Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)

Simulation and computational analysis of 6-gingerol and 6-shogaol is done to evaluate their binding affinity against ERα. Active site prediction was done using Computed Atlas of Surface Topography of Proteins (CASTp) to determine the binding pocket of ERα. Molecular docking and molecular dynamics (M...

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Main Authors:	Sharif, Faez, Mohd Yunus, Afdzal, Saedudin, RD Rohmat, Abdul Hamid, Azzmer Azzar, Kasim, Shahreen
Format:	Article
Language:	English English English
Published:	Penerbit UTHM 2018
Subjects:	Q Science (General)
Online Access:	http://irep.iium.edu.my/68126/ http://irep.iium.edu.my/68126/ http://irep.iium.edu.my/68126/1/68126_Molecular%20docking%20and%20dynamics%20%28MD%29.pdf http://irep.iium.edu.my/68126/2/68126_Molecular%20docking%20and%20dynamics%20%28MD%29_SCOPUS.pdf http://irep.iium.edu.my/68126/3/68126_Molecular%20docking%20and%20dynamics%20%28MD%29_WOS.pdf

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spelling	iium-681262019-02-13T04:12:18Z http://irep.iium.edu.my/68126/ Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ) Sharif, Faez Mohd Yunus, Afdzal Saedudin, RD Rohmat Abdul Hamid, Azzmer Azzar Kasim, Shahreen Q Science (General) Simulation and computational analysis of 6-gingerol and 6-shogaol is done to evaluate their binding affinity against ERα. Active site prediction was done using Computed Atlas of Surface Topography of Proteins (CASTp) to determine the binding pocket of ERα. Molecular docking and molecular dynamics (MD) simulation were done to assess the binding affinity and stability of the ligand-ERα complexes formed. Results showed that Tamoxifen have lowest binding energy (-9.61 ± 0.39 kcal/mol) followed by 6-gingerol (-6.59 ± 0.29 kcal/mol) and 6-shogaol (-5.70 ± 0.36 kcal/mol). Inhibition constant (Ki) range of TMX-ERα was found to be drastically lower than both 6GN-ERα and 6SG-ERα. Based on the difference in the binding energy range and inhibition constant, 6-gingerol and 6-shogaol showed less potential in substituting tamoxifen for the inhibition of ERɑ. Docking complexes formed was supported with stability in root mean square deviation (RMSD) and total binding energy of the complexes. The study is concluded that 6-gingerol have high level of interactions with the ERα active site in terms of hydrogen bonding whereas hydrophobic interactions are observed with both 6-gingerol and 6-shogaol. However, both ginger bioactive compounds poses low potential as substitute in comparison with tamoxifen against ERα. Penerbit UTHM 2018 Article PeerReviewed application/pdf en http://irep.iium.edu.my/68126/1/68126_Molecular%20docking%20and%20dynamics%20%28MD%29.pdf application/pdf en http://irep.iium.edu.my/68126/2/68126_Molecular%20docking%20and%20dynamics%20%28MD%29_SCOPUS.pdf application/pdf en http://irep.iium.edu.my/68126/3/68126_Molecular%20docking%20and%20dynamics%20%28MD%29_WOS.pdf Sharif, Faez and Mohd Yunus, Afdzal and Saedudin, RD Rohmat and Abdul Hamid, Azzmer Azzar and Kasim, Shahreen (2018) Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ). International Journal of Integrated Engineering, 10 (6 Special Issue 2018: Data Information Engineering). pp. 119-127. ISSN 2229-838X E-ISSN 2600-7916 http://penerbit.uthm.edu.my/ojs/index.php/ijie/article/view/2771/1770
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English English
topic	Q Science (General)
spellingShingle	Q Science (General) Sharif, Faez Mohd Yunus, Afdzal Saedudin, RD Rohmat Abdul Hamid, Azzmer Azzar Kasim, Shahreen Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)
description	Simulation and computational analysis of 6-gingerol and 6-shogaol is done to evaluate their binding affinity against ERα. Active site prediction was done using Computed Atlas of Surface Topography of Proteins (CASTp) to determine the binding pocket of ERα. Molecular docking and molecular dynamics (MD) simulation were done to assess the binding affinity and stability of the ligand-ERα complexes formed. Results showed that Tamoxifen have lowest binding energy (-9.61 ± 0.39 kcal/mol) followed by 6-gingerol (-6.59 ± 0.29 kcal/mol) and 6-shogaol (-5.70 ± 0.36 kcal/mol). Inhibition constant (Ki) range of TMX-ERα was found to be drastically lower than both 6GN-ERα and 6SG-ERα. Based on the difference in the binding energy range and inhibition constant, 6-gingerol and 6-shogaol showed less potential in substituting tamoxifen for the inhibition of ERɑ. Docking complexes formed was supported with stability in root mean square deviation (RMSD) and total binding energy of the complexes. The study is concluded that 6-gingerol have high level of interactions with the ERα active site in terms of hydrogen bonding whereas hydrophobic interactions are observed with both 6-gingerol and 6-shogaol. However, both ginger bioactive compounds poses low potential as substitute in comparison with tamoxifen against ERα.
format	Article
author	Sharif, Faez Mohd Yunus, Afdzal Saedudin, RD Rohmat Abdul Hamid, Azzmer Azzar Kasim, Shahreen
author_facet	Sharif, Faez Mohd Yunus, Afdzal Saedudin, RD Rohmat Abdul Hamid, Azzmer Azzar Kasim, Shahreen
author_sort	Sharif, Faez
title	Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)
title_short	Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)
title_full	Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)
title_fullStr	Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)
title_full_unstemmed	Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)
title_sort	molecular docking and dynamics (md) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (erɑ)
publisher	Penerbit UTHM
publishDate	2018
url	http://irep.iium.edu.my/68126/ http://irep.iium.edu.my/68126/ http://irep.iium.edu.my/68126/1/68126_Molecular%20docking%20and%20dynamics%20%28MD%29.pdf http://irep.iium.edu.my/68126/2/68126_Molecular%20docking%20and%20dynamics%20%28MD%29_SCOPUS.pdf http://irep.iium.edu.my/68126/3/68126_Molecular%20docking%20and%20dynamics%20%28MD%29_WOS.pdf
first_indexed	2023-09-18T21:36:42Z
last_indexed	2023-09-18T21:36:42Z
_version_	1777412868172414976

Molecular docking and dynamics (MD) simulation of 6-gingerol and 6-shogaol against human estrogen receptor alpha (ERɑ)

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