Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli a...

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Bibliographic Details
Published in:Advances in Bioinformatics 2014, Vol.2014 (2014), p.f1-12
Main Authors: Raharjo, Sentot Joko, Mahdi, Chanif, Nurdiana, Nurdiana, Kikuchi, Takheshi, Fatchiyah, Fatchiyah
Format: Article
Language:English
Subjects:
Alcohol
Analgesics
Analysis
Chemical properties
COX-2 inhibitors
Enzymes
Force and energy
Graduate studies
Kinases
Laboratories
Ligands
Methods
Molecular weight
Prostaglandins
Proteins
Science
Software
Solvents
Studies
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Summary:To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2.
ISSN:1687-8027
1687-8035
DOI:10.1155/2014/850628