Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

Data-Driven Approaches to Predict Dendrimer Cytotoxicity

Dendrimers are employed as functional elements in contrast agents and are proposed as nontoxic vehicles for drug delivery. Toxicity is a property that is to be evaluated for this novel class of bionanomaterials for in vivo applications. The current research is hampered due to the lack of structured data sets for toxicity studies for dendrimers. In this work, we have built a data set by curating literature for toxicity data and augmented it with structural and physicochemical features. We present a comprehensive, feature-rich database of dendrimer toxicity measured across various cell lines for prediction, design, and optimization studies. We have also explored novel computational approaches for predicting dendrimer cytotoxicity. We demonstrate superior outcomes for toxicity prediction using essential regression in the space of small data sets.

Cell internalization kinetics and surface charge accessibility of surface-modified PAMAM dendrimers

Surface-modified PAMAM dendrimers have important applications in drug delivery, yet a gap remains about the role that surface functionalization plays on their cell internalization capacity. We examined the cell internalization kinetics of PAMAM dendrimers that were surface-modified with acetyl, folate and poly(ethylene glycol), as model functional groups differing in size, charge, and chemical functionality. Dendrimers with 25% functionalization were internalized by HEK cells, but with slower rates and lower maximum uptakes than the native dendrimer between 1-6 h of incubation. Dendrimers with 50% functionalization exhibited negligible internalization capacities at all incubation times. Molecular dynamics simulations revealed that the solvent accessibility of the cationic surface charges is a key factor affecting cell internalization, unlike the total charge, functionality or size of surface-modified PAMAM dendrimers. These findings provide valuable insights to assist the design of PAMAM-based systems for drug delivery applications.

Efficient Removal of Uranyl Ions Using PAMAM Dendrimer: Simulation and Experiment

In this work, using atomistic molecular dynamics (MD) simulations and polymer-assisted ultrafiltration experiments, we explore the adsorption and removal of uranyl ions from aqueous solutions using poly(amidoamine) (PAMAM) dendrimers. The effects of uranyl ion concentration and the pH of the solution were examined for PAMAM dendrimers of generations 3, 4, and 5. Our simulation results show that PAMAM has a high adsorption capacity for the uranyl ions. The adsorption capacity increases with increasing concentration of uranyl ions for all 3 generations of PAMAM in agreement with experimental findings. We find that the number of uranyl ions bound to PAMAM is significantly higher in acidic solutions (pH < 3) as compared to neutral solutions (pH ∼ 7) for all uranyl ion concentrations. Additionally, we find an increase in the number of adsorbed uranyl ions to PAMAM with the increase in the dendrimer generation. This increase is due to the greater number of binding sites present for higher-generation PAMAM dendrimers. Our simulation study shows that nitrate ions form a solvation shell around uranyl ions, which allows them to bind to PAMAM binding sites, including the amide, amine, and carbonyl groups. In polymer-assisted ultrafiltration (PAUF) experiments, the removal percentage of uranyl ions by G3 PAMAM dendrimer increased from 36.3% to 42.6% as the metal ion concentration increased from 2.1 × 10^-5 M to 10.5 × 10^-5 M at a pH of 2. Our combined experiment and simulation study suggests that PAMAM is an effective adsorbent for removing uranyl ions from aqueous solutions.

Effect of Ionization Degree of Poly(amidoamine) Dendrimer and 5-Fluorouracil on the Efficiency of Complex Formation-A Theoretical and Experimental Approach

Due to their unique structure, poly(amidoamine) (PAMAM) dendrimers can bind active ingredients in two ways: inside the structure or on their surface. The location of drug molecules significantly impacts the kinetics of active substance release and the mechanism of internalization into the cell. This study focuses on the effect of the protonation degree of the G4PAMAM dendrimer and the anticancer drug 5-fluorouracil (5FU) on the efficiency of complex formation. The most favorable conditions for constructing the G4PAMAM-5FU complex are a low degree of protonation of the dendrimer molecule with the drug simultaneously present in a deprotonated form. The fluorine components in the XPS spectra confirm the formation of the stable complex. Through SAXS and DLS methods, a decrease in the dendrimer's molecular size resulting from protonation changes at alkaline conditions was demonstrated. The gradual closure of the dendrimer structure observed at high pH values makes it difficult for the 5FU molecules to migrate to the interior of the support structure, thereby promoting drug immobilization on the surface. The ¹H NMR and DOSY spectra indicate that electrostatic interactions determine the complex formation process. Through MD simulations, the localization profile and the number of 5FU molecules forming the complex were visualized on an atomic scale.

Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations

Angiotensin-(1-7) re-balance the Renin-Angiotensin system affected during several pathologies, including the new COVID-19; cardiovascular diseases; and cancer. However, one of the limiting factors for its therapeutic use is its short half-life, which might be overcome with the use of dendrimers as nanoprotectors. In this work, we addressed the following issues: (1) the capacity of our computational protocol to reproduce the experimental structural features of the (hydroxyl/amino)-terminated PAMAM dendrimers as well as the Angiotensin-(1-7) peptide; (2) the coupling of Angiotensin-(1-7) to (hydroxyl/amino)-terminated PAMAM dendrimers in order to gain insight into the structural basis of its molecular binding; (3) the capacity of the dendrimers to protect Angiotensin-(1-7); and (4) the effect of pH changes on the peptide binding and covering. Our Molecular-Dynamics/Metadynamics-based computational protocol well modeled the structural experimental features reported in the literature and our double-docking approach was able to provide reasonable initial structures for stable complexes. At neutral pH, PAMAM dendrimers with both terminal types were able to interact stably with 3 Angiotensin-(1-7) peptides through ASP1, TYR4 and PRO7 key amino acids. In general, they bind on the surface in the case of the hydroxyl-terminated compact dendrimer and in the internal zone in the case of the amino-terminated open dendrimer. At acidic pH, PAMAM dendrimers with both terminal groups are still able to interact with peptides either internalized or in its periphery, however, the number of contacts, the percentage of coverage and the number of hydrogen bonds are lesser than at neutral pH, suggesting a state for peptide release. In summary, amino-terminated PAMAM dendrimer showed slightly better features to bind, load and protect Angiotensin-(1-7) peptides.

Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH₄⁺ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH₄⁺ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

Dynamics of Human Serum Transferrin in Varying Physicochemical Conditions Explored by Using Molecular Dynamics Simulations

Conformational stability of human serum transferrin (Tf) at varying pH values and salt and excipient concentrations were investigated using molecular dynamics (MD) simulations, and the results are compared with previously published small-angle X-ray scattering (SAXS) experiments. SAXS study showed that at pH 5, Tf is predominantly present in a partially open (PO) form, and the factions of PO differ based on the physicochemical condition and drift toward the closed form (HO) as the pH increases. Tf is a bilobal glycoprotein that is composed of homologous halves termed the N- and C-lobes. The current study shows that the protonation of Y188 and K206 at pH 5 is the primary conformational drive into PO, which shifts toward the closed (HO) conformer as the pH increases. Furthermore, at pH 6.5, PO is unfavorable due to negative charge-charge repulsion at the N/C-lobe interface linker region causing increased hinge distance when compared to HO, which has favorable attractive electrostatic interactions in this region. Subsequently, the effect of salt concentration was studied at 70 and 140 mM NaCl. At 70 mM NaCl and pH 5, chloride ions bind strongly in the N-lobe iron-binding site, whereas these interactions are weak at pH 6.5. With increasing salt concentration at pH 5, the regions surrounding the N-lobe iron-binding site are saturated, and as a consequence, sodium and chloride ions accumulate into the bulk. Additionally, protein-excipient interactions were investigated. At pH 5, the excipients interact in similar loop regions, E89-T93, and D416-D420, located in the N- and C-lobes of the HO conformer, respectively. It is anticipated that interactions of additives in these two loop regions cause conformational changes that lead to iron-coordinating residues in the N-lobe to drift away from iron and thus drive HO to PO conversion. Furthermore, at pH 6.5 and 140 mM histidine, these interactions are negligible leading to the stabilization of HO.

Spontaneously Restoring Specific Bioaffinity of RGD in Linear RGD-containing Peptides by Conjugation with Zwitterionic Dendrimers

Peptides are more versatile than small molecule drugs, but their specific bioaffinities are usually lower than their original native proteins because of the loss of preferred conformations. To overcome this key obstacle, we demonstrated a hydrogen bond-induced conformational constraint method to enhance the specific bioaffinities of peptides to achieve a high success rate by using linear RGD-containing peptides as a model of bioactive peptides. By performing molecular simulation, we found that the chemically immobilized linear CRGDS via cysteine (C) at the N-terminus on zwitterionic PAMAM G-5 can not only spontaneously restore the natural conformation of the RGD segment through the assistance of the dynamic hydrogen bond from serine (S) at the C-terminus of the peptide, but it can also narrow the distribution of all possible conformations. Consequently, the conjugates showed comparable or even better high affinity than native proteins without the use of conventional, labor-intensive, synthesis-based structure search methods to construct a binding conformation. In addition, the conjugates showed globular protein-like characteristics chemically, physically, and physiologically. They exhibited not only high efficacy and biosafety both in vitro and in vivo, but they also showed extremely high thermostability even upon boiling in a solution. This approach offers great design flexibility for reviving functional peptides without impairing their high specific affinity for their targets. STATEMENT OF SIGNIFICANCE: : In this work, we developed a swift approach to spontaneously restore the natural conformation of a linear peptide from a nature protein and thus enhance its specific bioaffinity instead of constructing a binding conformation by the labor-intensive, synthesis-based structure search method. In details, our new approach involves dynamically constraining the linear peptide on a zwitterionic PAMAM G-5 surface by a combination of chemical bonding at one terminus and dynamic hydrogen bonding at the other terminus of the linear peptide. The zwitterionic background offers abundant interaction sites for hydrogen bonding as well as resistance to nonspecific interactions. This approach fully restores the specific bioaffinity of RGD segments on a zwitterionic PAMAM G-5 through only one conjugation point at the C-terminus of the peptide. Moreover, the bioaffinity of all three types of RGD-containing peptides is successfully restored, which indicates the high rate of success of this approach in affinity restoring.

Drug-dendrimer complexes and conjugates: Detailed furtherance through theory and experiments

Dendritic nanovectors-based drug delivery has gained significant attention in the past couple of decades. Dendrimers play a crucial role in deciding the solubility of sparingly soluble drug molecules and help in improving pharmacokinetics. A few important steps in drug delivery through dendrimers, such as drug encapsulation, formulation, and target-specific delivery, play an important role in deciding the fate of a drug molecule. It is also of prime importance to understand the interactions between a drug molecule and dendrimers at atomistic levels to decode the mechanism of action of drug-dendrimer complexes and their reliability in terms of drug delivery. Colossal progress in current experimental and computational approaches in the field has resulted in a vast amount of data that needs to be curated to be further implemented efficiently. Improved computational power has led to greater accuracy and prompt predictions of properties of drug-dendrimer complexes and their mechanism of action. The current review encapsulates the pioneering work in the field, experimental achievements in terms of drug delivery, and newer computational techniques employed in the advancement of the field.

Uncovering a Hub Signaling Pathway of Antimicrobial-Antifungal-Anticancer Peptides’ Axis on Short Cationic Peptides via Network Pharmacology Study

Short cationic peptides (SCPs) with therapeutic efficacy of antimicrobial peptides (AMPs), antifungal peptides (AFPs), and anticancer peptides (ACPs) are known as an enhancement of the host defense system. Here, we investigated the uppermost peptide(s), hub signaling pathway(s), and their associated target(s) through network pharmacology. Firstly, we selected SCPs with positive amino acid residues on N- and C- terminals under 500 Dalton via RStudio. Secondly, the overlapping targets between the bacteria-responsive targets (TTD and OMIM) and AMPs’ targets were visualized by VENNY 2.1. Thirdly, the overlapping targets between AFPs’ targets and fungal-responsive targets were exhibited by VENNY 2.1. Fourthly, the overlapping targets between cancer-related targets (TTD and OMIM) and fungal-responsive targets were displayed by VENNY 2.1. Finally, a molecular docking study (MDS) was carried out to discover the most potent peptides on a hub signaling pathway. A total of 1833 SCPs were identified, and AMPs’, AFPs’, and ACPs’ filtration suggested that 197 peptides (30 targets), 81 peptides (6 targets), and 59 peptides (4 targets) were connected, respectively. The AMPs―AFPs―ACPs’ axis indicated that 27 peptides (2 targets) were associated. Each hub signaling pathway for the enhancement of the host defense system was “Inactivation of Rap1 signaling pathway on AMPs”, “Activation of Notch signaling pathway on AMPs―AFPs’ axis”, and “Inactivation of HIF-1 signaling pathway on AMPs―AFPs―ACPs’ axis”. The most potent peptides were assessed via MDS; finally, HPIK on STAT3 and HVTK on NOS2 and on HIF-1 signaling pathway were the most stable complexes. Furthermore, the two peptides had better affinity scores than standard inhibitors (Stattic, 1400 W). Overall, the most potent SCPs for the human defense system were HPIK on STAT3 and HVTK on NOS2, which might inactivate the HIF-1 signaling pathway.

Exploring Dendrimer Nanoparticles for Chronic Wound Healing

The United States spends billions of dollars to treat chronic wounds each year. Wound healing is complex in nature which involves several intricate multiphase processes that can be delayed for a number of reasons leading to the development of chronic wounds. Wound healing therapies range from topical preparations to surgical repair with treatment options that vary based on other underlying factors like co-infection, age, or co-morbidities such as diabetes. Historically, micelles and liposomes are some of the nanoparticle drug delivery systems explored to treat chronic wounds; however, recent data suggests that dendrimers have shown potential to rival these systems in treating chronic wounds as well as other diseases. This mini review examines advances in dendrimer nanoparticle drug delivery systems to treat chronic wounds.

Noncovalent Interactions with PAMAM and PPI Dendrimers Promote the Cellular Uptake and Photodynamic Activity of Rose Bengal: The Role of the Dendrimer Structure

Rose bengal is an anionic dye considered as a potential photosensitizer for anticancer photodynamic therapy. The clinical utility of rose bengal is hampered by its short half-life, limited transmembrane transport, aggregation, and self-quenching; consequently, efficient drug carriers that overcome these obstacles are urgently required. In this study, we performed multilevel in vitro and in silico characterization of interactions between rose bengal and cationic poly(amidoamine) (PAMAM) and poly(propyleneimine) (PPI) dendrimers of the third and fourth generation and assessed the ability of the resultant complexes to modulate the photosensitizing properties of the drug. We focused on explaining the molecular basis of this phenomenon and proved that the generation- and structure-dependent binding of the dye by the dendrimers increases the cellular uptake and production of singlet oxygen and intracellular reactive oxygen species, leading to an increase in phototoxicity. We conclude that the application of dendrimer carriers could enable the design of efficient photodynamic therapies based on rose bengal.

Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms

Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse-grained MARTINI models and structure-based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.

Drug-Loading Capacity of PAMAM Dendrimers Encapsulating Quercetin Molecules: A Molecular Dynamics Study with the 2016H66 Force Field

The complexation of quercetin molecules with poly(amidoamine) (PAMAM) dendrimers of generation 0-3 was studied by molecular dynamics simulations. Three main points were addressed: (i) the effect of starting from different initial structures; (ii) the performance of the 2016H66 force field (recently validated in the context of dendrimer simulations) in predicting the experimental drug(quercetin)-loading capacity of PAMAM dendrimers; and (iii) the stability of quercetin-PAMAM complexes and their interactions. Initial structures generated by different restraint protocols led to faster convergence compared to initial structures generated by randomly placing the drug molecules in the simulation box. The simulations yielded meta-stable complexes where the loading numbers have converged to average values and were compared to experimentally obtained values. Once the first meta-stable state was reached, the drug-dendrimer complexes did not deviate significantly throughout the simulation. They were characterized in terms of structural properties, such as the radius of gyration and radial distribution functions. The results suggest that quercetin molecules interact mostly with the internal dendrimer monomers rather than to their surface.

Slightly congested amino terminal dendrimers. The synthesis of amide-based stable structures on a large scale

Preparation of a new family of stable and aqueous soluble high-generation aliphatic polyamide amino terminal dendrimers. Promising scaffolds for applications where the combination of stability, multivalence and efficient conjugation is required.

Conformational properties of complexes of poly(propylene imine) dendrimers with linear polyelectrolytes in dilute solutions

This study investigates the conformational properties of complexes of poly(propylene imine) dendrimers with a linear polyelectrolyte (LPE) at neutral pH in an aqueous solution via molecular dynamics simulations. Various conformational properties, such as the atomic density profile, counterion density distribution, charge distribution, cavity volume, and the static structure factor are studied as a function of the charge and chain length of the LPE. The lower generation dendrimer complexes encapsulate the shorter linear PE chains, while the longer PE chains are adsorbed on the dendrimer surface that screen the surface charge and prevent the penetration of the counterions and water molecules. However, the overall charge of the higher generation dendrimers is not neutralized by the charge of the PE chains, which results in chloride counterion penetration within the dendrimers. The adsorption of the PE chains on the dendrimers is also verified from the charge distribution of the dendrimer-PE complexes. The charge on the lower generation dendrimer complexes is overcompensated by the longer PE chains resulting in an overall negative charge on the complexes, while the PE chains do not completely neutralize the charge of the higher generation dendrimers and produce positively charged complexes. The results of the structure factor indicate a conformational transition of the dendrimer-PE complexes from a dense compact structure to an open one with an increase in the PE chain length. This transition is characterized by an increase in the cavity volume in dendrimers with an increase in the PE chain length.

Polyamidoamine-based nanovector for the efficient delivery of methotrexate to U87 glioma cells

The purpose of this study was to design a polyamidoamine (PAMAM)-based nanovector for the efficient delivery of methotrexate to U87 glioma cells. To this end, 0-100% acetylated PAMAM dendrimers of the fourth generation were synthesized and evaluated using drug encapsulation measurements, molecular dynamics simulations, neurotoxicity assays and neuronal internalization experiments. The best system was tested as a nanovector for methotrexate delivery to U87 glioma cells. The authors found that 25% acetylated PAMAM dendrimers of the fourth-generation combine low intrinsic toxicity, large drug complexation capacity and efficient internalization into hippocampal neurons. Nanovector complexation enhances the cytotoxic response of methotrexate against U87 glioma cells compared with free drug solutions. In conclusion, 25% acetylated PAMAM dendrimers of the fourth-generation increase drug uptake by glioma cells and thereby act as efficient nanovectors for methotrexate delivery.

Conformations of poly(propylene imine) dendrimers in an ionic liquid at different pH

The conformational behavior of poly(propylene imine) (PPI) dendrimers at three different solution pH is studied in an ionic liquid (IL) solvent, 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), through molecular dynamics (MD) simulations. The size, shape, density distribution, structure factor, and the scattering intensity are evaluated to probe the conformational transition of dendrimers as a function of pH. The results of the radial atomic and terminal amine group density distribution at low pH indicate a shift in the density towards the periphery of the dendrimers due to the electrostatic repulsion between the charged tertiary amine groups within the dendrimers. The [BMIM] cations are not encapsulated within dendrimers and predominantly reside near the periphery. The extensive back-folding of the outer branches due to the electrostatic repulsion between the solvent cations and the peripheral charged amine groups at neutral and low pH results in a dense compact structure in [BMIM]Cl as compared to that in water, as evident from the results of the structure factor and scattering intensity. The structural analysis in terms of the fractal dimension reveals that the lower generation dendrimers exhibit conformational transition as a function of pH, while the higher generations exhibit a highly compact structure at all solution pH. However, PPI dendrimers at low pH exhibit more free volume as compared to that at high pH, which may be utilized to accommodate specific guest molecules.

Small angle X-ray scattering and molecular dynamic simulations provide molecular insight for stability of recombinant human transferrin

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Combination of SAXS and MD simulations can explain the molecular background for the stability studies.

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Destabilizing excipients in general induce opening of the N-lobe by binding to specific residues in the protein.

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The fully open conformation of transferrin is not seen without aggregation.

Transferrin is an attractive candidate for drug delivery due to its ability to cross the blood brain barrier. However, in order to be able to use it for therapeutic purposes, it is important to investigate how its stability depends on different formulation conditions. Combining high-throughput thermal and chemical denaturation studies with small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations, it was possible to connect the stability of transferrin with its conformational changes. Lowering pH induces opening of the transferrin N-lobe, which results in a negative effect on the stability. Presence of NaCl or arginine at low pH enhances the opening and has a negative impact on the overall protein stability.

Statement of Significance

Protein-based therapeutics have become an essential part of medical treatment. They are highly specific, have high affinity and fewer off-target effects. However, stabilization of proteins is critical, time-consuming, and expensive, and it is not yet possible to predict the behavior of proteins under different conditions. The current work is focused on a molecular understanding of the stability of human serum transferrin; a protein which is abundant in blood serum, may pass the blood brain barrier and therefore with high potential in drug delivery. Combination of high throughput unfolding techniques and structural studies, using small angle X-ray scattering and molecular dynamic simulations, allows us to understand the behavior of transferrin on a molecular level.

How Spherical Are Gaseous Low Charged Dendrimer Ions: A Molecular Dynamics/Ion Mobility Study?

The globular shape of gaseous ions, resulting from the ionization of large molecules such as polymers and proteins, is a recurring subject that has undergone a renewed interest with the advent of ion mobility spectrometry (IMS), especially in conjunction with theoretical chemistry techniques such as Molecular Dynamics (MD). Globular conformations result from a fine balance between entropy and enthalpy considerations. For multiply charged ions isolated in the gas phase of a mass spectrometer, the Coulombic repulsion between the different charges tends to prevent the ions from adopting a compact, and folded 3D structure. In the present paper, we closely associate data from IMS experiments and MD simulations to unambiguously access the conformations of dendrimer ions in the gas phase with special attention paid to the dendrimer structure, the generation, and the charge state. By doing so, we here combine a set of structural tools able to evaluate the (non)globular shape of ions based on both experimental and theoretical results.

An update on the use of molecular modeling in dendrimers design for biomedical applications: are we using its full potential?

INTRODUCTION

Dendrimers are well-defined hyperbranched polymers built from a variety of different monomers and with tuneable properties that make them suitable for different biomedical applications. Their three-dimensional (3D) structure cannot be usually determined experimentally due to their inherent nature of repeating patterns in the topology, failure to crystalize, and/or high flexibility. Therefore, their conformations and interactions at the atomistic level can be studied only by using computational chemistry methods, including molecular dynamics, Monte Carlo simulations, and molecular docking.

AREAS COVERED

In this review, the methods that could be utilized in computer-aided dendrimer design are considered, providing a list of approaches to generate initial 3D coordinates and selected examples of applications of relevant molecular modeling methods.

EXPERT OPINION

Computational chemistry provides an invaluable set of tools to study dendrimers and their interactions with drugs and biological targets. There is a gap in the software development that is dedicated to study of these highly variable and complex systems that could be overcome by the integration of already established approaches for topology generation and open source molecular modeling libraries. Furthermore, it would be highly beneficial to collate already built 3D models of various dendrimers with corresponding relevant experimental data.

Modulating Interdendrimer Interactions through Surface Adsorption

Physical confinement of polymers not only affects their structure but also modifies their effective interaction profiles. In this article, we investigate the nature of graphene-adsorbed poly(amidoamine) (PAMAM) dendrimers' interactions using fully atomistic molecular dynamics simulations. Using the umbrella sampling technique, we calculate the potential of mean force (PMF) profiles for the interaction between two graphene-adsorbed PAMAM dendrimers of generations 3 and 4 as a function of their protonation levels. We find that the attractive PMF profile observed for the interaction between two nonprotonated (high pH) PAMAM dendrimers in bulk becomes repulsive upon adsorption. Also, the repulsive interdendrimer interactions known in bulk for the protonated dendrimers become enhanced for the adsorbed case. We further explain these weakened interactions by explicitly showing that the dendrimer-graphene interaction is an order of magnitude larger than the dendrimer-dendrimer bulk interaction. Using the force integration method, we obtain the contributions from various subinteractions present in the system, that is, dendrimer-water, dendrimer-ions, dendrimer-graphene, and dendrimer-dendrimer to the total PMF. From these contributions, we conclude that the reduced dendrimer-dendrimer interactions in the adsorbed case, as compared to those in bulk, lead to the enhanced repulsive effective interdendrimer interactions. Our PMF profiles fit well with the sum of exponential and Gaussian functions, proposed in the bulk interdendrimer interaction study. We hope the current results provide the microscopic origin of how adsorption weakens the interpolymer interactions in general.

Orientational Relaxation of Poly(propylene imine) Dendrimers at Different pH

The dilute solution dynamics of poly(propylene imine) (PPI) dendrimers is investigated at three different solution pH through molecular dynamics (MD) simulations. The dynamics of PPI dendrimers is characterized by both global and local relaxations that occur at different time and length scales. While the global dynamics may be described in terms of rotational diffusion, the local motion may be characterized through orientational relaxation dynamics measured in terms of the time autocorrelation function (ACF), second-order orientational ACF, and the spin-lattice relaxation rate. The global motion of dendrimers decreases with an increase in the size from high pH to low pH with increasing generations of growth. The results reveal that the segments at low pH relax faster than those at high pH, and the local mobility of the segments near the periphery is higher than the core segments. This observation is also evident from the spectral density and spin-lattice relaxation rate. High values of the spectral density at higher frequencies imply higher segmental mobility of the dendrimer at low pH relative to that at high pH. A shift in the maximum of the spin-lattice relaxation rate toward lower frequencies with decreasing generations indicates the dependence of local mobility on the topological distance of the segment from the periphery at all pH conditions.

Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations

Modern nanotechnology research has generated numerous experimental data for various nanomaterials. However, the few nanomaterial databases available are not suitable for modeling studies due to the way they are curated. Here, we report the construction of a large nanomaterial database containing annotated nanostructures suited for modeling research. The database, which is publicly available through http://www.pubvinas.com/, contains 705 unique nanomaterials covering 11 material types. Each nanomaterial has up to six physicochemical properties and/or bioactivities, resulting in more than ten endpoints in the database. All the nanostructures are annotated and transformed into protein data bank files, which are downloadable by researchers worldwide. Furthermore, the nanostructure annotation procedure generates 2142 nanodescriptors for all nanomaterials for machine learning purposes, which are also available through the portal. This database provides a public resource for data-driven nanoinformatics modeling research aimed at rational nanomaterial design and other areas of modern computational nanotechnology.

Complexation of peptide epitopes with G4-PAMAM dendrimer through ligand diffusion molecular dynamic simulations

Peptide epitopes from HIV-1 gp120 have been used to block the gp120-CD4 complex, whereas their poor absorbable or immunogenic properties prevent them from coupling to generation four polyamidoamine (PAMAM-G4) dendrimers. PAMAM-G4 are synthetic nanoparticles that are relatively nontoxic and nonimmunogenic have been employed as nanocarriers. In a previous study, two peptide epitopes (ABC and PGV04) from gp120 located at the protein-protein interface of the gp120-CD4 complex were identified through protein-protein dissociation. Then, their complexation with G4-PAMAM was evaluated through experimental and theoretical approaches, revealing a stoichiometry of 1:8/9 for G4-PAMAM and ABC or PGV04, respectively, providing important information that can be used to gain insight into the structural and energetic basis of the molecular binding of these G4-PAMAM-peptide systems. In this contribution, we performed ligand diffusion molecular dynamic simulations (LDMDSs) using 1.5 μs combined with the molecular mechanics generalized Born surface area (MMGBSA) approach, a strategy that successfully reproduced experimentally encapsulation on PAMAM-G4-ligand complexes, to explore the mechanism through which ABC and PGV04 are encapsulated by PAMAM-G4 under neutral and acid conditions. Our results reproduce the reported PAMAM-G4-peptide complex stoichiometry, revealing a slower peptide delivery at neutral conditions and a spontaneous release under acidic conditions. LDMDSs show that several peptides can reach stable G4-PAMAM complexes at neutral pH, and only a few are able to encapsulate on dendrimers without impacting dendrimer sphericity. Energetic analysis exploring different generalized Born models revealed that the ABC peptide has better binding properties than PGV04.

Prediction of MAYV peptide antigens for immunodiagnostic tests by immunoinformatics and molecular dynamics simulations

The Mayaro virus is endemic to South America, and the possible involvement of Aedes spp. mosquitoes in its transmission is a risk factor for outbreaks of greater proportions. The virus causes a potentially disabling illness known as Mayaro fever, which is similar to that caused by the chikungunya virus. The cocirculation of both viruses, with their clinical and structural similarities, and the absence of prophylactic and therapeutic measures highlight the need for studies that seek to understand the Mayaro virus. Using approaches in silico, we identified an antigenic and specific epitope (p_MAYV4) in domain A of the E2 glycoprotein of the Mayaro virus. This epitope was theoretically predicted to be stable and exposed on the surface of the protein, where it showed key properties that enable its interaction with neutralizing antibodies. These characteristics make it an interesting target for the development of immunodiagnostic platforms. Molecular dynamics simulation-based structural analysis showed that the PHE95 residue in the E1 fusion loop region is conserved among Alphavirus family members. PHE95 interacts with the hydrophobic residues of the E2 glycoprotein to form a cage-shaped structure that is critical to assemble and stabilize the E1/E2 heterodimer. These results provide important insights useful for the advancement of diagnostic platforms and the study of therapeutic alternatives.

Complexation of methotrexate via ligand diffusion molecular dynamic simulations under neutral, basic, and acidic conditions

Methotrexate (MTX), an FDA-approved drug employed in the treatment of several types of cancer and autoimmune diseases, is characterized by its poor solubility. Therefore, new strategies have been implemented such as coupling to nanocarriers to increase its solubility. Previous experimental studies have demonstrated complexation of MTX to polyamidoamine of a generation four (PAMAM-G4) dendrimer with a complex stoichiometry of 19/22:1 under neutral conditions, providing important information that can be used to further elucidate the structural and energetic basis of the molecular binding of MTX and PAMAM-G4. In this study, we performed ligand diffusion molecular dynamic simulations (LDMDSs), using 3 μs combined with the molecular mechanics generalized surface area (MMGBSA) approach employing saturating concentrations of MTX to explore the mechanism through which MTX is complexed by PAMAM-G4 at neutral, basic, and acidic conditions. Our results reproduce the reported complex stoichiometry between MTX and PAMAM-G4 in neutral conditions. Binding free energy values suggest a much slower release in neutral and acidic conditions, consistent with the controlled rate of drug release into the bloodstream and when reaching the acidic environment of tumor tissues. Altogether, the methodology employed and the results may be useful in the evaluation of other drugs of pharmaceutical interest.

Synthesis of Amino Terminal Clicked Dendrimers. Approaches to the Application as a Biomarker

Herein, we present an easy and efficient synthesis of amino terminal dendrons, combining protection/deprotection reactions with copper-catalyzed azide alkyne cycloaddition in a convergent way. This new approach affords dendrons in gram scale with excellent yields and easy purification. By choosing the appropriate azido-functionalized core, these dendrons lead to a more efficient and controlled convergent synthesis of dendrimers with different sizes and shapes and multivalence. The amino terminal dendrimers were analyzed by diffusion-ordered spectroscopy experiments. The observed dendrimer size is in excellent correlation with the expected size and shape by molecular dynamic simulations. The construction of these kinds of nanostructures, in a simple and efficient way, opens new opportunities for biomedical applications. Moreover, by choosing the appropriate core, these versatile macromolecules become an excellent fluorescent biomarker.

Understanding the Thermodynamics of the Binding of PAMAM Dendrimers to Graphene: A Combined Analytical and Simulation Study

We investigate the thermodynamics of the binding of a poly(amidoamine) dendrimer to an uncharged graphene sheet as a function of the pH level using umbrella sampling simulations and a mean-field theory for generations three and four. We find that the dendrimer strongly binds to the graphene sheet ( O (100) kcal/mol) from our potential of mean force (PMF) calculations. In specific, we find that the dendrimer binds the most at neutral pH (∼7) and the least at low pH (∼4). We explain this nonmonotonic nature of the dendrimer's adsorption by studying the interactions contributing to the PMF, i.e., the dendrimer-graphene, dendrimer-water, and dendrimer-ion interactions. We also corroborate our PMF calculations with molecular mechanics generalized Born surface area analysis and free energies obtained from a mean-field theory of Flory-Huggins-Debye-Hückel type [ Muthukumar , M. , J. Chem. Phys. 2010 , 132 , 084901 ], including electrostatic interactions. We find that the van der Waals interactions between the dendrimer and the graphene alone cannot capture the accurate trends in the binding free energies (BEs) as a function of pH. The solvent and the counterions present in the system are also found to have a major influence on these trends. We demonstrate that the dendrimer-graphene and dendrimer-water interactions become favorable, whereas the dendrimer-ion interaction becomes unfavorable, as the dendrimer binds to graphene. These opposing effects lead to the observed nonmonotonicity in the BE trends. Our theoretical model also reproduces these trends in the subinteractions contributing to the PMF. To the best of our knowledge, this is a novel attempt where an equivalence between theory and simulations is made in the context of the dendrimer's adsorption.

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.

Zn2+-triggered self-assembly of Gonadorelin [6-D-Phe] to produce nanostructures and fibrils

A synthetic derivative, GnRH [6-D-Phe], stable against enzymatic degradation, self-assembles and forms nanostructures and fibrils upon a pH shift in the presence of different concentrations of Zn²⁺in vitro. Attenuated Total Reflection Fourier Transform Infrared spectroscopy (ATR–FTIR) revealed the existence of higher order assembly of Zn²⁺: GnRH [6-D-Phe]. Nuclear Magnetic Resonance spectroscopy (NMR) indicated a weak interaction between Zn²⁺ and GnRH [6-D-Phe]. Atomic Force Microscopy (AFM) showed the existence of GnRH [6-D-Phe] oligomers and fibrils. Molecular Dynamic (MD) simulation of the 10:1 Zn²⁺: GnRH [6-D-Phe] explored the interaction and dimerization processes. In contrast to already existing short peptide fibrils, GnRH [6-D-Phe] nanostructures and fibrils form in a Tris-buffered pH environment in a controlled manner through a temperature reduction and a pH shift. The lyophilized Zn²⁺: GnRH [6-D-Phe] assembly was tested as a platform for the sustained delivery of GnRH [6-D-Phe] and incorporated into two different oil vehicle matrices. The in vitro release was slow and continuous over 14 days and not influenced by the oil matrix.

Dendrimeric Antigens for Drug Allergy Diagnosis: A New Approach for Basophil Activation Tests

Dendrimeric Antigens (DeAns) consist of dendrimers decorated with multiple units of drug antigenic determinants. These conjugates have been shown to be a powerful tool for diagnosing penicillin allergy using in vitro immunoassays, in which they are recognized by specific IgE from allergic patients. Here we propose a new diagnostic approach using DeAns in cellular tests, in which recognition occurs through IgE bound to the basophil surface. Both IgE molecular recognition and subsequent cell activation may be influenced by the tridimensional architecture and size of the immunogens. Structural features of benzylpenicilloyl-DeAn and amoxicilloyl-DeAn (G2 and G4 PAMAM) were studied by diffusion Nuclear Magnetic Resonance (NMR) experiments and are discussed in relation to molecular dynamics simulation (MDS) observations. IgE recognition was clinically evaluated using the basophil activation test (BAT) for allergic patients and tolerant subjects. Diffusion NMR experiments, MDS and cellular studies provide evidence that the size of the DeAn, its antigen composition and tridimensional distribution play key roles in IgE-antigen recognition at the effector cell surface. These results indicate that the fourth generation DeAns induce a higher level of basophil activation in allergic patients. This approach can be considered as a potential complementary diagnostic method for evaluating penicillin allergy.

pH and generation dependent morphologies of PAMAM dendrimers on a graphene substrate

The adsorption of PAMAM dendrimers at solid/water interfaces has been extensively studied, and is mainly driven by electrostatic and van der Waals interactions between the substrate and the dendrimers. However, the pH dependence of the adsorption driven predominantly by the van der Waals interactions is poorly explored, although it is crucial for investigating the potentiality of these dendrimers in supercapacitors and surface patterning. Motivated by this aspect, we have studied the adsorption behavior of PAMAM dendrimers of generations 2 (G2) to 5 (G5) with pH and salt concentration variation, on a charge neutral graphene substrate, using fully atomistic molecular dynamics simulations. The instantaneous snapshots from our simulations illustrate that the dendrimers deform significantly from their bulk structures. Based on various structural property calculations, we classify the adsorbed dendrimer morphologies into five categories and map them to a phase diagram. Interestingly, the morphologies we report here have striking analogies with those reported in star-polymer adsorption studies. From the fractional contacts and other structural property analyses we find that the deformations are more pronounced at neutral pH as compared to high and low pH. Higher generation dendrimers resist deformation following the deformation trend, G2 > G3 > G4 > G5 at any given pH level. As the adsorption here is mainly driven by van der Waals interactions, we observe no desorption of the dendrimers as the salt molarity is increased, unlike that reported in the electrostatically driven adsorption studies.

Translocation of Bioactive Molecules through Carbon Nanotubes Embedded in the Lipid Membrane

One of the major challenges of nanomedicine and gene therapy is the effective translocation of drugs and genes across cell membranes. In this study, we describe a systematic procedure that could be useful for efficient drug and gene delivery into the cell. Using fully atomistic molecular dynamics (MD) simulations, we show that molecules of various shapes, sizes, and chemistries can be spontaneously encapsulated in a single-walled carbon nanotube (SWCNT) embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer, as we have exemplified with dendrimers, asiRNA, ssDNA, and ubiquitin protein. We compute the free energy gain by the molecules upon their entry inside the SWCNT channel to quantify the stability of these molecules inside the channel as well as to understand the spontaneity of the process. The free energy profiles suggest that all molecules can enter the channel without facing any energy barrier but experience a strong energy barrier (≫k_BT) to translocate across the channel. We propose a theoretical model for the estimation of encapsulation and translocation times of the molecules. Whereas the model predicts the encapsulation time to be of the order of few nanoseconds, which match reasonably well with those obtained from the simulations, it predicts the translocation time to be astronomically large for each molecule considered in this study. This eliminates the possibility of passive diffusion of the molecules through the CNT-nanopore spanning across the membrane. To counter this, we put forward a mechanical method of ejecting the encapsulated molecules by pushing them with other free-floating SWCNTs of diameter smaller than the pore diameter. The feasibility of the proposed method is also demonstrated by performing MD simulations. The generic strategy described here should work for other molecules as well and hence could be potentially useful for drug- and gene-delivery applications.

Dendrimer-functionalized electrospun nanofibres as dual-action water treatment membranes

This work reports the preparation of composite electrospun membranes combining antimicrobial action with the capacity of retaining low-molecular weight non-polar pollutants. The membranes were electrospun blends of polyvinyl alcohol (PVA) and poly(acrylic acid) (PAA) stabilized using heat curing. The membranes were functionalized by grafting amino-terminated poly(amidoamine) (PAMAM) G3 dendrimers. The antimicrobial effect was assessed using strains of Escherichia coli and Staphylococcus aureus by tracking their capacity to form new colonies and their metabolic impairment upon contact with membranes. The antimicrobial activity was particularly high to the gram-positive bacterium S. aureus with a 3-log reduction in their capacity to colonize dendrimer-functionalized membranes with respect to neat PVA/PAA fibers. The effect to gram-positive bacteria was attributed to the interaction of dendrimers with the negatively charged bacterial membranes and resulted in membranes essentially free of bacterial colonization after 20h in contact with cultures at 36°C. The adsorption of toluene on PAA/PVA fibers and on dendrimer-functionalized membranes was assayed using toluene over a broad concentration range. The host-guest encapsulation of toluene inside dendrimer molecules was computed through docking studies, which allowed calculating a maximum capacity of 14 molecules of toluene per molecule of PAMAM G3. The theoretical prediction was in good agreement with the experimental capacity at the higher concentrations assayed.

Binding free energy calculations using MMPB/GBSA approaches for PAMAM-G4-drug complexes at neutral, basic and acid pH conditions

Dendrimers are synthetic macromolecules with a highly-branched structure and high concentration of surface groups. Among dendrimers, Poly(amidoamine) (PAMAM) has received substantial attention as a novel drug carrier and delivery system. Depending on the generation and type of terminal groups, dendrimer toxicity could change and include cytotoxicity. Although PAMAM is water soluble, molecular modeling of the dendrimer-drug complex is considered challenging for exploring the conformational mobility of dendrimers and atomic specific interactions during the dendrimer-drug association. However, conventional protocols for predicting binding affinities have been designed for small protein molecules or protein-protein complexes that can be applied to study the dendrimer-drug association. In this work, we performed docking calculations for a set of 94 previously reported compounds on PAMAM of fourth generation (G4-PAMAM) to select six compounds, cromoglicic acid (CRO) - a mast cell stabilizer, Fusidic acid (FUS) - a bacteriostatic antibiotic, and Methotrexate (MTX) - a chemotherapy agent and immune system suppressant, which have the highest affinities for G4-PAMAM, and Lidocaine (LDC) - used to numb tissue in a specific area and for ventricular tachycardia treatment, Metoprolol (MET) - a β₁ receptor blocker, and Pindolol (PIN) - a β blocker, which have the lowest affinities for the G4-PAMAM dendrimer, to perform MD simulations combined with the molecular mechanics generalized/Poisson-Boltzmann surface area MMGBSA/MMPBSA approach to investigate the interactions of generating 4 charge-neutral, charge-basic and charge-acid G4-PAMAM dendrimers. In addition, to validate these theoretical G4-PAMAM-drug complexes, the complexes were experimentally conjugated to determine their stability in aqueous solubility studies immediately and over one year. Our results show that among the different commercial drugs, both charged and neutral PAMAM have the most favorable binding free energies for CRO, MTX, and FUS, which appears to be due to a complex counterbalance of electrostatics and van der Waals interactions. These theoretical and aqueous solubility studies supported the high affinity of methotrexate for the G4-PAMAM-drug due to its carboxyl and aryl moieties that favor its accommodation by noncovalent interactions.

PAMAM dendrimer: a pH-controlled nanosponge

Using fully atomistic molecular dynamics simulation that are several hundred nanoseconds long, we demonstrate the pH-controlled sponge action of PAMAM dendrimer. We show how at varying pH levels, the PAMAM dendrimer acts as a wet sponge; at neutral or low pH levels, the dendrimer expands noticeably and the interior of the dendrimer opens up to host several hundreds to thousands of water molecules depending on the generation number. Increasing the pH (i.e., going from low pH to high pH) leads to the collapse of the dendrimer size, thereby expelling the inner water, which mimics the ‘sponge’ action. As the dendrimer size swells up at a neutral pH or low pH due to the electrostatic repulsion between the primary and tertiary amines that are protonated at this pH, there is dramatic increase in the available solvent accessible surface area (SASA), as well as solvent accessible volume (SAV).