Multiscale Modeling and Simulation of Nano‐Carriers Delivery through Biological Barriers—A Review

Single core and multicore aggregates from a polymer mixture: A dissipative particle dynamics study

HYPOTHESIS

Multicore block copolymer aggregates correspond to self-assembly such that the polymer system spontaneously phase separates to multiple, droplet-like cores differing in the composition from the polymer surroundings. Such multiple core aggregates are highly useful capsules for different applications, e.g., drug transport, catalysis, controlled solvation, and chemical reactions platforms. We postulate that polymer system composition provides a direct means for designing polymer systems that self-assemble to such morphologies and controlling the assembly response.

SIMULATIONS

Using dissipative particle dynamics (DPD) simulations, we examine the self-assembly of a mixture of highly and weakly solvophobic homopolymers and an amphiphilic block copolymer in the presence of solvent. We map the multicore vs single core (core-shell particles) assembly response and aggregate structure in terms of block copolymer concentration, polymer component ratios, and chain length of the weakly solvophobic homopolymer.

FINDINGS

For fixed components and polymer chemistries, the amount of block copolymer is the key to controlling single core vs multicore aggregation. We find a polymer system dependent critical copolymer concentration for the multicore aggregation and that a minimum level of incompatibility between the solvent and the weakly solvophobic component is required for multicore assembly. We discuss the implications for polymer system design for multicore assemblies. In summary, the study presents guidelines to produce multicore aggregates and to tune the assembly from multicore aggregation to single core core-shell particles.

Computational modeling of passive transport of functionalized nanoparticles

Functionalized nanoparticles (NPs) are complex objects present in a variety of systems ranging from synthetic grafted nanoparticles to viruses. The morphology and number of the decorating groups can vary widely between systems. Thus, the modeling of functionalized NPs typically considers simplified spherical objects as a first-order approximation. At the nanoscale label, complex hydrodynamic interactions are expected to emerge as the morphological features of the particles change, and they can be further amplified when the NPs are confined or near walls. Direct estimation of these variations can be inferred via diffusion coefficients of the NPs. However, the evaluation of the coefficients requires an improved representation of the NPs morphology to reproduce important features hidden by simplified spherical models. Here, we characterize the passive transport of free and confined functionalized nanoparticles using the Rigid Multi-Blob (RMB) method. The main advantage of RMB is its versatility to approximate the mobility of complex structures at the nanoscale with significant accuracy and reduced computational cost. In particular, we investigate the effect of functional groups' distribution, size, and morphology over nanoparticle translational and rotational diffusion. We identify that the presence of functional groups significantly affects the rotational diffusion of the nanoparticles; moreover, the morphology of the groups and number induce characteristic mobility reduction compared to non-functionalized nanoparticles. Confined NPs also evidenced important alterations in their diffusivity, with distinctive signatures in the off-diagonal contributions of the rotational diffusion. These results can be exploited in various applications, including biomedical, polymer nanocomposite fabrication, drug delivery, and imaging.

Effects of Shape on Interaction Dynamics of Tetrahedral Nanoplastics and the Cell Membrane

Cellular uptake of nanoplastics is instrumental in their environmental accumulation and transfer to humans through the food chain. Despite extensive studies using spherical plastic nanoparticles, the influence of the morphological characteristics of environmentally released nanoplastics is understudied. Using dissipative particle dynamics simulations, we modeled the interactions between a cell membrane and hydrophobic nanotetrahedra, which feature high shape anisotropy and large surface curvature seen for environmental nanoplastics. We observe robust uptake of nanotetrahedra with sharp vertices and edges by the lipid membrane. Two local energy minimum configurations of nanotetrahedra embedded in the membrane bilayer were identified for particles of large sizes. Further analysis of particle dynamics within the membrane shows that the two interaction states exhibit distinct translational and rotational dynamics in the directions normal and parallel to the plane of the membrane. The membrane confinement significantly arrests the out-of-plane motion, resulting in caged translation and subdiffusive rotation. While the in-plane diffusion remains Brownian, we find that the translational and rotational modes decouple from each other as the particle size increases. The rotational diffusion decreases by a greater extent compared to the translational diffusion, deviating from the continuum theory predictions. These results provide fundamental insights into the shape effect on the nanoparticle dynamics in crowded lipid membranes.

Fluorescent Multifunctional Organic Nanoparticles for Drug Delivery and Bioimaging: A Tutorial Review

Fluorescent organic nanoparticles (FONs) are a large family of nanostructures constituted by organic components that emit light in different spectral regions upon excitation, due to the presence of organic fluorophores. FONs are of great interest for numerous biological and medical applications, due to their high tunability in terms of composition, morphology, surface functionalization, and optical properties. Multifunctional FONs combine several functionalities in a single nanostructure (emission of light, carriers for drug-delivery, functionalization with targeting ligands, etc.), opening the possibility of using the same nanoparticle for diagnosis and therapy. The preparation, characterization, and application of these multifunctional FONs require a multidisciplinary approach. In this review, we present FONs following a tutorial approach, with the aim of providing a general overview of the different aspects of the design, preparation, and characterization of FONs. The review encompasses the most common FONs developed to date, the description of the most important features of fluorophores that determine the optical properties of FONs, an overview of the preparation methods and of the optical characterization techniques, and the description of the theoretical approaches that are currently adopted for modeling FONs. The last part of the review is devoted to a non-exhaustive selection of some recent biomedical applications of FONs.

Modeling Polyzwitterion-Based Drug Delivery Platforms: A Perspective of the Current State-of-the-Art and Beyond

Drug delivery platforms are anticipated to have biocompatible and bioinert surfaces. PEGylation of drug carriers is the most approved method since it improves water solubility and colloid stability and decreases the drug vehicles’ interactions with blood components. Although this approach extends their biocompatibility, biorecognition mechanisms prevent them from biodistribution and thus efficient drug transfer. Recent studies have shown (poly)zwitterions to be alternatives for PEG with superior biocompatibility. (Poly)zwitterions are super hydrophilic, mainly stimuli-responsive, easy to functionalize and they display an extremely low protein adsorption and long biodistribution time. These unique characteristics make them already promising candidates as drug delivery carriers. Furthermore, since they have highly dense charged groups with opposite signs, (poly)zwitterions are intensely hydrated under physiological conditions. This exceptional hydration potential makes them ideal for the design of therapeutic vehicles with antifouling capability, i.e., preventing undesired sorption of biologics from the human body in the drug delivery vehicle. Therefore, (poly)zwitterionic materials have been broadly applied in stimuli-responsive “intelligent” drug delivery systems as well as tumor-targeting carriers because of their excellent biocompatibility, low cytotoxicity, insignificant immunogenicity, high stability, and long circulation time. To tailor (poly)zwitterionic drug vehicles, an interpretation of the structural and stimuli-responsive behavior of this type of polymer is essential. To this end, a direct study of molecular-level interactions, orientations, configurations, and physicochemical properties of (poly)zwitterions is required, which can be achieved via molecular modeling, which has become an influential tool for discovering new materials and understanding diverse material phenomena. As the essential bridge between science and engineering, molecular simulations enable the fundamental understanding of the encapsulation and release behavior of intelligent drug-loaded (poly)zwitterion nanoparticles and can help us to systematically design their next generations. When combined with experiments, modeling can make quantitative predictions. This perspective article aims to illustrate key recent developments in (poly)zwitterion-based drug delivery systems. We summarize how to use predictive multiscale molecular modeling techniques to successfully boost the development of intelligent multifunctional (poly)zwitterions-based systems.

Engineered strategies to enhance tumor penetration of drug-loaded nanoparticles

Nanocarriers have been widely employed in preclinical studies and clinical trials for the delivery of anticancer drugs. The most important causes of failure in clinical translation of nanocarriers is their inefficient accumulation and penetration which arises from special characteristics of tumor microenvironment such as insufficient blood supply, dense extracellular matrix, and elevated interstitial fluid pressure. Various strategies such as engineering extracellular matrix, optimizing the physicochemical properties of nanocarriers have been proposed to increase the depth of tumor penetration; however, these strategies have not been very successful so far. Novel strategies such as transformable nanocarriers, transcellular transport of peptide-modified nanocarriers, and bio-inspired carriers have recently been emerged as an advanced generation of drug carriers. In this study, the latest developments of nanocarrier-based drug delivery to solid tumor are presented with their possible limitations. Then, the prospects of advanced drug delivery systems are discussed in detail.

Ferroptosis in cancer therapeutics: a materials chemistry perspective

Ferroptosis, distinct from apoptosis, is a regulated form of cell death caused by lipid peroxidation that has attracted extensive research interest since it was first defined in 2012. Over the past five years, an increasing number of studies have revealed the close relationship between ferroptosis and materials chemistry, in particular nanobiotechnology, and have concluded that nanotechnology-triggered ferroptosis is an efficient and promising antitumor strategy that provides an alternative therapeutic approach, especially for apoptosis-resistant tumors. In this review, we summarize recent advances in ferroptosis-induced tumor therapy at the intersection of materials chemistry, redox biology, and tumor biology. The biological features and molecular mechanisms of ferroptosis are first outlined, followed by a summary of the feasible strategies to induce ferroptosis using nanomaterials and the applications of ferroptosis in combined tumor therapy. Finally, the existing challenges and future development directions in this emerging field are discussed, with the aim of promoting the progress of ferroptosis-based oncotherapy in materials science and nanoscience and enriching the antitumor arsenal.

Interfacial behavior of phospholipid monolayers revealed by mesoscopic simulation

A mesoscopic model with molecular resolution is presented for dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl oleoyl phosphatidylcholine (POPC) monolayer simulations at the air-water interface using many-body dissipative particle dynamics (MDPD). The parameterization scheme is rigorously based on reproducing the physical properties of water and alkane and the interfacial property of the phospholipid monolayer by comparison with experimental results. Using much less computing cost, these MDPD simulations yield a similar surface pressure-area isotherm as well as similar pressure-related morphologies as all-atom simulations and experiments. Moreover, the compressibility modulus, order parameter of lipid tails, and thickness of the phospholipid monolayer are quantitatively in line with the all-atom simulations and experiments. This model also captures the sensitive changes in the pressure-area isotherms of mixed DPPC/POPC monolayers with altered mixing ratios, indicating that the model is promising for applications with complex natural phospholipid monolayers. These results demonstrate a significant improvement of quantitative phospholipid monolayer simulations over previous coarse-grained models.

Computer Simulations on a pH-Responsive Anticancer Drug Delivery System Using Zwitterion-Grafted Polyamidoamine Dendrimer Unimolecular Micelles

Unimolecular micelles have attracted wide attention in the field of drug delivery because of their thermodynamic stability and uniform size distribution. However, their drug loading/release mechanisms at the molecular level have been poorly understood. In this work, the stability and drug loading/release behaviors of unimolecular micelles formed using generation-5 polyamidoamine-graft-poly(carboxybetaine methacrylate) (PAMAM(G5)-PCBMA) were studied by dissipative particle dynamics simulations. In addition, the unimolecular micelles formed using generation-5 polyamidoamine-graft-poly(ethyleneglycol methacrylate) (PAMAM(G5)-PEGMA) were used as a comparison. The simulation results showed that PAMAM(G5)-PCBMA can spontaneously form core-shell unimolecular micelles. The PAMAM(G5) dendrimer constitutes a hydrophobic core to load the doxorubicin (DOX), while the zwitterionic PCBMA serves as a protective shell to improve the stability of the unimolecular micelle. The DOX can be encapsulated into the cavity of PAMAM(G5) at the physiological pH 7.4. The drug loading efficiency and drug loading content showed some regularities with the increase in the drug concentration. At the acidic pH 5.0, the loaded DOX can be released gradually from the hydrophobic core. The comparison of DOX-loaded morphologies between the PAMAM(G5)-PCBMA system and PAMAM(G5)-PEGMA system showed that the former has better monodisperse stability. This work could offer theoretical guidance for the design and development of promising unimolecular micelles for drug delivery.

Molecular Modelling Guided Modulation of Molecular Shape and Charge for Design of Smart Self-Assembled Polymeric Drug Transporters

Nanomedicine employs molecular materials for prevention and treatment of disease. Recently, smart nanoparticle (NP)-based drug delivery systems were developed for the advanced transport of drug molecules. Rationally engineered organic and inorganic NP platforms hold the promise of improving drug targeting, solubility, prolonged circulation, and tissue penetration. However, despite great progress in the synthesis of NP building blocks, more interdisciplinary research is needed to understand their self-assembly and optimize their performance as smart nanocarriers. Multi-scale modeling and simulations provide a valuable ally to experiment by mapping the potential energy landscape of self-assembly, translocation, and delivery of smart drug-loaded NPs. Here, we highlight key recent advances to illustrate the concepts, methods, and applications of smart polymer-based NP drug delivery. We summarize the key design principles emerging for advanced multifunctional polymer topologies, illustrating how the unusual architecture and chemistry of dendritic polymers, self-assembling polyelectrolytes and cyclic polymers can provide exceptional drug delivery platforms. We provide a roadmap outlining the opportunities and challenges for the effective use of predictive multiscale molecular modeling techniques to accelerate the development of smart polymer-based drug delivery systems.

Nanoscale covalent organic frameworks as theranostic platforms for oncotherapy: synthesis, functionalization, and applications

Cancer nanomedicine is one of the most promising domains that has emerged in the continuing search for cancer diagnosis and treatment. The rapid development of nanomaterials and nanotechnology provide a vast array of materials for use in cancer nanomedicine. Among the various nanomaterials, covalent organic frameworks (COFs) are becoming an attractive class of upstarts owing to their high crystallinity, structural regularity, inherent porosity, extensive functionality, design flexibility, and good biocompatibility. In this comprehensive review, recent developments and key achievements of COFs are provided, including their structural design, synthesis methods, nanocrystallization, and functionalization strategies. Subsequently, a systematic overview of the potential oncotherapy applications achieved till date in the fast-growing field of COFs is provided with the aim to inspire further contributions and developments to this nascent but promising field. Finally, development opportunities, critical challenges, and some personal perspectives for COF-based cancer therapeutics are presented.

Mechanistic modeling of spontaneous penetration of carbon nanocones into membrane vesicles

Carbon nanocones (CNCs) are promising drug delivery systems that can be functionalized with a variety of biomolecules (such as proteins, peptides, or antibodies), which allow for site-specific, targeted payload delivery to particular cells and organs. However, considerable uncertainty exists with respect to the toxicity of CNCs on their conical shape, and the underlying mechanism that leads to the penetration of CNCs (especially the truncated ones) in and through the cell membrane is not yet well understood. Using a coarse-grained dissipative particle dynamics method, we systematically investigate the spontaneous penetration of untruncated and truncated CNCs into membrane vesicles. For untruncated CNCs, the simulation results show that both pristine and oxidized ones can spontaneously penetrate across or be attached to the vesicle surface without membrane rupture, indicating low or insignificant toxicity. However, for truncated CNCs, we find that both the apex angle and aspect ratio can influence the CNC-membrane interactions and CNC-induced toxicity: a higher apex angle (and/or a lower aspect ratio) yields a higher toxicity of truncated CNCs. Further free energy analysis reveals that the lowest free energy path during the penetration is associated with CNC's orientation and rotation. For a truncated CNC with a low aspect ratio and high apex angle, it tends to rotate itself to a preferred standing-up fashion inside the vesicle membrane, posing an enhanced toxicity of CNCs. These findings may provide useful guidelines for designing effective CNC vehicles for drug delivery.

Adsorption of Phospholipids at the Air-Water Surface

Phospholipids are ubiquitous components of biomembranes and common biomaterials used in many bioengineering applications. Understanding adsorption of phospholipids at the air-water surface plays an important role in the study of pulmonary surfactants and cell membranes. To date, however, the biophysical mechanisms of phospholipid adsorption are still unknown. It is challenging to reveal the molecular structure of adsorbed phospholipid films. Using combined experiments with constrained drop surfactometry and molecular dynamics simulations, here, we studied the biophysical mechanisms of dipalmitoylphosphatidylcholine (DPPC) adsorption at the air-water surface. It was found that the DPPC film adsorbed from vesicles showed distinct equilibrium surface tensions from the DPPC monolayer spread via organic solvents. Our simulations revealed that only the outer leaflet of the DPPC vesicle is capable of unzipping and spreading at the air-water surface, whereas the inner leaflet remains intact and forms an inverted micelle to the interfacial monolayer. This inverted micelle increases the local curvature of the monolayer, thus leading to a loosely packed monolayer at the air-water surface and hence a higher equilibrium surface tension. These findings provide novel insights, to our knowledge, into the mechanism of the phospholipid and pulmonary surfactant adsorption and may help understand the structure-function correlation in biomembranes.

Controlling the Interaction of Nanoparticles with Cell Membranes by the Polymeric Tether

The well control over the cell-nanoparticle interaction can be of great importance and necessity for different biomedical applications. In this work, we propose a new and simple way (i.e., polymeric tether) to tuning the interaction between nanoparticles and cell membranes by dissipative particle dynamics simulations. It is found that the linked nanoparticles (via polymeric tether) can show some cooperation during the cellular uptake and thereby have a higher wrapping degree than the single nanoparticle. The effect of the property of the polymer on the wrapping is also investigated, and it is found that the length, rigidity, and hydrophobicity of the polymer play an important role. More interestingly, the uptake of linked nanoparticles could be adjusted to the firm adhesion via two rigid polymeric tethers. The present study may provide some useful guidelines for novel design of functional nanomaterials in the experiments.

BODIPY-Decorated Nanoscale Covalent Organic Frameworks for Photodynamic Therapy

Covalent organic frameworks (COFs), an emerging class of organic porous materials, have attracted intense attention due to their versatile applications. However, the deliberate fabrication of COF-based nanomaterials for nanomedical application remains challenging due to difficulty in their size- and structure-controlled synthesis and poor aqueous dispersibility. Herein, we report two boron-dipyrromethene (BODIPY)-decorated nanoscale COFs (NCOFs), which were prepared by the Schiff-base condensation of the free end -CHO (bonding defects in COFs) on the established imine-based NCOFs with the amino-substituted organic photosensitizer BODIPY via "bonding defects functionalization" approach. Thus BODIPY has been successfully nanocrystallized via the NCOF platform, and can be used for photodynamic therapy (PDT) to treat tumors. These NCOF-based PDT agents featured nanometer size (∼110 nm), low dark toxicity, and high phototoxicity as evidenced by in vitro and in vivo experiments. Moreover, the "bonding defects functionalization" approach might open up new avenues for the fabrication of additional COF-based platforms for biomedical treatment.