Navegando por Assunto "Molecular Docking"

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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)
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.