Computer simulation of the role of protein corona in cellular delivery of nanoparticles

Effect of Nanoparticle Curvature on Its Interaction with Serum Proteins

The size or the curvature of nanoparticles (NPs) plays an important role in regulating the composition of the protein corona. However, the molecular mechanisms of how curvature affects the interaction of NPs with serum proteins still remain elusive. In this study, we employ all-atom molecular dynamics simulations to investigate the interactions between two typical serum proteins and PEGylated Au NPs with three different surface curvatures (0, 0.1, and 0.5 nm-1, respectively). The results show that for proteins with a regular shape, the binding strength between the serum protein and Au NPs decreases with increasing curvature. For irregularly shaped proteins with noticeable grooves, the binding strength between the protein and Au NPs does not change obviously with increasing curvature in the cases of smaller curvature. However, as the curvature continues to increase, Au NPs may act as ligands firmly adsorbed in the protein grooves, significantly enhancing the binding strength. Overall, our findings suggest that the impact of NP curvature on protein adsorption may be nonmonotonic, which may provide useful guidelines for better design of functionalized NPs in biomedical applications.

Engineering the protein corona: Strategies, effects, and future directions in nanoparticle therapeutics

Nanoparticles (NPs) serve as versatile delivery systems for anticancer, antibacterial, and antioxidant agents. The manipulation of protein-NP interactions within biological systems is crucial to the application of NPs in drug delivery and cancer nanotherapeutics. The protein corona (PC) that forms on the surface of NPs is the interface between biomacromolecules and NPs and significantly influences their pharmacokinetics and pharmacodynamics. Upon encountering proteins, NPs undergo surface alterations that facilitate their clearance from circulation by the mononuclear phagocytic system (MPS). PC behavior depends largely on the biological microenvironment and the physicochemical properties of the NPs. This review describes various strategies employed to engineer PC compositions on NP surfaces. The effects of NP characteristics such as size, shape, surface modification and protein precoating on PC performance were explored. In addition, this study addresses these challenges and guides the future directions of this evolving field.

Instability of membranes containing ionizable cationic lipids: Effects of the repulsive range of headgroups and tail structures

The stability of membranes formed by ionizable cationic lipids, which constitute the primary components in lipid nanoparticles capable of endosomal escape, is explored using coarse-grained dissipative particle dynamics. Three types of ionizable model lipids with different tail structures are considered. Endosome acidification causes the ionization of lipids, leading to an increased repulsive range between their headgroups. When electrostatic repulsion is modeled as a conservative force with a long-range cutoff distance (rc,HH), the membrane and vesicle experience a loss of structural integrity and develop holes as rc,HH is beyond a critical value, which varies with the tail structure. When Coulombic repulsion is explicitly incorporated and intensified, a fully ionized lipid membrane undergoes a loss of structural integrity, displaying a qualitative similarity to the effect observed with the increase in rc,HH on the membrane stability. Qualitatively similar results are obtained for partially ionized membranes as the fraction of charged lipids increases. The stability of a mixed lipid membrane containing both ionizable and conventional lipids is also investigated. The disruption of the bilayer structure occurs for a sufficiently high charged fraction. The membrane instability can be attributed to the decrease in the packing parameter, which significantly deviates from unity as the interaction range increases.

Mechanism of RGD-conjugated nanodevice binding to its target protein integrin αVβ3 by atomistic molecular dynamics and machine learning

Active targeting strategies have been proposed to enhance the selective uptake of nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the effectiveness of this approach. However, no mechanistic studies have yet revealed the atomistic details of the interactions between ligand-activated NPs and integrins. As a case study, here we investigate, by means of advanced molecular dynamics simulations (MD) and machine learning methods (namely equilibrium MD, binding free energy calculations and training of self-organized maps), the interaction of a cyclic-RGD-conjugated PEGylated TiO2 NP (the nanodevice) with the extracellular segment of integrin αVβ3 (the target), the latter experimentally well-known to be over-expressed in several solid tumors. Firstly, we proved that the cyclic-RGD ligand binding to the integrin pocket is established and kept stable even in the presence of the cumbersome realistic model of the nanodevice. In this respect, the unsupervised machine learning analysis allowed a detailed comparison of the ligand/integrin binding in the presence and in the absence of the nanodevice, which unveiled differences in the chemical features. Then, we discovered that unbound cyclic RGDs conjugated to the NP largely contribute to the interactions between the nanodevice and the integrin. Finally, by increasing the density of cyclic RGDs on the PEGylated TiO2 NP, we observed a proportional enhancement of the nanodevice/target binding. All these findings can be exploited to achieve an improved targeting selectivity and cellular uptake, and thus a more successful clinical outcome.

Separation of protein corona from nanoparticles under intracellular acidic conditions: effect of protonation on nanoparticle-protein and protein-protein interactions

Protein coronas separate from nanoparticles under intracellular acidic conditions however, competitive adsorption of multiple proteins and their protein network formation under different pH conditions have not yet been systematically studied at the atomic scale. Herein, we report all-atom molecular dynamics simulations of plasma proteins (human serum albumin and immunoglobulin gamma-1 chain C) adsorbed to 10 nm-sized carboxyl-terminated polystyrene (PS) nanoparticles at different protonation states that mimic extracellular and intracellular pH conditions of 7, 6-5, and 4.5. Binding free energies are calculated from umbrella sampling simulations, showing the significantly weakened binding between PS particles and proteins at the protonation state at pH 4.5, in agreement with experiments showing the separation of protein corona from nanoparticles at pH 4.5. Mixtures of multiple proteins and PS particles are also simulated, showing much less protein adsorption and protein cluster formation at the protonation state at pH 4.5 than that at higher pH values, which are further confirmed by calculating the diffusivities and hydrodynamic radii of individual proteins. In particular, electrostatic particle-protein and protein-protein interactions are significantly weakened by a combination of particle and protein protonation rather than by particle protonation alone, to an extent dependent on different proteins. These findings help explain the experimental observations regarding separation of protein corona from nanoparticles under intracellular acidic conditions at pH 4.5 but not at higher pH, supporting that acidification cannot be the only reason for this separation during the process of endosome maturation.

Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation

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

Differences in protein distribution, conformation, and dynamics in hard and soft coronas: dependence on protein and particle electrostatics

We perform all-atom molecular dynamics simulations of a 9 nm-thick protein layer, which consists of serum albumin (SA) or a mixture of SA and immunoglobulin gamma-1, formed on 10 nm-sized cationic, anionic, and neutral polystyrene particles. More than half of the proteins are densely concentrated within a distance of ∼3 nm from the particle surface, while fewer proteins are broadly distributed in the range of 3-9 nm from the particle. This compares favorably with the experimental observations of a hard corona as the first layer adjacent to the particle and a soft corona as a loose protein-network. The conformation and diffusivity of the proteins vary in different positions of the layer, and are to an extent dependent on the protein and particle electrostatics. These, combined with free energy calculations, show that the protein and particle charges do not significantly modify the strength of protein-particle binding but do influence the distribution of proteins in the layer. In particular, a free protein more strongly binds to the complex of a protein and particle than to either one, showing the synergistic effect of already adsorbed proteins and a particle. This helps explain the experimental observation regarding the formation of a denser protein layer and the stronger protein-protein interaction in the hard corona than the soft corona.

Plasma metabolites-based design of long-acting peptides and their anticancer evaluation

Antimicrobial peptides (AMPs) are generally small cationic amphipathic peptides, which are thought to be ideal antineoplastic agents, owing to their favorable selectivity to cancer cells and the ability to overcome drug-resistance. In this study, an anticancer AMP (Mastoparan (INLKALAALAKKIL-NH2)) was selected as the lead compound and a series of Mastoparan derivatives were designed. Preliminary studies verified that an analogue of Mastoparan, KM8 (KLLKINLKALAALAKKIL-NH2), exhibited prominent selective antitumor effects. Instead, it presents a significant defect of metabolic instability, with a half-life in plasma of only about 0.5 h. Metabolite profiling of KM8 was performed and indicated the structure ₉AL₁₀ in peptide sequence could be the fragile site for KM8. Thus, the Aib (unnatural amnio acid) was employed to substitute the ₉Ala residue in KM8, and generating a long-acting KM8 derivative, namely KM8-Aib. Further investigations revealed KM8-Aib possessed higher metabolic stability, more potent anticancer activity in vitro & in vivo, and lower toxicity. Therefore, KM8-Aib is suggested be a potential antimalignant agent that worthy of more in-depth study.

The effects of serum albumin pre-adsorption of nanoparticles on protein corona and membrane interaction: A molecular simulation study

As a platform to deliver imaging and therapeutic agents to targeted sites in vivo, nanoparticles (NPs) have widespread applications in diagnosis and treatment of cancer. However, the poor in vivo delivery efficiency of nanoparticles limits its potential for further application. Once enter the physiological environment, nanoparticles immediately interact with proteins and form protein corona, which changes the physicochemical properties of nanoparticle surface and further affects their transport. In this study, we performed molecular dynamics simulations to study the adsorption mechanism of nanoparticles with various surface modifications and different proteins (e.g., human serum albumin, complement protein C3b), and their interactions with cell membrane. The results show that protein human serum albumin prefers to interact with hydrophobic and positively charged nanoparticles, while the protein C3b prefers the hydrophobic and charged nanoparticles. The pre-adsorption of human serum albumin on the nanoparticle surface obviously decreases the interaction of nanoparticle with C3b. Furthermore, the high amount of protein pre-adsorption could decrease the probability of nanoparticle-membrane interaction. These results indicate that appropriate modification of nanoparticles with protein provides nanoparticles with better capability of targeting, which could be used to guide nanoparticle design and improve transport efficiency.

The effect of biomolecular corona on adsorption onto and desorption from a model lipid membrane

The current lack of insight into nanoparticle-cell membrane interactions hampers smart design strategies and thereby the development of effective nanodrugs. Quantitative and methodical approaches utilizing cell membrane models offer an opportunity to unravel particle-membrane interactions in a detailed manner under well controlled conditions. Here we use total internal reflection microscopy for real-time studies of the non-specific interactions between nanoparticles and a model cell membrane at 50 ms temporal resolution over a time course of several minutes. Maintaining a simple lipid bilayer system across conditions, adsorption and desorption were quantified as a function of biomolecular corona, particle size and fluid flow. The presence of a biomolecular corona reduced both the particle adsorption rate onto the membrane and the duration of adhesion, compared to pristine particle conditions. Particle size, on the other hand, was only observed to affect the adsorption rate. The introduction of flow reduced the number of adsorption events, but increased the residence time. Lastly, altering the composition of the membrane itself resulted in a decreased number of adsorption events onto negatively charged bilayers compared to neutral bilayers. Overall, a model membrane system offers a facile platform for real-time imaging of individual adsorption-desorption processes, revealing complex adsorption kinetics, governed by particle surface energy, size dependent interaction forces, flow and membrane composition.

The Interaction Between Cholesterol-Modified Amino-Pullulan Nanoparticles and Human Serum Albumin: Importance of Nanoparticle Positive Surface Charge

To study the interaction of nanoparticles (NPs) and human serum albumin (HSA), we designed three different aminosubstituted hydrophobically cholesterol-modified pullulan NPs (CHPN NPs). Dynamic light scattering (DLS) revealed sizes of 145, 156, and 254 nm and zeta potentials of 0.835, 7.22, and 11.7 mV for CHPN1, CHPN2, and CHPN3 NPs, respectively. Isothermal titration calorimetry (ITC) revealed that the binding constants were (1.59±0.45)×105 M−1, (2.08±0.26)×104 M−1, and (2.71±0.92)×104 M−1, respectively, and HSA coverage was (1.52±0.12), (0.518±0.316), and (0.092±0.015). Fluorescence spectroscopy of HSA revealed that the fluorescence intensity was quenched by CHPN NPs, which was maintained with a long final complexation period. Circular dichroism (CD) revealed a quick decrease in the α-helix content of HSA to 39.1% after the final complexation. NPs with a more positive charge led to a greater decrease in α-helix content than occurred in other NPs, so the NP surface charge played a role in the HSA–NP interaction. After HSA binding, the surface charge was −3.66±0.12 for CHPN1, −2.65±0.06 for CHPN2 and −1.12±0.28 mV for CHPN3 NPs. The NP surface property changed because of HSA binding, which is important for NP applications.

Nanomaterials-based photosensitizers and delivery systems for photodynamic cancer therapy

The increasing cancer morbidity and mortality requires the development of high-efficiency and low-toxicity anticancer approaches. In recent years, photodynamic therapy (PDT) has attracted much attention in cancer therapy due to its non-invasive features and low side effects. Photosensitizer (PS) is one of the key factors of PDT, and its successful delivery largely determines the outcome of PDT. Although a few PS molecules have been approved for clinical use, PDT is still limited by the low stability and poor tumor targeting capacity of PSs. Various nanomaterial systems have shown great potentials in improving PDT, such as metal nanoparticles, graphene-based nanomaterials, liposomes, ROS-sensitive nanocarriers and supramolecular nanomaterials. The small molecular PSs can be loaded in functional nanomaterials to enhance the PS stability and tumor targeted delivery, and some functionalized nanomaterials themselves can be directly used as PSs. Herein, we aim to provide a comprehensive understanding of PDT, and summarize the recent progress of nanomaterials-based PSs and delivery systems in anticancer PDT. In addition, the concerns of nanomaterials-based PDT including low tumor targeting capacity, limited light penetration, hypoxia and nonspecific protein corona formation are discussed. The possible solutions to these concerns are also discussed.

Effect of dopamine-functionalization, charge and pH on protein corona formation around TiO2 nanoparticles

Inorganic nanoparticles (NPs) are gaining increasing attention in nanomedicine because of their stimuli responsiveness, which allows combining therapy with diagnosis. However, little information is known about their interaction with intracellular or plasma proteins when they are introduced in a biological environment. Here we present atomistic molecular dynamics (MD) simulations investigating the case study of dopamine-functionalized TiO₂ nanoparticles and two proteins that are overexpressed in cancer cells, i.e. PARP1 and HSP90, since experiments proved them to be the main components of the corona in cell cultures. The mechanism and the nature of the interaction (electrostatic, van der Waals, H-bonds, etc.) is unravelled by defining the protein residues that are more frequently in contact with the NPs, the extent of contact surface area and the variations in the protein secondary structures, at different pH and ionic strength conditions of the solution where they are immersed to simulate a realistic biological environment. The effects of the NP surface functionalization and charge are also considered. Our MD results suggest that less acidic intracellular pH conditions in the presence of cytosolic ionic strength enhance PARP1 interaction with the nanoparticle, whereas the HSP90 contribution is partly weakened, providing a rational explanation to existing experimental observations.

Engineering surface patterns on nanoparticles: New insights on nano-bio interactions

The surface properties of nanoparticles affect their fates in biological systems. Based on nanotechnology and methodology, pioneering works have explored the effects of chemical surface patterns on the behavior of...

Reversible Immunoaffinity Interface Enables Dynamic Manipulation of Trapping Force for Accumulated Capture and Efficient Release of Circulating Rare Cells

Controllable assembly and disassembly of recognition interface are vital for bioanalysis. Herein, a strategy of dynamic manipulation of trapping force by engineering a dynamic and reversible immunoaffinity microinterface (DynarFace) in a herringbone chip (DynarFace-Chip) for liquid biopsy is proposed. The DynarFace is assembled by magnetically attracting immunomagnetic beads (IMBs) on chip substrate, with merits of convenient operation and reversible assembly. The DynarFace allows accumulating attachment of IMBs on circulating rare cell (CRC) surfaces during hydrodynamically enhanced interface collision, where accumulatively enhanced magnetic trapping force improves capture efficiency toward CRCs with medium expression of biomarkers from blood samples by 134.81% compared with traditional non-dynamic interfaces. Moreover, magnet withdrawing-induced disappearance of trapping force affords DynarFace disassembly and CRC release with high efficiency (>98%) and high viability (≈98%), compatible with downstream in vitro culture and gene analysis of CRCs. This DynarFace strategy opens a new avenue to accumulated capture and reversible release of CRCs, holding great potential for liquid biopsy-based precision medicine.

Polyelectrolyte Encapsulation and Confinement within Protein Cage-Inspired Nanocompartments

Protein cages are nanocompartments with a well-defined structure and monodisperse size. They are composed of several individual subunits and can be categorized as viral and non-viral protein cages. Native viral cages often exhibit a cationic interior, which binds the anionic nucleic acid genome through electrostatic interactions leading to efficient encapsulation. Non-viral cages can carry various cargo, ranging from small molecules to inorganic nanoparticles. Both cage types can be functionalized at targeted locations through genetic engineering or chemical modification to entrap materials through interactions that are inaccessible to wild-type cages. Moreover, the limited number of constitutional subunits ease the modification efforts, because a single modification on the subunit can lead to multiple functional sites on the cage surface. Increasing efforts have also been dedicated to the assembly of protein cage-mimicking structures or templated protein coatings. This review focuses on native and modified protein cages that have been used to encapsulate and package polyelectrolyte cargos and on the electrostatic interactions that are the driving force for the assembly of such structures. Selective encapsulation can protect the payload from the surroundings, shield the potential toxicity or even enhance the intended performance of the payload, which is appealing in drug or gene delivery and imaging.

Molecular Modeling of Protein Corona Formation and Its Interactions with Nanoparticles and Cell Membranes for Nanomedicine Applications

The conformations and surface properties of nanoparticles have been modified to improve the efficiency of drug delivery. However, when nanoparticles flow through the bloodstream, they interact with various plasma proteins, leading to the formation of protein layers on the nanoparticle surface, called protein corona. Experiments have shown that protein corona modulates nanoparticle size, shape, and surface properties and, thus, influence the aggregation of nanoparticles and their interactions with cell membranes, which can increases or decreases the delivery efficiency. To complement these experimental findings and understand atomic-level phenomena that cannot be captured by experiments, molecular dynamics (MD) simulations have been performed for the past decade. Here, we aim to review the critical role of MD simulations to understand (1) the conformation, binding site, and strength of plasma proteins that are adsorbed onto nanoparticle surfaces, (2) the competitive adsorption and desorption of plasma proteins on nanoparticle surfaces, and (3) the interactions between protein-coated nanoparticles and cell membranes. MD simulations have successfully predicted the competitive binding and conformation of protein corona and its effect on the nanoparticle-nanoparticle and nanoparticle-membrane interactions. In particular, simulations have uncovered the mechanism regarding the competitive adsorption and desorption of plasma proteins, which helps to explain the Vroman effect. Overall, these findings indicate that simulations can now provide predications in excellent agreement with experimental observations as well as atomic-scale insights into protein corona formation and interactions.

Effect of Protein Corona on Nanoparticle-Lipid Membrane Binding: The Binding Strength and Dynamics

All-atom molecular dynamics simulations of the 10 nm-sized anionic polystyrene (PS) particle complexed with plasma proteins (human serum albumin, immunoglobulin gamma-1 chain-C, and apolipoprotein A-I) adsorbed onto lipid bilayers [asymmetrically composed of extracellular (zwitterionic) and cytosolic (anionic) leaflets] are performed. Free energies calculated from umbrella sampling simulations show that proteins on the particle more weakly bind to the zwitterionic leaflet than do bare particles, in agreement with experiments showing the suppression of the particle-bilayer binding by protein corona. Proteins on the particle interact more strongly with the anionic leaflet than with the zwitterionic leaflet because of charge interactions between cationic protein residues and anionic lipid headgroups, to an extent dependent on various plasma proteins. In particular, hydrogen bonds between proteins and zwitterionic leaflets restrict the motion of lipids and thus reduce the lateral dynamics of bilayers, while the tight binding between proteins and anionic leaflets disrupts the helical structure of proteins and disorders lipids, leading to an increase in the lateral dynamics of bilayers. These findings help explain the experimental observation regarding the fact that the bilayer dynamics decreases when interacting with protein corona and suggest that the effect of protein corona on the binding strength and bilayer dynamics depends on protein types and bilayer charges.

Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations

The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.

Acidity constant and DFT-based modelling of pH-responsive alendronate loading and releasing on propylamine-modified silica surface

A computational methodology that couples the acidity (K_a) and density functional theory (DFT) calculations has been developed to explain the pH-dependent drug loading on and releasing from mesoporous silica nanoparticles.

Unbound Natural Organic Matter Competes with Nanoparticles for Internalization Receptors During Cell Uptake

Natural organic matter (NOM) that forms coronas on the surface of engineered nanoparticles (NPs) affects their stability, bio-uptake, and toxicity. After corona formation, a large amount of unbound NOM remains in the environment and their effects on organismal uptake of NPs remain unknown. Here, the effects of unbound NOM on the uptake of polyacrylate-coated hematite NPs (HemNPs) by the protozoan Tetrahymena thermophila were examined. HemNPs were well-dispersed without any detectable NOM adsorption. Kinetics experiments showed that unbound NOM decreased the uptake of HemNPs with greater inhibition at lower concentrations of the particles in the presence of NOM of higher molecular weight. The unbound NOM suppressed clathrin-mediated endocytosis but not the phagocytosis of HemNPs. Confirmation of these events was obtained using label-free hyperspectral stimulated Raman spectroscopy imaging and dissipative particle dynamics simulation. Overall, the present study demonstrates that unbound NOM can compete with HemNPs for internalization receptors on the surface of T. thermophila and inhibit particle uptake, highlighting the need to consider the direct effects of unbound NOM in bioapplication studies and in safety evaluations of NPs.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

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.

Insights into Characterization Methods and Biomedical Applications of Nanoparticle-Protein Corona

Nanoparticles (NPs) exposed to a biological milieu will strongly interact with proteins, forming "coronas" on the surfaces of the NPs. The protein coronas (PCs) affect the properties of the NPs and provide a new biological identity to the particles in the biological environment. The characterization of NP-PC complexes has attracted enormous research attention, owing to the crucial effects of the properties of an NP-PC on its interactions with living systems, as well as the diverse applications of NP-PC complexes. The analysis of NP-PC complexes without a well-considered approach will inevitably lead to misunderstandings and inappropriate applications of NPs. This review introduces methods for the characterization of NP-PC complexes and investigates their recent applications in biomedicine. Furthermore, the review evaluates these characterization methods based on comprehensive critical views and provides future perspectives regarding the applications of NP-PC complexes.

Drug Delivery System Based on pH-Sensitive Biocompatible Poly(2-vinyl pyridine)-b-poly(ethylene oxide) Nanomicelles Loaded with Curcumin and 5-Fluorouracil

Smart polymeric micelles (PMs) are of practical interest as nanocarriers for the encapsulation and controlled release of hydrophobic drugs. Two hydrophobic drugs, naturally-based curcumin (Cur) and synthetic 5-fluorouracil (5-FU), were loaded into the PMs formed by a well-defined pH-sensitive poly(2-vinyl pyridine)-b-poly(ethylene oxide) (P2VP₉₀-b-PEO₃₉₈) block copolymer. The influence of the drug loading on the micellar sizes was investigated by dynamic light scattering (DLS) and it appears that the size of the PMs increases from around 60 to 100 nm when Cur is loaded. On the contrary, the loading of the 5-FU has a smaller effect on the micellar sizes. This difference can be attributed to higher molar mass of Cur with respect to 5-FU but also to higher loading efficiency of Cur, 6.4%, compared to that of 5-FU, 5.8%. In vitro drug release was studied at pH 2, 6.8, and 7.4, and it was observed that the pH controls the release of both drugs. At pH 2, where the P2VP sequences from the “frozen-in” micellar core are protonated, the drug release efficiencies exceed 90%. Moreover, it was demonstrated, by in vitro assays, that these PMs are hemocompatible and biocompatible. Furthermore, the PMs protect the Cur against the photo-degradation, whereas the non-ionic PEO corona limits the adsorption of bovine serum albumin (BSA) protein on the surface. This study demonstrates that these pH-sensitive PMs are suitable for practical utilization as human-safe and smart, injectable drug delivery systems.

Advances in Nanoparticles as Anticancer Drug Delivery Vector: Need of this Century

Background:

Nanotechnology has contributed a great deal to the field of medical science. Smart drugdelivery vectors, combined with stimuli-based characteristics, are becoming increasingly important. The use of external and internal stimulating factors can have enormous benefits and increase the targeting efficiency of nanotechnology platforms. The pH values of tumor vascular tissues are acidic in nature, allowing the improved targeting of anticancer drug payloads using drug-delivery vectors. Nanopolymers are smart drug-delivery vectors that have recently been developed and recommended for use by scientists because of their potential targeting capabilities, non-toxicity and biocompatibility, and make them ideal nanocarriers for personalized drug delivery.

Method:

The present review article provides an overview of current advances in the use of nanoparticles (NPs) as anticancer drug-delivery vectors.

Results:

This article reviews the molecular basis for the use of NPs in medicine, including personalized medicine, personalized therapy, emerging vistas in anticancer therapy, nanopolymer targeting, passive and active targeting transports, pH-responsive drug carriers, biological barriers, computer-aided drug design, future challenges and perspectives, biodegradability and safety.

Conclusions:

This article will benefit academia, researchers, clinicians, and government authorities by providing a basis for further research advancements.

Effects of titanium dioxide and zinc oxide nano-materials on lipid order in model membranes

Engineered nano-materials (ENM) have been reported to affect lipid membrane permeability in cell models, but a mechanistic understanding of how these materials interact with biological membranes has not been described. To assess mechanisms of permeability, liposomes composed of DOPC, DOPS, or POPC, with or without cholesterol, were used as model membranes for measuring ENM-induced changes to lipid order to improve our understanding of ENM effects on membrane permeability. Liposomes were treated with either titanium dioxide (TiO₂) or zinc oxide (ZnO) ENM, and changes to lipid order were measured by time-resolved fluorescence anisotropy of a lipophilic probe, Di-4-ANEPPDHQ. Both ENM increased lipid order in two lipid models differing in headgroup charge. TiO₂ increased lipid order of POPC liposomes (neutral charge), while ZnO acted primarily on DOPS liposomes (negative charge). Addition of cholesterol to these models significantly increased lipid order while in some cases attenuated ENM-induced changes to lipid order. To assess the ability of ENM to induce membrane permeability, liposomes composed of the above lipids were assayed for membrane permeability by calcein leakage in response to ENM. Both ENM caused a dose-dependent increase in permeability in all liposome models tested, and the addition of cholesterol to the liposome models neither blocked nor reduced calcein leakage. Together, these experiments show that ENM increased permeability of small molecules (calcein) from model liposomes, and that the magnitude of the effect of ENM on lipid order depended on ENM surface charge, lipid head group charge and the presence of cholesterol in the membrane.

Enhancing the targeting ability of nanoparticles via protected copolymers

It is important to maintain the balance between therapeutic efficiency and cytotoxicity when using nanomaterials for biomedical applications. Here, we propose a new method (i.e., non-covalent coating of protected copolymers onto the nanoparticle surface) to enhance the active targeting of nanoparticles to the cancer cells by combining the dissipative particle dynamics simulation and in vitro experiments. When coating the protected copolymer onto the nanoparticle surface, the uptake efficiency could be greatly altered due to the competition between the copolymer-ligand interaction and the receptor-ligand interaction-the non-covalent coating is more efficient than the covalent coating. Furthermore, the effect of the physicochemical properties of the protected copolymer on the targeting ability of nanoparticles was also investigated. This study offers useful insight into the optimal design of nanocarriers in biomedicine.

Protein corona impact on nanoparticle-cell interactions: toward an energy-based model of endocytosis

Upon incubation of nanoparticles in biological fluids, a new layer called the protein corona is formed on their surface affecting the interactions between nanoparticles and targeted cells during the endocytosis process. In the present study, a mathematical model based on the diffusion of membrane mobile receptors is proposed. Opposing the endocytosis proceeding, membrane bending and tension energies are named as resistant energy. Also, the binding energy and free-energy associated with the configurational entropy are collectively termed promoter energy. Utilizing this model, endocytosis of gold nanoparticle (GNP) is simulated to explore the biological media effect. The results reveal that there exists a nanoparticle size of 60 nm at which, the endocytosis time is at a minimum. It has been illustrated that, although for sufficiently small particles of diameter 30nm, membrane tension has a negligible contribution (<10%) in the resistant energy, it noticeably increases the endocytosis processing time for large particles. Therefore, we report several parametric studies to provide a better insight into the effects of biological media on the ingestion of nanoparticles. Through a detailed analysis of the engulfment of the nanoparticles, it is shown that the nanoparticle radius corresponding to the quickest possible ingestion time is affected in the presence of corona. Moreover, it is found that the formation of this layer does not only affect the endocytosis time but also can lead to incomplete engulfment by decreasing the ligand density on the nanoparticle surface. Use of the proposed model can play a significant role in advancing the design of nanoparticles in targeted drug delivery applications.

Effects of Nanoparticle Electrostatics and Protein-Protein Interactions on Corona Formation: Conformation and Hydrodynamics

All-atom molecular dynamics simulations of plasma proteins (human serum albumin, fibrinogen, immunoglobulin gamma-1 chain-C, complement C3, and apolipoprotein A-I) adsorbed onto 10 nm sized cationic, anionic, and neutral polystyrene (PS) particles in water are performed. In simulations of a single protein with a PS particle, proteins eventually bind to all PS particles, regardless of particle charge, in agreement with experiments showing the binding between anionic proteins and particles, which is further confirmed by calculating the binding free energies from umbrella sampling simulations. Simulations of mixtures of multiple proteins and a PS particle show the formation of the protein layer on the surface via the adsorption competition between proteins, which influences the binding affinity and structure of adsorbed proteins. In particular, diffusivities are much higher for proteins bound to the particle surface or to the boundary of the protein layer than for those bound to both the particle surface and other proteins, indicating the dependence of protein mobility on their positions in the layer. These findings help to explain in detail experimental observations regarding the replacement of plasma proteins at the early stage of corona formation and the difference in the binding strength of proteins in inner and outer protein-layers.

Long-Acting Paliperidone Parenteral Formulations Based on Polycaprolactone Nanoparticles; the Influence of Stabilizer and Chitosan on In Vitro Release, Protein Adsorption, and Cytotoxicity

Long-acting preparations containing the antipsychotic paliperidone for intramuscular injection has drawn considerable attention to achieve harmless long-term treatment. This study aimed to develop paliperidone loaded polycaprolactone (PCL) nanoparticles and investigate the influence of PCL/drug ratio, stabilizer type, and chitosan coating on physicochemical properties, protein adsorption, and cellular toxicity. Results showed that chitosan coating produced enlarged particle sizes, shifted the surface charges from negative into positive and did not influence encapsulation efficiencies. Chitosan coating relatively sustained the drug release especially in pluronic stabilized formulations. Pluronic F127 based formulations exhibited the least protein adsorption (384.3 μg/mL). Chitosan coating of Tween 80 and polyvinyl alcohol stabilized formulations significantly (p < 0.05) increased protein adsorption. Cellular viability was concentration-dependent and negatively affected by stabilizers. All formulations did not show cellular death at 1.56 μg/mL. Inflammatory responses and oxidative stress were less affected by Tween 80 compared with other stabilizers. Chitosan minimized all aspects of cellular toxicity. Collectively, stabilizer type and chitosan coating play critical roles in developing safe and effective long-acting PCL nanoparticles intended for parenteral drug delivery. The coated formulations containing Tween 80 and Pluronic F127 as stabilizers are warranted a future in vivo study to delineate its safety and efficacy profiles.

Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations

Due to different interactions between lipids and proteins, a plasma membrane can segregate into different membrane domains. Among them, ordered functional membrane domains are defined as "lipid rafts", which play key roles in many biological processes (e.g., signal transduction, endocytosis, etc.) in the cell. Hence, it will be of much biological significance to monitor and even regulate the dynamics of lipid rafts. In this work, we designed a ligand-modified spherical nanoparticle with coarse-grained molecular dynamics simulations, which can be encapsulated into the hydrophobic region of the lipid membrane and specifically target either raft or non-raft membrane domains. The preferred localization of the nanoparticle can be tuned by adjusting ligand hydrophobicity, length and density. Generally, more hydrophobic nanoparticles tend to target the raft domain, while less hydrophobic nanoparticles prefer the non-raft domain. Besides, ligand length and density jointly determine the exposure of nanoparticle cores and thus affect the roles of ligands in nanoparticles' final localization. Our results may provide insights into the experimental design of functional nanoparticles, targeting the lipid raft and regulating its dynamics.

Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives

Injection of nanoparticles (NP) into the bloodstream leads to the formation of a so-called "nano-bio" interface where dynamic interactions between nanoparticle surfaces and blood components take place. A common consequence is the formation of the protein corona, that is, a network of adsorbed proteins that can strongly alter the surface properties of the nanoparticle. The protein corona and the resulting structural changes experienced by adsorbed proteins can lead to substantial deviations from the expected cellular uptake as well as biological responses such as NP aggregation and NP-induced protein fibrillation, NP interference with enzymatic activity, or the exposure of new antigenic epitopes. Achieving a detailed understanding of the nano-bio interface is still challenging due to the synergistic effects of several influencing factors like pH, ionic strength, and hydrophobic effects, to name just a few. Because of the multiscale complexity of the system, modeling approaches at a molecular level represent the ideal choice for a detailed understanding of the driving forces and, in particular, the early events at the nano-bio interface. This review aims at exploring and discussing the opportunities and perspectives offered by molecular modeling in this field through selected examples from literature.

Tailoring the component of protein corona via simple chemistry

Control over the protein corona of nanomaterials allows them to function better. Here, by taking graphene/gold as examples, we comprehensively assessed the association of surface properties with the protein corona. As revealed by in vitro measurements and computations, the interaction between graphene/gold and HSA/IgE was inversely correlated with the hydroxyl group availability, whereas the interaction between that and ApoE was comparatively less relevant. Molecular simulations revealed that the number and the distribution of surface hydroxyl groups could regulate the manner in which nanomaterials interact with proteins. Moreover, we validated that ApoE pre-adsorption before injection enhances the blood circulation of nanomaterials relative to their pristine and IgE-coated counterparts. This benefit can be attributed to the invulnerability of the complementary system provided by ApoE, whose encasement does not increase cytotoxicity. Overall, this study offers a robust yet simple way to create protein corona enriched in dysopsonins to realize better delivery efficacy.

The interaction between proteins and nanomaterials is complex and of interest for controlling nanoparticle fate. Here, using experimental and computational methods, the authors report on the effect of hydroxyl groups on protein interaction and how they can be used to enhance circulation times.

Interplay between ligand mobility and nanoparticle geometry during cellular uptake of PEGylated liposomes and bicelles

We explore the cellular uptake process of PEGylated liposomes and bicelles by investigating their membrane wrapping process using large-scale molecular dynamics simulations. We find that due to the mobility of ligands on the liposome/bicelle, the membrane wrapping process of a PEGylated liposome/bicelle can be divided into two stages, whose transition is determined by a critical wrapping fraction fc; it is reached when all the ligands are exhausted and bound to receptors within the cell membrane. Before this critical scenario is approached, the grafted polyethylene glycol (PEG) polymers aggregate together within the membrane-wrapped region of the liposome/bicelle, driven by ligand-receptor binding. For wrapping fractions f > fc, membrane wrapping cannot proceed unless a compressive membrane tension is provided. By systematically varying the membrane tension and PEG molar ratio, we establish phase diagrams about wrapping states for both PEGylated liposomes and bicelles. According to these diagrams, we find that the absolute value of the compressive membrane tension required by a fully wrapped PEGylated bicelle is smaller than that of the PEGylated liposome, indicating that the PEGylated bicelle is easily internalized by cells. Further theoretical analysis reveals that compared to a liposome, the flatter surface at the top of a bicelle makes it energetically more favored beyond the critical wrapping fraction fc. Our simulations confirm that the interplay between ligand mobility and NP geometry can significantly change the understanding about the influence of NP geometry on the membrane wrapping process. It can help us to better understand the cellular uptake process of the PEGylated liposome/bicelle and to improve the design of lipid-like NPs for drug delivery.

Nanoformulation properties, characterization, and behavior in complex biological matrices: Challenges and opportunities for brain-targeted drug delivery applications and enhanced translational potential

Nanocarriers (synthetic/cell-based have attracted enormous interest for various therapeutic indications, including neurodegenerative disorders. A broader understanding of the impact of nanomedicines design is now required to enhance their translational potential. Nanoformulations in vivo journey is significantly affected by their physicochemical properties including the size, shape, hydrophobicity, elasticity, and surface charge/chemistry/morphology, which play a role as an interface with the biological environment. Understanding protein corona formation is crucial in characterizing nanocarriers and evaluating their interactions with biological systems. In this review, the types and properties of the brain-targeted nanocarriers are discussed. The biological factors and nanocarriers properties affecting their in vivo behavior are elaborated. The compositional description of cell culture and biological matrices, including proteins potentially relevant to protein corona built-up on nanoformulation especially for brain administration, is provided. Analytical techniques of characterizing nanocarriers in complex matrices, their advantages, limitations, and implementation challenges in industrial GMP environment are discussed. The uses of orthogonal complementary characterization approaches of nanocarriers are also covered.

Electrostatic complex of neurotrophin 4 with dendrimer nanoparticles: controlled release of protein in vitro and in vivo

Background: NT4 has been regarded as a promising therapeutic protein for treatment of damaged retinal pigment epithelium cells.

Purpose: Here, we studied physicochemical parameters of an NT4–polyamidoamine (PAMAM) electrostatic complex, which can provide a sustained concentration of protein in intraocular space over an extended period after delivery. Adsorption/desorption of NT4 molecules to/from positively charged PAMAM dendrimers were precisely determined to control the concentration of bounded/unbounded protein molecules, diffusion coefficient, and size of a protein-laden dendrimer structure. We determined kinetics of NT4 desorption in PBS, vitreous, and damaged retina.

Methods: Initially, adsorption of NT4 molecules on PAMAM dendrimers was studied in PBS using dynamic light scattering, electrophoresis, solution depletion, ELISA, and atomic force microscopy. This allowed us precisely to determine desorption of NT4 from nanoparticles under in situ conditions. The maximum coverage of irreversibly adsorbed NT4 determined by ELISA allowed us to devise a robust procedure for preparing stable and well-controlled coverage of NT4 on PAMAM nanoparticles. Thereafter, we studied diffusion of nanospheres containing NT4 molecules by injecting them into vitreous cavities of mice exposed to intravenous injections of sodium iodate and evaluated their intraocular desorption kinetics from drug carriers in vivo.

Results: Our measurements revealed NT4–dendrimer nanoparticles can be used for continuous neurotrophic factor delivery, enhancing its distribution into mouse vitreous, as well as damaged retina over 28 days of postinjury observation.

Conclusion: Understanding of polyvalent neurotrophin interactions with dendrimer nanoparticles might be useful to obtain well-ordered protein layers, targeting future development of drug-delivery systems, especially for neuroprotection of damaged retinal neurons.

Design of Small Nanoparticles Decorated with Amphiphilic Ligands: Self-Preservation Effect and Translocation into a Plasma Membrane

Design of nanoparticles (NPs) for biomedical applications requires a thorough understanding of cascades of nano-bio interactions at different interfaces. Here, we take into account the cascading effect of NP functionalization on interactions with target cell membranes by determining coatings of biomolecules in biological media. Cell culture experiments show that NPs with more hydrophobic surfaces are heavily ingested by cells in both the A549 and HEK293 cell lines. However, before reaching the target cell, both the identity and amount of recruited biomolecules can be influenced by the pristine NPs' hydrophobicity. Dissipative particle dynamics (DPD) simulations show that hydrophobic NPs acquire coatings of more biomolecules, which may conceal the properties of the as-engineered NPs and impact the targeting specificity. Based on these results, we propose an amphiphilic ligand coating on NPs. DPD simulations reveal the design principle, following which the amphiphilic ligands first curl in solvent to reduce the surface hydrophobicity, thus suppressing the assemblage of biomolecules. Upon attaching to the membrane, the curled ligands extend and rearrange to gain contacts with lipid tails, thus dragging NPs into the membrane for translocation. Three NP-membrane interaction states are identified that are found to depend on the NP size and membrane surface tension. These results can provide useful guidelines to fabricate ligand-coated NPs for practical use in targeted drug delivery, and motivate further studies of nano-bio-interactions with more consideration of cascading effects.

Microscopy and Cell Biology: New Methods and New Questions

Understanding the cellular basis of human health and disease requires the spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Just as these imaging methods allow researchers to address new biological questions, progress in biological sciences will drive the development of new imaging methods. We highlight four topics in cell biology that illustrate the need for new imaging tools: nanoparticle-cell interactions, intracellular redox chemistry, neuroscience, and the increasing use of spheroids and organoids. Overall, our goal is to provide a brief overview of individual imaging methods and highlight recent advances in the use of microscopy for cell biology.

Role of Ligand Conformation on Nanoparticle-Protein Interactions

Engineered biomedical nanoparticles (NPs) administered via intravenous routes are prone to associate to serum proteins. The protein corona can mask the NP surface functionalization and hamper the delivery of the NP to its biological target. The design of corona-free NPs relies on our understanding of the chemical-physical features of the NP surface driving the interaction with serum proteins. Here, we address, by computational means, the interaction between human serum albumin (HSA) and a prototypical monolayer-protected Au nanoparticle. We show that both the chemical composition (charge, hydrophobicity) and the conformational preferences of the ligands decorating the NP surface affect the NP propensity to bind HSA.

Impact of soft protein interactions on the excretion, extent of receptor occupancy and tumor accumulation of ultrasmall metal nanoparticles: a compartmental model simulation

Ultrasmall metal nanoparticles (NPs) are next-generation nano-based platforms for in vivo disease diagnosis and treatment. Due to their small size below the kidney filtration threshold and marked resistance to nonspecific serum protein adsorption, ultrasmall NPs can be rapidly excreted through the kidneys and escape liver uptake. However, although ultrasmall particles may be deemed highly resistant to protein adsorption, the real extent of this resistance is not known. Here, a simple compartmental model simulation was therefore implemented to understand how NP behavior in vivo could be modulated by soft, transient NP–plasma protein interactions characterized by dissociation constants in the millimolar range. In Model 1, ultrasmall NPs functionalized with a targeting probe, plasma proteins and target receptors were assumed to co-exist within a single compartment. Simulations were performed to understand the synergistic effect of soft interactions, systemic clearance and NP size on receptor occupancy in the single compartment. The results revealed the existence of a narrow range of ultraweak affinities and optimal particle sizes leading to greater target occupancy. In Model 2, simulations were performed to understand the impact of soft interactions on NP accumulation into a peripheral (tumor) compartment. The results revealed that soft interactions – but not active targeting – enhanced tumor uptake levels when tumor accumulation was limited by ‘fast’ plasma clearance and ‘slow’ vascular extravasation. The simple model presented here provides a basic framework to quantitatively understand the blood and tumor pharmacokinetics of ultrasmall NPs under the influence of transient protein interactions.

A compartmental model simulation shows that the blood and tumor pharmacokinetics of ultrasmall metal nanoparticles can be modulated by soft interactions with plasma proteins.