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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
Published: Penerbit UTHM 2018
Subjects:
TP248.13-248.65 Biotechnology
Online Access:http://eprints.uthm.edu.my/3646/1/AJ%202018%20%28707%29%20Molecular%20Docking%20and%20Dynamics%20%28MD%29%20simulation%20of%206-gingerol%20and%206-shogaol%20against%20human%20Estrogen%20Receptor%20Alpha%20%28ER%C9%91%29.pdf
http://eprints.uthm.edu.my/3646/
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spelling my.uthm.eprints.36462021-11-21T04:51:37Z http://eprints.uthm.edu.my/3646/ 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 TP248.13-248.65 Biotechnology 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 text en http://eprints.uthm.edu.my/3646/1/AJ%202018%20%28707%29%20Molecular%20Docking%20and%20Dynamics%20%28MD%29%20simulation%20of%206-gingerol%20and%206-shogaol%20against%20human%20Estrogen%20Receptor%20Alpha%20%28ER%C9%91%29.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). pp. 119-127. ISSN 2229-838X
institution Universiti Tun Hussein Onn Malaysia
building UTHM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Tun Hussein Onn Malaysia
content_source UTHM Institutional Repository
url_provider http://eprints.uthm.edu.my/
language English
topic TP248.13-248.65 Biotechnology
spellingShingle TP248.13-248.65 Biotechnology
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://eprints.uthm.edu.my/3646/1/AJ%202018%20%28707%29%20Molecular%20Docking%20and%20Dynamics%20%28MD%29%20simulation%20of%206-gingerol%20and%206-shogaol%20against%20human%20Estrogen%20Receptor%20Alpha%20%28ER%C9%91%29.pdf
http://eprints.uthm.edu.my/3646/
_version_ 1738581150478106624
score 13.211869

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