New insights into the binding mode of melanin concentrating hormone receptor-1 antagonists: Homology modeling and explicit membrane molecular dynamics simulation study

Journal of Chemical Information and Modeling

Volumn 51, Issue 3, 2011, Pages 635-646

  Helal, Mohamed A ^a   Chittiboyina, Amar G ^a   Avery, Mitchell A ^a,b  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b UNIVERSITY OF MISSISSIPPI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CRYSTAL STRUCTURE; LIGANDS; MAMMALS; MELANIN;

AQUEOUS ENVIRONMENT; CHEMICAL DIVERSITY; ENERGY HOMEOSTASIS; ENERGY MINIMIZATION; HOMOLOGY MODELING; HORMONE RECEPTORS; MOLECULAR DYNAMICS SIMULATIONS; REFINEMENT PROCESS;

MOLECULAR DYNAMICS;

HYPOPHYSIS HORMONE; HYPOTHALAMUS HORMONE; MELANIN; MELANIN CONCENTRATING HORMONE; MELANIN-CONCENTRATING HORMONE;

ANIMAL; ARTICLE; CHEMISTRY; DRUG ANTAGONISM; MOLECULAR DYNAMICS;

ANIMALS; HYPOTHALAMIC HORMONES; MELANINS; MOLECULAR DYNAMICS SIMULATION; PITUITARY HORMONES;

EID: 79953226342     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100355c     Document Type: Article

References (52)

1. World Health Organization. http://www.who.int/nutrition/topics/obesity/ en/ (accessed December 28, 2010).
2. Dannenberg, A. L.; Burton, D. C.; Jackson, R. J. Economic and environmental costs of obesity: the impact on airlines Am. J. Prev. Med. 2004, 27, 264-271
3. Haslam, D. W.; James, W. P. Obesity Lancet 2005, 366, 1197-1209 (Pubitemid 41393598)
4. Kawauchi, H.; Kawazoe, I.; Tsubokawa, M.; Kishida, M.; Baker, B. I. Characterization of melanin-concentrating hormone in chum salmon pituitaries Nature 1983, 305, 321-323 (Pubitemid 13010926)
5. Bittencourt, J. C.; Presse, F.; Arias, C.; Peto, C.; Vaughan, J.; Nahon, J. L.; Vale, W.; Sawchenko, P. E. The melanin-concentrating hormone system of the rat brain: an immuno- and hybridization histochemical characterization J. Comp. Neurol. 1992, 319, 218-245
6. Chambers, J.; Ames, R. S.; Bergsma, D.; Muir, A.; Fitzgerald, L. R.; Hervieu, G.; Dytko, G. M.; Foley, J. J.; Martin, J.; Liu, W. S.; Park, J.; Ellis, C.; Ganguly, S.; Konchar, S.; Cluderay, J.; Leslie, R.; Wilson, S.; Sarau, H. M. Melanin-concentrating hormone is the cognate ligand for the orphan G-protein-coupled receptor SLC-1 Nature 1999, 400, 261-265 (Pubitemid 29334140)
7. Hill, J.; Duckworth, M.; Murdock, P.; Rennie, G.; Sabido-David, C.; Ames, R. S.; Szekeres, P.; Wilson, S.; Bergsma, D. J.; Gloger, I. S.; Levy, D. S.; Chambers, J. K.; Muir, A. I. Molecular cloning and functional characterization of MCH2, a novel human MCH receptor J. Biol. Chem. 2001, 276, 20125-20129
8. Kokkotou, E. G.; N., T.; Mastaitis, J. W.; Slieker, L; Maratos-Flier Melanin-Concentrating Hormone Receptor Is a Target of Leptin Action in the Mouse Brain Endocrinology 2002, 142, 680-688
9. Chen, Y.; Hu, C.; Hsu, C. K.; Zhang, Q.; Bi, C.; Asnicar, M.; Hsiung, H. M.; Fox, N.; Slieker, L. J.; Yang, D. D.; Heiman, M. L.; Shi, Y. Targeted disruption of the melanin-concentrating hormone receptor-1 results in hyperphagia and resistance to diet-induced obesity Endocrinology 2002, 143, 2469-2477 (Pubitemid 34701307)
10. Borowsky, B.; Durkin, M. M.; Ogozalek, K.; Marzabadi, M. R.; DeLeon, J.; Lagu, B.; Heurich, R.; Lichtblau, H.; Shaposhnik, Z.; Daniewska, I.; Blackburn, T. P.; Branchek, T. A.; Gerald, C.; Vaysse, P. J.; Forray, C. Antidepressant, anxiolytic and anorectic effects of a melanin-concentrating hormone-1 receptor antagonist Nat. Med. 2002, 8, 825-830
11. Tan, C. P.; Sano, H.; Iwaasa, H.; Pan, J.; Sailer, A. W.; Hreniuk, D. L.; Feighner, S. D.; Palyha, O. C.; Pong, S. S.; Figueroa, D. J.; Austin, C. P.; Jiang, M. M.; Yu, H.; Ito, J.; Ito, M.; Guan, X. M.; MacNeil, D. J.; Kanatani, A.; Van der Ploeg, L. H.; Howard, A. D. Melanin-concentrating hormone receptor subtypes 1 and 2: species-specific gene expression Genomics 2002, 79, 785-792 (Pubitemid 34595312)
12. Takekawa, S.; Asami, A.; Ishihara, Y.; Terauchi, J.; Kato, K.; Shimomura, Y.; Mori, M.; Murakoshi, H.; Suzuki, N.; Nishimura, O.; Fujino, M. T-226296: a novel, orally active and selective melanin-concentrating hormone receptor antagonist Eur. J. Pharmacol. 2002, 438, 129-135 (Pubitemid 34241500)
13. Tavares, F. X.; Al-Barazanji, K. A.; Bishop, M. J.; Britt, C. S.; Carlton, D. L.; Cooper, J. P.; Feldman, P. L.; Garrido, D. M.; Goetz, A. S.; Grizzle, M. K.; Hertzog, D. L.; Ignar, D. M.; Lang, D. G.; McIntyre, M. S.; Ott, R. J.; Peat, A. J.; Zhou, H. Q. 6-(4-chlorophenyl)-3-substituted-thieno[3,2-d] pyrimidin-4(3H)-one-based melanin-concentrating hormone receptor 1 antagonist J. Med. Chem. 2006, 49, 7108-7118 (Pubitemid 44888834)
14. Ito, M.; Ishihara, A.; Gomori, A.; Egashira, S.; Matsushita, H.; Mashiko, S.; Ito, J.; Nakase, K.; Haga, Y.; Iwaasa, H.; Suzuki, T.; Ohtake, N.; Moriya, M.; Sato, N.; MacNeil, D. J.; Takenaga, N.; Tokita, S.; Kanatani, A. Melanin-concentrating hormone 1-receptor antagonist suppresses body weight gain correlated with high receptor occupancy levels in diet-induced obesity mice Eur. J. Pharmacol. 2009, 624, 77-83
15. Ito, M.; Ishihara, A.; Gomori, A.; Matsushita, H.; Metzger, J. M.; Marsh, D. J.; Haga, Y.; Iwaasa, H.; Tokita, S.; Takenaga, N.; Sato, N.; MacNeil, D. J.; Moriya, M.; Kanatani, A. Mechanism of the anti-obesity effects induced by a novel melanin-concentrating hormone 1-receptor antagonist in mice Br. J. Pharmacol. 2010, 159, 374-383
16. Handlon, A. L.; Zhou, H. Melanin-concentrating hormone-1 receptor antagonists for the treatment of obesity J. Med. Chem. 2006, 49, 4017-4022 (Pubitemid 44043104)
17. Becker, O. M.; Shacham, S.; Marantz, Y.; Noiman, S. Modeling the 3D structure of GPCRs: advances and application to drug discovery Curr. Opin. Drug Discovery Dev. 2003, 6, 353-361 (Pubitemid 36702308)
18. Vitale, R. M.; Pedone, C.; De Benedetti, P. G.; Fanelli, F. Structural features of the inactive and active states of the melanin-concentrating hormone receptors: insights from molecular simulations Proteins 2004, 56, 430-448 (Pubitemid 38924958)
19. Clark, D. E.; Higgs, C.; Wren, S. P.; Dyke, H. J.; Wong, M.; Norman, D.; Lockey, P. M.; Roach, A. G. A virtual screening approach to finding novel and potent antagonists at the melanin-concentrating hormone 1 receptor J. Med. Chem. 2004, 47, 3962-3971 (Pubitemid 38970958)
20. Ulven, T.; Frimurer, T. M.; Receveur, J. M.; Little, P. B.; Rist, O.; Norregaard, P. K.; Hogberg, T. 6-Acylamino-2-aminoquinolines as potent melanin-concentrating hormone 1 receptor antagonists. Identification, structure-activity relationship, and investigation of binding mode J. Med. Chem. 2005, 48, 5684-5697 (Pubitemid 41298343)
21. Tavares, F. X.; Al-Barazanji, K. A.; Bigham, E. C.; Bishop, M. J.; Britt, C. S.; Carlton, D. L.; Feldman, P. L.; Goetz, A. S.; Grizzle, M. K.; Guo, Y. C.; Handlon, A. L.; Hertzog, D. L.; Ignar, D. M.; Lang, D. G.; Ott, R. J.; Peat, A. J.; Zhou, H. Q. Potent, selective, and orally efficacious antagonists of melanin-concentrating hormone receptor 1 J. Med. Chem. 2006, 49, 7095-7107 (Pubitemid 44888833)
22. Witty, D. R.; Bateson, J. H.; Hervieu, G. J.; Jeffrey, P.; Johnson, C. N.; Muir, A. I.; O'Hanlon, P. J.; Stemp, G.; Stevens, A. J.; Thewlis, K. M.; Wilson, S.; Winborn, K. Y. SAR of biphenyl carboxamide ligands of the human melanin-concentrating hormone receptor 1 (MCH R1): discovery of antagonist SB-568849 Bioorg. Med. Chem. Lett. 2006, 16, 4865-4871 (Pubitemid 44177772)
23. Cavasotto, C. N.; Orry, A. J.; Murgolo, N. J.; Czarniecki, M. F.; Kocsi, S. A.; Hawes, B. E.; O'Neill, K. A.; Hine, H.; Burton, M. S.; Voigt, J. H.; Abagyan, R. A.; Bayne, M. L.; Monsma, F. J., Jr. Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening J. Med. Chem. 2008, 51, 581-588 (Pubitemid 351252286)
24. Giordanetto, F.; Karlsson, O.; Lindberg, J.; Larsson, L. O.; Linusson, A.; Evertsson, E.; Morgan, D. G.; Inghardt, T. Discovery of cyclopentane- and cyclohexane-trans-1,3-diamines as potent melanin-concentrating hormone receptor 1 antagonists Bioorg. Med. Chem. Lett. 2007, 17, 4232-4241 (Pubitemid 47028598)
25. Cavasotto, C. N.; Phatak, S. S. Homology modeling in drug discovery: current trends and applications Drug Discovery Today 2009, 14 (13-14) 676-683
26. Konc, J.; Janezic, D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment Bioinformatics 2010, 26 (9) 1160-11688
27. Bairoch, A.; Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Nucleic Acids Res. 2000, 28 (1) 45-48 (Pubitemid 30047711)
28. Okada, T.; Sugihara, M.; Bondar, A. N.; Elstner, M.; Entel, P.; Buss, V. The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure J. Mol. Biol. 2004, 342 (2) 571-583 (Pubitemid 39149759)
29. Clustalw2. http://www.ebi.ac.uk/Tools/clustalw2/index.html (accessed December 28, 2010).
30. TMPRED. http://ch.embnet.org./software/TMPRED-form.html (accessed December 28, 2010).
31. Clark, M.; Cramer, R. D., III; Van Opdenbosch, N. Validation of the general purpose tripos 5.2 force field J. Comput. Chem. 1989, 10, 982-991
32. Lovell, S. C.; Word, J. M.; Richardson, J. S.; Richardson, D. C. The Penultimate Rotamer Library Proteins: Struct., Funct., Genet. 2000, 40, 389-408 (Pubitemid 30624447)
33. Gasteiger, J. M. M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges Tetrahedron 1980, 36 (22) 3219-3228
34. Fletcher, R.; Reeves, C. M. Function Minimization by Conjugate Gradients Comp. J. 1965, 7, 149-154
35. Macdonald, D.; Murgolo, N.; Zhang, R.; Durkin, J. P.; Yao, X.; Strader, C. D.; Graziano, M. P. Molecular characterization of the melanin-concentrating hormone/receptor complex: identification of critical residues involved in binding and activation Mol. Pharmacol. 2000, 58 (1) 217-225 (Pubitemid 30452545)
36. Halgren, T. Merck molecular force field. I Basis, form, scope, parametization, and performance of MMFF94 J. Comput. Chem. 1996, 17, 490-498
37. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267 (3) 727-748 (Pubitemid 27170693)
38. Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Yibing, S.; Shaw, D. E. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (SC06), Tampa, FL, 2006; ACM Press: New York, 2006.
39. Humphrey, W.; Dalke, A.; Schulten, K. VMD: visual molecular dynamics J. Mol. Graphics 1996, 14 (1) 33-38 (Pubitemid 26152973)
40. Palczewski, K.; Kumasaka, T.; Hori, T.; Behnke, C. A.; Motoshima, H.; Fox, B. A.; Le Trong, I.; Teller, D. C.; Okada, T.; Stenkamp, R. E.; Yamamoto, M.; Miyano, M. Crystal structure of rhodopsin: A G protein-coupled receptor Science 2000, 289 (5480) 739-745 (Pubitemid 30650186)
41. Filipek, S.; Teller, D. C.; Palczewski, K.; Stenkamp, R. The crystallographic model of rhodopsin and its use in studies of other G protein-coupled receptors Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 375-397 (Pubitemid 37056234)
42. Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234 (3) 779-815 (Pubitemid 24007801)
43. Tirado-Rives, W. L. J. a. J. The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
44. Kimura, S. R.; Tebben, A. J.; Langley, D. R. Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach Proteins 2008, 71 (4) 1919-1929 (Pubitemid 351732945)
45. Itai, A.; Toriumi, Y.; Tomioka, N.; Kagechika, H.; Azumaya, I.; Shudo, K. Stereochemistry of N-methylbenzanilide and benzanilide Tet. Lett. 1989, 30, 6177-6180 (Pubitemid 19280181)
46. Kagechika, H.; Himi, T.; Kawachi, E.; Shudo, K. Retinobenzoic acids. 4. Conformation of aromatic amides with retinoidal activity. Importance of trans-amide structure for the activity J. Med. Chem. 1989, 32 (10) 2292-2296 (Pubitemid 19245889)
47. Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.; Rasmussen, S. G.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Kuhn, P.; Weis, W. I.; Kobilka, B. K.; Stevens, R. C. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor Science 2007, 318 (5854) 1258-1265 (Pubitemid 350172884)
48. Strahs, D.; Weinstein, H. Comparative modeling and molecular dynamics studies of the delta, kappa and mu opioid receptors Protein Eng. 1997, 10 (9) 1019-1038 (Pubitemid 28004648)
49. Boeckler, F.; Lanig, H.; Gmeiner, P. Modeling the similarity and divergence of dopamine D2-like receptors and identification of validated ligand-receptor complexes J. Med. Chem. 2005, 48 (3) 694-709 (Pubitemid 40209092)
50. Meyers, K. M.; Mendez-Andino, J.; Colson, A. O.; Hu, X. E.; Wos, J. A.; Mitchell, M. C.; Hodge, K.; Howard, J.; Paris, J. L.; Dowty, M. E.; Obringer, C. M.; Reizes, O. Novel pyrazolopiperazinone- and pyrrolopiperazinone-based MCH-R1 antagonists Bioorg. Med. Chem. Lett. 2007, 17 (3) 657-661 (Pubitemid 46108574)
51. Mirzadegan, T.; Benko, G.; Filipek, S.; Palczewski, K. Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin Biochemistry 2003, 42 (10) 2759-2767 (Pubitemid 36331518)
52. Kristiansen, K.; Kroeze, W. K.; Willins, D. L.; Gelber, E. I.; Savage, J. E.; Glennon, R. A.; Roth, B. L. A highly conserved aspartic acid (Asp-155) anchors the terminal amine moiety of tryptamines and is involved in membrane targeting of the 5-HT(2A) serotonin receptor but does not participate in activation via a "salt-bridge disruption" mechanism J. Pharmacol. Exp. Ther. 2000, 293 (3) 735-746