Standard

DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal. / Garkusha, Nadezhda A.; Anikeeva, Oksana P.; Bayıl, Imren et al.
In: Journal of the Indian Chemical Society, Vol. 100, No. 3, 100926, 01.03.2023.

Research output: Contribution to journal › Article › peer-review

Harvard

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, vol. 100, no. 3, 100926. https://doi.org/10.1016/j.jics.2023.100926

APA

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

Vancouver

Garkusha NA, Anikeeva OP, Bayıl I, Taskin-Tok T, Safin DA. DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal. Journal of the Indian Chemical Society. 2023 Mar 1;100(3):100926. doi: 10.1016/j.jics.2023.100926

Author

Garkusha, Nadezhda A. ; Anikeeva, Oksana P. ; Bayıl, Imren et al. / DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal. In: Journal of the Indian Chemical Society. 2023 ; Vol. 100, No. 3.

BibTeX

@article{933e50d026894d8ca2f4da406fb84452,
title = "DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal",
abstract = "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.",
author = "Garkusha, {Nadezhda A.} and Anikeeva, {Oksana P.} and Imren Bayıl and Tugba Taskin-Tok and Safin, {Damir A.}",
note = "The numerical calculations were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources).",
year = "2023",
month = mar,
day = "1",
doi = "10.1016/j.jics.2023.100926",
language = "English",
volume = "100",
journal = "Journal of the Indian Chemical Society",
issn = "0019-4522",
publisher = "Elsevier BV",
number = "3",

}

RIS

TY - JOUR

T1 - DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal

AU - Garkusha, Nadezhda A.

AU - Anikeeva, Oksana P.

AU - Bayıl, Imren

AU - Taskin-Tok, Tugba

AU - Safin, Damir A.

N1 - The numerical calculations were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources).

PY - 2023/3/1

Y1 - 2023/3/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?partnerID=8YFLogxK&scp=85147587576

UR - https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=tsmetrics&SrcApp=tsm_test&DestApp=WOS_CPL&DestLinkType=FullRecord&KeyUT=000944340100001

U2 - 10.1016/j.jics.2023.100926

DO - 10.1016/j.jics.2023.100926

M3 - Article

VL - 100

JO - Journal of the Indian Chemical Society

JF - Journal of the Indian Chemical Society

SN - 0019-4522

IS - 3

M1 - 100926

ER -

ID: 35500317