Navegando por Assunto "Molecular dynamics"

Agora exibindo 1 - 10 de 10

Acesso aberto (Open Access)
Dinâmica molecular de armazenamento de H2 em nanotubos de carbono sob ação de campo elétrico externo
(Universidade Federal do Pará, 2016-01-27) AIRES, Júlio Cesar Nunes; CHAVES NETO, Antônio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
Several thermodynamic properties were analyzed through computer simulations systems, in which we used a carbon nanotube a gas molecule (H2), the very low initial temperature of 10-3K order. This H2 molecule was chosen because of its properties are of great application in different branches of study, the physical sciences, chemical and biological. The H2 molecule is individually relaxed inside and outside the nanotube during simulations. Each system was under the influence of a uniform electric field parallel to the carbon nanotube and the thermal effect on the initial temperature in the simulations generating the evanescent effect. Due to the electric field, the molecule rotates at a low temperature in orbit about the carbon nanotube while increasing the value of the electric field permitted the variation of the radius of the orbit atoms. The calculated amounts were the following: kinetic energy, potential energy, the total energy, temperature variation in situ, the molar entropy and the mean radius of the orbit atoms. The data suggest the action of the electric field is sufficient only to generate the evanescent attractive potential and this system can be used as a sensor selector atoms.
Acesso aberto (Open Access)
O estudo da docagem e dinâmica molecular de potenciais fármacos: rodatina, scedapina C e cequinadolina A, utilizados no tratamento da SARS-COV-2
(Universidade Federal do Pará, 2022-05-06) LIMA, Antonio Sanderlei dos Santos; ALMEIDA, Ossalin de; http://lattes.cnpq.br/7040173036131516; HTTPS://ORCID.ORG/0000-0003-3895-0952; CHAVES NETO, Antônio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
Due to the study of new drugs to combat the SARS-COV-2 virus, which is causing the COVID-19 pandemic. In this work, we address the use of three drugs (Rhodatin, Scedapin C and Scequinadoline A) as possible inhibitors of SARS-CoV-2, as they have several interactive properties, showing potential to be used in the treatment of COVID19 disease. Molecular docking provided information about the affinity energy which was -8.186, -9.617, -7.866, -7.601, -7.527 kcal/mol, for the best conformations with Scequinadoline A. Molecular couplings and affinity energy showed the residues of the site macrostructures, and analyzed the electrostatic potential map to predict some promising candidates for virus antagonists. Molecular dynamics techniques were used, where the targets were the external structures of the virus, but specifically the envelope protein, main protease, Spike glycoprotein. Using the GROMACS 2021.2 modules, the results showed that the ligands have characteristics of interaction over time. Molecular dynamics provided values between 1.5 and 4.5Å for the mean square deviation of atomic positions. Among the results obtained through molecular dynamics, it was noted that the hydrogen bonds, when compared to the calculation of the square root of the mean square deviation, underwent a change in the amount of hydrogen bonds in the bonding process, according to the proximity of the ligand used to filter out unrealistic poses in the snap, and also improved the accuracy of binding energy calculation. Analysis of molecular couplings showed that the S-gly active site residues strongly interacted with the three drugs. The reuse of these drugs in the fight against SARSCoV-2 may be candidates via virus antagonists, which if confirmed through experimental approaches, can contribute to the resolution of the global crisis of the COVID-19 pandemic.
Acesso aberto (Open Access)
Estudo do mecanismo conformacional da proteína 3-hidroxi-3- metilglutaril Coenzima A Redutase (HMGR) com as estatinas e substrato através de Dinâmica Molecular, PCA e Energia Livre
(Universidade Federal do Pará, 2017-08-03) COSTA, Clauber Henrique Souza da; SILVA, Jerônimo Lameira; http://lattes.cnpq.br/7711489635465954; https://orcid.org/0000-0001-7270-1517
Cholesterol is a substance of paramount importance for all animals. However, its high level in the human body is linked to the two major diseases that kill the world: ischemic heart disease and stroke. One of the synthetic drugs used in the treatment of hypercholesterolemia are statins, inhibitors of 3-hydroxy-3-methylglutaryl Cozyme A reductase (HMGR), which act primarily on the liver by inhibiting a conversion of the HMG-CoA substrate into mevalonic acid, which is the metabolite Cholesterol precursor. Studies Molecular Dynamics (MD) combined with Principal Component Analysis (PCA) were performed to verify the mechanism of the changes in the Cterminal Flap domain form (residues His861, Leu862, Val863, Lys864, Ser865 and Hys866) after binding substrate and efficient statins in inhibiting the HMGR enzyme. A total of 500 ns of MD simulation time were performed in this study. Binding Free Energies calculations were used, which estimate that the structural mechanism of the Flap is related to an action of the HMGR protein, since domain control or access to the active site of the enzyme. The results also show that the structural modification of Flap increases the energy contribution of the system by involving larger interactions with catalytic residues and, consequently, an ability to inhibit cholesterol production, as observed for the catalytic His866, which has a very favorable contribution when the Flap is in the closed state, with energy of -14,802 Kcal/mol, and when the Flap passes to the open state the contribution is less favorable, with -1,022 Kcal/mol, for 1 inhibitor, showing that in the closed state the catalytic residue is directly involved and contributes in a favorable way to the system, leading to a better understanding of the conformational changes of HMGR after a binding of statin derivatives and HMG-CoA substrate.
Acesso aberto (Open Access)
Interações de carvão ativado, fármacos e libidibia ferrea contra o vírus SARS-COV-2
(Universidade Federal do Pará, 2021-08-25) ARAÚJO, Herica Daniele Costa; CHAVES NETO, Antonio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
The high rates of infection and mortality from Severe Acute Respiratory Syndrome (SARS-CoV-2) or COVID-19 infection has caused severe socio-economic impacts worldwide. Transmission basically occurs through contact with bodily fluids. In the airways, by spraying droplets and/or aerosols suspended in the environment and/or deposited on surfaces. The effectiveness of using effective masks to contain contagion is a necessity. The present work evaluated the adsorption capacity of filters containing activated carbon and modified activated carbon during nanofiltration in masks with greater efficiency. The possible interactions between Spike (S) and membrane (M) proteins with activated carbon oxygen non-modified and activated carbon oxygen modified were evaluated by docking and molecular dynamics. Autodock Vina 4.2.6 and AMBER 16 software were used in the simulations. Results of the formed ligand-receptor complexes had the affinity energy, the root mean-square deviation (RMSD) and the Gibbs free energy of binding evaluated. Activated carbon oxygen modified showed greater spontaneity in protein interactions. And, another front to combat the coronavirus was addressed in this work: the treatment of the infected, as evaluations of the inhibitory action of the active principles of retroviral drugs known in the literature, as well as new compounds from the Brazilian Amazon flora were docked with proteins S, M and envelope (E). Three drugs (Colchicine, Nafamostat and Selinexor) and three compounds originated from Libidibia ferrea or Caesalpinia ferrea (Elagic Acid, Pauferrol A and Sitosterol) interacted as ligands. And, after docking, the most favorable affinity energies of the active sites established between ligands and receptors were graphically demonstrated. The docking was carried out through the SwissDock server. The interactions of the ligands Pauferrol A and Colchicine on the proteins contained in the viral surface were highlighted.
Acesso aberto (Open Access)
Interações de ftalocianinas de Co, Cu e não metálicas com estruturas externas de SARS-CoV-2 utilizando docking e dinâmica molecular
(Universidade Federal do Pará, 2021-12-22) ALENCAR, Wilson Luna Machado; CHAVES NETO, Antonio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
Acesso aberto (Open Access)
Interações de Quantum Dot com estruturas externas de vírus Nipah utilizando docking e dinâmica molecular
(Universidade Federal do Pará, 2023-01-30) ALMEIDA, Aguinaldo Pantoja de; OLIVEIRA, Mozaniel Santana de; http://lattes.cnpq.br/0810227136654245; HTTPS://ORCID.ORG/0000-0002-4076-2443; CHAVES NETO, Antônio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
Performing the interaction of the outermost protein of the Nipah virus with fourteen structures with possible potential for the emission of quantum dots, using anchoring and molecular dynamics, using molecular docking platforms: CB Docking, Swiss DOCK, AutoDock Vina 4.2.6 to perform a comparison of results explaining the best values, in addition to using Gromacs 2022 to make ligand trajectories in relation to time. The mostly hydrophobic complexes at the receptor binding site. The tolerance energy results tolerated the partial loads of the tips which showed better stability, the RMSD results also respected this premise. Thus, the set formed by combining proteins with a quantum dot has the potential to more efficiently adsorbing of the protein components of the virus. Molecular dynamics and docking studies and verification of binding energy revealed strong and stable binding between para QD K and QD-G and QD-F with the macrostructure of NIPAH virus. It was established in the docking studies, that the binders have emission energy scores of -13,658 kcal/mol, -13.6 kcal/mol, -13.9 kcal/mol, for K, G and F respectively. The same result was applied in the Gibbs free energy verification study with values for F of 239.00 kcal/mol, G of 246.65 kcal/mol and K of 259.52 kcal/mol.
Acesso aberto (Open Access)
Investigação computacional de bromo-ariloxi-2-acetamida etil-benzimidazólicos como inibidores não-peptídicos da proteinase cruzaína de trypanosoma cruzi
(Universidade Federal do Pará, 2017-11-17) FERREIRA, Fábio Jorge de Nazaré; ALENCAR, Nelson Alberto Nascimento de; http://lattes.cnpq.br/3035968396241810; https://orcid.org/ 0000-0002-5763-7024; CARNEIRO, Agnaldo da Silva; http://lattes.cnpq.br/8915348778787525
Chagas’ disease is an infection caused by the Trypanosoma Cruzi flagellated protozoan transmitted by insects (gnat) known in Brazil as “barbeiro” (barber). In the Amazon region, studies have shown that oral contamination has been frequent. The only available drugs for the treatment of Chagas’ disease - Benzonidazole (Rochagan R , Roche) and Nifurtimox (Lampit R , Bayer) - have shown limited efficiency and severe side effects. Cruzain is an enzyme present at all stages of the life cycle of T. cruzi and is the most abundant of the family of papain cysteine proteases found in the parasite, being a promising enzymatic target for the design and development of inhibitors against the disease. Non-peptidic non covalently bound to the enzyme were synthesized and evaluated biologically in vitro and in vivo by Ferreira et al. (2014) analogs of the 8D (or B95) leader compound (crystallographic), yielding a series of active compounds, of which the most powerful are: 8K, 8L and 8R. This work investigated the potential interactions and energies of the cruzain (PDB code: 3KKU) complexed with these four ligands by means of computational tools in order to help elucidate their potential inhibition activity in this enzyme. The computational protocol (parameters, topologies, coordinates, minimizations, thermalizations and productions) was the same for each system. In the final stage of molecular dynamics (MD) production, each system was simulated for a period of 100 ns, to which the mean square deviation (RMSD) stability values of the enzyme and the marked change in 8L ligand conformation were analyzed. The quality of the simulation was also evaluated through potential, kinetic and total energy, volume and temperature graphs. Interactions of hydrogen bonds of the ligands with some amino acid residues belonging to the catalytic site were analyzed. The interaction between the ASP161 and the 8R ligand is emphasized, being ratified by the energy decomposition by residue showing that ASP161 has the best contribution. In terms of binding free energy, the ∆Gtotal follows the experimental trend, pointing the 8R ligand as the most favorable to the reaction having a theoretical value of -30.04kcal.mol−1. This spontaneity is ratified by means of the values obtained with the SIE method, whose theoretical value was -7.54 kcal.mol−1. The results of this work should favor the optimization of compound 8R or development of a series of analogs of this molecule in order to be used as a possible drug for the treatment of Chagas’ disease.
Acesso aberto (Open Access)
Nanofiltração de hormônios e metais pesados em nanotubos de carbono e de boro por dinâmica molecular
(Universidade Federal do Pará, 2020-02-27) CAVALEIRO, Rosely Maria dos Santos; CHAVES NETO, Antonio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
Sewage treatment stations receive various effluents and perform the selective filtering of molecules that can, if they persist in the water, contaminate or the environment. Selection processes initiated by larger sections down to nanoparticles. Among the molecules called emerging contaminants are hormones and heavy metals that impact on graves consequences on organisms by endocrine-disrupting action. When surface waters receive effluents with traces of contamination and hormones or heavy metals, they will cause diseases in living beings, especially in pregnant women and children, as well as interfering in the chains of DNA, also affecting the next generations. This study of molecular tests carried out with nanofiltration: water with hormones and water with heavy metals filtered through carbon nanotubes and boron nitrogen, under the action of 8 (eight) electric fields lasting 100 (hundred) ps. The study hormones were: estrone, estradiol, estriol, progesterone, ethinylestradiol, levonorgestrel, diethylbestrol, and heavy metal ions: lead, cadmium, iron, zinc, and mercury. Each of the hormone molecules and the heavy metal were filtered through two nanotubes, under the same boundary conditions. The selected results that allow creating nanofiltration systems that can be removed micropollutants using carbon nanotubes or boron nitride activated by the uniform electrical fields from 10-5 a.u. to 10-8 a.u.
Acesso aberto (Open Access)
Sensores de narcóticos, gás natural e syngás utilizando nanotubos de carbono sob ação de campo elétrico externo
(Universidade Federal do Pará, 2021-02-15) AIRES, Júlio Cesar Nunes; CHAVES NETO, Antonio Maia de Jesus; http://lattes.cnpq.br/3507474637884699; https://orcid.org/0000-0002-9730-3512
This work presents an analysis of the molecular dynamics between several illicit drugs: benzoylmethylecgonine, diacetylmorphine, 3,4 methylenedioxymethamphetamine, D-Deoxefedrine, lysergic acid diethylamide and, interacting with a section of carbon nanotubes at low initial temperature, corresponding to 10-3 K, and under a uniform electric field, like a drug detection system. In addition to the analysis of the behavior of natural gas molecules and SYNGAS interacting with a carbon nanotube at an initial simulation temperature of 300K, with all systems being relaxed by 50 ps outside the carbon nanotube, describing each possible arrangement for capture; a constant external electric field was then applied to the systems, longitudinally, along the length of the carbon nanotube, promoting an evanescent effect, capable of trapping them orbiting the carbon nanotube. Simulations for electric field intensities within a range of 10-5 to 10-1 a.u. were performed, to verify the behavior of drugs, while for the molecules that comprise Natural Gas and SYNGAS, a range of 10-8 to 10-1 a.u. was adopted. Average orbital radii were estimated, in addition to a number of thermodynamic properties. Our results indicate that the combination of a uniform external electric field and van der Waals interactions in a carbon-derived nanotube is enough to create an evanescent field of attractive potential, modeling it as a system for the detection of temperature and drug rays .
Acesso aberto (Open Access)
Simulação computacional da adsorção dos poluentes benzeno, tolueno e p-xileno sobre carvão ativado
(Universidade Federal do Pará, 2013-12-27) COSTA, Wanessa Almeida da; MARTELLI, Marlice Cruz; http://lattes.cnpq.br/1213009262936026; BRASIL, Davi do Socorro Barros; http://lattes.cnpq.br/0931007460545219
The greatest problems of groundwater and soil contamination are assigned to monoaromatic hydrocarbons which are the most soluble and the most mobile constituents of the fraction of certain substances, such as gasoline. To remove these contaminants, adsorption by activated carbon is the most widely used method, for it presents a significant ability to adsorb organic low molecular weight components, such as benzene, toluene and p-xylene. In this work, we verified the adsorption on activated carbon thereof via computer simulation. As base, we used the postulated model of charcoal prepared by Bourke et al. (2007). Several steps have been completed since the design of the structures of carbon and pollutants to the molecular dynamics phase. For the conformational analysis of the coal’s structure, it was used the semi-empirical method PM3 and for the molecular dynamics technique, the AMBER force field FF99SB. The structure went through a heating at constant pressure until it reaches a final temperature of 298K (25ºC), being its information collected every 50 ps. Subsequently, the structure was submited to equilibrium system at a constant temperature of 298K (25ºC) for 500ps for its information can be analyzed. Finally, the system was then submited to molecular dynamics during 30ns. After analyzing the results, it was found that the ether, lactone and carbonyl (ketone) groups present in the structure of activated carbon provide to it acid feature and because of this and its consequent negative surface charge, adsorption has become viable once the pollutants had positive surface charge, which supports the view that is already known about this type of phenomenon.