Impact of Single-Walled Carbon Nanotube Functionalization on Ion and Water Molecule Transport at the Nanoscale.

Nanofluidics has a very promising future owing to its numerous applications in many domains. It remains, however, very difficult to understand the basic physico-chemical principles that control the behavior of solvents confined in nanometric channels. Here, water and ion transport in carbon nanotubes is investigated using classical force field molecular dynamics simulations. By combining one single walled carbon nanotube (uniformly charged or not) with two perforated graphene sheets, we mimic single nanopore devices similar to experimental ones. The graphitic edges delimit two reservoirs of water and ions in the simulation cell from which a voltage is imposed through the application of an external electric field. By analyzing the evolution of the electrolyte conductivity, the role of the carbon nanotube geometric parameters (radius and chirality) and of the functionalization of the carbon nanotube entrances with OH or COO- groups is investigated for different concentrations of group functions.

Modeling the Cellular Uptake of Functionalized Carbon Nanohorns Loaded with Cisplatin through a Breast Cancer Cell Membrane.

The cisplatin encapsulation into carbon nanohorns (CNH) is a promising nanoformulation to circumvent the drug dissipation and to specifically accumulate it in tumor sites. Herein, biased molecular dynamics simulations were used to analyze the transmembrane transport of the CNH loaded with cisplatin through a breast cancer cell membrane prototype. The simulations revealed a four-stage mechanism: approach, insertion, permeation, and internalization. Despite the lowest structural disturbance of the membrane provided by the nanocarrier, the average free energy barrier for the translocation was 55.2 kcal mol-1, suggesting that the passive process is kinetically unfavorable. In contrast, the free energy profiles revealed potential wells of -6.8 kcal mol-1 along the insertion stage in the polar heads region of the membrane, which might enhance the retention of the drug in tumor sites; therefore, the most likely cisplatin delivery mechanism should involve the adsorption and retention of CNH on the surface of cancer cells, allowing the loaded cisplatin be slowly released and passively transported through the cell membrane.

Translocation Processes of Pt(II)-Based Drugs through Human Breast Cancer Cell Membrane: In Silico Experiments.

Breast cancer is one of the most frequent modalities of cancer worldwide, with notable mortality. The medication based on platinum drugs (cisplatin (cddp), carboplatin (cpx), and oxaliplatin (oxa)) is a conventional chemotherapy despite severe side effects and the development of drug resistance. In order to provide a deeper molecular description of the influx and efflux processes of platinum drugs through breast cancer tissues, this study focuses on molecular dynamics (MD) simulations of the passive translocation process through a realistic plasma membrane prototype of human breast cancer cell (c_memb). The results showed that the permeation events were mainly mediated by neutral lipids (DOPC, DOPE, and cholesterol), producing a low and temporary membrane deformation. The drug insertion in the region of polar heads was the most favorable stage of the translocation mechanism, especially for cddp and oxa with potential wells of -8.6 and -9.8 kcal mol-1, respectively. However, the potentials of mean force (PMF) revealed unfavorable kinetics for the permeation of these drugs through lipid tails, with energy barriers of 28.3 (cddp), 32.2 (cpx), and 30.4 kcal mol-1 (oxa). The low permeability coefficients (P) of cpx and oxa, which were 3 and 1 orders of magnitude inferior than for cddp, resulted from the high energy barriers for their traslocation processes through the membrane. The obtained results provide a more accurate picture of the permeation of Pt(II)-based drugs through breast cancer cells, which may be relevant for the design and evaluation of new platinum complexes.

Ultrasensitive Detection of Aß42 Seeds in Cerebrospinal Fluid with a Nanopipette-Based Real-Time Fast Amyloid Seeding and Translocation Assay.

In this work, early-stage Aß42 aggregates were detected using a real-time fast amyloid seeding and translocation (RT-FAST) assay. Specifically, Aß42 monomers were incubated in buffer solution with and without preformed Aß42 seeds in a quartz nanopipette coated with L-DOPA. Then, formed Aß42 aggregates were analyzed on flyby resistive pulse sensing at various incubation time points. Aß42 aggregates were detected only in the sample with Aß42 seeds after 180 min of incubation, giving an on/off readout of the presence of preformed seeds. Moreover, this RT-FAST assay could detect preformed seeds spiked in 4% cerebrospinal fluid/buffer solution. However, in this condition, the time to detect the first aggregates was increased. Analysis of Cy3-labeled Aß42 monomer adsorption on a quartz substrate after L-DOPA coating by confocal fluorescence spectroscopy and molecular dynamics simulation showed the huge influence of Aß42 adsorption on the aggregation process.

Nanovectorization of Ivermectin to avoid overdose of drugs.

Ivermectin is an antiparasitic drug that results in the death of the targeted parasites using several mechanical actions. While very well supported, it can induce in rare cases, adverse effects including coma and respiratory failure in case of overdose. This problem should be solved especially in an emergency situation. For instance, the first pandemic of the 21th century was officially declared in early 2020, and while several vaccines around the worlds have been used, an effective treatment against this new strain of coronavirus, better known as SARS-CoV-2, should also be considered, especially given the massive appearance of variants. From all the tested therapies, Ivermectin showed a potential reduction of the viral portability, but sparked significant debate around the dose needed to achieve these positive results. To answer this general question, we propose, using simulations, to show that the nanovectorization of Ivermectin on BN oxide nanosheets can increase the transfer of the drug to its target and thus decrease the quantity of drug necessary to cope with the disease. This first application could help science to develop such nanocargo to avoid adverse effects.Communicated by Ramaswamy H. Sarma.

Investigation of α-Synuclein and Amyloid-ß(42)-E22Δ Oligomers Using SiN Nanopore Functionalized with L-Dopa.

Solid-state nanopores are an emerging technology used as a high-throughput, label-free analytical method for the characterization of protein aggregation in an aqueous solution. In this work, we used Levodopamine to coat a silicon nitride nanopore surface that was fabricated through a dielectric breakdown in order to reduce the unspecific adsorption. The coating of inner nanopore wall by investigation of the translocation of heparin. The functionalized nanopore was used to investigate the aggregation of amyloid-ß and α-synuclein, two biomarkers of degenerative diseases. In the first application, we demonstrate that the α-synuclein WT is more prone to form dimers than the variant A53T. In the second one, we show for the Aß(42)-E22Δ (Osaka mutant) that the addition of Aß(42)-WT monomers increases the polymorphism of oligomers, while the incubation with Aß(42)-WT fibrils generates larger aggregates.

Conical nanopores highlight the pro-aggregating effects of pyrimethanil fungicide on Aß(1-42) peptides and dimeric splitting phenomena.

The Aß(1-42) aggregation is a key event in the physiopathology of Alzheimer's disease (AD). Exogenous factors such as environmental pollutants, and more particularly pesticides, can corrupt Aß(1-42) assembly and could influence the occurrence and pathophysiology of AD. However, pesticide involvement in the early stages of Aß(1-42) aggregation is still unknown. Here, we employed conical track-etched nanopore in order to analyse the Aß(1-42) fibril formation in the presence of pyrimethanil, a widely used fungicide belonging to the anilinopyrimidine class. Our results evidenced a pro-aggregating effect of pyrimethanil on Aß(1-42). Aß(1-42) assemblies were successfully detected using conical nanopore coated with PEG. Using an analytical model, the large current blockades observed (>0.7) were assigned to species with size close to the sensing pore. The long dwell times (hundreds ms scale) were interpreted by the possible interactions amyloid/PEG using molecular dynamic simulation. Such interaction could leave until splitting phenomena of the dimer structure. Our work also evidences that the pyrimethanil induce an aggregation of Aß(1-42) mechanism in two steps including the reorganization prior the elongation phase.

Detection of Amyloid-ß Fibrils Using Track-Etched Nanopores: Effect of Geometry and Crowding.

Several neurodegenerative diseases have been linked to proteins or peptides that are prone to aggregate in different brain regions. Aggregation of amyloid-ß (Aß) peptides is recognized as the main cause of Alzheimer's disease (AD) progression, leading to the formation of toxic Aß oligomers and amyloid fibrils. The molecular mechanism of Aß aggregation is complex and still not fully understood. Nanopore technology provides a new way to obtain kinetic and morphological aspects of Aß aggregation at a single-molecule scale without labeling by detecting the electrochemical signal of the peptides when they pass through the hole. Here, we investigate the influence of nanoscale geometry (conical and bullet-like shape) of a track-etched nanopore pore and the effect of molecular crowding (polyethylene glycol-functionalized pores) on Aß fibril sensing and analysis. Various Aß fibril samples that differed by their length were produced by sonication of fibrils obtained in the presence of epigallocatechin gallate. The conical nanopore functionalized with polyethylene glycol (PEG) 5 kDa is suitable for discrimination of the fibril size from relative current blockade. The bullet-like-shaped nanopore enhances the amplitude of the current and increases the dwell time, allowing us to well discern the fibrils. Finally, the nanopore crowded with PEG 20 kDa enhances the relative current blockade and increases the dwell time; however, the discrimination is not improved compared to the "bullet-shaped" nanopore.

Impact of surface state on polyethylene glycol conformation confined inside a nanopore.

Solid-state nanopores are a promising platform for characterizing proteins. In order to improve their lifetime and prevent fouling, Polyethylene Glycol (PEG) grafting is one of the most efficient and low-cost solutions. Different models to calculate the PEG thickness do not consider their interaction with the nanopore inner surface nor the effect of confinement. Here, we investigate by molecular dynamic simulation the PEG conformation inside a nanopore in the case of hydrophobic and hydrophilic nanopores. Our results reveal that the nanopore inner surface plays a role in the PEG organization and, thus, in the speed of the salt constituent. The resulting pair interaction between PEG and its environment clearly shows a more important affinity for K+ compared to Li+ cations.

Breaking the Controversy of the Electropolymerization of Pyrrole Mechanisms by the Effective Screening Medium Quantum Charged Model Interface.

Several mechanisms for the electropolymerization of pyrrole have been proposed since the first report 40 years ago. However, none of them were consensual despite a range of assumptions. We simulated and explained the preliminary steps governing the electropolymerization of pyrrole in a charged model interface using first-principles molecular dynamics calculations to solve the problem. We have shown under these conditions that adjacent pyrrole molecules in water can react together, causing their electropolymerization at the interface with a biased platinum electrode in anodic oxidation. In this work, the effective screening medium method that prevents energy divergence of the system was applied to different configurations of pyrrole, water, and electrolyte molecules to best screen the phase space. Furthermore, we worked on a Pt(100) electrode surface in an aqueous electrolyte to be as close as possible to the experimental conditions, MD taking the average of their different orientations.

Conformation of Polyethylene Glycol inside Confined Space: Simulation and Experimental Approaches.

The modification of the inner nanopore wall by polymers is currently used to change the specific properties of the nanosystem. Among them, the polyethylene glycol (PEG) is the most used to prevent the fouling and ensure the wettability. However, its properties depend mainly on the chain structure that is very difficult to estimate inside this confined space. Combining experimental and simulation approaches, we provide an insight to the consequence of the PEG presence inside the nanopore on the nanopore properties. We show, in particular, that the cation type in the electrolyte, together with the type of electrolyte (water or urea), is at the origin of the ion transport modification in the nanopore.

From Behavior of Water on Hydrophobic Graphene Surfaces to Ultra-Confinement of Water in Carbon Nanotubes.

In recent years and with the achievement of nanotechnologies, the development of experiments based on carbon nanotubes has allowed to increase the ionic permeability and/or selectivity in nanodevices. However, this new technology opens the way to many questionable observations, to which theoretical work can answer using several approximations. One of them concerns the appearance of a negative charge on the carbon surface, when the latter is apparently neutral. Using first-principles density functional theory combined with molecular dynamics, we develop here several simulations on different systems in order to understand the reactivity of the carbon surface in low or ultra-high confinement. According to our calculations, there is high affinity of the carbon atom to the hydrogen ion in every situation, and to a lesser extent for the hydroxyl ion. The latter can only occur when the first hydrogen attack has been achieved. As a consequence, the functionalization of the carbon surface in the presence of an aqueous medium is activated by its protonation, then allowing the reactivity of the anion.

A potential solution to avoid overdose of mixed drugs in the event of Covid-19: Nanomedicine at the heart of the Covid-19 pandemic.

Since 2020, the world is facing the first global pandemic of 21st century. Among all the solutions proposed to treat this new strain of coronavirus, named SARS-CoV-2, the vaccine seems a promising way but the delays are too long to be implemented quickly. In the emergency, a dual therapy has shown its effectiveness but has also provoked a set of debates around the dangerousness of a particular molecule, hydroxychloroquine. In particular, the doses to be delivered, according to the studies, were well beyond the acceptable doses to support the treatment without side effects. We propose here to use all the advantages of nanovectorization to address this question of concentration. Using quantum and classical simulations we will show in particular that drug transport on boron nitrogen oxide nanosheets increases the effectiveness of the action of these drugs. This will definitely allow to decrease the drug quantity needing to face the disease.

Ligand nanovectorization using graphene to target cellular death receptors of cancer cell.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is nowadays envisaged as a natural cytokine useful in nanomedicine to eradicate the cancer cells and not the healthy surrounding ones. However, it suffers from cell resistance and strong dispersion in body to prove its efficiency. The understanding at the molecular level of the TRAIL interaction with death receptors (DRs) on cancer cells is thus of fundamental importance to improve its action. We demonstrate here via molecular simulations that TRAIL can bind to its both agonistic DRs (ie, DR4 and DR5) with a preference for DR4. In this study, the role of a graphene nanoflake as a potential cargo for TRAIL is examined. Furthermore, both TRAIL self-assembling and TRAIL affinity when adsorbed on graphene are considered to enhance efficacy toward the targeted cancer cell. Our modelization results show that TRAIL can bind to DR4 and DR5 when transported by graphene nanoflake, as a proof of concept.

Polynucleotide differentiation using hybrid solid-state nanopore functionalizing with α-hemolysin.

We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.

From Anodic Oxidation of Aliphatic α-Amino Acids to Polypeptides by Quantum Electrochemistry Approach: Beyond Miller-Urey Experiments.

For years, polypeptide formation has fascinated the scientific world because its understanding could lead to one of the possible explanations for the origin of life. Anodic oxidation of aliphatic α-amino acids in aqueous electrolytes can result either in their decomposition or in their polymerization into polypeptide. This behavior depends experimentally on both amino acid concentration and pH. The elucidation of the involved mechanisms remains a challenge because of the multitude of products which can be obtained. In this context, the electrochemical behavior of glycine and alanine on a biased platinum surface was examined at the nanoscale by quantum electrochemistry via the effective screening medium method. Several electrochemical systems with different concentrations and pH values have been explored. Simulations of the anodic oxidation of the amino acids have not only confirmed their electropolymerization and decomposition at high and low concentrations, respectively, but also have revealed unsuspected mechanisms at the origin of polypeptide formation. This sheds new light on electrochemistry of α-amino acids, on occurrence of polypeptides, and more generally on organic electrochemistry.

Influence of nanotube section on carboplatin confinement.

The confinement of anticancer carboplatin molecules (CBPT) in boron nitride nanotubes (BNNTs) with various sections was studied by means of density functional theory and molecular dynamic simulations. We show that the molecular insertion in BNNT is favored depending on the tube radius. The range of the energy adsorption varied from -1 eV to -2 eV depending on BNNT dimension. We also determined the critical diameter for the possible vectorization of the anticancer molecule. Indeed, the hydrophobicity of small BNNT radius R < 5.5 Å) is so large that CBPT encapsulation is impossible to achieve. On the contrary, a larger radius could offer an ideal situation to enhance drug delivery and allow a progressive release of the therapeutic near its target. Comparison with carbon nanotubes allowed us to draw conclusions on the best adapted nanovector for CBPT.

Unexpected ionic transport behavior in hydrophobic and uncharged conical nanopores.

We investigated ionic transport behavior in the case of uncharged conical nanopores. To do so, we designed conical nanopores using atomic layer deposition of Al2O3/ZnO nanolaminates and then coated these with trimethylsilane. The experimental results are supported by molecular dynamics simulations. The ionic transport reveals an unexpected behavior: (i) a current rectification and (ii) a constant conductance at low salt concentration which are usually reported for charged conical nanopore. To explain these results, we have considered different assumptions: (i) a default of functionalization, (ii) the adsorption anion and (iii) the slippage. The first one was refuted by the study of the poly-l-lysine transport through the nanopore. To verify the second assumption, we investigate the effect of pH on the current rectification and the molecular dynamics simulations. Finally our study demonstrates that the unexpected ionic transport is provided to a predominant effect of slippage due to the water organization at the solid/liquid interface.

The encapsulation of the gemcitabine anticancer drug into grapheme nest: a theoretical study.

The efficient transport of a drug molecule until its target cell constitutes a significant challenge for delivery processes. To achieve such objectives, solid nanocapsules that protect the immune system during the transport should be developed and controlled at the nanoscale level. From this point of view, nanostructures based on graphene sheets could present some promising properties due to their ultimate size and dimension. In this work, we present theoretical results using DFT calculations, dealing with a graphene-based delivery system. Indeed, we demonstrate the stability of the gemcitabine anticancer molecule when it is encapsulated into two concave graphene sheets organized as a nest. Quantum calculations showed that the most stable state is located inside the nest, which is then formed by two layers distanced 6 Å from each other. For all the optimized systems, we focused on the dependence of the interaction energy on the molecule displacements during its entrance in the graphene nest and its exit from it. We also analyzed their consequence on the local morphological and electronic charge properties. Graphical Abstract Adsorption energy (in eV) of gemcitabine drug during its encapsulation inside the nest of grapheneand its release from it.

Simulations of a Graphene Nanoflake as a Nanovector To Improve ZnPc Phototherapy Toxicity: From Vacuum to Cell Membrane.

We propose a new approach to improving photodynamic therapy (PDT) by transporting zinc phthalocyanine (ZnPc) in biological systems via a graphene nanoflake, to increase its targeting. Indeed, by means of time-dependent density functional theory simulations, we show that the ZnPc molecule in interaction with a graphene nanoflake preserves its optical properties not only in a vacuum but also in water. Moreover, molecular dynamic simulations demonstrate that the graphene nanoflake/ZnPc association, as a carrier, permits one to stabilize the ZnPc/graphene nanoflake system on the cellular membrane, which was not possible when using ZnPc alone. We finally conclude that the graphene nanoflake is a good candidate to transport and stabilize the ZnPc molecule near the cell membrane for a longer time than the isolated ZnPc molecule. In this way, the choice of the graphene nanoflake as a nanovector paves the way to ZnPc PDT improvement.