Effects of PEGylation on the Size and Internal Structure of Dendrimers: Self-Penetration of Long PEG Chains into the Dendrimer Core

Computer simulation of the structural properties of fatty-acid modified PAMAM dendrimers at pH 5 and 7

In this work, we performed coarse-grained molecular dynamics (CGMD) simulations of G3, G4, and G5 polyamidoamine (PAMAM) dendrimers grafting with fatty acid (FTA) chains. The FTA chains of varying length and grafting densities (50% and 100% of surface terminals) correspond to pH 7 and 5, respectively. Our findings suggested that the structural properties of dendrimers were determined by dendrimer generation, polymerization degrees, and pH. With one exception, the size of the FTA grafting dendrimer shrank after fatty acid attachment. Because of the protonation of the dendrimer's interior amines at low pH, the FTA chains are distributed at the dendrimer's surface group. At pH 7, the FTA chains that have aggregated in the interior of the dendrimer cause chain crowding. Our research provided references on drug encapsulation and the lower toxicity of these hydrophobically modified nanoparticles.

Charge shielding effects of PEG bound to NH2-terminated PAMAM dendrimers - an experimental approach

Cationic poly(amido amine) (PAMAM) dendrimers exhibit great potential for use in drug delivery, but their high charge density leads to an inherent cytotoxicity. To increase biocompatibility, many studies have attached poly(ethylene glycol) (PEG) chains to the dendrimer surface. It is unclear how these tethered PEG chains influence the physicochemical properties of the dendrimer. Here, we develop a fluorescence-based assay utilizing anionic biological tissue to quantify the electrostatic binding affinity of a library of PEG-PAMAM conjugates with various PEG chain lengths and grafting densities. We find that covalently bound PEG chains reduce the electrostatic binding affinity more significantly than what can be achieved through covalent bonds only. Contrary to previous thought, this reduction is not explained by the steric hindrance effects of PEG chains, suggesting that other, non-covalent interactions between PEG and PAMAM are present. Using acetylated PAMAM conjugates, we convert electrostatic binding affinity to the number of charged amines accessible to the physiological environment. These data, coupled with ¹H-NMR, allows us to study more closely the non-covalent interactions between PEG and PAMAM. We find that increasing PEG chain length increases the number of non-covalent interactions. Additionally, at low grafting densities, increasing the number of PEG chains on the PAMAM surface also increases the non-covalent interactions. At higher grafting densities, however, PEG chains sterically repel one another, forcing chains to elongate away from the surface and reducing the number of interactions between PAMAM and individual PEG chains. The data presented here provides a framework for a more precise mechanistic understanding of how the length and density of tethered PEG chains on PAMAM dendrimers influence drug delivery properties.

An Insight into Advances in Developing Nanotechnology Based Therapeutics, Drug Delivery, Diagnostics and Vaccines: Multidimensional Applications in Tuberculosis Disease Management

Tuberculosis (TB), one of the deadliest contagious diseases, is a major concern worldwide. Long-term treatment, a high pill burden, limited compliance, and strict administration schedules are all variables that contribute to the development of MDR and XDR tuberculosis patients. The rise of multidrug-resistant strains and a scarcity of anti-TB medications pose a threat to TB control in the future. As a result, a strong and effective system is required to overcome technological limitations and improve the efficacy of therapeutic medications, which is still a huge problem for pharmacological technology. Nanotechnology offers an interesting opportunity for accurate identification of mycobacterial strains and improved medication treatment possibilities for tuberculosis. Nano medicine in tuberculosis is an emerging research field that provides the possibility of efficient medication delivery using nanoparticles and a decrease in drug dosages and adverse effects to boost patient compliance with therapy and recovery. Due to their fascinating characteristics, this strategy is useful in overcoming the abnormalities associated with traditional therapy and leads to some optimization of the therapeutic impact. It also decreases the dosing frequency and eliminates the problem of low compliance. To develop modern diagnosis techniques, upgraded treatment, and possible prevention of tuberculosis, the nanoparticle-based tests have demonstrated considerable advances. The literature search was conducted using Scopus, PubMed, Google Scholar, and Elsevier databases only. This article examines the possibility of employing nanotechnology for TB diagnosis, nanotechnology-based medicine delivery systems, and prevention for the successful elimination of TB illnesses.

Self-Organization of Mobile, Polyelectrolytic Dendrons on Stable, Amphiphile-Based Spherical Surfaces

Spherical surfaces bearing mobile, solvophilic chains are ubiquitous. These systems are found in nature in the form of biological cells bearing carbohydrate chains, or glycans, or in drug delivery systems such as vesicles bearing polyethylene glycol chains and carrying therapeutic molecules. The self-organization of the chains on the spherical surface dictates the stability and functionality of the latter and is determined by key factors such as the interchain, chain-surface interactions, excluded volume, concentration of the chains, and external environment. This study develops a fundamental understanding of how these factors control the organization of mobile, solvophilic chains while preserving the stability of the spherical surface. To that end, the study focuses on the organization of polyamidoamine dendrons on the surface of a dipalmitoylphosphatidylcholine-based vesicle. The excluded volume of the chains and the external environment are, respectively, controlled via the dendron generation and the pH. For acidic and basic pH environments, the dendrons are extended away from the surface. As a consequence, the vesicles are able to accommodate significantly higher concentration of dendrons on their surface without rupturing. For acidic pH, the dendrons change their conformation to avoid intermeshing. However for basic pH, the dendrons only change their conformation at extremely high concentrations due to excluded volume effects. These conformational changes are attributed to the number of protonated dendron residues that vary as a function of pH. The results from this study will advance diverse subdisciplines within cell biology, biomedicine, and pharmaceuticals.

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

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

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

The branching angle effect on the properties of rigid dendrimers studied by Monte Carlo simulation

We studied the properties of rigid dendrimers with different branching angles by means of Monte Carlo simulations on a coarse-grained level. It was found that the terminal groups of dendrimers with both rigid and flexible spacers could locate near the center of the molecule. In flexible dendrimers, the wide distribution is attributed to the back folding of flexible spacers, while in rigid dendrimers, it is caused by the branching angle effect that a branch will grow laterally due to the restriction of a non-zero branching angle. It has been established that the branching angle is a key parameter for rigid dendrimers, which can be applied to tune the properties of rigid dendrimers: decreasing branching angle is helpful to obtain dendrimers with a larger size, lower density, and more terminal groups locating at periphery.

Dendronized vesicles: formation, self-organization of dendron-grafted amphiphiles and stability

Fundamental bacterial functions like quorum sensing can be targeted to replace conventional antibiotic therapies. Nanoparticles or vesicles that bind interfacially to charged biomolecules could be used to block quorum sensing pathways in bacteria. Towards this goal, dendronized vesicles (DVs) encompassing polyamidoamine dendron-grafted amphiphiles (PDAs) and dipalmitoyl-sn-glycero-3-phosphocholine lipids are investigated using the molecular dynamics simulation technique in conjunction with an explicit solvent coarse-grained force field. The key physical factors determining the stability of DVs as a function of the dendron generation and relative concentration are identified. The threshold concentration of each dendron generation that yields stable DVs is determined. Dendrons with lower generations rupture the DVs at high relative concentrations due to the electrostatic repulsions between the terminally protonated amines. Whereas, dendrons with intermediate generations demonstrate a mushroom-to-brush transition. Conformational changes in the dendrons expand the outer DV surface, resulting in instability in the DV bilayer. DVs encompassing dendrons with higher generations incur stresses on the bilayer due to their high charge density and spontaneous curvature. The self-organization of PDAs on the DV surface are examined to understand how the asymmetric stresses are minimized across the bilayer. A set of conditions are determined to be conducive for the formation of a single cluster of PDAs that decorates the DV surface like a mesh. Results from this study can potentially guide the design and synthesis of nanoparticles which target quorum sensing pathways in bacteria towards the prevention and treatment of bacterial infections. Furthermore, these nanoparticles can be used in diverse applications in biomedicine, energy or electronics that require synthetic dendronized cells or the adsorption and transport of charged species.

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.

The ENUF method-Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application

Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between charged particles constitute a prominent factor in determining structures and states of model systems. How to efficiently calculate electrostatic interactions in simulation systems subjected to partial or full periodic boundary conditions has been a grand challenging task. In the past decades, a large variety of computational schemes has been proposed, among which the Ewald summation method is the most reliable route to accurately deal with electrostatic interactions between charged particles in simulation systems. In addition, extensive efforts have been done to improve computational efficiencies of the Ewald summation based methods. Representative examples are approaches based on cutoffs, reaction fields, multi-poles, multi-grids, and particle-mesh schemes. We sketched an ENUF method, an abbreviation for the Ewald summation method based on the nonuniform fast Fourier transform technique, and have implemented this method in particle-based simulation packages to calculate electrostatic energies and forces at micro- and mesoscopic levels. Extensive computational studies of conformational properties of polyelectrolytes, dendrimer-membrane complexes, and ionic fluids demonstrated that the ENUF method and its derivatives conserve both energy and momentum to floating point accuracy, and exhibit a computational complexity of O N log N with optimal physical parameters. These ENUF based methods are attractive alternatives in molecular simulations where high accuracy and efficiency of simulation methods are needed to accelerate calculations of electrostatic interactions at extended spatiotemporal scales.

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.

Structural behavior of amphiphilic polyion complexes interacting with saturated lipid membranes investigated by coarse-grained molecular dynamic simulations

Neutral polyelectrolyte complexes (PECs) made from an amphiphilic multiblock copolymer of type (A_nB_n)_m and an oppositely charged polyion and interacting with a dipalmitoylphosphatidylcholine (DPPC) lipid membrane.

Effect of pH on Size and Internal Structure of Poly(propylene imine) Dendrimers: A Molecular Dynamics Simulation Study

The behavior of poly(propylene imine) dendrimers at three different solution pH is investigated through molecular dynamics (MD) simulations in explicit solvent. MD simulations provide an insight into the conformational properties of dendrimers via the evaluation of their size, shape, radial density distribution, static structure factor, and scattering intensity. The size of the dendrimer increases from high solution pH to low pH. The internal structure of the dendrimer is quantified in terms of the radial atomic density profile and the terminal amine group density distribution. While the radial atomic density distribution shifts away from the core of the dendrimer with decreasing pH, a significant degree of back-folding of the outer generations is observed at high pH for higher generations of growth. Results from the structure factor and scattering intensity indicate two types of conformational transitions: (i) as a function of the solution pH, where the dendrimer evolves from an expanded structure at low pH to a highly compact one at high pH (except for higher generations), and (ii) with increasing generations, where the open structure of the dendrimer at lower generations transforms to a compact structure at higher generations at both high and low pH, characterized by a change in the fractal dimension.

A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites

By employing coarse grained (CG) molecular dynamics (MD) simulation, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube (CNT)-dendrimer composites has been studied, to find a stable composite with high solubility in water and the capability to be used in drug delivery applications. For this purpose, composites consisting of core-shell dendrimer complexes including: [PPI{core}-PAMAM{shell}], [PAMAM{core}-polyethyleneglycol (PEG){shell}] and [PAMAM{core}-fattyacid (FTA){shell}] were constructed. A new CG model for the fatty acid (FTA) molecules as functionalized to the dendrimer was developed, which, unlike the previous models, could generate the structural conformations of the FTA properly. The obtained results indicated that the dendrimer complexes with short FTA chains can form stable composites with the CNT. Also, it was found that the pristine PAMAM and PPI-PAMAM with small PPI, and PAMAM-PEG dendrimers with short PEG chains, can distribute their chains into the water medium and interact with the CNT efficiently, to form a stable water-soluble CNT-dendrimer composite. The results demonstrated that the structural difference between the interior and exterior of a core-shell dendrimer complex can prevent the core and the interior layers of the dendrimer complex from interacting with the CNT. An overall analysis of the results manifested that the CNT-PAMAM:4-PEG:4 is the most stable composite, due to strong binding of the dendrimer with the CNT while also having high solubility in water, and its core retains its structure properly and unchanged, suitable for encapsulating drugs in the targeted delivery applications.

Mechanisms underlying interactions between PAMAM dendron-grafted surfaces with DPPC membranes

Biofouling is a pervasive problem which demands the creation of smart, antifouling surfaces. Towards this end, we examine the interactions between a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer and a polyamidoamine (PAMAM) dendron-grafted surface. In addition, we investigate the impact of dendron generation on the system behavior. To resolve the multiscale dynamical processes occurring over a large spatial scale, we employ Molecular Dynamics simulations with a coarse-grained implicit solvent force field. Our results demonstrate the transient and equilibrium system dynamics to be determined by the PAMAM dendron generation along with the underlying mechanisms. Higher generation dendrons are observed to favor penetration of the DPPC molecules into the dendron branches, thereby enabling sustained interactions between the membrane and the dendron-grafted surface. Under equilibrium, the membrane adopts a bowl-shaped morphology whose dimensions are determined by the dendron generation and density of interactions. The results from our study can be used to guide the design of novel surfaces with selective antifouling properties which can prevent the adsorption of microorganisms onto lipid membranes.

The interactions between a DPPC lipid membrane and a PAMAM dendron-grafted surface.

Solid-State Fluorescence of Fluorine-Modified Carbon Nanodots Aggregates Triggered by Poly(ethylene glycol)

Solid-state fluorescent carbon quantum dots (QDs) can be used for the encryption of security information. Controlling the dispersion and aggregation of the QDs is crucial for switching their solid-state fluorescence "on" and "off." The use of polymers has been proposed to slightly separate the QDs inside aggregates to trigger their fluorescence. However, the complex interactions between the QDs and flexible polymer chains make this process challenging. Here, fluorine-modified carbon nanodots (FCDs) were used in a solution as the printing ink. After printing, the FCDs were aggregated on paper via hydrogen bonds, thereby quenching the fluorescence. After a poly(ethylene glycol) (PEG) treatment, the FCDs exhibited yellow solid-state fluorescence due to an increased interdot spacing. The fluorescence intensity and emission wavelength could be tuned by varying the molecular weight and quantity of PEG used. Finally, we demonstrated a high-resolution encryption and decryption system based on the PEG-triggered fluorescence of FCDs.

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

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

Exploring the Structural Properties of Positively Charged Peptide Dendrimers

We report a combined experimental and computational approach to study the structural behavior of positively charged peptide dendrimers. Third-generation dendrimers containing combinations of positive/neutral amino acid residues in the different dendrimer generations were synthesized and their overall size evaluated using diffusion NMR. Molecular dynamics simulations were performed to obtain a comprehensive description of the molecular-level phenomena substantiating the structural differences observed. Comparison of the results presented with previous findings reveals a striking charge-dependent tendency in these systems, where the simple number and placement of charged amino acids in the sequence allows an extensive control over the exhibited structural features. Indeed, we observe that peptide dendrimers bearing progressively higher amounts of charged residues are characterized by an increasing structural plasticity, with a myriad of conformational states equally accessible to them. On the other hand, dendrimers containing only small amounts of charged residues evidence, to some extent, a characteristic structural rigidity.

Hybrid Dendrimers of PPI(core)-PAMAM(shell): A Molecular Dynamics Simulation Study

The structural properties of hybrid dendrimers PPI(core)-PAMAM(shell) for application in drug delivery are studied by coarse-grained molecular dynamics simulation, and their capacity to encapsulate drug guest molecules such as pyrene is investigated by changing the core (PPI) in the PPI-PAMAM hybrids. For this purpose, a coarse-grained model for PPI dendrimer is developed and is used to predict the structural properties as a function of PPI core size, such as the size of hybrid dendrimers, the depth of water penetration, the extent of back-folding of their chain terminals, the size and distribution of created cavities, and asphericity. The results show that the location of pyrene in the interior structure of the hybrids is independent of PPI core size and the branching chains create a barrier against the penetrating molecules in the shell of PPI. Then, by adding the PAMAM to the surface of PPI, this barrier is removed, and this will enhance the encapsulation capacity of the hybrid.

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.

Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH

Highly branched polymers such as polyamidoamine (PAMAM) dendrimers are promising macromolecules in the realm of nanobiotechnology due to their high surface coverage of tunable functional groups. Modeling efforts of PAMAM can provide structural and morphological properties, but the inclusion of solvents and the exponential growth of atoms with generations make atomistic simulations computationally expensive. We apply an implicit solvent coarse-grained model, called the Dry Martini force field, to PAMAM dendrimers. The reduced number of particles and the absence of a solvent allow the capture of longer spatiotemporal scales. This study characterizes PAMAM dendrimers of generations one through seven in acidic, neutral, and basic pH environments. Comparison with existing literature, both experimental and theoretical, is done using measurements of the radius of gyration, moment of inertia, radial distributions, and scaling exponents. Additionally, ion coordination distributions are studied to provide insight into the effects of interior and exterior protonation on counter ions. This model serves as a starting point for future designs of larger functionalized dendrimers.

Design of PAMAM-COO dendron-grafted surfaces to promote Pb(ii) ion adsorption

A coarse-grained molecular dynamics study of carboxylate functionalized polyamidoamine (PAMAM-COO) dendrons grafted onto a surface for the adsorption of Pb ions.

Facile construction of well-defined fullerene–dendrimer supramolecular nanocomposites for bioapplications

Well-defined supramolecular nanocomposites with biofunctions were facilely fabricated through complexation of carboxyfullerenes with poly(ethylene glycol)-modified poly(amidoamine) dendrimers.

Role of hydrophilicity and length of diblock arms for determining star polymer physical properties

We present a molecular simulation study of star polymers consisting of 16 diblock copolymer arms bound to a small adamantane core by varying both arm length and the outer hydrophilic block when attached to the same hydrophobic block of poly-δ-valerolactone. Here we consider two biocompatible star polymers in which the hydrophilic block is composed of polyethylene glycol (PEG) or polymethyloxazoline (POXA) in addition to a polycarbonate-based polymer with a pendant hydrophilic group (PC1). We find that the different hydrophilic blocks of the star polymers show qualitatively different trends in their interactions with aqueous solvent, orientational time correlation functions, and orientational correlation between pairs of monomers of their polymeric arms in solution, in which we find that the PEG polymers are more thermosensitive compared with the POXA and PC1 star polymers over the physiological temperature range we have investigated.