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Advances in Bioinformatics
Volume 2014 (2014), Article ID 850628, 12 pages
Research Article

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

1Biology Doctoral Program, Faculty of Science, Brawijaya University, Malang 65141, Indonesia
2Academic of Pharmacy and Food Analysis, Putra Indonesia Malang, Malang 65123, Indonesia
3Chemistry Department, Faculty of Science, Brawijaya University, Malang 65123, Indonesia
4Medicine Pharmacology, Faculty of Medicine, Brawijaya University, Malang 65141, Indonesia
5Graduate Life Science School, Ritsumeikan University, Biwako Kutsasu Campus, Kutsasu, Shiga 525-8577, Japan
6Biology Department, Faculty of Science, Brawijaya University, Malang 65141, Indonesia

Received 5 May 2014; Revised 7 July 2014; Accepted 8 July 2014; Published 17 November 2014

Academic Editor: Huixiao Hong

Copyright © 2014 Sentot Joko Raharjo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.