Uptake and translocation mechanisms of cationic amino derivatives functionalized on pristine C60 by lipid membranes: a molecular dynamics simulation study

Computational Indicator Approach for Assessment of Nanotoxicity of Two-Dimensional Nanomaterials

The increasing growth in the development of various novel nanomaterials and their biomedical applications has drawn increasing attention to their biological safety and potential health impact. The most commonly used methods for nanomaterial toxicity assessment are based on laboratory experiments. In recent years, with the aid of computer modeling and data science, several in silico methods for the cytotoxicity prediction of nanomaterials have been developed. An affordable, cost-effective numerical modeling approach thus can reduce the need for in vitro and in vivo testing and predict the properties of designed or developed nanomaterials. We propose here a new in silico method for rapid cytotoxicity assessment of two-dimensional nanomaterials of arbitrary chemical composition by using free energy analysis and molecular dynamics simulations, which can be expressed by a computational indicator of nanotoxicity (CIN_2D). We applied this approach to five well-known two-dimensional nanomaterials promising for biomedical applications: graphene, graphene oxide, layered double hydroxide, aloohene, and hexagonal boron nitride nanosheets. The results corroborate the available laboratory biosafety data for these nanomaterials, supporting the applicability of the developed method for predictive nanotoxicity assessment of two-dimensional nanomaterials.

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.

Carbon Nanomaterials for Targeted Cancer Therapy Drugs: A Critical Review

Cancer represents one of the main causes of human death in developed countries. Most current therapies, unfortunately, carry a number of side effects, such as toxicity and damage to healthy cells, as well as the risk of resistance and recurrence. Therefore, cancer research is trying to develop therapeutic procedures with minimal negative consequences. The use of nanomaterial-based systems appears to be one of them. In recent years, great progress has been made in the field using nanomaterials with high potential in biomedical applications. Carbon nanomaterials, thanks to their unique physicochemical properties, are gaining more and more popularity in cancer therapy. They are valued especially for their ability to deliver drugs or small therapeutic molecules to these cells. Through surface functionalization, they can specifically target tumor tissues, increasing the therapeutic potential and significantly reducing the adverse effects of therapy. Their potential future use could, therefore, be as vehicles for drug delivery. This review presents the latest findings of research studies using carbon nanomaterials in the treatment of various types of cancer. To carry out this study, different databases such as Web of Science, PubMed, MEDLINE and Google Scholar were employed. The findings of research studies chosen from more than 2000 viewed scientific publications from the last 15 years were compared.

Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations

Protonation states of amino acids crossing lipid bilayers from multidimensional free energy surfaces.

Counterintuitive cooperative endocytosis of like-charged nanoparticles in cellular internalization: computer simulation and experiment

The nanoparticles (NPs) functionalized with charged ligands are of particular significance due to their potential drug/gene delivery and biomedical applications. However, the molecular mechanism of endocytosis of the charged NPs by cells, especially the effect of the NP-NP and NP-biomembrane interactions on the internalization pathways is still poorly understood. In this work, we systematically investigate the internalization behaviors of the positively charged NPs by combining experiment technology and dissipative particle dynamics (DPD) simulation. We experimentally find an interesting but highly counterintuitive phenomenon, i.e. the multiple positively charged NPs prefer to enter cells cooperatively although the like-charged NPs have obvious electrostatic repulsion. Furthermore, we adopt the DPD simulation to confirm the experimental findings, and reveal that the mechanism of the cooperative endocytosis between like-charged NPs is definitely caused by the interplay of particle size, the charged ligand density on particle surface and local concentration of NPs. Importantly, we not only observe the normal cooperative endocytosis of like-charged NPs in cell biomembrane like neutral NP case, but also predict the 'bud' cooperative endocytosis of like-charged NPs which is absence in the neutral NP case. The results indicate that electrostatic repulsion between the positively charged nanoparticles plays an important role in the 'bud' cooperative endocytosis of like-charged NPs.

Mechanism of ROS scavenging and antioxidant signalling by redox metallic and fullerene nanomaterials: Potential implications in ROS associated degenerative disorders

BACKGROUND

The balance between oxidation and anti-oxidation is believed to be critical in maintaining healthy biological systems. However, our endogenous antioxidant defense systems are incomplete without exogenous antioxidants and, therefore, there is a continuous demand for exogenous antioxidants to prevent stress and ageing associated disorders. Nanotechnology has yielded enormous variety of nanomaterials (NMs) of which metallic and carbonic (mainly fullerenes) NMs, with redox property, have been found to be strong scavengers of ROS and antioxidants in preclinical in vitro and in vivo models.

SCOPE OF REVIEW

Redox activity of metal based NMs and membrane translocation time of fullerene NMs seem to be the major determinants in ROS scavenging potential exhibited by these NMs. A comprehensive knowledge about the effects of ROS scavenging NMs in cellular antioxidant signalling is largely lacking. This review compiles the mechanisms of ROS scavenging as well as antioxidant signalling of the aforementioned metallic and fullerene NMs.

MAJOR CONCLUSIONS

Direct interaction between NMs and proteins does greatly affect the corona/adsorption formation dynamics but such interaction does not provide the explanation behind diverse biological outcomes induced by NMs. Indirect interaction, however, that could occur via NMs uptake and dissolution, NMs ROS induction and ROS scavenging property, and NMs membrane translocation time seem to work as a central mode of interaction.

GENERAL SIGNIFICANCE

The usage of potential antioxidant NMs in biological systems would greatly impact the field of nanomedicine. ROS scavenging NMs hold great promise in the future treatment of ROS related degenerative disorders.

Lipid monolayer disruption caused by aggregated carbon nanoparticles

Carbon nanoparticles (CNP) have significant impact on the Pulmonary Surfactant (PS), the first biological barrier in the respiratory system.

Conformation-dependent translocation of a star polymer through a nanochannel

The translocation process of star polymers through a nanochannel is investigated by dissipative particle dynamics simulations. The translocation process is strongly influenced by the star arm arrangement as the polymer enters the channel, and a scaling relation between the translocation time [Formula: see text] and the total number of beads N tot is obtained. Qualitative agreements are found with predictions of the nucleation and growth model for linear block co-polymer translocation. In the intermediate stage where the center of the star polymer is at the channel entrance, the translocation time is found to have power law-dependence on the number of arms outside the channel and very weakly dependent on the number of arms in the channel. Increasing the total number of star arms also increases the star translocation time.

Comparative computational study of interaction of C60-fullerene and tris-malonyl-C60-fullerene isomers with lipid bilayer: relation to their antioxidant effect

Oxidative stress induced by excessive production of reactive oxygen species (ROS) has been implicated in the etiology of many human diseases. It has been reported that fullerenes and some of their derivatives–carboxyfullerenes–exhibits a strong free radical scavenging capacity. The permeation of C₆₀-fullerene and its amphiphilic derivatives–C₃-tris-malonic-C₆₀-fullerene (C₃) and D₃-tris-malonyl-C₆₀-fullerene (D₃)–through a lipid bilayer mimicking the eukaryotic cell membrane was studied using molecular dynamics (MD) simulations. The free energy profiles along the normal to the bilayer composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) for C₆₀, C₃ and D₃ were calculated. We found that C₆₀ molecules alone or in clusters spontaneously translocate to the hydrophobic core of the membrane and stay inside the bilayer during the whole period of simulation time. The incorporation of cluster of fullerenes inside the bilayer changes properties of the bilayer and leads to its deformation. In simulations of the tris-malonic fullerenes we discovered that both isomers, C₃ and D₃, adsorb at the surface of the bilayer but only C₃ tends to be buried in the area of the lipid headgroups forming hydrophobic contacts with the lipid tails. We hypothesize that such position has implications for ROS scavenging mechanism in the specific cell compartments.

Membrane monolayer protrusion mediates a new nanoparticle wrapping pathway

Understanding how nanoparticles (NPs) interact with the lipid membrane is of importance for their potential applications in biomedicine and cytotoxic effects. In this paper, with the aid of computer simulation techniques, we report that NPs can be wrapped by lipid membranes in a pathway different from the conventional endocytic pathway. Our simulation results show that under the conditions of strong NP-membrane adhesion and low membrane tension, NPs can be wrapped by membranes with a pathway regulated by membrane monolayer protrusion. We also find that in the monolayer protrusion mediated wrapping pathway NPs are first trapped in the membrane and the subsequent NP internalization can be achieved by several means, including decreasing the membrane tension, breaking the membrane symmetry between upper and lower leaflets, and exerting an external force on the NPs. The findings from our simulations are well supported by the free energy analysis.

Interaction of fullerene chains and a lipid membrane via computer simulations

Coarse-grained molecular dynamics simulations were employed to study the fullerene polymers with various functionalization degrees interacting with the DPPC membrane. Structure, dynamics, and thermodynamics of systems were analyzed.

Fullerene-biomolecule conjugates and their biomedicinal applications

Fullerenes are among the strongest antioxidants and are characterized as “radical sponges.” The research on biomedicinal applications of fullerenes has achieved significant progress since the landmark publication by Friedman et al in 1993. Fullerene–biomolecule conjugates have become an important area of research during the past 2 decades. By a thorough literature search, we attempt to update the information about the synthesis of different types of fullerene–biomolecule conjugates, including fullerene-containing amino acids and peptides, oligonucleotides, sugars, and esters. Moreover, we also discuss in this review recently reported data on the biological and pharmaceutical utilities of these compounds and some other fullerene derivatives of biomedical importance. While within the fullerene–biomolecule conjugates, in which fullerene may act as both an antioxidant and a carrier, specific targeting biomolecules conjugated to fullerene will undoubtedly strengthen the delivery of functional fullerenes to sites of clinical interest.

Membrane perturbation by carbon nanotube insertion: pathways to internalization

Carbon nanotubes (CNTs) can penetrate the membranes of cells, offering prospects for nanomedicine but problems for nanotoxicity. Molecular simulations are used to provide a systematic analysis of the interactions of single-walled and multi-walled CNTs of different radii with a model lipid bilayer membrane. The simulations allow characterization of the mechanism of spontaneous exothermic insertion of CNTs into lipid bilayer membranes. The size and type of CNT determine the nature and extent of the local perturbation of the bilayer. Single-walled CNTs are shown to insert via a two-step mechanism with initial transient formation of a water filled pore followed by full insertion of the CNT into the bilayer. The latter stage is associated with formation of a persistent inverted micelle arrangement of lipid molecules trapped inside the CNT. This suggests a possible vehicle for nano-encapsulation of drugs, enabling their entry into and subsequent release within cells following endocytosis of CNT-containing membranes.

How do functionalized carbon nanotubes land on, bind to and pierce through model and plasma membranes

Study of the mechanisms understanding how chemically functionalized carbon nanotubes internalize into mammalian cells is important in view of their design as new tools for therapeutic and diagnostic applications. The initial contact between the nanotube and the cell membrane allows elucidation of the types of interaction that are occurring and the contribution from the types of functional groups at the nanotube surface. Here we offer a combination of experimental and theoretical evidence of the initial phases of interaction between functionalized carbon nanotubes with model and cellular membranes. Both experimental and theoretical data reveal the critical parameters to determine direct translocation of the nanotubes through the membrane into the cytoplasm as a result of three distinct processes that can be summarized as landing, piercing and uptake.

Lipid nanotechnology

Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices and machines derived from engineering, physics, materials science, chemistry and biology. These devices have found applications in biomedical sciences, such as targeted drug delivery, bio-imaging, sensing and diagnosis of pathologies at early stages. In these applications, nano-devices typically interface with the plasma membrane of cells. On the other hand, naturally occurring nanostructures in biology have been a source of inspiration for new nanotechnological designs and hybrid nanostructures made of biological and non-biological, organic and inorganic building blocks. Lipids, with their amphiphilicity, diversity of head and tail chemistry, and antifouling properties that block nonspecific binding to lipid-coated surfaces, provide a powerful toolbox for nanotechnology. This review discusses the progress in the emerging field of lipid nanotechnology.

Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion

Carbon nanotubes have been proposed to be efficient nanovectors able to deliver genetic or therapeutic cargo into living cells. However, a direct evidence of the molecular mechanism of their translocation across cell membranes is still needed. Here, we report on an extensive computational study of short (5 nm length) pristine and functionalized single-walled carbon nanotubes uptake by phospholipid bilayer models using all-atom molecular dynamics simulations. Our data support the hypothesis of a direct translocation of the nanotubes through the phospholipid membrane. We find that insertion of neat nanotubes within the bilayer is a “nanoneedle” like process, which can often be divided in three consecutive steps: landing and floating, penetration of the lipid headgroup area and finally sliding into the membrane core. The presence of functional groups at moderate concentrations does not modify the overall scheme of diffusion mechanism, provided that their deprotonated state favors translocation through the lipid bilayer.