Comparative modeling of human kappa opioid receptor and docking analysis with the peptide YFa

Journal of Molecular Graphics and Modelling

Volumn 33, Issue , 2012, Pages 44-51

  Patra, Mahesh Chandra ^a   Kumar, Krishan ^a   Pasha, Santosh ^a   Chopra, Madhu ^b  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b UNIVERSITY OF DELHI   (India)

Author keywords

G protein coupled receptor; Homology modeling; Kappa opioid receptor; Molecular docking; Molecular dynamics simulation

Indexed keywords

G PROTEIN COUPLED RECEPTORS; HOMOLOGY MODELING; KAPPA OPIOID RECEPTOR; MOLECULAR DOCKING; MOLECULAR DYNAMICS SIMULATION;

AMINO ACIDS; COMPUTER SIMULATION; CRYSTAL STRUCTURE; DRUG INTERACTIONS; DYNAMICS; HYDROGEN BONDS; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODELING; OPTIMIZATION; PEPTIDES; PHOSPHOLIPIDS;

BINDING ENERGY;

AMINO ACID DERIVATIVE; KAPPA OPIATE RECEPTOR; PEPTIDE DERIVATIVE; RHODOPSIN; TYROSYLGLYCYLGLYCYLPHENYLALANYLMETHIONYLLYSYLLYSYLPHENYLALANYLMETHIONYLARGINYLPHENYLALANINE; UNCLASSIFIED DRUG;

ARTICLE; COW; CRYSTAL STRUCTURE; ENERGY; HYDROGEN BOND; HYDROPHOBICITY; IN VITRO STUDY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PHOSPHOLIPID BILAYER; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HUMANS; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PEPTIDES; PHOSPHOLIPIDS; PROTEIN CONFORMATION; RECEPTORS, OPIOID, KAPPA; STRUCTURAL HOMOLOGY, PROTEIN;

BOVINAE;

EID: 84855220150     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.10.007     Document Type: Article

References (39)

1. B.L. Kieffer Recent advances in molecular recognition and signal transduction of active peptides: receptors for opioid peptides Cell. Mol. Neurobiol. 15 1995 615 635 (Pubitemid 26019815)
2. R. Fredriksson, M.C. Lagerstrom, L.G. Lundin, and H.B. Schioth The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints Mol. Pharmacol. 63 2003 1256 1272 (Pubitemid 36627220)
3. P.G. Fine, and K.P. Russell The endogenous opioid system A Clinical Guide to Opioid Analgesia 2004 McGraw Hill Chapter 2, pp. 9-16
4. P.Y. Law, Y.H. Wong, and H.H. Loh Molecular mechanisms and regulation of opioid receptor signaling Annu. Rev. Pharmacol. Toxicol. 40 2000 389 430 (Pubitemid 30340688)
5. G. Gaibelet, E. Meilhoc, J. Riond, I. Saves, T. Exner, L. Liaubet, B. Nurnberg, J.M. Masson, and L.J. Emorine Nonselective coupling of the human μ-opioid receptor to multiple inhibitory G-protein isoforms Eur. J. Biochem. 261 1999 517 523 (Pubitemid 29187499)
6. K. Lundstrom Structural genomics for membrane proteins Cell. Mol. Life Sci. 63 2006 2597 2607 (Pubitemid 44800714)
7. K. Lundstrom Structural genomics on membrane proteins: mini review Comb. Chem. High Throughput Screen. 7 2004 431 439 (Pubitemid 39108265)
8. K. Haeyoung, K. Raynor, and T. Reisine Amino acids in the cloned mouse kappa receptor that are necessary for high affinity agonist binding but not antagonist binding Regul. Pept. 54 1994 155 156 (Pubitemid 24360378)
9. F. Meng, M.T. Hoversten, R.C. Thompson, L. Taylor, S.J. Watson, and H. Akil A chimeric study of the molecular basis of affinity and selectivity of the κ and the δ opioid receptors: potential role of extracellular domains J. Biol. Chem. 270 1995 12730 12736
10. J.C. Xue, C. Chen, J. Zhu, S.P. Kunapuli, J.K. Riel, L. Yu, and L.Y. Liu-Chen The third extracellular loop of the μ opioid receptor is important for agonist selectivity J. Biol. Chem. 270 1995 12977 12979
11. F. Meng, Y. Ueda, M.T. Hoversten, R.C. Thompson, L. Taylor, S.J. Watson, and H. Akil Mapping the receptor domains critical for the binding selectivity of delta-opioid receptor ligands Eur. J. Pharmacol. 311 1996 285 292 (Pubitemid 26330386)
12. B.E. Kane, B. Svensson, and D.M. Ferguson Molecular recognition of opioid receptor ligands AAPS J. 8 2006 126 137
13. J.B. Wang, P.S. Johnson, J.M. Wu, W.F. Wang, and G.R. Uhl Human κ opiate receptor second extracellular loop elevates dynorphin's affinity for human μ/κ chimeras J. Biol. Chem. 269 1994 25966 25969 (Pubitemid 24328398)
14. H. Teschemacher, K.E. Opheim, B.M. Cox, and A. Goldstein A Peptide-like substance from pituitary that acts like morphine. I. Isolation Life Sci. 16 1975 1771 1775
15. P.J. Conn, A. Christopoulos, and C.W. Lindsley Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders Nat. Rev. Drug Discov. 8 2009 41 54
16. K. Mohr, C. Tränkle, E. Kostenis, E. Barocelli, M. De Amici, and U. Holzgrabe Themed section: molecular pharmacology of g protein-coupled receptors Br. J. Pharmacol. 159 2010 997 1008
17. R. Schwyzer Peptide-membrane interactions and a new principle in quantitative structure-activity relationships Biopolymers 31 1991 785 792
18. S. Gupta, S. Pasha, Y.K. Gupta, and D.K. Bhardwaj Chimeric peptide of Metenkephalin and FMRFa induces antinociception and attenuates development of tolerance to morphine antinociception Peptides 20 1999 471 478 (Pubitemid 29458990)
19. I.D. Vats, K.S. Dolt, K. Kumar, J. Karar, M. Nath, A. Mohan, M.A. Pasha, and S. Pasha YFa, a chimeric opioid peptide, induces kappa-specific antinociception with no tolerance development during 6 days of chronic treatment J. Neurosci. Res. 86 2008 1599 1607 (Pubitemid 351642453)
20. K. Gupta, I.D. Vats, Y.K. Gupta, K. Saleem, and S. Pasha Lack of tolerance and morphine-induced cross-tolerance to the analgesia of chimeric peptide of Met-enkephalin and FMRFa Peptides 29 2008 2266 2267
21. K. Kumar, S. Kumar, R.K. Kurupati, M.K. Seth, A. Mohan, M.E. Hussain, and S. Pasha Intracellular cAMP assay and Eu-GTP-γS binding studies of chimeric opioid peptide YFa Eur. J. Pharmacol. 650 2010 28 33
22. N. Eswar, M.A. Marti-Renom, B. Webb, M.S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, and A. Sali Comparative protein structure modeling with MODELLER Curr. Prot. Bioinfor. Supplement 15 2006 5.6.1-5.6.30
23. T. Okada, M. Sugihara, A.N. Bondar, M. Elstner, P. Entel, and V. Buss The retinal conformation and its environment in rhodopsin in light of a new 2.2. A crystal structure J. Mol. Biol. 342 2004 571 583 (Pubitemid 39149759)
24. A. Fiser, R.K. Do, and A. Sali Modeling of loops in protein structures Protein Sci. 9 2000 1753 1773
25. T.L. Gioannini, Y.F. Liu, Y.H. Park, J.M. Hiller, and E.J. Simon Evidence for the presence of disulfide bridges in opioid receptors essential for ligand binding. Possible role in receptor activation J. Mol. Recognit. 2 1989 44 48
26. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J. Berendsen GROMACS: fast, flexible, and free J. Comput. Chem. 26 2005 1701 1718 (Pubitemid 43076182)
27. O. Berger, O. Edholm, and F. Jahnig Molecular dynamics simulations of fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure and constant temperature Biophys. J. 72 1997 2002 2013 (Pubitemid 27184429)
28. SYBYL, Version 8.0, Tripos International, 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA.
29. A.N. Jain Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine J. Med. Chem. 46 2003 499 511 (Pubitemid 36182752)
30. R.D. Clark, A. Strizhev, J.M. Leonard, J.F. Blake, and J.B. Matthew Consensus scoring for ligand/protein interactions J. Mol. Graphics Modell. 20 2002 281 295 (Pubitemid 34017546)
31. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan Stereochemistry of polypeptide chain configurations J. Mol. Biol. 7 1963 95 99
32. J.A. Ballesteros, and H. Weinstein Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors Methods Neurosci. 25 1995 366 428
33. P. Coward, H.G. Wada, M.S. Falk, S.D.H. Chan, F. Meng, H. Akil, and B.R. Conklin Controlling signaling with a specifically designed Gi-coupled receptor Proc. Natl. Acad. Sci. U.S.A. 95 1998 352 357
34. I.D. Pogozheva, A.L. Lomize, and H.I. Mosberg Opioid receptor 3-dimensional structures from distance geometry calculations with hydrogen bonding constraints Biophys. J. 75 1998 612 634 (Pubitemid 28357504)
35. I.D. Pogozheva, M.J. Przydzial, and H.I. Mosberg Homology modeling of opioid receptor-ligand complexes using experimental constraints AAPS J. 7 2005 E434 E448
36. J.C. Xue, C. Chen, and J. Zhu Differential binding domains of peptide and non-peptide ligands in the cloned rat kappa opioid receptor J. Biol. Chem. 269 1994 30195 30199
37. D.M. Ferguson, S. Kramer, T.G. Metzger, P.Y. Law, and P.S. Portoghese Isosteric replacement of acidic with neutral residues in extracellular loop-2 of the kappa-opioid receptor does not affect dynorphin A(1-13) affinity and function J. Med. Chem. 43 2000 1251 1252 (Pubitemid 30212565)
38. A. Corbett, S. Paterson, and H. Kosterlitz Selectivity of ligands for opioid receptors A. Herz, Handbook of Experimental Pharmacology vol. 104/I 1993 Springer-Verlag Berlin 645 679
39. G. Paterlini, P. Portoghese, and D. Ferguson Molecular simulation of dynorphin A-(1-10) binding to extracellular loop 2 of the kappa-opioid receptor: a model for receptor activation J. Med. Chem. 40 1997 3254 3262 (Pubitemid 27413750)