Investigation of graphene-based nanomaterial as nanocarrier for adsorption of paclitaxel anticancer drug: a molecular dynamics simulation study

A DFT study of sulforaphane adsorption on the group III nitrides (B12N12, Al12N12 and Ga12N12) nanocages

In this paper, the adsorption behavior of group III nitrides (B12N12, Al12N12, and Ga12N12) nanocages to sulforaphane (SF) anticancer medicine were studied by density functional theory (DFT). The adsorption energy, solvation energy, desorption time and related quantum molecular descriptors were calculated in neutral and acidic solutions. When the drugs were adsorbed to nanocages, the structure of nanocages and drugs changed after adsorption, indicating that the process was effective adsorption. The adsorption energy and solvation energy of the complexes created after adsorption were negative values, which indicated that the structure of complexes formed by adsorption were stable. According to charge decomposition analysis (CDA) and natural bonding orbitals (NBO), drugs act as charge donors and nanocages act as charge acceptors, so that the charge flows from drugs to nanocages. Thermodynamic calculations demonstrate that drugs adsorption on nanocages is a spontaneous exothermic process. The calculation of quantum molecular descriptors confirmed that drugs adsorption on nanocages increased the chemical reactivity and solubility of drugs, which facilitated its transfer in biological fluids. Both interaction region index (IRI) and topological analysis of atom in molecule (AIM) revealed Van Der Waals interaction between drugs and nanocages. Protonation studies demonstrated that acidic circumstances could improve the polarity of complexes, increase the solvation effect, and boost drugs release in target cancer cells. The results of this work indicate that X12N12(X = B, Al, Ga) nanocages can be used as the delivery vehicle of SF drug.Communicated by Ramaswamy H. Sarma.

The computational quantum mechanical investigation of the functionalized boron nitride nanocage as the smart carriers for favipiravir drug delivery: a DFT and QTAIM analysis

Favipiravir (FPV) is an antiviral drug used for the cure of Influenza virus, Ebola virus, Lassa virus etc. because it has excellent preventing ability of entry/exit of the virus into/from the human cells. Boron nitride nanocages have already drawn enormous attention as the delivery vehicle of various drug molecules for their nontoxicity and other lucrative properties. In this research, we have scrutinized the adsorption mechanism of FPV molecule on the exterior surface of pristine, Zn functionalized, and Ni functionalized B12N12 (BN, Zn f-BN, and Ni f-BN) nanocages by applying the DFT/QTAIM method and B3LYP/6-31G(d,p) approach. The adsorption energy (E_Ad) data reveal that the functionalized BN adsorbents can adsorb FPV drug very efficiently compared with the pristine adsorbent (Highest E_Ad is -56.40 kcal/mol for FPV adsorbed Ni f-BN complex). The reduction of the HOMO-LUMO gap up to 67.79% indicates that this drug can be detected by the produced electrical signal very promisingly in the case of f-BN nanocages. The topological parameters also validate the ability of the f-BN nanocages to adsorb the FPV molecule. The effect of the biological environment of our investigated structures has been studied by using water as a solvent, and spontaneous adsorption with high solubility is observed in our calculations. This analysis also reveals that f-BN nanocages can be a potential nanocarrier for the delivery of FPV drug molecule.Communicated by Ramaswamy H. Sarma.

Multifunctional graphene oxide nanoparticles for drug delivery in cancer

Recent advancements in nanotechnology have enabled us to develop sophisticated multifunctional nanoparticles or nanosystems for targeted diagnosis and treatment of several illnesses, including cancers. To effectively treat any solid tumor, the therapy should preferably target just the malignant cells/tissue with minor damage to normal cells/tissues. Graphene oxide (GO) nanoparticles have gained considerable interest owing to their two-dimensional planar structure, chemical/mechanical stability, excellent photosensitivity, superb conductivity, high surface area, and good biocompatibility in cancer therapy. Many compounds have been functionalized on the surface of GO to increase their biological applications and minimize cytotoxicity. The review presents an overview of the physicochemical characteristics, strategies for various modifications, toxicity and biocompatibility of graphene and graphene oxide, current trends in developing GO-based nano constructs as a drug delivery cargo and other biological applications, including chemo-photothermal therapy, chemo-photodynamic therapy, bioimaging, and theragnosis in cancer. Further, the review discusses the challenges and opportunities of GO, GO-based nanomaterials for the said applications. Overall, the review focuses on the therapeutic potential of strategically developed GO nanomedicines and comprehensively discusses their opportunities and challenges in cancer therapy.

Optimization of the Urea Removal in a Wearable Dialysis Device Using Nitrogen-Doped and Phosphorus-Doped Graphene

Dialysis has been recognized as an essential treatment for end-stage renal disease (ESRD). This therapy, however, suffers from several limitations leading to numerous complications in the patients. As dialysis cannot completely substitute healthy kidney functions, the health condition of an ESRD patient is ultimately affected. Wearable artificial kidney (WAK) can resolve the restrictions of blood purification by the dialysis method. However, absorbing large amounts of urea produced in the body is one of the main challenges of these WAK and overcoming this is necessary to improve both functionality and footprint of the device. This study investigates the adsorption capabilities of N- and P-doped graphene nanosorbents for the first time by using molecular dynamic simulation. Urea removal on carbon nanosheets was simulated with different percentages of phosphorus and nitrogen dopants along with the pristine graphene. Specifically, the effects of interaction energy, adsorption percentage, gyration radius, hydrogen bonding, and other molecular dynamic analyses on urea removal were also investigated. The results from this study match well with the existing research, demonstrating the accuracy of the model. The results further suggest that graphene nanosheets doped by 10% nitrogen are likely the most effective in removing urea given that it is associated with the maximum radial distribution function (RDF), the maximum reduction in gyration radius, a high number of hydrogen bonds, and the most negative adsorption energy. This molecular study offers attractive suggestions for the novel adsorbents of artificial kidney devices and paves the way for the development of novel and enhanced urea adsorbents.

Theoretical assessments on the interaction between amino acids and the g-Mg3N2 monolayer: dispersion corrected DFT and DFT-MD simulations

The interaction of a few amino acids (AAs) with the graphene-like magnesium nitride (g-Mg₃N₂) monolayer has been investigated with density functional theory (DFT) simulations. The Mg site was found to cause significant attraction with the polar active sites of AAs. Such AAs, are capable of producing electrostatics bonding with -48.012 (kcal mol^-1) of interaction energy for tyrosine. The good consistency of the DFT interaction energy with the second-order Møller-Plesset method was found. Furthermore, the DFT-MD simulation of the tyrosine/g-Mg₃N₂ system demonstrated that this host-guest system is stable at ambient conditions. The electronic structures and quantum molecular descriptors were calculated, and the results revealed that the g-Mg₃N₂ monolayer is sensitive to the interaction with AAs. Our first-principles outcomes suggest comprehensive visions into the functionalization of g-Mg₃N₂, and anticipate its applicability as an unprecedented nanovector for AAs. In addition, g-Mg₃N₂ nanosheets can be utilized as biosensors for biomolecules detection. These are very hopeful for promising biological and pharmaceutical applications of g-Mg₃N₂.

Assessment of the effect of external and internal triggers on adsorption and release of paclitaxel from the PEI functionalized silicene nanosheet: A molecular dynamic simulation

In order to examine the adsorption mechanisms of paclitaxel (PTX) on silicene nanosheet (SNS) molecular dynamics (MD) simulations are carried out. The MD outcomes show that the adsorption of PTX on the pristine SNS is exothermic and spontaneous. The interaction between the PTX molecule and the pristine SNS is mainly due to the formation of π-π interactions through their aromatic rings, which are supplemented by X-π (X = N-H, C-H, and CO) interactions. Upon functionalization of SNS by Polyethylenimine (PEI), drug molecules prefer to bind to the nanocarrier instead of the polymer. In the functionalized SNS (f-SNS), the binding energy of the drug with the nanocarrier becomes stronger in comparison to the SNS case (E_ads: -2468.91 vs -840.95 kJ/mol). At the acidic condition, protonation of drug and PEI cause that the interaction between PTX and the nanocarrier become weaker and drug molecules could release from the nanocarrier surface. Finally, two f-SNS and protonated f-SNS (f-pSNS) systems are induced by the electric field (EF). Evaluation of the dynamic properties of these systems (with strengths 0.5 and 1 V/nm) shows that the electric field could be acted as a stimulus for drug release from nanocarriers. The obtained results from this study provide valuable information about the loading/release mechanisms of PTX on/from the SNS surface.

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.

Graphene-Based Nanoparticles as Potential Treatment Options for Parkinson's Disease: A Molecular Dynamics Study

INTRODUCTION

The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson's disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients' quality of life. However, if these medications are stopped, symptoms of the disease will recur even more severely. Therefore, the improvement of therapies targeting more basic mechanisms like prevention of amyloid formation seems to be critical. It has been shown that the interactions between monolayers like graphene and amyloids could prevent their fibrillation.

METHODS

For the first time, the impact of four types of last-generation graphene-based nanostructures on the prevention of α-synuclein amyloid fibrillation was investigated in this study by using molecular dynamics simulation tools.

RESULTS

Although all monolayers were shown to prevent amyloid fibrillation, nitrogen-doped graphene (N-Graphene) caused the most instability in the secondary structure of α-synuclein amyloids. Moreover, among the four monolayers, N-Graphene was shown to present the highest absolute value of interaction energy, the lowest contact level of amyloid particles, the highest number of hydrogen bonds between water and amyloid molecules, the highest instability caused in α-synuclein particles, and the most significant decrease in the compactness of α-synuclein protein.

DISCUSSION

Ultimately, it was concluded that N-Graphene could be the most effective monolayer to disrupt amyloid fibrillation, and consequently, prevent the progression of Parkinson's disease.

Molecular Interpretation of Pharmaceuticals’ Adsorption on Carbon Nanomaterials: Theory Meets Experiments

The ability of carbon-based nanomaterials (CNM) to interact with a variety of pharmaceutical drugs can be exploited in many applications. In particular, they have been studied both as carriers for in vivo drug delivery and as sorbents for the treatment of water polluted by pharmaceuticals. In recent years, the large number of experimental studies was also assisted by computational work as a tool to provide understanding at molecular level of structural and thermodynamic aspects of adsorption processes. Quantum mechanical methods, especially based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were mainly applied to study adsorption/release of various drugs. This review aims to compare results obtained by theory and experiments, focusing on the adsorption of three classes of compounds: (i) simple organic model molecules; (ii) antimicrobials; (iii) cytostatics. Generally, a good agreement between experimental data (e.g. energies of adsorption, spectroscopic properties, adsorption isotherms, type of interactions, emerged from this review) and theoretical results can be reached, provided that a selection of the correct level of theory is performed. Computational studies are shown to be a valuable tool for investigating such systems and ultimately provide useful insights to guide CNMs materials development and design.

Modified gaphene oxide (GO) particles in peptide hydrogels: a hybrid system enabling scheduled delivery of synergistic combinations of chemotherapeutics

The scheduled delivery of synergistic drug combinations is increasingly recognized as highly effective against advanced solid tumors. Of particular interest are composite systems that release a sequence of drugs with defined kinetics and molar ratios to enhance therapeutic effect, while minimizing the dose to patients. In this work, we developed a homogeneous composite comprising modified graphene oxide (GO) nanoparticles embedded in a Max8 peptide hydrogel, which provides controlled kinetics and molar ratios of release of doxorubicin (DOX) and gemcitabine (GEM). First, modified GO nanoparticles (tGO) were designed to afford high DOX loading and sustained release (18.9% over 72 h and 31.4% over 4 weeks). Molecular dynamics simulations were utilized to model the mechanism of DOX loading as a function of surface modification. In parallel, a Max8 hydrogel was developed to release GEM with faster kinetics and achieve a 10-fold molar ratio to DOX. The selected DOX/tGO nanoparticles were suspended in a GEM/Max8 hydrogel matrix, and the resulting composite was tested against a triple negative breast cancer cell line, MDA-MB-231. Notably, the composite formulation afforded a combination index of 0.093 ± 0.001, indicating a much stronger synergism compared to the DOX-GEM combination co-administered in solution (CI = 0.396 ± 0.034).

Computational insights into the sorption mechanism of environmental contaminants by carbon nanoparticles through molecular dynamics simulation and density functional theory

Carbon nanomaterials like carbon nanotube, graphene or graphene oxide could significantly enhance contaminant sorption in aqueous solutions, offering a promising opportunity in water and air purification for removal of environmental contaminants.

Development and evaluation of a pH-responsive and water-soluble drug delivery system based on smart polymer coating of graphene nanosheets: an in silico study

The objective of this study is to develop a controlled and water-soluble delivery system for doxorubicin (DOX) based on the coating of graphene (G) with a smart polymer. A combination of polyethyleneimine (PEI) and G–DOX is investigated by performing density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Several parameters have been employed to evaluate the effect of PEI on the adsorption and release mechanisms of DOX. The obtained results indicated that the binding energy of the drug molecule on G in the presence of PEI is enhanced by about 20% under neutral conditions, whereas the drug absorption becomes weaker in an acidic environment so that DOX could be separated from the carrier surface using near-infrared radiation (NIR). Based on the atom in molecule (AIM) theory, two hydrogen bonds with strengths of about −12.59 and −39.99 kJ mol⁻¹ have been established. Furthermore, evaluating the dynamic behavior of the designed systems in water solution shows that the polymer in physiological pH rapidly adsorbed on the drug–carrier complex. However, at acidic pH, it is quickly desorbed from the carrier surface and the G–DOX complex can be exposed to cancer cells. The obtained results of the present research may be used in future experimental work to design smart DDSs.

The objective of this study is to develop a controlled and water-soluble delivery system for doxorubicin (DOX) based on the coating of graphene (G) with a smart polymer.

Investigation on absorption and release of mercaptopurine anticancer drug from modified polylactic acid as polymer carrier by molecular dynamic simulation

The absorption and release of 6-mercaptopurine anticancer drug was investigated in biodegradable and biocompatible polymer of polylactic acid (PLA) using molecular dynamics simulation. For this purpose, the amount of mixing energy, radius of gyration, mean squared displacement and radial distribution function were computed and compared in concentrations of 5-36 wt% of 6-mercaptopurine drug. The simulation results show that increasing the concentration of the drug reduces mixing energy and PLA polymer carrier is able to carry 35.8 wt% of 6-mercaptopurine anticancer drug. Based on these results, the amount of 6-mercaptopurine release from PLA carrier 35.8 wt% of it in water environment is zero due to hydrophobic property of PLA and 6-mercaptopurine. Finally, polyethylene glycol (PEG) polymer with different percentages (10-30 wt%) was used to modify PLA carrier. The simulation results show that the rate of drug release increases by increasing the concentration of PEG polymer in the modified PLA carrier and also with increasing the percentage of drug loaded in the carrier and also the optimum weight percentage of PEG in modified PLA carrier for 35.8 wt% of drug concentration is 11 wt% and the rate of drug release is slower and equal to 4.4 molecules/ns.

Graphene oxide as selective transporter of flavonols for physiological target DNA: A two-color fluorescence approach

Our study determines the selectivity of graphene oxide (GO) to recognize its ligands (e.g. flavonoids) in facilitating the binding with their respective cellular targets. The polyhydroxy phenolic compounds, flavonoids, have a broad spectrum of therapeutic activities with high potency and low systemic toxicity. Despite the vast medicinal importance, their bioavailability is low. In this exploratory study, GO has been used as the transporter of three flavonols fisetin (3, 7, 3', 4'-OH flavone), quercetin (3, 5, 7, 3', 4'-OH flavone), and morin (3, 5, 7, 2', 4'-OH flavone) for the physiological target DNA. Calf thymus DNA is chosen as the model physiological target. Characterization of GO is performed using FTIR, Raman and dynamic light scattering (DLS) spectroscopy. The strong absorption peak at 1730 cm-1 indicated the presence of carbonyl groups (C=O) at the edges of GO. The presence of sp3 carbons due to oxidation of sp2 carbons in GO is further proved by Raman spectroscopy. DLS provided the average size of the GO particles to be ~9 μm. The dual luminescence behavior of the flavonols has been used in this study for the noninvasive sensing of the GO-flavonol and GO-flavonol-DNA interactions; as well as for the selectivity of GO for one flavonol over other in transferring the ligand to DNA. Furthermore, circular dichroism (CD) indicated that the optical activity of GO undergoes drastic change when conjugated with flavonols. Molecular modeling corroborated the findings from the binding studies. GO provides high promise as facilitators for drug delivery.

Folate receptor targeted delivery of paclitaxel to breast cancer cells via folic acid conjugated graphene oxide grafted methyl acrylate nanocarrier

The adaptability, joint with a large surface area, electronic flexibility, high intrinsic mobility, high mechanical strength and supreme thermal conductivity have condensed graphene family materials attractive as technological tools of the drug delivery system. In this present study, investigate a modified graphene oxide-methyl acrylate (GO-g-MA) nanocarrier for targeted anti-cancer drug delivery in breast cancer cells and the GO-g-MA fascinated with folic acidas a targeting ligand to target the cancer cells. Paclitaxel (PTX) was assembled through π-π stacking, hydrophophic interaction on the surface of the GO-g-MA/FA carrier. Structural modification of GO-g-MA, functionalization of targeting ligands GO-g-MA/FA and drug loaded GO-g-MA/FA-PTX was characterized and confirmed through FTIR, XRD, SEM,TEM and AFM analysis. The in-vitro drug release pattern of PTX from the GO-g-MA/FA was examined in different pH ranges. An MTT assay was performed to evaluate the cytotoxicity behaviour of the carrier and PTX loaded nanocarrier in the human breast cancer cell line (MDA-MB-231). GO-g-MA/FA-PTX carrier showed that 39% of cytotoxic effect. Furthermore, the in-vivo (DMBA induced breast cancer rats) studies were carried out and treatment with PTX- loaded GO-g-MA/FA nanocarrier attenuates the levels of mitochondrial citric acids enzymes to near normal.

Assessment of the chitosan-functionalized graphene oxide as a carrier for loading thioguanine, an antitumor drug and effect of urea on adsorption process: Combination of DFT computational and molecular dynamics simulation studies

In this study, the interaction thioguanine (TG) anticancer drug with the functionalized graphene oxide (GO) nanosheet surface is theoretically studied in both gas phase and separately in physiological media using the density functional theory (DFT) calculations. DFT calculations indicated the adsorption and solvation energies are negative for f-GONS/TG complexes which propose the adsorption process of TG molecule onto the f-GONS surface is possible from the energetic viewpoint. QTAIM calculations confirm the nature of partially covalent-partially electrostatic between drug and nanosheet. These results are sorely relevant that an approach for loading of TG molecule is the chemical modification of GO using covalent functionalization which can serve as a nanocarrier to load drug molecules. Moreover, to understand the effect of urea on the nature of the interaction between TG and f-GONS, molecular dynamics (MD) simulation was employed. The results indicated that in the presence of urea the adsorption process gets affected and leads to instability of system, while the affinity of the TG for adsorption onto GO surface is increased in pure water. Communicated by Ramaswamy H. Sarma.

Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery

The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.