Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics.

The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values ​​of - 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and - 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.

Interactions of Ozone-Functionalized Activated Charcoal with SARS-Cov-2 Proteases Using Molecular Docking and Dynamics.

The high contamination by the SARS-Cov-2 virus has led to the search for ways to minimize contagion. Masks are used as part of a strategy of measures to suppress transmission and save lives. However, they are not sufficient to provide an adequate level of protection against COVID-19. Activated charcoal has an efficient antibacterial action, adsorption and low cost. Here, the interaction between two molecules of activated carbon was analyzed, interacting with two structures of the SARS-Cov-2, through docking and molecular dynamics using the platforms Autodock Vina 4.2.6, Gaussian 09 and Amber 16. As a result, the complexes from ozone-functionalized coal to viral structures happen mainly through hydrophobic interactions at the binding site of each receptor. The values of the mean square deviations of the two systems formed by ligands/receptors and showed better stability. The results of Gibbs free energy showed a better interaction between proteins and functionalized charcoal, with △Gtotal values of -48.530 and -38.882 kcal/mol. Thus, the set formed by combinations of proteins with functionalized activated carbon tends to more efficiently adsorb the protein components of the coronavirus to the pores of the activated carbon with ozone during filtration.

Hormones Nanofiltration in Carbon Nanotubes and Boron Nitride Nanotubes Using Uniform External Electric Field Through Molecular Dynamics.

Hormones are a dangerous group of molecules that can cause harm to humans. This study based on classical molecular dynamics proposes the nanofiltration of wastewater contaminated by hormones from a computer simulation study, in which the water and the hormone were filtered in two single-walled nanotube compositions. The calculations were carried out by changing the intensities of the electric field that acted as a force exerting pressure on the filtration along the nanotube, in the simulation time of 100 ps. The hormones studied were estrone, estradiol, estriol, progesterone, ethinylestradiol, diethylbestrol, and levonorgestrel in carbon nanotubes (CNTs) and boron nitride (BNNTs). The most efficient nanofiltrations were for fields with low intensities in the order of 10-8 au and 10-7 au. The studied nanotubes can be used in membranes for nanofiltration in water treatment plants due to the evanescent field potential caused by the action of the electric field inside. Our data showed that the action of EF in conjunction with the van der Walls forces of the nanotubes is sufficient to generate the attractive potential. Evaluating the transport of water molecules in CNTs and BNNTs, under the influence of the electric field, a sequence of simulations with the same boundary conditions was carried out, seeking to know the percentage of water molecules filtered in the nanotubes.

Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol.

Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.

Polysaccharides obtained from natural edible sources and their role in modulating the immune system: Biologically active potential that can be exploited against COVID-19.

BACKGROUND: The global crisis caused by the outbreak of severe acute respiratory syndrome caused by the SARS-CoV-2 virus, better known as COVID-19, brought the need to improve the population's immunity. The foods rich in polysaccharides with immunomodulation properties are among the most highly rated to be used as immune response modulators. Thus, the use of polysaccharides obtained from food offers an innovative strategy to prevent serious side effects of viral infections. SCOPE AND APPROACH: This review revisits the current studies on the pathophysiology of SARS-CoV-2, its characteristics, target cell interactions, and the possibility of using polysaccharides from functional foods as activators of the immune response. Several natural foods are explored for the possibility of being used to obtain polysaccharides with immunomodulatory potential. And finally, we address expectations for the use of polysaccharides in the development of potential therapies and vaccines. KEY FINDINGS AND CONCLUSIONS: The negative consequences of the SARS-CoV-2 pandemic across the world are unprecedented, thousands of lives lost, increasing inequalities, and incalculable economic losses. On the other hand, great scientific advances have been made regarding the understanding of the disease and forms of treatment. Polysaccharides, due to their characteristics, have the potential to be used as potential drugs with the ability to modulate the immune response. In addition, they can be used safely, as they have no toxic effects, are biocompatible and biodegradable. Finally, these biopolymers can still be used in the development of new therapies and vaccines.

Influence of grilling pretreatment and optimization of sous vide processing parameters on the physicochemical and microbiological quality of pirarucu fillet.

The demand for high-quality food products has promoted the study of techniques for its processing and conservation. The present research aimed to evaluate the influence of grilling pretreatment on the physical characteristics of pirarucu fillets and the heat transfer process by a computational modelling, and to optimize the sous vide process parameters. Before and after the sous vide process, the samples were analysed for microbiological, chemical and physical characteristics. There was no significant difference between the total experimental time of grilling and that obtained by computational modelling. Immersion in brine for 300 s in combination with grilling at 200 ℃/120 s was selected because of its water-holding capacity (%) 79.40 ± 0.31, texture (N) 1.91 ± 0.40 and value of L* 74.44 ± 0.38 in the fillets. Cooking at 60 ℃ for 568.8 s were the best sous vide parameters obtained, with highest water-holding capacity (%) 93.60, texture (N) 6.24, ΔE* 7.43, and with microbiological loads below 6 log CFU/g and 7 log MPN/g in the final product. Useful information obtained from this study highlighted the brine and grill pretreatment in combination with sous vide proved it is a potential solution for developing pirarucu products even at an industrial scale.

Chemical Composition, Antimicrobial Properties of Siparuna guianensis Essential Oil and a Molecular Docking and Dynamics Molecular Study of its Major Chemical Constituent.

The essential oil of Siparuna guianensis was obtained by hydrodistillation. The identification of the chemical compounds was performed by gas chromatography coupled with mass spectrometry (GC/MS). Antimicrobial activity was investigated for four microorganisms: Streptococcus mutans (ATCC 3440), Enterococcus faecalis (ATCC 4083), Escherichia coli (ATCC 25922), and Candida albicans (ATCC-10231). The studies of doping and molecular dynamics were performed with the molecule that presented the highest concentration of drug-target proteins, 1IYL (C. albicans), 1C14 (E. coli), 2WE5 (E. faecalis), and 4TQX (S. mutans). The main compounds identified were: Curzerene (7.1%), γ-Elemene (7.04%), Germacrene D (7.61%), trans-ß-Elemenone (11.78%), and Atractylone (18.65%). Gram positive bacteria and fungi were the most susceptible to the effects of the essential oil. The results obtained in the simulation showed that the major compound atractylone interacts with the catalytic sites of the target proteins, forming energetically favourable systems and remaining stable during the period of molecular dynamics.

Chemical profile of Lippia thymoides, evaluation of the acetylcholinesterase inhibitory activity of its essential oil, and molecular docking and molecular dynamics simulations.

The essential oils of the fresh and dry flowers, leaves, branches, and roots of Lippia thymoides were obtained by hydrodistillation and analyzed using gas chromatography (GC) and GC-mass spectrometry (MS). The acetylcholinesterase inhibitory activity of the essential oil of fresh leaves was investigated on silica gel plates. The interactions of the key compounds with acetylcholinesterase were simulated by molecular docking and molecular dynamics studies. In total, 75 compounds were identified, and oxygenated monoterpenes were the dominant components of all the plant parts, ranging from 19.48% to 84.99%. In the roots, the main compounds were saturated and unsaturated fatty acids, having contents varying from 39.5% to 32.17%, respectively. In the evaluation of the anticholinesterase activity, the essential oils (detection limit (DL) = 0.1 ng/spot) were found to be about ten times less active than that of physostigmine (DL = 0.01ng/spot), whereas thymol and thymol acetate presented DL values each of 0.01 ng/spot, equivalent to that of the positive control. Based on the docking and molecular dynamics studies, thymol and thymol acetate interact with the catalytic residues Ser203 and His447 of the active site of acetylcholinesterase. The binding free energies (ΔGbind) for these ligands were -18.49 and -26.88 kcal/mol, demonstrating that the ligands are able to interact with the protein and inhibit their catalytic activity.