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DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine

In this work, quantum chemical descriptors and a vibrational analysis of 4-Phenylpyrimidine (4-PPy) were also investigated. Through conformational analysis, the most stable conformer can be determined. The geometry of the molecular structure was optimized by using the density functional theory (DFT)...

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Autor principal: Celik, Sibel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier B.V. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9803264/
https://www.ncbi.nlm.nih.gov/pubmed/36619799
http://dx.doi.org/10.1016/j.molstruc.2022.134895
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author Celik, Sibel
author_facet Celik, Sibel
author_sort Celik, Sibel
collection PubMed
description In this work, quantum chemical descriptors and a vibrational analysis of 4-Phenylpyrimidine (4-PPy) were also investigated. Through conformational analysis, the most stable conformer can be determined. The geometry of the molecular structure was optimized by using the density functional theory (DFT) at the B3LYP/6–311++G(d,p) level. The theoretically obtained FT-IR and FT-Raman spectral data agree with the experimental results. UV–Vis was done in the gas phase along with different solvents by the TD-DFT method and the PCM solvent model. Molecular electrostatic potential, natural bond orbital analysis, nonlinear optical properties, and global chemical reactivity parameters were described through the DFT method. Besides, the chemical implications of a molecule were explained using an electron localization function and a local orbital locator. We attempted to detect the antiviral activity of the 4-PPy compound by predicting molecular docking into coronavirus 2 (SARS-n-CoV-2) protein structures (6LU7, 6M03, and 6W63), because COVID-19 is known to have serious adverse effects in all areas of human life worldwide, and possible drugs need to be investigated for this. The results of the docking simulation demonstrate good affinities for binding to the receptors.
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spelling pubmed-98032642023-01-04 DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine Celik, Sibel J Mol Struct Article In this work, quantum chemical descriptors and a vibrational analysis of 4-Phenylpyrimidine (4-PPy) were also investigated. Through conformational analysis, the most stable conformer can be determined. The geometry of the molecular structure was optimized by using the density functional theory (DFT) at the B3LYP/6–311++G(d,p) level. The theoretically obtained FT-IR and FT-Raman spectral data agree with the experimental results. UV–Vis was done in the gas phase along with different solvents by the TD-DFT method and the PCM solvent model. Molecular electrostatic potential, natural bond orbital analysis, nonlinear optical properties, and global chemical reactivity parameters were described through the DFT method. Besides, the chemical implications of a molecule were explained using an electron localization function and a local orbital locator. We attempted to detect the antiviral activity of the 4-PPy compound by predicting molecular docking into coronavirus 2 (SARS-n-CoV-2) protein structures (6LU7, 6M03, and 6W63), because COVID-19 is known to have serious adverse effects in all areas of human life worldwide, and possible drugs need to be investigated for this. The results of the docking simulation demonstrate good affinities for binding to the receptors. Elsevier B.V. 2023-04-05 2022-12-30 /pmc/articles/PMC9803264/ /pubmed/36619799 http://dx.doi.org/10.1016/j.molstruc.2022.134895 Text en © 2022 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Celik, Sibel
DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine
title DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine
title_full DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine
title_fullStr DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine
title_full_unstemmed DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine
title_short DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine
title_sort dft investigations and molecular docking as potent inhibitors of sars-cov-2 main protease of 4-phenylpyrimidine
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9803264/
https://www.ncbi.nlm.nih.gov/pubmed/36619799
http://dx.doi.org/10.1016/j.molstruc.2022.134895
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