SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics.

Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values ​​for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.

Evaluation of the biological activities of Copaiba (Copaifera spp): a comprehensive review based on scientometric analysis.

Copaíba oil-resin is extracted from the trunk of the Copaíba tree and has medicinal, cosmetic, and industrial properties. As a result, widespread knowledge about the use of Copaíba oil-resin has evolved, attracting the scientific community's attention. This paper aims to map the global knowledge production regarding the biological activities of Copaíba (Copaifera spp.). Bibliometric methodological instruments were used to conduct a search of the Web of Science-Core Collection database. The search resulted in 822 references. After screening titles and abstracts, 581 references did not meet the eligibility criteria, leaving 246 references for full-text examination. Subsequently, 15 studies were excluded, resulting in a final set of 232 records for the bibliometric analysis. In vitro was the most published study type, mainly from Brazil, from 2010 to 2020. Regarding the authors, Bastos, JK, and Ambrosio, SR were the ones with the most significant number of papers included. The most frequent keywords were Copaíba oil, Copaíba, and Copaifera. Our findings revealed global study trends about Copaíba, mainly related to its various effects and use over time. In general, all countries have conducted more research on antimicrobial and anti-inflammatory activities, also exposing its antioxidant and healing properties. Copaifera reticulata was the most investigated, followed by Copaifera langsdorffi and Copaifera multijuga in both in vitro and in vivo studies. Therefore, there is a need for human reports, given the promising results that Copaíba oils have been demonstrating.

First report on the Annona exsucca DC. Essential oil and in silico identification of potential biological targets of its major compounds.

In the present study, the essential oil (EO) of Annona exsucca DC. or Rollinia exsucca was extracted by hydrodistillation, and the identification and quantification of volatile compounds were performed by GC-MS and GC-FID. A. exsucca leaves were collected from the Magalhães Barata, northeast of the State of Pará (Brazil) in March and September of 2019. Moreover, we used computational approaches to evaluate possible biological targets for the major compounds of the EO. In the sample obtained in March, 50 compounds were identified, with hydrocarbon sesquiterpenes being the predominant ones with the content of 80.52%. In the sample collected in September, 58 compounds were identified, and the chemical class of hydrocarbon monoterpenes and sesquiterpenes were the dominant ones with contents of 43.36 and 31.29%, respectively. Computational methods demonstrated that some major compounds have potential biological activity against some strains of pathogenic bacteria, as well as against molecular targets involved in cancer development.

Lamiaceae Essential Oils, Phytochemical Profile, Antioxidant, and Biological Activities.

Medicinal and aromatic plants present important active compounds that have potential for use in food, pharmaceutical, and agriculture industries. In this sense, the present work aimed to conduct a literature review on the potential applications of essential oils from Lamiaceae species. Antioxidant, anti-inflammatory, and antimicrobial activities were evaluated. The importance of this study is demonstrated as a way to theoretically provide information on the use of different plants belonging to the Lamiaceae family, especially with regard to the physical, chemical, and biological properties of its essential oils.

Chemical Composition and Antibacterial Activity of the Lippia origanoides Kunth Essential Oil from the Carajás National Forest, Brazil.

Species of the genus Lippia are rich in essential oils and have shown antibacterial properties, which may be related to oils' chemical composition. The present work aimed to evaluate the antimicrobial potential of Lippia origanoides Kunth against two bacteria strains: Escherichia coli and Staphylococcus aureus. Leaf essential oils were obtained by hydrodistillation in a modified Clevenger-type apparatus, and their chemical composition was determined by gas chromatography coupled to mass spectrometry (GC/MS) and flame ionization detection (GC/FID). We identified 28 compounds, representing 98.87% of the total concentration of the essential oil. The compounds identified at the highest concentrations were 1,8-cineole (35.04%), carvacrol (11.32%), p-cymene (8.53%), α-pinene (7.17%), and γ-terpinene (7.16%). The leaf essential oil of L. origanoides showed antibacterial action on biological isolates of Escherichia coli and Staphylococcus aureus. For Escherichia coli, the oil presented bactericidal action at concentrations of 5-20 µL/mL. Regarding Staphylococcus aureus, the bactericidal effect was noted at 20 µL/mL and the bacteriostatic action was noted around 2.5-10 µL/mL. Given the results obtained, L. origanoides essential oil showed promising biological potential against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, thus encouraging further studies on substances isolated from this species to contribute to the development of new antimicrobial drugs.

Extraction Yield, Chemical Composition, Preliminary Toxicity of Bignonia nocturna (Bignoniaceae) Essential Oil and in Silico Evaluation of the Interaction.

Bignonia nocturna (Bignoniaceae) is a plant used for medicinal purposes by the Amazonian indigenous peoples. To date, there have been no reported studies on its toxicity. The present study aimed to evaluate the chemical composition of essential oils obtained from Bignonia nocturna by different extraction techniques. In addition, an in silico study of the molecular interactions was performed using molecular docking and molecular dynamics. The extractions were carried out by hydrodistillation, simultaneous distillation-extraction, and steam distillation, using samples collected from the Amazon in summer and winter. The chemical composition was analyzed by GC/FID and GC/MS, and the cytotoxic activity in Artemia salina Leach was evaluated. The maximum yield (1.38 % w/w) was obtained by hydrodistillation. The results indicated that benzaldehyde predominated in all the fractions of both the volatile concentrate and the essential oils. In addition, the oil proved to be highly toxic to Artemia salina. The computer simulation results indicated that benzaldehyde strongly interacts with acetylcholinesterase, which is the likely interaction mechanism responsible for the cytotoxicity.

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.

Insight into the Interaction Mechanism of Nicotine, NNK, and NNN with Cytochrome P450 2A13 Based on Molecular Dynamics Simulation.

Tobacco smoke contains various cancer-causing toxic substances, including nicotine and nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN). The cytochrome 2A13 is involved in nicotine metabolism and in the activation of the pro-carcinogenic agents NNK and NNN, by means of α-hydroxylation reactions. Despite the significance of cytochrome 2A13 in the biotransformation of these molecules, its conformational mechanism and the molecular basis involved in the process are not fully understood. In this study, we used molecular dynamics and principal component analysis simulations for an in-depth analysis of the essential protein motions involved in the interaction of cytochrome 2A13 with its substrates. We also evaluated the interaction of these substrates with the amino acid residues in the binding pocket of cytochrome 2A13. Furthermore, we quantified the nature of these chemical interactions from free energy calculations using the Molecular Mechanics/Generalized Born Surface Area method. The ligands remained favorably oriented toward compound I (cytochrome P450 O═FeIV state), to undergo α-hydroxylation. The hydrogen bond with asparagine 297 was essential to maintaining the substrates in a favorable catalytic orientation. The plot of first principal motion vs second principal motion revealed that the enzyme's interaction with nicotine and NNK involved different conformational subgroups, whereas the conformational subgroups in the interaction with NNN are more similar. These results provide new mechanistic insights into the mode of interaction of the substrates with the active site of cytochrome 2A13, in the presence of compound I, which is essential for α-hydroxylation.