Recent advances in the analysis of nanoparticle-protein coronas

PROTCROWN: A Manually Curated Resource of Protein Corona Data for Unlocking the Potential of Protein-Nanoparticle Interactions

The emergence of the "Protein Corona" is a pivotal concept in bioinformatics and nanotechnology, crucial for understanding nanomedicine delivery and nanoparticle-biological entity interactions. After entering a biological fluid, such as blood, nanoparticles (NPs, such as nanomedical carriers) are quickly coated with proteins, forming a protein interface layer called the protein corona. An in-depth investigation into the protein corona is essential for elucidating the biological ramifications of NPs and their prospective applications within the medical field and beyond. To advance our understanding of the intricate interactions between NPs and biological systems, we have developed PROTCROWN, the inaugural protein corona database. This resource systematically curates and organizes data relevant to the protein corona, facilitating advanced analysis and research in the field. It provides a convenient data query platform for researchers and supports data visualization and analysis. Our database, PROTCROWN, is accessible at http://www.protcrown.cn.

In situ characterization techniques of protein corona around nanomaterials

Nanoparticles (NPs) inevitably interact with proteins upon exposure to biological fluids, leading to the formation of an adsorption layer known as the "protein corona". This corona imparts NPs with a new biological identity, directly influencing their interactions with living systems and dictating their fates in vivo. Thus, gaining a comprehensive understanding of the dynamic interplay between NPs and proteins in biological fluids is crucial for predicting therapeutic effects and advancing the clinical translation of nanomedicines. Numerous methods have been established to decode the protein corona fingerprints. However, these methods primarily rely on prior isolation of NP-protein complex from the surrounding medium by centrifugation, resulting in the loss of outer-layer proteins that directly interact with the biological system and determine the in vivo fate of NPs. We discuss here separation techniques as well as in situ characterization methods tailored for comprehensively unraveling the inherent complexities of NP-protein interactions, highlighting the challenges of in situ protein corona characterization and its significance for nanomedicine development and clinical translation.

An insight into impact of nanomaterials toxicity on human health

In recent years, advances in nanotechnology have significantly influenced electronics manufacturing, industrial processes, and medical research. Various industries have seen a surge in the use of nanomaterials. However, several researchers have raised the alarm about the toxicological nature of nanomaterials, which appear to be quite different from their crude forms. This altered nature can be attributed to their unique physicochemical profile. They can adversely affect human health and the environment. Nanomaterials that have been released into the environment tend to accumulate over time and can cause a significant impact on the ecosystem and organisms with adverse health effects. Increased use of nanoparticles has led to increased human exposure in their daily lives, making them more vulnerable to nanoparticle toxicity. Because of their small size, nanomaterials can readily cross biological membranes and enter cells, tissues, and organs. Therefore, the effect of nanomaterials on the human environment is of particular concern. The toxicological effects of nanomaterials and their mechanisms of action are being researched worldwide. Technological advances also support monitoring new nanomaterials marketed for industrial and household purposes. It is a challenging area because of the exceptional physicochemical properties of nanomaterials. This updated review focuses on the diverse toxicological perspective of nanomaterials. We have discussed the use of different types of nanoparticles and their physiochemical properties responsible for toxicity, routes of exposure, bio-distribution, and mechanism of toxicity. The review also includes various in vivo and in vitro methods of assessing the toxicity of nanomaterials. Finally, this review will provide a detailed insight into nano material-induced toxicological response, which can be beneficial in designing safe and effective nanoparticles.

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.

Real-Time Optical Tracking of Protein Corona Formation on Single Nanoparticles in Serum

The formation of a protein corona, where proteins spontaneously adhere to the surface of nanomaterials in biological environments, leads to changes in their physicochemical properties and subsequently affects their intended biomedical functionalities. Most current methods to study protein corona formation are ensemble-averaging and either require fluorescent labeling, washing steps, or are only applicable to specific types of particles. Here we introduce real-time all-optical nanoparticle analysis by scattering microscopy (RONAS) to track the formation of protein corona in full serum, at the single-particle level, without any labeling. RONAS uses optical scattering microscopy and enables real-time and in situ tracking of protein adsorption on metallic and dielectric nanoparticles with different geometries directly in blood serum. We analyzed the adsorbed protein mass, the affinity, and the kinetics of the protein adsorption at the single particle level. While there is a high degree of heterogeneity from particle to particle, the predominant factor in protein adsorption is surface chemistry rather than the underlying nanoparticle material or size. RONAS offers an in-depth understanding of the mechanisms related to protein coronas and, thus, enables the development of strategies to engineer efficient bionanomaterials.

The immune-stealth polymeric coating on drug delivery nanocarriers: In vitro engineering and in vivo fate

Although essential nanosystems such as nanoparticles and nanocarriers are desirable options for transporting various drug molecules into the biological environment, they rapidly remove from the circulatory system due to their interaction with multiple in vivo barriers, especially the immune barrier, which will result in their short-term effects. In order to improve their effectiveness and durability in the circulatory system, the polymer coatings can use to cover the surface of nanoparticles and nanocarriers to conceal them from the immune system. Due to their different properties (like charge, elasticity, and hydrophilicity/hydrophobicity), these coatings can improve drug delivery nanosystem durability and therapeutic applications. The mentioned coatings have different types and are divided into various categories, such as synthetic polymers, polysaccharides, and zwitterionic polymers. Each of these polymers has unique properties based on its category, origin, and chemical structure that make them suitable for producing stealth drug delivery nanocarriers. In this review article, we have tried to explain the importance of these diverse polymer coatings in determining the fate of drug nanocarriers and then introduced the different types of these coatings and, finally, described various methods that directly and indirectly analyze the nanocoatings to determine the stability of nanoparticles in the body.

Design of Synthetic Hydrogel Compositions for Noncovalent Protein Recognition

Multifunctional hydrogels composed of segments with ionizable, hydrophilic, and hydrophobic monomers have been optimized for sensing, bioseparation, and therapeutic applications. While the "biological identity" of bound proteins from biofluids underlies device performance in each context, design rules that predict protein binding outcomes from hydrogel design parameters are lacking. Uniquely, hydrogel designs that influence protein affinity (e.g., ionizable monomers, hydrophobic moieties, conjugated ligands, cross-linking) also affect physical properties (e.g., matrix stiffness, volumetric swelling). Here, we evaluated the influence of hydrophobic comonomer steric bulk and quantity on the protein recognition characteristics of ionizable microscale hydrogels (microgels) while controlling for swelling. Using a library synthesis approach, we identified compositions that balance the practical balance between protein-microgel affinity and the loaded mass at saturation. Intermediate quantities (10-30 mol %) of hydrophobic comonomer increased the equilibrium binding of certain model proteins (lysozyme, lactoferrin) in buffer conditions that favored complementary electrostatic interactions. Solvent-accessible surface area analysis of model proteins identified arginine content as highly predictive of model proteins' binding to our library of hydrogels containing acidic and hydrophobic comonomers. Taken together, we established an empirical framework for characterizing the molecular recognition properties of multifunctional hydrogels. Our study is the first to identify solvent-accessible arginine as an important predictor for protein binding to hydrogels containing both acidic and hydrophobic subunits.

Toxicity of metal-based nanoparticles: Challenges in the nano era

With the rapid progress of nanotechnology, various nanoparticles (NPs) have been applicated in our daily life. In the field of nanotechnology, metal-based NPs are an important component of engineered NPs, including metal and metal oxide NPs, with a variety of biomedical applications. However, the unique physicochemical properties of metal-based NPs confer not only promising biological effects but also pose unexpected toxic threats to human body at the same time. For safer application of metal-based NPs in humans, we should have a comprehensive understanding of NP toxicity. In this review, we summarize our current knowledge about metal-based NPs, including the physicochemical properties affecting their toxicity, mechanisms of their toxicity, their toxicological assessment, the potential strategies to mitigate their toxicity and current status of regulatory movement on their toxicity. Hopefully, in the near future, through the convergence of related disciplines, the development of nanotoxicity research will be significantly promoted, thereby making the application of metal-based NPs in humans much safer.

Nano-bio interactions: A major principle in the dynamic biological processes of nano-assemblies

Controllable nano-assembly with stimuli-responsive groups is emerging as a powerful strategy to generate theranostic nanosystems that meet unique requirements in modern medicine. However, this prospective field is still in a proof-of-concept stage due to the gaps in our understanding of complex-(nano-assemblies)-complex-(biosystems) interactions. Indeed, stimuli-responsive assembly-disassembly is, in and of itself, a process of nano-bio interactions, the key steps for biological fate and functional activity of nano-assemblies. To provide a comprehensive understanding of these interactions in this review, we first propose a 4W1H principle (Where, When, What, Which and How) to delineate the relevant dynamic biological processes, behaviour and fate of nano-assemblies. We further summarize several key parameters that govern effective nano-bio interactions. The effects of these kinetic parameters on ADMET processes (absorption, distribution, metabolism, excretion and transformation) are then discussed. Furthermore, we provide an overview of the challenges facing the evaluation of nano-bio interactions of assembled nanodrugs. We finally conclude with future perspectives on safe-by-design and application-driven-design of nano-assemblies. This review will highlight the dynamic biological and physicochemical parameters of nano-bio interactions and bridge discrete concepts to build a full spectrum understanding of the biological outcomes of nano-assemblies. These principles are expected to pave the way for future development and clinical translation of precise, safe and effective nanomedicines with intelligent theranostic features.

Nutrient molecule corona: An update for nanomaterial-food component interactions

The adsorption of biological molecules to nanomaterials (NMs) will significantly impact NMs' behavior in complex microenvironments. Previously we proposed the need to consider the interactions between food components and NMs for the evaluation of oral toxicity of NMs. This review updated this concept as nutrient molecule corona, that the adsorption of nutrient molecules alters the uptake of nutrient molecules and/or NMs, as well as the signaling pathways to induce a combined toxicity due to the biologically active nature of nutrient molecules. Even with the presence of protein corona, nutrient molecules may still bind to NMs to change the identities of NMs in vivo. Furthermore, this review proposed the binding of excessive nutrient molecules to NMs to induce a combined toxicity under pathological conditions such as metabolic diseases. The structures of nutrient molecules and physicochemical properties of NMs determine nutrient molecule corona formation, and these aspects should be considered to limit the unwanted effects brought by nutrient molecule corona. In conclusion, similar to other biological molecule corona, the formation of nutrient molecule corona due to the presence of food components or excessive nutrient molecules in pathophysiological microenvironments will alter the behaviors of NMs.

VEGF Overexpression Significantly Increases Nanoparticle-Mediated siRNA Delivery and Target-Gene Downregulation

The availability of nanoparticles (NPs) to deliver small interfering RNA (siRNA) has significantly expanded the specificity and range of ‘druggable’ targets for precision medicine in cancer. This is especially important for cancers such as triple negative breast cancer (TNBC) for which there are no targeted treatments. Our purpose here was to understand the role of tumor vasculature and vascular endothelial growth factor (VEGF) overexpression in a TNBC xenograft in improving the delivery and function of siRNA NPs using in vivo as well as ex vivo imaging. We used triple negative MDA-MB-231 human breast cancer xenografts derived from cells engineered to overexpress VEGF to understand the role of VEGF and vascularization in NP delivery and function. We used polyethylene glycol (PEG) conjugated polyethylenimine (PEI) NPs to deliver siRNA that downregulates choline kinase alpha (Chkα), an enzyme that is associated with malignant transformation and tumor progression. Because Chkα converts choline to phosphocholine, effective delivery of Chkα siRNA NPs resulted in functional changes of a significant decrease in phosphocholine and total choline that was detected with ¹H magnetic resonance spectroscopy (MRS). We observed a significant increase in NP delivery and a significant decrease in Chkα and phosphocholine in VEGF overexpressing xenografts. Our results demonstrated the importance of tumor vascularization in achieving effective siRNA delivery and downregulation of the target gene Chkα and its function.

Designing the Surface Chemistry of Inorganic Nanocrystals for Cancer Imaging and Therapy

Inorganic nanocrystals, such as gold, iron oxide and semiconductor quantum dots, offer promising prospects for cancer diagnostics, imaging and therapy, due to their specific plasmonic, magnetic or fluorescent properties. The organic coating, or surface ligands, of these nanoparticles ensures their colloidal stability in complex biological fluids and enables their functionalization with targeting functions. It also controls the interactions of the nanoparticle with biomolecules in their environment. It therefore plays a crucial role in determining nanoparticle biodistribution and, ultimately, the imaging or therapeutic efficiency. This review summarizes the various strategies used to develop optimal surface chemistries for the in vivo preclinical and clinical application of inorganic nanocrystals. It discusses the current understanding of the influence of the nanoparticle surface chemistry on its colloidal stability, interaction with proteins, biodistribution and tumor uptake, and the requirements to develop an optimal surface chemistry.

Quantification of Available Ligand Density on the Surface of Targeted Liposomal Nanomedicines at the Single-Particle Level

Active targeting has been hailed as one of the most promising strategies to further enhance the therapeutic efficacy of liposomal nanomedicines. Owing to the critical role of ligand density in mediating cellular uptake and the intrinsic heterogeneity of liposomal formulations, precise quantification of the surface ligand density on a single-particle basis is of fundamental importance. In this work, we report a method to simultaneously measure the particle size and the number of ligands on the same liposomal nanoparticles by nanoflow cytometry. Then the ligand density for each individual liposome can be determined. With an analysis rate up to 10 000 particles per minute, a statistically representative distribution of ligand density could be determined in minutes. By utilizing fluorescently labeled recombinant receptors as the detection probe against the conjugated ligands, only those available for cell targeting can be exclusively detected. The influence of ligand input, conjugation strategy, and the polyethylene glycol spacer length on the available ligand density of folate-modified liposomes was investigated. The correlation between the available ligand density and cell targeting capability was assessed in a quantitative perspective for liposomes modified with three different targeting moieties. The optimal ligand density was determined to be 0.5-2.0, 0.7, and 0.2 ligand per 100 nm² for folate-, transferrin-, and HER2-antibody-conjugated liposomes, respectively. These optimal values agreed well with the spike density of the natural counterparts, viruses. The as-developed approach is generally applicable to a wide range of active-targeting nanocarriers.

Inside the Protein Corona: From Binding Parameters to Unstained Hard and Soft Coronas Visualization

Proteins spontaneously adsorb on nanoparticle surfaces when injected into the bloodstream. It drastically modifies the nanoparticle's fate and how they interact with organs and cells. Although this protein layer (protein corona) has been widely studied, the robustness of the most employed characterization methods and the visualization of its unstained fractions remain open questions. Here, synchrotron-based small-angle X-ray scattering was used to follow the corona formation and estimate binding parameters. At the same time, transmission electron microscopy under cryogenic conditions associated with cross-correlation image processing and energy-filtered transmission electron microscopy allowed to determine protein corona morphology and thickness together with the visualization of its unstained hard and soft fractions. The above-presented strategy shows tremendous potential for deciphering fundamental protein corona aspects and can contribute to rational medical nanoparticle engineering.

Size, shape, charge and "stealthy" surface: Carrier properties affect the drug circulation time in vivo

The present review sets out to discuss recent developments of the effects and mechanisms of carrier properties on their circulation time. For most drugs, sufficient in vivo circulation time is the basis of high bioavailability. Drug carrier plays an irreplaceable role in helping drug avoid being quickly recognized and cleared by mononuclear phagocyte system, to give drug enough time to arrive at targeted organ and tissue to play its therapeutic effect. The physical and chemical properties of drug carriers, such as size, shape, surface charge and surface modification, would affect their in vivo circulation time, metabolic behavior and biodistribution. The final circulation time of carriers is determined by the balance between macrophage recognitions, blood vessel penetration and urine excretion. Therefore, when designing the drug delivery system, we should pay much attention to the properties of drug carriers to get enough in vivo circulation time to arrive at target site eventually. This article mainly reviews the effect of carrier size, size, surface charge and surface properties on its circulation time in vivo, and discusses the mechanism of these properties affecting circulation time. This review has reference significance for the research of long-circulation drug delivery system.

How to effectively prepare a sample for bottom-up proteomic analysis of nanoparticle protein corona? A critical review

Since the interest in the biomedical applications of inorganic nanoparticles (NPs) has rapidly grown over the last decades, there is a need for a thorough characterization of bio-nano interactions. NPs introduced to the body (mostly intravenously) encounter plasma proteins, that instantly create a so-called "protein corona" on the NPs surface, giving the nanomaterial a new biological identity. Type of the proteins that interact with NPs may affect the in vivo fate of NPs. For that reason, it is particularly important to establish analytical methods capable of corona protein identification. Bottom-up proteomics is most often used for that purpose. A crucial part of the experiment is sample preparation, as it is already proven that different protocols may lead to distinct results. This review is aimed at providing a characterization of two main stages of sample preparation: separation of NPs with protein corona from the unbound proteins and the digestion of corona proteins. Separation techniques such as centrifugation, magnetic separation, and chromatography and three digestion methods (in-gel, in-solution, and on-particle) are described with special emphasis paid on their advantages and disadvantages as well as their influence on the result of identification. This paper also indicates the need for standardization of protein corona identification protocols, as some of the proteins may be preferentially detected while applying a particular digestion procedure.

Protein corona precoating on redox-responsive chitosan-based nano-carriers for improving the therapeutic effect of nucleic acid drugs

Spontaneous formation of protein corona on chitosan-based nano-carriers is inevitable once they enter the blood, which is considered to be an important factor that weakens the delivery efficiency and therapeutic effect of nucleic acid drugs. For this, cyclic RGDyK peptide (cRGD) modified bovine serum albumin (BSA) was designed as a corona to precoat on redox-responsive chitosan-based nano-carriers (TsR NPs) before administration. The effects of the precoating corona on the pharmaceutical properties and delivery efficiency of the nano-carriers and the therapeutic effect of model siRNA (siVEGF) were investigated. The results showed that BSA-cRGD formed steady corona around TsR NPs, which enhanced targeting ability to cancer cells and reduced serum proteins adsorption. The Bc corona improved the stability and biocompatibility of TsR NPs, increased the intracellular uptake, facilitated the lysosomal escape and maintained their redox-sensitive responsiveness, resulting in enhanced gene silencing efficiency and anti-tumor proliferation effects both in vitro and in vivo.

Tailoring Antifouling Properties of Nanocarriers via Entropic Collision of Polymer Grafting

Polymer graftings (PGs) are widely employed in antifouling surfaces and drug delivery systems to regulate the interaction with a foreign environment. Through molecular dynamics simulations and scaling theory analysis, we investigate the physical antifouling properties of PGs via their collision behaviors. Compared with mushroom-like PGs with low grafting density, we find brush-like PGs with high grafting density could generate large deformation-induced entropic repulsive force during a collision, revealing a microscopic mechanism for the hop motions of polymer-grafted nanoparticles for drug delivery observed in experiment. In addition, the collision elasticity of PGs is found to decay with the collision velocity by a power law, i.e., a concise dynamic scaling despite the complex process involved, which is beyond expectation. These results elucidate the dynamic interacting mechanism of PGs, which are of immediate interest for a fundamental understanding of the antifouling performance of PGs and the rational design of PG-coated nanoparticles in nanomedicine for drug delivery.

Biological effects of formation of protein corona onto nanoparticles

Administration of nanomaterials based medicinal and drug carrier systems into systemic circulation brings about interaction of blood components e.g. albumin and globulin proteins with these nanosystems. These blood or serum proteins either get loosely attached over these nanocarriers and form soft protein corona or are tightly adsorbed over nanoparticles and hard protein corona formation occurs. Formation of protein corona has significant implications over a wide array of physicochemical and medicinal attributes. Almost all pharmacological, toxicological and carrier characteristics of nanoparticles get prominently touched by the protein corona formation. It is this interaction of nanoparticle protein corona that decides and influences fate of nanomaterials-based systems. In this article, authors reviewed several diverse aspects of protein corona formation and its implications on various possible outcomes in vivo and in vitro. A brief description regarding formation and types of protein corona has been included along with mechanisms and pharmacokinetic, pharmacological behavior and toxicological profiles of nanoparticles has been described. Finally, significance of protein corona in context of its in vivo and in vitro behavior, involvement of biomolecules at nanoparticle plasma interface and other interfaces and effects of protein corona on biocompatibility characteristics have also been touched upon.