Molecular dynamics studies of polysaccharide carrier based on starch in dental cavities

Space Station-like Composite Nanoparticles for Co-Delivery of Multiple Natural Compounds from Chinese Medicine and Hydrogen in Combating Sensorineural Hearing Loss

Ototoxic drugs such as aminoglycoside antibiotics and cisplatin (CDDP) can cause sensorineural hearing loss (SNHL), which is closely related to oxidative stress and the acidification of the inner ear microenvironment. Effective treatment of SNHL often requires multifaceted approach due to the complex pathology, and drug combination therapy is expected to be at the forefront of modern hearing loss treatment. Here, space-station-like composite nanoparticles (CCC@mPP NPs) with pH/oxidation dual responsiveness and multidrug simultaneous delivery capability were constructed and then loaded with various drugs including panax notoginseng saponins (PNS), tanshinone IIA (TSIIA), and ammonia borane (AB) to provide robust protection against SNHL. Molecular dynamics simulation revealed that carboxymethyl chitosan/calcium carbonate-chitosan (CCC) NPs and monomethoxy poly(ethylene glycol)-PLGA (mPP) NPs can rendezvous and dock primarily by hydrogen bonding, and electrostatic forces may be involved. Moreover, CCC@mPP NPs crossed the round window membrane (RWM) and entered the inner ear through endocytosis and paracellular pathway. The docking state was basically maintained during this process, which created favorable conditions for multidrug delivery. This nanosystem was highly sensitive to pH and reactive oxygen species (ROS) changes, as evidenced by the restricted release of payload at alkaline condition (pH 7.4) without ROS, while significantly promoting the release in acidic condition (pH 5.0 and 6.0) with ROS. TSIIA/PNS/AB-loaded CCC@mPP NPs almost completely preserved the hair cells and remained the hearing threshold shift within normal limits in aminoglycoside- or CDDP-treated guinea pigs. Further experiments demonstrated that the protective mechanisms of TSIIA/PNS/AB-loaded CCC@mPP NPs involved direct and indirect scavenging of excessive ROS, and reduced release of pro-inflammatory cytokines. Both in vitro and in vivo experiments showed the high biocompatibility of the composite NPs, even after long-term administration. Collectively, this work suggests that composite NPs is an ideal multi-drug-delivery vehicle and open new avenues for inner ear disease therapies.

Controlled Drug Release from Nanoengineered Polysaccharides

Polysaccharides are naturally occurring complex molecules with exceptional physicochemical properties and bioactivities. They originate from plant, animal, and microbial-based resources and processes and can be chemically modified. The biocompatibility and biodegradability of polysaccharides enable their increased use in nanoscale synthesis and engineering for drug encapsulation and release. This review focuses on sustained drug release studies from nanoscale polysaccharides in the fields of nanotechnology and biomedical sciences. Particular emphasis is placed on drug release kinetics and relevant mathematical models. An effective release model can be used to envision the behavior of specific nanoscale polysaccharide matrices and reduce impending experimental trial and error, saving time and resources. A robust model can also assist in translating from in vitro to in vivo experiments. The main aim of this review is to demonstrate that any study that establishes sustained release from nanoscale polysaccharide matrices should be accompanied by a detailed analysis of drug release kinetics by modeling since sustained release from polysaccharides not only involves diffusion and degradation but also surface erosion, complicated swelling dynamics, crosslinking, and drug-polymer interactions. As such, in the first part, we discuss the classification and role of polysaccharides in various applications and later elaborate on the specific pharmaceutical processes of polysaccharides in ionic gelling, stabilization, cross-linking, grafting, and encapsulation of drugs. We also document several drug release models applied to nanoscale hydrogels, nanofibers, and nanoparticles of polysaccharides and conclude that, at times, more than one model can accurately describe the sustained release profiles, indicating the existence of release mechanisms running in parallel. Finally, we conclude with the future opportunities and advanced applications of nanoengineered polysaccharides and their theranostic aptitudes for future clinical applications.

Effective removal of methylene blue with zero-valent iron/tea residual biochar composite: Performance and mechanism

Zero-valent iron (Fe⁰)-modified biochar (BFN) was prepared via low-temperature pyrolysis of tea residue (TR) and ferric nitrate hexahydrate (FN) coupled with NaOH activation for the removal of methylene blue (MB). BFN exhibited a specific surface area of 382.66 m²·g^-1, an average pore diameter of 4.97 nm and an equilibrium adsorption capacity as high as 452.5 mg·g^-1 of 0.33 g·L^-1 toward 150 mg·L^-1 MB within 60 min at 30 °C and pH 7.0. The recovered MB is far below of the removal rate in each of adsorption-desorption cycle because the removal mechanism is that MB molecular was firstly chemically adsorbed, then it was reduced and mineralized by BFN with the formation of nitrate, sulfate, CO₂ and H₂O.

Atomistic insight into 2D COFs as antiviral agents against SARS-CoV-2

The recent pandemic of COVID-19 has raised global health concerns. Preventing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) activity in the body is a very promising method to overcome the COVID-19 pandemic. One of the prevention methods is constraining the binding process among the human cell receptor-ACE2 and coronavirus spike protein. In the research done, the effect of deformation of the spike protein structure, due to the covalent organic frameworks (COFs), in reducing the interactions of ACE2 and the spike protein by the computational method was investigated. In this regard, atomic analysis of the interactions of ACE2 and the spike protein is provided using a molecular dynamics simulation. First, we investigated the interactions of the three different COFs, including COF-78, DAAQ-TFP, and COF-OEt, with the spike protein by analyzing the bond energies, as well as structural changes of the spike protein. Then, intermolecular interactions of the deformed spike protein along with ACE2 were assessed to clarify the protein's fusion after the deformation. As indicated by the results, although all introduced COFs deformed the spike protein in an effective way, COF-78 showed the best performance in the prevention of spike protein-ACE2 interactions by changing the molecular structure of the protein. Indeed, the interaction analysis of the deformed spike protein by COF-78 with the ACE2 showed that their interactions had the lowest absolute value of energy, along with the least amount of hydrogen bonds, in which the compaction of the protein was lower compared to the other deformed proteins. Moreover, having a high contact area with an aqueous media as well as severe fluctuations during the simulation time confirmed the positive performance of COF-78. In the current study, we aimed to introduce novel materials and COVID-19 prevention methodology that can be used in face masks and for surface disinfection.

Polysaccharide-Based Micro- and Nanosized Drug Delivery Systems for Potential Application in the Pediatric Dentistry

The intensive development of micro- and nanotechnologies in recent years has offered a wide horizon of new possibilities for drug delivery in dentistry. The use of polymeric drug carriers turned out to be a very successful technique for formulating micro- and nanoparticles with controlled or targeted drug release in the oral cavity. Such innovative strategies have the potential to provide an improved therapeutic approach to prevention and treatment of various oral diseases not only for adults, but also in the pediatric dental practice. Due to their biocompatibility, biotolerance and biodegradability, naturally occurring polysaccharides like chitosan, alginate, pectin, dextran, starch, etc., are among the most preferred materials for preparation of micro- and nano-devices for drug delivery, offering simple particle-forming characteristics and easily tunable properties of the formulated structures. Their low immunogenicity and low toxicity provide an advantage over most synthetic polymers for the development of pediatric formulations. This review is focused on micro- and nanoscale polysaccharide biomaterials as dental drug carriers, with an emphasis on their potential application in pediatric dentistry.

Effect of ZnO-based nanophotocatalyst on degradation of aniline

In this research, a zinc oxide/copper oxide/graphene oxide (ZnO/CuO/GO) nanophotocatalyst was synthesized for photodegradation of aniline as a pollutant, upon exposure to ultraviolet light (UV). Three variables including initial aniline concentration, the nanophotocatalyst dosage, and pH were designed. The statistical test and optimal conditions were determined. The consequences specified that the optimum values of pH, initial aniline concentration, the dosage of nanophotocatalyst, and the reaction time were 6, 150 ppm, 1 g/L, and 3 h, respectively. The obtained results revealed that the photodegradation of aniline was enhanced with doping zinc oxide and CuO on the graphene oxide. Under optimal conditions, 97% photodegradation of aniline was observed. The mechanism of aniline degradation with nanophotocatalyst was evaluated by molecular dynamic (MD) graphs. The interactions between nanophotocatalysts and aniline were considered by energy, density graph.

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 Dynamics Simulations with NAMD2

X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.

Investigating the effect of starch/Fe3O4 nanoparticles on biodesulfurization using molecular dynamic simulation

The application of dibenzothiophene (DBT) as a source of energy leads to air pollution. The key solution to overcome this drawback is desulfurization. Magnetic nanoparticles have shown an excellent performance in the desulfurization of dibenzothiophene. In this study, molecular dynamic (MD) simulation was considered for the first time to gain insight about the molecule interactions in the biodesulfurization (BDS) process of DBT using Rhodococcus erythropolis IGTS8, in the presence and absence of starch/magnetic nanoparticles. According to the MD simulation results, the density of the system in the presence of starch/Fe₃O₄ was ascending while in the absence of these nanoparticles, the density was descending. Starch/magnetic nanoparticles caused more rapid equilibrium state in the biodesulfurization process. The energy diagram showed that magnetic nanoparticles decrease the energy fluctuation and increase the difference of non-bounding energy and potential energy (8 times) compared to (BDS) without nanoparticle, which reflects higher bounded energy in the system using starch/magnetic nanoparticles. The height of RDF peak in the presence of starch/Fe₃O₄ was 4 times more than the RDF peak in the absence of nanoparticle. In addition, the nanoparticles decreased the fluctuations around optimal temperature in BDS up to 5% compared to other state.

Effect of starch/CNT on biodesulfurization using molecular dynamic simulation

Nowadays, fossil fuel is the most important source of energy. However, the sulfur oxide release through oxidation of the available sulfur and the resultant air pollution has turned into an issue. In biodesulfurization (BDS) process, the sulfur from the recalcitrant organic compounds dissolved in crude oil fractions will be removed biologically. Carbon nanotubes (CNTs) exhibit good catalytic performance in dibenzothiophene (DBT) oxidation. Molecular dynamic simulation is the best and the only way to reach this end. Through this study, molecular dynamic simulations are applied to compute the effects of starch/CNTs on BDS process of DBT during 5 ns. The changes of cell length, energy, dynamic temperature, relative concentration of DBT, and radial distribution function (RDF) in the absence and presence of starch/CNTs were investigated. Regarding to the energy diagram, the fluctuation because of temperature fluctuations reaches the stable state. The high level of the first peak in RDF diagram showed the high and long desulfurization by microorganism. All the results showed stable and reasonable equilibrium state of the system. According to the graphs, the simultaneous in the presence of starch/CNT and Rhodococcus erythropolis increase the removal efficiency of nitrate reached 85% and in the absence of nanoparticle was 35.44%.

Polyhydroxybutyrate Production from Natural Gas in A Bubble Column Bioreactor: Simulation Using COMSOL

In this study, the simulation of microorganism ability for the production of poly-β-hydroxybutyrate (PHB) from natural gas (as a carbon source) was carried out. Based on the Taguchi algorithm, the optimum situations for PHB production from natural gas in the columnar bubble reactor with 30 cm length and 1.5 cm diameter at a temperature of 32 °C was evaluated. So, the volume ratio of air to methane of 50:50 was calculated. The simulation was carried out by COMSOL software with two-dimensional symmetric mode. Mass transfer, momentum, density-time, and density-place were investigated. The maximum production of biomass concentration reached was 1.63 g/L, which shows a 10% difference in contrast to the number of experimental results. Furthermore, the consequence of inlet gas rate on concentration and gas hold up was investigated Andres the simulation results were confirmed to experimental results with less than 20% error.