Theoretical and computational studies of dendrimers as delivery vectors

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.

Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?

Gene therapy enables the introduction of nucleic acids like DNA and RNA into host cells, and is expected to revolutionize the treatment of a wide range of diseases. This growth has been further accelerated by the discovery of CRISPR/Cas technology, which allows accurate genomic editing in a broad range of cells and organisms in vitro and in vivo. Despite many advances in gene delivery and the development of various viral and non-viral gene delivery vectors, the lack of highly efficient non-viral systems with low cellular toxicity remains a challenge. The application of cutting-edge technologies such as artificial intelligence (AI) has great potential to find new paradigms to solve this issue. Herein, we review AI and its major subfields including machine learning (ML), neural networks (NNs), expert systems, deep learning (DL), computer vision and robotics. We discuss the potential of AI-based models and algorithms in the design of targeted gene delivery vehicles capable of crossing extracellular and intracellular barriers by viral mimicry strategies. We finally discuss the role of AI in improving the function of CRISPR/Cas systems, developing novel nanobots, and mRNA vaccine carriers.

Engineering of 177Lu-labeled gold encapsulated into dendrimeric nanomaterials for the treatment of lung cancer

As a novel type of theranostic radioactive agents, ¹⁷⁷Lu-labeled nanomaterials conjugated to macromolecules have been described. The study aimed to fabricate PAMAM-G4-(¹⁷⁷Lu-dendrimer)-bombesin-folate in the dendrimeric cavity, assess the radiopharmaceutical ability for specifically targeted radiotherapy and simultaneously detects gastrin-releasing peptide receptors (GRPR) and folate receptors (FRs) overexpressed in lung carcinoma cells, respectively. In an aqueous-basic media, p-SCN-benzyl-DOTA was conjugated to the dendrimer. This dendrimer was formed by activating the carboxylic acid groups of DOTA-folic acid and bombesin with HATU and conjugating them to develop the dendrimer. As part of this process, the conjugate was combined with 1% HAuCl₄, added NaBH₄ and filtered by ultrafiltration. Infrared, UV-Vis, TEM analysis, dynamic light scattering (DLS), and fluorescence spectroscopy were employed to observe the composition of the fabricated sample. Radio-labeled ¹⁷⁷LuCl₃ was used to label the conjugate, which was then evaluated using the radio-HPLC method. Findings demonstrated dendrimeric functionalization with remarkable radiochemical composition purity up to >96%. Because of fluorescence studies, it was determined that the occurrence of AuNMs in the dendrimeric cavities gives beneficial photo-physical characteristics to the radiopharmaceutical for bio-imaging. HEL-299 lung cancer cells exhibited a selective absorption of the drug (%). It might be helpful as nuclear and optical imaging agents for lung cancers that overexpress FRs and GRPR and as a specific target for radiation therapy if combined with folate-bombesin.

Molecular Simulation Studies on the Interactions of Bilirubin at Different States with a Lipid Bilayer

The unconjugated bilirubin (BR) may penetrate through the cell membrane and cause a severe cytotoxicity. However, the molecular mechanism underlying the penetration of BR into the cell membrane is still largely unknown. In this work, we systematically investigate the interaction of BR and a lipid bilayer under different conditions by using all-atom molecular dynamics simulations. It is found that BR at the Z,Z conformation can easily enter into the interior of the lipid bilayer due to its hydrophobicity. However, when BR transforms from the Z,Z conformation to the E,E conformation (after the blue-light emission), its penetration ability is greatly reduced (especially at its ionized state). This study may offer useful physical insights into the effect of phototherapy on the penetration behavior and the cytotoxicity of the unconjugated BR.

Phase equilibria and conformational behavior of dendrimers in porous media: Towards chromatographic analysis of dendrimers

HYPOTHESIS

The intricate entropy-enthalpy interplay of dendrimers confined in pores affects their conformation and retention in the porous stationary phase. This work aims at providing important insights into its impacts on partitioning and chromatographic separation in both size-exclusion chromatography (SEC) and interaction chromatography (IC) regimes.

SIMULATIONS

Using Monte Carlo (MC) simulations, we investigated the bulk-pore phase equilibria and the conformational behavior of flexible dendrimers differing in generation, in spacer length and in fraction of modified terminal groups interacting differently with pore walls than the majority building units.

FINDINGS

With increasing interaction strength, a distinct transition from a roughly spherical shape caused by simultaneous interactions with two walls to an ellipsoidal (or even disklike) conformation tenaciously adhering to only one wall was observed for moderately confined dendrimers. The strongly deformed dendrimers subjected to severe confinement gain high energy and the samples differing in the degree of modification become chromatographically discernable thanks to large energy differences. Consequently, our results suggest that the column fillings with fairly narrow pores which are ineffective in SEC, are highly efficient separation media for dendrimer studies by IC above the critical adsorption point (CAP). Overall, our simulations reveal useful information for advancing and optimizing experimental liquid chromatography studies of dendrimers.

Application of Non-Viral Vectors in Drug Delivery and Gene Therapy

Vectors and carriers play an indispensable role in gene therapy and drug delivery. Non-viral vectors are widely developed and applied in clinical practice due to their low immunogenicity, good biocompatibility, easy synthesis and modification, and low cost of production. This review summarized a variety of non-viral vectors and carriers including polymers, liposomes, gold nanoparticles, mesoporous silica nanoparticles and carbon nanotubes from the aspects of physicochemical characteristics, synthesis methods, functional modifications, and research applications. Notably, non-viral vectors can enhance the absorption of cargos, prolong the circulation time, improve therapeutic effects, and provide targeted delivery. Additional studies focused on recent innovation of novel synthesis techniques for vector materials. We also elaborated on the problems and future research directions in the development of non-viral vectors, which provided a theoretical basis for their broad applications.

Nanomaterial-based delivery vehicles for therapeutic cancer vaccine development

Nanomaterial-based delivery vehicles such as lipid-based, polymer-based, inorganics-based, and bio-inspired vehicles often carry distinct and attractive advantages in the development of therapeutic cancer vaccines. Based on various delivery vehicles, specifically designed nanomaterials-based vaccines are highly advantageous in boosting therapeutic and prophylactic antitumor immunities. Specifically, therapeutic vaccines featuring unique properties have made major contributions to the enhancement of antigen immunogenicity, encapsulation efficiency, biocompatibility, and stability, as well as promoting antigen cross-presentation and specific CD8+ T cell responses. However, for clinical applications, tumor-associated antigen-derived vaccines could be an obstacle, involving immune tolerance and deficiency of tumor specificities, in achieving maximum therapeutic indices. However, when using bioinformatics predictions with emerging innovations of in silico tools, neoantigen-based therapeutic vaccines might become potent personalized vaccines for tumor treatments. In this review, we summarize the development of preclinical therapeutic cancer vaccines and the advancements of nanomaterial-based delivery vehicles for cancer immunotherapies, which provide the basis for a personalized vaccine delivery platform. Moreover, we review the existing challenges and future perspectives of nanomaterial-based personalized vaccines for novel tumor immunotherapies.

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.

Understanding the Interaction of Polyelectrolyte Architectures with Proteins and Biosystems

The counterions neutralizing the charges on polyelectrolytes such as DNA or heparin may dissociate in water and greatly influence the interaction of such polyelectrolytes with biomolecules, particularly proteins. In this Review we give an overview of studies on the interaction of proteins with polyelectrolytes and how this knowledge can be used for medical applications. Counterion release was identified as the main driving force for the binding of proteins to polyelectrolytes: Patches of positive charge become multivalent counterions of the polyelectrolyte and lead to the release of counterions from the polyelectrolyte and a concomitant increase in entropy. This is shown from investigations on the interaction of proteins with natural and synthetic polyelectrolytes. Special emphasis is paid to sulfated dendritic polyglycerols (dPGS). The Review demonstrates that we are moving to a better understanding of charge-charge interactions in systems of biological relevance. Research along these lines will aid and promote the design of synthetic polyelectrolytes for medical applications.

Ion-mediated interactions between like-charged polyelectrolytes with bending flexibility

Ion-mediated interactions between polyelectrolytes (PEs) are crucial to the properties of flexible biopolymers such as nucleic acids and proteins but the effect of PE flexibility on such interactions has not been explicitly addressed until now. In this work, the potentials of mean force (PMFs) between like-charged PEs with different bending flexibility have been investigated by Monte Carlo simulations and a cylindrical confinement around each PE was involved to model two PEs in an array. We found that in the absence of trivalent salt, the PMFs between like-charged PEs in an array are apparently repulsive while the bending flexibility can visibly decrease the repulsive PMFs. With the addition of high trivalent salt, the PMFs become significantly attractive whereas the attractive PMFs can be apparently weakened by the bending flexibility. Our analyses reveal that the effect of bending flexibility is attributed to the increased PE conformational space, which allows the PEs to fluctuate away to decrease the monovalent ion-mediated repulsion or to weaken the trivalent ion-mediated attraction through disrupting trivalent ion-bridging configuration. Additionally, our further calculations show that the effect of bending flexibility on the ion-mediated interactions is less apparent for PEs without cylindrical confinement.

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.

Computational design of Janus polymersomes with controllable fission from double emulsions

Janus polymer vesicles (polymersomes) with biphasic membranes have special properties and potential applications in many fields. The big barrier for the preparation of Janus polymersomes lies in the difficulty of complete lateral microphase separation of polymers along the vesicle membrane due to the limited mobility. Herein, we present a systematic simulation study to provide a new strategy for the fabrication of Janus polymersomes based on water-in-oil-in-water double emulsions. Two incompatible block copolymers of AB and AC completely separate into two hemispheres of the polymersome driven by the dewetting of double emulsions, followed by the stabilization of the Janus structure with the block copolymers BC at the interface between AB and AC hemispheres. The simulation results demonstrate the formation of Janus polymersomes in a wide range of the incompatibility between blocks B and C. In addition, the morphologies of the Janus polymersomes can be readily regulated by changing the number of copolymers BC, the ratio of AB to AC, and the dewetting rate of organic solvents. Both the Janus and patchy polymersomes can be obtained through the adjustment of the dewetting rate. Besides, by introducing stimulus-cleavable copolymers of BC, the Janus polymersomes can perform controllable fission. Further comparison with similar experiments has also demonstrated the feasibility of our strategy. We believe the present work will be useful for the fabrication of polymersomes with controlled patches in a large quantity, and the stimulus-responsive fission process will also make the polymersomes promising in some applications like controlled drug delivery and cytomimetic membrane communication.

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.

Multifunctional Smart Yolk-Shell Nanostructure with Mesoporous MnO2 Shell for Enhanced Cancer Therapy

Manganese dioxide (MnO₂) nanostructures have aroused great interest among analytical and biological medicine researchers as a unique type of tumor microenvironment (TME)-responsive nanomaterial. However, reliable approaches for synthesizing yolk-shell nanostructures (YSNs) with mesoporous MnO₂ shell still remain exciting challenges. Herein, a YSN (size, ∼75 nm) containing a mesoporous MnO₂ shell and Er³⁺-doped upconversion/downconversion nanoparticle (UCNP) core with a large cavity is demonstrated for the first time. This nanostructure not only integrates diverse functional components including MnO₂, UCNPs, and YSNs into one system but also endows a size-controllable hollow cavity and thickness-tunable MnO₂ layers, which can load various guest molecules like photosensitizers, methylene blue (MB), and the anticancer drugs doxorubicin (DOX). NIR-II fluorescence and photoacoustic (PA) imaging from UCNP and MB, respectively, can monitor the enrichment of the nanomaterials in the tumors for guiding chemo-photodynamic therapy (PDT) in vivo. In the TME, degradation of the mMnO₂ shell by H₂O₂ and GSH not only generates Mn²⁺ for tumor-specific T₁-MR imaging but also releases O₂ and drugs for tumor-specific treatment. The result confirmed that imaging-guided enhanced chemo-PDT combination therapy that benefited from the unique structural features of YSNs could substantially improve the therapeutic effectiveness toward malignant tumors compared to monotherapy.

Controlling ion transport in a C2N-based nanochannel with tunable interlayer spacing

Selective ion transport through a nanochannel formed by stacked two-dimensional materials plays a key role in water desalination, nanofiltration, and ion separation. Although there have been many functional nanomaterials used in these applications, how to well control ion transport in a laminar structure so as to obtain the desired selectivity still remains a challenging problem. In the present work, the transport of ions through a C₂N-based nanochannel is investigated by using all-atom molecular dynamics simulation. It is found that C₂N-based nanochannels with different interlayer spacing posses diverse ion selectivity, which is mainly attributed to the distinct loading capability among ions and the different velocity of ions inside the nanochannel. Moreover, we also find that the ion selectivity is dependent on the electric field, but nearly independent of the salt concentration. The present study may provide some physical insights into the experimental design of C₂N-based nanodevices in nanofiltration.

Individual Roles of Peptides PGLa and Magainin 2 in Synergistic Membrane Poration

Synergy between antimicrobial peptides PGLa and Magainin 2 (MAG2) provides an efficient way to enhance their antimicrobial ability. However, the underlying molecular mechanism of such synergy, especially the individual roles of each peptide, remains poorly understood. We combined a giant unilamellar vesicle leakage assay, in situ interfacial photovoltage testing, and molecular dynamics to investigate membrane poration under the action of PGLa, MAG2, or a PGLa/MAG2 mixture. Our results clearly show the different membrane action modes of the three systems and demonstrate the importance of forming PGLa-MAG2 heterodimers in the membrane poration process. PGLa inserted into and extracted from a membrane rapidly and continually with minimal aggregation and produced only transient, small pores. In contrast, MAG2 peptides tended to aggregate together on the membrane surface or only shallowly embed in the membrane. Additionally, the PGLa and MAG2 residues were well integrated into the membrane via the formation of PGLa-MAG2 heterodimers. The membrane defect produced by the rapid insertion of PGLa was stabilized by MAG2, which further recruited other peptides for the formation of PGLa-MAG2 heterodimers and even heterodimer clusters. Growth in pore size then occurred in a step-by-step process involving the formation and assembly of heterodimer clusters within the membrane. Our results provide insight into the complicated synergy that occurs between PGLa and MAG2 during membrane poration and will assist in the design of new antimicrobial peptides.

Enhancing the targeting ability of nanoparticles via protected copolymers

It is important to maintain the balance between therapeutic efficiency and cytotoxicity when using nanomaterials for biomedical applications. Here, we propose a new method (i.e., non-covalent coating of protected copolymers onto the nanoparticle surface) to enhance the active targeting of nanoparticles to the cancer cells by combining the dissipative particle dynamics simulation and in vitro experiments. When coating the protected copolymer onto the nanoparticle surface, the uptake efficiency could be greatly altered due to the competition between the copolymer-ligand interaction and the receptor-ligand interaction-the non-covalent coating is more efficient than the covalent coating. Furthermore, the effect of the physicochemical properties of the protected copolymer on the targeting ability of nanoparticles was also investigated. This study offers useful insight into the optimal design of nanocarriers in biomedicine.

Lipid-specific interactions determine the organization and dynamics of membrane-active peptide melittin

The cell membranes of different cells deviate significantly in lipid compositions and thus provide varying biological environments to modulate the diffusion, organization and the resultant function of biomacromolecules. However, the detailed modulation mechanism remains elusive especially in consideration of the current overuse of the simplified membrane models such as the pure phosphatidylcholine (PC) membrane. In this work, with the typical membrane-active peptide melittin, we demonstrated that a more complicated membrane environment, such as the bacterial (IME) or plasma membrane (PM), would significantly change the organization and dynamics of melittin, by using molecular dynamics simulations as a "computational microscope". It was found that in these membrane systems, adding melittin would cause a varying degree of reduction in the lateral diffusion of lipids due to the different assembly states of peptides. Melittin tended to aggregate to oligomers in the pure PC membrane, mostly as a tetramer or trimer, while in IME or PM, its degree of oligomerization was significantly reduced. More surprisingly, melittin displayed a strong affinity with ganglioside GM3 in PM, leading to the formation of melittin-GM3 nanoclusters, which hindered its diffusion and further oligomerization. Additionally, small changes in the residue sequence of melittin could modulate the degree or structure of the peptide oligomer. Our work provides a typical example of a study on the organization and dynamics of pore-forming peptides in specific membrane environments and has great significance on the optimization of peptide sequences and the design of helix bundles in the membrane for target biological function.

Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations

Due to different interactions between lipids and proteins, a plasma membrane can segregate into different membrane domains. Among them, ordered functional membrane domains are defined as "lipid rafts", which play key roles in many biological processes (e.g., signal transduction, endocytosis, etc.) in the cell. Hence, it will be of much biological significance to monitor and even regulate the dynamics of lipid rafts. In this work, we designed a ligand-modified spherical nanoparticle with coarse-grained molecular dynamics simulations, which can be encapsulated into the hydrophobic region of the lipid membrane and specifically target either raft or non-raft membrane domains. The preferred localization of the nanoparticle can be tuned by adjusting ligand hydrophobicity, length and density. Generally, more hydrophobic nanoparticles tend to target the raft domain, while less hydrophobic nanoparticles prefer the non-raft domain. Besides, ligand length and density jointly determine the exposure of nanoparticle cores and thus affect the roles of ligands in nanoparticles' final localization. Our results may provide insights into the experimental design of functional nanoparticles, targeting the lipid raft and regulating its dynamics.

Study on the interfacial properties of polymers around a nanoparticle

The interfacial properties of polymer chains on spherical nanoparticles are investigated using off-lattice Monte Carlo simulations.

Acid-Triggered Charge-Convertible Graphene-Based All-in-One Nanocomplex for Enhanced Genetic Phototherapy of Triple-Negative Breast Cancer

Highly efficient and stimulus-responsive nanomedicines for cancer treatment are currently receiving tremendous attention. In this study, an acid-triggered charge-reversible graphene-based all-in-one nanocomplex is appropriately designed by surface modification with multilayer polymers and simultaneous co-transportation of photosensitizer indocyanine green (ICG) and oligonucleotide inhibitor of miR-21 (miR-21i) to achieve highly efficient genetic phototherapy in a controlled manner. The nanocomplex (denoted as GPCP/miR-21i/ICG) effectively protects miR-21i from degradation and exhibits excellent photothermal/photochemical reactive oxygen species (ROS) generation as well as fluorescence imaging ability. The cargoes ICG and miR-21i can significantly be released at acidic pH compared with normal physiological medium and escaped from endosomes/lysosomes due to the acid-triggered charge reversal effect. Typically, the released miR-21i downregulate the endogenous miR-21 and result in the upregulation of the target proteins PTEN and Bax, thus increasing the phototherapeutic efficiency of ICG. High in vivo anticancer efficiency against the MDA-MB-231 triple-negative breast cancer (TNBC) model is obtained due to the combination of genetic regulation of miR-21i and the photokilling effect of ICG. This work highlights the great potential of this smart nanocomplex as an attractive modality of gene-photo combined treatment of cancer, especially for intractable TNBC.

Controlling the Interaction of Nanoparticles with Cell Membranes by the Polymeric Tether

The well control over the cell-nanoparticle interaction can be of great importance and necessity for different biomedical applications. In this work, we propose a new and simple way (i.e., polymeric tether) to tuning the interaction between nanoparticles and cell membranes by dissipative particle dynamics simulations. It is found that the linked nanoparticles (via polymeric tether) can show some cooperation during the cellular uptake and thereby have a higher wrapping degree than the single nanoparticle. The effect of the property of the polymer on the wrapping is also investigated, and it is found that the length, rigidity, and hydrophobicity of the polymer play an important role. More interestingly, the uptake of linked nanoparticles could be adjusted to the firm adhesion via two rigid polymeric tethers. The present study may provide some useful guidelines for novel design of functional nanomaterials in the experiments.

How Melittin Inserts into Cell Membrane: Conformational Changes, Inter-Peptide Cooperation, and Disturbance on the Membrane

Antimicrobial peptides (AMPs), as a key component of the immune defense systems of organisms, are a promising solution to the serious threat of drug-resistant bacteria to public health. As one of the most representative and extensively studied AMPs, melittin has exceptional broad-spectrum activities against microorganisms, including both Gram-positive and Gram-negative bacteria. Unfortunately, the action mechanism of melittin with bacterial membranes, especially the underlying physics of peptide-induced membrane poration behaviors, is still poorly understood, which hampers efforts to develop melittin-based drugs or agents for clinical applications. In this mini-review, we focus on recent advances with respect to the membrane insertion behavior of melittin mostly from a computational aspect. Membrane insertion is a prerequisite and key step for forming transmembrane pores and bacterial killing by melittin, whose occurrence is based on overcoming a high free-energy barrier during the transition of melittin molecules from a membrane surface-binding state to a transmembrane-inserting state. Here, intriguing simulation results on such transition are highlighted from both kinetic and thermodynamic aspects. The conformational changes and inter-peptide cooperation of melittin molecules, as well as melittin-induced disturbances to membrane structure, such as deformation and lipid extraction, are regarded as key factors influencing the insertion of peptides into membranes. The associated intermediate states in peptide conformations, lipid arrangements, membrane structure, and mechanical properties during this process are specifically discussed. Finally, potential strategies for enhancing the poration ability and improving the antimicrobial performance of AMPs are included as well.

Drug-Conjugated Dendrimer Hydrogel Enables Sustained Drug Release via a Self-Cleaving Mechanism

In this study, the anticancer drug, camptothecin (CPT), was covalently grafted onto polyamidoamine (PAMAM) dendrimer surface and then reacted with polyethylene glycol diacrylate (PEG-DA) to form dendrimer hydrogel (DH-G3-CPT) with low cross-linking density. In this novel drug delivery system, CPT was cleaved from dendrimer via the ammonolysis of ester bonds and then diffused out of the hydrogel network, thus leading to significantly prolonged drug release. The self-cleaving release kinetics of camptothecin can be further tuned by pH. This DH-G3-CPT drug delivery system has both injectability and sustained drug release. It showed an excellent tumor inhibition effect following intratumoral injection in a head and neck cancer model of mouse.

Poly(amidoamine) Dendrimer as a Respiratory Nanocarrier: Insights from Experiments and Molecular Dynamics Simulations

Pulmonary drug delivery is superior to the systemic administration in treating lung diseases. An optimal respiratory nanocarrier should be able to efficiently and safely cross the pulmonary surfactant film, which serves as the first biological barrier for respiratory delivery and plays paramount roles in maintaining the proper mechanics of breathing. In this work, we focused on the interactions between poly(amidoamine) (PAMAM) dendrimers and a model pulmonary surfactant. With combined Langmuir monolayer experiments and coarse-grained molecular dynamics simulations, we studied the effect of environmental temperature, size, and surface property of PAMAM dendrimers (G3-OH, G3-NH₂, G5-OH, and G5-NH₂) on the dipalmitoylphosphatidylcholine (DPPC) monolayer. Our simulations indicated that the environmental temperature could significantly affect the influence of PAMAM dendrimers on the DPPC monolayer. Therefore, results obtained at room temperature cannot be directly applied to elucidate interactions at body temperature. Simulations at body temperature found that all tested PAMAM dendrimers can easily penetrate the lipid monolayer during the monolayer expansion process (mimicking "inhalation"), and the cationic PAMAM dendrimers (-NH₂) show promising penetration ability during the monolayer compression process (mimicking "expiration"). Larger PAMAM dendrimers (G5) adsorbed onto the lipid monolayer tend to induce structural collapse and inhibit normal phase transitions of the lipid monolayer. These adverse effects could be mitigated in the subsequent expansion-compression cycle. These findings suggest that the PAMAM dendrimer may be used as a potential respiratory drug nanocarrier.

Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications

Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.

Penetration of nanoparticles across a lipid bilayer: effects of particle stiffness and surface hydrophobicity

The cellular uptake of nanoparticles (NPs) has drawn significant attention due to their great importance and potential in drug delivery, bioimaging, and specific targeting. Here, we conduct a computational study on the translocation process of soft nanoparticles with different elasticities and surface hydrophobicities through a lipid bilayer membrane. It is shown that the translocation abilities of hydrophilic NPs can be enhanced by increasing their stiffness, while the penetrability of hydrophobic NPs is weakened by increasing the particle stiffness. The free energy analysis indicates that rigid hydrophilic NPs and soft hydrophobic NPs encounter lower energy barriers during penetration. In direct translocation, different deformation modes are observed for NPs with different surface hydrophobicities during cellular internalization. Further, deformation analysis demonstrates that hydrophilic NPs are flattened in the membrane plane, while hydrophobic NPs are elongated along the membrane norm during penetration. We conclude that the elasticity of NPs has an obvious impact on their ability to penetrate across the lipid bilayer membrane through different morphological responses of hydrophilic and hydrophobic NPs. These results shed light on the coupled effects of particle elasticity and surface hydrophobicity on the cellular uptake of elastic NPs, which may provide useful guidelines for designing effective nanocarrier systems for drug delivery.

Globule-stretch transition of a self-attracting chain in the repulsive active particle bath

Folding and unfolding of a chain structure are often manipulated in experiments by tuning the pH, temperature, single-molecule forces or shear fields. Here, we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting chain in a suspension of self-propelling particles (SPPs). As the propelling force increases, the globule-stretch (G-S) transition of the chain occurs due to the enhanced disturbance from the SPPs. Two distinct mechanisms of the transition in the limits of low and high rotational diffusion rates of SPPs have been observed: shear-induced stretching at a low rate and collision-induced melting at a high rate. The G-S and S-G (stretch-globule) curves form a hysteresis loop at the low rate, while they merge at the high rate. Besides, we find that two competing effects result in a non-monotonic dependence of the G-S transition on SPP density at the low rate. Our results suggest an alternative approach to manipulating the folding and unfolding of (bio)polymers by utilizing active agents.

Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations

Polyamidoamine (PAMAM) dendrimers, a class of polymeric nanoparticles (NPs) with highly-controllable sizes and surface chemistry, are promising candidates for many biomedical applications, including drug and gene delivery, imaging, and inhibition of amyloid aggregation. In circulation, binding of serum proteins with dendritic NPs renders the formation of protein corona and alters the biological identity of the NP core, which may subsequently elicit immunoresponse and cytotoxicity. Understanding the effects of PAMAM size and surface chemistry on serum protein binding is, therefore, crucial to enable their broad biomedical applications. Here, by applying atomistic discrete molecular dynamics (DMD) simulations, we first uncovered the binding of PAMAM with HSA and Ig and detailed the dependences of such binding on PAMAM size and surface modification. Compared to either anionic or cationic surfaces, modifications with neutral phosphorylcholine (PC), polyethylene glycol (PEG), and hydroxyls (OH) significantly reduced binding with proteins. The relatively strong binding between proteins and PAMAM dendrimers with charged surface groups was mainly driven by electrostatic interactions as well as hydrophobic interactions. Using steered DMD (SDMD) simulations, we conducted a force-pulling experiment in silico estimating the critical forces separating PAMAM-protein complexes and deriving the corresponding free energy barriers for dissociation. The SDMD-derived HSA-binding affinities were consistent with existing experimental measurements. Our results highlighted the association dynamics of protein-dendrimer interactions and binding affinities, whose implications range from fundamental nanobio interfacial phenomena to the development of "stealth NPs".

Charge and hydration structure of dendritic polyelectrolytes: molecular simulations of polyglycerol sulphate

Macromolecules based on dendritic or hyperbranched polyelectrolytes have been emerging as high potential candidates for biomedical applications. Here we study the charge and solvation structure of dendritic polyglycerol sulphate (dPGS) of generations 0 to 3 in aqueous sodium chloride solution by explicit-solvent molecular dynamics computer simulations. We characterize dPGS by calculating several important properties such as relevant dPGS radii, molecular distributions, the solvent accessible surface area, and the partial molecular volume. In particular, as the dPGS exhibits high charge renormalization effects, we address the challenges of how to obtain a well-defined effective charge and surface potential of dPGS for practical applications. We compare implicit- and explicit-solvent approaches in our all-atom simulations with the coarse-grained simulations from our previous work. We find consistent values for the effective electrostatic size (i.e., the location of the effective charge of a Debye-Hückel sphere) within all the approaches, deviating at most by the size of a water molecule. Finally, the excess chemical potential of water insertion into dPGS and its thermodynamic signature are presented and rationalized.

Influence of PPH dendrimers' surface functions on the activation of human monocytes: a study of their interactions with pure lipid model systems

The influence of surface functions on the interactions between Poly(PhosphorHydrazone) PPH dendrimers and human monocytes is discussed on the basis of complementary biological and physicochemical studies on membrane models (monolayers and multi-lamellar vesicles). The studies were performed on both an active and non-toxic phosphonic acid capped dendrimer and a non-active but toxic carboxylic acid capped one. On the one hand, comparative studies of the behaviour of DPPC monolayers in the presence or absence of PPH dendrimers in the subphase showed differences in the phase transitions, highlighting interactions between both dendrimers and phospholipid monolayers, with a larger incidence for the carboxylic acid capped dendrimer (negative control), validating its cellular toxicity. On the other hand, comparative biological studies (activation of human monocytes and binding of fluorescent dendrimers on human monocytes) show the pre-eminence of phosphonic acid capped dendrimers towards specific binding and subsequent activation of human monocytes.

Exploring the trans-membrane dynamic mechanisms of single polyamidoamine nano-drugs via a “force tracing” technique

Considerable success has been achieved in the drug delivery of nano-drugs for chemotherapy, but the main obstacles in understanding the drug delivery dynamic mechanisms for nano-drug applications stem from technical limitations.

Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson-Boltzmann theory and Monte Carlo simulations

Ion-mediated interactions between like-charged polyelectrolytes have been paid much attention, and the Poisson-Boltzmann (PB) theory has been shown to fail in qualitatively predicting multivalent ion-mediated like-charge attraction. However, inadequate attention has been paid to the ion-mediated interactions between oppositely charged polyelectrolytes. In this work, the potentials of mean force (PMF) between oppositely charged nanoparticles in 1:1 and 2:2 salt solutions were investigated by Monte Carlo simulations and the PB theory. Our calculations show that the PMFs between oppositely charged nanoparticles are generally attractive in 1:1 and 2:2 salt solutions and that such attractive PMFs become weaker at higher 1:1 or 2:2 salt concentrations. The comprehensive comparisons show that the PB theory can quantitatively predict the PMFs between oppositely charged nanoparticles in 1:1 salt solutions, except for the slight deviation at very high 1:1 salt concentration. However, for 2:2 salt solutions, the PB theory generally overestimates the attractive PMF between oppositely charged nanoparticles, and this overestimation becomes more pronounced for nanoparticles with higher charge density and for higher 2:2 salt concentration. Our microscopic analyses suggest that the overestimation of the PB theory on the attractive PMFs for 2:2 salt solutions is attributed to the underestimation of divalent ions bound to nanoparticles.

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).