Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4

Graphene quantum dots blocking the channel egresses of cytochrome P450 enzyme (CYP3A4) reveals potential toxicity

Graphene quantum dots (GQDs) have garnered significant attention, particularly in the biomedical domain. However, extensive research reveals a dichotomy concerning the potential toxicity of GQDs, presenting contrasting outcomes. Therefore, a comprehensive understanding of GQD biosafety necessitates a detailed supplementation of their toxicity profile. In this study, employing a molecular dynamics (MD) simulation approach, we systematically investigate the potential toxicity of GQDs on the CYP3A4 enzyme. We construct two distinct simulation systems, wherein a CYP3A4 protein is enveloped by either GQDs or GOQDs (graphene oxide quantum dots). Our results elucidate that GQDs come into direct contact with the bottleneck residues of Channels 2a and 2b of CYP3A4. Furthermore, GQDs entirely cover the exits of Channels 2a and 2b, implying a significant hindrance posed by GQDs to these channels and consequently leading to toxicity towards CYP3A4. In-depth analysis reveals that the adsorption of GQDs to the exits of Channels 2a and 2b is driven by a synergistic interplay of hydrophobic and van der Waals (vdW) interactions. In contrast, GOQDs only partially obstruct Channel 1 of CYP3A4, indicating a weaker influence on CYP3A4 compared to GQDs. Our findings underscore the potential deleterious impact of GQDs on the CYP3A4 enzyme, providing crucial molecular insights into GQD toxicology.

Short-Term Intravenous Administration of Carbon Nano-Onions is Non-Toxic in Female Mice

Background

A nanoscale drug carrier could have a variety of therapeutic and diagnostic uses provided that the carrier is biocompatible in vivo. Carbon nano-onions (CNOs) have shown promising results as a nanocarrier for drug delivery. However, the systemic effect of CNOs in rodents is unknown. Therefore, we investigated the toxicity of CNOs following intravenous administration in female BALB/c mice.

Results

Single or repeated administration of oxi-CNOs (125, 250 or 500 µg) did not affect mouse behavior or organ weight and there was also no evidence of hepatotoxicity or nephrotoxicity. Histological examination of organ slices revealed a significant dose-dependent accumulation of CNO aggregates in the spleen, liver and lungs (p<0.05, ANOVA), with a trace amount of aggregates appearing in the kidneys. However, CNO aggregates in the liver did not affect CYP450 enzymes, as total hepatic CYP450 as well as CYP3A catalytic activity, as meased by erythromycin N-demethylation, and protein levels showed no significant changes between the treatment groups compared to vehicle control. CNOs also failed to act as competitive inhibitors of CYP3A in vitro in both mouse and human liver microsomes. Furthermore, CNOs did not cause oxidative stress, as indicated by the unchanged malondialdehyde levels and superoxide dismutase activity in liver microsomes and organ homogenates.

Conclusion

This study provides the first evidence that short-term intravenous administration of oxi-CNOs is non-toxic to female mice and thus could be a promising novel and safe drug carrier.

Adsorption of Peptides onto Carbon Nanotubes Grafted with Poly(ethylene Oxide) Chains: A Molecular Dynamics Simulation Study

Carbon nanotubes (CNTs) display exceptional properties that predispose them to wide use in technological or biomedical applications. To remove the toxicity of CNTs and to protect them against undesired protein adsorption, coverage of the CNT sidewall with poly(ethylene oxide) (PEO) is often considered. However, controversial results on the antifouling effectiveness of PEO layers have been reported so far. In this work, the interactions of pristine CNT and CNT covered with the PEO chains at different grafting densities with polyglycine, polyserine, and polyvaline are studied using molecular dynamics simulations in vacuum, water, and saline environments. The peptides are adsorbed on CNT in all investigated systems; however, the adsorption strength is reduced in aqueous environments. Save for one case, addition of NaCl at a physiological concentration to water does not appreciably influence the adsorption and structure of the peptides or the grafted PEO layer. It turns out that the flexibility of the peptide backbone allows the peptide to adopt more asymmetric conformations which may be inserted deeper into the grafted PEO layer. Water molecules disrupt the internal hydrogen bonds in the peptides, as well as the hydrogen bonds formed between the peptides and the PEO chains.

Sub-Lethal Concentrations of Graphene Oxide Trigger Acute-Phase Response and Impairment of Phase-I Xenobiotic Metabolism in Upcyte® Hepatocytes

The impact of graphene oxide on hepatic functional cells represents a crucial evaluation step for its potential application in nanomedicine. Primary human hepatocytes are the gold standard for studying drug toxicity and metabolism; however, current technical limitations may slow down the large-scale diffusion of this cellular tool for in vitro investigations. To assess the potential hepatotoxicity of graphene oxide, we propose an alternative cell model, the second-generation upcyte^® hepatocytes, which show metabolic and functional profiles akin to primary human hepatocytes. Cells were acutely exposed to sub-lethal concentrations of graphene oxide (≤80 μg/ml) for 24 h and stress-related cell responses (such as apoptosis, oxidative stress, and inflammatory response) were evaluated, along with a broad investigation of graphene oxide impact on specialized hepatic functions. Results show a mild activation of early apoptosis but not oxidative stress or inflammatory response in our cell model. Notably, while graphene oxide clearly impacted phase-I drug-metabolism enzymes (e.g., CYP3A4, CYP2C9) through the inhibition of gene expression and metabolic activity, conversely, no effect was observed for phase-II enzyme GST and phase-III efflux transporter ABCG2. The GO-induced impairment of CYP3A4 occurs concomitantly with the activation of an early acute-phase response, characterized by altered levels of gene expression and protein production of relevant acute-phase proteins (i.e., CRP, Albumin, TFR, TTR). These data suggest that graphene oxide induces an acute phase response, which is in line with recent in vivo findings. In conclusion, upcyte^® hepatocytes appear a reliable in vitro model for assessing nanomaterial-induced hepatotoxicity, specifically showing that sub-lethal doses of graphene oxide have a negative impact on the specialized hepatic functions of these cells. The impairment of the cytochrome P450 system, along with the activation of an acute-phase response, may suggest potential detrimental consequences for human health, as altered detoxification from xenobiotics and drugs.

Photoluminescent Semiconducting Graphene Nanoribbons via Longitudinally Unzipping Single-Walled Carbon Nanotubes

The lack of a sizeable band gap has so far prevented graphene from building effective electronic and optoelectronic devices despite its numerous exceptional properties. Intensive theoretical research reveals that a band gap larger than 1 eV can only be achieved in sub-3 nm wide graphene nanoribbons (GNRs), but real fabrication of such ultranarrow GNRs still remains a critical challenge. Herein, we demonstrate an approach for the synthesis of ultranarrow and photoluminescent semiconducting GNRs by longitudinally unzipping single-walled carbon nanotubes. Atomic force microscopy reveals the unzipping process, and the resulting 2.2 nm wide GNRs are found to emit strong and sharp photoluminescence at ∼685 nm, demonstrating a very desirable semiconducting nature. This band gap of 1.8 eV is further confirmed by follow-up photoconductivity measurements, where a considerable photocurrent is generated, as the excitation wavelength becomes shorter than 700 nm. More importantly, our fabricated GNR field-effect transistors (FETs), by employing the hexagonal boron nitride-encapsulated heterostructure to achieve edge-bonded contacts, demonstrate a high current on/off ratio beyond 105 and carrier mobility of 840 cm2/V s, approaching the theoretical scattering limit in semiconducting GNRs at room temperature. Especially, highly aligned GNR bundles with lengths up to a millimeter are also achieved by prepatterning a template, and the fabricated GNR bundle FETs show a high on/off ratio reaching 105, well-defined saturation currents, and strong light-emitting properties. Therefore, GNRs produced by this method open a door for promising applications in graphene-based electronics and optoelectronics.

Thin films of functionalized carbon nanotubes support long-term maintenance and cardio-neuronal differentiation of canine induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) are a promising cell source for regenerative medicine. However, their feeder-free maintenance in undifferentiated states remains challenging. In recent past extensive studies have been directed using pristine or functionalized carbon nanotube in tissue engineering. Here we proposed thin films of functionalized carbon nanotubes (OH-single-walled CNTs [SWCNTs] and OH-multiwalled CNTs [MWCNTs]), as alternatives for the feeder-free in vitro culture of canine iPSCs (ciPSCs), considered as the cellular model. The ciPSC colonies could maintain their dome-shaped compactness and other characteristics when propagated on CNT films. Concomitantly, high cell viability and upregulation of pluripotency-associated genes and cell adhesion molecules were observed, further supported by molecular docking. Moreover, CNTs did not have profound toxic effects compared to feeder cultures as evident by cytocompatibility studies. Further, cardiac and neuronal differentiation of ciPSCs was induced on these films to determine their influence on the differentiation process. The cells retained differentiation potential and the nanotopographical features of the substrates provided positive cues to enhance differentiation to both lineages as evident by immunocytochemical staining and marker gene expression. Overall, OH-SWCNT provided better cues, maintained pluripotency, and induced the differentiation of ciPSCs. These results indicate that OH-functionalized CNT films could be used as alternatives for the feeder-free maintenance of ciPSCs towards prospective utilization in regenerative medicine.

Improved Biomedical Properties of Polydopamine-Coated Carbon Nanotubes

Carbon nanotubes (CNTs) due to their outstanding mechanical, thermal, chemical, and optical properties were utilized as a base material and were coated with polydopamine (PDA) (PDA@CNT) via the simple self-polymerization of dopamine (DA). Then, PDA@CNT coatings of up to five layers were examined for potential biomedical applications. The success of multiple coating of CNTs with PDA was confirmed via increased weight loss values with the increased number of PDA coatings of CNTs at 500 °C by thermogravimetric analysis. The surface area of bare CNTs was measured as 263.9 m2/g and decreased to 197.0 m2/g after a 5th coating with PDA. Furthermore, the antioxidant activities of CNT and PDA@CNTs were determined via total flavonoid content (TFC), total phenol content (TPC), and Fe(III)-reducing antioxidant power (FRAP) tests, revealing the increased antioxidant ability of PDA@CNTs with the increasing numbers of PDA coatings. Moreover, a higher inhibition percentage of the activity of the alpha-glucosidase enzyme with 95.1 ± 2.9% inhibition at 6 mg/mL PDA-1st@CNTs concentration was found. The CNT and PDA@CNTs exhibited blood compatibility, less than a 2.5% hemolysis ratio, and more than 85% blood clotting indexes. The minimum inhibition concentration (MIC) of PDA-5th@CNTs against E. coli and S. aureus bacteria was determined as 10 mg/mL.

Unexpected spontaneous dynamic oxygen migration on carbon nanotubes

Combining density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations, we show that oxygen functional groups exhibit unexpected spontaneous dynamic behaviors on the interior surface of single-walled carbon nanotubes (SWCNTs). The hydroxyl and epoxy migrations are achieved by the C-O bond breaking/reforming reactions or the proton transfer reaction between the neighboring epoxy and hydroxyl groups. It is demonstrated that the spontaneous dynamic characteristic is attributed to the sharply reduced energy barrier less than or comparable to thermal fluctuations. We also observe a stable intermediate state with a dangling C-O bond, which permits the successive migration of the oxygen functional groups. However, on the exterior surface of SWCNTs, it is difficult for the oxygen groups to migrate spontaneously because there are relatively high energy barriers, and the dangling C-O bond prefers to transform into the more stable epoxy configuration. The spontaneous oxygen migration is further confirmed by the oxygen migration process using DFT calculations and AIMD simulations at room temperature. Our work provides a new understanding of the behavior of oxygen functional groups at interfaces and gives a potential route to design new carbon-based dynamic materials.

Nanoparticulate Drug Delivery Strategies to Address Intestinal Cytochrome P450 CYP3A4 Metabolism towards Personalized Medicine

Drug dosing in clinical practice, which determines optimal efficacy, toxicity or ineffectiveness, is critical to patients' outcomes. However, many orally administered therapeutic drugs are susceptible to biotransformation by a group of important oxidative enzymes, known as cytochrome P450s (CYPs). In particular, CYP3A4 is a low specificity isoenzyme of the CYPs family, which contributes to the metabolism of approximately 50% of all marketed drugs. Induction or inhibition of CYP3A4 activity results in the varied oral bioavailability and unwanted drug-drug, drug-food, and drug-herb interactions. This review explores the need for addressing intestinal CYP3A4 metabolism and investigates the opportunities to incorporate lipid-based oral drug delivery to enable precise dosing. A variety of lipid- and lipid-polymer hybrid-nanoparticles are highlighted to improve drug bioavailability. These drug carriers are designed to target different intestinal regions, including (1) local saturation or inhibition of CYP3A4 activity at duodenum and proximal jejunum; (2) CYP3A4 bypass via lymphatic absorption; (3) pH-responsive drug release or vitamin-B12 targeted cellular uptake in the distal intestine. Exploitation of lipidic nanosystems not only revives drugs removed from clinical practice due to serious drug-drug interactions, but also provide alternative approaches to reduce pharmacokinetic variability.

Enhancing the enzymatic inhibition performance of Cu-based metal-organic frameworks by shortening the organic ligands

Creating more exposed active sites on the metal-organic framework (MOF) surface is crucial for enhancing the recognition ability of MOF artificial receptors. Here, a copper-based MOF Cu(im)₂ (im = imidazole) was utilized to act as an artificial receptor, inhibiting the activity of α-chymotrypsin. The shortest diazole ligand reduced the distance between regenerative copper sites, creating as many active sites as possible on the MOF unit surface. The amount of copper(ii) centers on the Cu(im)₂ surface was calculated to be 4.96 × 10⁶μm^-2. Thus, Cu(im)₂ showed exceedingly higher inhibition performance than other copper-based MOFs. The ChT activity was almost inhibited (88.8%) after the incubation with only 20 μg mL^-1 Cu(im)₂ for 10 min. The binding between ChT and Cu(im)₂ was very fast with high affinity. Further results proved that Cu(im)₂ inhibited the activity of ChT through electrostatic interactions and coordination interactions via the mixed inhibition mode. This strategy to use short ligands to create more active sites on the MOF surface provides a new direction to enhance the inhibition efficiency.

Brave new world revisited: Focus on nanomedicine

Nanomedicine is at a crossroads: with relatively few success stories in terms of clinical translation despite more and more research on increasingly sophisticated nanomaterials, it is important to consider whether we are on the right track. Indeed, it is crucial that we address the fact that while considerable efforts are being made to overcome barriers to translation from the bench to the clinic, scientists are still struggling to decipher fundamental aspects of nanomaterial interactions with biological systems. We believe that a key to the successful adoption of nanomedicines in oncology and beyond lies in a deeper understanding of underlying biological processes and in decoding interactions between engineered nanomaterials and biological systems. Here we provide an overview of progress in nanomedicine during the past 5 years.

Effect of Graphene Family Materials on Multiple Myeloma and Non-Hodgkin's Lymphoma Cell Lines

The interest around the graphene family of materials is constantly growing due to their potential application in biomedical fields. The effect of graphene and its derivatives on cells varies amongst studies depending on the cell and tissue type. Since the toxicity against non-adherent cell lines has barely been studied, we investigated the effect of graphene and two different graphene oxides against four multiple myeloma cell lines, namely KMS-12-BM, H929, U226, and MM.1S, as well as two non-Hodgkin lymphoma cells lines, namely KARPAS299 and DOHH-2. We performed two types of viability assays, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide conversion) and ATP (adenosine triphosphate detection), flow cytometry analysis of apoptosis induction and cell cycle, cell morphology, and direct interaction analysis using two approaches-visualization of living cells by two different systems, and visualization of fixed and dyed cells. Our results revealed that graphene and graphene oxides exhibit low to moderate cytotoxicity against cells, despite visible interaction between the cells and graphene oxide. This creates possibilities for the application of the selected graphene materials for drug delivery systems or theragnostics in hematological malignancies; however, further detailed studies are necessary to explain the nature of interactions between the cells and the materials.

Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains

Tungsten oxide nanodot (WO_3-x ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO_3-x and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations. Our results show that WO_3-x interacts only weakly with the key residues at the putative proline-rich motif (PRM) ligand-binding site of both domains. More importantly, our free energy landscape calculations reveal that the binding strength between WO_3-x and WW/SH3 is weaker than that of the native PRM ligand with WW/SH3, implying that WO_3-x has a limited inhibitory effect over PRM on both the WW and SH3 domains. These findings suggest that the cytotoxic effects of WO_3-x on the key modular protein domains could be very mild, which provides new insights for the future potential biomedical applications of this nanomaterial.

Coexposure to environmental concentrations of cis-bifenthrin and graphene oxide: Adverse effects on the nervous system during metamorphic development of Xenopus laevis

Despite the great concerns associated with the combined biological effects of nanoparticles and insecticides, the current understanding of the corresponding ecological risks remains limited. Xenopus laevis (X. laevis) tadpoles were exposed to various concentrations of typical pyrethroid (cis-bifenthrin; cis-BF), either alone or in combination with graphene oxide (GO), for 21 days. The presence of GO resulted in increased bioconcentration of cis-BF and a higher 1S-enantiomer fraction. Exposure to cis-BF and GO caused further reduction in pre-metamorphic developmental rates and activated dopaminergic, noradrenergic, and serotonergic neurotransmitter systems. Reduced tadpole activity and levels of genomic DNA methylation at cytosine nucleotides (5hmC) were observed in the coexposure groups. These results indicate that GO enhance the bioconcentration of cis-BF and promote the conversion of its 1R-enantiomer to the 1S form, which lead to disruption of neurotransmitter systems as well as interference in metamorphic development.

Impact of Gold Nanoparticles on Testosterone Metabolism in Human Liver Microsomes

Gold nanoparticle (AuNP)-protein corona complexes can alter cytochrome P450 (CYP)-mediated testosterone (TST) metabolism by altering their physicochemical properties. We investigated the impact of NP size, surface chemistry, and protein corona in TST metabolism in pooled human liver microsomes (pHLM) employing 40 and 80 nm AuNP functionalized with branched polyethylenimine (BPEI), lipoic acid (LA), and polyethylene glycol (PEG) as well as human plasma protein corona (PC). Individual variation in AuNP-mediated TST metabolism was also characterized among single donor HLM that contained different levels of CYP activities. Inhibitory effects of 40 nm AuNP and to a lesser degree of 80 nm AuNP occurred for the production of a total of five hydroxylated metabolites of TST in pHLM but PC alleviated them. Meanwhile, naked AuNP increased androstenedione production. Interindividual variation in TST metabolism occurred within single donor HLM. In most cases, 40 and 80 nm naked and PC AuNP essentially suppressed TST metabolism at non-inhibitory concentration but PC PEG-AuNP increased androstenedione. These studies contribute to a better understanding of the role of AuNP as TST disruptor by altering TST metabolism and could be utilized to screen other NP as potential endocrine disruptor.

Nanostructures of diamond, graphene oxide and graphite inhibit CYP1A2, CYP2D6 and CYP3A4 enzymes and downregulate their genes in liver cells

INTRODUCTION AND OBJECTIVE

Currently, carbon nanostructures are vastly explored materials with potential for future employment in biomedicine. The possibility of employment of diamond nanoparticles (DN), graphene oxide (GO) or graphite nanoparticles (GN) for in vivo applications raises a question of their safety. Even though they do not induce a direct toxic effect, due to their unique properties, they can still interact with molecular pathways. The objective of this study was to assess if DN, GO and GN affect three isoforms of cytochrome P450 (CYP) enzymes, namely, CYP1A2, CYP2D6 and CYP3A4, expressed in the liver.

METHODS

Dose-dependent effect of the DN, GO and GN nanostructures on the catalytic activity of CYPs was examined using microsome-based model. Cytotoxicity of DN, GO and GN, as well as the influence of the nanostructures on mRNA expression of CYP genes and CYP-associated receptor genes were studied in vitro using HepG2 and HepaRG cell lines.

RESULTS

All three nanostructures interacted with the CYP enzymes and inhibited their catalytic activity in microsomal-based models. CYP gene expression at the mRNA level was also downregulated in HepG2 and HepaRG cell lines. Among the three nanostructures, GO showed the most significant influence on the enzymes, while DN was the most inert.

CONCLUSION

Our findings revealed that DN, GO and GN might interfere with xenobiotic and drug metabolism in the liver by interactions with CYP isoenzymes responsible for the process. Such results should be considered if DN, GO and GN are used in medical applications.

Designed Functional Dispersion for Insulin Protection from Pepsin Degradation and Skeletal Muscle Cell Proliferation: In Silico and In Vitro Study

Functionalized single-walled carbon nanotubes with polyethylene glycol (PEGylated SWCNTs) are a promising nanomaterial that recently has emerged as the most attractive "cargo" to deliver chemicals, peptides, DNA and RNAs into cells. Insulin therapy is a recommended therapy to treat diabetes mellitus despite its side effects. Recently, functional dispersion made up of bioactive peptides, bioactive compounds and functionalized carbon nanomaterials such as PEGylated SWCNTs have proved to possess promising applications in nanomedicine. In the present study, molecular modeling simulations are utilized to assist in designing insulin hormone-PEGylated SWCNT composites, also called functional dispersion; to achieve this experimentally, an ultrasonication tool was utilized. Enzymatic degradation assay revealed that the designed functional dispersion protects about 70% of free insulin from pepsin. In addition, sulforhodamine B (SRB) assay, the quantification of insulin and glucose levels in differentiated skeletal muscle cell supernatants, reveals that functional dispersion regulates glucose and insulin levels to promote skeletal muscle cell proliferation. These findings offer new perspectives for designed functional dispersion, as potential pharmaceutical preparations to improve insulin therapy and promote skeletal muscle cell health.

Nanoresolution patterning of hydrogenated graphene by electron beam induced C-H dissociation

Direct writing of semi-conductive or insulative nanopatterns on graphene surfaces is one of the major challenges in the application of graphene in flexible and transparent electronic devices. Here, we demonstrate that nanoresolution patterning on hydrogenated graphene can be approached by using electron beam induced C-H dissociation when the electron accelerating voltage is beyond a critical voltage of 3 kV. The resolution of the patterning reaches 18 nm and remains constant as the accelerating voltage is beyond 15 kV. The origin of the nanoresolution pattering as well as the dependence of the resolution on voltage in this technique is well explained by studying the cross-section of the C-H bond under electron impact. This work constitutes a new approach to fabricate graphene-based electronic nanodevices, with the reduced hydrogenated graphene channel utilized as conductive or semi-conductive counterpart in the structure.

Exfoliated Nanosheets of a CuII Coordination Polymer Modulate Enzyme Activity of α-Chymotrypsin

A 2D coordination polymer derived from 5-azidoisophthalic acid (AIA) and Cu(NO₃ )₂ was designed with the aim of modulating the activity of a digestive enzyme α-chymotrypsin (ChT). The coordination polymer namely {[Cu_0.5 (μ-AIA)_0.5 (H₂ O)]⋅2 H₂ O}_α (CP1) was successfully synthesized and fully characterized by single-crystal X-ray diffraction (SXRD). An exfoliated nanosheet (ENS) of CP1 was readily produced by overnight stirring of hand-ground CP1 crystals dispersed in DMSO. ENS(CP1) was demonstrated to be acting as an inhibitor of ChT; as much as ≈97 % inhibition of ChT was achieved with 100 μm of ENS(CP1) using N-succinyl-l-phenylalanine-p-nitroanilide (SPNA) as substrate. Enzyme kinetics data revealed that the inhibition of ChT followed a competitive pathway. An enzyme assay under varying ionic strength and varying concentration of free histidine revealed that the active site His-57 participated in coordination with the Cu^II metal center of ENS(CP1) thereby preventing the substrate (SPNA) from binding with the enzyme resulting in efficient inhibition.

Comparison of conventional and advanced in vitro models in the toxicity testing of nanoparticles

Humans are exposed to a wide variety of nanoparticles (NPs) present in the environment, in consumer, health and medical products, and in food. Conventional cytotoxicity testing compared to animal testing is less expensive, faster and avoids ethical problems at the expense of a lower predictive value. New cellular models and exposure conditions have been developed to overcome the limitations of conventional cell culture and obtain more predictive data. The use of three-dimensional culture, co-culture and inclusion of mechanical stimulation can provide physiologically more relevant culture conditions. These systems are particularly relevant for oral, respiratory and intravenous exposure to NPs and it may be assumed that physiologically relevant application of the NPs can improve the predictive value of in vitro testing. Various groups have used advanced culture and exposure systems, but few direct comparisons between data from conventional cultures and from advanced systems exist. In silico models may present another option to predict human health risk by NPs without using animal studies. In the absence of validation, the question whether these alternative models provide more predictive data than conventional testing remains elusive.

The potential impact of carboxylic-functionalized multi-walled carbon nanotubes on trypsin: A Comprehensive spectroscopic and molecular dynamics simulation study

In this study, we report a detailed experimental, binding free energy calculation and molecular dynamics (MD) simulation investigation of the interactions of carboxylic-functionalized multi-walled carbon nanotubes (COOH-f-MWCNTs) with porcine trypsin (pTry). The enzyme exhibits decreased thermostability at 330K in the presence of COOH-f-MWCNTs. Furthermore, the activity of pTry also decreases in the presence of COOH-f-MWCNTs. The restricted diffusion of the substrate to the active site of the enzyme was observed in the experiment. The MD simulation analysis suggested that this could be because of the blocking of the S1 pocket of pTry, which plays a vital role in the substrate selectivity. The intrinsic fluorescence of pTry is quenched with increase in the COOH-f-MWCNTs concentration. Circular dichroism (CD) and UV–visible absorption spectroscopies indicate the ability of COOH-f-MWCNTs to experience conformational change in the native structure of the enzyme. The binding free energy calculations also show that electrostatics, π-cation, and π-π stacking interactions play important roles in the binding of the carboxylated CNTs with pTry. The MD simulation results demonstrated that the carboxylated CNTs adsorb to the enzyme stronger than the CNT without the–COOH groups. Our observations can provide an example of the nanoscale toxicity of COOH-f-MWCNTs for proteins, which is a critical issue for in vivo application of COOH-f-MWCNTs.

Effect of single-walled carbon nanotubes on cytochrome P450 activity in human liver microsomes in vitro

Single-walled carbon nanotubes (SWCNTs) are made from a rolled single sheet of graphene with a diameter in the nanometer range. SWCNTs are potential carriers for drug delivery systems because antibodies or drugs can be loaded on their surface; however, their effect on the activities of cytochrome P450 (CYP) remains unclear. The aim of this study was to investigate the effect of two kinds of SWCNTs with different lengths (FH-P- and SO-SWCNTs) on human CYP activity. In addition, other nano-sized carbon materials, such as carbon black, fullerene-C₆₀ , and fullerene-C₇₀ were also evaluated to compare their effects on CYP activities. Ten CYP substrates (phenacetin, coumarin, bupropion, paclitaxel, tolbutamide, S-mephenytoin, dextromethorphan, chlorzoxazone, midazolam, and testosterone) were used. Testosterone 6β-hydroxylation and midazolam 1'-hydroxylation, which are catalysed by both CYP3A4 and CYP3A5 in liver microsomes, were decreased by 25% and 45%, respectively, in the presence of 0.1 mg/ml SO-SWCNT. Dextromethorphan O-demethylation, which is catalysed mainly by CYP2D6, was decreased by 40% in the presence of SO-SWCNT. Other CYP activities, however, were not attenuated by SO-SWCNT. FH-P-SWCNT, carbon black, fullerene-C₆₀ , and fullerene-C₇₀ at 0.1 mg/ml had no effect on CYP activities. The K_i values for testosterone 6β-hydroxylation, midazolam 1'-hydroxylation, and dextromethorphan O-demethylation in liver microsomes were 136, 34, and 56 μg/ml, respectively. SO-SWCNT was determined to be a competitive inhibitor of CYP3A4, CYP3A5, and CYP2D6. These results suggest that the effect of SO-SWCNT differs among CYP isoforms, and that the inhibition potency depends on the physicochemical properties of the nanocarbons.

Extension of coarse-grained UNRES force field to treat carbon nanotubes

Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3-4 order of magnitude larger timescale than using regular all-atom force fields. Graphical abstract Bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ.

Exploring the Nanotoxicology of MoS2: A Study on the Interaction of MoS2 Nanoflakes and K+ Channels

Molybdenum disulfide (MoS₂) nanomaterial has recently found various applications in the biomedical field mainly due to its outstanding physicochemical properties. However, little is known about its interactions with biological systems at the atomic level, which intimately relates to the biocompatibility of the material. To provide insights into the effects of MoS₂ in biological entities, we investigated the interactions of MoS₂ with proteins from a functionally important membrane family, the ubiquitous potassium (K⁺) channels. Here, we study four representative K⁺ channels-KcsA, Kir3.2, the Kv1.2 paddle chimera, and K2P2-to investigate their interactions with a triangular MoS₂ nanoflake using Molecular Dynamics (MD) simulations combined with electrophysiology experiments. These particular K⁺ channels were selected based on the diversity in their structure; that is, although these K⁺ channels display similar structural motifs, they also contain significant differences related to their particular function. Our results indicate that the MoS₂ nanoflake is able to stably bind to three out of the four channels, albeit through distinct binding modes. The binding mode between each channel and MoS₂ underlies the specific deleterious influence on the channel's basic physiological function: For KcsA, MoS₂ binds on the extracellular loops, which indirectly destroys the delicate structure of the selectivity filter causing a strong leak of K⁺ ions. In the binding mode with Kir3.2, the MoS₂ nanoflake completely covers the entrance to the channel pore affecting the normal ion conduction. For the Kv1.2 chimera, the MoS₂ nanoflake prefers to bind into a crevice located at the extracellular side of the Voltage Sensor Domain (VSD). Interestingly, the crevice involves the N-terminal segment of S4, a crucial transmembrane helix which directly controls the gating process of the Kv1.2 chimera channel by electromechanical coupling the VSD to the transmembrane electric field. MoS₂ in contact with S4 from the Kv1.2 chimera, potentially influences the channel's gating process from open to closed states. In all three systems, the van der Waals contribution to the total energy dominates the binding interactions; also, hydrophobic residues contribute the most contact points, which agrees with the strong hydrophobic character of the MoS₂ nanomaterial. Electrophysiology recordings using two-electrode voltage-clamp show that currents of Kir3.2 and Kv1.2 are both blocked by the MoS₂ nanoflakes in a concentration-dependent way. While the background K⁺ channel, K2P2 (TREK-1), identified as a negative control, is not blocked by the MoS₂ nanoflakes. The large and rigid extracellular domain of K2P2 appears to protect the channel from disturbance by the nanoflakes. Intrinsic chemical properties of MoS₂, together with the specific features of the channels, such as the electrostatic character and complex surface architecture, determine the critical details of the binding events. These findings might shed light on the potential nanotoxicology of MoS₂ nanomaterials and help us to understand the underlying molecular mechanism.

Concentration-dependent binding of CdSe quantum dots on the SH3 domain

Quantum dots (QDs) are being used increasingly in applications for solar panels, consumer electronics, and biomedical imaging. For biomedical applications, QDs are typically coated with a biocompatible molecule for the system of interest. Experiments have indicated a QD dose-dependent and surface coating-dependent toxicity, with a portion of the toxicity being ascribed to interference with biomolecules. In this work, the interaction of trioctylphosphine oxide (TOPO) coated (CdSe)₁₃ QDs with the SRC homology 3 domain (SH3) protein domain are explored using molecular dynamics simulations. The results of this research agree well with experiments that show that at the lowest concentration, the QDs have little affinity for the native proline-rich motif (PRM) binding site of SH3. At higher concentrations, the QDs aggregate and increasingly prefer the PRM binding site, indicating that the normal SH3 function is impeded. This binding dependence is attributed to changes in the local density of the surface coated TOPO molecules upon aggregation. These results present possible interesting QD toxicity patterns and reveal the interdependence between dose and surface coating effects in QD toxicity.

Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery

The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.

The Dispersion State of Tangled Multi-Walled Carbon Nanotubes Affects Their Cytotoxicity

The medical applications of carbon nanotubes (CNTs) have garnered much attention. However, evaluating the safety of CNTs remains difficult, and no consensus has been reached. Moreover, assessing the biosafety of multi-walled CNTs (MWCNTs), which can become tangled during manufacturing, is challenging because they do not readily disperse. We studied how the dispersion state of tangled MWCNTs affects their cytotoxicity, using three sonicators. Flotube 9110 (FT9110), tangled MWCNTs, were dispersed in two dispersants (fetal bovine serum and polysorbate 80) using a new type of sonicator (PR-1) and two conventional sonicators. The size and cytotoxicity of the dispersed FT9110 were measured using the BEAS-2B human bronchial epithelial cell line. The PR-1 dispersed the FT9110 to agglomerates <200 nm in diameter; FT9110 dispersed with the PR-1 did not show cytotoxicity regardless of dispersant. The other sonicators dispersed the FT9110 to particles >1000 nm in diameter, and cytotoxicity depended on the dispersant. We found that excluding cells adhered to agglomerated FT9110 before evaluating cytotoxicity can lead to false-positive results. The PR-1 sonicator dispersed tangled FT9110 to many single fibers, which showed lower cytotoxicity than conventionally-sonicated MWCNTs. We suggest that dispersion state should be accounted for when evaluating the cytotoxicity of MWCNTs.