Influence of ligand distribution on uptake efficiency

Computer-aided nanodrug discovery: recent progress and future prospects

Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.

Virus-Shaped Mesoporous Silica Nanostars to Improve the Transport of Drugs across the Blood-Brain Barrier

Conditions affecting the brain are the second leading cause of death globally. One of the main challenges for drugs targeting brain diseases is passing the blood-brain barrier (BBB). Here, the effectiveness of mesoporous silica nanostars (MSiNSs) with two different spike lengths to cross an in vitro BBB multicellular model was evaluated and compared to spherical nanoparticles (MSiNP). A modified sol-gel single-micelle epitaxial growth was used to produce MSiNS, which showed no cytotoxicity or immunogenicity at concentrations of up to 1 μg mL-1 in peripheral blood mononuclear and neuronal cells. The nanostar MSiNS effectively penetrated the BBB model after 24 h, and MSiNS-1 with a shorter spike length (9 ± 2 nm) crossed the in vitro BBB model more rapidly than the MSiNS-2 with longer spikes (18 ± 4 nm) or spherical MSiNP at 96 h, which accumulated in the apical and basolateral sides, respectively. Molecular dynamic simulations illustrated an increase in configurational flexibility of the lipid bilayer during contact with the MSiNS, resulting in wrapping, whereas the MSiNP suppressed membrane fluctuations. This work advances an effective brain drug delivery system based on virus-like shaped MSiNS for the treatment of different brain diseases and a mechanism for their interaction with lipid bilayers.

Uncovering the Importance of Ligand Mobility on Cellular Uptake of Nanoparticles: Insights from Experimental, Computational, and Theoretical Investigations

The cellular uptake of nanoparticles (NPs) by biological cells is an important and fundamental process in drug delivery. Previous studies reveal that the physicochemical properties of nanoparticles as well as those of functionalized ligands can both critically affect the uptake behaviors. However, the effect of the conjugation strategy (i.e., the "bond" between the ligand and the NP) on the cellular uptake is overlooked and remains largely elusive. Here, by taking the broadly employed gold nanoparticle as an example, we comprehensively assessed the relationship between the conjugation strategy and uptake behaviors by introducing three ligands with the same functional terminal but different anchoring sites. As revealed by in vitro cell experiments and multiscale molecular simulations, the uptake efficiency of gold NPs was positively correlated with the strength of the "bond" and more specifically the ligand mobility on the NP surface. Moreover, we validated the results presented above by proposing a thermodynamic theory for the wrapping of NPs with mobile ligands. Further, we also showed that the endocytic pathway of NPs was highly dependent on ligand mobility. Overall, this study uncovered a vital role of conjugation strategy in the cellular uptake and may provide useful guidelines for tailoring the biobehaviors of nanoparticles.

Controlling the Nucleation and Growth of Au on a-Se Nanospheres to Enhance Their Cellular Uptake and Cytotoxicity

We report a method to experimentally control the heterogeneous nucleation and growth of Au nanoparticles on the surface of amorphous Se (a-Se) nanospheres. When a Au^III precursor is added into a colloidal suspension of a-Se nanospheres, galvanic replacement occurs between them and the resultant Au⁰ atoms then heterogeneously nucleate and grow from the surface of the a-Se nanospheres. As a unique feature of this system, the Au⁰ atoms can only be produced on the surface of the a-Se nanospheres in the nucleation stage. Once Au nuclei are formed on the surface at the very beginning of a synthesis, they will serve as the preferential sites for further deposition of Au⁰ atoms, making it possible to control the number of Au nanoparticles on each nanosphere and the morphology of the final product. The dependence of the initial reduction rate on the pH can be used to obtain Se-Au hybrid nanoparticles containing one, two, three, and multiple Au nanoparticles on the surface of each a-Se nanosphere. The presence of Au patches on the hybrid nanoparticles offers an experimental handle to optimize the ligand distribution for the achievement of enhanced cellular uptake and cytotoxicity for the a-Se nanospheres.

Synergistic Entry of Individual Nanoparticles into Mammalian Cells Driven by Free Energy Decline and Regulated by Their Sizes

Cell entry is one of the common prerequisites for nanomaterial applications. Despite extensive studies on a homogeneous group of nanoparticles (NPs), fewer studies have been performed when two or more types of NPs were coadministrated. We previously described a synergistic cell entry process for two heterogeneous groups of NPs, where NPs functionalized with TAT (transactivator of transcription) peptide (T-NPs) stimulate the cellular uptake of coadministered unfunctionalized NPs (bystander NPs, B-NPs). Here, we show that the synergistic cell entry of NPs is driven by free energy decline and depends on B-NP sizes. Simulations showed that when separately placed initially, two NPs first move toward each other instead of initiating cell entry individually. Only T-NP invokes an inward bending of membrane mimicking endocytosis, which attracts the nearby NPs into the same "vesicle". A two-phase free energy decline of the entire system occurred as two NPs get closer until contact, which is likely the thermodynamic driver for synergistic NP coentry. Experimentally, we found that T-NPs increase the apparent affinity of B-NPs to plasma membrane, suggesting that T-NPs help B-NPs "trapped" in the endocytic vesicles. Next, we varied the sizes of B-NPs and found that bystander activity peaks around 50 nm. Simulations also showed that the size of B-NPs influences the free energy decline, and thus the tendency and dynamics of NP coentry. These efforts provide a system to further understand the synergistic cell entry among individual NPs or multiple NP types on a biophysical basis and shed light on the future design of nanostructures for intracellular delivery.

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...

Effect of micro- and nanoparticle shape on biological processes

In the drug delivery field, there is beyond doubt that the shape of micro- and nanoparticles (M&NPs) critically affects their biological fate. Herein, following an introduction describing recent technological advances for designing nonspherical M&NPs, we highlight the role of particle shape in cell capture, subcellular distribution, intracellular drug delivery, and cytotoxicity. Then, we discuss theoretical approaches for understanding the effect of particle shape on internalization by the cell membrane. Subsequently, recent advances on shape-dependent behaviors of M&NPs in the systemic circulation are detailed. In particular, the interaction of M&NPs with blood proteins, biodistribution, and circulation under flow conditions are analyzed. Finally, the hurdles and future directions for developing nonspherical M&NPs are underscored.

Tuning cellular uptake of nanoparticles via ligand density: Contribution of configurational entropy

The bioactivity of nanoparticles (NPs) crucially depends on their ability to cross biological membranes. A fundamental understanding of cell-NP interaction is hence essential to improve the performance of the NP-based biomedical applications. Although extensive studies of cellular uptake have converged upon the idea that the uptake process is mainly regulated by the elastic deformation of the cell membrane or NP, recent experimental observations indicate the ligand density as another critical factor in modulating NP uptake into cells. In this study, we propose a theoretical model of the wrapping of an elastic vesicle NP by a finite lipid membrane to depict the relevant energetic and morphological evolutions during the wrapping process driven by forming receptor-ligand bonds. In this model, the deformations of the membrane and the vesicle NP are assumed to follow the continuum Canham-Helfrich framework, whereas the change of configurational entropy of receptors is described from statistical thermodynamics. Results show that the ligand density strongly affects the binding energy and configurational entropy of free receptors, thereby altering the morphology of the vesicle-membrane system in the steady wrapping state. For the wrapping process by the finite lipid membrane, we also find that there exists optimal ligand density for the maximum wrapping degree. These predictions are consistent with relevant experimental observations reported in the literature. We have further observed that there are transitions of various wrapping phases (no wrapping, partial wrapping, and full wrapping) in terms of ligand density, membrane tension, and molecular binding energy. In particular, the ligand and receptor shortage regimes for the small and high ligand density are, respectively, identified. These results may provide guidelines for the rational design of nanocarriers for drug delivery.

Geometallurgical Characterisation with Portable FTIR: Application to Sediment-Hosted Cu-Co Ores

Cobalt (Co) mine production primarily originates from the sediment-hosted copper (Cu) deposits of the Democratic Republic of Congo (DRC). These deposits usually consist of three ore zones with a supergene oxide ore blanket overlying a transition zone which grades into a sulphide zone at depth. Each of these zones display a mineral assemblage with varying gangue mineralogy and, most importantly, a distinct state of oxidation of the mineralisation. This has direct implications for Cu and Co extraction during mineral processing as it dictates which processing method is to be used (i.e., leaching vs. flotation) and affects the performance of these. To optimise resource efficiency, reduce technical risks and environmental impacts, comprehensive understanding of variation of ore mineralogy and texture in the deposit is essential. By defining geometallurgical ore types according to their inferred metallurgical behaviour, this information can serve to classify the resources and improve resource management. To obtain insight into the spatial distribution of mineral grades, it is necessary to develop techniques that have the potential to measure rapidly and, preferably, within the mine at relatively low-cost. In this study, the application of portable Fourier transformed infrared (FTIR) spectroscopy is investigated to measure the mineralogy of drill core samples. A set of samples from a sediment-hosted Cu-Co deposit in DRC was selected to test this approach. Results were validated using automated mineralogy (QEMSCAN). Prediction of gangue and target mineral grades from the FTIR spectra was achieved through partial least squares regression (PLS-R) combined with competitive adaptive reweighted sampling (CARS). It is shown that the modal mineralogy obtained from FTIR can be used to classify the ore according to type of mineralisation and gangue mineralogy into geometallurgical ore types. This classification supports selection of a suitable processing route and is likely to affect the overall process performance.

Role of Ligand Distribution in the Cytoskeleton-Associated Endocytosis of Ellipsoidal Nanoparticles

Nanoparticle (NP)–cell interaction mediated by receptor–ligand bonds is a crucial phenomenon in pathology, cellular immunity, and drug delivery systems, and relies strongly on the shape of NPs and the stiffness of the cell. Given this significance, a fundamental question is raised on how the ligand distribution may affect the membrane wrapping of non-spherical NPs under the influence of cytoskeleton deformation. To address this issue, in this work we use a coupled elasticity–diffusion model to systematically investigate the role of ligand distribution in the cytoskeleton-associated endocytosis of ellipsoidal NPs for different NP shapes, sizes, cytoskeleton stiffness, and the initial receptor densities. In this model, we have taken into account the effects of receptor diffusion, receptor–ligand binding, cytoskeleton and membrane deformations, and changes in the configuration entropy of receptors. By solving this model, we find that the uptake process can be significantly influenced by the ligand distribution. Additionally, there exists an optimal state of such a distribution, which corresponds to the fastest uptake efficiency and depends on the NP aspect ratio and cytoskeleton stiffness. We also find that the optimal distribution usually needs local ligand density to be sufficiently high at the large curvature region. Furthermore, the optimal state of NP entry into cells can tolerate slight changes to the corresponding optimal distribution of the ligands. The tolerance to such a change is enhanced as the average receptor density and NP size increase. These results may provide guidelines to control NP–cell interactions and improve the efficiency of target drug delivery systems.

Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study

Functionalized metal nanoparticles (NPs) hold great promise as innovative tools in nanomedicine. However, one of the main challenges is how to optimize their association with the cell membrane, which is critical for their effective delivery. Recent findings show high cellular uptake rates for NPs coated with the polycationic cell-penetrating peptide gH625-644 (gH), although the underlying internalization mechanism is poorly understood. Here, we use extended coarse-grained simulations and free energy calculations to study systems that simultaneously include metal NPs, peptides, lipids, and sterols. In particular, we investigate the first encounter between multicomponent model membranes and 2.5 nm metal NPs coated with gH (gHNPs), based on the evidence from scanning transmission electron microscopy. By comparing multiple membrane and (membranotropic) NP models, we found that gHNP internalization occurs by forming an intermediate state characterized by specific stabilizing interactions formed by peptide-coated nanoparticles with multicomponent model membranes. This association mechanism is mainly characterized by interactions of gH with the extracellular solvent and the polar membrane surface. At the same time, the NP core interacts with the transmembrane (cholesterol-rich) fatty phase.

Elucidating Carbohydrate-Protein Interactions Using Nanoparticle-Based Approaches

Carbohydrates are present on every living cell and coordinate important processes such as self/non-self discrimination. They are amongst the first molecular determinants to be encountered when cellular interactions are initiated. In particular, they resemble essential molecular fingerprints such as pathogen-, danger-, and self-associated molecular patterns guiding key decision-making in cellular immunology. Therefore, a deeper understanding of how cellular receptors of the immune system recognize incoming particles, based on their carbohydrate signature and how this information is translated into a biological response, will enable us to surgically manipulate them and holds promise for novel therapies. One approach to elucidate these early recognition events of carbohydrate interactions at cellular surfaces is the use of nanoparticles coated with defined carbohydrate structures. These particles are captured by carbohydrate receptors and initiate a cellular cytokine response. In the case of endocytic receptors, the capturing enables the engulfment of exogenous particles. Thereafter, the particles are sorted and degraded during their passage in the endolysosomal pathway. Overall, these processes are dependent on the nature of the endocytic carbohydrate receptors and consequently reflect upon the carbohydrate patterns on the exogenous particle surface. This interplay is still an under-studied subject. In this review, we summarize the application of nanoparticles as a promising tool to monitor complex carbohydrate-protein interactions in a cellular context and their application in areas of biomedicine.

Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures

In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry.

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.

Effect of Physico-Chemical Properties of Nanoparticles on Their Intracellular Uptake

Cellular internalization of inorganic, lipidic and polymeric nanoparticles is of great significance in the quest to develop effective formulations for the treatment of high morbidity rate diseases. Understanding nanoparticle–cell interactions plays a key role in therapeutic interventions, and it continues to be a topic of great interest to both chemists and biologists. The mechanistic evaluation of cellular uptake is quite complex and is continuously being aided by the design of nanocarriers with desired physico-chemical properties. The progress in biomedicine, including enhancing the rate of uptake by the cells, is being made through the development of structure–property relationships in nanoparticles. We summarize here investigations related to transport pathways through active and passive mechanisms, and the role played by physico-chemical properties of nanoparticles, including size, geometry or shape, core-corona structure, surface chemistry, ligand binding and mechanical effects, in influencing intracellular delivery. It is becoming clear that designing nanoparticles with specific surface composition, and engineered physical and mechanical characteristics, can facilitate their internalization more efficiently into the targeted cells, as well as enhance the rate of cellular uptake.

Gold Nanoparticle Mediated Multi-Modal CT Imaging of Hsp70 Membrane-Positive Tumors

Imaging techniques such as computed tomographies (CT) play a major role in clinical imaging and diagnosis of malignant lesions. In recent years, metal nanoparticle platforms enabled effective payload delivery for several imaging techniques. Due to the possibility of surface modification, metal nanoparticles are predestined to facilitate molecular tumor targeting. In this work, we demonstrate the feasibility of anti-plasma membrane Heat shock protein 70 (Hsp70) antibody functionalized gold nanoparticles (cmHsp70.1-AuNPs) for tumor-specific multimodal imaging. Membrane-associated Hsp70 is exclusively presented on the plasma membrane of malignant cells of multiple tumor entities but not on corresponding normal cells, predestining this target for a tumor-selective in vivo imaging. In vitro microscopic analysis revealed the presence of cmHsp70.1-AuNPs in the cytosol of tumor cell lines after internalization via the endo-lysosomal pathway. In preclinical models, the biodistribution as well as the intratumoral enrichment of AuNPs were examined 24 h after i.v. injection in tumor-bearing mice. In parallel to spectral CT analysis, histological analysis confirmed the presence of AuNPs within tumor cells. In contrast to control AuNPs, a significant enrichment of cmHsp70.1-AuNPs has been detected selectively inside tumor cells in different tumor mouse models. Furthermore, a machine-learning approach was developed to analyze AuNP accumulations in tumor tissues and organs. In summary, utilizing mHsp70 on tumor cells as a target for the guidance of cmHsp70.1-AuNPs facilitates an enrichment and uniform distribution of nanoparticles in mHsp70-expressing tumor cells that enables various microscopic imaging techniques and spectral-CT-based tumor delineation in vivo.

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.

Role of Surface RGD Patterns on Protein Nanocages in Tumor Targeting Revealed Using Precise Discrete Models

The effectiveness of active targeting in cancer nanomedicine is becoming increasingly more debatable. Here, the role of the ligand functionalization patterns (number and distribution) on nanoparticle surfaces in tumor targeting is investigated using a 9 nm sized miniferritin protein nanocage, Dps modified with Arg-Gly-Asp (RGD) ligands whose functionalization patterns are precisely controlled. In vitro and in vivo experiments show that RGD modification endows Dps with tumor targeting capacity no matter what the surface pattern is. The tumor targeting of 2-ligand Dps, which is better than that of 1-ligand Dps, rivals or surpasses that of the 12- or 24-ligand Dps. The 12-ligand Dps with clustered RGD distribution shows 2.3 times the in vivo targeting efficiency of that with even distribution. The surface ligand pattern effects are correlated at least to receptor clustering and opsonization. This study provides insights into the understanding of the controversial findings on active tumor targeting in the literature and highlights the necessity of precise functionalization to achieve optimal active targeting in developing cancer nanomedicine.

Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces

At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes where, among other functions, they control cell adhesion, motility and tissue formation. Besides being central to several biological processes, multivalent interactions mediated by reactive linkers confined to deformable substrates underpin the design of synthetic-biological platforms and advanced biomimetic materials. Here we review recent advances on the experimental study and theoretical modelling of a heterogeneous class of biomimetic systems in which synthetic linkers mediate multivalent interactions between fluid and deformable colloidal units, including lipid vesicles and emulsion droplets. Linkers are often prepared from synthetic DNA nanostructures, enabling full programmability of the thermodynamic and kinetic properties of their mutual interactions. The coupling of the statistical effects of multivalent interactions with substrate fluidity and deformability gives rise to a rich emerging phenomenology that, in the context of self-assembled soft materials, has been shown to produce exotic phase behaviour, stimuli-responsiveness, and kinetic programmability of the self-assembly process. Applications to (synthetic) biology will also be reviewed.

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.

Multivalent Binding of a Ligand-Coated Particle: Role of Shape, Size, and Ligand Heterogeneity

We utilize a multiscale modeling framework to study the effect of shape, size, and ligand composition on the efficacy of binding of a ligand-coated particle to a substrate functionalized with the target receptors. First, we show how molecular dynamics along with steered molecular dynamics calculations can be used to accurately parameterize the molecular-binding free energy and the effective spring constant for a receptor-ligand pair. We demonstrate this for two ligands that bind to the α₅β₁-domain of integrin. Next, we show how these effective potentials can be used to build computational models at the meso- and continuum-scales. These models incorporate the molecular nature of the receptor-ligand interactions and yet provide an inexpensive route to study the multivalent interaction of receptors and ligands through the construction of Bell potentials customized to the molecular identities. We quantify the binding efficacy of the ligand-coated-particle in terms of its multivalency, binding free-energy landscape, and the losses in the configurational entropies. We show that 1) the binding avidity for particle sizes less than 350 nm is set by the competition between the enthalpic and entropic contributions, whereas that for sizes above 350 nm is dominated by the enthalpy of binding; 2) anisotropic particles display higher levels of multivalent binding compared to those of spherical particles; and 3) variations in ligand composition can alter binding avidity without altering the average multivalency. The methods and results presented here have wide applications in the rational design of functionalized carriers and also in understanding cell adhesion.

Directional and Rotational Motions of Nanoparticles on Plasma Membranes as Local Probes of Surface Tension Propagation

Mechanical heterogeneity is ubiquitous in plasma membranes and of essential importance to cellular functioning. As a feedback of mechanical stimuli, local surface tension can be readily changed and immediately propagated through the membrane, influencing structures and dynamics of both inclusions and membrane-associated proteins. Using the nonequilibrium coarse-grained membrane simulation, here we investigate the inter-related processes of tension propagation, lipid diffusion, and transport of nanoparticles (NPs) adhering on the membrane of constant tension gradient, mimicking that of migrating cells or cells under prolonged stimulation. Our results demonstrate that the lipid bilayer membrane can by itself propagate surface tension in defined rates and pathways to reach a dynamic equilibrium state where surface tension is linearly distributed along the gradient maintained by the directional flow-like motion of lipids. Such lipid flow exerts shearing forces to transport adhesive NPs toward the region of a larger surface tension. Under certain conditions, the shearing force can generate nonzero torques driving the rotational motion of NPs, with the direction of the NP rotation determined by the NP-membrane interaction state as functions of both NP property and local membrane surface tension. Such features endow NPs with promising applications ranging from biosensing to targeted drug delivery.

Kinetics of Nanoparticle-Membrane Adhesion Mediated by Multivalent Interactions

Multivalent adhesive interactions mediated by a large number of ligands and receptors underpin many biological processes, including cell adhesion and the uptake of particles, viruses, parasites, and nanomedical vectors. In materials science, multivalent interactions between colloidal particles have enabled unprecedented control over the phase behavior of self-assembled materials. Theoretical and experimental studies have pinpointed the relationship between equilibrium states and microscopic system parameters such as the ligand-receptor binding strength and their density. In regimes of strong interactions, however, kinetic factors are expected to slow down equilibration and lead to the emergence of long-lived out-of-equilibrium states that may significantly influence the outcome of self-assembly experiments and the adhesion of particles to biological membranes. Here we experimentally investigate the kinetics of adhesion of nanoparticles to biomimetic lipid membranes. Multivalent interactions are reproduced by strongly interacting DNA constructs, playing the role of both ligands and receptors. The rate of nanoparticle adhesion is investigated as a function of the surface density of membrane-anchored receptors and the bulk concentration of nanoparticles and is observed to decrease substantially in regimes where the number of available receptors is limited compared to the overall number of ligands. We attribute such peculiar behavior to the rapid sequestration of available receptors after initial nanoparticle adsorption. The experimental trends and the proposed interpretation are supported by numerical simulations.

Galactose:PEGamine coated gold nanoparticles adhere to filopodia and cause extrinsic apoptosis

Ultra-small gold nanoparticles, surface functionalised with a 50 : 50 ratio of a thiolated α-galactose derivative and a thiolated hexaethylene glycol amine, are toxic to HSC-3 oral squamous carcinoma cells. Differences in nanoparticle toxicity were found to be related to the synthesis duration, with 1 h reaction nanoparticles being less toxic than 5 h reaction nanoparticles. The ligand density decreased with longer reaction time, although the size, charge and ligand ratio remained similar. The concentration of sodium borohydride in the reaction decreased logarithmically over 5 h but remained within a concentration range sufficient to desorb weakly bound ligands, possibly explaining the observed gradual decrease in ligand density. Nanoparticle toxicity was abrogated by inhibition of either caspase 3/7 or caspase 8, but not by inhibition of caspase 9, consistent with extrinsic apoptosis. Electron microscopic analysis of cellular uptake demonstrated predominantly cytoplasmic localization. However, when energy-dependent transport was inhibited, by lowering the temperature to 4 °C, a remarkable adhesion of nanoparticles to filopodia was observed. Inhibition of filopodial assembly with a fascin inhibitor prevented nanoparticle adhesion to HSC-3 cells at 4 °C, while fascin inhibition at 37 °C resulted in less cytoplasmic uptake. More adhesion to HSC-3 filopodia was seen with the higher toxicity 5 h reaction time nanoparticles than with the 1 h nanoparticles. By including two further cell types (HaCaT keratinocytes and hCMEC/D3 endothelial cells), a pattern of increasing toxicity with filopodial binding of 5 h reaction nanoparticles became apparent.

Controlling Cargo Trafficking in Multicomponent Membranes

Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such "inert" components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.

Understanding receptor-mediated endocytosis of elastic nanoparticles through coarse grained molecular dynamic simulation

For nanoparticle (NP)-based drug delivery platforms, the elasticity of the NPs has a significant influence on their blood circulation time and cellular uptake efficiency. However, due to the complexity of the endocytosis process and the inconsistency in the definition of elasticity for NPs in experiments, the understanding about the receptor-mediated endocytosis process of elastic NPs is still limited. In this work, we developed a coarse-grained molecular dynamics (CGMD) model for elastic NPs. The energy change of the elastic NPs can be precisely controlled by the bond, area, volume and bending potentials of this CGMD model. To represent liposomes with different elasticities, we systematically varied the bending rigidity of elastic NPs in CGMD simulations. Additionally, we changed the radius of the elastic NPs to explore the potential size effect. Through virtual nano-indentation tests, we found that the effective stiffness of elastic NPs was determined by their bending rigidity and size. Afterwards, we investigated the receptor-mediated endocytosis process of elastic NPs with different sizes and bending rigidities. We found that the membrane wrapping of soft NPs was faster than that of the stiff ones at the early stage, due to the NP deformation induced large contact area between the NPs and the membrane. However, because of the large energy penalties induced by the NP deformation, the membrane wrapping speed of soft NPs slows down during the late stage. Eventually, the soft NPs are wrapped less efficiently than the stiff ones during the membrane wrapping process. Through systematic CGMD simulations, we found a scaling law between the cellular uptake efficiency and the phenomenal bending rigidity of elastic NPs, which agrees reasonably well with experimental observations. Furthermore, we observed that the membrane wrapping efficiencies of soft and stiff NPs with large sizes were close to each other, due to the stronger ligand-receptor binding force and smaller difference in the stiffness of elastic NPs. Our computational model provides an effective tool to investigate the receptor-mediated endocytosis of elastic NPs with well controlled mechanical properties. This study can also be applied to guide the design of NP-based drug carriers with high efficacy, by utilizing their elastic properties.

Aggregation of polyethylene glycol polymers suppresses receptor-mediated endocytosis of PEGylated liposomes

The PEGylated liposome, composed of an aqueous core and a fluid state lipid bilayer shell, is one of the few Food and Drug Administration (FDA) approved drug delivery platforms. To prevent the absorption of serum proteins, the surface of a liposome is decorated by hydrophilic and bio-compatible polyethylene glycol (PEG) polymers, which can significantly extend the blood circulation time of liposomes. In this work, with the help of dissipative particle dynamics (DPD) simulations, we explore how the tethered PEG polymers will affect the membrane wrapping process of PEGylated liposomes during endocytosis. Specifically, we compare the membrane wrapping process of a PEGylated rigid nanoparticle (NP) with a PEGylated liposome under identical conditions. Due to the mobility of grafted PEG polymers on the liposome's surface, the complete wrapping of a PEGylated liposome can be dramatically delayed and blocked, in comparison with a PEGylated rigid NP. For the first time, we observe the aggregation of PEG polymers in the contact region between a PEGylated liposome and the membrane, which in turn leads to a ligand-free region on the surface of the liposome during endocytosis. Subsequently, the partially wrapped PEGylated liposome can be bounced back to a less wrapped state. Through free energy analysis, we find that the aggregation of PEG polymers during the membrane wrapping process of a PEGylated liposome introduces a dramatic free energy penalty of about ∼800k_BT, which is almost twice that of a PEGylated rigid NP. Here k_B and T are the Boltzmann constant and temperature, respectively. Such a large energy barrier and the existence of a ligand-free region on the surface of PEGlylated liposomes prevent their membrane wrapping, thereby reducing the chance of internalization by tumor cells. Therefore, our DPD simulation results provide a possible explanation for the inefficient cellular uptake of PEGylated liposomes. In addition, we suggest that by increasing the repulsive interactions between grafted PEG polymers it might be possible to limit their aggregation, and in turn, facilitate the internalization of PEGylated liposomes. The current study provides fundamental insights into the endocytosis of PEGylated liposomes, which could help to design this platform with high efficacy for drug delivery.

Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity

Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.

Design of Multivalent Inhibitors for Preventing Cellular Uptake

Cellular entry, the first crucial step of viral infection, can be inhibited by molecules adsorbed on the virus surface. However, apart from using stronger affinity, little is known about the properties of such inhibitors that could increase their effectiveness. Our simulations showed that multivalent inhibitors can be designed to be much more efficient than their monovalent counterparts. For example, for our particular simulation model, a single multivalent inhibitor spanning 5 to 6 binding sites is enough to prevent the uptake compared to the required 1/3 of all the receptor binding sites needed to be blocked by monovalent inhibitors. Interestingly, multivalent inhibitors are more efficient in inhibiting the uptake not only due to their increased affinity but mainly due to the co-localization of the inhibited receptor binding sites at the virion's surface. Furthermore, we show that Janus-like inhibitors do not induce virus aggregation. Our findings may be generalized to other uptake processes including bacteria and drug-delivery.

Multivalent ligand-receptor-mediated interaction of small filled vesicles with a cellular membrane

The ligand-receptor-mediated contacts of small sub-100-nm-sized lipid vesicles (or nanoparticles) with the cellular membrane are of interest in the contexts of cell-to-cell communication, endocytosis of membrane-coated virions, and drug (RNA) delivery. In all these cases, the interior of vesicles is filled by biologically relevant content. Despite the diversity of such systems, the corresponding ligand-receptor interaction possesses universal features. One of them is that the vesicle-membrane contacts can be accompanied by the redistribution of ligands and receptors between the contact and contact-free regions. In particular, the concentrations of ligands and receptors may become appreciably higher in the contact regions and their composition may there be different compared to that in the suspended state in the solution. A statistical model presented herein describes the corresponding distribution of various ligands and receptors and allows one to calculate the related change of the free energy with variation of the vesicle-engulfment extent. The results obtained are used to clarify the necessary conditions for the vesicle-assisted pathway of drug delivery.

Can dual-ligand targeting enhance cellular uptake of nanoparticles?

Dual ligand targeting to different types of over-expressed receptors on cell surfaces is a promising strategy in nanomedicine. Here, by using dissipative particle dynamics simulations, the effect of the surface distribution and physicochemical properties of dual ligands on the cellular uptake of nanoparticles is systematically studied. It is found that the spontaneous rearrangement of dual ligands (from random to patterned distribution) on the nanoparticle surface can enhance the cellular uptake of nanoparticles. While the short length of ligands may restrict the ligand rearrangement, nanoparticles coated with short dual ligands cannot be fully wrapped by cell membranes unless the dual ligands are initially separated on the nanoparticle surface. Besides, when there exists a length mismatch or non-specific interaction between the dual ligands, dual-ligand targeting cannot enhance the uptake efficiency, either. Further, we also provide the design guidelines for surface decoration, and find that the Janus nanoparticle can make the most of dual-ligand targeting. These results can help understand how to better use dual ligands to achieve efficient cellular uptake, which may provide significant insights into the optimal design of future nanomaterials in drug delivery.

Cellular Internalization of Rod-Like Nanoparticles with Various Surface Patterns: Novel Entry Pathway and Controllable Uptake Capacity

The cellular internalization of rod-like nanoparticles (NPs) is investigated in a combined experimental and simulation study. These rod-like nanoparticles with smooth, abacus-like (i.e., beads-on-wires), and helical surface patterns are prepared by the cooperative self-assembly of poly(γ-benzyl-l-glutamate)-block-poly(ethylene glycol) (PBLG-b-PEG) block copolymers and PBLG homopolymers. All three types of NPs can be internalized via endocytosis. Helical NPs exhibit the best endocytic efficacy, followed by smooth NPs and abacus-like NPs. Coarse-grained molecular dynamics simulations are used to examine the endocytic efficiency of these NPs. The NPs with helical and abacus-like surfaces can be endocytosed via novel "standing up" (tip entry) and "gyroscope-like" (precession) pathways, respectively, which are distinct from the pathway of traditional NPs with smooth surfaces. This finding indicates that the cellular internalization capacity and pathways can be regulated by introducing stripe patterns (helical and abacus-like) onto the surface of rod-like NPs. The results of this study may lead to novel applications of biomaterials, such as advanced drug delivery systems.

Effects of ligand distribution on receptor-diffusion-mediated cellular uptake of nanoparticles

Biophysical-factor-dependent cellular uptake of nanoparticles (NPs) through receptor-diffusion-mediated endocytosis bears significance in pathology, cellular immunity and drug-delivery systems. Advanced nanotechnology of NP synthesis provides methods for modifying NP surface with different ligand distributions. However, no report discusses effects of ligand distribution on NP surface on receptor-diffusion-mediated cellular uptake. In this article, we used a statistical dynamics model of receptor-diffusion-mediated endocytosis to examine ligand-distribution-dependent cellular uptake dynamics by considering that ligand-receptor complexes drive engulfing to overcome resistance to membrane deformation and changes in configuration entropy of receptors. Results showed that cellular internalization of NPs strongly depended on ligand distribution and that cellular-uptake efficiency of NPs was high when ligand distribution was within a range around uniform distribution. This feature of endocytosis ensures robust infection ability of viruses to enter host cells. Interestingly, results also indicated that optimal ligand distribution associated with highest cellular-uptake efficiency slightly depends on distribution pattern of ligands and density of receptors, and the optimal distribution becomes uniform when receptor density is sufficiently large. Position of initial contact point is also a factor affecting dynamic wrapping. This study explains why most enveloped viruses present almost homogeneous ligand distribution and is useful in designing controlled-release drug-delivery systems.

Interaction Pathways between Plasma Membrane and Block Copolymer Micelles

In this work, the interactions between block copolymer micelles (BCMs) and plasma membranes were investigated by performing coarse-grained molecular dynamics (CGMD) simulations. Different binding strengths between the BCMs and the membranes were tested, and four interaction pathways were discovered: attachment, semiendocytosis, endocytosis, and fusion. Endocytosis was the most efficient way for the BCMs to be taken up, and fusion could lead to cytotoxicity. Unlike rigid particles, deformation of the BCMs strongly affected the interaction pathways. We examined the effects of changing the aggregation number of the BCMs (N_agg), the chain length of the polymer (N_b), and the chain stiffness of the hydrophobic block (k_a), and we learned that smaller N_agg and lower N_b could lead to weaker cellular uptake capacities, whereas larger N_agg and higher N_b gave rise to higher cytotoxicities. Moreover, a weaker chain stiffness of the hydrophobic block could be more favorable for obtaining BCMs with higher internalization efficacies and lower cytotoxicities. The results of these simulations could aid in the design of BCMs with desirable cellular internalization capacities and lower cytotoxicities. Such BCMs could be useful in drug-delivery systems.

Kinetics of receptor-mediated endocytosis of elastic nanoparticles

It is now widely recognized that mechanical properties play critical roles in the cell uptake of nanomaterials. Here we conduct a theoretical study on the kinetics of receptor-mediated endocytosis of elastic nanoparticles that is limited by receptor diffusion, specifically focusing on how the uptake rate depends on the nanoparticle stiffness and size, membrane tension and binding strength between membrane receptors and ligands grafted on the nanoparticle surface. It is shown that, while soft nanoparticles are energetically less prone to full wrapping than stiff ones, the wrapping of the former is kinetically faster than that of the latter. Spherical and cylindrical elastic nanoparticles show dramatic differences in the effect of stiffness on the uptake rate. Additional theoretical analysis is performed to investigate the role of the stochastic receptor-ligand binding in the endocytosis of elastic nanoparticles. The relation between the uptake efficiency and uptake proneness is discussed. This study provides new insight into the elasticity effects on cell uptake and may serve as a design guideline for the controlled endocytosis and diagnostics delivery.

Facilitating the Clinical Integration of Nanomedicines: The Roles of Theoretical and Computational Scientists

Since the launch of multiple research initiatives on nanotechnology applied to medicine in the early 2000s, a plethora of nanomedicines have been developed that exhibit great therapeutic efficacy in preclinical models but yet minimal impact in daily clinical practice. The successful and complete clinical fruition of nanomedicines requires addressing three major technical challenges: improving loading efficacy and on-command release, modulating recognition and sequestration by immune cells, and maximizing accumulation at biological targets. In this Perspective, I describe how theoretical and computational models can help address each of these challenges. This armamentarium represents an ideal tool for maximizing the therapeutic efficacy of nanomedicines, thus facilitating their integration into daily clinical operations.

Imaging of Hsp70-positive tumors with cmHsp70.1 antibody-conjugated gold nanoparticles

Real-time imaging of small tumors is still one of the challenges in cancer diagnosis, prognosis, and monitoring of clinical outcome. Targeting novel biomarkers that are selectively expressed on a large variety of different tumors but not normal cells has the potential to improve the imaging capacity of existing methods such as computed tomography. Herein, we present a novel technique using cmHsp70.1 monoclonal antibody-conjugated spherical gold nanoparticles for quantification of the targeted uptake of gold nanoparticles into membrane Hsp70-positive tumor cells. Upon binding, cmHsp70.1-conjugated gold nanoparticles but not nanoparticles coupled to an isotype-matched IgG1 antibody or empty nanoparticles are rapidly taken up by highly malignant Hsp70 membrane-positive mouse tumor cells. After 24 hours, the cmHsp70.1-conjugated gold nanoparticles are found to be enriched in the perinuclear region. Specificity for membrane Hsp70 was shown by using an Hsp70 knockout tumor cell system. Toxic side effects of the cmHsp70.1-conjugated nanoparticles are not observed at a concentration of 1–10 µg/mL. Experiments are ongoing to evaluate whether cmHsp70.1 antibody-conjugated gold nanoparticles are suitable for the detection of membrane-Hsp70-positive tumors in vivo.