Nanoparticles In Biological Environments Research Articles

The role of protein corona in advancing plasma proteomics.

The protein corona, a layer of biomolecules forming around nanoparticles in biological environments, critically influences nanoparticle interactions with biosystems, affecting pharmacokinetics and biological outcomes. Initially, the protein corona presented challenges for nanomedicine and nanotoxicology, such as nutrient depletion in cell cultures and masking of nanoparticle-targeting species. However, recent advancements have highlighted its potential in environmental toxicity, proteomics, and immunology. This viewpoint focuses on leveraging the protein corona to enhance the depth of plasma proteome analysis, addressing challenges posed by the high dynamic range of protein concentrations in plasma. The protein corona simplifies sample preparation, enriches low-abundance proteins, and improves proteome coverage. Innovations include using diverse nanoparticles and spiking small molecules to increase the number of quantified proteins. Reproducibility issues across core facilities necessitate standardized protocols. Moreover, top-down proteomics enables proteoform-specific measurements, providing deeper insights into protein corona composition. Future research should aim at improving top-down proteomics techniques and integrating protein corona studies and proteomics for personalized medicine and advanced diagnostics.

Biodegradation of Oxide Nanoparticles in Apoferritin Protein Media: A Systematic Electrochemical Approach

AbstractFunctional oxide nanoparticles are extensively utilized in the last decades for biomedical purposes due to their unique functional properties. Nevertheless, their biodegradation mechanism by biological species, particularly by proteins at oxide/protein interfaces, still remains limited. Here, a systematic approaches is provided to investigate electrochemical behavior, electronic properties, and biodegradation mechanism of cobalt ferrite (CFO) and cobalt ferrite‐bismuth ferrite (CFO‐BFO) core‐shell nanoparticles in apoferritin‐containing media. Scanning Kelvin probe force microscopy results indicate that the presence of a thin shell (≈5 nm) of BFO on CFO causes a significant increase in surface potential. The potentiodynamic polarization measurements in different solutions showed higher anodic current densities for both samples when decreasing pH and increasing apoferritin concentration. Notably, CFO‐BFO exhibits lower anodic current densities than CFO due to a slightly higher flat band potential and lower donor density distribution on CFO‐BFO than on CFO, which results in lower electrochemical activity. Long‐term monitoring reveals that biodegradation of both nanoparticles is accelerated by high apoferritin concentrations and acidic media, resulting in the decrease of electrochemical potentials and impedance values, and enhancement of metal ion release. Thus, this systematic biodegradation study can help to predict the lifespan and toxicity of these functional nanoparticles in biological environments.

Evidence-Based Prediction of Cellular Toxicity for Amorphous Silica Nanoparticles.

Developing a generalized model for a robust prediction of nanotoxicity is critical for designing safe nanoparticles. However, complex toxicity mechanisms of nanoparticles in biological environments, such as biomolecular corona formation, prevent a reliable nanotoxicity prediction. This is exacerbated by the potential evaluation bias caused by internal validation, which is not fully appreciated. Herein, we propose an evidence-based prediction method for distinguishing between cytotoxic and noncytotoxic nanoparticles at a given condition by uniting literature data mining and machine learning. We illustrate the proposed method for amorphous silica nanoparticles (SiO2-NPs). SiO2-NPs are currently considered a safety concern; however, they are still widely produced and used in various consumer products. We generated the most diverse attributes of SiO2-NP cellular toxicity to date, using >100 publications, and built predictive models, with algorithms ranging from linear to nonlinear (deep neural network, kernel, and tree-based) classifiers. These models were validated using internal (4124-sample) and external (905-sample) data sets. The resultant categorical boosting (CatBoost) model outperformed other algorithms. We then identified 13 key attributes, including concentration, serum, cell, size, time, surface, and assay type, which can explain SiO2-NP toxicity, using the Shapley Additive exPlanation values in the CatBoost model. The serum attribute underscores the importance of nanoparticle-corona complexes for nanotoxicity prediction. We further show that internal validation does not guarantee generalizability. In general, safe SiO2-NPs can be obtained by modifying their surfaces and using low concentrations. Our work provides a strategy for predicting and explaining the toxicity of any type of engineered nanoparticles in real-world practice.

Dual-Labelled Nanoparticles Inform on the Stability of Fluorescent Labels In Vivo.

Fluorescent labelling is commonly used to monitor the biodistribution of nanomedicines. However, meaningful interpretation of the results requires that the fluorescent label remains attached to the nanomedicine. In this work, we explore the stability of three fluorophores (BODIPY650, Cyanine 5 and AZ647) attached to polymeric hydrophobic biodegradable anchors. Using dual-labelled poly(ethylene glycol)-b-poly(lactic acid) (PEG-PLA) nanoparticles that are both radioactive and fluorescent, we investigated how the properties of the fluorophores impact the stability of the labelling in vitro and in vivo. Results suggest that the more hydrophilic dye (AZ647) is released faster from nanoparticles, and that this instability results in misinterpretation of in vivo data. While hydrophobic dyes are likely more suitable to track nanoparticles in biological environments, quenching of the fluorescence inside the nanoparticles can also introduce artefacts. Altogether, this work raises awareness about the importance of stable labelling methods when investigating the biological fate of nanomedicines.

Biomolecular engineering of drugs loading in Riboflavin-targeted polymeric devices: simulation and experimental

The synthesis of polymeric nanoparticles (NPs) with efficient drug loading content and targeting moieties is an attractive field and remains a challenge in drug delivery systems. Atomistic investigations can provide an in-depth understanding of delivery devices and reduce the number of expensive experiments. In this paper, we studied the self-assembly of poly (lactic-co-glycolic acid)-b-poly (ethylene glycol) with different molecular weights and surface compositions. The innovation of this molecular study is the loading of an antitumor drug (docetaxel) on a targeting ligand (riboflavin). According to this work, a novel, biocompatible and targeted system for cancer treatment has been developed. The obtained results revealed a correlation between polymer molecular weight and the stability of particles. In this line, samples including 20 and 10 w/w% moiety NPs formed from polymers with 3 and 4.5 kDa backbone sizes, respectively, are the stable models with the highest drug loading and entrapment efficiencies. Next, we evaluated NP morphology and found that NPs have a core/shell structure consisting of a hydrophobic core with a shell of poly (ethylene glycol) and riboflavin. Interestingly, morphology assessments confirmed that the targeting moiety located on the surface can improve drug delivery to receptors and cancerous cells. The developed models provided significant insight into the structure and morphology of NPs before the synthesis and further analysis of NPs in biological environments. However, in the best cases of this system, Dynamic Light Scattering (DLS) tests were also taken and the results were consistent with the results obtained from All Atom and Coarse Grained simulations.

Predicting the Physicochemical Properties and Biological Activities of Monolayer-Protected Gold Nanoparticles Using Simulation-Derived Descriptors.

Gold nanoparticles are versatile materials for biological applications because their properties can be modulated by assembling ligands on their surface to form monolayers. However, the physicochemical properties and behaviors of monolayer-protected nanoparticles in biological environments are difficult to anticipate because they emerge from the interplay of ligand-ligand and ligand-solvent interactions that cannot be readily inferred from ligand chemical structure alone. In this work, we demonstrate that quantitative nanostructure-activity relationship (QNAR) models can employ descriptors calculated from molecular dynamics simulations to predict nanoparticle properties and cellular uptake. We performed atomistic molecular dynamics simulations of 154 monolayer-protected gold nanoparticles and calculated a small library of simulation-derived descriptors that capture nanoparticle structural and chemical properties in aqueous solution. We then parametrized QNAR models using interpretable regression algorithms to predict experimental measurements of nanoparticle octanol-water partition coefficients, zeta potentials, and cellular uptake obtained from a curated database. These models reveal that simulation-derived descriptors can accurately predict experimental trends and provide physical insight into what descriptors are most important for obtaining desired nanoparticle properties or behaviors in biological environments. Finally, we demonstrate model generalizability by predicting cell uptake trends for 12 nanoparticles not included in the original data set. These results demonstrate that QNAR models parametrized with simulation-derived descriptors are accurate, generalizable computational tools that could be used to guide the design of monolayer-protected gold nanoparticles for biological applications without laborious trial-and-error experimentation.

Inside Cover: Implications of Quenching‐to‐Dequenching Switch in Quantitative Cell Uptake and Biodistribution of Dye‐Labeled Nanoparticles (Angew. Chem. Int. Ed. 28/2021)

A quenching-to-dequenching switch of fluorescence-labeled nanoparticles in biological environments is unveiled by Chun-Xia Zhao and co-workers in their Research Article on page 15426. With dye molecules in a solid state, the release and/or degradation of the dye-labeled nanoparticles in biological environments led to a several-fold increase in fluorescence intensity due to the state switch, which has significant implications in quantitative cell uptake and biodistribution studies.

Facile construction of beads-on-a-string complexes of polymeric micelles and DNA via tunable electrostatic interactions

Inspired by the structure of chromatin fibers, the compaction of DNA by cationic nanoparticles has received much attention in the fields of nanomaterials and biotechnology. However, the fabrication of artificial chromatin-biomimetic assemblies of DNA and nanoparticles in biological environments is still a challenge due to their dependence on uncontrollable electrostatic interactions. Herein, block and random copolymerization of 2-(diisopropylamino)ethyl methacrylate (DPA) and 2-(dimethylamino)ethyl methacrylate (DMA) were used to regulate the charge density and distribution of cationic polyethylene glycol-b-poly(tertiary amine methacrylate) micelles, adjusting the electrostatic interaction between the micelles and DNA. We showed that the assembled PEG-b-PDMA-b-PDPA micelle/DNA system exhibited a strong electrostatic interactions between the micelles and DNA, causing uncontrollable intrachain flocculation. However, the assembled PEG-b-P(DMA-r-DPA) micelle/DNA system showed relatively week, tunable electrostatic interactions, leading to an open -chromatin-like structure

Multiscale simulations of the hydration shells surrounding spherical Fe3O4 nanoparticles and effect on magnetic properties.

Iron oxide magnetic nanoparticles (NPs) are excellent systems in catalysis and in nanomedicine, where they are mostly immersed in aqueous media. Even though the NP solvation by water is expected to play an active role, the detailed structural insight at the nanostructure oxide/water interface is still missing. Here, based on our previous efforts to obtain accurate models of dehydrated Fe3O4 NPs and of their magnetic properties and through multiscale molecular dynamics simulations combining the density functional tight binding method and force field, we unravel the atomistic details of the short range (chemical) and long range (physical) interfacial effects when magnetite nanoparticles are immersed in water. The influence of the first hydration shell on the structural, electronic and magnetic properties of Fe3O4 NPs is revealed by high-level hybrid density functional calculations. Hydrated Fe3O4 NPs possess larger magnetic moment than dehydrated ones. This work bridges the large gap between experimental studies on solvated Fe3O4 NPs and theoretical investigations on flat Fe3O4 surfaces covered with water and paves the way for further study of Fe3O4 NPs in biological environments.

Toward Diffusion Measurements of Colloidal Nanoparticles in Biological Environments by Nuclear Magnetic Resonance.

Protein corona formation on the surface of nanoparticles (NPs) is observed in situ by measuring diffusion coefficients of the NPs under the presence of proteins with a 19 F nuclear magnetic resonance (NMR) based methodology. Formation of a protein corona reduces the diffusion coefficient of the NPs, based on an increase in their effective hydrodynamic radii. With this methodology it is demonstrated that the apparent dissociation constant of protein-NP complexes may vary over at least nine orders of magnitude for different types of proteins, in line with the Vroman effect. Using this methodology, the interaction between one type of protein and one type of nanoparticle can be studied quantitatively. Due to the NMR-based detection, this methodology has no interference by absorption/scattering effects, by which optical detection schemes are affected. By using the potential of the NMR chemical shift, the detection of multiple 19 F signals simultaneously opens the possibility to study the diffusion of several NPs at the same time. The 19 F labeling of the NPs has negligible effect on their acute toxicity and moderate effect on NPs uptake by cells.

Eu-Doped Citrate-Coated Carbonated Apatite Luminescent Nanoprobes for Drug Delivery.

In the field of Nanomedicine, there is an increasing demand for new inorganic nanophosphors with low cytotoxicity and efficient loading-release ability of drugs for applications in bioimaging and drug delivery. This work assesses the potentiality of matured Eu-doped citrate-coated carbonated apatite nanoparticles to be used as theranostic platforms, for bioimaging, as luminescent nanoprobes, and for drug delivery applications, using Doxorubicin as a model drug. The drug adsorption isotherm fits the Langmuir–Freundlich (LF) model, showing that the Eu:cit-cAp nanoparticles can carry a maximum of 0.29 ± 0.02 mg Doxo mg Eu:cit-cAp−1 (Qmax). The affinity constant KFL for this binding is 44 ± 2 mL mg−1, and the cooperativity coefficient r is 6 ± 1. The nanoparticle suspensions presented charge reversion from negative to positive after loading with Doxo as revealed by the ζ-potential versus pH characterization. The release of drug from the loaded nanoparticles was found to be strongly pH-dependent, being around 5 wt % at physiological pH 7.4 and 20 wt % at pH 5, in experiments lasting 24 h. Luminescence spectroscopic measurements of Doxo-loaded nanoparticles revealed the increase of luminescence with a decrease in the amount of adsorbed Doxo, due to the so-called inner filter effect. The nanoparticles free of Doxo were cytocompatible when interacted with two human cell lines derived respectively from a gastric carcinoma (GTL-16), and a hepatocarcinoma (Huh7), while Doxo-loaded nanoparticles displayed significant toxicity in a dose-dependent relationship. Therefore, the new nanoassemblies might have a dual function, as nanoprobes in bioimaging by detecting the fate of the nanoparticles in biological environments, and for monitoring the delivery of the drug in such environments, by measuring the rise of the luminescence provided by the desorption of Doxo.

Synthesis of bismuth nanoparticles for biomedical applications

Bismuth is a biocompatible material that can be employed in the form of nanoparticles to be used as a possible alternative contrast medium for diagnostics. In particular, it has been prepared as spherical nanoparticles in liquid solution by using the technique of the pulsed laser ablation in water. The high atomic number Bi nanoparticles in the solution show surface plasmon resonance effects, high mass absorption coefficient for soft X-ray interaction and high electron and nuclear stopping powers for electrons and ion beams. This biocompatible solution can be injected into living systems, such as mice, in order to study the up-take effect in different organs with a high contrast spatial localization of the X-ray images in the tissues in which the nanoparticles are confined. The high contrast medium for high-resolution imaging in biological systems can be also used as targeting for successive exposure to ionizing radiation during radiotherapy or hyperthermia of diseased cells. The obtained results demonstrate high contrast images of Bi nanoparticles in biological environment by using the X-ray fluorescence in the electron microscopy and the X-ray absorption in mice.

Assembly and Degradation of Inorganic Nanoparticles in Biological Environments.

In solution, nanoparticles may be conceptually compartmentalized into cores and engineered surface coatings. Recent advances allow for simple and accurate characterization of nanoparticle cores and surface shells. After introduction into a complex biological environment, adsorption of biological molecules to the nanoparticle surface as well as a loss of original surface components occur. Thus, colloidal nanoparticles in the context of the biological environment are hybrid materials with complex structure, which may result in different chemical, physical, and biological outcomes as compared to the original engineered nanoparticles. In this review, we will discuss building up an engineered inorganic nanoparticle from its inside core to its outside surface and following its degradation in a biological environment from its outside to its inside. This will involve the way to synthesize selected inorganic nanoparticles. Then, we will discuss the environmental changes upon exposure of these nanoparticles to biological media and their uptake by cells. Next, the intracellular fate of nanoparticles and their degradation will be discussed. Based on these examples, the need to see nanoparticles in the context of the biological environment as dynamic hybrid materials will be highlighted.

Tunable photocycle kinetics of a hybrid bacteriorhodopsin/quantum dot system

The inclusion of inorganic nanoparticles in biological environments has led to the creation of hybrid nanosystems that are employed in a variety of applications. One such system includes quantum dots (QDs) coupled with the photoactive protein, bacteriorhodopsin (BR), which has been explored in developing enhanced photovoltaic devices. In this work, we have discovered that the kinetics of the BR photocycle can be manipulated using CdSe/CdS (core/shell) QDs. The photocycle lifetime of protein samples with varying QD amounts were monitored using time-resolved absorption spectroscopy. Concentration-dependent elongations of the bR and M state lifetimes were observed in the kinetic traces, thus suggesting that excitonic coupling occurs between BR and QDs. We propose that the pairing of BR with QDs has the potential to be utilized in protein-based computing applications, specifically for real-time holographic processors, which depend on the temporal dynamics of the bR and M photointermediates.

Stability and Mobility of Magnetic Nanoparticles in Biological Environments Determined from Dynamic Magnetic Susceptibility Measurements.

Low tumor accumulation following systemic delivery remains a key challenge for advancing many cancer nanomedicines. One obstacle in engineering nanoparticles for high tumor accumulation is a lack of techniques to monitor their stability and mobility in situ. One way to monitor the stability and mobility of magnetic nanoparticles biological fluids in situ is through dynamic magnetic susceptibility measurements (DMS), which under certain conditions provide a measure of the particle's rotational diffusivity. For magnetic nanoparticles modified to have commonly used biomedical surface coatings, we describe a systematic comparison of DMS measurements in wholeblood and tumor tissue explants. DMS measurements clearly demonstrated that stability and mobility changed over time and from one medium to another for each different coating. It was found that nanoparticles coated with covalently grafted, dense layers of PEG were the only ones to show good stability and mobility in all settings tested. These studies illustrate the utility of DMS measurements to estimate the stability and mobility of nanoparticles in situ,andwhich can provide insights that lead to engineering better nanoparticles for in vivo use.

The interplay of nanointerface curvature and calcium binding in weak polyelectrolyte-coated nanoparticles.

When engineering nanomaterials for application in biological systems, it is important to understand how multivalent ions, such as calcium, affect the structural and chemical properties of polymer-modified nanoconstructs. In this work, a recently developed molecular theory was employed to study the effect of surface curvature on the calcium-induced collapse of end-tethered weak polyelectrolytes. In particular, we focused on cylindrical and spherical nanoparticles coated with poly(acrylic acid) in the presence of different amounts of Ca2+ ions. We describe the structural changes that grafted polyelectrolytes undergo as a function of calcium concentration, surface curvature, and morphology. The polymer layers collapse in aqueous solutions that contain sufficient amounts of Ca2+ ions. This collapse, due to the formation of calcium bridges, is not only controlled by the calcium ion concentration but also strongly influenced by the curvature of the tethering surface. The transition from a swollen to a collapsed layer as a function of calcium concentration broadens and shifts to lower amounts of calcium ions as a function of the radius of cylindrical and spherical nanoparticles. The results show how the interplay between calcium binding and surface curvature governs the structural and functional properties of the polymer molecules. This would directly impact the fate of weak polyelectrolyte-coated nanoparticles in biological environments, in which calcium levels are tightly regulated. Understanding such interplay would also contribute to the rational design and optimization of smart interfaces with applications in, e.g., salt-sensitive and ion-responsive materials and devices.

How protein coronas determine the fate of engineered nanoparticles in biological environment.

Nanomedicine is a booming medical field that utilises nanoparticles (NPs) for the development of medicines, medical devices, and diagnostic tools. The behaviour of NPs in vivo may be quite complex due to their interactions with biological molecules. These interactions in biological fluids result in NPs being enveloped by dynamic protein coronas, which serve as an interface between NPs and their environment (blood, cell, tissue). How will the corona interact with this environment will depend on the biological, chemical, and physical properties of NPs, the properties of the proteins that make the corona, as well as the biological environment. This review summarises the main characteristics of protein corona and describes its dynamic nature. It also presents the most common analytical methods to study the corona, including examples of protein corona composition for the most common NPs used in biomedicine. This knowledge is necessary to design NPs that will create a corona with a desired efficiency and safety in clinical use.

Detection of Cancer-Specific Proteases Using Magnetic Relaxation of Peptide-Conjugated Nanoparticles in Biological Environment.

Protease expression is closely linked to malignant phenotypes of different solid tumors; as such, their detection is promising for diagnosis and treatment of cancers, Alzheimer's, and vascular diseases. Here, we describe a new method for detecting proteases by sensitively monitoring the magnetic relaxation of monodisperse iron oxide nanoparticles (IONPs) using magnetic particle spectrometer (MPS). In this assay, tailored peptides functioning as activatable nanosensors link magnetic nanoparticles and possess selective sites that are recognizeable and cleaveable by specific proteases. When these linker peptides, labeled with biotin at N- and C-terminals, are added to the neutravidin functionalized IONPs, nanoparticles aggregate, resulting in well-defined changes in the MPS signal. However, as designed, in the presence of proteases these peptides are cleaved at predetermined sites, redispersing IONPs, and returning the MPS signal(s) close to its preaggregation state. These changes observed in all aspects of the MPS signal (peak intensity, its position as a function of field amplitude, and full width at half-maximum-when combined, these three also eliminate false positives), help to detect specific proteases, relying only on the magnetic relaxation characteristics of the functionalized nanoparticles. We demonstrate the general utility of this assay by detecting one each from the two general classes of proteases: trypsin (digestive serine protease, involved in various cancers, promoting proliferation, invasion, and metastasis) and matrix metalloproteinase (MMP-2, observed through metastasis and tumor angiogenesis). This MPS based protease-assay is rapid, reproducible, and highly sensitive and can form the basis of a feasible, high-throughput method for detection of various other proteases.

Visualization, quantification and coordination of Ag+ ions released from silver nanoparticles in hepatocytes.

Silver nanoparticles (AgNPs) can enter eukaryotic cells and exert toxic effects, most probably as a consequence of the release of Ag+ ions. Due to the elusive nature of Ag+ ionic species, quantitative information concerning AgNP intracellular dissolution is missing. By using a synchrotron nanoprobe, silver is visualized and quantified in hepatocytes (HepG2) exposed to AgNPs; the synergistic use of electron microscopy allows for the discrimination between nanoparticular and ionic forms of silver within a single cell. AgNPs are located in endocytosis vesicles, while the visualized Ag+ ions diffuse in the cell. The averaged NP dissolution rates, measured by X-ray absorption spectroscopy, highlight the faster dissolution of citrate-coated AgNPs with respect to the less toxic PVP-coated AgNPs; these results are confirmed at the single-cell level. The released Ag+ ions recombine with thiol-bearing biomolecules: the Ag-S distances measured in cellulo, and the quantitative evaluation of gene expression, provide independent evidence of the involvement of glutathione and metallothioneins in Ag+ binding. The combined use of cutting-edge imaging techniques, atomic spectroscopy and molecular biology brings insight into the fate of AgNPs in hepatocytes, and more generally into the physicochemical transformations of metallic nanoparticles in biological environments and the resulting disruption of metal homeostasis.

Glycans as Biofunctional Ligands for Gold Nanorods: Stability and Targeting in Protein-Rich Media

Poly(ethylene glycol) (PEG) has become the gold standard for stabilization of plasmonic nanoparticles (NPs) in biofluids, because it prevents aggregation while minimizing unspecific interactions with proteins. Application of Au NPs in biological environments requires the use of ligands that can target selected receptors, even in the presence of protein-rich media. We demonstrate here the stabilizing effect of low-molecular-weight glycans on both spherical and rod-like plasmonic NPs under physiological conditions, as bench-marked against the well-established PEG ligands. Glycan-coated NPs are resistant to adsorption of proteins from serum-containing media and avoid phagocytosis by macrophage-like cells, but retain selectivity toward carbohydrate-binding proteins in protein-rich biological media. These results open the way toward the design of efficient therapeutic/diagnostic glycan-decorated plasmonic nanotools for specific biological applications.