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Amphiphilic ABA-triblock copolymers, comprised of poly(2-oxazoline) and poly(2-oxazine) blocks, can solubilize poorly water-soluble molecules; they form micelles with exceptionally high drug loading. In previous work, experimental studies have shown that even minor structural changes can have a significant impact on the maximum loading capacity for several different drugs. In an effort to shed light on the molecular interactions underlying the structure-property-relationships we performed all-atom molecular dynamics simulations on a selection of curcumin-loaded polymer micelles that have been experimentally characterized in detail. We investigated polymer-drug interactions in different micelle compositions, i.e. different drug loadings as well as variation of polymer structures of the inner hydrophobic core and the outer hydrophilic shell. Interestingly, the system with the highest experimental loading capacity also showed the highest amount of drug molecules encapsulated by the hydrophobic core in silico. Furthermore, in systems with a lower loading capacity the outer A blocks showed a greater extent of entanglement with the inner B blocks. Our results from hydrogen bond analyses corroborate the hypotheses of previous experimental studies: poly(2-butyl-2-oxazoline) B blocks, found experimentally to have a reduced loading capacity for curcumin in comparision to poly(2-propyl-2-oxazine), established fewer but longer-lasting hydrogen bonds. This possibly results from the additional methylene group in the backbone of poly(2-propyl-2-oxazine) to allow for different sidechain conformations around the hydrophobic cargo, compared to poly(2-butyl-2-oxazoline). This was further investigated by an unsupervised clustering of monomers within smaller model systems mimicking the different micelle compartments. In addition, an exchange of the hydrophilic poly(2-methyl-2-oxazoline) A blocks with the slightly more hydrophobic poly(2-ethyl-2-oxazoline) leads to a higher percentage of A blocks interacting with hydrophobic drugs and a reduced hydration of the corona; this suggests an impairment of micelle solubility or colloidal stability. This study demonstrates how all-atom molecular dynamics simulations can help in dissecting the effects of small structural changes in poly(2-oxazoline)-based micelles; we argue that it will pave the way for a more rational a priori design based approach to the development of drug delivery systems in the future.

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.

Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but highly lipophilic (clogP = 6.46) DAG mimetic. Although a less lipophilic pyrimidine analog, PYR-IgP (clogP = 3.30), gave positive results in computational docking, it unexpectedly presented greatly diminished binding to PKC in vitro. Through more rigorous computational molecular modeling, we reveal that, unlike HMI-1a3, PYR-1gP forms an intramolecular hydrogen bond, which both obstructs binding and reorients PYR-1gP in the membrane in a fashion that prevents it from correctly accessing the PKC C1 domain. Our results highlight the great value of molecular dynamics simulations as a key component for the drug design process of ligands targeting weakly membrane-associated proteins, where simulation in the relevant membrane environment is crucial for obtaining biologically applicable results.

The lipid second messenger diacylglycerol (DAG) is known for its involvement in many types of cellular signaling, especially as an endogenous agonist for protein kinase C (PKC). Evidence has emerged that the degree of saturation of the DAG molecules can affect PKC activation. DAG molecules with different acyl chain saturation have not only been observed to induce varying extents of PKC activation, but also to express selectivity towards different PKC isozymes. Both qualities are important for precise therapeutic activation of PKC; understanding DAG behavior at the molecular level in different environments has much potential in the development of drugs to target PKC. We used molecular dynamics simulations to study the behavior of two different unsaturated DAG species in lipid environments with varying degrees of unsaturation. We focus on phosphatidylethanolamine (PE) instead of phosphatidylcholine (PC) to more accurately model the relevant biomembranes. The effect of cholesterol (CHOL) on these systems was also explored. We found that both high level of unsaturation in the acyl chains of the DAG species and presence of CHOL in the surrounding membrane increase DAG molecule availability at the lipid–water interface. This can partially explain the previously observed differences in PKC activation strength and specificity, the complete mechanism is, however, likely to be more complex. Our simulations coupled with the current understanding of lipids highlight the need for more simulations of biologically accurate lipid environments in order to determine the correct correlations between molecular mechanisms and biological behavior when studying PKC activation.

Cardiac Repair In article number 2204666, Qiang Zhao, Xiaofeng Ye, Xianming Deng, Hélder A. Santos, and co-workers introduce a microfluidics-assisted single step, green synthesis method for producing targeting ligands free heart homing nanoparticles in a tailored manner. The developed microfluidic platform facilitates an economically feasible and simple yet robust synthesis procedure for nanoparticle production, which shows great clinical translational potential as an alternative post-conditioning routine after revascularization surgery.

Adsorptive fouling, by phenolic compounds, is a serious issue regarding the development and use of membrane based filtration technologies for water purification and wastewater treatment. We have developed a novel, combined, protocol of Raman spectroscopy and surface plasmon resonance (SPR) experiments, along with molecular dynamics (MD) simulation, to study the interaction of vanillin, a model phenolic compound, with the polyethersulfone (PES) surface of a membrane. The adsorption of vanillin to the PES surface was found to be highly pH dependent; the source of this was determined, by MD simulation, to be the stronger interaction with the protonated form of vanillin, predominant at low pH. Vanillin interacts with the PES surface, both through entropy driven, hydrophobic, interactions and, for the case of the protonated form, H-bonding of the hydroxyl group with the sulphur oxygens of the PES molecules. In addition to general insight into the fouling process that can be used to develop new methods to inhibit adsorptive fouling, our results also elucidate the specific interaction of the PES membrane with vanillin that can be used in the development of anti-fouling coatings, based on the structure of vanillin. Post-print / Final draft

Cholesterol plays a crucial role in modulating the physicochemical properties of biomembranes, both increasing mechanical strength and decreasing permeability. Cholesterol is also a common component of vesicle-based delivery systems, including liposome-based drug delivery systems (LDSs). However, its effect on the partitioning of drug molecules to lipid membranes is very poorly recognized. Herein, we performed a combined experimental/computational study of the potential for the use of the LDS formulation for the delivery of the antifungal drug itraconazole (ITZ). We consider the addition of cholesterol to the lipid membrane. Since ITZ is only weakly soluble in water, its bioavailability is limited. Use of an LDS has thus been proposed. We studied lipid membranes composed of cholesterol, 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), and ITZ using a combination of computational molecular dynamics (MD) simulations of lipid bilayers and Brewster angle microscopy (BAM) experiments of monolayers. Both experimental and computational results show separation of cholesterol and ITZ. Cholesterol has a strong preference to orient parallel to the bilayer normal. However, ITZ, a long and relatively rigid molecule with weakly hydrophilic groups along the backbone, predominantly locates below the interface between the hydrocarbon chain region and the polar region of the membrane, with its backbone oriented parallel to the membrane surface; the orthogonal orientation in the membrane could be the cause of the observed separation. In addition, fluorescence measurements demonstrated that the affinity of ITZ for the lipid membrane is decreased by the presence of cholesterol, which is thus probably not a suitable formulation component of an LDS designed for ITZ delivery.

Glyceryl monostearate (GMS) is a single-tailed lipidic monoglyceride commonly used as a nontoxic food additive. In this study, we have investigated GMS, specifically its self-assembling properties and subsequent application in drug delivery. Results from in silico modeling, corroborated by complementary small-angle neutron scattering, demonstrated vesicle formation; associated phase transitions were analyzed using differential scanning calorimetry; dynamic light scattering revealed particle size alterations that occurred in the transition region. Spherical morphology of unilamellar vesicles was visualized using transmission electron microscopy imaging. Further, hydrophilic and hydrophobic drug loading in GMS vesicles and their amenability to surface modification for hepatic targeting have, in this study, been both predicted through molecular simulation study and demonstrated experimentally. The influence of hepatotropic ligands on the stability of drug-loaded GMS vesicles vis-a-vis cholesterol has also been investigated; the resulting GMS-based drug delivery vehicle, its properties enhanced through surface decoration, is envisaged to achieve targeted delivery of its payload to hepatocytes.

Supported lipid bilayers (SLBs) have been used extensively as an effective model of biological membranes, in the context of in vitro biophysics research, and the membranes of liposomes, in the context of the development of nanoscale drug delivery devices. Despite numerous surface-sensitive techniques having been applied to their study, the comprehensive optical characterization of SLBs using surface plasmon resonance (SPR) has not been conducted. In this study, Fresnel multilayer analysis is utilized to effectively calculate layer parameters (thickness and refractive indices) with the aid of dual-wavelength and dispersion coefficient analysis, in which the linear change in the refractive index as a function of wavelength is assumed. Using complementary information from impedance-based quartz crystal microbalance experiments, biophysical properties, for example, area-per-lipid-molecule and the quantity of lipid-associated water molecules, are calculated for different lipid types and mixtures, one of which is representative of a raft-forming lipid mixture. It is proposed that the hydration layer beneath the bilayer is, in fact, an integral part of the measured optical signal. Also, the traditional Jung model analysis and the ratio of SPR responses are investigated in terms of assessing the structure of the lipid layer that is formed.

The soluble oligomeric form of the amyloid beta (Aβ) peptide is the major causative agent in the molecular pathogenesis of Alzheimer's disease (AD). We have previously developed a pyrroline-nitroxyl fluorene compound (SLF) that blocks the toxicity of Aβ. Here we introduce the multi-parametric surface plasmon resonance (MP-SPR) approach to quantify SLF binding and effect on the self-association of the peptide via a label-free, real-time approach. Kinetic analysis of SLF binding to Aβ and measurements of layer thickness alterations inform on the mechanism underlying the ability of SLF to inhibit Aβ toxicity and its progression towards larger oligomeric assemblies. Depending on the oligomeric state of Aβ, distinct binding affinities for SLF are revealed. The Aβ monomer and dimer uniquely possess sub-nanomolar affinity for SLF via a non-specific mode of binding. SLF binding is weaker in oligomeric Aβ, which displays an affinity for SLF on the order of 100 μM. To complement these experiments we carried out molecular docking and molecular dynamics simulations to explore how SLF interacts with the Aβ peptide. The MP-SPR results together with in silico modeling provide affinity data for the SLF-Aβ interaction and allow us to develop a new general method for examining protein aggregation.

Combined experimental and computational studies of lipid membranes and liposomes, with the aim to attain mechanistic understanding, result in a synergy that makes possible the rational design of liposomal drug delivery system (LDS) based therapies. The LDS is the leading form of nanoscale drug delivery platform, an avenue in drug research, known as "nanomedicine", that holds the promise to transcend the current paradigm of drug development that has led to diminishing returns. Unfortunately this field of research has, so far, been far more successful in generating publications than new drug therapies. This partly results from the trial and error based methodologies used. We discuss experimental techniques capable of obtaining mechanistic insight into LDS structure and behavior. Insight obtained purely experimentally is, however, limited; computational modeling using molecular dynamics simulation can provide insight not otherwise available. We review computational research, that makes use of the multiscale modeling paradigm, simulating the phospholipid membrane with all atom resolution and the entire liposome with coarse grained models. We discuss in greater detail the computational modeling of liposome PEGylation. Overall, we wish to convey the power that lies in the combined use of experimental and computational methodologies; we hope to provide a roadmap for the rational design of LDS based therapies. Computational modeling is able to provide mechanistic insight that explains the context of experimental results and can also take the lead and inspire new directions for experimental research into LDS development. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β

We assess the stability of two previously suggested binding modes for the neuropeptide orexin-A in the OX2 receptor through extensive molecular dynamics simulations. As the activation determinants of the receptor remain unknown, we simulated an unliganded receptor and two small-molecular ligands, the antagonist suvorexant and the agonist Nag26 for comparison. Each system was simulated in pure POPC membrane as well as in the 25% cholesterol–POPC membrane. In total, we carried out 36 μs of simulations. Through this set of simulations, we report a stable binding mode for the C-terminus of orexin-A. In addition, we suggest interactions that would promote orexin receptor activation, as well as others that would stabilize the inactive state.

Cationization of nanocarriers has been sought after as a viable strategy to surmount cellular barriers that impede intracellular drug and gene delivery. A plethora of cationic compounds including both lipids and polymers have been designed and developed for efficient cellular penetration. The toxicity of these cationic agents, however, precludes their use in drug delivery. Conjugation with biomolecules like sugars and amino acids to produce novel cationic agents is being investigated to generate biocompatible molecules to achieve safe drug delivery. In this study, we propose to mitigate the toxicity of stearylamine, a cationic lipid, by tethering it to arginine, to yield a novel cationic ligand. Ligand loaded liposomes and nanoparticles were fabricated and evaluated for their surface charge and cellular uptake. Furthermore, molecular dynamics simulations were utilized as a tool to understand the accessibility of the novel ligand and stearylamine loaded liposomal systems. This paper presents the one pot synthesis of a novel stearylated arginine dipeptide and its incorporation in delivery systems along with its in vitro and in vivo toxicity evaluation.

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 (Chin)]; (b) mPEG molecular weight (2 kDa mPEG and 5 kDa mPEG(114)); and (c) mPEG shape (linear and branched PEG). In vitro results demonstrated that branched (mPEG(114))(2)-DSPE confers the highest stealth properties to liposomes (similar to 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 mPEG(114)-Chol had 3.2- and similar to 2.1-fold higher area under curve (AUC) than naked liposomes and branched (mPEG(114))(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 mPEG(114)-DSPE yielded coated liposomes with the best in vitro stealth performance. Nevertheless, the in vivo AUC of liposomes decorated with linear mPEG(114)-DSPE was lower than that obtained with liposomes decorated with linear mPEG(114)-Chol. Computational molecular dynamics modeling provided additional insights that complement the experimental results.

Light triggered drug delivery systems offer attractive possibilities for sophisticated therapy, providing both temporal and spatial control of drug release. We have developed light triggered liposomes with clinically approved indocyanine green (ICG) as the light sensitizing compound. Amphiphilic ICG can be localized in different compartments of the liposomes, but the effect of its presence, on both triggered release and long term stability, has not been studied. In this work, we report that ICG localization has a significant effect on the properties of the liposomes. Polyethylene glycol (PEG) coating of the liposomes leads to binding and stabilization of the ICG molecules on the surface of the lipid bilayer. This formulation showed both good storage stability in buffer solution (at +4-37 degrees C) and adequate stability in serum and vitreous (at +37 degrees C). The combination of ICG within the lipid bilayer and PEG coating lead to poor stability at elevated temperatures of +22 degrees C and +37 degrees C. The mechanisms of the increased instability due to ICG insertion in the lipid bilayer was elucidated with molecular dynamics simulations. Significant PEG insertion into the bilayer was induced in the presence of ICG in the lipid bilayer. Finally, feasibility of freeze-drying as a long term storage method for the ICG liposomes was demonstrated. Overall, this is the first detailed study on the interactions of lipid bilayer, light sensitizer (ICG) and PEG coating on the liposome stability. The localization of the light triggering agent significantly alters the structure of the liposomes and it is important to consider these aspects in triggered drug delivery system design.

Peptide therapeutics have the potential to self-associate, leading to aggregation and fibrillation. Noncovalent PEGylation offers a strategy to improve their physical stability; an understanding of the behavior of the resulting polymer/ peptide complexes is, however, required. In this study, we have performed a set of experiments with additional mechanistic insight provided by in silico simulations to characterize the molecular organization of these complexes. We used palmitoylated vasoactive intestinal peptide (VIP-palm) stabilized by methoxy-poly(ethylene glycol)(skDa)-cholane (PEG-cholane) as our model system. Homogeneous supramolecular assemblies were found only when complexes of PEG-cholane/VIP-palm exceeded a molar ratio of 2:1; at and above this ratio, the simulations showed minimal exposure of VIP-palm to the solvent. Supramolecular assemblies formed, composed of, on average, 9-11 PEG-cholane/VIP-palm complexes with 2:1 stoichiometry. Our in silico results showed the structural content of the helical conformation in VIP-palm increases when it is complexed with the PEG-cholane molecule; this behavior becomes yet more pronounced when these complexes assemble into larger supramolecular assemblies. Our experimental results support this: the extent to which VIP-palm loses helical structure as a result of thermal denaturation was inversely related to the PEG-cholane:VIP-palm molar ratio. The addition of divalent buffer species and increasing the ionic strength of the solution both accelerate the formation of VIP-palm fibrils, which was partially and fully suppressed by 2 and >4 mol equivalents of PEG-cholane, respectively. We conclude that the relative freedom of the VIP-palm backbone to adopt nonhelical conformations is a key step in the aggregation pathway.

The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β2,2-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial agents, we have performed an in silico investigation of four leading β2,2-amino acid derivatives, interacting with models of both bacterial (target) and eukaryotic (host) membranes, using molecular dynamics simulation with a model with all-atom resolution. We found an unexpected result that could shed light on the mechanism of action of these antimicrobial agents: the molecules assume a conformation where one of the hydrophobic arms is directed downward into the membrane core while the other is directed upwards, out of the membrane and exposed above the position of the membrane headgroups; we dubbed this conformation the “can-can pose”. Intriguingly, the can-can pose was most closely linked to the choice of headgroup. Also, the compound previously found to be most effective against biofilms displayed the strongest extent of this behavior and, additionally, this behavior was more pronounced for this compound in the bacterial than in the eukaryotic membrane. We hypothesize that adopting the can-can pose could possibly disrupt the protective peptidoglycan macronet found on the exterior of the bacterial membrane.

Nelfinavir mesylate (NFV), a human immunodeficiency virus (HIV) protease inhibitor, is an integral component of highly active anti retro viral therapy (HAART) for management of AIDS. NFV possesses pH-dependent solubility and has low and variable bioavailability hampering its use in therapeutics. Lipid-based particulates have shown to improve solubility of poorly water soluble drugs and oral absorption, thereby aiding in improved bioavailability. The current study compares potential of vesicular and solid lipid nanocarriers of NFV with drug nanocrystallites and microvesicular systems like cochleates in improving bioavailability of NFV. The paper outlines investigation of systems using in vitro models like in vitro lipolysis, in vitro release, and permeation through cell lines to predict the in vivo potential of nanocarriers. Finally, in vivo pharmacokinetic study is reported which provided proof of concept in sync with results from in vitro studies. Graphical Abstract ᅟ.

The enzyme catechol-O-methyltransferase (COMT) has water soluble (S-COMT) and membrane associated (MB-COMT), bitopic, isoforms. Of these MB-COMT is a drug target in relation to the treatment of Parkinson's disease. Using a combination of computational and experimental protocols, we have determined the substrate selection mechanism specific to MB-COMT. We show: (1) substrates with preferred affinity for MB-COMT over S-COMT orient in the membrane in a fashion conducive to catalysis from the membrane surface and (2) binding of COMT to its cofactor ADOMET induces conformational change that drives the catalytic surface of the protein to the membrane surface, where the substrates and Mg2+ ions, required for catalysis, are found. Bioinformatics analysis reveals evidence of this mechanism in other proteins, including several existing drug targets. The development of new COMT inhibitors with preferential affinity for MB-COMT over S-COMT is now possible and insight of broader relevance, into the function of bitopic enzymes, is provided.

The application of Raman spectroscopy as a monitoring technique for bioprocesses is severely limited by a large background signal originating from fluorescing compounds in the culture media. Here, we compare time-gated Raman (TG-Raman)-, continuous wave NIR-process Raman (NIR-Raman), and continuous wave micro-Raman (micro-Raman) approaches in combination with surface enhanced Raman spectroscopy (SERS) for their potential to overcome this limit. For that purpose, we monitored metabolite concentrations of Escherichia coli bioreactor cultivations in cell-free supernatant samples. We investigated concentration transients of glucose, acetate, AMP, and cAMP at alternating substrate availability, from deficiency to excess. Raman and SERS signals were compared to off-line metabolite analysis of carbohydrates, carboxylic acids, and nucleotides. Results demonstrate that SERS, in almost all cases, led to a higher number of identifiable signals and better resolved spectra. Spectra derived from the TG-Raman were comparable to those of micro-Raman resulting in well-discernable Raman peaks, which allowed for the identification of a higher number of compounds. In contrast, NIR-Raman provided a superior performance for the quantitative evaluation of analytes, both with and without SERS nanoparticles when using multivariate data analysis. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1533-1542, 2018.

Antibacterial drug-loaded electrospun nano- and microfibrous dressings are of major interest as novel topical drug delivery systems in wound care. In this study, chloramphenicol (CAM)-loaded polycaprolactone (PCL) and PCL/poly(ethylene oxide) (PEO) fiber mats were electrospun and characterized in terms of morphology, drug distribution, physicochemical properties, drug release, swelling, cytotoxicity, and antibacterial activity. Computational modeling together with physicochemical analysis helped to elucidate possible interactions between the drug and carrier polymers. Strong interactions between PCL and CAM together with hydrophobicity of the system resulted in much slower drug release compared to the hydrophilic ternary system of PCL/PEO/CAM. Cytotoxicity studies confirmed safety of the fiber mats to murine NIH 3T3 cells. Disc diffusion assay demonstrated that both fast and slow release fiber mats reached effective concentrations and had similar antibacterial activity. A biofilm formation assay revealed that both blank matrices are good substrates for the bacterial attachment and formation of biofilm. Importantly, prolonged release of CAM from drug-loaded fibers helps to avoid biofilm formation onto the dressing and hence avoids the treatment failure.

Sterically stabilized liposomes (SSLs) (PEGylated liposomes) are applied as e ff ective drug delivery vehicles. Under- standing the interactions between hydrophobic compounds and PEGylated membranes is therefore important to determine the e ff ectiveness of PEGylated liposomes for delivery of drugs or other bioactive substances. In this study, we have combined fl uorescence quenching analysis (FQA) experiments and all-atom molecular dynamics (MD) simulations to study the e ff ect of membrane PEGylation on the location and orientation of 5,10,15,20-tetrakis(4- hydroxyphenyl)porphyrin (p-THPP) that has been used in our study as a model hydrophobic compound. First, we consider the properties of p-THPP in the presence of di ff erent fl uid phosphatidylcholine bilayers that we use as model systems for protein-free cell membranes. Next, we studied the interaction between PEGylated membranes and p-THPP. Our MD simulation results indicated that the arrangement of p-THPP within zwitterionic membranes is dependent on their free volume, and p-THPP solubilized in PEGylated liposomes is localized in two preferred positions: deep within the membrane (close to the center of the bilayer) and in the outer PEG corona (p-THPP molecules being wrapped with the polymer chains). Fluorescence quenching methods con fi rmed the results of atomistic MD simulations and showed two populations of p-THPP molecules as in MD simulations. Our results provide both an explanation for the experimental observation that PEGylation improves the drug-loading e ffi ciency of membranes and also a more detailed molecular-level description of the interactions between porphyrins and lipid membranes.

Despite doxorubicin being commonly used in chemotherapy there still remain significant holes in our knowledge regarding its delivery efficacy and an observed resistance mechanism that is postulated to involve the cell membrane. One possible mechanism is the efflux by protein P-gp, which is found predominantly in cholesterol enriched domains. Thereby, a hypothesis for the vulnerability of doxorubicin to efflux through P-gp is its enhanced affinity for the ordered cholesterol rich regions of the plasma membrane. Thus, we have studied doxorubicin’s interaction with model membranes in a cholesterol rich, ordered environment and in liquid-disordered cholesterol poor environment. We have combined three separate experimental protocols: UV-Vis spectrophotometry, fluorescence quenching and steady-state anisotropy and computational molecular dynamics modeling. Our results show that the presence of cholesterol induces a change in membrane structure and doesn’t impair doxorubicin’s membrane partitioning, but reduces drug’s influence on membrane fluidity without directly interacting with it. It is thus possible that the resistance mechanism that lowers the efficacy of doxorubicin, results from an increased density in membrane regions where the efflux proteins are present. This work represents a successful approach, combining experimental and computational studies of membrane based systems to unveil the behavior of drugs and candidate drug molecules.

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.

We have performed molecular dynamics simulations of lipid bilayers composed of inverse-phosphatidylcholines (CPe), an analog of phosphatidylcholine (PC) with the choline group directly bound to the glycerol backbone and the phosphate group freely protruding into the water phase. Synthetic phospholipids with the CPe headgroup have been proposed for use as drug delivery liposomes. Our simulation results show that the CPe lipids were characterized by a larger area per lipid molecule than the PC lipids. This can partly explain experimental results that show a higher permeability of small solutes through the membranes of liposomes composed of them. Unlike the PC headgroup, the CPe headgroup was found not to bind sodium ions at the water membrane interface. Both lipid types were found to bind calcium ions but do not bind potassium ions. Inversion of the choline group was found to decrease hydration of the membrane in the carbonyl region of the bilayer as well as hydration of the choline group. From analyzing th...

PEGylation has been used successfully to increase the circulation time of drug delivery liposomes by providing an external steric sheath. In all FDA approved PEGylated drug delivery liposomes, cholesterol is a key component. In a continuation of our previous work we have simulated a PEGylated membrane with cholesterol added to the membrane formulation to determine the effect on membrane structure of the cholesterol–PEG interaction. We show that, like the case for the liquid crystalline membrane, PEG enters into the lipid bilayer, however, in a specific fashion: the PEG winds along the β face of the cholesterol. Additionally, PEG interferes with the role cholesterol plays in structuring and compacting the membrane; when the membrane is PEGylated, the area per lipid increases, rather than decreases, with increasing cholesterol. Our studies provide mechanistic explanations for existing experimental results concerning the effect of adding cholesterol to the PEGylated liposome, including alteration to the lipo...

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.

Uptake of piroxicam, a non-steroidal anti-inflammatory drug, from the intestines after oral intake is limited due to its low solubility and its wide use is associated with several side effects related to the gastrointestinal tract. In this study, all-atom molecular dynamics (MD) simulations and fluorescent spectroscopy were employed to investigate the interaction of piroxicam in neutral, zwitterionic, and cationic forms with lipid bilayers composed of phosphatidylcholine, cholesterol, and PEGylated lipids. Our study was aimed to assess the potential for encapsulation of piroxicam in liposomal carriers and to shed more light on the process of gastrointestinal tract injury by the drug. Through both the MD simulations and laser scanning confocal microscopy, we have demonstrated that all forms of piroxicam can associate with the lipid bilayers and locate close to the water-membrane interface. Conventional liposomes used in drug delivery are usually stabilized by the addition of cholesterol and have their bloodstream lifetime extended through the inclusion of PEGylated lipids in the formulation to create a protective polymer corona. For this reason, we tested the effect of these two modifications on the behavior of piroxicam in the membrane. When the bilayer was PEGylated, piroxicam localize to the PEG layer and within the lipid headgroup region. This suggests that PEGylated liposomes are capable of carrying a larger quantity of piroxicam than the conventional ones. (C) 2017 Elsevier B.V. All rights reserved.

Light-triggered drug delivery systems enable site-specific and time-controlled drug release. In previous work, we have achieved this with liposomes containing gold nanoparticles in the aqueous core. Gold nanoparticles absorb near-infrared light and release the energy as heat that increases the permeability of the liposomal bilayer, thus releasing the contents of the liposome. In this work, we replaced the gold nanoparticles with the clinically approved imaging agent indocyanine green (ICG). The ICG liposomes were stable at storage conditions (4-22 °C) and at body temperature, and fast near-infrared (IR) light-triggered drug release was achieved with optimized phospholipid composition and a 1:50 ICG-to-lipid molar ratio. Encapsulated small molecular calcein and FITC-dextran (up to 20 kDa) were completely released from the liposomes after light exposure for 15 s. Location of ICG in the PEG layer of the liposomes was simulated with molecular dynamics. ICG has important benefits as a light-triggering agent in liposomes: fast content release, improved stability, improved possibility of liposomal size control, regulatory approval to use in humans, and the possibility of imaging the in vivo location of the liposomes based on the fluorescence of ICG. Near-infrared light used as a triggering mechanism has good tissue penetration and safety. Thus, ICG liposomes are an attractive option for light-controlled and efficient delivery of small and large drug molecules.

The rapid and accurate detection of food pathogens plays a critical role in the early prevention of foodborne epidemics. Current bacteria identification practices, including colony counting, polymerase chain reaction (PCR) and immunological methods, are time consuming and labour intensive; they are not ideal for achieving the required immediate diagnosis. Different SERS substrates have been studied for the detection of foodborne microbes. The majority of the approaches are either based on costly patterning techniques on silicon or glass wafers or on methods which have not been tested in large scale fabrication. We demonstrate the feasibility of analyte specific sensing using mass-produced, polymer-based low-cost SERS substrate in analysing the chosen model microbe with biological recognition. The use of this novel roll-to-roll fabricated SERS substrate was combined with optimised gold nanoparticles to increase the detection sensitivity. Distinctive SERS spectral bands were recorded for Listeria innocua ATCC 33090 using an in-house build (785 nm) near infra red (NIR) Raman system. Results were compared to both those found in the literature and the results obtained from a commercial time-gated Raman system with a 532 nm wavelength laser excitation. The effect of the SERS enhancer metal and the excitation wavelength on the detected spectra was found to be negligible. The hypothesis that disagreements within the literature regarding bacterial spectra results from conditions present during the detection process has not been supported. The sensitivity of our SERS detection was improved through optimization of the concentration of the sample inside the hydrophobic polydimethylsiloxane (PDMS) wells. Immunomagnetic separation (IMS) beads were used to assist the accumulation of bacteria into the path of the beam of the excitation laser. With this combination we have detected Listeria with gold enhanced SERS in a label free manner from such low sample concentrations as 10(4) CFU ml(-1).

We have used computational fluid dynamics modeling (CFD) to synchronize the flow conditions in the flow channels of two complementary surface-sensitive characterization techniques: surface plasmon resonance (SPR) and quartz crystal microbalance (QCM). Since the footprint of the flow channels of the two devices is specified by their function, the flow behavior can only be varied either by altering the height of the flow channel, or altering the volumetric rate of flow (flow rate) through the channel. The relevant quantity that must be calibrated is the shear strain on the measurement surface (center and bottom) of the flow channel. Our CFD modeling shows that the flow behavior is in the Stokes flow regime. We were thus able to generate a scaling expression with parameters for flow rate and flow channel height for each of the two devices: f QCM = 2.64 f SPR ( h QCM / h SPR ) 2 , where f QCM and f SPR are the flow rates in the SPR and QCM flow channels, respectively, and h QCM / h SPR is the ratio of the heights of the two channels. We demonstrate the success of our calibration procedure through the combined use of commercially available SPR and QCM flow channel devices on both a biomolecular interaction system of surface immobilized biotin and streptavidin and a targeted drug delivery model system of biotinylated liposomes interacting with a streptavidin functionalized surface.

J. Neurochem. (2012) 122, 681–690. Abstract The interactions of the neurotransmitter dopamine, and its precursor l-dopa, with membrane lipids were investigated through a set of molecular dynamic simulations with all atom resolution. The results obtained indicate that both dopamine and l-dopa have a pronounced association with the lipid head groups, predominantly mediated through H-bonds. As a result the molecules are anchored to the interfacial region of the membrane. The strength of this interaction is dependent on lipid composition – the presence of phosphatidylserine leads to an increase in the strength of this interaction, resulting in an H-bond network with a lifetime much longer than the timescale of our simulations. Also, bilayers that include sphingomieline and cholesterol interact strongly with dopamine and l-dopa. We postulate that the high membrane association that we have observed for both dopamine and l-dopa could have the following effects: 1) when on the plasma membrane exterior, favour the availability of these compounds for cell membrane uptake processes and, 2) when on an internal membrane surface, accentuate the importance of membrane-bound metabolizing enzymes over their soluble counterparts.

Altered prolyl oligopeptidase (PREP) activity is found in many common neurological and other genetic disorders, and in some cases PREP inhibition may be a promising treatment. The active site of PREP resides in an internal cavity; in addition to the direct interaction between active site and substrate or inhibitor, the pathway to reach the active site (the gating mechanism) must be understood for more rational inhibitor design and understanding PREP function. The gating mechanism of PREP has been investigated through molecular dynamics (MD) simulation combined with crystallographic and mutagenesis studies. The MD results indicate the inter-domain loop structure, comprised of 3 loops at residues, 189-209 (loop A), 577-608 (loop B), and 636-646 (loop C) (porcine PREP numbering), are important components of the gating mechanism. The results from enzyme kinetics of PREP variants also support this hypothesis: When loop A is (1) locked to loop B through a disulphide bridge, all enzyme activity is halted, (2) nicked, enzyme activity is increased, and (3) removed, enzyme activity is only reduced. Limited proteolysis study also supports the hypothesis of a loop A driven gating mechanism. The MD results show a stable network of H-bonds that hold the two protein domains together. Crystallographic study indicates that a set of known PREP inhibitors inhabit a common binding conformation, and this H-bond network is not significantly altered. Thus the domain separation, seen to occur in lower taxa, is not involved in the gating mechanism for mammalian PREP. In two of the MD simulations we observed a conformational change that involved the breaking of the H-bond network holding loops A and B together. We also found that this network was more stable when the active site was occupied, thus decreasing the likelihood of this transition.

PEGylation is an effective mechanism to prolong the bloodstream lifetime, and thus efficacy, of drug delivery liposomes. The mechanism through which poly(ethylene glycol) (PEG) increases bloodstream lifetime is, however, not completely understood. The interaction with salt ions found in the bloodstream is known to play a role in this. We have used all-atom molecular dynamics simulation to study the effect of PEGylated lipid density, salt concentration, and the interaction with KCl and CaCl(2) salts in addition to NaCl. Increasing the PEGylated lipid concentration in the formulation from 1:18 to 1:9 molar density decreased the extent to which the Cl(-) ions penetrated the PEG layer, thus causing the PEG layer to become effectively positively charged. The interaction of the PEG with the K(+) ions was weaker than for the Na(+) ions, and nonexistent for the Ca(2+) ions. This work expands on our previous work where we studied the gel and liquid crystalline membranes in physiological salt concentration. Our results provide both an explanation for the experimental observation that PEGylation inhibits calcium-induced liposome fusion and further insight into the mechanisms through which PEG may inhibit uptake of the liposome by the reticuloendothilial system (RES).

Biomolecules and drug delivery agents, such as liposomes, are often delivered intracellularly with help of cell penetrating peptides (CPPs) and, in particular, Tat peptide. Tat peptide acts as a membrane shuttle; the structural determinants of transport and the manner by which the peptide crosses the lipid bilayer are, however, still unknown. The roles of direct membrane translocation, endocytosis and cell surface proteoglycans, in particular, remain elusive. Our study aimed to explore the relationship between structure and activity of Tat peptide and its uptake mechanism. For this purpose we introduced several modifications (e.g. lipophilic, aromatic, neutral and non-natural amino acids) into the original Tat sequence. We studied the interaction of the peptides with a model lipid membrane and with three cell lines, a phagocytic cell line (human retinal pigment epithelium cell line, ARPE-19), a non-phagocytic cell line (Chinese hamster ovary cells, CHO wt) and a mutant form of the latter cell line deficient in glycosaminoglycans chondroitin sulfate and heparan sulfate (CHO-pgsB 618). The amino acid residues introduced into the original sequence of Tat peptide failed to influence cellular uptake, indicating that the cationic charge alone may be responsible for translocation. Clear discrepancy between permeation activity of the peptides into cells and their interaction with lipid bilayers of liposomes indicated the limited value of the model membrane in predicting cellular peptide delivery. Cell uptake of Tat peptide was unspecific, took place either by phagocytosis or pinocytosis, and was inhibited by cell-surface glycosaminoglycans. The internalized peptides were localized in vesicles and unable to reach the cell nuclei. In conclusion, we show that Tat-related peptides enter cells on the basis of their cationic charge following different endocytosis pathways and that glycosaminoglycans on the cell surface negatively affect their uptake. This lack of specificity should be taken into account when exploiting Tat peptide as vehicle for intracellular delivery of biomacromolecules.

The ATP binding cassette (ABC) transporter family of proteins contains members involved in ATP-mediated import or export of ligands at the cell membrane. For the case of exporters, the translocation mechanism involves a large-scale conformational change that involves a clothespin-like motion from an inward-facing open state, able to bind ligands and adenosine triphosphate (ATP), to an outward-facing closed state. Our work focuses on SAV1866, a bacterial member of the ABC transporter family for which the structure is known for the closed state. To evaluate the ability of this protein to undergo conformational changes at physiological temperature, we first performed conventional molecular dynamics (MD) on the cocrystallized adenosine diphosphate (ADP)-bound structure and on a nucleotide-free structure. With this assessment of SAV1866's stability, conformational changes were induced by steered molecular dynamics (SMD), in which the nucleotide binding domains (NBD) were pushed apart, simulating the ATP hydrolysis energy expenditure. We found that the transmembrane domain is not easily perturbed by large-scale motions of the NBDs.

We summarize our recent work, using all atom molecular dynamics simulation to study the role of poly(ethylene glycol) (PEG) in drug delivery. We have simulated the drug delivery liposome membrane, in both the Gel and Liquid crystalline states. The simulations of the PEGylated membrane have been carried out in the presence of a physiological concentration of NaCl, and two other salts encountered in physiological conditions, KCL and CaCl 2 . We also simulated targeting moieties on the PEGylated membrane, comparing the behavior of two targeting moieties. We also simulated PEG with three drug molecules for which it is used as a delivery aid: paclitaxel, piroxicam, and hematoporphyrin. We found that the specific properties of PEG, its solubility in both polar and non-polar solvents, and its acting as a polymer electrolyte, have a significant e_ect on its behavior when used in drug delivery.

We have studied the effect of dendrimer generation on the interaction between dsDNA and the PAMAM dendrimer using force biased simulation of dsDNA with three generations of dendrimer: G3, G4, and G5. Our results for the potential of mean force (PMF) and the dendrimer asphericity along the binding pathway, combined with visualization of the simulations, demonstrate that dendrimer generation has a pronounced impact on the interaction. The PMF increases linearly with increasing generation of the dendrimer. While, in agreement with previous results, we see an increase in the extent to which the dendrimer bends the dsDNA with increasing dendrimer generation, we also see that the deformation of the dendrimer is greater with smaller generation of the dendrimer. The larger dendrimer forces the dsDNA to conform to its structure, while the smaller dendrimer is forced to conform to the structure of the dsDNA. Monitoring the number of bound cations at different values of force bias distance shows the expected effect of ions being expelled when the dendrimer binds dsDNA.

Prolyl oligopeptidase (POP), a member of the prolyl endopeptidase family, is known to play a role in several neurological disorders. Its primary function is to cleave a wide range of small oligopeptides, including neuroactive peptides. We have used force biased molecular dynamics simulation to study the binding mechanism of POP. We examined three possible binding pathways using Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) on a crystal structure of porcine POP with bound Z-pro-prolinal (ZPP). Using SMD, an exit pathway between the first and seventh blade of the β-propeller domain of POP was found to be a nonviable route. US on binding pathways through the β-propeller tunnel and the TYR190-GLN208 flexible loop at the interface between both POP domains allowed us to isolate the flexible loop pathway as the most probable. Further analysis of that pathway suggests a long-range covariation of the interdomain H-bond network, which indicates the possibility of large-scale domain reorientation observed in bacterial homologues and hypothesized to also occur in human POP.