Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase

This study was conducted to search for potential aldose reductase (AR) inhibitors among the chosen catechin derivatives using computational methods. Molecular docking, molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation were per...

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Main Author:	Soib’, Shikin Faezah
Format:	Thesis
Language:	English
Published:	2019
Subjects:	QD1-999 Chemistry
Online Access:	http://eprints.usm.my/49338/1/shikin%20faezah%20cut.pdf
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id	my-usm-ep.49338
record_format	uketd_dc
spelling	my-usm-ep.493382021-06-22T10:03:30Z Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase 2019-08 Soib’, Shikin Faezah QD1-999 Chemistry This study was conducted to search for potential aldose reductase (AR) inhibitors among the chosen catechin derivatives using computational methods. Molecular docking, molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation were performed to investigate the interactions of AR with the catechin derivatives. A total of 14 ligands of catechin derivatives were submitted for molecular docking. Molecular docking results revealed ligand 2 (3-o-octanoylcatechin) has the best interactions and lowest binding energy with AR. A 100 ns molecular dynamics (MD) simulation was conducted for both AR/NADP+/quercetin (standard) and AR/NADP+/ligand 2. The results of MD analysis confirmed the stability of the AR/NADP+/ligand 2 complex based on the results of root-mean-square deviation (RMSD), radius of gyration (Rg) and secondary structure analysis. The root-mean-square fluctuations (RMSF) results indicated that there are no major changes in the structure and conformation of the protein upon the binding of ligand 2. The hydrogen bond analysis showed that ligand 2 has a high number and occupancy of intermolecular hydrogen bond formation with Trp111 (43.2 %), Glu120 (24.3 %), His110 (24.2 %), Gln49 (8.5 %) and Val47 (2.0 %) throughout the simulation compared with quercetin. The MM-PBSA free energy calculation showed lower total binding energy of ligand 2 (-127.62 ± 10.82 kJ/mol) compared with quercetin (-50.10 ± 9.74 kJ/mol). 2019-08 Thesis http://eprints.usm.my/49338/ http://eprints.usm.my/49338/1/shikin%20faezah%20cut.pdf application/pdf en public masters Universiti Sains Malaysia Pusat Pengajian Sains Kimia
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	QD1-999 Chemistry
spellingShingle	QD1-999 Chemistry Soib’, Shikin Faezah Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase
description	This study was conducted to search for potential aldose reductase (AR) inhibitors among the chosen catechin derivatives using computational methods. Molecular docking, molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation were performed to investigate the interactions of AR with the catechin derivatives. A total of 14 ligands of catechin derivatives were submitted for molecular docking. Molecular docking results revealed ligand 2 (3-o-octanoylcatechin) has the best interactions and lowest binding energy with AR. A 100 ns molecular dynamics (MD) simulation was conducted for both AR/NADP+/quercetin (standard) and AR/NADP+/ligand 2. The results of MD analysis confirmed the stability of the AR/NADP+/ligand 2 complex based on the results of root-mean-square deviation (RMSD), radius of gyration (Rg) and secondary structure analysis. The root-mean-square fluctuations (RMSF) results indicated that there are no major changes in the structure and conformation of the protein upon the binding of ligand 2. The hydrogen bond analysis showed that ligand 2 has a high number and occupancy of intermolecular hydrogen bond formation with Trp111 (43.2 %), Glu120 (24.3 %), His110 (24.2 %), Gln49 (8.5 %) and Val47 (2.0 %) throughout the simulation compared with quercetin. The MM-PBSA free energy calculation showed lower total binding energy of ligand 2 (-127.62 ± 10.82 kJ/mol) compared with quercetin (-50.10 ± 9.74 kJ/mol).
format	Thesis
qualification_level	Master's degree
author	Soib’, Shikin Faezah
author_facet	Soib’, Shikin Faezah
author_sort	Soib’, Shikin Faezah
title	Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase
title_short	Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase
title_full	Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase
title_fullStr	Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase
title_full_unstemmed	Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase
title_sort	molecular docking and molecular dynamics of 3-o-octanoylcatechin interactions against aldose reductase
granting_institution	Universiti Sains Malaysia
granting_department	Pusat Pengajian Sains Kimia
publishDate	2019
url	http://eprints.usm.my/49338/1/shikin%20faezah%20cut.pdf
_version_	1747821992499740672

Molecular Docking And Molecular Dynamics Of 3-O-Octanoylcatechin Interactions Against Aldose Reductase

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