Navegando por Assunto "Molecular dynamics and free energy"

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Interações com nanotubos de carbono e pontos quânticos de óxido de grafeno com estruturas externas do Sars-cov-2 via simulações de dinâmica e docagem molecular
(Universidade Federal do Pará, 2023-06-02) LOBATO, Júlio César Mendes; OLIVEIRA, Mozaniel Santana de; http://lattes.cnpq.br/0810227136654245; https://orcid.org/0000-0002-4076-2443; CHAVES NETO, Antonio Maia de Jesus; Lattes: 3507474637884699
The interaction between nanoparticles and SARS-CoV-2 virus proteins was evaluated using ligands such as single-walled carbon nanotubes (NTCPUs) and receptors including envelope protein (E-pro), major protease (M-pro) and Spike glycoprotein (Sgly). Molecular docking modeling and molecular dynamics techniques were applied. Molecular dynamics revealed root mean square shift of atomic positions ranging from 0.5Å to 3.0Å. The results indicated that the zigzag nanotube showed better affinity energy, with binding free energy values of -9.48, -9.98 and -10.08 kcal/mol for E-pro, M-pro and S-gly, respectively. Furthermore, the mean square deviation of the atomic positions remained more stable for this type of nanotube, indicating a high probability of binding to the active sites of the macromolecules. Molecular couplings and binding free energy showed strong interaction between NTCPUs and residues of the S-gly active site, with values of -112.73, -94.38 and -80.49 kcal/mol for zigzag, chiral and armchair ligands, respectively. In a second step, five graphene oxide (GO) quantum dots smaller than 20 nm were used as ligands, interacting only with the spike receptors of three different strains: S-GLY-OMICRON, S-GLY-KAPPA and S-GLY-DELTA. Comparing the two ligands, it was observed that the S-GLY-OMICRON/OG-E interaction showed better affinity with Gibbs free energy of 172.2510 KJ/mol, compared to the better affinity of carbon nanotubes, S-gly/zig-zag, with ΔG of -112.73 KJ/mol. The eight proposed ligands have a high probability of binding to the active sites of the macrostructures. In conclusion, both carbon nanotubes and OG showed promise for application in SARS-CoV-2 inhibitor products, such as the development of materials for the manufacture of personal protective equipment, sprays and waterproofing solutions in general.