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http://dx.doi.org/10.13160/ricns.2013.6.1.016

Homology Modeling of GPR18 Receptor, an Orphan G-protein-coupled Receptor  

Kothandan, Gugan (Department of Biochemistry, Centre for Bioinformatics, University of Madras, Guindy Campus)
Cho, Seung Joo (Department of Bio-New Drug Development College of Medicine, Chosun University)
Publication Information
Journal of Integrative Natural Science / v.6, no.1, 2013 , pp. 16-20 More about this Journal
Abstract
G-protein-coupled receptor (GPCR) superfamily is the largest known receptor family, characterized by seven transmembrane domains and considered to be an important drug target. In this study we focused on an orphan GPCR termed as GPR18. As there is no X-ray crystal structure has been reported for this receptor, we report on a homology model of GPR18. Template structure with high homology was used for modeling and ten models were developed. A model was selected and refined by energy minimization. The selected model was further validated using various parameters. Our results could be a starting point for further structure based drug design.
Keywords
Structure-Based Drug Design; Homology Modeling; GPR18; GPCR;
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1 A. Sali and T. L. Blundell, "Comparative protein modeling by satisfaction of spatial restraints", J. Mol. Biol., Vol. 234, pp. 779-815, 1993.   DOI   ScienceOn
2 A. Fiser, R. K. Do, and A. Sali, "Modeling of loops in protein structures", Protein Sci., Vol. 9, pp. 1753-1773, 2002.
3 R. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, "Procheck-a program to check the stereochemical quality of protein structures", J. Appl. Cryst., Vol. 26, pp. 283-291, 1993.   DOI   ScienceOn
4 C. Colovos and T.O. Yeates, "Verification of protein structures: patterns of nonbonded atomic interactions", Protein Sci., Vol. 2, pp. 1511-1519, 1993.   DOI   ScienceOn
5 A. A. Thompson, W. Liu, E. Chun, V. Katritch, H. Wu, E. Vardy, X. P. Huang, C. Trapella, R. Guerrini, G. Clo, B. L. Roth, V. Cherezov, and R. C. Stevens, "Structure of the nociceptin/orphanin FQ receptor in complex with a pepti de mimetic", Nature, Vol. 485, pp. 395-399, 2012.   DOI   ScienceOn
6 Y. Qin, E. M. E. Verdegaal, M. Siderius, J. P. Bebelman, M. J. Smit, R. Leurs, R. Willemze, C. P. Tensen, and S. Osanto, "Quantitative expression proling of G-protein-coupled receptors (GPCRs) in metastatic melanoma: the constitutively active orphan GPCR GPR18 as novel drug target", Pig. Cell Melanoma R., Vol. 24, pp. 207-218, 2010.
7 M. D. Thompson, W. M. Burnham, and D. E. Cole, "The G protein-coupled receptors: pharmacogenetics and disease", Crit. Rev. Clin. Lab. Sci., Vol. 42, pp. 311-392, 2005.   DOI   ScienceOn
8 R. J. Lefkowitz, "Historical review: a brief history and personal retrospective of seven-transmembrane receptors", Trends Pharmacol., Sci., Vol. 25, pp. 413-422, 2004.   DOI   ScienceOn
9 S. Schlyer and R. Horuk, "I want a new drug: Gprotein-coupled receptors", Drug Discov. Today, Vol. 11, pp. 481-493, 2006.   DOI   ScienceOn
10 M. Kohno, H. Hasegawa, A. Inoue, M. Muraoka, T. Miyazaki, K. Oka, and M. Yasukawa, "Identification of N-arachidonylglycine as the endogenous ligand for orphan G-protein-coupled receptor GPR18", Biochem. Biophys. Res. Commun., Vol. 347, pp. 827-832, 2006.   DOI   ScienceOn
11 G. Kothandan, T. Madhavan, C. G. Gadhe, and S. J. Cho, "Pseudoreceptor: Concept and an overview", J. Chosun Natural Sci., Vol. 5, pp. 216-219, 2012.   DOI   ScienceOn
12 S. J. Cho, "Meaning and definition of partial charges", J. Chosun Natural Sci., Vol. 3, pp. 231-236, 2010.   과학기술학회마을
13 G. Kothandan and S. J. Cho, "Prediction of binding free energy calculation using molecular mechanics/ Poisson-Boltzmann surface area (MM-PBSA) method in drug discovery: A short review", J. Chosun Natural Sci., Vol. 2, pp. 55-58, 2009.
14 S. J. Cho, "Search space reduction techniques in small molecular docking", J. Chosun Natural Sci. Vol. 3, pp. 143-147, 2010.   과학기술학회마을
15 S. J. Cho, "Calculation and application of partial charges", J. Chosun Natural Sci., Vol. 3, pp. 226-230, 2010.
16 S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic local alignment search tool", J. Mol. Biol., Vol. 215, pp 403-410, 1990.   DOI
17 S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res., Vol. 50, pp. 3389-3402, 1997.
18 H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, "The protein data bank", Nucleic Acids Res., Vol. 28, pp. 235-242, 2000.   DOI
19 J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice", Nucleic Acids Res., Vol. 22, pp. 4673-4680, 1994.   DOI
20 N. Eswar, B. John, N. Mirkovic, A. Fiser, V. A. Ilyin, U. Pieper, A. C. Stuart, M. A. Marti-Renom, M. S. Madhusudhan, B. Yerkovich, and A. Sali, "Tools for comparative protein structure modeling and analysis", Nucleic Acids Res., Vol. 31, pp. 3375-3380, 2003.   DOI   ScienceOn