Mart. Bioactive Molecules: Promising Agents to Modulate the NLRP3 Inflammasome.

Inflammation is a vital mechanism that defends the organism against infections and restores homeostasis. However, when inflammation becomes uncontrolled, it leads to chronic inflammation. The NLRP3 inflammasome is crucial in chronic inflammatory responses and has become a focal point in research for new anti-inflammatory therapies.

Ascorbic acid and ascorbyl palmitate-loaded liposomes: Development, characterization, stability evaluation, in vitro security profile, antimicrobial and antioxidant activities.

The objective of this work was to prepare and characterize liposomes containing co-encapsulated ascorbic acid (AA) and ascorbyl palmitate (AP), as well as to evaluate their stability, cytotoxicity, antioxidant, and antimicrobial activity. Through the pre-formulation studies, it was possible to improve the formulation, as leaving it more stable and with a greater antioxidant activity, resulting in a formulation designated LIP-AAP, with 161 nm vesicle size, 0.215 polydispersity index, -31.

Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation.

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the etiological agent responsible for the global outbreak of COVID-19 (Coronavirus Disease 2019). The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a vital role in mediating viral replication and transcription. In this study, a comprehensive computational approach was employed to investigate the binding affinity, selectivity, and stability of natural product candidates as potential new antivirals acting on the viral polyprotein processing mediated by SARS-CoV-2 Mpro.

Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis.

Context: Heparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations.

Ab initio study of water anchored in graphene pristine and vacancy-type defects.

Context: In this paper, we have addressed two issues that are relevant to the interaction of water in pristine and vacant graphene through first-principles calculations based on the Density Functional Theory (DFT). The results showed that for the interaction of pristine graphene with water, the DOWN configuration (with the hydrogen atoms facing downwards) was the most stable, presenting binding energies in the order of -13.62 kJ/mol at a distance of 2.

Comparison of three cyclodextrins to optimize bisphenol A extraction from source water: Computational, spectroscopic, and analytical studies.

Computationally and spectroscopically assisted analytical comparative investigation into the extraction of bisphenol A using three cyclodextrins, that is, α, β, and γ respectively, were performed. A simple, self-tailored μ-solid-phase extraction podium was used to extract bisphenol A from water samples, and high-performance liquid chromatography-ultraviolet was used for the qualitative and quantitative analysis of bisphenol A. Density functional theory first principle calculations, attenuated total reflectance Fourier-transform infrared spectroscopy and Fourier-transform Raman spectroscopy data supports the analytical selection of β-cyclodextrin as the adsorbent for bisphenol A extraction.

Graphene oxide and flavonoids as potential inhibitors of the spike protein of SARS-CoV-2 variants and interaction between ligands: a parallel study of molecular docking and DFT.

Nanocarriers allow the connection between biomolecules and other structures to enhance the treatment efficacy, through the biomolecule's properties to an existing drug, or to allow a better and specific delivery. Apigenin and orientin are biomolecules with excellent therapeutic properties that are proposed in the fight against COVID-19. Besides that, graphene oxide is a nanomaterial that exhibits antiviral activity and is used as a nanocarrier of several drugs.

Influence of magnetite incorporation into chitosan on the adsorption of the methotrexate and in vitro cytotoxicity.

Emerging pollutants are a group of substances involved in environmental contamination resulting mostly from incomplete drug metabolism, associated with inadequate disposal and ineffective effluent treatment techniques. Methotrexate (MTX), for instance, is excreted at high concentrations in unchanged form through the urine. Although the MTX is still effective in cancer and autoimmune disease treatment, this drug shows the ability of bioaccumulation and toxicity to the organism.

Ab initio simulations of black and blue phosphorene functionalised with chemical groups for biomolecule anchoring.

Black and blue phosphorene (2D-dimensional allotropes of phosphorus) have shown fascinating electronic, optical, and magnetic properties, with promising technological applications. In this work, we studied the adsorption of amine, hydroxyl, amide, and carboxyl groups onto both black and blue phosphorenes, in order to analyse the effects of biomolecule anchoring on the structural and electronic properties of phosphenes, using density functional simulations. Analyses were carried out of six different configurations for each chemical group functionalised on black and blue phosphorene.

Corrigendum to: Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures.

Due to an oversight of the publisher, Page no 2310 was missing in the published paper and page no 2311 repeated twice in the article entitled "Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures, 2020, 20(25), 2308-2325 [1]. The page no 2310 is added in the article and the repetition of page no 2311 is corrected. The original article can be found online at https://doi.

Theoretical study of small aromatic molecules adsorbed in pristine and functionalised graphene.

Small aromatic molecules are precursors for several biological systems such as DNA, proteins, drugs, and are also present in several pollutants. The understanding of the interaction of these small aromatic molecules with pristine and functionalised graphene (fGr) can generate different applications. We performed ab initio simulations based on the density functional theory to evaluate the interaction between the aromatic compounds, benzene, benzoic acid, aniline and phenol, with pristine and fGr.

Density functional theory study of π-aromatic interaction of benzene, phenol, catechol, dopamine isolated dimers and adsorbed on graphene surface.

We analyze the influence of different groups on the intermolecular energy of aromatic homodimers and on the interaction between a single aromatic molecule and a graphene surface. The analysis is performed for benzene, phenol, catechol, and dopamine. For calculating the energies, we employ density functional theory within the local density approximation (LDA-DFT).

Computational MitoTarget Scanning Based on Topological Vacancies of Single-Walled Carbon Nanotubes with the Human Mitochondrial Voltage-Dependent Anion Channel (hVDAC1).

We present an in silico approach for modeling the noncovalent interactions between the human mitochondrial voltage-dependent anion channel (hVDAC1) and a family of single-walled carbon nanotubes (SWCNTs) with a defined pattern of topological vacancies ( v = 1-16), obtained by removing atoms from the SWCNT surface. The general results showed more stable docking interaction complexes (SWCNT-hVDAC1), with more negative Gibbs free energy of binding affinity values, and a strong dependence on the vacancy number ( R = 0.93) and vacancy formation energy ( R = 0.

Interactions of graphene derivatives with glutamate-neurotransmitter: A parallel first principles - Docking investigation.

Glutamate plays an important role in excitatory neurotransmission, learning, and memory processes, and under pathological conditions it is directly associated with several chronic neurological disorders, such as depression, epilepsy, schizophrenia, and Parkinson's. Therefore, the detection and quantification of Glutamate is important for the rapid diagnosis of these diseases. Using first principles and molecular docking simulations we have evaluated the energetic, structural, and binding properties of graphene derivatives, such as pristine graphene (pristine-Gr) and oxidized graphene with carboxylic (Gr-COOH), carbonyl (Gr-COH), hydroxyl (Gr-OH), and epoxy (-O-) groups interacting with the glutamate neurotransmitter.

A simulation environment for polymeric nanoparticles based on multi-agent systems.

Production and characterization of polymeric nanoparticles, as colloidal dispersions, are processes that require time and technical skills to make the results accurate. Computational simulations in nanoscience have been used to help in these processes and provide agility and support to reach results: stability and quality in dispersions. Multi-Agent System for Polymeric Nanoparticles (MASPN) is an innovative and original simulation environment with features to demonstrate interactions of particles from physical-chemical parameters, ensuring Brownian motion of particles and attractive and repulsive behaviour.

Modeling drug-drug interactions of AZD1208 with Vincristine and Daunorubicin on ligand-extrusion binding TMD-domains of multidrug resistance P-glycoprotein (ABCB1).

In the present study, the molecular docking mechanism based on pharmacodynamic interactions between the ligands AZD1208 and recognized chemotherapy agents (Vincristine and Daunorubicin) with human ATP-binding cassette (ABC) transporters (ABCB1) was investigated. For the first time, were combined an in silico approaches like molecular docking and ab initio computational simulation based on Density Functional Theory (DFT) to explain the drug-drug interaction mechanism of aforementioned chemotherapy ligands with the transmembrane ligand extrusion binding domains (TMDs) of ABCB1. In this regard, the theoretical pharmacodynamic interactions were characterized by using the Gibbs free energy (FEB, kcal/mol) from the best ABCB1-ligand docking complexes.

Cytoprotection of lipoic acid against toxicity induced by saxitoxin in hippocampal cell line HT-22 through in silico modeling and in vitro assays.

Saxitoxins (STXs) are potent neurotoxins that block voltage-gated channels in neurons and induce cytotoxicity. These toxins not only can generate reactive oxygen species but also can alter antioxidant levels, promoting oxidative stress. Under this pro-oxidant situation, the use of the antioxidant lipoic acid (LA) can represent a chemoprotective alternative to minimize the deleterious effects induced by neurotoxins as STXs.

Influence of concentration and position of carboxyl groups on the electronic properties of single-walled carbon nanotubes.

The effects of attaching COOH groups at different sites and in various concentrations on electronic and structural properties of (8,0) single-walled carbon nanotubes (SWNT) were investigated using ab initio calculations. The binding energies and the charge transfers between the COOH functional groups and the tube were calculated for several configurations and a novel feature in the electronic structure of these groups was observed. The electronic character of these systems can be modulated by playing with the concentration and the position of the carboxyl groups bonded on the tube wall.

Interactions of iron-oxide filled carbon nanotubes with gas molecules.

This work presents a study on iron-oxide filled carbon nanotubes (CNTs) and their interaction with the surrounding atmosphere. Theoretical and experimental methods were employed to determine the interaction mechanism between the CNTs and some gases, such as O2 and N2. The electrical behavior of these CNTs under different atmospheric conditions was studied through resistance measurements, and for comparison, similar studies were conducted on non-filled carbon nanotubes.

Metal-doped carbon nanotubes interacting with vitamin C.

In this paper, the structural, electronic and magnetic properties of carbon nanotubes doped with Al, Fe, Mn and Ti atoms interacting with vitamin C molecules are studied through first principles simulations based on the density functional theory. The charge transfers are obtained from the vitamins into the tubes for adsorption and substitutional doping cases. The highest binding energies of vitamin C molecules are calculated for the Al substitutional and Ti adsorbed cases, with values of about 1.

Adsorption of Reactive Blue 4 dye from water solutions by carbon nanotubes: experiment and theory.

Multi-walled and single-walled carbon nanotubes were used as nanoadsorbents for the successful removal of Reactive Blue 4 textile dye from aqueous solutions. The adsorbents were characterised by infrared and Raman spectroscopy, N(2) adsorption/desorption isotherms and scanning and transmission electron microscopy. The effects of pH, shaking time and temperature on adsorption capacity were studied.

Carbon nanostructures interacting with vitamins A, B3 and C: ab initio simulations.

The energetic and structural properties of fullerenes, carbon nanotubes and graphene interacting with vitamins A, B3 and C were studied by first principles simulations. These vitamins, which have antioxidant activities, give support to the cellular metabolism, have biochemical, therapeutic and cosmetic functions, and when combined with carbon nanostructures may have their chemical instability controlled. In this work, the results illustrate that the strongest interaction is between vitamin A and graphene.