Molecular dynamics simulation of Doxorubicin loading with N-isopropyl acrylamide carbon nanotube in a drug delivery system

Metal-Organic Frameworks for Cisplatin Delivery to Cancer Cells: A Molecular Dynamics Simulation

Metal-organic frameworks (MOFs) are utilized as nanocarriers to enhance the efficiency of chemotherapy drugs, including cisplatin, which exhibit limitations such as side effects and resistance mechanisms. To evaluate the role of MOFs, we employed a molecular dynamics simulation, which, unlike other experiments, is cost-effective, less dangerous, and provides accurate results. Furthermore, we conducted molecular docking simulations to understand the interaction between cisplatin and MOF, as well as their internal interactions and how they bind to each other. Cisplatin and MOF molecules were parametrized using the Avogadro software and x2top command in GROMACS 5.1.2 and optimized by CP2K software; the Charmm-GUI site parametrized the cell cancer membrane. Three molecular dynamics simulations were conducted in four stages at various pHs, followed by simulated umbrella sampling. The simulations analyzed the pH responsiveness, total energy, Gibbs free energy, gyration radius, radial distribution function (RDF), solvent accessible surface area, and nanoparticles' toxicity. Results demonstrated that a neutral pH level (7.4) has greater adsorption and interaction compared to acidic pH values (6.4 and 5.4) because it displays the highest total energy (-17.1 kJ/mol), the highest RDF value (6.66), and the shortest distance (0.51 nm). Furthermore, the combination of cisplatin and MOFs displayed increased penetration compared to that of their individual forms. This study highlights the suitability of MOFs as nanocarriers and identifies the optimal pH values for desirable outcomes. Thus, it provides future studies with appropriate data to conduct their experiments in assessing MOFs.

Molecular dynamics investigation on synthesis of a pH- and temperature-sensitive carbon nanotube loaded with doxorubicin

The many exotic properties of carbon nanotubes (CNTs) make them a powerful attraction in the field of drug delivery systems (DDS). In this work, based on quantum chemical calculation and molecular simulation techniques, polyacrylic acid (PAA) and N-isopropyl acrylamide (NIP) are selected and acted simultaneously on the CNT to form a stable system (FCNT). As a potential DDS, FCNT captures the dispersed doxorubicin (DOX) molecules around it and maintains a stable configuration. In these processes, electrostatic and van der Waals forces act synergistically, with van der Waals forces dominating. Compared to NIP, PAA molecules exhibit stronger adhesion and encapsulation efficiency to CNT and stronger adsorption capacity to DOX. This study reveals the mechanism of action among PAA, NIP, CNT, and DOX, providing feasibility verification and prospective guidance for the experimental synthesis of PAA-NIP-CNT-type multifunctional DDS, and also broadening the idea for exploring more efficient DDS suitable for DOX.

Nanotube breakthroughs: unveiling the potential of carbon nanotubes as a dual therapeutic arsenal for Alzheimer's disease and brain tumors

Alzheimer's disease (AD) and brain tumors are debilitating neurological conditions that pose significant challenges in current medical practices. Existing treatment options for AD primarily focus on symptom management, and brain tumors often require aggressive therapeutic approaches. Novel disease-modifying strategies and therapeutic agents are urgently needed to address the underlying causes of AD pathogenesis and improve brain tumor management. In recent years, nanoparticles (NPs) have shown promise as valuable tools in diagnosing and managing various brain disorders, including AD. Among these, carbon nanotubes (CNTs) have garnered attention for their unique properties and biomedical potential. Their ability to cross the blood-brain barrier (BBB) with ease opens up new possibilities for targeted drug delivery and neuroprotection. This literature review aims to explore the versatile nature of CNTs, which can be functionalized with various biomolecules or substances due to their sp2 hybridization. This adaptability enables them to specifically target cells and deliver medications under specific environmental conditions. Moreover, CNTs possess an exceptional capacity to penetrate cell membranes, making them valuable tools in the treatment of AD and brain tumors. By delving into the role of CNTs in biomedicine, this review sheds light on their potential in managing AD, offering a glimpse of hope for effective disease-modifying options. Understanding the mechanisms of CNTs' action and their capabilities in targeting and delivering medication to affected cells will pave the way for innovative therapeutic strategies that can improve the lives of those afflicted with these devastating neurological conditions. The exploration of CNTs as a dual therapeutic arsenal for both brain tumors and Alzheimer's disease holds great promise and may usher in a new era of effective treatment strategies for these challenging conditions.

Exploring the benefits of functionally graded carbon nanotubes (FG-CNTs) as a platform for targeted drug delivery systems

BACKGROUND AND OBJECTIVE

Modern therapeutic systems have benefited from the use of functionally graded carbon nanotubes (FG-CNTs) to enhance their efficiency. Various studies have shown that the study of dynamic response and stability of fluid-conveying FG-nanotubes can be improved by considering a Multiphysics framework for the modeling of such a complex biological environment. However, despite noticing important aspects in modeling, the previous studies have drawbacks such as underrepresenting the effect of varying composition of the nanotube on magnetic drug release in drug delivery systems. The present work has the novelty of studying the combined effects of fluid flow, magnetic field, small-scale parameters, and functionally graded material on the performance of FG-CNTs for drug delivery applications. Additionally, the lack of an inclusive parametric study is resolved in the present study by evaluating the significance of different geometrical and physical parameters. As such, the achievements support the development of an efficient drug delivery treatment.

METHODS

The Euler-Bernoulli beam theory is implemented to model the nanotube and Hamilton's principle based on Eringen's nonlocal elasticity theory is used to derive the constitutive equations of motion. To add the effect of slip velocity on the CNT's wall, a correction factor is applied to velocity based on the Beskok-Karniadakis model.

RESULTS

demonstrate that the dimensionless critical flow velocity increases by 227% as the magnetic field intensity increases from 0 to 20 T, and improves the system stability. On the contrary, drug loading on the CNT has the opposite effect, as the critical velocity decreases from 10.1 to 8.38 using a linear function for drug loading, and it decreases to 7.95 using an exponential function. By employing a hybrid load distribution, an optimum material distribution can be achieved.

CONCLUSIONS

To benefit from the potential of CNTs in drug delivery systems while minimizing the instability problems, a suitable design for the drug loading is required prior to the clinical implementation of the nanotube.

Synthesis of single-walled carbon nanotubes functionalized with platinum nanoparticles to sense breast cancer cells in 4T1 model to X-ray radiation

In recent years, various types of radiosensitizers have been developed to address the challenges of cancer radiotherapy. Here, platinum-functionalized oxygenated single-walled carbon nanotubes (O-SWCNTs-Pt) coated with folic acid (FA) and bovine serum albumin (BSA) (O-SWCNTs-Pt-BSA-FA) were synthesized, characterized, and used as radiosensitizers to improve the therapeutic efficacy of X-rays in a mouse model of breast cancer (4T1) in vitro. The nanosensitizer was characterized by different techniques, such as transmission electron microscopy (TEM), selected area electron diffraction (SAED), dynamic light scattering (DLS), zeta potential, X-ray diffraction (XRD), ultraviolet-visible (UV-visible), and Fourier transform infrared (FTIR) spectrometry. The evaluation of cell viability with nanocarriers O-SWCNTs-BSA, O-SWCNTs-Pt-BSA, Pt-BSA-FA, and O-SWCNTs-Pt-BSA-FA is reported at the concentrations of 10, 30, and 90 μg/mL by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in the presence and absence of X-rays at 4 and 8 Gy. The results showed that administration of O-SWCNTs-BSA, O-SWCNTs-Pt-BSA, Pt-BSA-FA, and O-SWCNTs-Pt-BSA-FA + 8 Gy at a concentration of 90 μg/mL reduced survival by 75.31, 65.32, 67.35, and 60.35%, respectively. O-SWCNTs-Pt-BSA-FA has a hydrodynamic size of 88.57 nm and a surface charge of -29 mV, which indicates special stability. Compared with O-SWCNTs-BSA, O-SWCNTs-Pt-BSA, and Pt-BSA-FA, it has very strong cell-killing activity in the 4T1 cell line. It is also noteworthy that SWCNTs can act as a controlled release and delivery system for PtNPs due to their unique properties and easy penetration into biological membranes. As a result, the  new nanosensitizer may play a role in cancer treatment in conjunction with radiotherapy technology. Graphical abstract.

The effect of initial temperature on the mechanical interaction of 3DN5/5OTF protein-based structures using molecular dynamics simulation

Nowadays, advances in science and technology in biological macromolecules have led to the early detection and treatment of cancer-based cells. In this study, molecular dynamics (MD) simulation examines atomic interactions between 3DN5 and 5OTF structures. Technically, the effect of the initial temperature on the atomic behavior (AB) of the simulated samples is investigated. The stability of simulated structures is examined with changes in temperature and kinetic energy (KE) quantities. The biomechanical interaction is examined by the radius of gyration (RoG), interaction energy (IE), and interaction force (IF). The results show that the RoG changes from a numerical value of 40.25 to 41.33 Å, and the IE and IF converge to -552.38 kcal/mol and - 207.10 kcal/mol.Å after 10 ns, respectively. Due to the temperature effect on the AB of the structures, the RoG increases by increasing the initial temperature from 41.33 to 58.91 Å. By increasing the initial temperature to 350 K, the IE increases from -551.38 to -500.11 kcal/mol, and the IF increases from -207.10 to -183.39 kcal/mol.Å. Finally, the results of these studies are expected to lead to early detection and treatment of cancer cells.

Caenorhabditis elegans as a Prediction Platform for Nanotechnology-Based Strategies: Insights on Analytical Challenges

Nanotechnology-based strategies have played a pivotal role in innovative products in different technological fields, including medicine, agriculture, and engineering. The redesign of the nanometric scale has improved drug targeting and delivery, diagnosis, water treatment, and analytical methods. Although efficiency brings benefits, toxicity in organisms and the environment is a concern, particularly in light of global climate change and plastic disposal in the environment. Therefore, to measure such effects, alternative models enable the assessment of impacts on both functional properties and toxicity. Caenorhabditis elegans is a nematode model that poses valuable advantages such as transparency, sensibility in responding to exogenous compounds, fast response to perturbations besides the possibility to replicate human disease through transgenics. Herein, we discuss the applications of C. elegans to nanomaterial safety and efficacy evaluations from one health perspective. We also highlight the directions for developing appropriate techniques to safely adopt magnetic and organic nanoparticles, and carbon nanosystems. A description was given of the specifics of targeting and treatment, especially for health purposes. Finally, we discuss C. elegans potential for studying the impacts caused by nanopesticides and nanoplastics as emerging contaminants, pointing out gaps in environmental studies related to toxicity, analytical methods, and future directions.

Molecular dynamics insight of interaction between the functionalized-carbon nanotube and cancerous cell membrane in doxorubicin delivery

BACKGROUND AND OBJECTIVE

Doxorubicin (DOX) is a known anticancer drug which is widely used in cancer therapy. Carbon nanotubes (CNTs) are among the most promising platforms for smart drug delivery applications. However, due to the toxicity and their low sulubility their application is limited and their functionalization with wide range of biomolecules are suggested. Therefore, the functionalized carbon nanotubes (f-CNT) with carboxyl (CNT-COO) and folic acid (CNT-COO-FA) were investigated as drug-carrier.

METHODS

Molecular dynamics (MD) simulation along with the Density Functional Theory (DFT) methods are being used to study the drug loading process on functionalized carbon nanotubes.

RESULTS

The results indicate that doxorubicin molecules interact more with CNT-COO-FA than CNT-COO. The embedded dipalmitoylphosphatidylcholine (DPPC) lipid bilayer with a folate receptor was considered a cancerous cell's representative model. Then the drug release from the f-CNTs near the lipid bilayer was simulated. The results showed that CNT-COO-FA with a pH and ligand-sensitive mechanism strongly interacts with cancerous cells, which led to higher drug release, in agreement with the experimental results. The conformational changes of the lipid bilayer and folate receptor during drug release were evaluated. The analysis showed that drug release from CNT-COO-FA has significantly changed lipid bilayer and receptor conformations. The obtained results were interpreted and justified by considering the molecular mechanisms which control the drug delivery in the studied systems.

CONCLUSIONS

Based on the obtained results, CNT-COO-FA has a better performance during the drug release compared to CNT-COO in delivering doxorubicin. Both pH and ligand sensitive mechanisms are found to be responsible for higher drug delivery efficiency of CNT-COO-FA. In contrast, CNT-COO can only enhance drug delivery efficiently with a pH-sensitive mechanism.

Fabrication of chitosan-gelatin films incorporated with thymol-loaded alginate microparticles for controlled drug delivery, antibacterial activity and wound healing: In-vitro and in-vivo studies

Previously, studies have demonstrated the unique characteristics of chitosan-gelatin films as wound dressings applications. However, their application has been limited due to their inadequacy of antimicrobial and anti-inflammatory characteristics. To improve the intended multifunctional characteristics of chitosan-gelatin film, in this study, we designed a novel composite film with the capability of controlled and prolonged release of thymol as a natural antioxidant and antimicrobial drug. Here, thymol-loaded ALG MPs (Thymol-ALG MPs) were prepared by electrospraying method and incorporated into the chitosan-gelatin film. The composite wound dressings of Thymol-ALG MPs incorporated in chitosan-gelatin film (CS-GEL/Thymol-ALG MPs) were characterized by in vitro and in vivo evaluations. The Thymol-ALG MPs demonstrated spherical and uniform morphology, with high encapsulation efficiency (88.9 ± 1.1 %). The CS-GEL/Thymol-ALG MPs exhibited high antibacterial activity against both Gram-positive and Gram-negative bacteria and no cytotoxicity for the L929 fibroblast cells. The release trend of thymol from CS-GEL/Thymol-ALG MPs and Thymol-ALG MPs followed a pseudo-Fickian diffusion mechanism. This wound dressing effectively accelerates the wound healing process at rats' full-thickness skin excisions. Also, the histological analysis demonstrated that the CS-GEL/Thymol-ALG MPs could significantly enhance epithelialization, collagen deposition, and induce skin regeneration. The present antibacterial composite film has promising characteristics for wound dressings applications.

Molecular Dynamics Simulation of Drug Solubilization Behavior in Surfactant and Cosolvent Injections

Surfactants and cosolvents are often combined to solubilize insoluble drugs in commercially available intravenous formulations to achieve better solubilization. In this study, six marketed parenteral formulations with surfactants and cosolvents were investigated on the aggregation processes of micelles, the structural characterization of micelles, and the properties of solvent using molecular dynamics simulations. The addition of cosolvents resulted in better hydration of the core and palisade regions of micelles and an increase in both radius of gyration (Rg) and the solvent accessible surface area (SASA), causing a rise in critical micelle concentration (CMC), which hindered the phase separation of micelles. At the same time, the presence of cosolvents disrupted the hydrogen bonding structure of water in solution, increasing the solubility of insoluble medicines. Therefore, the solubilization mechanism of the cosolvent and surfactant mixtures was successfully analyzed by molecular dynamics simulation, which will benefit future formulation development for drug delivery.

PNIPAM/Hexakis as a thermosensitive drug delivery system for biomedical and pharmaceutical applications

Many technologies ranging from drug delivery approaches to tissue engineering purposes are beginning to benefit from the unique ability of "smart polymers." As a special case, thermo-sensitive hydrogels have great potential, e.g. in actuators, microfluidics, sensors, or drug delivery systems. Here, the loading of Doxorubicin (DOX) with novel thermo-sensitive polymer N-isopropyl acrylamide (PNIPAM) and its copolymers are investigated in order to increase the Doxorubicin's drug efficacy on the targeted tumor site. Therefore, a rational design accurate based on the use of classical molecular dynamics (MD) and well-tempered metadynamics simulations allows for predicting and understanding the behavior of thermo-responsive polymers in the loading of DOX on Hexakis nano-channel at 298 and 320 K. Furthermore, this work investigates the efficacy of this drug carrier for the release of DOX in response to stimuli like variations in temperature and changes in the physiological pH. The study concludes that the Hexakis-polymer composite is capable of adsorbing the DOX at neutral pH and by increasing the temperature of the simulated systems from 298 to 320 K, the strength of intermolecular attraction decreases. In addition, the obtained results of MD simulation revealed that the dominant interaction between DOX and Hexakis in the DOX/polymer/Hexakis systems is the Lennard-Jones (LJ) term due to the formation of strong π-π interaction between the adsorbate and substrate surface. Obtained results show that a higher aggregation of DMA chains around the Hexakis and the formation of stronger bonds with DOX. The results of the well-tempered metadynamics simulations revealed that the order of insertion of drug and polymer into the system is a determining factor on the fate of the adsorption/desorption process. Overall, our results explain the temperature-dependent behavior of the PNIPAM polymers and the suitability of the polymer-Hexakis carrier for Doxorubicin delivery.

Broad-Spectrum Antimicrobial ZnMintPc Encapsulated in Magnetic-Nanocomposites with Graphene Oxide/MWCNTs Based on Bimodal Action of Photodynamic and Photothermal Effects

Microbial diseases have been declared one of the main threats to humanity, which is why, in recent years, great interest has been generated in the development of nanocomposites with antimicrobial capacity. The present work studied two magnetic nanocomposites based on graphene oxide (GO) and multiwall carbon nanotubes (MWCNTs). The synthesis of these magnetic nanocomposites consisted of three phases: first, the synthesis of iron magnetic nanoparticles (MNPs), second, the adsorption of the photosensitizer menthol-Zinc phthalocyanine (ZnMintPc) into MWCNTs and GO, and the third phase, encapsulation in poly (N-vinylcaprolactam-co-poly(ethylene glycol diacrylate)) poly (VCL-co-PEGDA) polymer VCL/PEGDA a biocompatible hydrogel, to obtain the magnetic nanocomposites VCL/PEGDA-MNPs-MWCNTs-ZnMintPc and VCL/PEGDA-MNPs-GO-ZnMintPc. In vitro studies were carried out using Escherichia coli and Staphylococcus aureus bacteria and the Candida albicans yeast based on the Photodynamic/Photothermal (PTT/PDT) effect. This research describes the nanocomposites' optical, morphological, magnetic, and photophysical characteristics and their application as antimicrobial agents. The antimicrobial effect of magnetics nanocomposites was evaluated based on the PDT/PTT effect. For this purpose, doses of 65 mW·cm-2 with 630 nm light were used. The VCL/PEGDA-MNPs-GO-ZnMintPc nanocomposite eliminated E. coli and S. aureus colonies, while the VCL/PEGDA-MNPs-MWCNTs-ZnMintPc nanocomposite was able to kill the three types of microorganisms. Consequently, the latter is considered a broad-spectrum antimicrobial agent in PDT and PTT.

Membrane Technological Pathways and Inherent Structure of Bacterial Cellulose Composites for Drug Delivery

This report summarizes efforts undertaken in the area of drug delivery, with a look at further efforts made in the area of bacterial cellulose (BC) biomedical applications in general. There are many current methodologies (past and present) for the creation of BC membrane composites custom-engineered with drug delivery functionality, with brief consideration for very close applications within the broader category of biomedicine. The most emphasis was placed on the crucial aspects that open the door to the possibility of drug delivery or the potential for use as drug carriers. Additionally, consideration has been given to laboratory explorations as well as already established BC-drug delivery systems (DDS) that are either on the market commercially or have been patented in anticipation of future commercialization. The cellulose producing strains, current synthesis and growth pathways, critical aspects and intrinsic morphological features of BC were given maximum consideration, among other crucial aspects of BC DDS.

Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation

The use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The encapsulation process was modelled, considering an aqueous solution, by a molecular dynamics (MD) simulation under a canonical NVT ensemble. The interactions between the atoms of Isatin were obtained from the DREIDING force filed. The storage capacity of the capped SWCNT host was evaluated to quantify its capacity to host multiple Isatin molecules. Our results show that the Isatin can be readily trapped inside the volume cavity of the capped SWCNT and it remained stable, as featured by a reduction in the van der Waals forces between Isatin guest and the SWCNT host (at approximately - 30 kcal mol^-1) at the end of the MD simulation (15 ns). Moreover, the free energy of encapsulation was found to be - 34 kcal mol^-1 suggesting that the Isatin insertion procedure into the SWCNT occurred spontaneously. As calculated, a capped SWCNT (10,10) with a length of 30 Å, was able to host eleven (11) molecules of Isatin, that all remained steadily encapsulated inside the SWCNT volume cavity, showing a potential for the use of carbon nanotubes as drug delivery cargo systems.

Experimental and Computational Study on the Microfluidic Control of Micellar Nanocarrier Properties

Microfluidic-based synthesis is a powerful technique to prepare well-defined homogenous nanoparticles (NPs). However, the mechanisms defining NP properties, especially size evolution in a microchannel, are not fully understood. Herein, microfluidic and bulk syntheses of riboflavin (RF)-targeted poly(lactic-co-glycolic acid)-poly(ethylene glycol) (PLGA-PEG-RF) micelles were evaluated experimentally and computationally. Using molecular dynamics (MD), a conventional "random" model for bulk self-assembly of PLGA-PEG-RF was simulated and a conceptual "interface" mechanism was proposed for the microfluidic self-assembly at an atomic scale. The simulation results were in agreement with the observed experimental outcomes. NPs produced by microfluidics were smaller than those prepared by the bulk method. The computational approach suggested that the size-determining factor in microfluidics is the boundary of solvents in the entrance region of the microchannel, explaining the size difference between the two experimental methods. Therefore, this computational approach can be a powerful tool to gain a deeper understanding and optimize NP synthesis.

Key Points in Remote-Controlled Drug Delivery: From the Carrier Design to Clinical Trials

The increased research activity aiming at improved delivery of pharmaceutical molecules indicates the expansion of the field. An efficient therapeutic delivery approach is based on the optimal choice of drug-carrying vehicle, successful targeting, and payload release enabling the site-specific accumulation of the therapeutic molecules. However, designing the formulation endowed with the targeting properties in vitro does not guarantee its selective delivery in vivo. The various biological barriers that the carrier encounters upon intravascular administration should be adequately addressed in its overall design to reduce the off-target effects and unwanted toxicity in vivo and thereby enhance the therapeutic efficacy of the payload. Here, we discuss the main parameters of remote-controlled drug delivery systems: (i) key principles of the carrier selection; (ii) the most significant physiological barriers and limitations associated with the drug delivery; (iii) major concepts for its targeting and cargo release stimulation by external stimuli in vivo. The clinical translation for drug delivery systems is also described along with the main challenges, key parameters, and examples of successfully translated drug delivery platforms. The essential steps on the way from drug delivery system design to clinical trials are summarized, arranged, and discussed.

Theoretical Encapsulation of Fluorouracil (5-FU) Anti-Cancer Chemotherapy Drug into Carbon Nanotubes (CNT) and Boron Nitride Nanotubes (BNNT)

INTRODUCTION

Chemotherapy with anti-cancer drugs is considered the most common approach for killing cancer cells in the human body. However, some barriers such as toxicity and side effects would limit its usage. In this regard, nano-based drug delivery systems have emerged as cost-effective and efficient for sustained and targeted drug delivery. Nanotubes such as carbon nanotubes (CNT) and boron nitride nanotubes (BNNT) are promising nanocarriers that provide the cargo with a large inner volume for encapsulation. However, understanding the insertion process of the anti-cancer drugs into the nanotubes and demonstrating drug-nanotube interactions starts with theoretical analysis.

METHODS

First, interactions parameters of the atoms of 5-FU were quantified from the DREIDING force field. Second, the storage capacity of BNNT (8,8) was simulated to count the number of drugs 5-FU encapsulated inside the cavity of the nanotubes. In terms of the encapsulation process of the one drug 5-FU into nanotubes, it was clarified that the drug 5-FU was more rapidly adsorbed into the cavity of the BNNT compared with the CNT due to the higher van der Waals (vdW) interaction energy between the drug and the BNNT.

RESULTS

The obtained values of free energy confirmed that the encapsulation process of the drug inside the CNT and BNNT occurred spontaneously with the free energies of -14 and -25 kcal·mol-1, respectively.

DISCUSSION

However, the lower value of the free energy in the system containing the BNNT unraveled more stability of the encapsulated drug inside the cavity of the BNNT comparing the system having CNT. The encapsulation of Fluorouracil (5-FU) anti-cancer chemotherapy drug (commercial name: Adrucil®) into CNT (8,8) and BNNT (8,8) with the length of 20 Å in an aqueous solution was discussed herein applying molecular dynamics (MD) simulation.

Atomic Scale Interactions between RNA and DNA Aptamers with the TNF-α Protein

Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for selecting the aptamer candidate with the highest binding strength to a target. We combine information from the binding free energy calculations, molecular docking, and molecular dynamics simulations to investigate the interactions of both aptamers with TNF-α. The results reveal that the RNA aptamer has a more stable structure relative to the DNA aptamer. Interaction of aptamers with TNF-α does not have any negative effect on its structure. The results of molecular docking and molecular dynamics simulations suggest that the RNA aptamer has a stronger interaction with the protein. Also, these findings illustrate that basic residues of TNF-α establish more atomic contacts with the aptamers compared to acidic or pH-neutral ones. Furthermore, binding energy calculations show that the interaction of the RNA aptamer with TNF-α is thermodynamically more favorable. In total, the findings of this study indicate that the RNA aptamer is a more suitable candidate for using as an apta-biosensor of TNF-α and, therefore, of greater potential use for the diagnosis of blood infections. Also, this study provides more information about aptamer-protein interactions and increases our understanding of this phenomenon.

Turning Toxic Nanomaterials into a Safe and Bioactive Nanocarrier for Co-delivery of DOX/pCRISPR

Hybrid bioactive inorganic-organic carbon-based nanocomposites of reduced graphene oxide (rGO) nanosheets enlarged with multi-walled carbon nanotubes (MWCNTs) were decorated to provide a suitable space for in situ growth of CoNi₂S₄ and green-synthesized ZnO nanoparticles. The ensuing nanocarrier supplied π-π interactions between the DOX drug and a stabilizing agent derived from leaf extracts on the surface of ZnO nanoparticles and hydrogen bonds; gene delivery of (p)CRISPR was also facilitated by chitosan and alginate renewable macromolecules. Also, these polymers can inhibit the potential interactions between the inorganic parts and cellular membranes to reduce the potential cytotoxicity. Nanocomposite/nanocarrier analyses and sustained DOX delivery (cytotoxicity analyses on HEK-293, PC12, HepG2, and HeLa cell lines after 24, 48, and 72 h) were indicative of an acceptable cell viability of up to 91.4 and 78.8% after 48 at low and high concentrations of 0.1 and 10 μg/mL, respectively. The MTT results indicate that by addition of DOX to the nanostructures, the relative cell viability increased after 72 h of treatment; since the inorganic compartments, specifically CoNi₂S₄, are toxic, this is a promising route to increase the bioavailability of the nanocarrier before reaching the targeted cells. Nanosystems were tagged with (p)CRISPR for co-transfer of the drug/genes, where confocal laser scanning microscopy (CLSM) pictures of the 4',6-diamidino-2-phenylindole (DAPI) were indicative of appropriate localization of DOX into the nanostructure with effective cell and drug delivery at varied pH. Also, the intrinsic toxicity of CoNi₂S₄ does not affect the morphology of the cells, which is a breakthrough. Furthermore, the CLSM images of the HEK-293 and HeLa cell displayed effective transport of (p)CRISPR into the cells with an enhanced green fluorescent protein (EGFP) of up to 8.3% for the HEK-293 cell line and 21.4% for the HeLa cell line, a record. Additionally, the specific morphology of the nanosystems before and after the drug/gene transport events, via images by TEM and FESEM, revealed an intact morphology for these biopolymers and their complete degradation after long-time usage.

Exploring pH dependent delivery of 5-fluorouracil from functionalized multi-walled carbon nanotubes

Multi-walled carbon nanotubes (MWCNTs) can be applied for pH-sensitive delivery of anticancer drugs. Due to the importance of 5-fluorouracil (5-FU) in different tumor therapy regimens, it has been widely used in different pH dependent drug delivery systems. To investigate the pH effects on loading (and release) of 5-FU on (and from) the functionalized MWCNTs and propose the optimum condition for drug delivery, both macroscopic and microscopic studies were carried out using chromatography and molecular dynamic simulation at different conditions. For both levels of studies, different analytical approaches were performed to assess the validity of the methods. The experimental results revealed that 5-FU has more binding affinity to the surface of the nanocarrier at physiological pH (pH = 7.4) and showed more release at acidic conditions (pH = 5.0). Meanwhile it has been observed that basic pH (pH = 9.0) can lead to a dramatic decrease effect on loading of the drug. The results of this study can be used to suggest the optimum pH levels for nanocarbon based formulations of 5-FU in cancer therapy.

Encapsulation and Release of Doxorubicin from TiO2 Nanotubes: Experiment, Density Functional Theory Calculations, and Molecular Dynamics Simulation

Titanium dioxide (TiO₂) nanotubes are attractive materials for drug-delivery systems because of their biocompatibility, chemical stability, and simple preparation. In this study, we loaded TiO₂ nanotubes with anticancer drug doxorubicin (DOX) experimentally and in all-atom molecular dynamics (MD) simulations. The release of doxorubicin from the nanotubes was studied by high-performance liquid chromatography (HPLC) and confocal Raman spectroscopy, and drug-release profiles were evaluated under various conditions. The polyethylene glycol (PEG) coating and capping of the nanotubes led to a marked increase in the water contact angles from about 16 to 33° in keeping with reduced wettability. The capping retarded the release rate without decreasing the overall release amount. The MD simulations further show that the DOX molecule diffusion coefficients (D_i) are in the order of 10^-10 m²/s. The DOX molecules show a plethora of short- and long-range H-bonding interactions with TiO₂ nanotube walls and water. Calculated radial distribution functions (RDFs) and combined radial/angular distribution functions (CDFs) allowed gauging the strength of these hydrogen bonds. The strength does not fully correlate with the pKa values of DOX atoms which we assign to the confinement of DOX and water in the tubes. The lifetimes of hydrogen bonds between the DOX atoms and water molecules are shorter than that of the DOX^...TiO₂ interactions, and DOX^...DOX aggregation does not play an important role. These results suggest TiO₂ nanotubes as promising candidates for controllable drug-delivery systems for DOX or similar antiproliferative molecules.

Boron Nitride Nanotube as an Antimicrobial Peptide Carrier: A Theoretical Insight

INTRODUCTION

Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance.

METHODS

In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation.

RESULTS

The peptide was absorbed into the BNNT by van der Waals (vdW) interaction between cRW3 and the BNNT, in which the vdW interaction decreased during the simulation process and reached the value of -142.7 kcal·mol-1 at 4 ns.

DISCUSSION

The increase in the potential mean force profile of the encapsulated peptide during the pulling process of cRW3 out of the nanotube showed that its insertion into the BNNT occurred spontaneously and that the inserted peptide had the desired stability. The energy barrier at the entrance of the BNNT caused a pause of 0.45 ns when half of the peptide was inside the BNNT during the encapsulation process. Therefore, during this period, the peptide experienced the weakest movement and the smallest conformational changes.

Computational modelling of nanotube delivery of anti-cancer drug into glutathione reductase enzyme

Density functional theory method combined with docking and molecular dynamics simulations are used to understand the interaction of carmustine with human glutathione reductase enzyme. The active site of the enzyme is evaluated by docking simulation is used for molecular dynamics simulation to deliver the carmustine molecule by (5,5) single walled carbon nanotube (SWCNT). Our model of carmustine in the active site of GR gives a negative binding energy that is further refined by QM/MM study in gas phase and solvent phase to confirm the stability of the drug molecule inside the active site. Once released from SWCNT, carmustine forms multiple polar and non-polar hydrogen bonding interactions with Tyr180, Phe209, Lys318, Ala319, Leu320, Leu321, Ile350, Thr352 and Val354 in the range of 2–4 Å. The SWCNT vehicle itself is held fix at its place due to multiple pi-pi stacking, pi-amide, pi-sigma interactions with the neighboring residues. These interactions in the range of 3–5 Å are crucial in holding the nanotube outside the drug binding region, hence, making an effective delivery. This study can be extended to envisage the potential applications of computational studies in the modification of known drugs to find newer targets and designing new and improved controlled drug delivery systems.

The Opportunities and Challenges of Silica Nanomaterial for Atherosclerosis

Atherosclerosis (AS) as the leading cause of cardiovascular and cerebrovascular events has been paid much attention all the time. With the continuous development of modern medical drug treatment, surgical treatment, interventional treatment and other methods, the mortality rate of AS has shown a downward trend, while the morbidity rate is still increasing. Oral lipid-lowering or anti-inflammatory drugs are generally used for early AS, but the relatively low accumulation efficiency in lesions and the unavoidable side effects required researchers to develop more effective drug delivery approaches for the therapy of AS. Mesoporous silica nanoparticles as nanocarrier for drug delivery have received extensive attentions due to their flexible size, high specific surface area, controlled pore volume, high drug loading capacity and excellent biocompatibility. Series of good reviews about the mesoporous silica nanoparticles loaded drugs for cancer therapy have been well documented. However, their roles as nanocarrier for drug delivery to treat AS have few reports. In this review, the applications and challenges of mesoporous silica nanomaterials in the field of the diagnosis and therapy of AS have been summarized. The classification, synthesis, formation mechanism, surface modification and functionalization of mesoporous silica nanomaterials which were closely related to the theranostic effect of AS have also been included. Last but not the least, the future prospects’ suggestions of mesoporous silica nanomaterial-based drug delivery system for AS are also provided.

Carbon Dots as Nanotherapeutics for Biomedical Application

Carbon nanodots are zero-dimensional spherical allotropes of carbon and are less than 10nm in size (ranging from 2-8nm). Based on their biocompatibility, remarkable water solubility, eco- friendliness, conductivity, desirable optical properties and low toxicity, carbon dots have revolutionized the biomedical field. In addition, they have intrinsic photo-luminesce to facilitate bio-imaging, bio-sensing and theranostics. Carbon dots are also ideal for targeted drug delivery. Through functionalization of their surfaces for attachment of receptor-specific ligands, they ultimately result in improved drug efficacy and a decrease in side-effects. This feature may be ideal for effective chemo-, gene- and antibiotic-therapy. Carbon dots also comply with green chemistry principles with regard to their safe, rapid and eco-friendly synthesis. Carbon dots thus, have significantly enhanced drug delivery and exhibit much promise for future biomedical applications. The purpose of this review is to elucidate the various applications of carbon dots in biomedical fields. In doing so, this review highlights the synthesis, surface functionalization and applicability of biodegradable polymers for the synthesis of carbon dots. It further highlights a myriad of biodegradable, biocompatible and cost-effective polymers that can be utilized for the fabrication of carbon dots. The limitations of these polymers are illustrated as well. Additionally, this review discusses the application of carbon dots in theranostics, chemo-sensing and targeted drug delivery systems. This review also serves to discuss the various properties of carbon dots which allow chemotherapy and gene therapy to be safer and more target-specific, resulting in the reduction of side effects experienced by patients and also the overall increase in patient compliance and quality of life.

ZIF-8 Modified Polypropylene Membrane: A Biomimetic Cell Culture Platform with a View to the Improvement of Guided Bone Regeneration

PURPOSE

Despite the significant advances in modeling of biomechanical aspects of cell microenvironment, it remains a major challenge to precisely mimic the physiological condition of the particular cell niche. Here, the metal-organic frameworks (MOFs) have been introduced as a feasible platform for multifactorial control of cell-substrate interaction, given the wide range of physical and mechanical properties of MOF materials and their structural flexibility.

RESULTS

In situ crystallization of zeolitic imidazolate framework-8 (ZIF-8) on the polydopamine (PDA)-modified membrane significantly raised surface energy, wettability, roughness, and stiffness of the substrate. This modulation led to an almost twofold increment in the primary attachment of dental pulp stem cells (DPSCs) compare to conventional plastic culture dishes. The findings indicate that polypropylene (PP) membrane modified by PDA/ZIF-8 coating effectively supports the growth and proliferation of DPSCs at a substantial rate. Further analysis also displayed the exaggerated multilineage differentiation of DPSCs with amplified level of autocrine cell fate determination signals, like BSP1, BMP2, PPARG, FABP4, ACAN, and COL2A. Notably, osteogenic markers were dramatically overexpressed (more than 100-folds rather than tissue culture plate) in response to biomechanical characteristics of the ZIF-8 layer.

CONCLUSION

Hence, surface modification of cell culture platforms with MOF nanostructures proposed as a powerful nanomedical approach for selectively guiding stem cells for tissue regeneration. In particular, PP/PDA/ZIF-8 membrane presented ideal characteristics for using as a barrier membrane for guided bone regeneration (GBR) in periodontal tissue engineering.

Simulation of blood flow into the popliteal artery to explain the effect of peripheral arterial disease: Investigation the conditions and effects of different foot states during the daily activity of the patient

BACKGROUND AND OBJECTIVE

Peripheral artery disease, one type of atherosclerosis, is a common medical condition in the world that results from plaque build-up in the peripheral blood vessels. The symptoms of this disease are the senses of pain and weakness in outer muscles.

METHODS

The artery under consideration is called the popliteal artery. In this model, the blood flow is considered as pulsating. Therefore the inlet boundary condition is taken as unsteady velocity, and the outlet boundary condition is taken the outflow. The inlet boundary condition represents the increasing systole flow and the decreasing diastole flow, which occur naturally in blood flow. Systolic flow occurs when the heart contracts and pumps blood into the arteries. The inlet blood flow is in the form of a sine-cosine parabolic profile.

RESULTS

The artery bends from the middle at an angle of 45°. As the bending of the artery begins, the flow field also takes a bent form. At this point, the flow bends from the outside of the top wall and enfolds the bottom wall in its bending. For different periods, the popliteal flow is closer to the lower bend when the inlet velocity is more significant. While the top wall experiences a low-intensity region along the bend, the bottom wall experiences the same effect just before and after the bend. As the blood flows along the bend, the flow path becomes significantly curved near the bend, similar to the model. The clotted artery exhibits a large increase in flow due to a reduction in the cross-section as a result of the clotting in half of the artery. The flow before the clotting is not considerably different from the main model of the straight artery.

CONCLUSIONS

Like shear stress, the pressure drop has a linear relationship with the blood HCT and, hence, the viscosity. The pressure drop decreases with the inlet velocity reaching its maximum value and then increases with the start of the acceleration reduction in the second and third-time steps. This indicates that the pressure drop has a stronger relationship with the acceleration than the inlet velocity.

Engineering the pH-Sensitivity of the Graphene and Carbon Nanotube Based Nanomedicines in Smart Cancer Therapy by Grafting Trimetyl Chitosan

PURPOSE

The aim of this study was to introduce a smart and responsive drug carrier for Doxorubicin (DOX) and Paclitaxel (PAX) for desirable therapeutic application.

METHOD

Loading and releasing of DOX and PAX from smart and pH-sensitive functionalized single-walled carbon nanotube (SWCNTs) and graphene carriers have been simulated by molecular dynamics. The influences of chitosan polymer on proposed carriers have been studied, and both carriers were functionalized with carboxyl groups to improve the loading and releasing properties of the drugs.

RESULTS

The results showed that DOX could be well adsorbed on both functionalized SWCNTs and graphene. In contrast, there was a weak electrostatic and Van der Waals interaction between both these drugs and carriers at cancerous tissues, which is highly favorable for cancer therapy. Adding trimethyl chitosan (TMC) polymer to carriers facilitated DOX release at acidic tissues. Furthermore, at blood pH, the PAX loaded on the functionalized SWCNTs carrier represented the highest dispersion of the drug while the DOX-graphene showed the highest concentration of the drug at a point. In addition, the mean-square displacement (MSD) results of PAX-graphene indicated that the PAX could be adsorbed quickly and be released slowly. Finally, functionalized graphene-TMC-PAX is a smart drug system with responsive behavior and controllable drug release, which are essential in cancer therapy.

CONCLUSION

Simultaneous application of the carboxyl group and TMC can optimize the pH sensitivity of the SWCNTs and graphene to prepare a novel and smart drug carrier for cancer therapy.

Computer modeling of pulsatile blood flow in elastic artery using a software program for application in biomedical engineering

BACKGROUND AND OBJECTIVE

Atherosclerosis-a condition in which an artery is constricted-alters blood flow in the artery, that can exacerbate the condition. Focusing on previous studies, it can be seen that the k-ε model has been used in the simulation. Therefore, the reverse flow on the back of stenosis is not well represented. In this study, the simulated results are much closer to clinical results, relying on the use of physiological pulses, and considering elasticity of the vessel wall, and the applying k-ω model. It can therefore be claimed that a much more accurate prediction will be made regarding the formation, development and progression of the disease.

METHODS

Modeling biological systems usually contain many parameters, which cannot be calculated experimentally, or are too costly and time consuming. In addition, it is occasionally required to examine the influence of different physical variables, which, given the complexity of the governing equations, make analytical methods feasible (or very limited). The present study is an attempt to investigate the turbulent pulsatile blood flow in an elastic artery with single and double stenoses using a finite element software program, ADINA 8.8.

RESULTS

According to the results, the k - ω turbulence model predicted a larger reverse flow in the post-stenotic region and between the two stenoses in comparison with the k - ε model. In other words, the k - ω model results suggest that a larger region is prone to atherosclerosis. In addition, that the k - ε model predicted a greater maximum shear stress at the throat and a shorter reverse flow region (Mean WSS < 0) in both stenosis scenarios. In other words, relative to the k - ε model, the k - ω model underestimated the damage to the plaque and the risk of its rupture though it predicted new stenosis developing behind the previous one. It was observed that the presence of a double stenosis causes the upstream pressure to reach the critical value in less time. Velocity profiles revealed that in the stenosis throat, the maximum velocity exceeds the normal biological state, which may cause disorders in the blood circulation.

CONCLUSIONS

The artery wall displacement results are suggestive of the greater difference between the two turbulence models in the case with double stenosis compared with single stenosis. Moreover, the difference between the two turbulence models in double stenosis is minimized in both post-stenotic and pre-stenotic regions.

Molecular insight into the smart functionalized TMC-Fullerene nanocarrier in the pH-responsive adsorption and release of anti-cancer drugs

The Doxorubicin (DOX) and Paclitaxel (PAX) are widely used for cancer-therapy. Herein, in the efforts devoted to developing smart drug carriers, the loading and releasing of the DOX and PAX on the pH sensitive functionalized Fullerene carrier was investigated by molecular dynamics (MD) simulations. The effects of chitosan polymer as a functionalizing agent of the Fullerene carrier was also studied. In addition, the Fullerene carrier was functionalized with carboxyl groups in order to improve the loading and releasing properties of the DOX and PAX. The results showed the DOX is well adsorbed on Fullerene which was functionalized with carboxyl group and it was released controllably in cancerous tissues. According to the results of the electrostatic and Van der Waals interactions, it was found that the functionalized Fullerene can be a proper carrier for DOX in comparison with PAX. Adding the trimethyl chitosan (TMC) polymer to the carrier could improve the Van der Waals attractions of the PAX and Fullerene which indicates that by passing the time at acidic pH, the Van der Waals energy reaches zero that leads to promote the release of the PAX in cancerous tissues. The carboxyl group which was employed as a functionalizing agent could also increase the number of hydrogen bonds for the PAX and DOX at acidic and neutral pH, respectively. Moreover, a significant rise in the number of hydrogen bonds between the PAX and Fullerene at neutral pH was achieved by adding the TMC to the carrier. A more decrease of gyration radius was obtained for the DOX at acidic pH which confirms that the DOX with TMC-Fullerene is a more stable carrier. So, this smart nanomedicine system is introduced as an promising composition for smart cancer therapy.

An insight into the role of riboflavin ligand in the self-assembly of poly(lactic-co-glycolic acid)-based nanoparticles - a molecular simulation and experimental approach

Nanoparticles (NPs) used for targeted delivery purposes are rapidly gaining importance in diagnostic and therapeutic fields. These agents have been studied extensively so far to reveal their optimal physicochemical properties including the effects of ligands and their density on the surface of NPs. This article was conducted through a computational approach (all-atom molecular dynamics simulations) to predict the stability of NPs based on a poly-lactic-co-glycolic acid (PLGA) hydrophobic core with a poly-ethylene glycol (PEG) hydrophilic shell and varying numbers of riboflavin (RF) molecules as ligands. Depending on the molecular weight of the polymers, the most stable composition of NPs was achieved at 20 wt% and 10 wt% PLGA-PEG-RF for PLGA3kDa-PEG2kDa and PLGA4.5kDa-PEG2kDa polymers, respectively. According to the simulations, riboflavin molecules were located on the surface of the NPs, which would indicate that riboflavin-bound PLGA-PEG NPs could be efficiently utilized for active targeting purposes. To scrutinize the simulation results, NPs with riboflavin ligands were synthesized and put into in vitro experiments. Outstandingly, the empirical outcomes revealed that the hydrodynamic sizes of NPs also met minimum points at 20 and 10 wt% for PLGA3kDa-PEG2kDa and PLGA4.5kDa-PEG2kDa, respectively. Moreover, similar trends in the gyration radius as a function of riboflavin content were observed in the simulation analysis and the experimental results, which would indicate that the method of molecular dynamics (MD) simulation is a reliable mathematical technique and could be applied for predicting the physicochemical properties of NPs.