Molecular Modeling of the Major Compounds of Sesquiterpenes Class in Copaiba Oil-resin

Silva, Nayara; Santos, César F.; Gonçalves, Luana; Braga, Francinaldo Sarges; Almeida, Jonathan Resende de; Lima, Clarissa Silva; Brasil, Davi; Silva, Carlos; Hage‐Melim, Lorane Izabel da Silva; Santos, Cleydson Breno Rodrigues dos

doi:10.9734/bjpr/2015/17591

Cited by 12 publications

(6 citation statements)

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“…The maps of molecular electrostatic potential (MEP) show the regions featured by colors that vary depending on the potential/charges. The positive regions (blue/green) indicate the portion of the molecule with the higher probability to suffer a nucleophilic attack, while the negative regions (green/red) indicate the regions that will perform nucleophilic attacks [ 35 ]; see Figure S1 in the supplementary material .…”

Section: Resultsmentioning

confidence: 99%

An Antioxidant Potential, Quantum-Chemical and Molecular Docking Study of the Major Chemical Constituents Present in the Leaves of Curatella americana Linn

et al. 2018

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Reactive oxygen species (ROS) are continuously generated in the normal biological systems, primarily by enzymes as xanthine oxidase (XO). The inappropriate scavenging or inhibition of ROS has been considered to be linked with aging, inflammatory disorders, and chronic diseases. Therefore, many plants and their products have been investigated as natural antioxidants for their potential use in preventive medicine. The leaves and bark extracts of Curatella americana Linn. were described in scientific research as anti-inflammatory, vasodilator, anti-ulcerogenic, and hypolipidemic effects. So, the aim of this study was to evaluate the antioxidant potentials of leaf hydroalcoholic extract from C. americana (HECA) through the scavenging DPPH assay and their main chemical constituents, evaluated by the following quantum chemical approaches (DFT B3LYP/6-31G**): Maps of Molecular Electrostatic Potential (MEP), Frontier Orbital’s (HOMO and LUMO) followed by multivariate analysis and molecular docking simulations with the xanthine oxidase enzyme. The hydroalcoholic extract showed significant antioxidant activity by free radical scavenging probably due to the great presence of flavonoids, which were grouped in the PCA and HCA analysis with the standard gallic acid. In the molecular docking study, the compounds studied presented the binding free energy (ΔG) values close each other, due to the similar interactions with amino acids residues at the activity site. The descriptors Gap and softness were important to characterize the molecules with antioxidant potential by capturing oxygen radicals.

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Section: Resultsmentioning

confidence: 99%

An Antioxidant Potential, Quantum-Chemical and Molecular Docking Study of the Major Chemical Constituents Present in the Leaves of Curatella americana Linn

et al. 2018

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“…Preadmet simulates tests for strains TA100 and TA1535, which serve to evaluate the mutagenic potential of molecules, ie the ability to generate mutation in an organism. This test simulates an environment in which a post-mitochondrial mouse liver supernatant mixture treated with a mixture of phenobarbital / β-naphthoflavone (s9) may be present or absent [ 45 , 46 ]. The in silico carcinogenicity test simulates the presence of the drug in the organism of rats and mice, and it is possible to evaluate if the drug has the power to generate tumors [ 47 ].…”

Section: Resultsmentioning

confidence: 99%

Virtual Screening and Statistical Analysis in the Design of New Caffeine Analogues Molecules with Potential Epithelial Anticancer Activity

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Cruz

et al. 2018

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About 132 thousand cases of melanoma (more severe type of skin cancer) were registered in 2014 according to the World Health Organization. This type of cancer significantly affects the quality of life of individuals. Caffeine has shown potential inhibitory effect against epithelial cancer. In this study, it was proposed to obtain new caffeine-based molecules with potential epithelial anticancer activity. For this, a training set of 21 molecules was used for pharmacophore perception procedures. Multiple linear regression analyses were used to propose mono-, bi-, tri-, and tetra-parametric models applied in the prediction of the activity. The generated pharmacophore was used to select 350 molecules available at the ZINCpharmer server, followed by reduction to 24 molecules, after selection using the Tanimoto index, yielding 10 molecules after final selection by predicted activity values > 1.5229. These ten mole-cules had better pharmacokinetic properties than the other ones used as reference and within the clinical-ly significant limits. Only two molecules show minor hits of toxicity and were submitted to molecular docking procedures, showing BFE (binding free energy) values lower than the reference values. Statisti-cal analyses indicated strong negative correlations between BFE and pharmacophoric properties (high influence on BFE lowering) and practically null correlation between BFE and BBB. The two most prom-ising molecules can be indicated as candidates for further in vitro and in vivo analyzes.

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“…Pharmacophore perception for the compounds was carried out using PharmaGist, and the top-ranked pre-alignment of the compounds had a score of 64.605 (see Figure 2), wherein Silva [22] and Padilha [23] independently reported similar score values in their studies, using the same the PharmaGist algorithm. The aligned compounds shared six spatial characteristics: two aromatic (AR) groups and four hydrogen acceptor (HA) groups, where the coordinates and the radius of the spatial characteristics are shown in Table 1.…”

Section: Pharmacophore Perception Using the Pharmagist And Discovery mentioning

confidence: 99%

“…The other models were unsatisfactory in the recovery of the known bioactive ligands, since many hypotheses did not obtain the necessary characteristics for interaction at the A2AAR receptor site [26]. Pharmacophore hypothese was classified according to the number of ligands aligned or that combined in order to generate a pharmacophore model that was satisfactory based on score, according to literature data [22,23,26]. The pharmacophore model chosen in pre-alignment via PharmaGist was used as input in the Discovery Studio, in order to refine the initial pharmacophore model.…”

Section: Pharmacophore Model Evaluationmentioning

confidence: 99%

“…After evaluating the parameters and the statistical quality, the parametric models (tetra-, pentaand hexaparametric) were applied to the set of seven compounds (22)(23)(24)(25)(26)(27)(28) in this study, called the test set (totaling 43.75% in relation to the number of compounds used in the training set; n = 16). Compounds were selected from the Pubchem database based on their respective EC 50 values, which were converted to pEC 50 .…”

Section: Quantitative Structure-activity Relationship (Qsar) Modelingmentioning

confidence: 99%

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Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches

et al. 2020

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Adenosine Receptor Type 2A (A2AAR) plays a role in important processes, such as anti-inflammatory ones. In this way, the present work aimed to search for compounds by pharmacophore-based virtual screening. The pharmacokinetic/toxicological profiles of the compounds, as well as a robust QSAR, predicted the binding modes via molecular docking. Finally, we used molecular dynamics to investigate the stability of interactions from ligand-A2AAR. For the search for A2AAR agonists, the UK-432097 and a set of 20 compounds available in the BindingDB database were studied. These compounds were used to generate pharmacophore models. Molecular properties were used for construction of the QSAR model by multiple linear regression for the prediction of biological activity. The best pharmacophore model was used by searching for commercial compounds in databases and the resulting compounds from the pharmacophore-based virtual screening were applied to the QSAR. Two compounds had promising activity due to their satisfactory pharmacokinetic/toxicological profiles and predictions via QSAR (Diverset 10002403 pEC50 = 7.54407; ZINC04257548 pEC50 = 7.38310). Moreover, they had satisfactory docking and molecular dynamics results compared to those obtained for Regadenoson (Lexiscan®), used as the positive control. These compounds can be used in biological assays (in vitro and in vivo) in order to confirm the potential activity agonist to A2AAR.

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Molecular Modeling of the Major Compounds of Sesquiterpenes Class in Copaiba Oil-resin

Cited by 12 publications

References 0 publications

An Antioxidant Potential, Quantum-Chemical and Molecular Docking Study of the Major Chemical Constituents Present in the Leaves of Curatella americana Linn

An Antioxidant Potential, Quantum-Chemical and Molecular Docking Study of the Major Chemical Constituents Present in the Leaves of Curatella americana Linn

Virtual Screening and Statistical Analysis in the Design of New Caffeine Analogues Molecules with Potential Epithelial Anticancer Activity

Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches

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