In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

Raihan Kenji Rizqillah; Jaka Fajar Fatriansyah; Fadilah; Sulhadi; Siti Wahyuni; Muhammad Arif Sudirman; Helya Chafshoh Nafisah; Sukma Dewi Lestari

doi:10.1051/bioconf/20214107002

In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

Raihan Kenji Rizqillah, Jaka Fajar Fatriansyah, Fadilah, Sulhadi, Siti Wahyuni, Muhammad Arif Sudirman, Helya Chafshoh Nafisah, Sukma Dewi Lestari

Department of Metallurgical and Material Engineering

Research output: Contribution to journal › Conference article › peer-review

1 Citation (Scopus)

Abstract

In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.

Original language	English
Article number	07002
Journal	BIO Web of Conferences
Volume	41
DOIs	https://doi.org/10.1051/bioconf/20214107002
Publication status	Published - 22 Dec 2021
Event	4th International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering, BioMIC 2021 - Virtual, Online, Indonesia Duration: 6 Oct 2021 → 7 Oct 2021

Keywords

Andrographis paniculata
In silico molecular docking
molecular dynamics
Remdesivir
SARS-CoV-2

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10.1051/bioconf/20214107002

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Rizqillah, R. K., Fatriansyah, J. F., Fadilah, Sulhadi, Wahyuni, S., Sudirman, M. A., Nafisah, H. C., & Lestari, S. D. (2021). In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease. BIO Web of Conferences, 41, Article 07002. https://doi.org/10.1051/bioconf/20214107002

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title = "In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease",

abstract = "In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.",

keywords = "Andrographis paniculata, In silico molecular docking, molecular dynamics, Remdesivir, SARS-CoV-2",

author = "Rizqillah, {Raihan Kenji} and Fatriansyah, {Jaka Fajar} and Fadilah and Sulhadi and Siti Wahyuni and Sudirman, {Muhammad Arif} and Nafisah, {Helya Chafshoh} and Lestari, {Sukma Dewi}",

note = "Publisher Copyright: {\textcopyright} The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/).; 4th International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering, BioMIC 2021 ; Conference date: 06-10-2021 Through 07-10-2021",

year = "2021",

month = dec,

day = "22",

doi = "10.1051/bioconf/20214107002",

language = "English",

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journal = "BIO Web of Conferences",

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Rizqillah, RK, Fatriansyah, JF, Fadilah, Sulhadi, Wahyuni, S, Sudirman, MA, Nafisah, HC & Lestari, SD 2021, 'In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease', BIO Web of Conferences, vol. 41, 07002. https://doi.org/10.1051/bioconf/20214107002

In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease. / Rizqillah, Raihan Kenji; Fatriansyah, Jaka Fajar; Fadilah et al.
In: BIO Web of Conferences, Vol. 41, 07002, 22.12.2021.

Research output: Contribution to journal › Conference article › peer-review

TY - JOUR

T1 - In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

AU - Rizqillah, Raihan Kenji

AU - Fatriansyah, Jaka Fajar

AU - Fadilah,

AU - Sulhadi,

AU - Wahyuni, Siti

AU - Sudirman, Muhammad Arif

AU - Nafisah, Helya Chafshoh

AU - Lestari, Sukma Dewi

N1 - Publisher Copyright: © The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/).

PY - 2021/12/22

Y1 - 2021/12/22

N2 - In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.

AB - In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy-7, 8, 2', 3'-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.

KW - Andrographis paniculata

KW - In silico molecular docking

KW - molecular dynamics

KW - Remdesivir

KW - SARS-CoV-2

UR - http://www.scopus.com/inward/record.url?scp=85169039022&partnerID=8YFLogxK

U2 - 10.1051/bioconf/20214107002

DO - 10.1051/bioconf/20214107002

M3 - Conference article

AN - SCOPUS:85169039022

SN - 2273-1709

VL - 41

JO - BIO Web of Conferences

JF - BIO Web of Conferences

M1 - 07002

T2 - 4th International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering, BioMIC 2021

Y2 - 6 October 2021 through 7 October 2021

ER -

Rizqillah RK, Fatriansyah JF, Fadilah, Sulhadi, Wahyuni S, Sudirman MA et al. In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease. BIO Web of Conferences. 2021 Dec 22;41:07002. doi: 10.1051/bioconf/20214107002

In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2',3'-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

Abstract

Keywords

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