Biosafety and bioapplication of nanomaterials by designing protein-nanoparticle interactions

Matrix metalloproteinase inhibitors (MMPIs) as attractive therapeutic targets: Recent progress and current challenges

Matrix metalloproteinase (MMP) plays an essential role in many physiological and pathological processes. An increase in MMP activity contributes to excessive degradation and remodeling of the extracellular matrix (ECM), which has been correlated with invasion and metastasis of tumors. Matrix metalloproteinase inhibitor (MMPI) has been developed as an attractive therapeutic target for decades, suggesting inspiring therapeutic effects in preclinical studies. However, achieving specificity remains an important challenge in the development of MMPIs, limiting their clinical application and bringing about the risk of biosafety. Nanomaterials can be used as alternative candidates for MMPI design, providing a new strategy for this problem. This report reviewed the research about MMPIs, summarized their MMPs activity regulation mechanisms, and discussed their failures in clinical trials. Furthermore, we outlined several schemes of MMPIs screening and design. Finally, we reviewed the therapeutic application prospects of MMPIs and discussed the remaining challenges and solutions, which may offer new insights for the development of MMPIs studies.

Engineered bovine serum albumin-based nanoparticles with pH-sensitivity for doxorubicin delivery and controlled release

In this work, we prepared a stimuli-responsive system for drug delivery and controlled release by engineering the bovine serum albumin (BSA). The doxorubicin (DOX)-loaded BSA nanoparticles (NPs) were conveniently prepared using desolvation method, followed by crosslinking through Schiff base bonds, leading to pH-sensitive DOX-loaded system (DOXs@BSA NPs). The resulted DOXs@BSA NPs showed high drug loading capacity (21.4%), and the particle size was about 130 nm with narrow polydispersity and high negative surface charge (-20.5 mV). The pH-sensitivity of DOXs@BSA NPs was evidenced by the size changes and charge reversal after incubation at different pH values. The DOXs@BSA NPs showed high serum stability which indicated the prolonged circulation time. The in vitro drug release experiment showed that the release of DOX was obviously accelerated by acidity because of disassembly of NPs induced by cleavage of Schiff base bonds. The drug release mechanism was thoroughly studied using a semi-empirical model, further confirming the pH played an important role in drug controlled release process. The results of cytotoxicity assay revealed that DOXs@BSA NPs exhibited much higher toxic effects for tumor cells in comparison to the free DOX control. Collectively, these results demonstrated that DOXs@BSA NPs might be potential application for drug delivery and controlled release in cancer chemotherapy. Moreover, this work also showed that preparation of stimuli-responsive drug delivery system by engineering the commercial biomaterials could be a promising method to develop multi-functional nanomedicine.

The Protein Corona Conundrum: Exploring the Advantages and Drawbacks of its Presence around Amphiphilic Nanoparticles

The success of targeted drug delivery systems still requires a detailed understanding about the biological consequences of self-developed biomolecular coronas around them, since this is the surface that interacts with living cells. Herein, we report the behavior of carbohydrate-decorated amphiphilic nanoparticles in a plasma environment with regard to the formation and biological consequences of the protein corona. Naked amphiphilic nanoparticles were produced through the self-assembly of azido-PEO₉₀₀-docosanoate molecules, and the coupling of N-acetylglucosamine via click chemistry enabled the fabrication of the corresponding bioactive glyco-nanostructures. Light scattering measurements, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, liquid chromatography-mass spectrometry, and the Pierce BCA protein assay all confirmed the presence of protein coronas around the self-assembled nanoparticles, regardless of the presence of the sugar residues, although it reduces the amount of adsorbed proteins. The protein coronas were formed mainly by human serum albumin, complement proteins, apolipoproteins, immunoglobulins, and proteins involved in the coagulation cascade (fibrinogen and prothrombin). While the presence of these protein coronas significantly reduced cellular uptake of the amphiphilic assemblies, they also notably reduced the cytotoxic and hemolytic effects that result from the contact of the nanoparticles with living cells. Accordingly, we highlight that protein coronas should not always be treated as artifacts that have to be avoided because they can also provide beneficial effects.

The Last Secret of Protein Folding: The Real Relationship Between Long-Range Interactions and Local Structures

The protein folding problem has been extensively studied for decades, and hundreds of thousands of protein structures have been solved. Yet, how proteins fold from a linear peptide chain to their unique 3D structures is not fully understood. With key clues having emerged unexpectedly from the field of nanoscience, a "Confined Lowest Energy Fragment" (CLEF) hypothesis was proposed. The CLEF hypothesis states that a protein chain can be divided into CLEFs, the semi-independent folding units, by a small number of key residues that form key long-range interactions. The native structure of a CLEF is the lowest energy state under the constraints of the key long-range interactions, but the native structure of the whole protein is not necessary the lowest energy state as Anfinsen's thermodynamic hypothesis suggested. The CLEF hypothesis proposes a unified CLEF mechanism for protein folding, basically a two-step process. In the first step, the favorable enthalpy of CLEFs for native structures quickly brings those residues for the key long-range interactions together, forming intermediates corresponding to the so-called hydrophobic collapse. In the second step, those collapsed key residues shuffle for the right combination to form the native key long-range interactions. The CLEF hypothesis provides a simple solution to all protein folding paradoxes, and proposes a "CLEF Age" or "Stone Age" for the prebiotic evolution of proteins.

Protein corona: Dr. Jekyll and Mr. Hyde of nanomedicine

Nanomedicine is an interdisciplinary field of research, comprising science, engineering, and medicine. Many are the clinical applications of nanomedicine, such as molecular imaging, medical diagnostics, targeted therapy, and image-guided surgery. Despite major advances during the past 20 years, many efforts must be done to understand the complex behavior of nanoparticles (NPs) under physiological conditions, the kinetic and thermodynamic principles, involved in the rational design of NP. Once administrated in physiological environment, NPs interact with biomolecules and they are surrounded by protein corona (PC) or biocorona. PC can trigger an immune response, affecting NPs toxicity and targeting capacity. This review aims to provide a detailed description of biocorona and of parameters that are able to control PC formation and composition. Indeed, the review provides an overview about the role of PC in the modulation of both cytotoxicity and immune response as well as in the control of targeting capacity.

DNA-nanoparticle interactions: Formation of a DNA corona and its effects on a protein corona

There has been much recent interest in the protein "corona," the nonspecific adsorption of proteins on the surface of nanoparticles used in biological applications. This research investigates an analogous DNA corona. We find that particles (200 nm and 1 μm) incubated with DNA form a DNA corona, with a higher concentration of DNA adsorbed on the surface of cationic nanoparticles. With protein present, a combined DNA and protein corona is formed although DNA in solution displaces protein from the nanoparticle surface. Displacement of protein from the nanoparticle surface is dependent on the concentration of DNA in solution and was also observed for planar surfaces. Overall, we expect this investigation of the DNA corona to be important for nanomedicine applications, as well as disease states, especially systemic lupus erythematosus, in which biological particles with bound DNA are important mediators of inflammation and thrombosis.

15 Years of Small: Research Trends in Nanosafety

In the field of nano- and microscale science and technology, Small has become one of the worldwide leading journals since its initiation 15 years ago. Among all the topics covered in Small, "nanosafety" has received growing interest over the years, which accounts for a large proportion of the total publications of Small. Herein, inspired by its coming Special Issue "Rethinking Nanosafety," a general bibliometric overview of the nanosafety studies that have been published in Small is presented. Using the data derived from the Web of Science Core Collection, the annual publication growth, most influential countries/institutions as well as the visualized collaborations between different countries and institutions based on CiteSpace software are presented. A special emphasis on the impact of the previous Special Issue from Small that is related to nanosafety research is given and the research trend from the most highly cited papers during last 15 years is analyzed. Lastly, future research directions are also proposed.

Automation and low-cost proteomics for characterization of the protein corona: experimental methods for big data

Nanoparticles used in biological settings are exposed to proteins that adsorb on the surface forming a protein corona. These adsorbed proteins dictate the subsequent cellular response. A major challenge has been predicting what proteins will adsorb on a given nanoparticle surface. Instead, each new nanoparticle and nanoparticle modification must be tested experimentally to determine what proteins adsorb on the surface. We propose that any future predictive ability will depend on large datasets of protein-nanoparticle interactions. As a first step towards this goal, we have developed an automated workflow using a liquid handling robot to form and isolate protein coronas. As this workflow depends on magnetic separation steps, we test the ability to embed magnetic nanoparticles within a protein nanoparticle. These experiments demonstrate that magnetic separation could be used for any type of nanoparticle in which a magnetic core can be embedded. Higher-throughput corona characterization will also require lower-cost approaches to proteomics. We report a comparison of fast, low-cost, and standard, slower, higher-cost liquid chromatography coupled with mass spectrometry to identify the protein corona. These methods will provide a step forward in the acquisition of the large datasets necessary to predict nanoparticle-protein interactions.

Characterization of the Specific Interactions between Nanoparticles and Proteins at Residue-Resolution by Alanine Scanning Mutagenesis

The interaction between nanoparticles and proteins is a central problem in the nano-bio-fields. However, it is still a great challenge to characterize the specific interaction between nanoparticles and proteins in structural details. Using the Goldbodies, the artificial antibodies created by grafting complementary-determining regions (CDRs) of natural antibodies onto gold nanoparticles, as the models, we manage to identify the key residues of the CDR peptides on gold nanoparticles for the specific interactions by alanine scanning mutagenesis. Each and every residue of the CDR peptides on two Goldbodies (which specifically bind with hen egg white lysozyme and epidermal growth factor receptor, respectively) is mutated to alanine one by one, generating a total of 18 single-mutants of the two Goldbodies. Experimental results reveal that the key residues of the CDR peptides for the specific interactions between the two Goldbodies and the corresponding antigens are exactly the same as those in the natural antibodies, thus proving that the correct conformations of the CDRs of natural antibodies have been successfully reconstructed on AuNPs. This is the first residue-resolution structural illustration for the specific interaction between a designed nanoparticle and a protein.

In-vitro interaction of cerium oxide nanoparticles with hemoglobin, insulin, and dsDNA at 310.15 K: Physicochemical, spectroscopic and in-silico study

Lanthanide nanoparticles and nanorods especially their biocompatible oxide forms like cerium oxide nanoparticles (CNPs) with therapeutic applications are used to cure neurological oxidative stresses. Thus it tempts to study their biocompatible aspects by interactions with several biologically significant molecules. In-Vitro interactions of 15-240 μM CNPs with water, Phosphate buffered saline (PBS), DMEM media, Insulin (Ins) hemoglobin (Hb) and ds-DNA at 37 °C were studied. Their physicochemical properties study by Borosil Mansingh Survismeter (BMS) showed the first order interaction with the protein-protein structure breaking behaviour of CNPs with Hb, Ins, and DNA. Zeta potential measurements of CNPs in different biological medium show a net increase in negative charge magnitude with good colloidal stability. K_b = 4 × 106 mM^-1 of CNPs-DNA infer noncovalent interactions. Circular dichroism and FTIR revealed a loss of secondary conformation with increasing CNPs concentration. In-silico molecular docking depicts CNP interaction via conventional hydrogen bonding, carbon hydrogen bonding and electrostatic interactions at the minor groove of DNA. The study reports in-dept unfolding functional mechanism investigated by physicochemical, spectroscopic, and In-Silico approaches of protein on interactions with CNPs for safer-by-design use in medicine and pharmaceutics. Fundamentally the CeO₂ in ~62% and Ce₂O₃ in ~38% with Ce⁴⁺ and Ce³⁺ oxidation potentials develop a unique case of electronic configurations with 4f⁰5d⁰6s⁰ and 4f¹5d⁰6s⁰ electrons respectively which these studies a novel one.

In Situ Investigation on the Protein Corona Formation of Quantum Dots by Using Fluorescence Resonance Energy Transfer

A fundamental understanding of nanoparticle-protein corona and its interactions with biological systems is essential for future application of engineered nanomaterials. In this work, fluorescence resonance energy transfer (FRET) is employed for studying the protein adsorption behavior of nanoparticles. The adsorption of human serum albumin (HSA) onto the surface of InP@ZnS quantum dots (QDs) with different chirality (d- and l-penicillamine) shows strong discernible differences in the binding behaviors including affinity and adsorption orientation that are obtained upon quantitative analysis of FRET data. Circular dichroism spectroscopy further confirms the differences in the conformational changes of HSA upon interaction with d- and l-chiral QD surfaces. Consequently, the formed protein corona on chiral surfaces may affect their following biological interactions, such as possible protein exchange with serum proteins plasma as well as cellular interactions. These results vividly illustrate the potential of the FRET method as a simple yet versatile platform for quantitatively investigating biological interactions of nanoparticles.

Mechanistic Understanding of the Biological Responses to Polymeric Nanoparticles

Polymeric nanoparticles play important roles in the delivery of a multitude of therapeutic and imaging contrast agents. Although these nanomaterials have shown tremendous potential in disease diagnosis and therapy, there have been many reports on the failure of these nanoparticles in realizing their intended objectives due to an individual or a combination of factors, which have collectively challenged the merit of nanomedicine for disease theranostics. Herein, we investigate the interactions of polymeric nanoparticles with biological entities from molecular to organism levels. Specifically, the protein corona formation, in vitro endothelial uptake, and in vivo circulation time of these nanoparticles are systematically probed. We identify the crucial role of nanocarrier lipophilicity, zeta-potential, and size in controlling the interactions between nanoparticles and biological systems and propose a two-step framework in formulating a single nanoparticle system to regulate multiple biological effects. This study provides insight into the rational design and optimization of the performance of polymeric nanoparticles to advance their theranostic and nanomedicine applications.

The interaction between nanoparticles-protein corona complex and cells and its toxic effect on cells

Once nanoparticles (NPs) contact with the biological fluids, the proteins immediately adsorb onto their surface, forming a layer called protein corona (PC), which bestows the biological identity on NPs. Importantly, the NPs-PC complex is the true identity of NPs in physiological environment. Based on the affinity and the binding and dissociation rate, PC is classified into soft protein corona, hard protein corona, and interfacial protein corona. Especially, the hard PC, a protein layer relatively stable and closer to their surface, plays particularly important role in the biological effects of the complex. However, the abundant corona proteins rarely correspond to the most abundant proteins found in biological fluids. The composition profile, formation and conformational change of PC can be affected by many factors. Here, the influence factors, not only the nature of NPs, but also surface chemistry and biological medium, are discussed. Likewise, the formed PC influences the interaction between NPs and cells, and the associated subsequent cellular uptake and cytotoxicity. The uncontrolled PC formation may induce undesirable and sometimes opposite results: increasing or inhibiting cellular uptake, hindering active targeting or contributing to passive targeting, mitigating or aggravating cytotoxicity, and stimulating or mitigating the immune response. In the present review, we discuss these aspects and hope to provide a valuable reference for controlling protein adsorption, predicting their behavior in vivo experiments and designing lower toxicity and enhanced targeting nanomedical materials for nanomedicine.

The effect of chitosan and PEG polymers on stabilization of GF-17 structure: A molecular dynamics study

We examine the interactions of chitosan and polyethylene glycol (PEG) with antimicrobial peptide GF-17 to identify a suitable carrier to improve the peptide drug delivery systems. To this end, the molecular dynamics simulations are used to determine the interactions of a typical antimicrobial peptide GF-17 with the chitosan and PEG polymers. The findings indicate the great potential of the peptide to maintain its secondary structure in the adjacent to chitosan polymers. During the interaction with chitosan polymers, the structure of the peptide has smaller fluctuations compared to the PEG polymers. Also, in the presence of both the polymers, the PEG polymers are situated closer to the peptide than chitosan polymers. Moreover, the analysis indicates that the acidic residues and phenylalanine play a crucial role in peptide-polymer interactions. This research provides a valuable insight into the design of polymer surfaces for drug delivery applications such as controlled-release peptide delivery systems.

Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications

Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.

Physicochemical interaction of cerium oxide nanoparticles with simulated biofluids, hemoglobin, insulin, and ds-DNA at 310.15 K

Interaction study in cerium oxide nanoparticles with biofluids and biomolecules via physicochemical, spectroscopic and in silico analytical approaches, showing conformational change.

Proteomic investigation on bio-corona of Au, Ag and Fe nanoparticles for the discovery of triple negative breast cancer serum protein biomarkers

Nowadays, there are no targeted therapeutic modalities for triple negative breast cancer (TNBC). This disease is associated with poor prognosis and worst clinical outcome because of the aggressive nature of the tumor, delayed diagnosis, and non-specific symptoms in the early stages. Therefore, identification of novel specific TNBC serum biomarkers for screening and therapeutic purposes remains an urgent clinical requirement. New user-friendly and cheap methods for biomarker identification are needed, and nanotechnology offers new opportunities. When dispersed in blood, nanoparticles (NPs) are covered by a protein shell termed "protein corona" (PC). While alterations in protein patterns are challeging to detect by conventional blood analyses, PC acts as a "nano-concentrator" of serum proteins with affinity for NPs' surface. So, the characterization of PC could allow the detection of otherwise undetectable changes in protein concentration at an early stage of the disease or after chemotherapy or surgery. To explore this research idea, serum samples from 8 triple negative breast cancer (TNBC) patients and 8 patients without malignancy were allowed to interact with gold nanoparticles (AuNPs: 10.02 ± 0.91 nm), silver nanoparticles (AgNPs: 9.73 ± 1.70 nm) and magnetic nanoparticles (MNPs: (9.30 ± 0.67 nm). Here, in order to identify biomarker candidates in serum of TNBC patients, these nanomaterials were combined with electrophoretic separation (SDS-PAGE) to performed qualitative and quantitative comparisons of the serum proteomes of TNBC patients (n = 8) and healthy controls (n = 8) by liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis. The results were validated through a sequential window acquisition of all theoretical mass spectra (SWATH) analysis, performed in total serum samples (patients and controls) using this approach as a multiple reaction monitoring (MRM) analysis. SIGNIFICANCE: It is well known that several proteins presented in human serum are important biomarkers for the diagnosis or prognosis of different diseases, as triple negative breast cancer (TNBC). Determining how nanomaterials as gold nanoparticles (AuNPs: 10.02 ± 0.91 nm), silver nanoparticles (AgNPs: 9.73 ± 1.70 nm) and magnetic nanoparticles (MNPs: (9.30 ± 0.67 nm) interact with human serum will assist not only in understanding their effects on the biological system (biocompability and toxicity), but also to obtain information for developing novel nanomaterials with high specificity and selectivity towards proteins with an important biological function (prognostic and diagnostic protein biomarkers).

Unexpected Size Effect: The Interplay between Different-Sized Nanoparticles in Their Cellular Uptake

The size effect on the cellular uptake of nanoparticles (NPs) has been extensively studied, but it is still not well understood. Herein, a reductionist approach is used to minimize all influencing factors except the particle size, and co-exposure of different-sized silica nanoparticles (SNPs) is adopted instead of the common single exposure. SNPs are found being internalized by Hela cells in serum-free medium mainly via clathrin-dependent endocytosis, thus simplifying the data analysis for reliable attribution to size effects. Remarkably, even though at conditions that the size effects seem very small or even undetectable in the common single exposure experiments, the co-exposure experiments reveal significant size effects due to an unexpected interplay between two different-sized SNPs. Namely, the bigger SNPs significantly promote the cellular uptake of the smaller ones, while the smaller SNPs inhibit the internalization of the bigger ones, with a total uptake increase of the particle number of SNPs in the cells. This strong interplay between different-sized NPs might unavoidably exist within most "single-sized" NP products, whose sizes actually distribute in certain ranges, thus urging reconsideration of the size effect on the cellular uptake of NPs, for the benefits of both bioapplications and safety assessment of nanomaterials.

Synthetic and biological identities of polymeric nanoparticles influencing the cellular delivery: An immunological link

Enhanced understanding of bio-nano interaction requires recognition of hidden factors such as protein corona, a layer of adsorbed protein around nano-systems. This study compares the biological identity and fingerprint profile of adsorbed proteins on PLGA-based nanoparticles through nano-liquid chromatography-tandem mass spectrometry. The total proteins identified in the corona of nanoparticles (NPs) with different in size, charge and compositions were classified based on molecular mass, isoelectric point and protein function. A higher abundance of complement proteins was observed in modified NPs with an increased size, while NPs with a positive surface charge exhibited the minimum adsorption for immunoglobulin proteins. A correlation of dysopsonin/opsonin ratio was found with cellular uptake of NPs exposed to two positive and negative Fc receptor cell lines. Although the higher abundance of dysopsonins such as apolipoproteins may cover the active sites of opsonins causing a lower uptake, the correlation of adsorbed dysopsonin/opsonin proteins on the NPs surface has an opposite trend with the intensity of cell uptake. Despite the reduced uptake of corona-coated NPs in comparison with pristine NPs, the dysopsonin/opsonin ratio controlled by the physicochemistry properties of NPs could potentially be used to tune up the cellular delivery of polymeric NPs.

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics

Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.

Target Site Delivery and Residence of Nanomedicines: Application of Quantitative Systems Pharmacology

Quantitative systems pharmacology (QSP), an emerging field that entails using modeling and computation to interpret, interrogate, and integrate drug effects spanning from the molecule to the whole organism to forecast treatment outcomes, is expected to enhance the efficiency of drug development. Since late 2017, the U.S. Food and Drug Administration has advocated the use of an analogous approach of model-informed drug development. This review focuses on issues pertaining to nanosized medicines (NP) and the potential utility of QSP to determine NP delivery and residence at extracellular or intracellular targets in vivo. The kinetic processes governing NP disposition and transport, interactions with biologic matrix components, binding and internalization in cells, and intracellular trafficking are determined, sometimes jointly, by NP properties (e.g., dimension, materials, surface charge and modifications, shape, and geometry) and target tissue properties (e.g., perfusion status, vessel pore size and wall thickness, vessel and cell density, composition of extracellular matrix, and void volume fraction). These various determinants, together with the heterogeneous tissue structures and microenvironment factors in solid tumors, lead to environment-, spatial-, and time-dependent changes in NP concentrations that are difficult to predict. Adding to the complexity is the recent discovery that NP surface-coating protein corona, whose composition depends on NP properties and which undergoes continuous evolution with time and local protein environments, is yet another unpredictable variable. Examples are provided to demonstrate the potential utility of QSP-based multiscale modeling to capture the physicochemical and biologic processes in equations to enable computational studies of the key kinetic processes in cancer treatments.

Oxidative Stress of Carbon Nanotubes on Proteins Is Mediated by Metals Originating from the Catalyst Remains

Nanomaterials introduced into biological systems are immediately coated by proteins in vivo. They induce oxidative stress on adsorbed proteins and hence alter the protein structures, which determines the fate pathways and biological impacts of nanomaterials. Carbon nanotubes (CNTs) have been suggested to cause protein oxidation. In this work, we discovered that CNTs induce oxidative stress on proteins in cooperation with coexisting metals originating from catalyst remains. Protein sulfhydryl groups were readily oxidized by the coexistence of CNTs and metals. Numerical simulations of the reaction demonstrated that the metals effectively mediate electron transfer between the CNTs and protein sulfhydryl groups. Thus, the coexistence of CNTs and metals, even in low concentrations, generates oxidative stress on proteins with high reaction rates. Metal catalysts used for CNT growth, in turn, catalyze the oxidation reaction of proteins. The proposed protein oxidation mechanism will advance the fundamental understanding of the biological safety and toxicity of nanomaterials synthesized using metal catalysts.

Systemic Bioequivalence Is Unlikely to Equal Target Site Bioequivalence for Nanotechnology Oncologic Products

Approval of generic drugs by the US Food and Drug Administration (FDA) requires the product to be pharmaceutically equivalent to the reference listed drug (RLD) and demonstrate bioequivalence (BE) in effectiveness when administered to patients under the conditions in the RLD product labeling. Effectiveness is determined by drug exposure at the target sites. However, since such measurement is usually unavailable, systemic exposure is assumed to equal target site exposure and systemic BE to equal target site BE. This assumption, while it often applies to small molecule drug products that are readily dissolved in biological fluids and systemically absorbed, is unlikely to apply to nanotechnology products (NP) that exist as heterogeneous systems and are subjected to dimension- and material-dependent changes. This commentary provides an overview of the intersecting and spatial-dependent processes and variables governing the delivery and residence of oncologic NP in solid tumors. In order to provide a quantitative perspective of the collective effects of these processes, we used quantitative systems pharmacology (QSP) multi-scale modeling to capture the physicochemical and biological events on several scales (whole-body, organ/suborgan, cell/subcellular, spatial locations, time). QSP is an emerging field that entails using modeling and computation to facilitate drug development; an analogous approach (i.e., model-informed drug development) is advocated by to FDA. The QSP model-based simulations illustrated that small changes in NP attributes (e.g., size variations during manufacturing, interactions with proteins in biological milieu) could lead to disproportionately large differences in target site exposure, rending systemic BE unlikely to equal target site BE.

Interaction of functionalized nanoparticles with serum proteins and its impact on colloidal stability and cargo leaching

The majority of effort in the area of polymeric nanocarriers is aimed at providing controlled drug delivery in vivo. Therefore, it is essential to understand the delicate interplay of polymeric NPs with serum proteins in order to forecast their performance in a biological system. In this study, the interaction of serum proteins with functionalized polymeric colloids as a function of particle charge and hydrophobicity was investigated. Moreover, impact on NP stability and cargo leaching was assessed. The hard protein corona of polymeric NPs with either uncharged methoxy groups (methoxy-NPs), positively charged amine groups (amine-NPs), negatively charged carboxylic acid groups (carboxyl-NPs) or zwitterionic NPs decorated with amine and carboxylic acid groups (zwitterion-NPs) was quantitatively and qualitatively analyzed and correlated with the respective colloidal stability using fluorescence resonance energy transfer. Positively charged amine-NPs displayed an enhanced interaction with serum proteins via electrostatic interactions resulting in a hard corona consisting of diverse protein components. As revealed by FRET and agarose gel electrophoresis, the enhanced adsorption of proteins onto the colloidal surface significantly altered the NP identity and severely impaired the colloidal integrity as the lipophilic cargo was continuously leached out of the hydrophobic NP core. These results highlight the importance of generating a profound knowledge of the bio-nano interface as adherence of biomolecules can severely compromise the performance of a colloidal drug delivery system by changing its identity and integrity.

Imaging and therapeutic applications of persistent luminescence nanomaterials

The development of probes for biomolecular imaging and diagnostics is a very active research area. Among the different imaging modalities, optics emerged since it is a noninvasive and cheap imaging technique allowing real time imaging. In vitro, this technique is very useful however in vivo, fluorescence suffers from low signal-to-noise ratio due to tissue autofluorescence under constant excitation. To address this limitation, novel types of optical nanoprobes are actually being developed and among them, persistent luminescence nanoparticles (PLNPs), with long lasting near-infrared (NIR) luminescence capability, allows doing optical imaging without constant excitation and so without autofluorescence. This review will begin by introducing the physical phenomenon associated to the long luminescence decay of such nanoprobes, from minutes to hours after ceasing the excitation. Then we will show how this property can be used to develop in vivo imaging probes and also more recently nanotheranostic agents. Finally, preliminary data on their biocompatibility will be mentioned and we will conclude by envisioning on the future applications and improvements of such nanomaterials.

A pH-based sensor array for the detection and identification of proteins using CdSe/ZnS quantum dots as an indicator

A novel and simple fluorescence sensor array was developed for the detection and identification of proteins using pH buffer solutions as sensing elements.

Toxicity of carbon nanotubes to white rot fungus Phanerochaete chrysosporium

Carbon nanotubes (CNTs) are widely used in diverse areas with increasing annual production, thus the environmental impact of CNTs needs thorough investigation. In this study, we evaluated the effect of pristine multi-walled CNTs (p-MWCNTs) and oxidized multi-walled CNTs (o-MWCNTs) on white rot fungus Phanerochaete chrysosporium, which is the decomposer in carbon cycle and also has many applications in environmental remediation. Both p-MWCNTs and o-MWCNTs had no influence on the dry weight increase of P. chrysosporium and the pH value of culture system. The fibrous structure of P. chrysosporium was disturbed by p-MWCNTs seriously, while o-MWCNTs had litter influence. The ultrastructural changes were more evident for P. chrysosporium exposed to p-MWCNTs and only p-MWCNTs could penetrate into the cell plasma. The chemical composition of P. chrysosporium was nearly unchanged according to the infrared spectra. The laccase activity was suppressed by p-MWCNTs, while o-MWCNTs showed stimulating effect. The decoloration of reactive brilliant red X-3B was not affected by both CNT samples. However, serious inhibition of wood degradation was observed in the p-MWCNTs exposed groups, suggesting the potential threat of CNTs to the decomposition of carbon cycle. The implication to the environmental risks and safe applications of carbon nanomaterials is discussed.

Understanding the elusive protein corona of thermoresponsive nanogels

Aim: We analyzed the protein corona of thermoresponsive, poly(N-isopropylacrylamide)- or poly(N-isopropylmethacrylamide)-based nanogels. Materials & methods: Traces of protein corona detected after incubation in human serum were characterized by proteomics and dynamic light scattering in undiluted serum. Results: Apolipoprotein B-100 and albumin were the main components of the protein coronae. For dendritic polyglycerol-poly(N-isopropylacrylamide) nanogels at 37°C, an increase in adsorbed immunoglobulin light chains was detected, followed by partially reversible nanogel aggregation. All nanogels in their hydrophilic state are colloidally stable in serum and bear a dysopsonin-rich protein corona. Conclusion: We observed strong changes in NG stability upon slight alterations in the composition of the protein coronae according to nanogel solvation state. Nanogels in their hydrophilic state possess safe protein coronae.

Inner-View of Nanomaterial Incited Protein Conformational Changes: Insights into Designable Interaction

Nanoparticle bioreactivity critically depends upon interaction between proteins and nanomaterials (NM). The formation of the "protein corona" (PC) is the effect of such nanoprotein interactions. PC has a wide usage in pharmaceuticals, drug delivery, medicine, and industrial biotechnology. Therefore, a detailed in-vitro, in-vivo, and in-silico understanding of nanoprotein interaction is fundamental and has a genuine contemporary appeal. NM surfaces can modify the protein conformation during interaction, or NMs themselves can lead to self-aggregations. Both phenomena can change the whole downstream bioreactivity of the concerned nanosystem. The main aim of this review is to understand the mechanistic view of NM-protein interaction and recapitulate the underlying physical chemistry behind the formation of such complicated macromolecular assemblies, to provide a critical overview of the different models describing NM induced structural and functional modification of proteins. The review also attempts to point out the current limitation in understanding the field and highlights the future scopes, involving a plausible proposition of how artificial intelligence could be aided to explore such systems for the prediction and directed design of the desired NM-protein interactions.

Generation of a Diligand Complex of Bovine Serum Albumin with Quercetin and Carbon Nanotubes for the Protection of Bioactive Quercetin and Reduction of Cytotoxicity

The interactions between proteins and bioactive ligands (such as flavonoids and nanomaterials) are vital to the design of effective protein carriers for the protection of bioactive molecules and reduction of the cytotoxicity of nanotubes. Bovine serum albumin (BSA) can bind various bioactive components and subsequently form protein-ligand complexes. Herein, the binding of BSA to quercetin and single-walled carbon nanotubes (SWCNTs) was investigated by using experimental and molecular-docking methods. The fluorescence intensity of BSA was decreased by both quercetin and SWCNTs in static quenching mode (i.e., compound formation), which was authenticated by Stern-Volmer calculations. Although quercetin showed a higher affinity for BSA than SWCNTs, the binding of both components to BSA was located in site I (subdomain IIA). BSA-diligand complexes were successfully generated when SWCNTs and quercetin, in that sequence, were added. The cytotoxicity of SWCNTs and the formation of reactive oxygen species in endothelial cells were decreased with the BSA-diligand complexes relative to those of SWCNTs or BSA-SWCNT corona, whereas the stability problems of quercetin were ameliorated in the BSA-diligand complex relative to in the free flavonoid. The BSA-diligand complex showed a better inhibitive effect on the cytotoxicity of SWCNTs than the BSA-SWCNT complex, and thus the coexistence of quercetin played a crucial role. These data demonstrate the advantages and possibility of designing BSA carriers for the protection of bioactive ligands and reduction of the cytotoxicity of nanotubes in functional-food and biomedical applications.

The Protein Corona as a Confounding Variable of Nanoparticle-Mediated Targeted Vaccine Delivery

Nanocarriers (NC) are very promising tools for cancer immunotherapy. Whereas conventional vaccines are based on the administration of an antigen and an adjuvant in an independent fashion, nanovaccines can facilitate cell-specific co-delivery of antigen and adjuvant. Furthermore, nanovaccines can be decorated on their surface with molecules that facilitate target-specific antigen delivery to certain antigen-presenting cell types or tumor cells. However, the target cell-specific uptake of nanovaccines is highly dependent on the modifications of the nanocarrier itself. One of these is the formation of a protein corona around NC after in vivo administration, which may potently affect cell-specific targeting and uptake of the NC. Understanding the formation and composition of the protein corona is, therefore, of major importance for the use of nanocarriers in vaccine approaches. This Mini Review will give a short overview of potential non-specific interactions of NC with body fluids or cell surfaces that need to be considered for the design of NC vaccines for immunotherapy of cancer.

Interaction of spin-labeled HPMA-based nanoparticles with human blood plasma proteins - the introduction of protein-corona-free polymer nanomedicine

In this paper, we revised the current understanding of the protein corona that is created on the surface of nanoparticles in blood plasma after an intravenous injection. We have focused on nanoparticles that have a proven therapeutic outcome. These nanoparticles are based on two types of biocompatible amphiphilic copolymers based on N-(2-hydroxypropyl)methacrylamide (HPMA): a block copolymer, poly(ε-caprolactone) (PCL)-b-poly(HPMA), and a statistical HPMA copolymer bearing cholesterol moieties, which have been tested both in vitro and in vivo. We studied the interaction of nanoparticles with blood plasma and selected blood plasma proteins by electron paramagnetic resonance (EPR), isothermal titration calorimetry, dynamic light scattering, and cryo-transmission electron microscopy. The copolymers were labeled with TEMPO radicals at the end of hydrophobic PCL or along the hydrophilic HPMA chains to monitor changes in polymer chain dynamics caused by protein adsorption. By EPR and other methods, we were able to probe specific interactions between nanoparticles and blood proteins, specifically low- and high-density lipoproteins, immunoglobulin G, human serum albumin (HSA), and human plasma. It was found that individual proteins and plasma have very low binding affinity to nanoparticles. We observed no hard corona around HPMA-based nanoparticles; with the exception of HSA the proteins showed no detectable binding to the nanoparticles. Our study confirms that a classical "hard corona-soft corona" paradigm is not valid for all types of nanoparticles and each system has a unique protein corona that is determined by the nature of the NP material.

Toxicity of Pristine and Chemically Functionalized Fullerenes to White Rot Fungus Phanerochaete chrysosporium

Fullerenes are widely produced and applied carbon nanomaterials that require a thorough investigation into their environmental hazards and risks. In this study, we compared the toxicity of pristine fullerene (C60) and carboxylated fullerene (C60-COOH) to white rot fungus Phanerochaete chrysosporium. The influence of fullerene on the weight increase, fibrous structure, ultrastructure, enzyme activity, and decomposition capability of P. chrysosporium was investigated to reflect the potential toxicity of fullerene. C60 did not change the fresh and dry weights of P. chrysosporium but C60-COOH inhibited the weight gain at high concentrations. Both C60 and C60-COOH destroyed the fibrous structure of the mycelia. The ultrastructure of P. chrysosporium was changed by C60-COOH. Pristine C60 did not affect the enzyme activity of the P. chrysosporium culture system while C60-COOH completely blocked the enzyme activity. Consequently, in the liquid culture, P. chrysosporium lost the decomposition activity at high C60-COOH concentrations. The decreased capability in degrading wood was observed for P. chrysosporium exposed to C60-COOH. Our results collectively indicate that chemical functionalization enhanced the toxicity of fullerene to white rot fungi and induced the loss of decomposition activity. The environmental risks of fullerene and its disturbance to the carbon cycle are discussed.

Impact of Anti-Biofouling Surface Coatings on the Properties of Nanomaterials and Their Biomedical Applications

Understanding and subsequently controlling non-specific interactions between engineered nanomaterials and biological environment have become increasingly important for further developing and advancing nanotechnology for biomedical applications. Such non-specific interactions, also known as the biofouling effect, mainly associate with the adsorption of biomolecules (such as proteins, DNAs, RNAs, and peptides) onto the surface of nanomaterials and the adhesion or uptake of nanomaterials by various cells. By altering the surface properties of nanomaterials the biofouling effect can lead to in situ changes of physicochemical properties, pharmacokinetics, functions, and toxicity of nanomaterials. This review provides discussions on the current understanding of the biofouling effect, the factors that affect the non-specific interactions associated with biofouling, and the impact of the biofouling effect on the performances and functions of nanomaterials. An overview of the development and applications of various anti-biofouling coating materials to preserve and improve the properties and functions of engineered nanomaterials for intended biomedical applications is also provided.

Advanced Nuclear and Related Techniques for Metallomics and Nanometallomics

Metallomics, focusing on the global and systematic understanding of the metal uptake, trafficking, role, and excretion in biological systems, has attracted more and more attention. Metal-related nanomaterials, including metallic and metal-containing nanomaterials, have unique properties compared to their macroscale counterparts and therefore require special attention. The absorption, distribution, metabolism, excretion (ADME) behavior of metal-related nanomaterials in the biological systems is influenced by their physicochemical properties, the exposure route, and the microenvironment of the deposition site. Nanomaterials not only may interact directly or indirectly with genes, proteins, and other molecules to bring genotoxicity, immunotoxicity, DNA damage, and cytotoxicity but may also stimulate the immune responses, circumvent tumor resistance, and inhibit tumor metastasis. Because of their advantages of absolute quantification, high sensitivity, excellent accuracy and precision, low matrix effects, and nondestructiveness, nuclear and related analytical techniques have been playing important roles in the study of metallomics and nanometallomics. In this chapter, we present a comprehensive overview of nuclear and related analytical techniques applied to the quantification of metallome and nanometallome, the biodistribution, bioaccumulation, and transformation of metallome and nanometallome in vivo, and the structural analysis. Besides, metallomics and nanometallomics need to cooperate with other -omics, like genomics, proteomics, and metabolomics, to obtain the knowledge of underlying mechanisms and therefore to improve the application performance and to reduce the potential risk of metallome and nanometallome.

Particle Targeting in Complex Biological Media

Over the past few decades, nanoengineered particles have gained increasing interest for applications in the biomedical realm, including diagnosis, imaging, and therapy. When functionalized with targeting ligands, these particles have the potential to interact with specific cells and tissues, and accumulate at desired target sites, reducing side effects and improve overall efficacy in applications such as vaccination and drug delivery. However, when targeted particles enter a complex biological environment, the adsorption of biomolecules and the formation of a surface coating (e.g., a protein corona) changes the properties of the carriers and can render their behavior unpredictable. For this reason, it is of importance to consider the potential challenges imposed by the biological environment at the early stages of particle design. This review describes parameters that affect the targeting ability of particulate drug carriers, with an emphasis on the effect of the protein corona. We highlight strategies for exploiting the protein corona to improve the targeting ability of particles. Finally, we provide suggestions for complementing current in vitro assays used for the evaluation of targeting and carrier efficacy with new and emerging techniques (e.g., 3D models and flow-based technologies) to advance fundamental understanding in bio-nano science and to accelerate the development of targeted particles for biomedical applications.

Artificial antibody created by conformational reconstruction of the complementary-determining region on gold nanoparticles

Mimicking protein-like specific interactions and functions has been a long-pursued goal in nanotechnology. The key challenge is to precisely organize nonfunctional surface groups on nanoparticles into specific 3D conformations to function in a concerted and orchestrated manner. Here, we develop a method to graft the complementary-determining regions of natural antibodies onto nanoparticles and reconstruct their “active” conformation to create nanoparticle-based artificial antibodies that recognize the corresponding antigens. Our work demonstrates that it is possible to create functions on nanoparticles by conformational engineering, namely tuning flexible surface groups into specific conformations. Our straightforward strategy could be used further to create other artificial antibodies for various applications and provides a new tool to understand the structure and folding of natural proteins.

To impart biomedical functions to nanoparticles (NPs), the common approach is to conjugate functional groups onto NPs by dint of the functions of those groups per se. It is still beyond current reach to create protein-like specific interactions and functions on NPs by conformational engineering of nonfunctional groups on NPs. Here, we develop a conformational engineering method to create an NP-based artificial antibody, denoted “Goldbody,” through conformational reconstruction of the complementary-determining regions (CDRs) of natural antibodies on gold NPs (AuNPs). The seemingly insurmountable task of controlling the conformation of the CDR loops, which are flexible and nonfunctional in the free form, was accomplished unexpectedly in a simple way. Upon anchoring both terminals of the free CDR loops on AuNPs, we managed to reconstruct the “active” conformation of the CDR loops by tuning the span between the two terminals and, as a result, the original specificity was successfully reconstructed on the AuNPs. Two Goldbodies have been created by this strategy to specifically bind with hen egg white lysozyme and epidermal growth factor receptor, with apparent affinities several orders of magnitude stronger than that of the original natural antibodies. Our work demonstrates that it is possible to create protein-like functions on NPs in a protein-like way, namely by tuning flexible surface groups to the correct conformation. Given the apparent merits, including good stability, of Goldbodies, we anticipate that a category of Goldbodies could be created to target different antigens and thus used as substitutes for natural antibodies in various applications.