DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal
Электронный научный архив УРФУ
Информация об архиве | Просмотр оригинала| Поле | Значение | |
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DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal
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| Автор |
Garkusha, N. A.
Anikeeva, O. P. Bayıl, I. Taskin-Tok, T. Safin, D. A. |
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| Тематика |
COMPUTATIONAL STUDY
COVID-19 DENSITY FUNCTIONAL THEORY MOLECULAR DOCKING MOLECULAR DYNAMICS SIMULATION PYRIDINE ALDEHYDE NICKEL PYRIDINE PYRIDOXAL RIBONUCLEASE VIRUS SPIKE PROTEIN ABSORPTION SPECTROSCOPY ARTICLE COMPUTER MODEL CORONAVIRUS DISEASE 2019 CRYSTAL STRUCTURE DENSITY FUNCTIONAL THEORY DRUG BIOAVAILABILITY GASTROINTESTINAL ABSORPTION HYDROGEN BOND MOLECULAR DOCKING MOLECULAR DYNAMICS MONKEYPOX VIRUS NONHUMAN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY PHYSIOLOGICAL PROCESS SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 |
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| Описание |
We report in silico studies of pyridoxal, which is of interest both as a precursor for further functionalization due to the presence of the aldehyde functionality, as well as a bioactive compound. So far, the crystal structure of pyridoxal has not been reported and, thus, we have optimized its structure both under water solvation and in gas phase using the DFT calculations. Under water solvation conditions the optimized structure of pyridoxal is 7.62 kcal/mol more favorable in comparison to that in gas phase. The DFT calculations were also applied to verify optical and electronic properties of the optimized structure of pyridoxal in water. The HOMO and LUMO were revealed to subtract a set of descriptors of the so-called global chemical reactivity as well as to probe pyridoxal as a potential corrosion inhibitor for some important metals used in implants. The title compound exhibits the best electron charge transfer from the molecule to the surface of Ni and Co. Some biological properties of pyridoxal were evaluated using the respective on-line tools. Molecular docking was additionally applied to study interaction of pyridoxal with some SARS-CoV-2 proteins as well as one of the monkeypox proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with nonstructural protein 15 (endoribonuclease) and Omicron Spike protein of SARS-CoV-2. Pyridoxal was found to be also active against the studied monkeypox protein. Interaction of pyridoxal with nonstructural protein 15 (endoribonuclease) was further studied using molecular dynamics simulation. © 2023 Indian Chemical Society
The numerical calculations were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). |
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| Дата |
2024-04-05T16:39:31Z
2024-04-05T16:39:31Z 2023 |
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| Тип |
Article
Journal article (info:eu-repo/semantics/article) |info:eu-repo/semantics/publishedVersion |
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| Идентификатор |
Garkusha, NA, Anikeeva, OP, Bayıl, I, Taskin-Tok, T & Safin, DA 2023, 'DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal', Journal of the Indian Chemical Society, Том. 100, № 3, 100926. https://doi.org/10.1016/j.jics.2023.100926
Garkusha, N. A., Anikeeva, O. P., Bayıl, I., Taskin-Tok, T., & Safin, D. A. (2023). DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal. Journal of the Indian Chemical Society, 100(3), [100926]. https://doi.org/10.1016/j.jics.2023.100926 0019-4522 Final All Open Access, Bronze https://www.scopus.com/inward/record.uri?eid=2-s2.0-85147587576&doi=10.1016%2fj.jics.2023.100926&partnerID=40&md5=ab6edf6cbaa9ba0acc97485bd10373dc https://doi.org/10.1016/j.jics.2023.100926 http://elar.urfu.ru/handle/10995/131158 10.1016/j.jics.2023.100926 85147587576 000944340100001 |
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| Язык |
en
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| Права |
Open access (info:eu-repo/semantics/openAccess)
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| Формат |
application/pdf
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| Издатель |
Elsevier B.V.
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| Источник |
Journal of the Indian Chemical Society
Journal of the Indian Chemical Society |
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