Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches

Stability and hydrogen bond occupancy analysis of flavonol derivative docked in DAPK1 have been carried out using molecular dynamics simulation approach. Six flavonol derivatives were docked in DAPK1 as protein target, then continued with molecular dynamics simulation. NVT and NPT ensembles were use...

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Autores principales:	Adi Tiara Zikri, Harno Dwi Pranowo, Winarto Haryadi
Formato:	article
Lenguaje:	EN
Publicado:	Department of Chemistry, Universitas Gadjah Mada 2020
Materias:	flavonol hydrogen bond occupancy molecular dynamics simulation Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/d9fb3d3a6b0742c498fdec4c2092b689
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spelling	oai:doaj.org-article:d9fb3d3a6b0742c498fdec4c2092b6892021-12-02T12:51:19ZStability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches1411-94202460-157810.22146/ijc.56087https://doaj.org/article/d9fb3d3a6b0742c498fdec4c2092b6892020-10-01T00:00:00Zhttps://jurnal.ugm.ac.id/ijc/article/view/56087https://doaj.org/toc/1411-9420https://doaj.org/toc/2460-1578Stability and hydrogen bond occupancy analysis of flavonol derivative docked in DAPK1 have been carried out using molecular dynamics simulation approach. Six flavonol derivatives were docked in DAPK1 as protein target, then continued with molecular dynamics simulation. NVT and NPT ensembles were used to equilibrate the system, followed by 20 ns sampling time for each system. Structural stability and hydrogen bond occupancy analyses were carried out at the NVT ensemble, while free binding energy analysis was done at NPT ensemble. From all compounds used in this work, compound B (5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one) has a similar interaction with reference ligands (quercetin, kaempferol, and fisetin), and the most stable complex system has the maximum RMSD around 2 Å. Compound C complex has -48.06 kJ/mol binding free energy score, and it was slightly different from quercetin, kaempferol, and fisetin complexes. Even though complex C has similar binding free energy with the reference compound, complex B shows more stable interactions due to their hydrogen bond and occupancy.Adi Tiara ZikriHarno Dwi PranowoWinarto HaryadiDepartment of Chemistry, Universitas Gadjah Madaarticleflavonolhydrogen bond occupancymolecular dynamics simulationChemistryQD1-999ENIndonesian Journal of Chemistry, Vol 21, Iss 2, Pp 383-390 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	flavonol hydrogen bond occupancy molecular dynamics simulation Chemistry QD1-999
spellingShingle	flavonol hydrogen bond occupancy molecular dynamics simulation Chemistry QD1-999 Adi Tiara Zikri Harno Dwi Pranowo Winarto Haryadi Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches
description	Stability and hydrogen bond occupancy analysis of flavonol derivative docked in DAPK1 have been carried out using molecular dynamics simulation approach. Six flavonol derivatives were docked in DAPK1 as protein target, then continued with molecular dynamics simulation. NVT and NPT ensembles were used to equilibrate the system, followed by 20 ns sampling time for each system. Structural stability and hydrogen bond occupancy analyses were carried out at the NVT ensemble, while free binding energy analysis was done at NPT ensemble. From all compounds used in this work, compound B (5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one) has a similar interaction with reference ligands (quercetin, kaempferol, and fisetin), and the most stable complex system has the maximum RMSD around 2 Å. Compound C complex has -48.06 kJ/mol binding free energy score, and it was slightly different from quercetin, kaempferol, and fisetin complexes. Even though complex C has similar binding free energy with the reference compound, complex B shows more stable interactions due to their hydrogen bond and occupancy.
format	article
author	Adi Tiara Zikri Harno Dwi Pranowo Winarto Haryadi
author_facet	Adi Tiara Zikri Harno Dwi Pranowo Winarto Haryadi
author_sort	Adi Tiara Zikri
title	Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches
title_short	Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches
title_full	Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches
title_fullStr	Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches
title_full_unstemmed	Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches
title_sort	stability, hydrogen bond occupancy analysis and binding free energy calculation from flavonol docked in dapk1 active site using molecular dynamic simulation approaches
publisher	Department of Chemistry, Universitas Gadjah Mada
publishDate	2020
url	https://doaj.org/article/d9fb3d3a6b0742c498fdec4c2092b689
work_keys_str_mv	AT aditiarazikri stabilityhydrogenbondoccupancyanalysisandbindingfreeenergycalculationfromflavonoldockedindapk1activesiteusingmoleculardynamicsimulationapproaches AT harnodwipranowo stabilityhydrogenbondoccupancyanalysisandbindingfreeenergycalculationfromflavonoldockedindapk1activesiteusingmoleculardynamicsimulationapproaches AT winartoharyadi stabilityhydrogenbondoccupancyanalysisandbindingfreeenergycalculationfromflavonoldockedindapk1activesiteusingmoleculardynamicsimulationapproaches
_version_	1718393655093362688

Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches

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