Probing the adsorption and release mechanisms of cytarabine anticancer drug on/from dopamine functionalized graphene oxide as a highly efficient drug delivery system

Comparison Between Molecular Dynamics Potentials for Simulation of Graphene-Based Nanomaterials for Biomedical Applications

OBJECTIVE

This article provides a substantial review of recent research and comparison on molecular dynamics potentials to determine which are most suitable for simulating the phenomena in graphene-based nanomaterials (GBNs).

SIGNIFICANCE

GBNs gain significant attention due to their remarkable properties and potential applications, notably in nanomedicine. However, the physical and chemical characteristics toward macromolecules that justify their nanomedical applications are not yet fully understood. The molecular interaction through molecular dynamic simulation offers the benefits for simulating inorganic molecules like GBNs, with necessary adjustments to account for physical and chemical interactions, or thermodynamic conditions.

METHOD

In this review, we explore various molecular dynamics potentials (force fields) used to simulate interactions and phenomena in graphene-based nanomaterials. Additionally, we offer a brief overview of the benefits and drawbacks of each force fields that available for analysis to assess which one is suitable to study the molecular interaction of graphene-based nanomaterials.

RESULT

We identify and compare various molecular dynamics potentials that available for analysing GBNs, providing insights into their suitability for simulating specific phenomena in graphene-based nanomaterials. The specification of each force fields and its purpose can be used for further application of molecular dynamics simulation on GBNs.

CONCLUSION

GBNs hold significant promise for applications like nanomedicine, but their physical and chemical properties must be thoroughly studied for safe clinical use. Molecular dynamics simulations, using either reactive or non-reactive MD potentials depending on the expected chemical changes, are essential for accurately modeling these properties, requiring careful selection based on the specific application.

Synthesis of chiral graphene structures and their comprehensive applications: a critical review

From a molecular viewpoint, chirality is a crucial factor in biological processes. Enantiomers of a molecule have identical chemical and physical properties, but chiral molecules found in species exist in one enantiomer form throughout life, growth, and evolution. Chiral graphene materials have considerable potential for application in various domains because of their unique structural framework, properties, and controlled synthesis, including chiral creation, segregation, and transmission. This review article provides an in-depth analysis of the synthesis of chiral graphene materials reported over the past decade, including chiral nanoribbons, chiral tunneling, chiral dichroism, chiral recognition, and chiral transfer. The second segment focuses on the diverse applications of chiral graphene in biological engineering, electrochemical sensors, and photodetectors. Finally, we discuss research challenges and potential future uses, along with probable outcomes.

Graphene Oxide (GO) for the Treatment of Bone Cancer: A Systematic Review and Bibliometric Analysis

Cancer is a severe disease that, in 2022, caused more than 9.89 million deaths worldwide. One worrisome type of cancer is bone cancer, such as osteosarcoma and Ewing tumors, which occur more frequently in infants. This study shows an active interest in the use of graphene oxide and its derivatives in therapy against bone cancer. We present a systematic review analyzing the current state of the art related to the use of GO in treating osteosarcoma, through evaluating the existing literature. In this sense, studies focused on GO-based nanomaterials for potential applications against osteosarcoma were reviewed, which has revealed that there is an excellent trend toward the use of GO-based nanomaterials, based on their thermal and anti-cancer activities, for the treatment of osteosarcoma through various therapeutic approaches. However, more research is needed to develop highly efficient localized therapies. It is suggested, therefore, that photodynamic therapy, photothermal therapy, and the use of nanocarriers should be considered as non-invasive, more specific, and efficient alternatives in the treatment of osteosarcoma. These options present promising approaches to enhance the effectiveness of therapy while also seeking to reduce side effects and minimize the damage to surrounding healthy tissues. The bibliometric analysis of photothermal and photochemical treatments of graphene oxide and reduced graphene oxide from January 2004 to December 2022 extracted 948 documents with its search strategy, mainly related to research papers, review papers, and conference papers, demonstrating a high-impact field supported by the need for more selective and efficient bone cancer therapies. The central countries leading the research are the United States, Iran, Italy, Germany, China, South Korea, and Australia, with strong collaborations worldwide. At the same time, the most-cited papers were published in journals with impact factors of more than 6.0 (2021), with more than 290 citations. Additionally, the journals that published the most on the topic are high impact factor journals, according to the analysis performed, demonstrating the high impact of the research field.

Theoretical aspects of interaction of the anticancer drug cytarabine with human serum albumin

Despite diagnostic and therapeutic methods, cancer is a major cause of death worldwide. Since anticancer drugs affect both normal and cancer cells, targeted drug delivery systems can play a key role in reducing the destructive effects of anticancer drugs on normal cells. In this regard, the use of stimulus-sensitive polymers has increased in recent years. This study has attempted to investigate interaction of the anticancer drug cytarabine with a stimuli-sensitive polymer, human serum albumin (HSA), one of the most abundant protein in blood plasma, via computational methods at both body temperature and tumor temperature. For this purpose, molecular docking was performed using Molegro virtual Docker software to select the best ligand in terms of binding energy to simulate molecular dynamics. Then, molecular dynamics simulation was performed on human serum albumin with code (1Ao6) and cytarabine with code (AR3), using Gromacs software and the results were presented in the graphs. The simulations were performed at 310 K (normal cell temperature) and 313 K (cancer cell temperature) in 100 ns. Results showed drug release occurred at a temperature of 313 K. These findings demonstrated the sensitivity of human serum albumin to temperature.

Application of DFT Calculations in Designing Polymer-Based Drug Delivery Systems: An Overview

Drug delivery systems transfer medications to target locations throughout the body. These systems are often made up of biodegradable and bioabsorbable polymers acting as delivery components. The introduction of density functional theory (DFT) has tremendously aided the application of computational material science in the design and development of drug delivery materials. The use of DFT and other computational approaches avoids time-consuming empirical processes. Therefore, this review explored how the DFT computation may be utilized to explain some of the features of polymer-based drug delivery systems. First, we went through the key aspects of DFT and provided some context. Then we looked at the essential characteristics of a polymer-based drug delivery system that DFT simulations could predict. We observed that the Gaussian software had been extensively employed by researchers, particularly with the B3LYP functional and 6-31G(d, p) basic sets for polymer-based drug delivery systems. However, to give researchers a choice of basis set for modelling complicated organic systems, such as polymer-drug complexes, we then offered possible resources and presented the future trend.

Hybrid hydrogels derived from renewable resources as a smart stimuli responsive soft material for drug delivery applications

The design and synthesis of amphiphilic molecules play a crucial role in fabricating smart functional materials via self-assembly. Especially, biologically significant natural molecules and their structural analogues have inspired chemists and made a major contribution to the development of advanced smart materials. In this report, a series of amphiphilic N-acyl amides were synthesized from natural precursors using a simple synthetic protocol. Interestingly, the self-assembly of amphiphiles 6a and 7a furnished a hydrogel and oleogel in vegetable oils. Morphological analysis of gels revealed the existence of a 3-dimensional fibrous network. Thermoresponsive and thixotropic behavior of these gels were evaluated using rheological analysis. A composite gel prepared by the encapsulation of curcumin in the hydrogel formed from 7a displayed a gel-sol transition in response to pH and could act as a dual channel responsive drug carrier.

Selective adsorption and dissociation of NO, NO2, and N2O molecules on Si-doped haeckelite boron nitride nanotube: an investigation for sensitive molecular sensors and catalysts

The current study describes the investigation of the adsorption NO, N₂O, and NO₂ on haeckelite boron nitride nanotube doped with Si (Si-doped haeck-BNNT) by means of density functional theory calculation (DFT). The obtained results confirmed the energetic stability of the optimized geometries and revealed that the adsorption of the gas molecules with the nanotube sidewall is a spontaneous process. The calculated work function of Si-doped haeck-BNNT in the presence of gas molecules is greater than that of a bare Si-doped haeck-BNNT sheet. The energy gap of the Si-doped haeck-BNNT is sensitive to the adsorption of the gas molecules, which implies possible future applications in gas sensors. For most of the adsorption configurations studied, the adsorption energies for the Si_B-doped haeck-BNNT are higher than those for Si_N-doped haeck-BNNTones. The N₂O gas molecule is totally dissociated into N₂ and O species through the adsorption process, while the other gas molecules retain their molecular forms. Thus, the Si_N-doped haeck-BNNT is a likely catalyst for dissociation of the N₂O gas molecule. Our findings divulge promising potential of the doped haeck-BNNT as a highly sensitive molecular sensor for NO and NO₂ detection and a catalyst for N₂O dissociation.

Biochemical, Ameliorative and Cytotoxic Effects of Newly Synthesized Curcumin Microemulsions: Evidence from In Vitro and In Vivo Studies

Curcumin is known to exhibit antioxidant and tissue-healing properties and has recently attracted the attention of the biomedical community for potential use in advanced therapies. This work reports the formulation and characterization of oil-in-water F127 microemulsions to enhance the bioavailability of curcumin Microemulsions showed a high encapsulation efficiency and prolonged release. To investigate the interactions of curcumin with one unit of the polymeric chain of surfactant F127, ethyl butyrate, and sodium octanoate, as well as the interaction between ethyl butyrate and one unit of the F127 polymer chain, the Density Functional Theory (DFT) calculations at the M06-2X level of theory, were performed in water solution. The MTT assay was used to assess the cytotoxicity of free and encapsulated curcumin on non-malignant and malignant cell lines. Combination effects were calculated according to Chou-Talalay's principles. Results of in vitro studies indicated that MCF7 and HepG2 cells were more sensitive to curcumin microemulsions. Moreover, a synergistic relationship was observed between curcumin microemulsions and cisplatin in all affected fractions of MCF7 and HepG2 cells (CI < 0.9). For in vivo investigation, thioacetamide-intoxicated rats received thioacetamide (100 mg/kg Sc) followed by curcumin microemulsions (30 mg/kg Ip). Thioacetamide-intoxicated rats showed elevated serum liver enzymes, blood urea nitrogen (BUN), and creatinine levels, and a significant reduction in liver superoxide dismutase (SOD) and catalase (CAT) activities (p < 0.05). Curcumin microemulsions reduced liver enzymes and serum creatinine and increased the activity of antioxidant enzymes in thioacetamide-treated rats in comparison to the untreated thioacetamide-intoxicated group. Histopathological investigations confirmed the biochemical findings. Overall, the current results showed the desirable hepatoprotective, nephroprotective, and anti-cancer effects of curcumin microemulsions.

A Review on Recent Advancements of Graphene and Graphene-Related Materials in Biological Applications

Graphene is the most outstanding material among the new nanostructured carbonaceous species discovered and produced. Graphene’s astonishing properties (i.e., electronic conductivity, mechanical robustness, large surface area) have led to a deep change in the material science field. In this review, after a brief overview of the main characteristics of graphene and related materials, we present an extensive overview of the most recent achievements in biological uses of graphene and related materials.

Investigation of nanotubes as the smart carriers for targeted delivery of mercaptopurine anticancer drug

Mercaptopurine (MCP) is an anticancer drug that is used to treat acute lymphoblastic leukemia. The therapeutic effect of the mercaptopurine limits its severe side effects like other cytotoxic (anti-cancer) drugs. Nanostructures or nanoparticles can be widely used as potential drug carriers for diagnosis and treatment of cancer. In the current study, the boron nitride nanotube (BNNT) and carbon nanotube (CNT) were studied as the delivery carriers of MCP using the density functional theory (DFT) calculations and molecular dynamics (MDs) simulation studies. To further understand the electronic properties of mercaptopurine, the partial density of states (PDOS) was calculated. The PDOS results depicted that the electronic features of the MCP do not change after the adsorption on the surface of the nanotubes. More stability of the MCP/BNNT complexes may be attributed to the existence of the intermolecular hydrogen bonds (H-bonds) between the hydrogen atoms of the MCP molecule and the N atoms of the BNNT. The results of the quantum theory of atoms in molecules (QTAIM) confirmed the presence of H-bonds in these complexes. Moreover, MD simulation studies were done in the presence of five drug molecules. The results revealed that the strongest van der Waals (vdW) interaction energy was found between the BNNT and MCP among the studied nanotubes, indicating the BNNT is a better nanocarrier than carbon nanotube for delivery of the MCP drug within the biological systems. In general, the obtained results may present helpful information on the nature of the interactions between mercaptopurine anticancer drug with BNNT and/or CNT.Communicated by Ramaswamy H. Sarma.

Sustained release of tulobuterol from graphene oxide laden hydrogel to manage asthma

Bronchial asthma is a chronic disease which is currently treated using various inhalants. However, the medication adherence with the inhalants is poor due to complex procedure to use them along with frequent dosing. In this paper, we have developed tulobuterol loaded Pluronic® F127-reduced graphene oxide transdermal hydrogel to sustain the release of tulobuterol to manage asthma for days. The synthesis of Pluronic^® F127-reduced graphene oxide was confirmed by Fourier transform infrared spectroscopy, X-ray diffraction, and Raman spectroscopy. The transmission electron microscope showed wrinkled flat nano sheets. The hydrogel showed sufficient mechanical properties for topical application and was safe in the skin irritation study (rabbit model). The ex vivo release data demonstrated the ability of reduced graphene oxide to sustain the release of tulobuterol for 72 h, due to strong π-π interaction between drug and graphene oxide. The pharmacokinetic profile in Sprague-Dawley rat model confirmed the potential of tulobuterol-Pluronic^® F127-reduced graphene oxide hydrogel to sustain the release of tulobuterol for effective management of asthma.

RETRACTED: Pluronic® F127 stabilized reduced graphene oxide hydrogel for the treatment of psoriasis: In vitro and in vivo studies

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editors. Significant similarities were noticed post-publication between this article and an article submitted to the journal on the same day, by an apparently unrelated research group: Hui Li, Yanlu Jia and Chunling Liu, Colloids and Surfaces B: Biointerfaces 195 (2020) 111259 https://doi.org/10.1016/j.colsurfb.2020.111259. Moreover, the authors did not respond to the journal request to comment on these similarities and to provide the raw data, and the Editors decided to retract the article. One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and genuine. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process. Although this article was published earlier than the article from Colloids and Surfaces B: Biointerfaces 195 (2020) 111259, the Editors decided to retract this article given the concerns on the reliability of the data.

RETRACTED: Pluronic® F127 stabilized reduced graphene oxide hydrogel for transdermal delivery of ondansetron: Ex vivo and animal studies

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editors. Significant similarities were noticed post-publication between this article and an article submitted to the journal on the same day, by an apparently unrelated research group: Qiang Li, Fangmei Li, Xixi Qi, Fuqiao Wei, Hongxiao Chen and Ting Wang, Colloids and Surfaces B: Biointerfaces 195 (2020) 111246 https://doi.org/10.1016/j.colsurfb.2020.111246. Moreover, the authors did not respond to the journal request to comment on these similarities and to provide the raw data, and the Editors decided to retract the article. One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and genuine. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

New insight into the molecular mechanism of the trehalose effect on urate oxidase stability

Urate oxidase (EC 1.7.3.3) is a key enzyme in the purine metabolism which is applied in the treatment of gout and also, as a diagnostic reagent for uric acid detection. In the current study, the trehalose (TRE) effects as an additive on the structural stability and function of uricase were investigated. For recombinant expression of UOX in E. coli BL21 cells, firstly the coding sequence was subcloned into the pET-28a vector and after induction with IPTG, the recombinant UOX was purified by affinity chromatography using a Ni-NTA agarose column. To specify the trehalose effects on the urate oxidase (UOX) structure, optimum pH, optimum temperature, kinetic and thermodynamic parameters and also, the intrinsic fluorescence of UOX in the absence and presence of trehalose were examined. The UOX half-life is 24.32 min at 40 °C, whereas the UOX-TRE has a higher half-life (32.09 min) at this temperature. Generally, our findings confirm that trehalose has a protective effect on the enzyme structure. Optimum pH and temperature were 9 and 25 °C, respectively for both the naked and treated enzymes and their activity retained 42.18 and 64.80%, respectively after 48 h of incubation at room temperature. Also, theoretical results indicate that the random coil of the enzyme was converted to α-helix and β-sheet in the presence of trehalose which may preserve the integrity of the active site of the enzyme and increased the enzymatic activity. The MD simulation results indicated greater stability of the uricase structure in the presence of trehalose.Communicated by Ramaswamy H. Sarma.