Kelson M T Oliveira | Universidade Federal do Amazonas (original) (raw)

Papers by Kelson M T Oliveira

Research paper thumbnail of Simulações De Docking e Dinâmica Molecular Na Busca De Fármacos Moduladores Do Sistema Neuroinflamatório Em Infecções Pelo SARSCOV-2

A Geração de Novos Conhecimentos na Química 2, 2021

Direitos para esta edição cedidos à Atena Editora pelos autores. Todo o conteúdo deste livro está... more Direitos para esta edição cedidos à Atena Editora pelos autores. Todo o conteúdo deste livro está licenciado sob uma Licença de Atribuição Creative Commons. Atribuição-Não-Comercial-NãoDerivativos 4.0 Internacional (CC BY-NC-ND 4.0).

Research paper thumbnail of New insights into structural, electronic, reactivity, spectroscopic and pharmacological properties of Bergenin: Experimental, DFT calculations, MD and docking simulations

Journal of Molecular Liquids, 2021

Abstract Bergenin is a polyphenol found in many medicinal plants that presents numerous activitie... more Abstract Bergenin is a polyphenol found in many medicinal plants that presents numerous activities, such as antiulcer, anti-inflammatory, antifungal, anticancer, antimicrobial, antidiabetic, antiviral and antioxidant, being, therefore, a research target nowadays. In the present study, bergenin, isolated from Endopleura uchi Huber Cuatrecasas plant, was studied through density functional theory (DFT) and time-dependent density functional theory (TD-DFT), at the B3LYP/6–311++G(2d,2p) and B3LYP-D3(BJ)/6–311+G(2d,p) levels, where the obtained optimized geometry, FT-IR and UV–Vis data were analyzed along with experimental data. The comparative IR studies, together with potential energy distribution (PED) calculation, enabled the assignment of the observed experimental IR bands, besides evaluating the existence of intermolecular H-bonds through dimers formation. The calculated electronic transitions are in good agreement with the experimental data, which allowed the characterization of the UV–Vis bands. HOMO-LUMO energy gaps, average local ionization energy (ALIE) surfaces and Fukui indices calculations were carried out, allowing to concisely evaluate the reactive sites of bergenin. Also, calculations of solvation free energies and free energies of association in water, methanol and ethanol were performed. Due to the know in vitro anti-inflammatory and anticancer activities presented by bergenin, molecular docking and molecular dynamic (MD) calculations were carried out in front of cyclooxygenases 1 and 2 and topoisomerases I and II, revealing good interactions of bergenin with the active site of the tested enzymes, justifying the experimental results found in literature.

Research paper thumbnail of Larvicidal, adulticidal and repellent activities against Aedes aegypti L. of two commonly used spices, Origanum vulgare L. and Thymus vulgaris L

South African Journal of Botany, 2021

Abstract The high incidence of dengue, chikungunya, and Zika indicates the importance of controll... more Abstract The high incidence of dengue, chikungunya, and Zika indicates the importance of controlling the vector of these arboviruses in the tropical and subtropical regions of the world. However, vector control is hindered by pesticide resistance and the limited success of biocontrol programs against Aedes mosquitoes. Despite these difficulties, the study of common plant species, including those with commercial value, can offer effective and ecological tools in the fight against mosquitoes. In the present study, the essential oils obtained from the aerial parts of Origanum vulgare L. and Thymus vulgaris L. were analyzed by GC–MS and evaluated for their larvicidal, adulticidal and repellent activities against Aedes aegypti L. The main constituents of the O. vulgare essential oil were terpinen-4-ol (17.4%), carvacrol (16.0%) and thymol (10.4%), and the main constituents of the T. vulgaris essential oil were thymol (40.0%), p-cymene (19.3%) and γ-terpinene (17.3%). Both essential oils were toxic to Ae. aegypti larvae with LC50 values of 37.5 μg/mL for O. vulgare and 38.9 μg/mL for T. vulgaris. For adult mosquitoes, the LC50 values were 14.3 and 11.7 μg/mL, respectively. The essential oils of O. vulgare and T. vulgaris showed a significant repellency effect, with values ranging from 8.9% to 37.8% and 4.4% to 68.9%, respectively. In addition, morphological differences between larvae treated with the EOs and the control group were evidenced by optical microscopy. Thus, the results suggest that the essential oils of O. vulgare and T. vulgaris have potential use as an ecofriendly source to develop new insecticides for the control of Ae. aegypti.

Research paper thumbnail of Experimental and theoretical study on spectral features, reactivity, solvation, topoisomerase I inhibition and in vitro cytotoxicity in human HepG2 cells of guadiscine and guadiscidine aporphine alkaloids

Journal of Molecular Structure, 2021

ABSTRACT In this study, guadiscine (G1) and guadiscidine (G2), 7,7-dimethylaporphine alkaloids fr... more ABSTRACT In this study, guadiscine (G1) and guadiscidine (G2), 7,7-dimethylaporphine alkaloids from Guatteria plants, have they geometric paramaters, vibrational behavior and quantum chemical properties (HOMO-LUMO, MEP, ALIE and Fukui indices) analyzed through a theoretical view, by density functional theory (DFT), using the Becker's three-parameter hybrid exchange functional combined with the Lee–Yang–Parr correlation functional (B3LYP) and 6-311G(2d,p) and 6-311G++(2df,3p) basis set. The obtained geometry data were compared with x-ray data for (−)-N-acetyl-anonaine showing close values. Vibrational analysis, together with potential energy distribution (PED) calculations, revealed several characteristic vibrations that characterize the 7,7 dimethylaporphine skeleton, besides enabling the observation of intermolecular H-bonds through dimers formation. Molecular dynamic simulations were carried out, allowing to evaluate the solvation free energies of G1 and G2 in water, methanol and ethanol, as well as the H-bonds formation between G1 and G2 and the tested solvents. The antineoplastic potential of the title molecules was evaluated via molecular docking calculations with topoisomerase I complexed with DNA. Guadiscine and guadiscidine showed, respectively, free binding energies of -8.0 and -8.5 kcal/mol, while topotecan, a DNA topoisomerase I inhibitor, showed a binding free energy value of -12 kcal/mol, indicating that the studied molecules are good topoisomerase I inhibitors. In vitro cytotoxicity assay with HepG2 cell line were performed, revealing significant antitumor potential of the studied molecules.

Research paper thumbnail of Structural, vibrational, UV–vis, quantum-chemical properties, molecular docking and anti-cancer activity study of annomontine and N-hydroxyannomontine β-carboline alkaloids: A combined experimental and DFT approach

Journal of Molecular Structure, 2018

A theoretical and experimental DFT study of the vibrational, structural and quantum properties of... more A theoretical and experimental DFT study of the vibrational, structural and quantum properties of annomontine (1) and N-hydroxyannomontine (2) alkaloids using the B3LYP exchange-correlation functional with 6-311G (2d, p) basis set is presented. The theoretical geometry optimization data of the two structures were compared with the X-ray data of (1) in the associated literature and a conformational study is presented for both molecules, providing a good comprehension of the conformational stability. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap and mapped molecular electrostatic potential surface (MEPS) calculations were also performed at the same calculation approach. The calculated UV spectra agreed well with the measured experimental data, with transitions assigned. The comparative IR studies confirmed the intramolecular hydrogen bonds of the conformations and the intermolecular hydrogen bonds of dimeric forms and also revealed several characteristic vibrations for the structures. Molecular docking studies with DNA Topoisomerase II-DNA complex showed binding free energies of À11.5 and À10.6 kcal/mol for 2 and 1 respectively, while for amsacrine, used for the treatment of leukemia, and doxorubicin, used for the treatment of breast cancer, bladder cancer, Kaposi's sarcoma, and acute lymphocytic leukemia, the presented binding free energies values are À10.0 and À9.9 kcal/mol respectively, revealing good bind affinities of the tested alkaloids with the complex. In vitro cytotoxicity assay revealed an expressive antitumor activity of N-hydroxyannomontine against human hepatocellular carcinoma cell line HepG2.

Research paper thumbnail of Theoretical and experimental study by DFT, molecular docking calculations and cytotoxicity assay of 7,7-dimethylaporphine alkaloids type isolated from Guatteria friesiana (Annonaceae)

Journal of Molecular Structure, 2019

A combined experimental and theoretical DFT study of the structural, vibrational and electronic p... more A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of 9-methoxyguatterfriesine (I), (R)-6,6a-dihydro-9methoxyguatterfriesine (II) and 4,5-dehydro-9-methoxyguatterfriesine (III) is presented using B3LYP exchange-correlation functional with 6-311G (2d, p) basis set. The theoretical geometry optimization data were compared with the X-ray data for (-)-N-acetylanonaine, showing close values. In addition, molecular electrostatic potential surface (MEPS) calculation, HOMO-LUMO energy gap, natural bond orbitals (NBOs) and first and second order hyperpolarizabilities were also performed with the same calculation level. Transitions for UV spectrum for the three structures were assigned and the calculated bands showed good agreement with the measured experimental data. The comparative IR studies showed intermolecular hydrogen bonds that stabilize dimeric forms proposed for the three molecules and also revealed several characteristic vibrations for the structures. Molecular docking studies with DNA Topoisomerase II-DNA complex showed binding free energies of-7.6,-7.5 and-8.7 kcal/mol, for I, II and III respectively, which indicate III as a better potential inhibitor for this enzyme. In vitro cytotoxicity assay revealed an expressive antitumor activity of III against HepG2 cell line.

Research paper thumbnail of Comparative Computational Study of SARS-CoV-2 Receptors Antagonists from Already Approved Drugs

According to the World Health Organisation, on March 27, 2020, the number of confirmed cases of C... more According to the World Health Organisation, on March 27, 2020, the number of confirmed cases of COVID-19 has already exceeded 509.000 with about of 23.000 deaths worldwide. Given this, the impact of COVID-19 on humanity cannot be overlooked, and basic research are urgently needed. This research aims to find antagonists already approved for another diseases, that may inhibit activity of the main protease (Mpro) of the SARS-CoV-2 virus, as well as modulate the ACE2 receptors, largely found in lung cells and reduce viral replication by inhibiting NSP12 RNA Polymerase. Docking molecular simulations were realized among a total of 28 ligands published in the literature against COVID-19. Docking studies were made with algorithm of AutoDock Vina 1.1.2 software. A structure-based virtual screening was performed with MTiOpenScreen. Subsequently, the physical-chemical and pharmacokinetic parameters were analyzed with SwissADME in order to select only the most promising ones. Finally, simulatio...

Research paper thumbnail of Novel route for the synthesis of azepine derivative using tin-based catalyst: Spectroscopic characterization and theoretical investigations

Journal of Molecular Structure, 2019

Synthesis of azepine-based compounds are of highly interest due to their vast applications in med... more Synthesis of azepine-based compounds are of highly interest due to their vast applications in medicinal filed. In this work, is described the synthesis of a azepine-based derivative, 11-methoxy-6,6a-dihydro-5H-dibenzo[b,e]azepine (MDDA) by new route using dibutyltin dilaurate (DBTDL) as catalyst. The structural elucidation of MDDA was done by FT-IR, 1 H NMR, and mass spectrometry techniques. Also is presented the experimental and theoretical DFT study of the vibrational, structural and quantum properties of MDDA using B3LYP exchange-correlation functional with 6-311G (2d, p) basis set. The theoretical DFT geometry optimization data was compared with the X-ray data in the associated literature promoting a good comprehension of the structural arrangement. In complementation, mapped molecular electrostatic potential surface (MEPS), HOMO-LUMO orbitals and NBO energy calculations were also performed using the same calculation approach. The calculated UV spectrum is in good agreement with the experimental one, making the bands assignments possible. The comparative IR studies clearly confirmed the intermolecular hydrogen bonds of the proposed dimeric form for MDDA and also showed several characteristic vibrations within the molecular structure.

Research paper thumbnail of Vibrational, structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: A theoretical approach for potentially bioactive molecules

Journal of Molecular Structure, 2017

, structural and electronic properties investigation by DFT calculations and molecular docking st... more , structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: a theoretical approach for potentially bioactive molecules, (2017), doi:

Research paper thumbnail of Aprendizagem da Língua Portuguesa com Dispositivos Móveis: Um Mapeamento Sistemático da Literatura

Anais do XXVI Simpósio Brasileiro de Informática na Educação (SBIE 2015), 2015

With the advance, popularization and mainly due to the great range of features that are added to ... more With the advance, popularization and mainly due to the great range of features that are added to them, the mobile devices have become more attractive for the pedagogical practices, such as teaching Portuguese Language (PL). This study aims to analyze scientific publications in order to identify mobile learning (m-learning) applications to PL, using a Systematic Literature Mapping (SLM) to provide a wide view of the mentioned area. Results have shown that the research on m-learning and PL in Brazil are still recent, but have also shown an increase of publications in the last few years. Resumo. Com o avanço, a popularização e principalmente devido à gama de recursos que agregam, os dispositivos móveis têm se tornado cada vez mais atrativos para as práticas pedagógicas, como, por exemplo, no ensino da Língua Portuguesa (LP). Este estudo tem por objetivo analisar publicações científicas com o propósito de identificar aplicações mobile learning (mlearning) para a LP, utilizando um Mapeamento Sistemático da Literatura (MSL), a fim de obter uma visão geral e ampla da área de pesquisa. Os resultados mostram que as pesquisas em m-learning e LP ainda são recentes, porém têm mostrado aumento de publicações nos últimos anos.

Research paper thumbnail of Trilhas de Aprendizagem em Ambientes Virtuais de Ensino-aprendizagem: Uma Revisão Sistemática da Literatura

Anais do XXVI Simpósio Brasileiro de Informática na Educação (SBIE 2015), 2015

The research presented in this paper is the result of a Systematic Literature Review that aimed t... more The research presented in this paper is the result of a Systematic Literature Review that aimed to identify how learning paths are represented within the e-learning systems. It was also verified if these representations include not only data structure and modeling of e-learning systems, but also the visualization of learning paths by teachers and students. Resumo. A pesquisa apresentada neste trabalho é resultado de uma Revisão Sistemática da Literatura que buscou identificar como as trilhas de aprendizagem são representadas nos sistemas e-learning. Foi verificado se essas representações contemplam apenas a estrutura de dados e modelagem dos sistemas de e-learning, ou se também há visualização das trilhas de aprendizagem pelos professores e alunos.

Research paper thumbnail of A multivariate study on flavonoid compounds scavenging the peroxynitrite free radical

Journal of Molecular Structure: THEOCHEM, 2007

The goal of this study is to select electronic properties (variables or descriptors) responsible ... more The goal of this study is to select electronic properties (variables or descriptors) responsible for peroxynitrite scavenging ability of a set of 24 flavonoids. To do so, electronic parameters were calculated by using DFT and chemometric methods (Principal Component Analysis, Hierarchical Cluster Analysis and K-Nearest Neighbor) in order to build models able to establish relationships between electronic features and the

Research paper thumbnail of Molecular modeling of the inhibition of enzyme PLA2from snake venom by dipyrone and 1-phenyl-3-methyl-5-pyrazolone

International Journal of Quantum Chemistry, 2008

Phospholipases A2 (PLA2) are enzymes that trigger the degradation cascade of the arachidonic acid... more Phospholipases A2 (PLA2) are enzymes that trigger the degradation cascade of the arachidonic acid, leading to the formation of pro-inflammatory eicosanoids. The selective inhibition of PLA2s is crucial in the search for a more efficient anti-inflammatory drug with fewer side effects than the drugs currently used. Hence, we studied the influences caused by two pyrazolonic inhibitors: dipyrone (DIP) and 1-phenyl-3-methyl-5-pyrazolone

Research paper thumbnail of Synthesis, Characterization and <I>In Vitro-In Vivo</I> Evaluation of Carboxymethylated Badam Gum Derivative for Improving Dissolution Behaviour of BCS Class-II Drug

Advanced Science, Engineering and Medicine, 2016

Research paper thumbnail of Improvement of SARS-CoV-2 macromolecule conformation by algorithmic structural prediction

2021 XLVII Latin American Computing Conference (CLEI)

A fast way to reconstruct the three-dimensional molecular conformation of SARS-CoV-2 virus protei... more A fast way to reconstruct the three-dimensional molecular conformation of SARS-CoV-2 virus proteins is addressed in this article, involving the most worrying variant discovered in patients from Brazil, the lineage BBB.1.1.28/$P$.1. The proposed methodology is based on the sequencing of virus proteins and that, through the incorporation of mutations in silico, which are then computationally reconstructed using an enumerative feasibility algorithm validated by the Ramachandran diagram and structural alignment, in addition to the subsequent study of structural stability through classical molecular dynamics. From the resulting structure to the ACE2-RBD complex, the valid solution presented 97.06% of the residues in the most favorable region while the reference crystallographic structure presented 95.0%, a difference therefore very small and revealing the great consistency of the developed algorithm. Another important result was the low RMSD alignment between the best solution by the BP algorithm and the reference structure, where we obtained 0.483Å. Finally, the molecular dynamics indicated greater structural stability in the ACE2-RBD interaction with the P.1 strain, which could be a plausible explanation for convergent evolution that provides an increase in the interaction affinity with the ACE2 receptor.

Research paper thumbnail of Molecular dynamics of the P.1 variant of SARS-CoV-2

All molecular dynamics simulations were performed in GROMACS 2019.1 software by Prof. Dr. Jonatha... more All molecular dynamics simulations were performed in GROMACS 2019.1 software by Prof. Dr. Jonathas N. Silva. The time interval for each simulation is 50ns. Among the crystallographic structures, we have the antibody-antigen complex containing the P.1 variant (PDB ID: 7NXB), and the respective wild-type structure (PDB ID: 7NX6) In preparing the topology, Na+ and Cl- ions were inserted to neutralize the system at a concentration of 0.15 mol/L. Trajectory files were simulated based on the CHARMM36 force field. We use a cubic solvation box, by the TIP3P water model. The production of trajectories was carried out using the NPT canonical cycle. The Parrinello–Rahman barostat was adopted to keep the pressure constant at 1 atm, while the Berendsen algorithm acted as a thermostat to keep the system temperature at 300 K.

Research paper thumbnail of Theoretical causes of the Brazilian P.1 and P.2 lineages of the SARS-CoV-2 virus through molecular dynamics

ABSTRACTThe new β-coronavirus has been causing sad losses around the world and the emergence of n... more ABSTRACTThe new β-coronavirus has been causing sad losses around the world and the emergence of new variants has caused great concern. This pandemic is of a proportion not seen since the Spanish Flu in 1918. Thus, throughout this research, the B.1.1.28 lineage of the P.1 clade (K417T, N501Y, E484K) that emerged in Brazil was studied, as well as the latest Delta variant. This is because the molecular mechanisms by which phenotypic changes in transmissibility or mortality remain unknown. Through molecular dynamics simulations with the NAMD 3 algorithm in the 50ns interval, it was possible to understand the impact on structural stabilization on the interaction of the ACE2-RBD complex, as well as simulations in 30ns for the neutralizing antibody P2B-2F6, with this antibody was derived from immune cells from patients infected with SARS-CoV-2. Although not all molecular dynamics analyzes support the hypothesis of greater stability in the face of mutations, there was a predominance of low ...

Research paper thumbnail of Synthetic Routes of the Fundamental Building Blocks of Life: Computational Study of The Reaction Free Energy

Revista Processos Químicos, 2015

Research paper thumbnail of Geometry and Stability of Molecular Clusters: Factor to Be Considered in Biomolecular Activity

Journal of the Brazilian Chemical Society, 2018

Betulinic and melaleucic acids, lupan-skeleton triterpenes with very similar structure, present m... more Betulinic and melaleucic acids, lupan-skeleton triterpenes with very similar structure, present marked differences in anti-malarial activity. While betulinic acid and some of its analogs exhibit strong activity, melaleucic acid is inactive. In the present work, a theoretical approach was used to explain such differences, using Austin Model 1 (AM1) and density functional theory (DFT)/ Becke, three-parameter, Lee-Yang-Parr (B3LYP) approaches, and AutoDock Vina calculations. The initial results showed no significant differences between structural and electronic properties. On the other hand, studies of the geometry of molecular clusters with both compounds revealed significant differences. Melaleucic acid clusters were shown to be stable enough to influence the substrate-protein interaction, unlike betulinic acid, which was unable to form clusters comparable to melaleucic acid ones. The present study suggests the molecular clusters as a new factor that has a great influence on the mechanism of biomolecular activity.

Research paper thumbnail of Theoretical Study of Metalloporphyrins Oxo-Dimers With Metals of the First and Second Transition Series

In this work were analyzed the structural properties of metalloporphyrins dimmers, with transitio... more In this work were analyzed the structural properties of metalloporphyrins dimmers, with transition metals, in which the monomers are aggregated through an oxo bridge. Five different basic structural conformations were found. The correlation of them with electronic structure of the monomers were observed. It was used the quantum method INDO.

Research paper thumbnail of Simulações De Docking e Dinâmica Molecular Na Busca De Fármacos Moduladores Do Sistema Neuroinflamatório Em Infecções Pelo SARSCOV-2

A Geração de Novos Conhecimentos na Química 2, 2021

Direitos para esta edição cedidos à Atena Editora pelos autores. Todo o conteúdo deste livro está... more Direitos para esta edição cedidos à Atena Editora pelos autores. Todo o conteúdo deste livro está licenciado sob uma Licença de Atribuição Creative Commons. Atribuição-Não-Comercial-NãoDerivativos 4.0 Internacional (CC BY-NC-ND 4.0).

Research paper thumbnail of New insights into structural, electronic, reactivity, spectroscopic and pharmacological properties of Bergenin: Experimental, DFT calculations, MD and docking simulations

Journal of Molecular Liquids, 2021

Abstract Bergenin is a polyphenol found in many medicinal plants that presents numerous activitie... more Abstract Bergenin is a polyphenol found in many medicinal plants that presents numerous activities, such as antiulcer, anti-inflammatory, antifungal, anticancer, antimicrobial, antidiabetic, antiviral and antioxidant, being, therefore, a research target nowadays. In the present study, bergenin, isolated from Endopleura uchi Huber Cuatrecasas plant, was studied through density functional theory (DFT) and time-dependent density functional theory (TD-DFT), at the B3LYP/6–311++G(2d,2p) and B3LYP-D3(BJ)/6–311+G(2d,p) levels, where the obtained optimized geometry, FT-IR and UV–Vis data were analyzed along with experimental data. The comparative IR studies, together with potential energy distribution (PED) calculation, enabled the assignment of the observed experimental IR bands, besides evaluating the existence of intermolecular H-bonds through dimers formation. The calculated electronic transitions are in good agreement with the experimental data, which allowed the characterization of the UV–Vis bands. HOMO-LUMO energy gaps, average local ionization energy (ALIE) surfaces and Fukui indices calculations were carried out, allowing to concisely evaluate the reactive sites of bergenin. Also, calculations of solvation free energies and free energies of association in water, methanol and ethanol were performed. Due to the know in vitro anti-inflammatory and anticancer activities presented by bergenin, molecular docking and molecular dynamic (MD) calculations were carried out in front of cyclooxygenases 1 and 2 and topoisomerases I and II, revealing good interactions of bergenin with the active site of the tested enzymes, justifying the experimental results found in literature.

Research paper thumbnail of Larvicidal, adulticidal and repellent activities against Aedes aegypti L. of two commonly used spices, Origanum vulgare L. and Thymus vulgaris L

South African Journal of Botany, 2021

Abstract The high incidence of dengue, chikungunya, and Zika indicates the importance of controll... more Abstract The high incidence of dengue, chikungunya, and Zika indicates the importance of controlling the vector of these arboviruses in the tropical and subtropical regions of the world. However, vector control is hindered by pesticide resistance and the limited success of biocontrol programs against Aedes mosquitoes. Despite these difficulties, the study of common plant species, including those with commercial value, can offer effective and ecological tools in the fight against mosquitoes. In the present study, the essential oils obtained from the aerial parts of Origanum vulgare L. and Thymus vulgaris L. were analyzed by GC–MS and evaluated for their larvicidal, adulticidal and repellent activities against Aedes aegypti L. The main constituents of the O. vulgare essential oil were terpinen-4-ol (17.4%), carvacrol (16.0%) and thymol (10.4%), and the main constituents of the T. vulgaris essential oil were thymol (40.0%), p-cymene (19.3%) and γ-terpinene (17.3%). Both essential oils were toxic to Ae. aegypti larvae with LC50 values of 37.5 μg/mL for O. vulgare and 38.9 μg/mL for T. vulgaris. For adult mosquitoes, the LC50 values were 14.3 and 11.7 μg/mL, respectively. The essential oils of O. vulgare and T. vulgaris showed a significant repellency effect, with values ranging from 8.9% to 37.8% and 4.4% to 68.9%, respectively. In addition, morphological differences between larvae treated with the EOs and the control group were evidenced by optical microscopy. Thus, the results suggest that the essential oils of O. vulgare and T. vulgaris have potential use as an ecofriendly source to develop new insecticides for the control of Ae. aegypti.

Research paper thumbnail of Experimental and theoretical study on spectral features, reactivity, solvation, topoisomerase I inhibition and in vitro cytotoxicity in human HepG2 cells of guadiscine and guadiscidine aporphine alkaloids

Journal of Molecular Structure, 2021

ABSTRACT In this study, guadiscine (G1) and guadiscidine (G2), 7,7-dimethylaporphine alkaloids fr... more ABSTRACT In this study, guadiscine (G1) and guadiscidine (G2), 7,7-dimethylaporphine alkaloids from Guatteria plants, have they geometric paramaters, vibrational behavior and quantum chemical properties (HOMO-LUMO, MEP, ALIE and Fukui indices) analyzed through a theoretical view, by density functional theory (DFT), using the Becker's three-parameter hybrid exchange functional combined with the Lee–Yang–Parr correlation functional (B3LYP) and 6-311G(2d,p) and 6-311G++(2df,3p) basis set. The obtained geometry data were compared with x-ray data for (−)-N-acetyl-anonaine showing close values. Vibrational analysis, together with potential energy distribution (PED) calculations, revealed several characteristic vibrations that characterize the 7,7 dimethylaporphine skeleton, besides enabling the observation of intermolecular H-bonds through dimers formation. Molecular dynamic simulations were carried out, allowing to evaluate the solvation free energies of G1 and G2 in water, methanol and ethanol, as well as the H-bonds formation between G1 and G2 and the tested solvents. The antineoplastic potential of the title molecules was evaluated via molecular docking calculations with topoisomerase I complexed with DNA. Guadiscine and guadiscidine showed, respectively, free binding energies of -8.0 and -8.5 kcal/mol, while topotecan, a DNA topoisomerase I inhibitor, showed a binding free energy value of -12 kcal/mol, indicating that the studied molecules are good topoisomerase I inhibitors. In vitro cytotoxicity assay with HepG2 cell line were performed, revealing significant antitumor potential of the studied molecules.

Research paper thumbnail of Structural, vibrational, UV–vis, quantum-chemical properties, molecular docking and anti-cancer activity study of annomontine and N-hydroxyannomontine β-carboline alkaloids: A combined experimental and DFT approach

Journal of Molecular Structure, 2018

A theoretical and experimental DFT study of the vibrational, structural and quantum properties of... more A theoretical and experimental DFT study of the vibrational, structural and quantum properties of annomontine (1) and N-hydroxyannomontine (2) alkaloids using the B3LYP exchange-correlation functional with 6-311G (2d, p) basis set is presented. The theoretical geometry optimization data of the two structures were compared with the X-ray data of (1) in the associated literature and a conformational study is presented for both molecules, providing a good comprehension of the conformational stability. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap and mapped molecular electrostatic potential surface (MEPS) calculations were also performed at the same calculation approach. The calculated UV spectra agreed well with the measured experimental data, with transitions assigned. The comparative IR studies confirmed the intramolecular hydrogen bonds of the conformations and the intermolecular hydrogen bonds of dimeric forms and also revealed several characteristic vibrations for the structures. Molecular docking studies with DNA Topoisomerase II-DNA complex showed binding free energies of À11.5 and À10.6 kcal/mol for 2 and 1 respectively, while for amsacrine, used for the treatment of leukemia, and doxorubicin, used for the treatment of breast cancer, bladder cancer, Kaposi's sarcoma, and acute lymphocytic leukemia, the presented binding free energies values are À10.0 and À9.9 kcal/mol respectively, revealing good bind affinities of the tested alkaloids with the complex. In vitro cytotoxicity assay revealed an expressive antitumor activity of N-hydroxyannomontine against human hepatocellular carcinoma cell line HepG2.

Research paper thumbnail of Theoretical and experimental study by DFT, molecular docking calculations and cytotoxicity assay of 7,7-dimethylaporphine alkaloids type isolated from Guatteria friesiana (Annonaceae)

Journal of Molecular Structure, 2019

A combined experimental and theoretical DFT study of the structural, vibrational and electronic p... more A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of 9-methoxyguatterfriesine (I), (R)-6,6a-dihydro-9methoxyguatterfriesine (II) and 4,5-dehydro-9-methoxyguatterfriesine (III) is presented using B3LYP exchange-correlation functional with 6-311G (2d, p) basis set. The theoretical geometry optimization data were compared with the X-ray data for (-)-N-acetylanonaine, showing close values. In addition, molecular electrostatic potential surface (MEPS) calculation, HOMO-LUMO energy gap, natural bond orbitals (NBOs) and first and second order hyperpolarizabilities were also performed with the same calculation level. Transitions for UV spectrum for the three structures were assigned and the calculated bands showed good agreement with the measured experimental data. The comparative IR studies showed intermolecular hydrogen bonds that stabilize dimeric forms proposed for the three molecules and also revealed several characteristic vibrations for the structures. Molecular docking studies with DNA Topoisomerase II-DNA complex showed binding free energies of-7.6,-7.5 and-8.7 kcal/mol, for I, II and III respectively, which indicate III as a better potential inhibitor for this enzyme. In vitro cytotoxicity assay revealed an expressive antitumor activity of III against HepG2 cell line.

Research paper thumbnail of Comparative Computational Study of SARS-CoV-2 Receptors Antagonists from Already Approved Drugs

According to the World Health Organisation, on March 27, 2020, the number of confirmed cases of C... more According to the World Health Organisation, on March 27, 2020, the number of confirmed cases of COVID-19 has already exceeded 509.000 with about of 23.000 deaths worldwide. Given this, the impact of COVID-19 on humanity cannot be overlooked, and basic research are urgently needed. This research aims to find antagonists already approved for another diseases, that may inhibit activity of the main protease (Mpro) of the SARS-CoV-2 virus, as well as modulate the ACE2 receptors, largely found in lung cells and reduce viral replication by inhibiting NSP12 RNA Polymerase. Docking molecular simulations were realized among a total of 28 ligands published in the literature against COVID-19. Docking studies were made with algorithm of AutoDock Vina 1.1.2 software. A structure-based virtual screening was performed with MTiOpenScreen. Subsequently, the physical-chemical and pharmacokinetic parameters were analyzed with SwissADME in order to select only the most promising ones. Finally, simulatio...

Research paper thumbnail of Novel route for the synthesis of azepine derivative using tin-based catalyst: Spectroscopic characterization and theoretical investigations

Journal of Molecular Structure, 2019

Synthesis of azepine-based compounds are of highly interest due to their vast applications in med... more Synthesis of azepine-based compounds are of highly interest due to their vast applications in medicinal filed. In this work, is described the synthesis of a azepine-based derivative, 11-methoxy-6,6a-dihydro-5H-dibenzo[b,e]azepine (MDDA) by new route using dibutyltin dilaurate (DBTDL) as catalyst. The structural elucidation of MDDA was done by FT-IR, 1 H NMR, and mass spectrometry techniques. Also is presented the experimental and theoretical DFT study of the vibrational, structural and quantum properties of MDDA using B3LYP exchange-correlation functional with 6-311G (2d, p) basis set. The theoretical DFT geometry optimization data was compared with the X-ray data in the associated literature promoting a good comprehension of the structural arrangement. In complementation, mapped molecular electrostatic potential surface (MEPS), HOMO-LUMO orbitals and NBO energy calculations were also performed using the same calculation approach. The calculated UV spectrum is in good agreement with the experimental one, making the bands assignments possible. The comparative IR studies clearly confirmed the intermolecular hydrogen bonds of the proposed dimeric form for MDDA and also showed several characteristic vibrations within the molecular structure.

Research paper thumbnail of Vibrational, structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: A theoretical approach for potentially bioactive molecules

Journal of Molecular Structure, 2017

, structural and electronic properties investigation by DFT calculations and molecular docking st... more , structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: a theoretical approach for potentially bioactive molecules, (2017), doi:

Research paper thumbnail of Aprendizagem da Língua Portuguesa com Dispositivos Móveis: Um Mapeamento Sistemático da Literatura

Anais do XXVI Simpósio Brasileiro de Informática na Educação (SBIE 2015), 2015

With the advance, popularization and mainly due to the great range of features that are added to ... more With the advance, popularization and mainly due to the great range of features that are added to them, the mobile devices have become more attractive for the pedagogical practices, such as teaching Portuguese Language (PL). This study aims to analyze scientific publications in order to identify mobile learning (m-learning) applications to PL, using a Systematic Literature Mapping (SLM) to provide a wide view of the mentioned area. Results have shown that the research on m-learning and PL in Brazil are still recent, but have also shown an increase of publications in the last few years. Resumo. Com o avanço, a popularização e principalmente devido à gama de recursos que agregam, os dispositivos móveis têm se tornado cada vez mais atrativos para as práticas pedagógicas, como, por exemplo, no ensino da Língua Portuguesa (LP). Este estudo tem por objetivo analisar publicações científicas com o propósito de identificar aplicações mobile learning (mlearning) para a LP, utilizando um Mapeamento Sistemático da Literatura (MSL), a fim de obter uma visão geral e ampla da área de pesquisa. Os resultados mostram que as pesquisas em m-learning e LP ainda são recentes, porém têm mostrado aumento de publicações nos últimos anos.

Research paper thumbnail of Trilhas de Aprendizagem em Ambientes Virtuais de Ensino-aprendizagem: Uma Revisão Sistemática da Literatura

Anais do XXVI Simpósio Brasileiro de Informática na Educação (SBIE 2015), 2015

The research presented in this paper is the result of a Systematic Literature Review that aimed t... more The research presented in this paper is the result of a Systematic Literature Review that aimed to identify how learning paths are represented within the e-learning systems. It was also verified if these representations include not only data structure and modeling of e-learning systems, but also the visualization of learning paths by teachers and students. Resumo. A pesquisa apresentada neste trabalho é resultado de uma Revisão Sistemática da Literatura que buscou identificar como as trilhas de aprendizagem são representadas nos sistemas e-learning. Foi verificado se essas representações contemplam apenas a estrutura de dados e modelagem dos sistemas de e-learning, ou se também há visualização das trilhas de aprendizagem pelos professores e alunos.

Research paper thumbnail of A multivariate study on flavonoid compounds scavenging the peroxynitrite free radical

Journal of Molecular Structure: THEOCHEM, 2007

The goal of this study is to select electronic properties (variables or descriptors) responsible ... more The goal of this study is to select electronic properties (variables or descriptors) responsible for peroxynitrite scavenging ability of a set of 24 flavonoids. To do so, electronic parameters were calculated by using DFT and chemometric methods (Principal Component Analysis, Hierarchical Cluster Analysis and K-Nearest Neighbor) in order to build models able to establish relationships between electronic features and the

Research paper thumbnail of Molecular modeling of the inhibition of enzyme PLA2from snake venom by dipyrone and 1-phenyl-3-methyl-5-pyrazolone

International Journal of Quantum Chemistry, 2008

Phospholipases A2 (PLA2) are enzymes that trigger the degradation cascade of the arachidonic acid... more Phospholipases A2 (PLA2) are enzymes that trigger the degradation cascade of the arachidonic acid, leading to the formation of pro-inflammatory eicosanoids. The selective inhibition of PLA2s is crucial in the search for a more efficient anti-inflammatory drug with fewer side effects than the drugs currently used. Hence, we studied the influences caused by two pyrazolonic inhibitors: dipyrone (DIP) and 1-phenyl-3-methyl-5-pyrazolone

Research paper thumbnail of Synthesis, Characterization and <I>In Vitro-In Vivo</I> Evaluation of Carboxymethylated Badam Gum Derivative for Improving Dissolution Behaviour of BCS Class-II Drug

Advanced Science, Engineering and Medicine, 2016

Research paper thumbnail of Improvement of SARS-CoV-2 macromolecule conformation by algorithmic structural prediction

2021 XLVII Latin American Computing Conference (CLEI)

A fast way to reconstruct the three-dimensional molecular conformation of SARS-CoV-2 virus protei... more A fast way to reconstruct the three-dimensional molecular conformation of SARS-CoV-2 virus proteins is addressed in this article, involving the most worrying variant discovered in patients from Brazil, the lineage BBB.1.1.28/$P$.1. The proposed methodology is based on the sequencing of virus proteins and that, through the incorporation of mutations in silico, which are then computationally reconstructed using an enumerative feasibility algorithm validated by the Ramachandran diagram and structural alignment, in addition to the subsequent study of structural stability through classical molecular dynamics. From the resulting structure to the ACE2-RBD complex, the valid solution presented 97.06% of the residues in the most favorable region while the reference crystallographic structure presented 95.0%, a difference therefore very small and revealing the great consistency of the developed algorithm. Another important result was the low RMSD alignment between the best solution by the BP algorithm and the reference structure, where we obtained 0.483Å. Finally, the molecular dynamics indicated greater structural stability in the ACE2-RBD interaction with the P.1 strain, which could be a plausible explanation for convergent evolution that provides an increase in the interaction affinity with the ACE2 receptor.

Research paper thumbnail of Molecular dynamics of the P.1 variant of SARS-CoV-2

All molecular dynamics simulations were performed in GROMACS 2019.1 software by Prof. Dr. Jonatha... more All molecular dynamics simulations were performed in GROMACS 2019.1 software by Prof. Dr. Jonathas N. Silva. The time interval for each simulation is 50ns. Among the crystallographic structures, we have the antibody-antigen complex containing the P.1 variant (PDB ID: 7NXB), and the respective wild-type structure (PDB ID: 7NX6) In preparing the topology, Na+ and Cl- ions were inserted to neutralize the system at a concentration of 0.15 mol/L. Trajectory files were simulated based on the CHARMM36 force field. We use a cubic solvation box, by the TIP3P water model. The production of trajectories was carried out using the NPT canonical cycle. The Parrinello–Rahman barostat was adopted to keep the pressure constant at 1 atm, while the Berendsen algorithm acted as a thermostat to keep the system temperature at 300 K.

Research paper thumbnail of Theoretical causes of the Brazilian P.1 and P.2 lineages of the SARS-CoV-2 virus through molecular dynamics

ABSTRACTThe new β-coronavirus has been causing sad losses around the world and the emergence of n... more ABSTRACTThe new β-coronavirus has been causing sad losses around the world and the emergence of new variants has caused great concern. This pandemic is of a proportion not seen since the Spanish Flu in 1918. Thus, throughout this research, the B.1.1.28 lineage of the P.1 clade (K417T, N501Y, E484K) that emerged in Brazil was studied, as well as the latest Delta variant. This is because the molecular mechanisms by which phenotypic changes in transmissibility or mortality remain unknown. Through molecular dynamics simulations with the NAMD 3 algorithm in the 50ns interval, it was possible to understand the impact on structural stabilization on the interaction of the ACE2-RBD complex, as well as simulations in 30ns for the neutralizing antibody P2B-2F6, with this antibody was derived from immune cells from patients infected with SARS-CoV-2. Although not all molecular dynamics analyzes support the hypothesis of greater stability in the face of mutations, there was a predominance of low ...

Research paper thumbnail of Synthetic Routes of the Fundamental Building Blocks of Life: Computational Study of The Reaction Free Energy

Revista Processos Químicos, 2015

Research paper thumbnail of Geometry and Stability of Molecular Clusters: Factor to Be Considered in Biomolecular Activity

Journal of the Brazilian Chemical Society, 2018

Betulinic and melaleucic acids, lupan-skeleton triterpenes with very similar structure, present m... more Betulinic and melaleucic acids, lupan-skeleton triterpenes with very similar structure, present marked differences in anti-malarial activity. While betulinic acid and some of its analogs exhibit strong activity, melaleucic acid is inactive. In the present work, a theoretical approach was used to explain such differences, using Austin Model 1 (AM1) and density functional theory (DFT)/ Becke, three-parameter, Lee-Yang-Parr (B3LYP) approaches, and AutoDock Vina calculations. The initial results showed no significant differences between structural and electronic properties. On the other hand, studies of the geometry of molecular clusters with both compounds revealed significant differences. Melaleucic acid clusters were shown to be stable enough to influence the substrate-protein interaction, unlike betulinic acid, which was unable to form clusters comparable to melaleucic acid ones. The present study suggests the molecular clusters as a new factor that has a great influence on the mechanism of biomolecular activity.

Research paper thumbnail of Theoretical Study of Metalloporphyrins Oxo-Dimers With Metals of the First and Second Transition Series

In this work were analyzed the structural properties of metalloporphyrins dimmers, with transitio... more In this work were analyzed the structural properties of metalloporphyrins dimmers, with transition metals, in which the monomers are aggregated through an oxo bridge. Five different basic structural conformations were found. The correlation of them with electronic structure of the monomers were observed. It was used the quantum method INDO.