Molecular Dynamics Simulation of PEGylated Bilayer Interacting with Salt Ions: A Model of the Liposome Surface in the Bloodstream

Molecular insights into the interactions between PEG carriers and drug molecules from Celastrus hindsii: a multi-scale simulation study

Efficient drug delivery is crucial for the creation of effective pharmaceutical treatments, and polyethylene glycol (PEG) carriers have been emerged as promising candidates for this purpose due to their bio-compatibility, enhancement of drug solubility, and stability. In this study, we utilized molecular simulations to examine the interactions between PEG carriers and selected drug molecules extracted from Celastrus hindsii: Hindsiilactone A, Hindsiiquinoflavan B, Maytenfolone A, and Celasdin B. The simulations provided detailed insights into the binding affinity, stability, and structural properties of these drug molecules when complexed with PEG carriers. A multi-scale approach combining density functional theory (DFT), extended tight-binding (xTB), and molecular dynamics (MD) simulations was conducted to investigate both unbound and bound states of PEG/drug systems. The results from DFT and xTB calculations revealed that the unbound complex has an unfavorable binding free energy, primarily due to negative contributions of delta solvation free energy and entropy. The MD simulations provided more detailed insights into the interactions between PEG and drug molecules in water solutions. By integrating the findings from the multi-scale simulations, a comprehensive picture of the unbound and bound states of PEG and drug systems were obtained. This information is valuable for understanding the molecular mechanisms governing the binding of drugs in PEG-based delivery platforms, and it contributes to the rational design and optimization of these systems.

A mechanistic study on the cellular uptake, intracellular trafficking, and antisense gene regulation of bottlebrush polymer-conjugated oligonucleotides

We have developed a non-cationic transfection vector in the form of bottlebrush polymer-antisense oligonucleotide (ASO) conjugates. Termed pacDNA (polymer-assisted compaction of DNA), these agents show improved biopharmaceutical characteristics and antisense potency in vivo while suppressing non-antisense side effects. Nonetheless, there still is a lack of the mechanistic understanding of the cellular uptake, subcellular trafficking, and gene knockdown with pacDNA. Here, we show that the pacDNA enters human non-small cell lung cancer cells (NCI-H358) predominantly by scavenger receptor-mediated endocytosis and macropinocytosis and trafficks via the endolysosomal pathway within the cell. The pacDNA significantly reduces a target gene expression (KRAS) in the protein level but not in the mRNA level, despite that the transfection of certain free ASOs causes ribonuclease H1 (RNase H)-dependent degradation of KRAS mRNA. In addition, the antisense activity of pacDNA is independent of ASO chemical modification, suggesting that the pacDNA always functions as a steric blocker.

Engineering and Validation of a Peptide-Stabilized Poly(lactic-co-glycolic) Acid Nanoparticle for Targeted Delivery of a Vascular Disruptive Agent in Cancer Therapy

Developing a biocompatible and biodegradable nanoparticle (NP) carrier that integrates drug-loading capability, active targeting, and imaging modality is extremely challenging. Herein, we report an NP with a core of poly(lactic-co-glycolic) acid (PLGA) chemically modified with the drug combretastatin A4 (CA4), a vascular disrupting agent (VDA) in clinical development for ovarian cancer (OvCA) therapy. The NP is stabilized with a short arginine-glycine-aspartic acid-phenylalanine x3 (RGDFFF) peptide via self-assembly of the peptide on the PLGA surface. Importantly, the use of our RGDFFF coating replaces the commonly used polyethylene glycol (PEG) polymer that itself often induces an unwanted immunogenic response. In addition, the RGD motif of the peptide is well-known to preferentially bind to αvβ3 integrin that is implicated in tumor angiogenesis and is exploited as the NP's targeting component. The NP is enhanced with an optical imaging fluorophore label via chemical modification of the PLGA. The RGDFFF-CA4 NPs are synthesized using a nanoprecipitation method and are ∼75 ± 3.7 nm in diameter, where a peptide coating comprises a 2-3 nm outer layer. The NPs are serum stable for 72 h. In vitro studies using human umbilical cord vascular endothelial cells (HUVEC) confirmed the high uptake and biological activity of the RGDFFF-CA4 NP. NP uptake and viability reduction were demonstrated in OvCA cells grown in culture, and the NPs efficiently accumulated in tumors in a preclinical OvCA mouse model. The RGDFFF NP did not induce an inflammatory response when cultured with immune cells. Finally, the NP was efficiently taken up by patient-derived OvCA cells, suggesting a potential for future clinical applications.

A Long-Circulating Vector for Aptamers Based upon Polyphosphodiester-Backboned Molecular Brushes

Aptamers face challenges for use outside the ideal conditions in which they are developed. These difficulties are most palpable in vivo due to nuclease activities, rapid clearance, and off-target binding. Herein, we demonstrate that a polyphosphodiester-backboned molecular brush can suppress enzymatic digestion, reduce non-specific cell uptake, enable long blood circulation, and rescue the bioactivity of a conjugated aptamer in vivo. The backbone along with the aptamer is assembled via solid-phase synthesis, followed by installation of poly(ethylene glycol) (PEG) side chains using a two-step process with near-quantitative efficiency. The synthesis allows for precise control over polymer size and architecture. Consisting entirely of building blocks that are generally recognized as safe for therapeutics, this novel molecular brush is expected to provide a highly translatable route for aptamer-based therapeutics.

Ferroptosis-induced anticancer effect of resveratrol with a biomimetic nano-delivery system in colorectal cancer treatment

Ferroptosis is a novel form of programmed cell death impelled by iron-dependent lipid peroxidation, which may be a potential strategy for cancer therapy. Here we demonstrated for the first time that Resveratrol (RSV), a traditional Chinese medicine (TCM) chemical monomer, could effectually inhibit the growth of colon cancer cells through the ROS-dependent ferroptosis pathway. Mechanistically, RSV evoked the increase of reactive oxygen species and lipid peroxidation in colorectal cancer cells, and eventually lead to ferroptosis. Furthermore, RSV could promote ferroptosis by downregulating the expression of the channel protein solute carrier family 7 member 11 (SLC7A11) and glutathione peroxidase 4 (GPX4). To improve the delivery efficiency of RSV, a biomimetic nanocarrier was developed by coating RSV-loaded poly(ε-caprolactone)–poly(ethylene glycol) (PCL-PEG) nanoparticles with erythrocyte membrane (RSV-NPs@RBCm). The RSV-NPs@RBCm provide the possibility to escape macrophage phagocytosis and have a long circulation effect. In addition, when coupled with a tumor-penetrating peptide iRGD, which could trigger enhanced tissue penetration tumor-specifically, the delivery of RSV-NPs@RBCm into tumors would be significantly improved results from the in vivo study demonstrated an excellent treatment efficacy for CRC. Altogether, our study highlighted the therapeutic potential of RSV as a ferroptosis-inducing anticancer agent and when loaded into a biomimetic nanoplatform, it might pave the way for the application of RSV loaded nanosystems for colorectal cancer treatment.

An update on dual targeting strategy for cancer treatment

The key issue in the treatment of solid tumors is the lack of efficient strategies for the targeted delivery and accumulation of therapeutic cargoes in the tumor microenvironment (TME). Targeting approaches are designed for more efficient delivery of therapeutic agents to cancer cells while minimizing drug toxicity to normal cells and off-targeting effects, while maximizing the eradication of cancer cells. The highly complicated interrelationship between the physicochemical properties of nanoparticles, and the physiological and pathological barriers that are required to cross, dictates the need for the success of targeting strategies. Dual targeting is an approach that uses both purely biological strategies and physicochemical responsive smart delivery strategies to increase the accumulation of nanoparticles within the TME and improve targeting efficiency towards cancer cells. In both approaches, either one single ligand is used for targeting a single receptor on different cells, or two different ligands for targeting two different receptors on the same or different cells. Smart delivery strategies are able to respond to triggers that are typical of specific disease sites, such as pH, certain specific enzymes, or redox conditions. These strategies are expected to lead to more precise targeting and better accumulation of nano-therapeutics. This review describes the classification and principles of dual targeting approaches and critically reviews the efficiency of dual targeting strategies, and the rationale behind the choice of ligands. We focus on new approaches for smart drug delivery in which synthetic and/or biological moieties are attached to nanoparticles by TME-specific responsive linkers and advanced camouflaged nanoparticles.

Fusion-Induced Growth of Biomimetic Polymersomes: Behavior of Poly(dimethylsiloxane)-Poly(ethylene oxide) Vesicles in Saline Solutions Under High Agitation

Giant unilamellar vesicles serve as membrane models and primitive mockups of natural cells. With respect to the latter use, amphiphilic polymers can be used to replace phospholipids in order to introduce certain favorable properties, ultimately allowing for the creation of truly synthetic cells. These new properties also enable the employment of new preparation procedures that are incompatible with the natural amphiphiles. Whereas the growth of lipid compartments to micrometer dimensions has been well established, growth of their synthetic analogs remains underexplored. Here, the influence of experimental parameters like salt type/concentration and magnitude of agitation on the fusion of nanometer-sized vesicles made of poly(dimethylsiloxane)-poly(ethylene oxide) graft copolymer (PDMS-g-PEO) is investigated in detail. To this end, dynamic light scattering, microscopy, and membrane mixing assays are employed, and the process at different time and length scales is analyzed. This optimized method is used as an easy tool to obtain giant vesicles, equipped with membrane and cytosolic biomachinery, in the presence of salts at physiological concentrations.

En route to dynamic life processes by SNARE-mediated fusion of polymer and hybrid membranes

A variety of artificial cells springs from the functionalization of liposomes with proteins. However, these models suffer from low durability without repair and replenishment mechanisms, which can be partly addressed by replacing the lipids with polymers. Yet natural membranes are also dynamically remodeled in multiple cellular processes. Here, we show that synthetic amphiphile membranes also undergo fusion, mediated by the protein machinery for synaptic secretion. We integrated fusogenic SNAREs in polymer and hybrid vesicles and observed efficient membrane and content mixing. We determined bending rigidity and pore edge tension as key parameters for fusion and described its plausible progression through cryo-EM snapshots. These findings demonstrate that dynamic membrane phenomena can be reconstituted in synthetic materials, thereby providing new tools for the assembly of synthetic protocells.

Mechanistic Insight into How PEGylation Reduces the Efficacy of pH-Sensitive Liposomes from Molecular Dynamics Simulations

Liposome-based drug delivery systems composed of DOPE stabilized with cholesteryl hemisuccinate (CHMS) have been proposed as a drug delivery mechanism with pH-triggered release as the anionic form (CHSa) is protonated (CHS) at reduced pH; PEGylation is known to decrease this pH sensitivity. In this manuscript, we set out to use molecular dynamics (MD) simulations with a model with all-atom resolution to provide insight into why incorporation of poly(ethyleneglycol) (PEG) into DOPE–CHMS liposomes reduces their pH sensitivity; we also address two additional questions: (1) How CHSa stabilizes DOPE bilayers into a lamellar conformation at a physiological pH of 7.4? and (2) how the change from CHSa to CHS at acidic pH triggers the destabilization of DOPE bilayers? We found that (A) CHSa stabilizes the DOPE lipid membrane by increasing the hydrophilicity of the bilayer surface, (B) when CHSa changes to CHS by pH reduction, DOPE bilayers are destabilized due to a reduction in bilayer hydrophilicity and a reduction in the area per lipid, and (C) PEG stabilizes DOPE bilayers into the lamellar phase, thus reducing the pH sensitivity of the liposomes by increasing the area per lipid through penetration into the bilayer, which is our main focus.

Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems

Lipid nanoparticles (LNPs) have been widely applied in drug and gene delivery. More than twenty years ago, DoxilTM was the first LNPs-based drug approved by the US Food and Drug Administration (FDA). Since then, with decades of research and development, more and more LNP-based therapeutics have been used to treat diverse diseases, which often offer the benefits of reduced toxicity and/or enhanced efficacy compared to the active ingredients alone. Here, we provide a review of recent advances in the development of efficient and robust LNPs for drug/gene delivery. We emphasize the importance of rationally combining experimental and computational approaches, especially those providing multiscale structural and functional information of LNPs, to the design of novel and powerful LNP-based delivery systems.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

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.

In Vitro and in Vivo Behavior of Liposomes Decorated with PEGs with Different Chemical Features

The colloidal stability, in vitro toxicity, cell association, and in vivo pharmacokinetic behavior of liposomes decorated with monomethoxy-poly(ethylene glycol)-lipids (mPEG-lipids) with different chemical features were comparatively investigated. Structural differences of the mPEG-lipids used in the study included: (a) surface-anchoring moiety [1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE), cholesterol (Chol), and cholane (Chln)]; (b) mPEG molecular weight (2 kDa mPEG₄₅ and 5 kDa mPEG₁₁₄); and (c) mPEG shape (linear and branched PEG). In vitro results demonstrated that branched (mPEG₁₁₄)₂-DSPE confers the highest stealth properties to liposomes (∼31-fold lower cell association than naked liposomes) with respect to all PEGylating agents tested. However, the pharmacokinetic studies showed that the use of cholesterol as anchoring group yields PEGylated liposomes with longer permeance in the circulation and higher systemic bioavailability among the tested formulations. Liposomes decorated with mPEG₁₁₄-Chol had 3.2- and ∼2.1-fold higher area under curve (AUC) than naked liposomes and branched (mPEG₁₁₄)₂-DSPE-coated liposomes, respectively, which reflects the high stability of this coating agent. By comparing the PEGylating agents with same size, namely, linear 5 kDa PEG derivatives, linear mPEG₁₁₄-DSPE yielded coated liposomes with the best in vitro stealth performance. Nevertheless, the in vivo AUC of liposomes decorated with linear mPEG₁₁₄-DSPE was lower than that obtained with liposomes decorated with linear mPEG₁₁₄-Chol. Computational molecular dynamics modeling provided additional insights that complement the experimental results.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

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.

Rational Design of Cancer Nanomedicine for Simultaneous Stealth Surface and Enhanced Cellular Uptake

Owing to the complex and still not fully understood physiological environment, the development of traditional nanosized drug delivery systems is very challenging for precision cancer therapy. It is very difficult to control the in vivo distribution of nanoparticles after intravenous injection. The ideal drug nanocarriers should not only have stealth surface for prolonged circulation time but also possess enhanced cellular internalization in tumor sites. Unfortunately, the stealth surface and enhanced cellular uptake seem contradictory to each other. How to integrate the two opposite aspects into one system is a very herculean but meaningful task. As an alternative drug delivery strategy, chameleon-like drug delivery systems were developed to achieve long circulation time while maintaining enhanced cancer cell uptake. Such drug nanocarriers can "turn off" their internalization ability during circulation. However, the enhanced cellular uptake can be readily activated upon arriving at tumor tissues. In this way, stealth surface and enhanced uptake are of dialectical unity in drug delivery. In this review, we focus on the surface engineering of drug nanocarriers to obtain simultaneous stealth surfaces in circulation and enhanced uptake in tumors. The current strategies and ongoing developments, including programmed tumor-targeting strategies and some specific zwitterionic surfaces, will be discussed in detail.

Cleavable PEGylation: a strategy for overcoming the "PEG dilemma" in efficient drug delivery

To prolong the circulation time of drug, PEGylation has been widely used via the enhanced permeability and retention (EPR) effect, thereby providing new hope for better treatment. However, PEGylation also brings the "PEG dilemma", which is difficult for the cellular absorption of drugs and subsequent endosomal escape. As a result, the activity of drugs is inevitably lost after PEG modification. To achieve successful drug delivery for effective treatment, the crucial issue associated with the use of PEG-lipids, that is, “PEG dilemma” must be addressed. In this paper, we introduced the development and application of nanocarriers with cleavable PEGylation, and discussed various strategies for overcoming the PEG dilemma. Compared to the traditional ones, the vehicle systems with different environmental-sensitive PEG-lipids were discussed, which cleavage can be achieved in response to the intracellular as well as the tumor microenvironment. This smart cleavable PEGylation provides us an efficient strategy to overcome “PEG dilemma”, thereby may be a good candidate for the cancer treatment in future.

Comparison of Carboxybetaine with Sulfobetaine as Lipid Headgroup Involved in Intermolecular Interaction between Lipids in the Membrane

Diacylglycerides (DAGs) constitute an important category of lipids owing to their ability to form a lipid membrane, which can be used in a wide variety of biomedical applications. DAGs often include a zwitterionic polar headgroup that can influence the properties of the lipid membrane (e.g., protein adsorption, ion binding, hydration, membrane fluidity, phase stability) and affect their applicability. To clarify the effect of the charge arrangement of zwitterionic headgroups on intermolecular interactions in the DAG bilayers, we investigated the intermolecular interaction between a naturally occurring DAG (1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)) and synthetic DAGs (which is called "inverse charge zwitterlipids (ICZLs)") whose headgroup charges were antiparallel with respect to those of DPPC. We used 1,2-dipalmitoyl-sn-glycero-3-carboxybetaine (DPCB) and 1,2-dipalmitoyl-sn-glycero-3-sulfobetaine (DPSB) as ICZLs and compared two combinations of the lipids (DPPC-DPCB and DPPC-DPSB). We obtained surface pressure-area (π-A) isotherms to elucidate the intermolecular interaction between the lipids in the monolayer at the air/water interface. We found shrinkage of the area per molecule in both lipid combinations, indicating that mixing DPPC with ICZLs results in an attractive intermolecular force. As an overall trend, the degree of shrinkage of the mixed monolayer and the thermodynamic favorability of mixing were greater in the DPPC-DPCB combination than in the DPPC-DPSB combination. These trends were also observed in the lipid bilayers, as determined from the gel-to-liquid crystal phase transition temperature (T c) of the aqueous dispersion of the lipid vesicles. In the highly compressed lipid monolayers and vesicles (lipid bilayer), the molar fractions of ICZLs, in which the intermolecular interaction reached a maximum, were 0.6-0.8 for the DPPC-DPCB combination and 0.5 (equimolar composition) for the DPPC-DPSB combination. Therefore, in the compressed monolayers and bilayers, the mechanism of intermolecular interaction between DPPC and DPCB is different from that between DPPC and DPSB.

Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles

In this study, the dopamine-lipid bilayer interactions were probed with three physiologically relevant ion compositions using atomistic molecular dynamics simulations and free energy calculations. The in silico results indicate that calcium is able to decrease significantly the binding of dopamine to a neutral (zwitterionic) phosphatidylcholine lipid bilayer model mimicking the inner leaflet of a presynaptic vesicle. We argue that the observed calcium-induced effect is likely in crucial role in the neurotransmitter release from the presynaptic vesicles docked in the active zone of nerve terminals. The inner leaflets of presynaptic vesicles, which are responsible for releasing neurotransmitters into the synaptic cleft, are mainly composed of neutral lipids such as phosphatidylcholine and phosphatidylethanolamine. The neutrality of the lipid head group region, enhanced by a low pH level, should limit membrane aggregation of transmitters. In addition, the simulations suggest that the high calcium levels inside presynaptic vesicles prevent even the most lipophilic transmitters such as dopamine from adhering to the inner leaflet surface, thus rendering unhindered neurotransmitter release feasible.

A computational study suggests that replacing PEG with PMOZ may increase exposure of hydrophobic targeting moiety

In a previous study we showed that the cause of failure of a new, proposed, targeting ligand, the AETP moiety, when attached to a PEGylated liposome, was occlusion by the poly(ethylene glycol) (PEG) layer due to its hydrophobic nature, given that PEG is not entirely hydrophilic. At the time we proposed that possible replacement with a more hydrophilic protective polymer could alleviate this problem. In this study we have used computational molecular dynamics modelling, using a model with all atom resolution, to suggest that a specific alternative protective polymer, poly(2-methyloxazoline) (PMOZ), would perform exactly this function. Our results show that when PEG is replaced by PMOZ the relative exposure to the solvent of AETP is increased to a level even greater than that we found in previous simulations for the RGD peptide, a targeting moiety that has previously been used successfully in PEGylated liposome based therapies. While the AETP moiety itself is no longer under consideration, the results of this computational study have broader significance: the use of PMOZ as an alternative polymer coating to PEG could be efficacious in the context of more hydrophobic targeting ligands. In addition to PMOZ we studied another polyoxazoline, poly(2-ethyloxazoline) (PEOZ), that has also been mooted as a possible alternate protective polymer. It was also found that the RDG peptide occlusion was significantly greater for the case of both oxazolines as opposed to PEG and that, unlike PEG, neither oxazoline entered the membrane. As far as we are aware this is the first time that polyoxazolines have been studied using molecular dynamics simulation with all atom resolution.

Effects of Membrane PEGylation on Entry and Location of Antifungal Drug Itraconazole and Their Pharmacological Implications

Itraconazole (ITZ) is an antifungal agent used clinically to treat mycotic infections. However, its therapeutic effects are limited by low solubility in aqueous media. Liposome-based delivery systems (LDS) have been proposed as a delivery mechanism for ITZ to alleviate this problem. Furthermore, PEGylation, the inclusion in the formulation of a protective "stealth sheath" of poly(ethylene glycol) around carrier particles, is widely used to increase circulation time in the bloodstream and hence efficacy. Together, these themes highlight the importance of mechanistic and structural understanding of ITZ incorporation into liposomes both with and without PEGylation because it can provide a potential foundation for the rational design of LDS-based systems for delivery of ITZ, using alternate protective polymers or formulations. Here we have combined atomistic simulations, cryo-TEM, Langmuir film balance, and fluorescence quenching experiments to explore how ITZ interacts with both pristine and PEGylated liposomes. We found that the drug can be incorporated into conventional and PEGylated liposomes for drug concentrations up to 15 mol % without phase separation. We observed that, in addition to its protective properties, PEGylation significantly increases the stability of liposomes that host ITZ. In a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer without PEGylation, ITZ was found to reside inside the lipid bilayer between the glycerol and the double-bond regions of POPC, adopting a largely parallel orientation along the membrane surface. In a PEGylated liposome, ITZ partitions mainly to the PEG layer. The results provide a solid basis for further development of liposome-based delivery systems.

Complexing Cations by Poly(ethylene oxide): Binding Site and Binding Mode

The binding of K⁺ and Ba²⁺ cations to short poly(ethylene oxide) (PEO) chains with ca. 4-25 monomeric units in methanol was studied by determining the effective charge of the polymer through a combination of electrophoretic NMR and diffusion NMR experiments. These cations were previously found to bind to long PEO chains in a similar strong manner. In addition, ¹H chemical shift and longitudinal spin relaxation rate changes upon binding were quantified. For both systems, binding was stronger for the short chains than that for the longer chains, which is attributed mainly to interactions between bound ions. For K⁺ ions, the equilibrium binding constant of a cation to a binding site was measured. For both cations, the binding site was estimated to consist of ca. six monomeric units that coordinated with the respective ions. For the systems with barium, a significant fraction of the bound ions are (BaAnion)⁺ ion pairs. This leads to a strong anion effect in the effective charge of the oligomers acquired upon barium ion binding. For K⁺, the coordinating oligomer segment remains rather mobile and individual oligomers exchange rapidly (≪s) between their free and ion-complexing states. In contrast, segmental dynamics slows significantly for the oligomer section that coordinates with the barium species, and for individual oligomers, binding and nonbinding sections do not exchange on the time scale of seconds. Hence, oligomers also exchange slowly (>s) between their free and barium complexing states.

Increased Binding of Calcium Ions at Positively Curved Phospholipid Membranes

Calcium ion is the ubiquitous messenger in cells and plays a key role in neuronal signaling and fusion of synaptic vesicles. These vesicles are typically ∼20-50 nm in diameter, and thus their interaction with calcium ions cannot be modeled faithfully with a conventional flat membrane bilayer setup. Within our newly developed molecular dynamics simulations setup, we characterize here interactions of the calcium ion with curved membrane interfaces with atomistic detail. The present molecular dynamics simulations together with time-dependent fluorescence shift experiments suggest that the mode and strength of interaction of calcium ion with a phospholipid bilayer depends on its curvature. Potential of mean force calculations demonstrate that the binding of calcium ion to the positively curved side of the bilayer is significantly stronger compared with that to a flat membrane.

Binding of Monovalent and Multivalent Metal Cations to Polyethylene Oxide in Methanol Probed by Electrophoretic and Diffusion NMR

Complex formation in methanol between monodisperse polyethylene oxide (PEO) and a large set of cations was studied by measuring the effective charge acquired by PEO upon complexation. Quantitative data were obtained at a low ionic strength of 2 mM (for some salts, also between 0.5 and 6 mM) by a combination of diffusion nuclear magnetic resonance (NMR) and electrophoretic NMR experiments. For strongly complexing cations, the magnitude of the acquired effective charge was on the order of 1 cation per 100 monomer units. For monovalent cations, the relative strength of binding varies as Na⁺ < K⁺ ≈ Rb⁺ ≈ Cs⁺, whereas Li⁺ exhibited no significant binding. All polyvalent cations bind very weakly, except for Ba²⁺ that exhibited strong binding. Anions do not bind, as is shown by the lack of response to the chemical nature of anionic species (perchlorate, iodide, or acetate). Diffusion experiments directly show that the acetate anion with monovalent cations does not associate with PEO. Considering all cations, we find that the observed binding does not follow any Hofmeister order. Instead, binding occurs below a critical surface charge density, which indicates that the degree of complexation is defined by the solvation shell. A large solvation shell prevents the binding of most multivalent ions.

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.

Molecular Dynamics Simulations of a Poly(ethylene glycol)-Grafted Polyamide Membrane and Its Interaction with a Calcium Alginate Gel

Molecular dynamics simulations are carried out to investigate the antifouling property of a polyethylene glycol (PEG)-grafted polyamide (PA) membrane. Our specific interest is the computational study of the interaction between a grafted PEG coating and an alginate gel foulant by a steered molecular dynamics approach. Simulation results show that the PEG coating can hold a tightly bound hydration water layer. When the alginate gel is dragged to approach the PEG coating surface, a strong repulsive hydration force is observed due to the compression of this hydration layer. Detailed calculations of the potential of mean force (PMF) show that the repulsive interaction between the alginate gel and the hydration water layer around the PEG coating has a dominant contribution to the total repulsive PMF. We have also studied the effect of the PEG coverage on the membrane-foulant interactions. We find that the alginate gel has a strong tendency to drift to the uncovered PA membrane surfaces (namely, the PEG hollows). However, direct attachment of the gel to the PA membrane surface can be avoided if the gel size is slightly larger than the PEG hollow site.

Functionalized lipids and surfactants for specific applications

Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

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.

Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes?

Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.

Cholesterol level affects surface charge of lipid membranes in saline solution

Cholesterol is an important component of all biological membranes as well as drug delivery liposomes. We show here that increasing the level of cholesterol in a phospholipid membrane decreases surface charge in the physiological environment. Through molecular dynamics simulation we have shown that increasing the level of cholesterol decreases Na+ ion binding. Complementary experimental ζ--potential measurements have shown a decreased ζ--potential with increasing cholesterol content, indicative of reduced surface charge. Both experiments and simulations have been carried out on both saturated 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and monounsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. This result is particularly important because membrane surface charge plays an important role in the interactions of biomembranes with peripheral membrane proteins and drug delivery liposomes with the immune system.

Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration

We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

Effects of PEGylation on the binding interaction of magainin 2 and tachyplesin I with lipid bilayer surface

Poly(ethylene glycol) (PEG)-grafted magainin 2 and tachyplesin I were simulated with lipid bilayers. In the simulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are wrapped by PEG chains. The α-helical structure of PEGylated magainin 2 is broken in water, while the β-sheet of PEGylated tachyplesin I keeps stable, similar to the structural behavior of unPEGylated peptides, in agreement with experiments. Simulations of PEGylated peptides with lipid bilayers show that PEG chains block the electrostatic interaction between cationic residues of peptides and anionic phosphates of lipids, leading to the less binding of the peptide to the bilayer surface, which is observed more significantly for magainin 2 than for tachyplesin I. Since the random-coiled magainin 2 can be more completely covered by PEGs than does the β-sheet tachyplesin I, the PEGylation effect on the decreased binding is larger for magainin 2, showing the dependence of PEGylation on the peptide structure. These simulation findings qualitatively support the experimental observation of the different extents of the reduced membrane-permeabilizing activity for PEGylated magainin 2 and tachyplesin I.

A photo-triggerable drug carrier based on cleavage of PEG lipids by photosensitiser-generated reactive singlet oxygen

To circumvent the limitations of polyethylene glycol (PEG) modified carriers, a photo-triggerable liposome was prepared which was modified by cholesterol derivatives via a cleavable vinyl ether linkage so that the PEGylated coating can be efficiently removed by a photoactivated fullerene. After the photocleavage of the PEG moiety, the intracellular uptake of the photo-triggerable liposome improved.