دورية أكاديمية
DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal
| العنوان: | DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal |
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| المؤلفون: | Garkusha, N. A., Anikeeva, O. P., Bayıl, I., Taskin-Tok, T., Safin, D. A. |
| المصدر: | Journal of the Indian Chemical Society |
| بيانات النشر: | Elsevier B.V. |
| سنة النشر: | 2023 |
| المجموعة: | Ural Federal University (URFU): ELAR / Уральский федеральный университет: электронный архив УрФУ |
| مصطلحات موضوعية: | COMPUTATIONAL STUDY, COVID-19, DENSITY FUNCTIONAL THEORY, MOLECULAR DOCKING, MOLECULAR DYNAMICS SIMULATION, PYRIDINE, ALDEHYDE, NICKEL, PYRIDOXAL, RIBONUCLEASE, VIRUS SPIKE PROTEIN, ABSORPTION SPECTROSCOPY, ARTICLE, COMPUTER MODEL, CORONAVIRUS DISEASE 2019, CRYSTAL STRUCTURE, DRUG BIOAVAILABILITY, GASTROINTESTINAL ABSORPTION, HYDROGEN BOND, MOLECULAR DYNAMICS, MONKEYPOX VIRUS, NONHUMAN, NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, PHYSIOLOGICAL PROCESS, SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 |
| الوصف: | 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). |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| ردمك: | 978-0-00-944340-4 0-00-944340-1 |
| تدمد: | 0019-4522 |
| العلاقة: | 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.2023.100926Test; 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.2023.100926Test; 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=ab6edf6cbaa9ba0acc97485bd10373dcTest; https://doi.org/10.1016/j.jics.2023.100926Test; http://elar.urfu.ru/handle/10995/131158Test; 85147587576; 000944340100001 |
| DOI: | 10.1016/j.jics.2023.100926 |
| الإتاحة: | https://doi.org/10.1016/j.jics.2023.100926Test http://elar.urfu.ru/handle/10995/131158Test |
| حقوق: | info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.67140903 |
| قاعدة البيانات: | BASE |
| ردمك: | 9780009443404 0009443401 |
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| تدمد: | 00194522 |
| DOI: | 10.1016/j.jics.2023.100926 |