflectivity and grazing incidence X-ray diffraction techniques. Results showed that attaching PEG to the headgroup of the lipids up to 15 mol % had limited effects on molecular packing of the lipid monolayers in the condensed phase at the gas-liquid interface and negligible effects on the enzyme adsorption to the interface. After enzyme-catalyzed degradation, equimolar fatty acids and lyso PC were generated. The fatty acids together with the subphase Ca²⁺ self-assembled into highly organized multilayer domains at the interface. The X-ray measurements unambiguously revealed that the densely packed PEG markedly hindered microphase separation and formation of the palmitic acid-Ca²⁺ complexes.

Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications

Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.

Formation and Properties of a Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed through Molecular Dynamics Simulations

We have carried out coarse-grained molecular dynamics (MD) simulations to study the self-assembly procedure of a system of randomly placed lipid molecules, water beads, and a nanoparticle (NP). The self-assembly results in the formation of the nanoparticle-supported lipid bilayer (NPSLBL), with the self-assembly mechanism being driven by events such as the formation of small lipid clusters, merging of the lipid clusters in the vicinity of the NP to form NP-embedded vesicle with a pore, and collapsing of that pore to eventually form the equilibrated NPSLBL system overcoming a large free-energy barrier. Subsequently, we quantify the properties and the configurations of this NPSLBL system. We reveal that unlike our proposition of an equal number of lipid molecules occupying the inner and outer leaflets in a recent report studying the properties of a preassembled lipid bilayer, the equilibrated self-assembled NPSLBL system demonstrates a much larger number of lipid molecules occupying the outer leaflet as compared to the inner leaflet. Second, the thickness of the water layer entrapped between the NP and the inner leaflet shows similar values as predicted by experiments and our previous study. Finally, we reveal that, similar to our previous study, the diffusivity of the lipid molecules in the outer leaflet is larger than that in the inner leaflet but, due to higher temperature employed during our simulations, are even larger than that predicted by our previous study.

Facile Mixing of Phospholipids Promotes Self-Assembly of Low-Molecular-Weight Biodegradable Block Co-Polymers into Functional Vesicular Architectures

In this work, we have used low-molecular-weight (PEG12-b-PCL6, PEG12-b-PCL9 or PEG16-b-PLA38; MW, 1.25-3.45 kDa) biodegradable block co-polymers to construct nano- and micron-scaled hybrid (polymer/lipid) vesicles, by solvent dispersion and electroformation methods, respectively. The hybrid vesicles exhibit physical properties (size, bilayer thickness and small molecule encapsulation) of a vesicular boundary, confirmed by cryogenic transmission electron microscopy, calcein leakage assay and dynamic light scattering. Importantly, we find that these low MW polymers, on their own, do not self-assemble into polymersomes at nano and micron scales. Using giant unilamellar vesicles (GUVs) model, their surface topographies are homogeneous, independent of cholesterol, suggesting more energetically favorable mixing of lipid and polymer. Despite this mixed topography with a bilayer thickness similar to that of a lipid bilayer, variation in surface topology is demonstrated using the interfacial sensitive phospholipase A2 (sPLA2). The biodegradable hybrid vesicles are less sensitive to the phospholipase digestion, reminiscent of PEGylated vesicles, and the degree of sensitivity is polymer-dependent, implying that the nano-scale surface topology can further be tuned by its chemical composition. Our results reveal and emphasize the role of phospholipids in promoting low MW polymers for spontaneous vesicular self-assembly, generating a functional hybrid lipid-polymer interface.

Structure and dynamics of lipid membranes interacting with antivirulence end-phosphorylated polyethylene glycol block copolymers

The structure and dynamics of lipid membranes in the presence of extracellular macromolecules are critical for cell membrane functions and many pharmaceutical applications. The pathogen virulence-suppressing end-phosphorylated polyethylene glycol (PEG) triblock copolymer (Pi-ABAPEG) markedly changes the interactions with lipid vesicle membranes and prevents PEG-induced vesicle phase separation in contrast to the unphosphorylated copolymer (ABAPEG). Pi-ABAPEG weakly absorbs on the surface of lipid vesicle membranes and slightly changes the structure of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar vesicles at 37 °C, as evidenced by small angle neutron scattering. X-ray reflectivity measurements confirm the weak adsorption of Pi-ABAPEG on DMPC monolayer, resulting in a more compact DMPC monolayer structure. Neutron spin-echo results show that the adsorption of Pi-ABAPEG on DMPC vesicle membranes increases the membrane bending modulus κ.

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.

Shape and Phase Transitions in a PEGylated Phospholipid System

Poly(ethylene glycol) (PEG) polymers and PEG-conjugated lipids are widely used in bioengineering and drug transport applications. A PEG layer in a drug carrier increases hydrophilic repulsion, inhibits membrane fusion and serum opsonin interactions, and prolongs the storage and circulation time. It can also change the carrier shape and have an influence on many properties related to the content release of the carrier. In this paper, we focus on the physicochemical effects of PEGylation in the lipid bilayer. We introduce laurdanC as a fluorophore for shape recognition and phase transition detection. Together with laurdanC, cryogenic transmission electron microscopy, differential scanning calorimetry, molecular dynamics simulations, and small-angle X-ray scattering/wide-angle X-ray scattering, we acquire information of the particle/bilayer morphology and phase behavior in systems containing 1,2-dipalmitoyl- sn-glycero-3-phosphocholine:1,2-distearoyl- sn-glycero-3-phosphoethanolamine-PEG(2000) with different fractions. We find that PEGylation leads to two important and potentially usable features of the system. (1) Spherical vesicles present a window of elevated chain-melting temperatures and (2) lipid packing shape-controlled liposome-to-bicelle transition. The first finding is significant for targets requiring multiple release sequences and the second enables tuning the release by composition and the PEG polymer length. Besides drug delivery systems, the findings can be used in other smart soft materials with trigger-polymers as well.

Role of Ligand Conformation on Nanoparticle-Protein Interactions

Engineered biomedical nanoparticles (NPs) administered via intravenous routes are prone to associate to serum proteins. The protein corona can mask the NP surface functionalization and hamper the delivery of the NP to its biological target. The design of corona-free NPs relies on our understanding of the chemical-physical features of the NP surface driving the interaction with serum proteins. Here, we address, by computational means, the interaction between human serum albumin (HSA) and a prototypical monolayer-protected Au nanoparticle. We show that both the chemical composition (charge, hydrophobicity) and the conformational preferences of the ligands decorating the NP surface affect the NP propensity to bind HSA.

Molecular-Level "Observations" of the Behavior of Gold Nanoparticles in Aqueous Solution and Interacting with a Lipid Bilayer Membrane

We use coarse-grained molecular dynamics simulations to "observe" details of interactions between ligand-covered gold nanoparticles and a lipid bilayer model membrane. In molecular dynamics simulations, one puts the individual atoms and groups of atoms of the physical system to be "observed" into a simulation box, specifies the forms of the potential energies of interactions between them (ultimately quantum based), and lets them individually move classically according to Newton's equations of motion, based on the forces arising from the assumed potential energy forms. The atoms that are chemically bonded to each other stay chemically bonded, following known potentials (force fields) that permit internal degrees of freedom (internal rotation, torsion, vibrations), and the interactions between nonbonded atoms are simplified to Lennard-Jones forms (in our case) and coulombic (where electrical charges are present) in which the parameters are previously optimized to reproduce thermodynamic properties or are based on quantum electronic calculations. The system is started out at a reasonable set of coordinates for all atoms or groups of atoms, and then permitted to develop according to the equations of motion, one small step (usually 10 fs time step) at a time, for millions of steps until the system is at a quasi-equilibrium (usually reached after hundreds of nanoseconds). We then let the system play out its motions further for many nanoseconds to observe the behavior, periodically taking snapshots (saving all positions and energies), and post-processing the snapshots to obtain various average descriptions of the system. Alkanethiols of various lengths serve as examples of hydrophobic ligands and methyl-terminated PEG with various numbers of monomer units serve as examples of hydrophilic ligands. Spherical gold particles of various diameters as well as gold nanorods form the core to which ligands are attached. The nanoparticles are characterized at the molecular level, especially the distributions of ligand configurations and their dependence on ligand length, and surface coverage. Self-assembly of the bilayer from an isotropic solution and observation of membrane properties that correspond well to experimental values validate the simulations. The mechanism of permeation of a gold NP coated with either a hydrophobic or a hydrophilic ligand, and its dependence on surface coverage, ligand length, core diameter, and core shape, is investigated. Lipid response such as lipid flip-flops, lipid extraction, and changes in order parameter of the lipid tails are examined in detail. The mechanism of permeation of a PEGylated nanorod is shown to occur by tilting, lying down, rotating, and straightening up. The nature of the information provided by molecular dynamics simulations permits understanding of the detailed behavior of gold nanoparticles interacting with lipid membranes which in turn helps to understand why some known systems work better than others and aids the design of new particles and improvement of methods for preparing existing ones.

The role of traction in membrane curvature generation

Curvature of biological membranes can be generated by a variety of molecular mechanisms including protein scaffolding, compositional heterogeneity, and cytoskeletal forces. These mechanisms have the net effect of generating tractions (force per unit length) on the bilayer that are translated into distinct shapes of the membrane. Here, we demonstrate how the local shape of the membrane can be used to infer the traction acting locally on the membrane. We show that buds and tubes, two common membrane deformations studied in trafficking processes, have different traction distributions along the membrane and that these tractions are specific to the molecular mechanism used to generate these shapes. Furthermore, we show that the magnitude of an axial force applied to the membrane as well as that of an effective line tension can be calculated from these tractions. Finally, we consider the sensitivity of these quantities with respect to uncertainties in material properties and follow with a discussion on sources of uncertainty in membrane shape.

Simulation of Mixed Self-Assembled Monolayers on Gold: Effect of Terminal Alkyl Anchor Chain and Monolayer Composition

Self-assembling monolayers provide a reproducible synthetic microenvironment for tethering lipid bilayers to incorporate proteins and lay the ground for numerous applications in nanotechnology and biomedical engineering. Although the structure of single-component monolayers is well investigated, there is far less insight into the molecular behavior at the interface of mixed monolayers at different mole fractions. Here, we present and apply a novel procedure to simulate and analyze multicomponent self-assemblies of alkanethiols over a wide range of mole concentrations of anchoring compounds. In particular, the structural features of monolayers consisting of a matrix compound and either a short (C₈) or a long (C₁₆) anchor compound on Au(111)-like surfaces were investigated first using coarse-grained and subsequently full-atomistic molecular dynamics simulations. Different scenarios of spatial distributions (random vs clustering) of anchoring molecules on flat surfaces were probed. The results of the simulations are in excellent agreement with the experimental data from ellipsometry and infrared reflection absorption spectroscopy. For short anchoring molecules, a random spatial distribution in the matrix is obtained. At low, experimentally relevant anchor compound mole fractions < 0.1, only for long-chain (C₁₆)-terminal alkyls, phase segregation and self-association of the anchoring molecules can be observed, which are also seen in experiment.

Transferable MARTINI Model of Poly(ethylene Oxide)

Motivated by the deficiencies of the previous MARTINI models of poly(ethylene oxide) (PEO), we present a new model featuring a high degree of transferability. The model is parametrized on (a) a set of 8 free energies of transfer of dimethoxyethane (PEO dimer) from water to solvents of varying polarity; (b) the radius of gyration in water at high dilution; and (c) matching angle and dihedral distributions from atomistic simulations. We demonstrate that our model behaves well in five different areas of application: (1) it produces accurate densities and phase behavior or small PEO oligomers and water mixtures; (2) it yields chain dimensions in good agreement with the experiment in three different solvents (water, diglyme, and benzene) over a broad range of molecular weights (∼1.2 kg/mol to 21 kg/mol); (3) it reproduces qualitatively the structural features of lipid bilayers containing PEGylated lipids in the brush and mushroom regime; (4) it is able to reproduce the phase behavior of several PEO-based nonionic surfactants in water; and (5) it can be combined with the existing MARTINI PS to model PS-PEO block copolymers. Overall, the new PEO model outperforms previous models and features a high degree of transferability.

Simulations Study of Single-Component and Mixed n-Alkyl-PEG Micelles

Here, we study one-component and mixed n-alkyl-poly(ethylene glycol) (C mE n) micelles with varying poly(ethylene glycol) (PEG) chain lengths n using coarse-grained molecular simulations. These nonionic alkyl-PEG surfactants and their aggregates are widely used in bio and chemical technology. As expected, the simulations show that increasing the PEG chain length decreases the alkyl-PEG micelle core diameter and the aggregation number but also enhances PEG chain penetration to the core region and spreads the micelle corona. Both the core and corona density are heavily dependent on the PEG chain length and decrease with increasing PEG length. Furthermore, we find that the alkyl-PEG surfactants exhibit two distinct micellization modes: surfactants with short PEG chains as their hydrophilic heads aggregate with the PEG heads relatively extended. Their aggregation number and the PEG corona density are dictated by the core carbon density. For longer PEG chains, the PEG sterics, that is, the volume occupied by the PEG head group, becomes the critical factor limiting the aggregation. Finally, simulations of binary mixtures of alkyl-PEGs of two different PEG chain lengths show that even in the absence of core-freezing, the surfactants prefer the aggregate size of their single-component solutions with the segregation propelled via enthalpic contributions. The findings, especially as they provide a handle on the density and the density profile of the aggregates, raise attention to effective packing shape as a design factor of micellar systems, for example, drug transport, solubilization, or partitioning.

Design of Polyphosphate Inhibitors: A Molecular Dynamics Investigation on Polyethylene Glycol-Linked Cationic Binding Groups

Inorganic polyphosphate (polyP) released by human platelets has recently been shown to activate blood clotting and identified as a potential target for the development of novel antithrombotics. Recent studies have shown that polymers with cationic binding groups (CBGs) inhibit polyP and attenuate thrombosis. However, a good molecular-level understanding of the binding mechanism is lacking for further drug development. While molecular dynamics (MD) simulation can provide molecule-level information, the time scale required to simulate these large biomacromolecules makes classical MD simulation impractical. To overcome this challenge, we employed metadynamics simulations with both all-atom and coarse-grained force fields. The force field parameters for polyethylene glycol (PEG) conjugated CBGs and polyP were developed to carry out coarse-grained MD simulations, which enabled simulations of these large biomacromolecules in a reasonable time scale. We found that the length of the PEG tail does not impact the interaction between the (PEG) _n-CBG and polyP. As expected, increasing the number of the charged tertiary amine groups in the head group strengthens its binding to polyP. Our simulation shows that (PEG) _n-CBG initially form aggregates, mostly with the PEG in the core and the hydrophilic CBG groups pointing toward water; then the aggregates approach the polyP and sandwich the polyP to form a complex. We found that the binding of (PEG) _n-CBG remains intact against various lengths of polyP. Binding thermodynamics for two of the (PEG) _n-CBG/polyP systems simulated were measured by isothermal titration calorimetry to confirm the key finding of the simulations that the length PEG tail does not influence ligand binding to polyP.

Characterizing the structure and properties of dry and wet polyethylene glycol using multi-scale simulations

Multi-scale simulations to study the structure and material properties of PEG in dry and wet conditions.

Self-Assembled Ligands Targeting TLR7: A Molecular Level Investigation

Toll-like receptors (TLRs) are pattern recognition transmembrane proteins that play an important role in innate immunity. In particular, TLR7 plays a role in detecting nucleic acids derived from viruses and bacteria. The huge number of pathologies in which TLR7 is involved has led to an increasing interest in developing new compounds targeting this protein. Several conjugation strategies were proposed for TLR7 agonists to increase the potency while maintaining a low toxicity. In this work, we focus the attention on two promising classes of TLR7 compounds derived from the same pharmacophore conjugated with phospholipid and polyethylene glycol (PEG). A multidisciplinary investigation has been carried out by molecular dynamics (MD), dynamic light scattering (DLS), electron paramagnetic resonance (EPR), and cytotoxicity assessment. DLS and MD indicated how only the phospholipid conjugation provides the compound abilities to self-assemble in an orderly fashion with a maximal pharmacophore exposition to the solvent. Further EPR and cytotoxicity experiments highlighted that phospholipid compounds organize in stable aggregates and well interact with TLR7, whereas PEG conjugation was characterized by poorly stable aggregates at the cells surface. The methodological framework proposed in this study may be used to investigate, at a molecular level, the interactions generally occurring between aggregated ligands, to be used as drugs, and protein receptors.

Effects of temperature and PEG grafting density on the translocation of PEGylated nanoparticles across asymmetric lipid membrane

Plasma membrane internalization of nanoparticles (NPs) is important for their biomedical applications such as drug-delivery carriers. On one hand, in order to improve their half-life in circulation, PEGylation has been widely used. However, it may hinder the NPs' membrane internalization ability. On the other hand, higher temperature could enhance the membrane permeability and may affect the NPs' ability to enter into or exit from cells. To make full use of their advantages, we systematically investigated the effects of temperature and PEG density on the translocation of PEGylated nanoparticles across the plasma asymmetric membrane of eukaryotic cells, using near-atom level coarse-grained molecular dynamics simulations. Our results showed that higher temperature could accelerate the translocation of NPs across membranes by making lipids more disorder and faster diffusion. On the contrary, steric hindrance effects of PEG would inhibit NPs' translocation process and promote lipids flip-flops. The PEG chains could rearrange themselves to minimize the contacts between PEG and lipid tails during the translocation, which was similar to 'snorkeling effect'. Moreover, lipid flip-flops were affected by PEGylated density as well as NPs' translocation direction. Higher PEG grafting density could promote lipid flip-flops, but inhibit lipid extraction from bilayers. The consequence of lipid flip-flop and extraction was that the membranes got more symmetric.

Adsorption of plasma proteins onto PEGylated single-walled carbon nanotubes: The effects of protein shape, PEG size and grafting density

Single-walled carbon nanotubes (SWCNTs) covalently functionalized or noncovalently coated with polyethylene glycol (PEG) of different sizes (M_w=2000 and 5000) and grafting densities (5-16 PEGs per SWCNT) are simulated with human fibrinogen (HFG) and serum albumin (HSA). Proteins migrate toward the SWCNT, but their adsorption extents differ. The extent of the HFG-SWCNT binding decreases with increasing PEG size and grafting density because PEGs more completely cover SWCNTs and thus block hydrophobic interactions between HFGs and SWCNTs, which occurs on PEG-functionalized SWCNTs but not on PEG-coated ones. In particular, the HFG-SWCNT binding significantly decreases in the transition region of PEG conformation from mushroom to brush, where PEGs extend like brushes as described in the Alexander-de Gennes theory. While the HFG adsorption is modulated by PEG conformation, the HSA adsorption is much weaker and less influenced by PEG, because spherical HSAs can bind to the restricted area of the SWCNT and thus cannot bind to the SWCNT as tightly as do linear HFGs. These findings agree with experiments showing less adsorption of proteins on the SWCNT functionalized with larger and more PEGs, and support experimental suggestions regarding the dependence of protein adsorption on protein shape and the mushroom-brush transition of PEG conformation.

Effect of Chain Length on the Partition Properties of Poly(ethylene oxide): Comparison between MARTINI Coarse-Grained and Atomistic Models

The MARTINI coarse-grained beads are parameterized to match the partition coefficients of several organic molecules in different solvents. Here, we test the method when modeling the partitioning properties of poly(ethylene oxide) between solvents of different polarities. We show that, among the existing models, the latest model developed by Lee and co-workers [ Lee , H. ; Pastor , R. W. J. Phys. Chem. B 2011 , 115 , 7830 - 7837 ] is the one that most successfully reproduces the hydration free energy of short oligomers, although it predicts highly negative solvation free energies in octanol and hexane. We develop a new CG model matching the solvation free energy of the monomer in different solvents and propose a simple method to select the Lennard-Jones parameters that reproduce the desired partition coefficients. The model correctly reproduces water/hexane partition properties for oligomers up to 10 monomers but still suffers from a transferability problem for larger molecular weight.

Hyper-cell-permeable micelles as a drug delivery carrier for effective cancer therapy

Although PEGylated liposomes (PEG-LS) have been intensively studied as drug-delivery vehicles, the rigidity and the hydrophilic PEG corona of liposomal membranes often limits cellular uptake, resulting in insufficient drug delivery to target cells. Thus, it is necessary to develop a new type of lipid-based self-assembled nanoparticles capable of enhanced cellular uptake, tissue penetration, and drug release than conventional PEGylated liposomes. Herein, we describe a simple modification of bicellar formulation in which the addition of a PEGylated phospholipid produced a dramatic physicochemical change in morphology, i.e., the disc-shaped bicelle became a uniformly distributed ultra-small (∼12 nm) spherical micelle. The transformed lipid-based nanoparticles, which we termed hyper-cell-permeable micelles (HCPMi), demonstrated not only prolonged stability in serum but also superior cellular and tumoral uptake compared to a conventional PEGylated liposomal system (PEG-LS). In addition, HCPMi showed rapid cellular uptake and subsequent cargo release into the cytoplasm of cancer cells. Cells treated with HCPMi loaded with docetaxel (DTX) had an IC₅₀ value of 0.16 μM, compared with 0.78 μM with PEG-LS loaded with DTX, a nearly five-fold decrease in cell viability, indicating excellent efficiency in HCPMi uptake and release. In vivo tumor imaging analysis indicated that HCPMi penetrated deep into the tumor core and achieved greater uptake than PEG-LS. Results of HCPMi (DTX) treatment of allograft and xenograft mice in vivo showed high tumoral uptake and appreciable tumor retardation, with ∼70% tumor weight reduction in the SCC-7 allograft model. Taken together, these findings indicate that HCPMi could be developed further as a highly competent lipid-based drug-delivery system.

Morphology-Induced Defects Enhance Lipid Transfer Rates

Molecular transfer between nanoparticles has been considered to have important implications regarding nanoparticle stability. Recently, the interparticle spontaneous lipid transfer rate constant for discoidal bicelles was found to be very different from spherical, unilamellar vesicles (ULVs). Here, we investigate the mechanism responsible for this discrepancy. Analysis of the data indicates that lipid transfer is entropically favorable, but enthalpically unfavorable with an activation energy that is independent of bicelle size and long- to short-chain lipid molar ratio. Moreover, molecular dynamics simulations reveal a lower lipid dissociation energy cost in the vicinity of interfaces ("defects") induced by the segregation of the long- and short-chain lipids in bicelles; these defects are not present in ULVs. Taken together, these results suggest that the enhanced lipid transfer observed in bicelles arises from interfacial defects as a result of the hydrophobic mismatch between the long- and short-chain lipid species. Finally, the observed lipid transfer rate is found to be independent of nanoparticle stability.

Mechanistic Studies on the Self-Assembly of PLGA Patchy Particles and Their Potential Applications in Biomedical Imaging

Currently, several challenges prevent poly(lactic-co-glycolic acid) (PLGA) particles from reaching clinical settings. Among these is a lack of understanding of the molecular mechanisms involved in the formation of these particles. We have been studying in depth the formation of patchy polymeric particles. These particles are made of PLGA and lipid-polymer functional groups. They have unique patch-core-shell structural features: hollow or solid hydrophobic cores and a patchy surface. Previously, we identified the shear stress as the most important parameter in a patchy particle's formation. Here, we investigated in detail the role of shear stress in the patchy particle's internal and external structure using an integrative experimental and computational approach. By cross-sectioning the multipatch particles, we found lipid-based structures embedded in the entire PLGA matrix, which represents a unique finding in the PLGA field. By developing novel computational fluid dynamics and molecular dynamics simulations, we found that the shear stress determines the internal structure of the patchy particles. Equally important, we discovered that these particles emit a photoacoustic (PA) signal in the optical clinical imaging window. Our results show that particles with multiple patches emit a higher PA signal than single-patch particles. This phenomenon most likely is due to the fact that multipatchy particles absorb more heat than single-patchy particles as shown by differential scanning calorimetry analysis. Furthermore, we demonstrated the use of patchy polymeric particles as photoacoustic molecular probes both in vitro and in vivo studies. The fundamental studies described here will help us to design more effective PLGA carriers for a number of medical applications as well as to accelerate their medical translation.

Simulated Permeation and Characterization of PEGylated Gold Nanoparticles in a Lipid Bilayer System

PEGylated gold nanoparticles are considered suitable nanocarriers for use in biomedical applications and targeted drug delivery systems. In our previous investigation with the alkanethiol-functionalized gold nanoparticle, we found that permeation across a protein-free phospholipid membrane resulted in damaging effects of lipid displacement and water and ion leakage. In the present study, we carry out a series of coarse-grained molecular simulations to explore permeation of lipid bilayer systems by a PEGylated gold nanoparticle, especially at the bulk-liquid-lipid interface as well as the interface between the two lipid leaflets. Initially, we examine molecular-level details of a PEGylated gold nanoparticle (constructed from cycled annealing) in water and find a distribution of ligand configurations (from mushroom to brush states) present in nanoparticles with medium to high surface coverage. We also find that the characteristic properties of the PEGylated gold nanoparticle do not change when it is placed in a salt solution. In our permeation studies, we investigate events of water and ion penetration as well as lipid translocation while varying the ligand length, nanoparticle surface coverage, and ion concentration gradient of our system. Results from our studies show the following: (1) The number of water molecules in the interior of the membrane during ligand-coated nanoparticle permeation increases with PEGn-SH surface coverage, ligand length, and permeation velocity but is not sensitive to the ion concentration gradient. (2) Lipid molecules do not leave the membrane; instead they complete trans-bilayer lipid flip-flop with longer ligands and higher surface coverages. (3) The lack of formation of stable water pores prevents ion translocation. (4) The PEGylated nanoparticle causes less damage to the membrane overall due to favorable interactions with the lipid headgroups which may explain why experimentalists observe endocytosis of PEGylated nanocarriers in vivo.

Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion

A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems

Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.