Binding of blood proteins to carbon nanotubes reduces cytotoxicity

Understanding the role of biomolecular coronas in human exposure to nanomaterials

Nanomaterials (NMs) are increasingly used in medical treatments, electronics, and food additives. However, nanosafety-the possible adverse effects of NMs on human health-is an area of active research. This review provides an overview of the influence of biomolecular coronas on NM transformation following various exposure routes. We discuss potential exposure pathways, including inhalation and ingestion, describing the physiology of exposure routes and emphasising the relevance of coronas in these environments. Additionally, we review other routes to NM exposure, such as synovial fluid, blood (translocation and injection), dermal and ocular exposure, as well as the dose and medium impact on NM interactions. We emphasize the need for an in-depth characterisation of coronas in different biological media, highlighting the need and opportunity to study lung and gastric fluids to understand NM behaviour and potential toxicity. Future research aims to predict better in vivo outcomes and address the complexities of NM interactions with biological systems.

Multifunctional biomolecular corona-inspired nanoremediation of antibiotic residues

Facing complex and variable emerging antibiotic pollutants, the traditional development of functional materials is a "trial-and-error" process based on physicochemical principles, where laborious steps and long timescales make it difficult to accelerate technical breakthroughs. Notably, natural biomolecular coronas derived from highly tolerant organisms under significant contamination scenarios can be used in conjunction with nanotechnology to tackling emerging contaminants of concern. Here, super worms (Tubifex tubifex) with high pollutant tolerance were integrated with nano-zero valent iron (nZVI) to effectively reduce the content of 17 antibiotics in wastewater within 7 d. Inspired by the synergistic remediation, nZVI-augmented worms were constructed as biological nanocomposites. Neither nZVI (0.3 to 3 g/L) nor worms (104 to 105 per liter) alone efficiently degraded florfenicol (FF, as a representative antibiotic), while their composite removed 87% of FF (3 μmol/L). Under antibiotic exposure, biomolecules secreted by worms formed a corona on and modified the nZVI particle surface, enabling the nano-bio interface greater functionality, including responsiveness, enrichment, and reduction. Mechanistically, FF exposure activated glucose-alanine cycle pathways that synthesize organic acids and amines as major metabolites, which were assembled into vesicles and secreted, thereby interacting with nZVI in a biologically response design strategy. Lactic acid and urea formed hydrogen bonds with FF, enriched analyte presence at the heterogeneous interface. Succinic and lactic acids corroded the nZVI passivation layer and promoted electron transfer through surface conjugation. This unique strategy highlights biomolecular coronas as a complex resource to augment nano-enabled technologies and will provide shortcuts for rational manipulation of nanomaterial surfaces with coordinated multifunctionalities.

Molecular insights into the phase transition of lysozyme into amyloid nanostructures: Implications of therapeutic strategies in diverse pathological conditions

Lysozyme, a well-known bacteriolytic enzyme, exhibits a fascinating yet complex behavior when it comes to protein aggregation. Under certain conditions, this enzyme undergoes flexible transformation, transitioning from partially unfolded intermediate units of native conformers into complex cross-β-rich nano fibrillar amyloid architectures. Formation of such lysozyme amyloids has been implicated in a multitude of pathological and medical severities, like hepatic dysfunction, hepatomegaly, splenic rupture as well as spleen dysfunction, nephropathy, sicca syndrome, renal dysfunction, renal amyloidosis, and systemic amyloidosis. In this comprehensive review, we have attempted to provide in-depth insights into the aggregating behavior of lysozyme across a spectrum of variables, including concentrations, temperatures, pH levels, and mutations. Our objective is to elucidate the underlying mechanisms that govern lysozyme's aggregation process and to unravel the complex interplay between its structural attributes. Moreover, this work has critically examined the latest advancements in the field, focusing specifically on novel strategies and systems, that have been implemented to delay or inhibit the lysozyme amyloidogenesis. Apart from this, we have tried to explore and advance our fundamental understanding of the complex processes involved in lysozyme aggregation. This will help the research community to lay a robust foundation for screening, designing, and formulating targeted anti-amyloid therapeutics offering improved treatment modalities and interventions not only for lysozyme-linked amyloidopathy but for a wide range of amyloid-related disorders.

Molecular Insights into the Binding and Conformational Changes of Hepcidin25 Blood Peptide with 4-Aminoantipyrine and Their Sorption Mechanism by Carboxylic-Functionalized Multiwalled Carbon Nanotubes: A Comprehensive Spectral Analysis and Molecular Dynamics Simulation Study

In this work, the main purpose is to analyze and understand the mechanism and thermodynamic interactions of carboxylic acid-functionalized multiwalled carbon nanotubes (cf-MWCNTs) and 4-aminoantipyrine (AAP) with human hepcidine25 (Hep25) using multispectroscopic and molecular docking modeling methods, binding free energy calculations, and molecular dynamics (MD) simulations under physiological conditions. AAP belongs to a class of persistent environmental contaminants, and its residue is a potential hazard to human health, exhibiting a high binding affinity with blood peptides. Hepcidin is a 25-residue peptide hormone with four disulfide bonds that regulates the iron balance in vertebrates and contributes to host immunity as a cysteine-rich antimicrobial peptide. Due to their diverse properties and pollutant absorption capabilities, CNTs demonstrate important biological effects in biological applications, particularly in the noncovalent interactions with blood peptides. A comprehensive molecular dynamics simulation integrated with molecular docking methodologies was employed to explore the binding free energy between AAP and Hep25, identify binding sites, elucidate thermodynamic characteristics, and evaluate the binding forces governing their interaction. The investigation delved into elucidating the precise binding site of AAP within the Hep25 protein and thoroughly analyzed the impact of AAP on the microenvironment and conformational dynamics of Hep25. The circular dichroism (CD) experimental results highlight a reduction in β-sheet composition following the introduction of AAP and cf-MWCNT. In addition, outcomes from fluorescence spectroscopy demonstrate that both cf-MWCNT and AAP significantly attenuated Hep-25 fluorescence via a static quenching mechanism. According to the MD simulations, the presence of AAP induces changes in the secondary structure of Hep25 and enhances its hydrophobicity. Additionally, our findings demonstrated that alongside the alteration in protein structure and functionality induced by contaminants, cf-MWCNTs possess the capability to mitigate the contaminant-induced effects on Hep25 activity while preserving the overarching structural integrity of Hep25. Based on the distance and RDF data, we found that during the simulation the presence of the cf-MWCNT causes the AAP to move away from the Hep25, and as a result fewer and weaker interactions of the AAP with the Hep25 will be observed. Likewise, free energy calculations indicate that the binding of Hep25 to AAP and cf-MWCNT involves electrostatic, π-cationic, and π-π stacking interactions. The research findings offer invaluable insights into the intricate influence of pollutants and carbon nanotubes on protein functionality within the circulatory system and their toxicity in vivo for prospective investigations.

Graphene Oxide Nanosheets Toxicity in Mice Is Dependent on Protein Corona Composition and Host Immunity

Two-dimension graphene oxide (GO) nanosheets with high and low serum protein binding profiles (high/low hard-bound protein corona/HChigh/low) are used in this study as model materials and screening tools to investigate the underlying roles of the protein corona on nanomaterial toxicities in vivo. We proposed that the in vivo biocompatibility/nanotoxicity of GO is protein corona-dependent and host immunity-dependent. The hypothesis was tested by injecting HChigh/low GO nanosheets in immunocompetent ICR/CD1 and immunodeficient NOD-scid II2rγnull mice and performed histopathological and hematological evaluation studies on days 1 and 14 post-injection. HClow GO induced more severe acute lung injury compared to HChigh GO in both immunocompetent and immunodeficient mice, with the effect being particularly pronounced in immunocompetent animals. Additionally, HClow GO caused more significant liver injury in both types of mice, with immunodeficient mice being more susceptible to its hepatotoxic effects. Moreover, administration of HClow GO resulted in increased hematological toxicity and elevated levels of serum pro-inflammatory cytokines in immunocompromised and immunocompetent mice, respectively. Correlation studies were conducted to explore the impact of distinct protein corona compositions on resulting toxicities in both immunocompetent and immunodeficient mice. This facilitated the identification of consistent patterns, aligning with those observed in vitro, thus indicating a robust in vitro-in vivo correlation. This research will advance our comprehension of how hard corona proteins interact with immune cells, leading to toxicity, and will facilitate the development of improved immune-modulating nanomaterials for therapeutic purposes.

Analysis of nanomaterial biocoronas in biological and environmental surroundings

A biomolecular coating, or biocorona, forms on the surface of engineered nanomaterials (ENMs) immediately as they enter biological or environmental systems, defining their biological and environmental identity and influencing their fate and performance. This biomolecular layer includes proteins (the protein corona) and other biomolecules, such as nucleic acids and metabolites. To ensure a meaningful and reproducible analysis of the ENMs-associated biocorona, it is essential to streamline procedures for its preparation, separation, identification and characterization, so that studies in different labs can be easily compared, and the information collected can be used to predict the composition, dynamics and properties of biocoronas acquired by other ENMs. Most studies focus on the protein corona as proteins are easier to monitor and characterize than other biomolecules and play crucial roles in receptor engagement and signaling; however, metabolites play equally critical roles in signaling. Here we describe how to reproducibly prepare and characterize biomolecule-coated ENMs, noting especially the steps that need optimization for different types of ENMs. The structure and composition of the biocoronas are characterized using general methods (transmission electron microscopy, dynamic light scattering, capillary electrophoresis-mass spectrometry and liquid chromatography-mass spectrometry) as well as advanced techniques, such as transmission electron cryomicroscopy, synchrotron-based X-ray absorption near edge structure and circular dichroism. We also discuss how to use molecular dynamic simulation to study and predict the interaction between ENMs and biomolecules and the resulting biocorona composition. The application of this protocol can provide mechanistic insights into the formation, composition and evolution of the ENM biocorona, ultimately facilitating the biomedical and agricultural application of ENMs and a better understanding of their impact in the environment.

Molecular Dynamic Simulations for Biopolymers with Biomedical Applications

Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.

Supramolecular interaction in the action of drug delivery systems

Complex diseases and diverse clinical needs necessitate drug delivery systems (DDSs), yet the current performance of DDSs is far from ideal. Supramolecular interactions play a pivotal role in various aspects of drug delivery, encompassing biocompatibility, drug loading, stability, crossing biological barriers, targeting, and controlled release. Nevertheless, despite having some understanding of the role of supramolecular interactions in drug delivery, their incorporation is frequently overlooked in the design and development of DDSs. This perspective provides a brief analysis of the involved supramolecular interactions in the action of drug delivery, with a primary emphasis on the DDSs employed in the clinic, mainly liposomes and polymers, and recognized phenomena in research, such as the protein corona. The supramolecular interactions implicated in various aspects of drug delivery systems, including biocompatibility, drug loading, stability, spatiotemporal distribution, and controlled release, were individually analyzed and discussed. This perspective aims to trigger a comprehensive and systematic consideration of supramolecular interactions in the further development of DDSs. Supramolecular interactions embody the true essence of the interplay between the majority of DDSs and biological systems.

Abrogation of ORF8-IRF3 binding interface with Carbon nanotube derivatives to rescue the host immune system against SARS-CoV-2 by using molecular screening and simulation approaches

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to over six million deaths worldwide. In human immune system, the type 1 interferon (IFN) pathway plays a crucial role in fighting viral infections. However, the ORF8 protein of the virus evade the immune system by interacting with IRF3, hindering its nuclear translocation and consequently downregulate the type I IFN signaling pathway. To block the binding of ORF8-IRF3 and inhibit viral pathogenesis a quick discovery of an inhibitor molecule is needed. Therefore, in the present study, the interface between the ORF8 and IRF3 was targeted on a high-affinity carbon nanotube by using computational tools. After analysis of 62 carbon nanotubes by multiple docking with the induced fit model, the top five compounds with high docking scores of - 7.94 kcal/mol, - 7.92 kcal/mol, - 7.28 kcal/mol, - 7.19 kcal/mol and - 7.09 kcal/mol (top hit1-5) were found to have inhibitory activity against the ORF8-IRF3 complex. Molecular dynamics analysis of the complexes revealed the high compactness of residues, stable binding, and strong hydrogen binding network among the ORF8-nanotubes complexes. Moreover, the total binding free energy for top hit1-5 was calculated to be - 43.21 ± 0.90 kcal/mol, - 41.17 ± 0.99 kcal/mol, - 48.85 ± 0.62 kcal/mol, - 43.49 ± 0.77 kcal/mol, and - 31.18 ± 0.78 kcal/mol respectively. These results strongly suggest that the identified top five nanotubes (hit1-5) possess significant potential for advancing and exploring innovative drug therapies. This underscores their suitability for subsequent in vivo and in vitro experiments, marking them as promising candidates worthy of further investigation.

Interfacial interactions between spider silk protein and cellulose studied by molecular dynamics simulation

CONTEXT

Due to their excellent biocompatibility and degradability, cellulose/spider silk protein composites hold a significant value in biomedical applications such as tissue engineering, drug delivery, and medical dressings. The interfacial interactions between cellulose and spider silk protein affect the properties of the composite. Therefore, it is important to understand the interfacial interactions between spider silk protein and cellulose to guide the design and optimization of composites. The study of the adsorption of protein on specific surfaces of cellulose crystal can be very complex using experimental methods. Molecular dynamics simulations allow the exploration of various physical and chemical changes at the atomic level of the material and enable an atomic description of the interactions between cellulose crystal planes and spider silk protein. In this study, molecular dynamics simulations were employed to investigate the interfacial interactions between spider silk protein (NTD) and cellulose surfaces. Findings of RMSD, RMSF, and secondary structure showed that the structure of NTD proteins remained unchanged during the adsorption process. Cellulose contact numbers and hydrogen bonding trends on different crystalline surfaces suggest that van der Waals forces and hydrogen bonding interactions drive the binding of proteins to cellulose. These findings reveal the interaction between cellulose and protein at the molecular level and provide theoretical guidance for the design and synthesis of cellulose/spider silk protein composites.

METHODS

MD simulations were all performed using the GROMACS-5.1 software package and run with CHARMM36 carbohydrate force field. Molecular dynamics simulations were performed for 500 ns for the simulated system.

Protein Corona-Mediated Inhibition of Nanozyme Activity: Impact of Protein Shape

During biomedical applications, nanozymes, exhibiting enzyme-like characteristics, inevitably come into contact with biological fluids in living systems, leading to the formation of a protein corona on their surface. Although it is acknowledged that molecular adsorption can influence the catalytic activity of nanozymes, there is a dearth of understanding regarding the impact of the protein corona on nanozyme activity and its determinant factors. In order to address this gap, we employed the AuNR@Pt@PDDAC [PDDAC, poly(diallyldimethylammonium chloride)] nanorod (NR) as a model nanozyme with multiple activities, including peroxidase, oxidase, and catalase-mimetic activities, to investigate the inhibitory effects of the protein corona on the catalytic activity. After the identification of major components in the plasma protein corona on the NR, we observed that spherical proteins and fibrous proteins induced distinct inhibitory effects on the catalytic activity of nanozymes. To elucidate the underlying mechanism, we uncovered that the adsorbed proteins assembled on the surface of the nanozymes, forming protein networks (PNs). Notably, the PNs derived from fibrous proteins exhibited a screen mesh-like structure with smaller pore sizes compared to those formed by spherical proteins. This structural disparity resulted in a reduced efficiency for the permeation of substrate molecules, leading to a more robust inhibition in activity. These findings underscore the significance of the protein shape as a crucial factor influencing nanozyme activity. This revelation provides valuable insights for the rational design and application of nanozymes in the biomedical fields.

Interaction of eugenol-based anti-tuberculosis nanoemulsion with bovine serum albumin: A spectroscopic study including Rifampicin, Isoniazid, Pyrazinamide, and Ethambutol

Tuberculosis (TB), a deadly infectious disease, is primarily caused by the bacterium Mycobacterium tuberculosis. The misuse of antibiotics has led to the development of drug resistance, prompting researchers to explore new technologies to combat multidrug-resistant Tuberculosis (MDR TB). Phospholipid-based nanotherapeutics, such as nanoemulsions, are gaining traction as they enhance drug solubility, stability, and bioavailability. Our study focuses on the interaction between Bovine Serum Albumin (BSA) and a drug-loaded nanoemulsion based on Eugenol. This nanoemulsion incorporates Eugenol, Clove, cinnamon oil, and first-line anti-tuberculosis drugs like Rifampicin, Isoniazid, Pyrazinamide, and Ethambutol. The primary objective is to assess the biosafety profile of the nanoemulsion upon interaction with BSA. We employed Fluorescence, UV-visible, and Fourier Transform Infrared Spectroscopy (FTIR) to analyze this interaction. UV-visible spectroscopy detected changes in hydrophobicity due to structural alterations in BSA near the tryptophan residue, leading to the formation of ground-state complexes. Fluorescence spectroscopy demonstrated that the nanoemulsion effectively quenched fluorescence originating from tryptophan and tyrosine residues. Studies using synchronous and three-dimensional spectroscopy point to a potential modification of the aromatic environment of BSA by the nanoemulsion. Resonance light scattering spectra indicated the formation of large aggregates due to the interaction with the nanoemulsion. The second derivative FTIR spectra showed an increase in the magnitude of secondary structure bands, suggesting a conformational shift. This research has significant pharmacological implications for developing safer, more targeted drug delivery systems. The information obtained from the interaction of the nanoemulsion with the blood carrier protein is vital for the future development of superior carriers with minimal adverse effects on patients. It is crucial to remember that conformational changes brought on by drug-ligand complexes attaching to carrier proteins may have negative consequences. Therefore, this study enhances the in vitro evaluation of potential adverse effects of the nanoemulsion on serum proteins.

The impact of chemical properties of the solid-liquid-adsorbate interfaces on the entropy-enthalpy compensation involved in adsorption

Despite extensive studies on the thermodynamic mechanism governing molecular adsorption at the solid-water interface, a comprehensive understanding of the crucial role of interface properties in mediating the entropy-enthalpy compensation during adsorption is lacking, particularly at a quantitative level. Herein, we employed two types of surface models (hydroxyapatite and graphene) along with a series of amino acids to successfully elucidate how distinct interfacial features dictate the delicate balance between entropy and enthalpy variations. The adsorption of all amino acids on the hydroxyapatite surface is an enthalpy-dominated process, where the water-induced enthalpic component of the free energy and the surface-adsorbate electrostatic interaction term alternatively act as the driving force for adsorption in different regions of the surface. Although favorable interactions are observed between amino acids and the graphene surface, the entropy-enthalpy compensation exhibits dependence on the molecular size of the adsorbates. For small amino acids, favorable enthalpy changes predominantly determine their adsorption behavior; however, larger amino acids tend to bind more tightly with the graphene surface, which is thermodynamically dominated by the entropy variations despite the structural characteristics of amino acids. This study reveals specific entropy-enthalpy mechanisms underlying amino acid adsorption at the solid-liquid interface, providing guidance for surface design and synthesis of new biomolecules.

Chiral nanomaterials in tissue engineering

Addressing significant medical challenges arising from tissue damage and organ failure, the field of tissue engineering has evolved to provide revolutionary approaches for regenerating functional tissues and organs. This involves employing various techniques, including the development and application of novel nanomaterials. Among them, chiral nanomaterials comprising non-superimposable nanostructures with their mirror images have recently emerged as innovative biomaterial candidates to guide tissue regeneration due to their unique characteristics. Chiral nanomaterials including chiral fibre supramolecular hydrogels, polymer-based chiral materials, self-assembling peptides, chiral-patterned surfaces, and the recently developed intrinsically chiroptical nanoparticles have demonstrated remarkable ability to regulate biological processes through routes such as enantioselective catalysis and enhanced antibacterial activity. Despite several recent reviews on chiral nanomaterials, limited attention has been given to the specific potential of these materials in facilitating tissue regeneration processes. Thus, this timely review aims to fill this gap by exploring the fundamental characteristics of chiral nanomaterials, including their chiroptical activities and analytical techniques. Also, the recent advancements in incorporating these materials in tissue engineering applications are highlighted. The review concludes by critically discussing the outlook of utilizing chiral nanomaterials in guiding future strategies for tissue engineering design.

Impact of Whey Protein Corona Formation around TiO2 Nanoparticles on Their Physiochemical Properties and Gastrointestinal Fate

Previously, we found that whey proteins form biomolecular coronas around titanium dioxide (TiO2) nanoparticles. Here, the gastrointestinal fate of whey protein-coated TiO2 nanoparticles and their interactions with gut microbiota were investigated. The antioxidant activity of protein-coated nanoparticles was enhanced after simulated digestion. The structure of the whey proteins was changed after they adsorbed to the surfaces of the TiO2 nanoparticles, which reduced their hydrolysis under simulated gastrointestinal conditions. The presence of protein coronas also regulated the impact of the TiO2 nanoparticles on colonic fermentation, including promoting the production of short-chain fatty acids. Bare TiO2 nanoparticles significantly increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria, but the presence of protein coronas alleviated this effect. In particular, the proportion of beneficial bacteria, such as Bacteroides and Bifidobacterium, was enhanced for the coated nanoparticles. Our results suggest that the formation of a whey protein corona around TiO2 nanoparticles may have beneficial effects on their behavior within the colon. This study provides valuable new insights into the potential impact of protein coronas on the gastrointestinal fate of inorganic nanoparticles.

Progress in regulating inflammatory biomaterials for intervertebral disc regeneration

Intervertebral disc degeneration (IVDD) is rising worldwide and leading to significant health issues and financial strain for patients. Traditional treatments for IVDD can alleviate pain but do not reverse disease progression, and surgical removal of the damaged disc may be required for advanced disease. The inflammatory microenvironment is a key driver in the development of disc degeneration. Suitable anti-inflammatory substances are critical for controlling inflammation in IVDD. Several treatment options, including glucocorticoids, non-steroidal anti-inflammatory drugs, and biotherapy, are being studied for their potential to reduce inflammation. However, anti-inflammatories often have a short half-life when applied directly and are quickly excreted, thus limiting their therapeutic effects. Biomaterial-based platforms are being explored as anti-inflammation therapeutic strategies for IVDD treatment. This review introduces the pathophysiology of IVDD and discusses anti-inflammatory therapeutics and the components of these unique biomaterial platforms as comprehensive treatment systems. We discuss the strengths, shortcomings, and development prospects for various biomaterials platforms used to modulate the inflammatory microenvironment, thus providing guidance for future breakthroughs in IVDD treatment.

Modulating the toxicity of engineered nanoparticles by controlling protein corona formation: Recent advances and future prospects

With the rapid development and widespread application of engineered nanoparticles (ENPs), understanding the fundamental interactions between ENPs and biological systems is essential to assess and predict the fate of ENPs in vivo. When ENPs are exposed to complex physiological environments, biomolecules quickly and inevitably adsorb to ENPs to form a biomolecule corona, such as a protein corona (PC). The formed PC has a significant effect on the physicochemical properties of ENPs and gives them a brand new identity in the biological environment, which determines the subsequent ENP-cell/tissue/organ interactions. Controlling the formation of PCs is therefore of utmost importance to accurately predict and optimize the behavior of ENPs within living organisms, as well as ensure the safety of their applications. In this review, we provide an overview of the fundamental aspects of the PC, including the formation mechanism, composition, and frequently used characterization techniques. We comprehensively discuss the potential impact of the PC on ENP toxicity, including cytotoxicity, immune response, and so on. Additionally, we summarize recent advancements in manipulating PC formation on ENPs to achieve the desired biological outcomes. We further discuss the challenges and prospects, aiming to provide valuable insights for a better understanding and prediction of ENP behaviors in vivo, as well as the development of low-toxicity ENPs.

Cytotoxicity prediction of nano metal oxides on different lung cells via Nano-QSAR

In recent years, nanomaterials have found extensive applications across diverse domains owing to their distinctive physical and chemical characteristics. It is of great importance in theoretical and practical terms to carry out the relationship between structural characteristics of nanomaterials and different cytotoxicity and to achieve practical assessment and prediction of cytotoxicity. This study investigated the intrinsic quantitative constitutive relationships between the cytotoxicity of nano-metal oxides on human normal lung epithelial cells and human lung adenocarcinoma cells. We first employed quasi-SMILES-based nanostructural descriptors by selecting the five physicochemical properties that are most closely related to the cytotoxicity of nanometal oxides, then established SMILES-based descriptors that can effectively describe and characterize the molecular structure of nanometal oxides, and then built the corresponding Nano-Quantitative Structure-Activity Relationship (Nano-QSAR) prediction models, finally, combined with the theory of reactive oxygen species (ROS) biotoxicity, to reveal the mechanism of toxicity and differences between the two cell types. The established model can efficiently and accurately predict the properties of targets, reveal the corresponding toxicity mechanisms, and guide the safe design, synthesis, and application of nanometal oxides.

Nanoinformatics based insights into the interaction of blood plasma proteins with carbon based nanomaterials: Implications for biomedical applications

In the past three decades, interest in using carbon-based nanomaterials (CBNs) in biomedical application has witnessed remarkable growth. Despite the rapid advancement, the translation of laboratory experimentation to clinical applications of nanomaterials is one of the major challenges. This might be attributed to poor understanding of bio-nano interface. Arguably, the most significant barrier is the complexity that arises by interplay of several factors like properties of nanomaterial (shape, size, surface chemistry), its interaction with suspending media (surface hydration and dehydration, surface reconstruction and release of free surface energy) and the interaction with biomolecules (conformational change in biomolecules, interaction with membrane and receptor). Tailoring a nanomaterial that minimally interacts with protein and lipids in the medium while effectively acts on target site in biological milieu has been very difficult. Computational methods and artificial intelligence techniques have displayed potential in effectively addressing this problem. Through predictive modelling and deep learning, computer-based methods have demonstrated the capability to create accurate models of interactions between nanoparticles and cell membranes, as well as the uptake of nanomaterials by cells. Computer-based simulations techniques enable these computational models to forecast how making particular alterations to a material's physical and chemical properties could enhance functional aspects, such as the retention of drugs, the process of cellular uptake and biocompatibility. We review the most recent progress regarding the bio-nano interface studies between the plasma proteins and CBNs with a special focus on computational simulations based on molecular dynamics and density functional theory.

Progress and challenges in the translation of cancer nanomedicines

With the booming development of nanotechnology, nanomedicines have made considerable progress in the pharmaceutical field. However, the number of nanodrugs approved for clinical treatment is very limited. The main obstacles stem from the complexity of nanomedicine composition, tumor heterogeneity, complexity and incomplete understanding of nanotumor interactions, uncontrollable scaling, high production costs, and uncertainty of regulations and standards. This review article described the current stage of nanomedicines and highlighted the challenges, strategies, and opportunities for clinical translation of nanomedicines.

Pulmonary Surfactant Homeostasis Dysfunction Mediates Multiwalled Carbon Nanotubes Induced Lung Fibrosis via Elevating Surface Tension

Multiwalled carbon nanotubes (MWCNTs) have been widely used in many disciplines and raised great concerns about their negative health impacts, especially environmental and occupational exposure. MWCNTs have been reported to induce fibrotic responses; however, the underlying mechanisms remain largely veiled. Here, we reported that MWCNTs inhalation induced lung fibrosis together with decreased lung compliance, increased elastance in the mice model, and elevated surface tension in vitro. Specifically, MWCNTs increased surface tension by impairing the function of the pulmonary surfactant. Mechanistically, MWCNTs induced lamellar body (LB) dysfunction through autophagy dysfunction, which then leads to surface tension elevated by pulmonary surfactant dysfunction in the context of lung fibrosis. This is a study to investigate the molecular mechanism of MWCNTs-induced lung fibrosis and focus on surface tension. A direct mechanistic link among impaired LBs, surface tension, and fibrosis has been established. This finding elucidates the detailed molecular mechanisms of lung fibrosis induced by MWCNTs. It also highlights that pulmonary surfactants are expected to be potential therapeutic targets for the prevention and treatment of lung fibrosis induced by MWCNTs.

Villin headpiece unfolding upon binding to boridene mediated by the "anchoring-perturbation" mechanism

We employ molecular dynamics (MD) simulations to investigate the influence of boridene on the behavior of a protein model, HP35, with the aim of assessing the potential biotoxicity of boridene. Our MD results reveal that HP35 can undergo unfolding via an "anchoring-perturbation" mechanism upon adsorption onto the boridene surface. Specifically, the third helix of HP35 becomes tightly anchored to the boridene surface through strong electrostatic interactions between the abundant molybdenum atoms on the boridene surface and the oxygen atoms on the HP35 backbone. Meanwhile, the first helix, experiencing continuous perturbation from the surrounding water solution over an extended period, suffers from potential breakage of hydrogen bonds, ultimately resulting in its unfolding. Our findings not only propose, for the first time to our knowledge, the "anchoring-perturbation" mechanism as a guiding principle for protein unfolding but also reveal the potential toxicity of boridene on protein structures.

Development of nano-delivery systems for loaded bioactive compounds: using molecular dynamics simulations

Over the past decade, a remarkable surge in the development of functional nano-delivery systems loaded with bioactive compounds for healthcare has been witnessed. Notably, the demanding requirements of high solubility, prolonged circulation, high tissue penetration capability, and strong targeting ability of nanocarriers have posed interdisciplinary research challenges to the community. While extensive experimental studies have been conducted to understand the construction of nano-delivery systems and their metabolic behavior in vivo, less is known about these molecular mechanisms and kinetic pathways during their metabolic process in vivo, and lacking effective means for high-throughput screening. Molecular dynamics (MD) simulation techniques provide a reliable tool for investigating the design of nano-delivery carriers encapsulating these functional ingredients, elucidating the synthesis, translocation, and delivery of nanocarriers. This review introduces the basic MD principles, discusses how to apply MD simulation to design nanocarriers, evaluates the ability of nanocarriers to adhere to or cross gastrointestinal mucosa, and regulates plasma proteins in vivo. Moreover, we presented the critical role of MD simulation in developing delivery systems for precise nutrition and prospects for the future. This review aims to provide insights into the implications of MD simulation techniques for designing and optimizing nano-delivery systems in the healthcare food industry.

Spatial mapping and quantitative evaluation of protein corona on PEGylated mesoporous silica particles by super-resolution fluorescence microscopy

Nanoparticles (NPs) adsorb serum proteins when exposed to biological fluids, forming a dynamic protein corona that has a profound impact on their overall biological profile and fate. Polyethylene glycol (PEG) modification is the most widely used strategy to mitigate and inhibit protein corona formation. Nevertheless, the accurate mapping and quantification of PEG inhibition effects on protein corona formation have scarcely been reported. Herein, we demonstrate the direct observation and quantification of protein corona adsorbed onto PEGylated mesoporous silica particles by direct stochastic optical reconstruction microscopy (dSTORM). The variation tendency of protein penetration depth in terms of PEG molecular weights and incubated time is investigated for the first time. The maximum penetration depths present slight increase with the prolonged incubation time, while they tend to remarkably decrease with increased chain length of modified PEG. Moreover, the co-localization of preformed protein corona with lysosomes and the destination of adsorbed protein are demonstrated. Our method provides important technical characterization information and in-depth understanding of protein corona adsorbed onto PEGylated mesoporous silica particles. This shines new light on the behaviors of silica materials in cells and may promote their practical applications in biomedicine.

Serum albumin acted as an effective carrier to improve the stability of bioactive flavonoid

The health-improving functions of bioactive flavonoids in vitro and in vivo are often limited by their low stability, which could be counteracted by the application of proteins as carriers of flavonoids. Clarification of the mechanism of protein-ligand interaction is crucial for the encapsulation of bioactive components. Herein, common plasma proteins [i.e., bovine serum albumin (BSA), human serum albumin (HSA), human immunoglobulin G (IgG) and fibrinogen (FG)] were compared for their binding characteristics to quercetin, the main component of flavonoids in human diet, in the absence and presence of free Cu2+ (an accelerator for flavonoids' instability) using multi-spectroscopic and computational methods. As a flexible open structure of proteins, both BSA and HSA were found to be the most promising carriers for quercetin and Cu2+ with an affinity on the order of 104 M-1. HSA-diligand complex (i.e., HSA-quercetin-Cu2+) was successfully generated when both quercetin and Cu2+ were added to the HSA solution. The stability and free radical scavenging activity of bioactive quercetin during incubation was promoted in the HSA-diligand complex relative to quercetin-Cu2+ complex. Quercetin/Cu2+ system could induce the formation of reactive oxygen species such as hydrogen peroxide (H2O2) and hydroxide radical (·OH), which were significantly suppressed upon HSA binding. Consistently, the cytotoxicity of the quercetin/Cu2+ system to endothelial cells was reduced in the HSA-diligand complex. These results demonstrate the possibility of developing serum albumin-based carriers for the protection of bioactive flavonoids in their nutritional application.

Therapeutic applications of carbon nanomaterials in renal cancer

Carbon nanomaterials (CNMs), including carbon nanotubes (CNTs), graphene, and nanodiamonds (NDs), have shown great promise in detecting and treating numerous cancers, including kidney cancer. CNMs can increase the sensitivity of diagnostic techniques for better kidney cancer identification and surveillance. They enable targeted medicine delivery specifically to tumour locations, with little effect on healthy tissue. Because of their unique chemical and physical characteristics, they can avoid the body's defence mechanisms, making it easier to accumulate where tumours exist. Consequently, CNMs provide more effective drug delivery to kidney cancer cells. It also helps in improving the efficacy of treatment. This review explores the potential of several CNMs in improving therapeutic strategies for kidney cancer. We briefly covered the physicochemical properties and therapeutic applications of CNMs. Additionally, we discussed how structural modifications in CNMs enhance their precision in treating renal cancer. A thorough overview of CNM-based gene, peptide, and drug delivery strategies for the treatment of renal cancer is presented in this review. It covers information on other CNM-based therapeutic approaches, such as hyperthermia, photodynamic therapy, and photoacoustic therapy. Also, the interactions of CNMs with the tumour microenvironment (TME) are explored, including modulation of the immune response, regulation of tumour hypoxia, interactions between CNMs and TME cells, effects of TME pH on CNMs, and more. Finally, potential side effects of CNMs, such as toxicity, bio corona formation, enzymatic degradation, and biocompatibility, are also discussed.

Formation and detection of biocoronas in the food industry and their fate in the human body

The rapid advancement of nanotechnology has opened up new avenues for applications in all stages of the food industry. Over the past decade, extensive research has emphasized that when nanoparticles (NPs) enter organisms, they spontaneously adsorbed biomolecules, leading to the formation of biocorona. This paper provided a detailed review of the process of biocorona formation in the food industry, including their classification and influencing factors. Additionally, various characterization methods to investigated the morphology and structure of biocoronas were introduced. As a real state of food industry nanoparticles in biological environments, the biocorona causes structural transformations of biomolecules bound to NPs, thus affecting their fate in the body. It can either promote or inhibit enzyme activity in the human environment, and may also positively or negatively affect the cellular uptake and toxicity of NPs. Since NPs present in the food industry will inevitably enter the human body, further investigations on biocoronas will offer valuable insights and perspectives on the safety of incorporating more NPs into the food industry.

Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene

There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.

Adsorption and encapsulation of melittin on covalently functionalized carbon nanotubes; a molecular dynamics simulation study

For the first time, molecular dynamics (MD) simulation was used to examine melittin's adsorption and encapsulation on covalently functionalized carbon nanotubes (fCNTs). The CNT wall and terminals were functionalized with carboxy, hydroxyl, and amine functional groups. The findings demonstrated that the melittin would be adsorbed on the fCNT's outer surface when just the CNT terminal is functionalized. On the other hand, melittin is encapsulated inside the nanotube space when the CNTs' walls and terminals are functionalized. Encapsulated melittin has an alpha-helix structure similar to melittin in a water medium. With the use of parameters like root mean square fluctuations (RMSF) and radius of gyration (Rg), the melittin conformational changes were evaluated. According to the findings, the amine functional group significantly alters the melittin's conformation. The wall and terminals fCNTs with hydroxyl and carboxyl could encapsulate melittin inside them with a stable structure. This result will be useful for the design of peptide carriers.

Current research trends of nanomedicines

Owing to the inherent shortcomings of traditional therapeutic drugs in terms of inadequate therapeutic efficacy and toxicity in clinical treatment, nanomedicine designs have received widespread attention with significantly improved efficacy and reduced non-target side effects. Nanomedicines hold tremendous theranostic potential for treating, monitoring, diagnosing, and controlling various diseases and are attracting an unfathomable amount of input of research resources. Against the backdrop of an exponentially growing number of publications, it is imperative to help the audience get a panorama image of the research activities in the field of nanomedicines. Herein, this review elaborates on the development trends of nanomedicines, emerging nanocarriers, in vivo fate and safety of nanomedicines, and their extensive applications. Moreover, the potential challenges and the obstacles hindering the clinical translation of nanomedicines are also discussed. The elaboration on various aspects of the research trends of nanomedicines may help enlighten the readers and set the route for future endeavors.

Serum albumin mitigated perfluorooctane sulfonate-induced cytotoxicity by affecting the cellular responses

During the wide applications of perfluorinated materials such as perfluorooctane sulfonate (PFOS) in commercial and industrial products, the potential toxicity of these engineered compounds has attracted more and more attention. As a typical environmental pollutant, PFOS could preferentially bind to albumin protein in vivo. However, the role of protein-PFOS interactions in the cytotoxicity of PFOS was not stressed enough. Herein, we investigated the interactions of PFOS with human serum albumin (HSA, the most abundant protein in human plasma) using both experimental and theoretical approaches. It was demonstrated that PFOS could mainly bind to the Sudlow site I of HSA to generate HSA-PFOS complex through hydrogen bonds and van der Waals forces. Toxicity assays with endothelial cells illustrated that the binding of HSA could significantly attenuate the intracellular uptake and subcellular distribution of PFOS, thereby inhibiting the formation of reactive oxygen species and toxicity for those HSA-bound PFOS. Similarly, the presence of fetal bovine serum in the cell culture media greatly reduced PFOS-caused cytotoxicity. Conclusively, our study reveals that the binding of albumin protein to PFOS could mitigate its toxicity by the modulation of cellular responses. The formation of protein-complexed contaminants would significantly reduce the bioavailability of these chemicals and subsequently mitigate their environmental toxicology to the human health.

Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations

The utilization of microbial cellulase enzymes for transforming plant biomass into biofuel or bioethanol, which can serve as a substitute for fossil fuel, is a subject of growing interest. Nonetheless, large-scale production of biofuel using cellulases is not economically feasible as the extraction of these enzymes from diverse microorganisms is an expensive process. To address this issue, immobilizing the enzyme to a substrate material, e.g., carbon nanotubes (CNTs), to recycle without a significant decline in its catalytic activity is a promising solution. Due to the hydrophobic nature of CNTs, we employed molecular docking and network analysis methodologies to identify potential CNT-binding sites on the outer surface of a wild-type cellulase enzyme, CelS. Classical molecular dynamics simulations of CNT-bound CelS through one of the selected binding sites resulted in negligible changes in the secondary structure of the enzyme and its catalytic domain, implying the least possible effect on the catalytic activity post-immobilization. Furthermore, our study reveals that while the unfolding near the CNT-binding region in CelS is more pronounced when the enzyme is interacting with a wider CNT, resulting in enhanced contact area and improved binding affinity, its impact on the overall CelS structure is relatively less significant when compared to thinner CNTs. Particularly, CNTs of diameter ∼12 Å can serve as a favorable option for substrate materials in cellulase immobilization. Our study also provides critical insights into the binding mechanisms between cellulase and CNTs, which could lead to the development of more efficient biocatalysts for biofuel production.

Unveiling the Effects of Carbon-Based Nanomaterials on Crop Growth: From Benefits to Detriments

To systematically assess the impact of typical CNMs on the growth effects of cereal crops, we conducted a meta-analysis of 48 independent studies worldwide. The pooled results showed that shoot weight (13.39%) and antioxidant metabolite content (SOD: 106.32%, POD: 32.29%, CAT: 22.63%) of cereal crops exposed to the presence of CNMs were significantly increased, but phytohormones secretion (17.84%) was inhibited. The results of subgroup analysis showed that there were differences in the results of different CNM types with the same exposure concentration on growth effects. Short-term exposure adversely affected the root and photosynthetic capacity of the crop, but prolonged exposure instead showed a promoting effect. Multiple linear regression analysis showed that the concentration of CNMs and cereal variety variables were significantly associated with changes in multiple growth effect values. This work could offer references and fresh perspectives for investigating how nanoparticles and crops interact.

The role of protein corona on nanodrugs for organ-targeting and its prospects of application

Nowadays, nanodrugs become a hotspot in the high-end medical field. They have the ability to deliver drugs to reach their destination more effectively due to their unique properties and flexible functionalization. However, the fate of nanodrugs in vivo is not the same as those presented in vitro, which indeed influenced their therapeutic efficacy in vivo. When entering the biological organism, nanodrugs will first come into contact with biological fluids and then be covered by some biomacromolecules, especially proteins. The proteins adsorbed on the surface of nanodrugs are known as protein corona (PC), which causes the loss of prospective organ-targeting abilities. Fortunately, the reasonable utilization of PC may determine the organ-targeting efficiency of systemically administered nanodrugs based on the diverse expression of receptors on cells in different organs. In addition, the nanodrugs for local administration targeting diverse lesion sites will also form unique PC, which plays an important role in the therapeutic effect of nanodrugs. This article introduced the formation of PC on the surface of nanodrugs and summarized the recent studies about the roles of diversified proteins adsorbed on nanodrugs and relevant protein for organ-targeting receptor through different administration pathways, which may deepen our understanding of the role that PC played on organ-targeting and improve the therapeutic efficacy of nanodrugs to promote their clinical translation.

The attenuating ability of deep eutectic solvents towards the carboxylated multiwalled carbon nanotubes induced denatured β-lactoglobulin structure

The stabilization of proteins has been a major challenge for their practical utilization in industrial applications. Proteins can easily lose their native conformation in the presence of denaturants, which unfolds the protein structure. Since the introduction of deep eutectic solvents (DESs), there are numerous studies in which DESs act as promising co-solvents that are biocompatible with biomolecules. DESs have emerged as sustainable biocatalytic media and an alternative to conventional organic solvents and ionic liquids (ILs). However, the superiority of DESs over the deleterious influence of denaturants on proteins is often neglected. To address this, we present the counteracting ability of biocompatible DESs, namely, choline chloride-glycerol (DES-1) and choline chloride-urea (DES-2), against the structural changes induced in β-lactoglobulin (Blg) by carboxylated multiwalled carbon nanotubes (CA-MWCNTs). The work is substantiated with various spectroscopic and thermal studies. The spectroscopic results revealed that the fluorescence emission intensity enhances for the protein in DESs. Contrary to this, the emission intensity extremely quenches in the presence of CA-MWCNTs. However, in the mixture of DESs and CA-MWCNTs, there was a slight increase in the fluorescence intensity. Circular dichroism spectral studies reflect the reappearance of the native band that was lost in the presence of CA-MWCNTs, which is a good indicator of the counteraction ability of DESs. Further, thermal fluorescence studies showed that the protein exhibited extremely great thermal stability in both DESs as well as in the mixture of DES-CA-MWCNTs compared to the protein in buffer. This study is also supported by dynamic light scattering and zeta potential measurements; the results reveal that DESs were successfully able to maintain the protein structure. The addition of CA-MWCNTs results in complex formation with the protein, which is indicated by the increased hydrodynamic size of the protein. The presence of DESs in the mixture of CA-MWCNTs and DESs was quite successful in eliminating the negative impact of CA-MWCNTs on protein structural alteration. DES-1 proved to be superior to DES-2 over counteraction against CA-MWCNTs and maintained the native conformation of the protein. Overall, both DESs act as recoiling media for both native and unfolded (denatured by CA-MWCNTs) Blg structures. Both the DESs can be described as potential co-solvents for Blg with increased structural and thermal stability of the protein. To the best of our knowledge, this study for the first time has demonstrated the role of choline-based DESs in the mixture with CA-MWCNTs in the structural transition of Blg. The DESs in the mixture successfully enhance the stability of the protein by reducing the perturbation caused by CA-MWCNTs and then amplifying the advantages of the DESs present in the mixture. Overall, these results might find implications for understanding the role of DES-CA-MWCNT mixtures in protein folding/unfolding and pave a new direction for the development of eco-friendly protein-protective solvents.

Binding of serum albumin to perfluorooctanoic acid reduced cytotoxicity

With the ubiquitous applications of perfluorinated compounds such as perfluorooctanoic acid (PFOA) in industrial and commercial products, the toxicity of these engineered materials in environmental and public health is received growing attention. As a typical organic pollutant, PFOA has been extensively found in wildlife and human bodies, and can preferentially bind to serum albumin in vivo. However, the importance of protein-PFOA interactions on the cytotoxicity of PFOA could not be stressed enough. In this study, we used both experimental and theoretical approaches, to investigate the interactions of PFOA with bovine serum albumin (BSA, the most abundant protein in blood). It was found that PFOA could mainly interact with Sudlow site I of BSA to form BSA-PFOA complex, in which van der Waals forces and hydrogen bonds played dominant roles. Moreover, the strong binding of BSA could greatly alter the cellular uptake and distribution of PFOA in human endothelial cells, and result in the decreases of reactive oxygen species formation and cytotoxicity for these BSA-coated PFOA. Consistently, the addition of fetal bovine serum into cell culture medium also significantly mitigated PFOA-induced cytotoxicity, which was attributed to the extracellular complexation between PFOA and serum proteins. Altogether, our study demonstrates that the binding of serum albumin to PFOA could reduce its toxicity by affecting the cellular responses.

Enzyme immobilization studied through molecular dynamic simulations

In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.

Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation

Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.

Nitrobenzene reduction promoted by the integration of carbon nanotubes and Geobacter sulfurreducens

Electron shuttles (ES) can mediate long-distance electron transfer between extracellular respiratory bacteria (ERB) and the surroundings. However, the effects of graphite structure in ES on the extracellular electron transfer (EET) process remain ambiguous. This work investigated the function of graphite structure in the process of nitrobenzene (NB) degradation by Geobacter sulfurreducens PCA, in which highly aromatic carbon nanotubes (CNTs) was studied as a typical ES. The results showed that the addition of 1.5 g L^-1 of CNTs improved the NB biodegradation up to 81.2%, plus 18.8% NB loss due to the adsorption property of CNTs, achieving complete removal of 200 μM NB within 9 h. The amendment of CNTs greatly increased the EET rate, indicating that graphite structure exhibited excellent electron shuttle performance. Furthermore, Raman spectrum proved that CNTs obtained better graphite structure after 90 h of cultivation with strain PCA, resulting in higher electrochemical performance. Also, CNTs was perceived as the "Contaminant Reservoir", which alleviated the toxic effect of NB and shortened the distance of EET process. Overall, this work focused on the effects of material graphite structure on the EET process, which enriched the understanding of the interaction between CNTs and ERB, and these results might promote their application in the in-situ bioremediation of nitroaromatic-polluted environment.

Carbon nanotube recognition by human Siglec-14 provokes inflammation

For the design and development of innovative carbon nanotube (CNT)-based tools and applications, an understanding of the molecular interactions between CNTs and biological systems is essential. In this study, a three-dimensional protein-structure-based in silico screen identified the paired immune receptors, sialic acid immunoglobulin-like binding lectin-5 (Siglec-5) and Siglec-14, as CNT-recognizing receptors. Molecular dynamics simulations showed the spatiotemporally stable association of aromatic residues on the extracellular loop of Siglec-5 with CNTs. Siglec-14 mediated spleen tyrosine kinase (Syk)-dependent phagocytosis of multiwalled CNTs and the subsequent secretion of interleukin-1β from human monocytes. Ectopic in vivo expression of human Siglec-14 on mouse alveolar macrophages resulted in enhanced recognition of multiwalled CNTs and exacerbated pulmonary inflammation. Furthermore, fostamatinib, a Syk inhibitor, blocked Siglec-14-mediated proinflammatory responses. These results indicate that Siglec-14 is a human activating receptor recognizing CNTs and that blockade of Siglec-14 and the Syk pathway may overcome CNT-induced inflammation.

Surface engineering of colloidal nanoparticles

Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications. Surface engineering of colloidal NPs can improve their stability in diverse solvents by inhibiting the interparticle attractive forces, thus providing a prerequisite for further particle manipulation, fabrication of the following materials and biological applications. During the last decades, surface engineering methods for colloidal NPs have been well-developed by numerous researchers. However, accurate control of surface properties is still an important topic. The emerging DNA/protein nanotechnology offers additional possibility of surface modification of NPs and programmable particle self-assembly. Here, we first briefly review the recent progress in surface engineering of colloidal NPs, focusing on the improved stability by grafting suitable small molecules, polymers or biological macromolecules. We then present the practical strategies for nucleic acid surface encoding of NPs and subsequent programmable assembly. Various exciting applications of these unique materials are summarized with a specific focus on the cellular uptake, bio-toxicity, imaging and diagnosis of colloidal NPs in vivo. With the growing interest in colloidal NPs in nano-biological research, we expect that this review can play an instructive role in engineering the surface properties for desired applications.

Nanomechanical Profiling of Aβ42 Oligomer-Induced Biological Changes in Single Hippocampus Neurons

Understanding how Aβ42 oligomers induce changes in neurons from a mechanobiological perspective has important implications in neuronal dysfunction relevant to neurodegenerative diseases. However, it remains challenging to profile the mechanical responses of neurons and correlate the mechanical signatures to the biological properties of neurons given the structural complexity of cells. Here, we quantitatively investigate the nanomechanical properties of primary hippocampus neurons upon exposure to Aβ42 oligomers at the single neuron level by using atomic force microscopy (AFM). We develop a method termed heterogeneity-load-unload nanomechanics (HLUN), which exploits the AFM force spectra in the whole loading-unloading cycle, allowing comprehensive profiling of the mechanical properties of living neurons. We extract four key nanomechanical parameters, including the apparent Young's modulus, cell spring constant, normalized hysteresis, and adhesion work, that serve as the nanomechanical signatures of neurons treated with Aβ42 oligomers. These parameters are well-correlated with neuronal height increase, cortical actin filament strengthening, and calcium concentration elevation. Thus, we establish an HLUN method-based AFM nanomechanical analysis tool for single neuron study and build an effective correlation between the nanomechanical profile of the single neurons and the biological effects triggered by Aβ42 oligomers. Our finding provides useful information on the dysfunction of neurons from the mechanobiological perspective.

Application of Computing as a High-Practicability and -Efficiency Auxiliary Tool in Nanodrugs Discovery

Research and development (R&D) of nanodrugs is a long, complex and uncertain process. Since the 1960s, computing has been used as an auxiliary tool in the field of drug discovery. Many cases have proven the practicability and efficiency of computing in drug discovery. Over the past decade, computing, especially model prediction and molecular simulation, has been gradually applied to nanodrug R&D, providing substantive solutions to many problems. Computing has made important contributions to promoting data-driven decision-making and reducing failure rates and time costs in discovery and development of nanodrugs. However, there are still a few articles to examine, and it is necessary to summarize the development of the research direction. In the review, we summarize application of computing in various stages of nanodrug R&D, including physicochemical properties and biological activities prediction, pharmacokinetics analysis, toxicological assessment and other related applications. Moreover, current challenges and future perspectives of the computing methods are also discussed, with a view to help computing become a high-practicability and -efficiency auxiliary tool in nanodrugs discovery and development.

The protein corona from nanomedicine to environmental science

The protein corona spontaneously develops and evolves on the surface of nanoscale materials when they are exposed to biological environments, altering their physiochemical properties and affecting their subsequent interactions with biosystems. In this Review, we provide an overview of the current state of protein corona research in nanomedicine. We next discuss remaining challenges in the research methodology and characterization of the protein corona that slow the development of nanoparticle therapeutics and diagnostics, and we address how artificial intelligence can advance protein corona research as a complement to experimental research efforts. We then review emerging opportunities provided by the protein corona to address major issues in healthcare and environmental sciences. This Review details how mechanistic insights into nanoparticle protein corona formation can broadly address unmet clinical and environmental needs, as well as enhance the safety and efficacy of nanobiotechnology products.

Identification and Biological Evaluation of a Water-Soluble Fullerene Nanomaterial as BTK Kinase Inhibitor

Introduction

Thanks to recent advances in synthetic methodology, water-soluble fullerene nanomaterials that interfere with biomolecules, especially DNA/RNA and selected proteins, have been found with tremendous potential for applications in nanomedicine. Herein, we describe the synthesis and evaluation of a water-soluble glycine-derived [60]fullerene hexakisadduct (HDGF) with T _h symmetry, which is a first-in-class BTK protein inhibitor.

Methods

We synthesized and characterized glycine derived [60]fullerene using NMR, ESI-MS, and ATR-FT-IR. DLS and zeta potential were measured and high-resolution transmission electron microscopy (HRTEM) observations were performed. The chemical composition of the water-soluble fullerene nanomaterial was examined by X-ray photoelectron spectrometry. To observe aggregate formation, the cryo-TEM analysis was carried out. The docking studies and molecular dynamic simulations were performed to determine interactions between HDGF and BTK. The in vitro cytotoxicity was evaluated on RAJI and K562 blood cancer cell lines. Subsequently, we examined the induction of cell death by autophagy and apoptosis by determining the expression levels of crucial genes and caspases. We investigated the direct association of HDGF on inhibition of the BTK signalling pathway by examining changes in the calcium levels in RAJI cells after treatment. The inhibitory potential of HDGF against non-receptor tyrosine kinases was evaluated. Finally, we assessed the effects of HDGF and ibrutinib on the expression of the BTK protein and downstream signal transduction in RAJI cells following anti-IgM stimulation.

Results

Computational studies revealed that the inhibitory activity of the obtained [60]fullerene derivative is multifaceted: it hampers the BTK active site, interacting directly with the catalytic residues, rendering it inaccessible to phosphorylation, and binds to residues that form the ATP binding pocket. The anticancer activity of produced carbon nanomaterial revealed that it inhibited the BTK protein and its downstream pathways, including PLC and Akt proteins, at the cellular level. The mechanistic studies suggested the formation of autophagosomes (increased gene expression of LC3 and p62) and two caspases (caspase-3 and -9) were responsible for the activation and progression of apoptosis.

Conclusion

These data illustrate the potential of fullerene-based BTK protein inhibitors as nanotherapeutics for blood cancer and provide helpful information to support the future development of fullerene nanomaterials as a novel class of enzyme inhibitors.

Covalent conjugation of proteins onto fluorescent single-walled carbon nanotubes for biological and medical applications

Single-walled carbon nanotubes (SWCNTs) have optical properties that are conducive for biological applications such as sensing, delivery, and imaging. These applications necessitate the immobilization of macromolecules that can serve as therapeutic drugs, molecular templates, or modulators of surface interactions. Although previous studies have focused on non-covalent immobilization strategies, recent advances have introduced covalent functional handles that can preserve or even enhance the SWCNT optical properties. This review presents an overview of covalent sidewall modifications of SWCNTs, with a focus on the latest generation of "sp³ defect" modifications. We summarize and compare the reaction conditions and the reported products of these sp³ chemistries. We further review the underlying photophysics governing SWCNT fluorescence and apply these principles to the fluorescence emitted from these covalently modified SWCNTs. Finally, we provide an outlook on additional chemistries that could be applied to covalently conjugate proteins to these chemically modified, fluorescent SWCNTs. We review the advantages of these approaches, emerging opportunities for further improvement, as well as their implications for enabling new technologies.

In vitro-in vivo correlation in nanocarriers: From protein corona to therapeutic implications

Understanding and establishing a link between the physicochemical characteristics of nanoparticles (NPs) and their biological interactions poses to be a great challenge in the field of nanotherapeutics. Recent analytical advancements concerning bio-nanointerfaces have accelerated the quest to comprehend the fate of nanocarrier systems in vivo. Scientists have discovered that protein corona, an adsorbed layer of biomolecules on the surface of NPs takes a leading part in interacting with cells and in the cellular uptake process, thereby determining the in vivo behaviour of NPs. Another useful method to assess the in vivo fate of NPs is by performing dissolution testing. This forms the basis for in vitro in vivo correlation (IVIVC), relating in vitro dissolution of NPs and their in vivo properties. Scientists are continuously directing their efforts towards establishing IVIVC for different nanocarrier systems while concurrently gaining insights into protein corona. This review primarily summarizes the importance of protein corona and its interaction with nanoparticles. It also gives an insight into the factors affecting the interaction and various in vitro dissolution media used for varied nanocarrier systems. The article concludes with a discussion of the limitations of IVIVC modelling and its position from a regulatory perspective.

The Effect of PEGylated Graphene Oxide Nanoparticles on the Th17-Polarization of Activated T Helpers

We investigated the direct effect of PEGylated graphene oxide (P-GO) nanoparticles on the differentiation, viability, and cytokine profile of activated T helper type 17 (Th17) in vitro. The subject of the study were cultures of "naive" T-helpers (CD4+) isolated by immunomagnetic separation and polarized into the Th17 phenotype with a TCR activator and cytokines. It was found that P-GO at low concentrations (5 µg/mL) had no effect on the parameters studied. The presence of high concentrations of P-GO in T-helper cultures (25 μg/mL) did not affect the number and viability of these cells. However, the percentage of proliferating T-helpers in these cultures was reduced. GO nanoparticles modified with linear polyethylene glycol (PEG) significantly increased the percentage of Th17/22 cells in cultures of Th17-polarized T helpers and the production of IFN-γ, whereas those modified with branched PEG suppressed the synthesis of IL-17. Thus, a low concentration of PEGylated GO nanoparticles (5 μg/mL), in contrast to a concentration of 25 μg/mL, has no effect on the Th17-polarization of T helpers, allowing their further use for in-depth studies of the functions of T lymphocytes and other immune cells. Overall, we have studied for the first time the direct effect of P-GO nanoparticles on the conversion of T helper cells to the Th17 phenotype.

Computational Investigation of Chirality-Based Separation of Carbon Nanotubes Using Tripeptide Library

Carbon nanotubes (CNT) have fascinating applications in flexible electronics, biosensors, and energy storage devices, and are classified as metallic or semiconducting based on their chirality. Semiconducting CNTs have been teased as a new material for building blocks in electronic devices, owing to their band gap resembling silicon. However, CNTs must be sorted into metallic and semiconducting for such applications. Formerly, gel chromatography, ultracentrifugation, size exclusion chromatography, and phage display libraries were utilized for sorting CNTs. Nevertheless, these techniques are either expensive or have poor efficiency. In this study, we utilize a novel technique of using a library of nine tripeptides with glycine as a central residue to study the effect of flanking residues for large-scale separation of CNTs. Through molecular dynamics, we found that the tripeptide combinations with threonine as one of the flanking residues have a high affinity for metallic CNTs, whereas those with flanking residues having uncharged and negatively charged polar groups show selectivity towards semiconducting CNTs. Furthermore, the role of interfacial water molecules and the ability of the tripeptides to form hydrogen bonds play a crucial role in sorting the CNTs. It is envisaged that CNTs can be sorted based on their chirality-selective interaction affinity to tripeptides.