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

Abstract

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-β-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.

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

“…For the HD extraction process, dry and fresh sample (40 g each) were used. The same proportion of water in relation to plant material was used, according to the literature [44,45] …”

Chemical Composition and Antioxidant Activity of Essential Oils from Eugenia patrisii Vahl, E. punicifolia (Kunth) DC., and Myrcia tomentosa (Aubl.) DC., Leaf of Family Myrtaceae

“…The chemical compositions of the EOs of E. patrisii, E. punicifolia, and M. tomentosa, were analyzed using a Shimadzu QP-2010 (Kyoto, Japan) plus gas chromatography system equipped with an Rtx-5MS capillary column (Restek Corporation, Bellefonte, PA USA) (30 m × 0.25 mm; 0.25 µm film thickness) coupled to a mass spectrometer (GC/MS) (Shimadzu, Kyoto, Japan). The program temperature was maintained at 60-240 • C at a rate of 3 • C/min, with an injector temperature of 250 • C, helium as the carrier gas (linear velocity of 32 cm/s, measured at 100 • C) and a splitless injection (1 µL of a 2:1000 hexane solution) using the same operating conditions as described in the literature [59,60]. Except for the carrier hydrogen gas, the components were quantified using gas chromatography (CG) on a Shimadzu QP-2010 system (Kyoto, Japan), equipped with a flame ionization detector (FID), under the same operating conditions as before.…”

GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe

“…Docking protocol was run in extra precision (XP) mode through Glide using OPLS_2005 forcefield with flexible ligand and rigid receptor conditions [41,42]. To evaluate the potential of each ligand as 3CL protease inhibitor of SARS-CoV-2, molecular mechanics-generalized Born surface area (MM-GBSA) was used for scoring the docked pose of the ligand [21,43,44].…”

“…In this present study, the isolation and identification of the bioactive compounds of Z. officinale (leaves, pseudostems and rhizomes), have been performed using combination of chromatographic/spectroscopic analysis and in silico methods. Many studies have reported this approach as successful strategy to discover potential bioactive compounds from the nature, as well as to determine their binding interaction mode on protein target [19][20][21]. Gas chromatography-mass spectrophotometry (GC-MS) was used to identify the major compounds for further isolation, liquid chromatography-mass spectrophotometry/mass spectrophotometry (LC-MS/MS) was used to identify the isolated compounds, and nuclear magnetic resonance (NMR) was used to elucidate the chemical structure of isolated compound.…”