Design maps for cellular uptake of gene nanovectors by computer simulation

Dynamic Processes and Mechanical Properties of Lipid-Nanoparticle Mixtures

In this study, we investigate the dynamic processes and mechanical properties of lipid nanoparticle mixtures in a melt via dissipation particle dynamic simulation. By investigating the distribution of nanoparticles in lamellar and hexagonal lipid matrices in equilibrium state and dynamic processes, we observe that the morphology of such composites depends not only on the geometric features of the lipid matrix but also on the concentration of nanoparticles. The dynamic processes are also demonstrated by calculating the average radius of gyration, which indicates the isotropic conformation of lipid molecules in the x-y plane and that the lipid chains are stretched in the z direction with the addition of nanoparticles. Meanwhile, we predict the mechanical properties of lipid-nanoparticle mixtures in lamellar structures by analyzing the interfacial tensions. Results show that the interfacial tension decreased with the increase in nanoparticle concentration. These results provide molecular-level information for the rational and a priori design of new lipid nanocomposites with ad hoc tailored properties.

Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties

The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated by using the phase diagrams based on the tail chain lengths for the two types of lipids. Several parameters, such as chain number and average radius of gyration, were employed to explore the structural formations of the membrane and perforated membrane in the dynamic processes. Interface tension was used to demonstrate the mechanical properties of the membrane and perforated membrane in the equilibrium state and dynamics processes. Results help us to understand the self-assembly mechanism of the biomolecule mixtures, which has a potential application for designing the lipid molecule-based bio-membranes in solutions.

Silk Nanocarrier Size Optimization for Enhanced Tumor Cell Penetration and Cytotoxicity In Vitro

Silk nanofibers are versatile carriers for hydrophobic and hydrophilic drugs, but fall short in terms of effective delivery to cells, which is essential for therapeutic benefits. Here, the size of silk nanofibers was tuned by ultrasonic treatment to improve the cell penetration features without impacting the structural features. The gradual decrease in silk nanofiber length from 1700 to 40 nm resulted in improved cell uptake. The internalized silk nanofiber carriers evaded lysosomes, which facilitated retention in cancer cells in vitro. The smaller sizes also facilitated enhanced penetration of tumor spheroids for improved delivery in vitro. The cytotoxicity of paclitaxel (PTX)-laden nanocarriers increased when the length of the silk nanocarriers decreased. Both the drug loading capacity and delivery of silk nanocarriers with optimized sizes suggest potential utility in cell treatments.

Asymmetric Lipid Membranes under Shear Flows: A Dissipative Particle Dynamics Study

We investigate the phase behavior of the asymmetric lipid membranes under shear flows, using the dissipative particle dynamics simulation. Two cases, the weak and strong shear flows, are considered for the asymmetric lipid microstructures. Three typical asymmetric structures, the membranes, tubes, and vesicle, are included in the phase diagrams, where the effect of two different types of lipid chain length on the formation of asymmetric membranes is evaluated. The dynamic processes are demonstrated for the asymmetric membranes by calculating the average radius of gyration and shape factor. The result indicates that different shear flows will affect the shape of the second type of lipid molecules; the shape of the first type of lipid molecules is more stable than that of the second type of lipid molecules. The mechanical properties are investigated for the asymmetric membranes by analyzing the interface tension. The results reveal an absolute pressure at the junctions of different types of particles under the weak shear flow; the other positions are almost in a state of no pressure; there is almost no pressure inside the asymmetric lipid membrane structure under the strong shear flow. The findings will help us to understand the potential applications of asymmetric lipid microstructures in the biological and medical fields.

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.

Predicting asymmetric phospholipid microstructures in solutions

Asymmetric phospholipid microstructures, such as asymmetric phospholipid membranes, have potential applications in biological and medicinal processes. Here, we used the dissipative particle dynamics simulation method to predict the asymmetric phospholipid microstructures in aqueous solutions. The asymmetric phospholipid membranes, tubes and vesicles are determined and characterized by the chain density distributions and order parameters. The phase diagrams are constructed to evaluate the effects of the chain length on the asymmetric structure formations at equilibrium states, while the average radius of gyration and shape factors are calculated to analyze the asymmetric structure formations in the non-equilibrium processes. Meanwhile, we predicted the mechanical properties of the asymmetric membranes by analyzing the spatial distributions of the interface tensions and osmotic pressures in solutions.

Advances in Nanoparticles as Anticancer Drug Delivery Vector: Need of this Century

Background:

Nanotechnology has contributed a great deal to the field of medical science. Smart drugdelivery vectors, combined with stimuli-based characteristics, are becoming increasingly important. The use of external and internal stimulating factors can have enormous benefits and increase the targeting efficiency of nanotechnology platforms. The pH values of tumor vascular tissues are acidic in nature, allowing the improved targeting of anticancer drug payloads using drug-delivery vectors. Nanopolymers are smart drug-delivery vectors that have recently been developed and recommended for use by scientists because of their potential targeting capabilities, non-toxicity and biocompatibility, and make them ideal nanocarriers for personalized drug delivery.

Method:

The present review article provides an overview of current advances in the use of nanoparticles (NPs) as anticancer drug-delivery vectors.

Results:

This article reviews the molecular basis for the use of NPs in medicine, including personalized medicine, personalized therapy, emerging vistas in anticancer therapy, nanopolymer targeting, passive and active targeting transports, pH-responsive drug carriers, biological barriers, computer-aided drug design, future challenges and perspectives, biodegradability and safety.

Conclusions:

This article will benefit academia, researchers, clinicians, and government authorities by providing a basis for further research advancements.

Molecular mechanism of HIV-1 TAT peptide and its conjugated gold nanoparticles translocating across lipid membranes

The trans-acting activator of transcription (TAT) peptide, which is derived from human immunodeficiency virus-1 (HIV-1), has been widely used as an effective nanocarrier to transport extracellular substances into cells. However, the underlying translocation mechanism of TAT peptide across cell membranes still remains controversial. Besides, the molecular process of TAT peptide facilitating the transport of extracellular substances into cells is largely unknown. In this study, we explore the interactions of TAT peptides and their conjugated gold nanoparticles with lipid membranes by coarse-grained molecular dynamics simulations. It is found that the TAT peptides can hardly penetrate through the membrane at low peptide concentrations; after the concentration increases to a threshold value, they can cross the membrane through an induced nanopore due to the transmembrane electrostatic potential difference. The translocation of TAT peptides is mainly caused by the overall structural changes of membranes. Furthermore, we demonstrate that the translocation of gold nanoparticles (AuNPs) across the membrane is significantly affected by the number of grafted TAT peptides on the particle surface. The transmembrane efficiency of AuNPs may even be reduced when a small number of peptides modify them; whereas, when the number of grafted peptides increases to a certain value, the TAT-AuNP complex can translocate across the membrane in a pore-mediated way. Based on our findings, an effective strategy has been proposed to enhance the delivery efficiency of AuNPs. The present study can improve our understanding of the interactions between TAT peptides and cell membranes; it may also give some insightful suggestions on the design and development of nanocarriers with high efficiency for the delivery of nanoparticles and drugs.

Self-assembly of phospholipid molecules in solutions under shear flows: Microstructures and phase diagrams

Shear-induced microstructures and their phase diagrams were investigated for phospholipid molecules in aqueous solution by dissipative particle dynamic simulation. Self-assembled microstructures, including spherical and cylindrical micelles, spherical vesicles, lamellae, undulated lamellae, perforated lamellae, and continuous networks, were observed under various shear flows and phospholipid concentrations, where the spatial inhomogeneity and symmetry were analysed. A series of phase diagrams were constructed based on the chain lengths under various phospholipid concentrations. The phase distributions showed that the structures with spherical symmetry could be shear-induced to structures with cylindrical symmetry in the dilute solutions. In the semi-concentrated solutions, the lamellae were located in most spaces under zero shear flows, which could be shear-induced into undulated lamellae and then into cylindrical micelles. For the concentrated solutions, the strong shear flows oriented the directions of multilayer lamellae and phase transitions appeared between several cylindrical network structures. These observations on shear-induced microstructures and their distributions revealed a promising approach that could be used to design bio-microstructures based on phospholipid molecules under shear flows.

Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity

Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.

Molecular dynamics study on the mechanism of polynucleotide encapsulation by chitosan

The safe and effective delivery of therapeutic genes into target cell interiors is of great importance in gene therapy. Chitosan has been extensively studied as a gene delivery carrier due to its good biocompatibility and biodegradability. Understanding the atomic interaction mechanism between chitosan and DNA is important in the design and application of chitosan-based drug and gene delivery systems. In this work, the interactions between single-stranded polynucleotides and different types of chitosan were systematically investigated by using molecular dynamics (MD) simulation. Our results demonstrate that the functional groups of chitosan, the types of base and length of polynucleotides regulate the interaction behavior between chitosan and polynucleotides. The encapsulation capacity of polynucleotide by chitosan is mainly balanced by two factors: the strength of polynucleotide binding to chitosan and the tendency of self-aggregation of polynucleotide in the solution. For -NH3+ chitosan, due to the strong electrostatic interaction, especially the H-bond between -NH3+ groups in chitosan and phosphate groups in polynucleotide, the aggregation effect could be partially eliminated. The good dispersal capacity of polynucleotides may improve the encapsulation of polynucleotides by chitosan, and hence increase the delivery and transfection efficiency of chitosan-based gene carrier.

Engineering approaches in siRNA delivery

siRNAs are very potent drug molecules, able to silence genes involved in pathologies development. siRNAs have virtually an unlimited therapeutic potential, particularly for the treatment of inflammatory diseases. However, their use in clinical practice is limited because of their unfavorable properties to interact and not to degrade in physiological environments. In particular they are large macromolecules, negatively charged, which undergo rapid degradation by plasmatic enzymes, are subject to fast renal clearance/hepatic sequestration, and can hardly cross cellular membranes. These aspects seriously impair siRNAs as therapeutics. As in all the other fields of science, siRNAs management can be advantaged by physical-mathematical descriptions (modeling) in order to clarify the involved phenomena from the preparative step of dosage systems to the description of drug-body interactions, which allows improving the design of delivery systems/processes/therapies. This review analyzes a few mathematical modeling approaches currently adopted to describe the siRNAs delivery, the main procedures in siRNAs vectors' production processes and siRNAs vectors' release from hydrogels, and the modeling of pharmacokinetics of siRNAs vectors. Furthermore, the use of physical models to study the siRNAs vectors' fate in blood stream and in the tissues is presented. The general view depicts a framework maybe not yet usable in therapeutics, but with promising possibilities for forthcoming applications.

Molecular Understanding of the Penetration of Functionalized Gold Nanoparticles into Asymmetric Membranes

In this work, the interactions between surface-functionalized gold nanoparticles (AuNPs) and asymmetric membranes and the associated cytotoxicity were explored by coarse-grained molecular dynamics simulations. Simulation results show that the surface chemistry of AuNPs and the asymmetry of lipid membranes play significant roles. AuNPs with different signs of charges spontaneously adhere to the membrane surface or penetrate the membrane core. Also, the asymmetric distribution of charged lipids in membranes can facilitate the penetration of cationic AuNPs. Increasing the surface charge density (SCD) of AuNPs can not only improve the penetration efficiency but also lead to more disruption of the membrane structure. Moreover, the flip-flop of charged lipids in the inner leaflet can be observed during the translocation of AuNPs with a high SCD. The breakdown of membrane asymmetry may hinder the cellular internalization of AuNPs in a direct penetration mechanism. More importantly, we demonstrate that the hydrophobic contact between protruding solvent-exposed lipid tails and the hydrophobic moieties of ligands can mediate the insertion of AuNPs with a low SCD into cell membranes, which will exhibit less cytotoxicity in most in vivo applications. This may open a new exciting avenue to developing nanocarriers with a higher translocation efficiency and a lower toxicity simultaneously for biomedical applications.

Design strategy of surface decoration for efficient delivery of nanoparticles by computer simulation

Understanding the role of surface decoration of nanoparticles in protein adsorption and cellular uptake is of great importance in biomedicine. Here, by using dissipative particle dynamics simulations, we take two typical coating polymers (i.e., hydrophilic and zwitterionic polymers) as an example, and systematically investigate their effect on cellular delivery of hydrophobic and charged nanoparticles (in the presence of serum protein). Our results show that though two types of polymers are charge-neutral and can both reduce the protein adsorption, there exist some differences between their ability of protein resistance, especially in the case of positively charged nanoparticles. Besides, it is found that the coating polymers may also greatly decrease the cellular uptake efficiency of nanoparticles. Nevertheless, and importantly, since the zwitterionic polymers may become positively charged under low pH environments, the nanoparticle can attach onto cell membrane more firmly than that coated with hydrophilic polymers, which can further enhance the active targeting of nanoparticles. Finally, we also provide the design maps for surface decoration to achieve efficient cellular delivery. These results can help better understand how to keep the balance between protein resistance and cell targeting, which may give some useful guidelines on optimal design of future nanomaterials in drug delivery.

Interaction of peptides with cell membranes: insights from molecular modeling

The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.

Designing new strategy for controlling DNA orientation in biosensors

Orientation controllable DNA biosensors hold great application potentials in recognizing small molecules and detecting DNA hybridization. Though electric field is usually used to control the orientation of DNA molecules, it is also of great importance and significance to seek for other triggered methods to control the DNA orientation. Here, we design a new strategy for controlling DNA orientation in biosensors. The main idea is to copolymerize DNA molecules with responsive polymers that can show swelling/deswelling transitions due to the change of external stimuli, and then graft the copolymers onto an uncharged substrate. In order to highlight the responsive characteristic, we take thermo-responsive polymers as an example, and reveal multi-responsive behavior and the underlying molecular mechanism of the DNA orientation by combining dissipative particle dynamics simulation and molecular theory. Since swelling/deswelling transitions can be also realized by using other stimuli-responsive (like pH and light) polymers, the present strategy is universal, which can enrich the methods of controlling DNA orientation and may assist with the design of the next generation of biosensors.

Theoretical and computational investigations of nanoparticle-biomembrane interactions in cellular delivery

With the rapid development of nanotechnology, nanoparticles have been widely used in many applications such as phototherapy, cell imaging, and drug/gene delivery. A better understanding of how nanoparticles interact with bio-system (especially cells) is of great importance for their potential biomedical applications. In this review, the current status and perspective of theoretical and computational investigations is presented on the nanoparticle-biomembrane interactions in cellular delivery. In particular, the determining parameters (including the properties of nanoparticles, cell membranes and environments) that govern the cellular uptake of nanoparticles (direct penetration and endocytosis) are discussed. Further, some special attention is paid to their interactions beyond the translocation of nanoparticles across membranes (e.g., nanoparticles escaping from endosome and entering into nucleus). Finally, a summary is given, and the challenging problems of this field in the future are identified.

Molecular modeling of membrane responses to the adsorption of rotating nanoparticles: promoted cell uptake and mechanical membrane rupture

Recently, a unique dynamic magnetic field was developed to induce the rotational movement of superparamagnetic iron oxide nanoparticles. This technique has been applied to remotely control both cellular internalization and apoptosis. Therefore, a thorough understanding of how a lipid membrane responds to the introduction of rotating NPs is quite important to promote the applications of this technique in a variety of biomedical area. Here, we performed Dissipative Particle Dynamics (DPD) simulations to systematically investigate the interaction mechanism between lipid membranes and rotating NPs. Two kinds of membrane responses are observed. One is the promoted cell uptake and the other is the mechanical membrane rupture. The promoting effect of NP rotation on the cell uptake is ascribed to the enhanced membrane monolayer protrusion, which can wrap the NP from the top side. Meanwhile, the rotating NP exerts a shearing force on the membrane. Accordingly, the membrane undergoes a local distortion around the NP. If the shearing force exceeds a critical value, the local membrane distortion develops into a mechanical rupture. A number of factors, like NP size, NP shape, ligand density and rotation speed, are critical in both of the above membrane responses.

Phase diagrams and morphological evolution in wrapping of rod-shaped elastic nanoparticles by cell membrane: a two-dimensional study

A fundamental understanding of cell-nanomaterial interaction is essential for biomedical diagnostics, therapeutics, and nanotoxicity. Here, we perform a theoretical analysis to investigate the phase diagram and morphological evolution of an elastic rod-shaped nanoparticle wrapped by a lipid membrane in two dimensions. We show that there exist five possible wrapping phases based on the stability of full wrapping, partial wrapping, and no wrapping states. The wrapping phases depend on the shape and size of the particle, adhesion energy, membrane tension, and bending rigidity ratio between the particle and membrane. While symmetric morphologies are observed in the early and late stages of wrapping, in between a soft rod-shaped nanoparticle undergoes a dramatic symmetry breaking morphological change while stiff and rigid nanoparticles experience a sharp reorientation. These results are of interest to the study of a range of phenomena including viral budding, exocytosis, as well as endocytosis or phagocytosis of elastic particles into cells.

Molecular modeling of polynucleotide complexes

Delivery of polynucleotides into patient cells is a promising strategy for treatment of genetic disorders. Gene therapy aims to either synthesize desired proteins (DNA delivery) or suppress expression of endogenous genes (siRNA delivery). Carriers constitute an important part of gene therapeutics due to limitations arising from the pharmacokinetics of polynucleotides. Non-viral carriers such as polymers and lipids protect polynucleotides from intra and extracellular threats and facilitate formation of cell-permeable nanoparticles through shielding and/or bridging multiple polynucleotide molecules. Formation of nanoparticulate systems with optimal features, their cellular uptake and intracellular trafficking are crucial steps for an effective gene therapy. Despite the great amount of experimental work pursued, critical features of the nanoparticles as well as their processing mechanisms are still under debate due to the lack of instrumentation at atomic resolution. Molecular modeling based computational approaches can shed light onto the atomic level details of gene delivery systems, thus provide valuable input that cannot be readily obtained with experimental techniques. Here, we review the molecular modeling research pursued on critical gene therapy steps, highlight the knowledge gaps in the field and providing future perspectives. Existing modeling studies revealed several important aspects of gene delivery, such as nanoparticle formation dynamics with various carriers, effect of carrier properties on complexation, carrier conformations in endosomal stages, and release of polynucleotides from carriers. Rate-limiting steps related to cellular events (i.e. internalization, endosomal escape, and nuclear uptake) are now beginning to be addressed by computational approaches. Limitations arising from current computational power and accuracy of modeling have been hindering the development of more realistic models. With the help of rapidly-growing computational power, the critical aspects of gene therapy are expected to be better investigated and direct comparison between more realistic molecular modeling and experiments may open the path for design of next generation gene therapeutics.