Docking of ubiquitin to gold nanoparticles

Molecular Docking Approach for Biological Interaction of Green Synthesized Nanoparticles

In recent years, significant progress has been made in the subject of nanotechnology, with a range of methods developed to synthesize precise-sized and shaped nanoparticles according to particular requirements. Often, the nanoparticles are created by employing dangerous reducing chemicals to reduce metal ions into uncharged nanoparticles. Green synthesis or biological approaches have been used recently to circumvent this issue because biological techniques are simple, inexpensive, safe, clean, and extremely productive. Nowadays, much research is being conducted on how different kinds of nanoparticles connect to proteins and nucleic acids using molecular docking models. Therefore, this review discusses the most recent advancements in molecular docking capacity to predict the interactions between various nanoparticles (NPs), such as ZnO, CuO, Ag, Au, and Fe3O4, and biological macromolecules.

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces

We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy

Despite great advances in protein structure analysis, label-free and ultrasensitive methods to obtain the natural and dynamic three-dimensional (3D) structures are still urgently needed. Surface-enhanced Raman spectroscopy (SERS) can be a good candidate, whereas the complexity originated from the interactions between the protein and the gradient surface electric field makes it extremely challenging to determine the protein structure. Here, we propose a deciphering strategy for accurate determination of 3D protein structure from experimental SERS spectra in seconds by simply summing SERS spectra of isolated amino acids in electric fields of different strength with their orientations in protein. The 3D protein structure can be reconstructed by comparing the experimental spectra obtained in a well-defined gap-mode SERS configuration with the simulated spectra. The gradient electric field endows SERS with a unique advantage to section biomolecules with atomic precision, which makes SERS a competent tool for monitoring biomolecular events under physiological conditions.

Molecular docking in organic, inorganic, and hybrid systems: a tutorial review

Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review.

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Effect of substrate charge density on the adsorption of intrinsically disordered protein amyloid β40: a molecular dynamics study

The inhibitory effect of negatively charged gold nanoparticles (AuNPs) on amyloidogenic protein fibrillation has been established from experiments and computer simulations. Here, we investigate the effect of the charge density (σ) of gold (Au) surfaces on the adsorption of the intrinsically disordered amyloid β40 (Aβ40) monomer using molecular dynamics (MD) simulations. On the basis of the binding free energy, some key residues (ARG5, LYS16, LYS28, LEU17-ALA21, ILE31-VAL38) were found to be responsible for preventing the β-sheet formation, which is known to be a precursor for fibrillation. Until a critical charge density (σ_c) of -0.167 e nm^-2, the key residues remained adsorbed on the Au slab. A saturation in the number of condensed counterions (Na⁺) on Aβ40 was also observed at σ_c. Beyond σ_c, the condensation of Na⁺ occurs only on the Au slab, leading to competition between positively charged key residues and condensed ions. This competition was found to be responsible for the lack of adsorption of the key residues, leading to β-sheet formation for σ > -0.167 e nm^-2. This study suggests that if the key residues are not adsorbed, then β-sheet formation is observed, which can then lead to the development of proto-fibrils and subsequently fibrillation. Therefore the surface should have an optimal charge density to be an effective inhibitor of fibrillation.

A review on microfluidic-assisted nanoparticle synthesis, and their applications using multiscale simulation methods

Recent years have witnessed an increased interest in the development of nanoparticles (NPs) owing to their potential use in a wide variety of biomedical applications, including drug delivery, imaging agents, gene therapy, and vaccines, where recently, lipid nanoparticle mRNA-based vaccines were developed to prevent SARS-CoV-2 causing COVID-19. NPs typically fall into two broad categories: organic and inorganic. Organic NPs mainly include lipid-based and polymer-based nanoparticles, such as liposomes, solid lipid nanoparticles, polymersomes, dendrimers, and polymer micelles. Gold and silver NPs, iron oxide NPs, quantum dots, and carbon and silica-based nanomaterials make up the bulk of the inorganic NPs. These NPs are prepared using a variety of top-down and bottom-up approaches. Microfluidics provide an attractive synthesis alternative and is advantageous compared to the conventional bulk methods. The microfluidic mixing-based production methods offer better control in achieving the desired size, morphology, shape, size distribution, and surface properties of the synthesized NPs. The technology also exhibits excellent process repeatability, fast handling, less sample usage, and yields greater encapsulation efficiencies. In this article, we provide a comprehensive review of the microfluidic-based passive and active mixing techniques for NP synthesis, and their latest developments. Additionally, a summary of microfluidic devices used for NP production is presented. Nonetheless, despite significant advancements in the experimental procedures, complete details of a nanoparticle-based system cannot be deduced from the experiments alone, and thus, multiscale computer simulations are utilized to perform systematic investigations. The work also details the most common multiscale simulation methods and their advancements in unveiling critical mechanisms involved in nanoparticle synthesis and the interaction of nanoparticles with other entities, especially in biomedical and therapeutic systems. Finally, an analysis is provided on the challenges in microfluidics related to nanoparticle synthesis and applications, and the future perspectives, such as large-scale NP synthesis, and hybrid formulations and devices.

Computational Biomaterials: Computational Simulations for Biomedicine

With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning, etc.), and the invention of high-performance computing equipment, computational simulation tools have sparked the fundamental mechanism-level explorations to predict the diverse physicochemical properties and biological effects of biomaterials and investigate their enormous application potential for disease prevention, diagnostics, and therapeutics. Herein, the term "computational biomaterials" is proposed and the computational methods currently used to explore the inherent properties of biomaterials, such as optical, magnetic, electronic, and acoustic properties, and the elucidation of corresponding biological behaviors/effects in the biomedical field are summarized/discussed. The theoretical calculation of the physiochemical properties/biological performance of biomaterials applied in disease diagnosis, drug delivery, disease therapeutics, and specific paradigms such as biomimetic biomaterials is discussed. Additionally, the biosafety evaluation applications of theoretical simulations of biomaterials are presented. Finally, the challenges and future prospects of such computational simulations for biomaterials development are clarified. It is anticipated that these simulations would offer various methodologies for facilitating the development and future clinical translations/utilization of versatile biomaterials.

Red Blood Cell Substitutes: Liposome Encapsulated Hemoglobin and Magnetite Nanoparticle Conjugates as Oxygen Carriers

The established blood donation and transfusion system has contributed a lot to human health and welfare, but for this system to function properly, it requires a sufficient number of healthy donors, which is not always possible. Pakistan was a country hit hardest by COVID-19 which additionally reduced the blood donation rates. In order to address such challenges, the present study focused on the development of RBC substitutes that can be transfused to all blood types. This paper reports the development and characterization of RBC substitutes by combining the strategies of conjugated and encapsulated hemoglobin where magnetite nanoparticles would act as the carrier of hemoglobin, and liposomes would separate internal and external environments. The interactions of hemoglobin variants with bare magnetite nanoparticles were studied through molecular docking studies. Moreover, nanoparticles were synthesized, and hemoglobin was purified from blood. These components were then used to make conjugates, and it was observed that only the hemoglobin HbA1 variant was making protein corona. These conjugates were then encapsulated in liposomes to make negatively charged RBC substitutes with a size range of 1-2 μm. Results suggest that these RBC substitutes work potentially in a similar way as natural RBCs work and can be used in the time of emergency.

Supercritical CO2 assisted extraction of essential oil and naringin from Citrus grandis peel: in vitro antimicrobial activity and docking study

The extraction of bioactive compounds, including essential oils and flavonoids, using organic solvents is a significant environmental concern. In this work, waste C. grandis peel was the ingredient used to extract essential oil and naringin by conducting a supercritical CO2 technique with a two stage process. In the first stage, the extraction with only supercritical CO2 solvent showed a significant enhancement of the d-limonene component, up to 95.66% compared with the hydro-distillation extraction (87.60%). The extraction of naringin using supercritical CO2 and ethanol as a co-solvent was done in the second stage of the process, followed by evaluating in vitro antimicrobial activity of both the essential oil and naringin. The essential oil indicated significant activity against M. catarrhalis (0.25 mg ml-1), S. pyogenes (1.0 mg ml-1), S. pneumoniae (1.0 mg ml-1). Whilst naringin gave good inhibition towards all tested microbial strains with MIC values in the range of 6.25-25.0 μM. In particular, naringin exhibited high antifungal activity against T. rubrum, T. mentagrophytes, and M. gypseum. The molecular docking study also confirmed that d-limonene inhibited bacterium M. catarrhalis well and that naringin possessed potential ligand interactions that proved the inhibition effective against fungi. Molecular dynamics simulations of naringin demonstrated the best docking model using Gromacs during simulation up to 100 ns to explore the stability of the complex naringin and crystal structure of enzyme 2VF5: PDB.

Size-dependent theoretical and experimental photothermal conversion efficiency of spherical gold nanoparticles

INTRODUCTION

Due to their biocompatible and plasmonic properties, gold nanoparticles (Au NPs) are good candidates to be photosensitizers in photothermal cancer therapy (PTT).

MATERIALS AND METHODS

In this paper, the dependence of the NIR-light-to-heat energy on Au NPs size was investigated. Moreover, to determine the photosensitizing properties of gold nanoparticles, PTT was conducted on two colon cell lines: SW480 and SW620 by irradiating them with two lasers having different wavelengths.

RESULTS

Transmission electron microscopy showed that the respective sizes of Au NPs were 10 nm, 12 nm and 16 nm. Moreover, local as well as global structural measurements showed that all synthesized Au NPs were crystalline and UV-Vis spectroscopy revealed that with increasing nanoparticles size the position of the surface Plasmon resonance (SPR) peaks is shifted to higher wavelengths. Decrease of cells viability was observed, when they were cultured with Au NPs and irradiated by 650 nm and 808 nm lasers. Moreover, FTIR and Raman spectra of cells, showed structural changes in DNA, phospholipids, proteins and cholesterol caused by the addition of nanoparticles and laser irradiation. The chemical changes were more pronounced in the cells cultured with Au NPs and irradiated by 650 nm lasers and these changes were dependent on the nanoparticle size. Moreover, the viability of cells investigated by the MTS assay showed, that the percentage of dead cells (∼40%) is the highest for cells cultured with 8 nm Au NPs and irradiated by the 650 nm laser. The photothermal conversion efficiency calculated from the experimental results showed a decrease of this parameter from 70% to 55% and from 61% to 48% with increasing particle size, for 650 nm and 808 nm lasers, respectively.

CONCLUSIONS

The obtained results showed that the photothermal conversion efficiency of Au NPs is size-tunable, and can be correlated with the absorption/extinction ratios calculated by the Mie theory.

Engineering the Aggregation of Dyes on Ligand-Shell Protected Gold Nanoparticles to Promote Plexcitons Formation

The ability to control the light–matter interaction in nanosystems is a major challenge in the field of innovative photonics applications. In this framework, plexcitons are promising hybrid light–matter states arising from the strong coupling between plasmonic and excitonic materials. However, strategies to precisely control the formation of plexcitons and to modulate the coupling between the plasmonic and molecular moieties are still poorly explored. In this work, the attention is focused on suspensions of hybrid nanosystems prepared by coupling cationic gold nanoparticles to tetraphenyl porphyrins in different aggregation states. The role of crucial parameters such as the dimension of nanoparticles, the pH of the solution, and the ratio between the nanoparticles and dye concentration was systematically investigated. A variety of structures and coupling regimes were obtained. The rationalization of the results allowed for the suggestion of important guidelines towards the control of plexcitonic systems.

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.

Evaluation of noble metal nanostructure-serum albumin interactions in 2D and 3D systems: Thermodynamics and possible mechanisms

In this review, we clearly highlight the importance of the detailed study of the interactions between noble metal colloids (nanoparticles (NPs) and nanoclusters (NCs)) with serum albumins (SAs) due to their rapidly growing presence in biomedical research. Besides the changes in the structure and optical property of SA, we demonstrate that the characteristic localized surface plasmon resonance (LSPR) feature of the colloidal noble metal NPs and the size- and structure-dependent photoluminescence (PL) property of the sub-nanometer sized NCs are also altered differently because of the interactions between them. Namely, for plasmonic NPs - SA interactions the PL quenching of SA (mainly static) is identified, while the SA cause PL enhancement of the ultra-small NCs after complexation. This review summarizes that the thermodynamic nature and the possible mechanisms of the binding processes are dependent partly on the size, morphology, and type of the noble metals, while the chemical structure as well as the charge of the stabilizing ligands have the most dominant effect on the change in optical features. In addition to the thermodynamic data and proposed binding mechanisms provided by three-dimensional spectroscopic techniques, the quantitative and real-time data of "quasi" two-dimensional sensor apparatus should also be considered to provide a comprehensive evaluation on many aspects of the particle/cluster - SA interactions.

Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach

We report on the first formulation of a novel polarizable QM/MM approach, where the density functional tight binding (DFTB) is coupled to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ) is then extended to the linear response within the TD-DFTB framework and challenged to study absorption spectra of large condensed-phase systems.

Nanotechnology-Based Delivery Systems for Antimicrobial Peptides

Antimicrobial resistance (AMR) is a significant threat to global health. The conventional antibiotic pool has been depleted, forcing the investigation of novel and alternative antimicrobial strategies. Antimicrobial peptides (AMPs) have shown potential as alternative diagnostic and therapeutic agents in biomedical applications. To date, over 3000 AMPs have been identified, but only a fraction of these have been approved for clinical trials. Their clinical applications are limited to topical application due to their systemic toxicity, susceptibility to protease degradation, short half-life, and rapid renal clearance. To circumvent these challenges and improve AMP’s efficacy, different approaches such as peptide chemical modifications and the development of AMP delivery systems have been employed. Nanomaterials have been shown to improve the activity of antimicrobial drugs by providing support and synergistic effect against pathogenic microbes. This paper describes the role of nanotechnology in the targeted delivery of AMPs, and some of the nano-based delivery strategies for AMPs are discussed with a clear focus on metallic nanoparticle (MNP) formulations.

Adsorption of the amyloid β40 monomer on charged gold nanoparticles and slabs: a molecular dynamics study

Negatively charged nanoparticles are known to inhibit the fibrillation of amyloidogenic protein amyloid β (Aβ40), though the overall charge on the protein is negative. In this work a molecular dynamics study is reported to investigate the interaction of Aβ40 on negatively charged gold nanoparticles (3-5 nm) and charged (positive and negative) and neutral gold slabs. The equilibrium structures of Aβ40 on gold surfaces are characterized using residue-specific contacts on the gold surface, secondary structure analysis and binding free energy calculations. The simulation results reveal that the Aβ40 protein in water interconverts into β-sheets, which are building blocks of the mature fibrils, whereas on gold nanoparticles Aβ40 unfolds and adsorbs. Both the negatively charged gold nanoparticles and gold slabs arrest the formation of β-sheets in Aβ40, whereas the positively charged gold slab does not inhibit the formation of β-sheets. The residue-specific interactions between Aβ40 and the gold surfaces are important in governing the adsorption of Aβ40 on charged surfaces.

Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles

Protein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse−grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS−capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems.

Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics

Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces. However, hydrodynamic and long-range electrostatic interactions cannot be fully treated with grid-based approaches alone. Here, we develop a treatment of both hydrodynamic and electrostatic interactions to include the presence of surfaces by modeling grid-based and long-range interactions. We describe its application to simulate the self-association and many-molecule adsorption of the well-characterized protein hen egg-white lysozyme to mica-like and silica-like surfaces. We find that the computational model can recover a number of experimental observables of the adsorption process and provide insights into their determinants. The computational model is implemented in the Simulation of Diffusional Association (SDA) software package.

Interaction of silver nanoparticles with catechol O-methyltransferase: Spectroscopic and simulation analyses

Catechol O-methyltransferase, an enzyme involved in the metabolism of catechol containing compounds, catalyzes the transfer of a methyl group between S-adenosylmethionine and the hydroxyl groups of the catechol. Furthermore it is considered a potential drug target for Parkinson’s disease as it metabolizes the drug levodopa. Consequently inhibitors of the enzyme would increase levels of levodopa. In this study, absorption, fluorescence and infrared spectroscopy as well as computational simulation studies investigated human soluble catechol O-methyltransferase interaction with silver nanoparticles. The nanoparticles form a corona with the enzyme and quenches the fluorescence of Trp143. This amino acid maintains the correct structural orientation for the catechol ring during catalysis through a static mechanism supported by a non-fluorescent fluorophore–nanoparticle complex. The enzyme has one binding site for AgNPs in a thermodynamically spontaneous binding driven by electrostatic interactions as confirmed by negative ΔG and ΔH and positive ΔS values. Fourier transform infrared spectroscopy within the amide I region of the enzyme indicated that the interaction causes relaxation of its β−structures, while simulation studies indicated the involvement of six polar amino acids. These findings suggest AgNPs influence the catalytic activity of catechol O-methyltransferase, and therefore have potential in controlling the activity of the enzyme.

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A recombinant soluble human catechol O-methyltransferase was inhibited by silver nanoparticles.

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Inhibition by AgNPs was concentration and size dependent.

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The binding mechanism was through spontaneous static quenching, driven by positive ΔS, and negative ΔH and ΔG.

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Stern-Volmer analysis suggested binding of AgNPs with Trp143.

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In silico indicate relaxation of β-sheets and the interaction of AgNPs with 6 amino acids in the enzyme’s helical structures.

In vivo Protein Corona Formation: Characterizations, Effects on Engineered Nanoparticles' Biobehaviors, and Applications

Understanding the basic interactions between engineered nanoparticles (ENPs) and biological systems is essential for evaluating ENPs’ safety and developing better nanomedicine. Profound interactions between ENPs and biomolecules such as proteins are inevitable to occur when ENPs are administered or exposed to biological systems, for example, through intravenous injection, oral, or respiration. As a key component of these interactions, protein corona (PC) is immediately formed surrounding the outlayer of ENPs. PC formation is crucial because it gives ENPs a new biological identity by altering not only the physiochemical properties, but also the biobehaviors of ENPs. In the past two decades, most investigations about PC formation were carried out with in vitro systems which could not represent the true events occurring within in vivo systems. Most recently, studies of in vivo PC formation were reported, and it was found that the protein compositions and structures were very different from those formed in vitro. Herein, we provide an in-time review of the recent investigations of this in vivo PC formation of ENPs. In this review, commonly used characterization methods and compositions of in vivo PC are summarized firstly. Next, we highlight the impacts of the in vivo PC formation on absorption, blood circulation, biodistribution, metabolism, and toxicity of administered ENPs. We also introduce the applications of modulating in vivo PC formation in nanomedicine. We further discuss the challenges and future perspectives.

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide-Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide-nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure-function relationship, for technological and nanomedical applications.

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.

Atomistic simulations of gold surface functionalization for nanoscale biosensors applications

A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.

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.

DFT study of cyclic glycine-alanine dipeptide binding to gold nanoclusters

In this work, we studied the interactions between cyclic glycine-alanine dipeptide c(GA) and gold nanoclusters (Au_nNCs, where n = 2-10) using density functional theory (DFT), atoms-in-molecules theory (AIM), and natural bond orbital analysis (NBO). This dipeptide (DP) consists of two amino acid residues (glycine and alanine); thus, the preference of both residues for binding to gold atoms was examined. The preference of alanine residue to the studied Au_nNCs was found to be greater than that of glycine residue. Two types of interactions were exhibited between the Au_nNCs and c(GA), the partially-covalent partially-electrostatic type and electrostatic interaction. Performance of two DFT functionals and different basis sets is assessed. The results benchmark the importance of the DFT functional with dispersion and long-range corrections, as well as the polarization functions in the basis sets for the gold lusters-peptide binding. The binding energy (ΔE_bind) values of the c(GA)-Au_nNCs complexes in gas and water implicit solvent were compared with those previously published for cyclic glycine-glycine DP-Au_nNCs complexes. It was found that the ΔE_bind values of the former complexes are greater than those of latter ones in water solvent.

Protein corona, understanding the nanoparticle-protein interactions and future perspectives: A critical review

Proteins are biopolymers of highly varied structures taking part in almost all processes occurring in living cells. When nanoparticles (NPs) interact with proteins in biological environments, they are surrounded by a layer of biomolecules, mainly proteins adsorbing to the surfaces. This protein rich layer formed around NPs is called the "protein corona". Consequential interactions between NPs and proteins are governed due to the characteristics of the corona. The features of NPs such as the size, surface chemistry, charge are the critical factors influencing the behavior of protein corona. Molecular properties and protein corona composition affect the cellular uptake of NPs. Understanding and analyzing protein corona formation in relation to protein-NP properties, and elucidating its biological implications play an important role in bio-related nano-research studies. Protein-NP interactions have been studied extensively for the purpose of investigating the potential use of NPs as carriers in drug delivery systems. Further study should focus on exploring the effects of various characteristic parameters, such as the particle size, modifier type, temperature, pH on protein-NP interactions, providing toxicity information of novel NPs. In this contribution, important aspects related to protein corona forming, influential factors, novel findings and future perspectives on protein-NP interactions are overviewed.

Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies

The high frequency of using engineered nanoparticles in various medical applications entails a deep understanding of their interaction with biological macromolecules. Molecular docking simulation is now widely used to study the binding of different types of nanoparticles with proteins and nucleic acids. This helps not only in understanding the mechanism of their biological action but also in predicting any potential toxicity. In this review, the computational techniques used in studying the nanoparticles interaction with biological macromolecules are covered. Then, a comprehensive overview of the docking studies performed on various types of nanoparticles will be offered. The implication of these predicted interactions in the biological activity and/or toxicity is also discussed for each type of nanoparticles.

Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface

We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria and their couplings to the electrostatic potential of the plane. Electrostatic interactions are described within a framework of the continuum Poisson-Boltzmann model, whereas protein-plane hydrodynamic interactions are evaluated based on analytical expressions for the position- and orientation-dependent near-wall friction tensor of a spheroid. The algorithm was applied to simulate near-surface diffusion of lysozyme in solutions having pH in the range 4-10 and ionic strengths of 10 and 150 mM. As a reference, we performed Brownian dynamics simulations in which the protein is assigned a fixed, most probable protonation state, appropriate for given solution conditions and unaffected by the presence of the charged plane, and Brownian dynamics simulations in which the protein probes possible protonation states with the pH-dependent probability, but these variations are not coupled to the electric field generated by the boundary. We show that electrostatic interactions with the negatively charged plane substantially modify probabilities of different protonation states of lysozyme and shift protonation equilibria of both acidic and basic amino acid side chains toward higher pH values. Consequently, equilibrium energy distributions, equilibrium position-orientation distributions, and functions that characterize rotational dynamics, which for a protein with multiple ionization sites, such as lysozyme, in the presence of a charged obstacle are pH-dependent, are significantly affected by the approach taken to incorporate the solution pH into simulations.

Molecular Dynamics Studies of Poly(Lactic Acid) Nanoparticles and Their Interactions with Vitamin E and TLR Agonists Pam1CSK4 and Pam3CSK4

Poly(lactic acid) (PLA) nanoparticles (NPs) are widely investigated due to their bioresorbable, biocompatible and low immunogen properties. Interestingly, many recent studies show that they can be efficiently used as drug delivery systems or as adjuvants to enhance vaccine efficacy. Our work focuses on the molecular mechanisms involved during the nanoprecipitation of PLA NPs from concentrated solutions of lactic acid polymeric chains, and their specific interactions with biologically relevant molecules. In this study, we evaluated the ability of a PLA-based nanoparticle drug carrier to vectorize either vitamin E or the Toll-like receptor (TLR) agonists Pam₁CSK₄ and Pam₃CSK₄, which are potent activators of the proinflammatory transcription factor NF-κB. We used dissipative particle dynamics (DPD) to simulate large systems mimicking the nanoprecipitation process for a complete NP. Our results evidenced that after the NP formation, Pam₁CSK₄ and Pam₃CSK₄ molecules end up located on the surface of the particle, interacting with the PLA chains via their fatty acid chains, whereas vitamin E molecules are buried deeper in the core of the particle. Our results allow for a better understanding of the molecular mechanisms responsible for the formation of the PLA NPs and their interactions with biological molecules located either on their surfaces or encapsulated within them. This work should allow for a rapid development of better biodegradable and safe vectorization systems with new drugs in the near future.

Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils

Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.

Formation of a Highly Stable and Nontoxic Protein Corona upon Interaction of Human α-1-Acid Glycoprotein (AGP) with Citrate-Stabilized Silver Nanoparticles

Given the importance of protein corona in determining cellular responses to nanoparticles, numerous studies have been devoted to finding stable, biocompatible, and nontoxic protein corona. In this work, the interaction between human α-1-acid glycoprotein (AGP) and citrate-stabilized silver (Ag-CIT) nanoparticles of about 10 nm was methodically studied using molecular docking simulation approach and various experimental techniques. It could be shown that a stable Ag-CIT/AGP bioconjugate was formed with a high binding constant of 10⁹ M^-1, several orders of magnitude larger than that of other highly abundant serum proteins. Formation of AGP corona was accompanied by conserving the native conformation of the protein and further associated with a considerable decrease in the cytotoxicity of the silver nanoparticles.

Effects of Orientation on the Stability and Affinity of Antibody-GNP Conjugation

In medicine, gold nanoparticles are widely used because of its unique properties. They are usually attached to a monoclonal antibody in treatment and diagnosis. Computational and laboratory work has demonstrated that the structure of the protein can change after interaction with gold nanoparticle and the effect of nanoparticle on the protein is dependent on the type of bond between them. Thus, finding out how nanoparticles affect the protein structure can help us to design the optimal complex of gold nanoparticle-antibody. In the present study, docking and molecular dynamic simulation were performed to obtain an insight at the molecular level in the binding of immunoglobulin G to the Gold nanoparticles, the structure change in immunoglobulin G, and binding energies of Fab and Fc domains of Immunoglobulin G to the GNP. We found the Fab region was more stable than the Fc region when bound to the GNP surface and it also had less structural changes. In neutral pH, Van der Waals interactions contribute more to the Fab-GNP interaction compared to electrostatic interactions; However, in Fc-GNP interaction, the main contributor is the electrostatic energy.

Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques

In the last decade, nanoparticles (NPs) have become a key tool in medicine and biotechnology as drug delivery systems, biosensors and diagnostic devices. The composition and surface chemistry of NPs vary based on the materials used: typically organic polymers, inorganic materials, or lipids. Nanoparticle classes can be further divided into sub-categories depending on the surface modification and functionalization. These surface properties matter when NPs are introduced into a physiological environment, as they will influence how nucleic acids, lipids, and proteins will interact with the NP surface. While small-molecule interactions are easily probed using NMR spectroscopy, studying protein-NP interactions using NMR introduces several challenges. For example, globular proteins may have a perturbed conformation when attached to a foreign surface, and the size of NP-protein conjugates can lead to excessive line broadening. Many of these challenges have been addressed, and NMR spectroscopy is becoming a mature technique for in situ analysis of NP binding behavior. It is therefore not surprising that NMR has been applied to NP systems and has been used to study biomolecules on NP surfaces. Important considerations include corona composition, protein behavior, and ligand architecture. These features are difficult to resolve using classical surface and material characterization strategies, and NMR provides a complementary avenue of characterization. In this review, we examine how solution NMR can be combined with other analytical techniques to investigate protein behavior on NP surfaces.

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Interaction of gold nanosurfaces/nanoparticles with collagen-like peptides

Nanotechnology has quickly emerged as a promising research field with potential effects in disease treatments. For example, gold nanoparticles (AuNPs) have been extensively used in diagnostics and therapeutics. When administrated into human tissues, AuNPs first encounter extracellular matrix (ECM) molecules. Amongst all the ECM components, collagen is the main tension-resisting constituent, whose biofunctional and mechanical properties are strongly dependent on its hierarchical structure. Therefore, an in-depth understanding of the structural response of collagen to the presence of gold nanosurfaces (AuNS) and AuNPs is crucial in terms of clinical applications of AuNPs. However, detailed understanding of the molecular-level and atomic-level interaction between AuNS/AuNPs and collagen in the ECM is elusive. In this study, comprehensive molecular dynamics (MD) simulations have been performed to investigate the molecular behaviour of a collagen molecule segment (CMS) in the presence of AuNS/AuNPs in explicit water, aiming to explore the interaction of AuNS/AuNPs with collagen triple helices at the molecular and atomic levels. The results show that the CMS forms a rapid association with AuNS/AuNPs and undergoes a severe unfolding upon adsorption on AuNS/AuNPs, indicating an unfolding propensity of gold surfaces. We conclude that collagen triple helices unfold readily on AuNS and bare AuNPs, due to the interaction of gold surfaces with the protein backbone. The revealed clear unfolding nature and the unravelled atomic-level unfolding mechanism of collagen triple helices onto AuNPs contribute to the development of AuNPs for biomedical and therapeutic applications, and the design of gold-binding proteins.

Controlling Redox Enzyme Orientation at Planar Electrodes

Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.

Enhancing using glucose encapsulation, the efficacy of CdO NPs against multi-drug resistant Escherichia coli

In this study, monodispersed, highly biocompatible and substantially stable glucose encapsulated CdO nanoparticles (G-CdO NPs) of uniform sizes were synthesized using a sol-gel route. In addition, naked CdO (n-CdO) NPs without any capping or surface functionalization were synthesized using the same method. These NPs were uniformly dispersed in an aqueous solution. The synthesis of G-CdO and n-CdO NP was confirmed by UV-Vis spectroscopy, transmission electron microscopy (TEM), zeta potential, and dynamic light scattering analyses. The average size of G-CdO and n-CdO NP was found to be 17±1and 27 ± 1 nm, under TEM, respectively. X-ray diffraction analysis of G-CdO and n-CdO NPs confirmed their sizes to be 18.83 and 28.41 nm, respectively, and revealed their cubic crystal structures with no impurity. The surface functionalization of G-CdO NPs with glucose was confirmed by Nuclear Magnetic Resonance and Fourier-transform infrared spectroscopy analyses. As per our knowledge, this is the first report to investigate the potencies of G-CdO and n-CdO NPs against gram-negative and gram-positive multi-drug resistant (MDR) bacteria. The minimum inhibitory concentrations of G-CdO and n-CdO NPs were6.42 and 16.29 μg/ml, respectively, against Escherichia coli (NCIM 2571-MDR), whereas 7.5 μg/ml & 11.6 μg/ml, respectively against S. aureus (NCIM- 2079) as determined by the double dilution method. The minimum bactericidal concentration was determined at the concentration for which no growth was observed. TEM analysis of E. coli cells treated with G-CdO NPs revealed cell shrinkage and degraded cell membranes, while the cell surfaces of untreated viable cells were smooth.

Specific Interaction Sites Determine Differential Adsorption of Protein Structural Isomers on Nanoparticle Surfaces

In biological systems, nanoparticles (NPs) elicit bioactivity upon interaction with proteins. As a result of post-translational modification, proteins occur in a variety of alternative covalent forms, including structural isomers, which present unique molecular surfaces. We aimed at a detailed description of the recognition of protein isomeric species by NP surfaces. The transient adsorption of isomeric ubiquitin (Ub) dimers by NPs was investigated by solution NMR spectroscopy. Lys63- and Lys48-linked Ub₂ were adsorbed by large anionic NPs with different affinities, whereas the binding strength was similar in the cases of smaller particles. After the incorporation of paramagnetic tags into NPs, the observed site-resolved paramagnetic footprints provided a high-resolution map of the different protein surfaces binding to NPs. The approach described could be extended to further protein isoforms and more specialized NP systems to allow better control of the interactions between NPs and protein targets.

Synthesis, Characterization, and Selective Delivery of DARPin-Gold Nanoparticle Conjugates to Cancer Cells

We demonstrate that the designed ankyrin repeat protein (DARPin)_9-29, which specifically targets human epidermal growth factor receptor 2 (HER 2), binds tightly to gold nanoparticles (GNPs). Binding of the protein strongly increases the colloidal stability of the particles. The results of experimental analysis and molecular dynamics simulations show that approximately 35 DARPin_9-29 molecules are bound to the surface of a 5 nm GNP and that the binding does not involve the receptor-binding domain of the protein. The confocal fluorescent microscopy studies show that the DARPin-coated GNP conjugate specifically interacts with the surface of human cancer cells overexpressing epidermal growth factor receptor 2 (HER2) and enters the cells by endocytosis. The high stability under physiological conditions and high affinity to the receptors overexpressed by cancer cells make conjugates of plasmonic gold nanostructures with DARPin molecules promising candidates for cancer therapy.

NanoEHS beyond Toxicity - Focusing on Biocorona

The first phase of environmental health and safety of nanomaterials (nanoEHS) studies has been mainly focused on evidence-based investigations that probe the impact of nanoparticles, nanomaterials and nano-enabled products on biological and ecological systems. The integration of multiple disciplines, including colloidal science, nanomaterial science, chemistry, toxicology/immunology and environmental science, is necessary to understand the implications of nanotechnology for both human health and the environment. While strides have been made in connecting the physicochemical properties of nanomaterials with their hazard potential in tiered models, fundamental understanding of nano-biomolecular interactions and their implications for nanoEHS is largely absent from the literature. Research on nano-biomolecular interactions within the context of natural systems not only provides important clues for deciphering nanotoxicity and nanoparticle-induced pathology, but also presents vast new opportunities for screening beneficial material properties and designing greener products from bottom up. This review highlights new opportunities concerning nano-biomolecular interactions beyond the scope of toxicity.