Ligand-based homology modeling as attractive tool to inspect GPCR structural plasticity

Current Pharmaceutical Design

Volumn 12, Issue 17, 2006, Pages 2175-2185

  Moro, Stefano ^a   Deflorian, Francesca ^a   Bacilieri, Magdalena ^a   Spalluto, Giampiero ^b  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF TRIESTE   (Italy)

Author keywords

Cross Docking; Ligand Based Homology Modeling; Pyrazolotriazolopyrimidines; Seven trans membrane (7TM) bundle; Y shaped 3D pharmacophore model

Indexed keywords

5,9 DIHYDRO 6 METHOXYCARBONYL 9 METHYL 2 PHENYL 1,2,4 TRIAZOLO[5,1 A][2,7]NAPHTHYRIDINE; 9 CHLORO 2 (2 FURYL) 5,6 DIHYDRO 5 IMINO 1,2,4 TRIAZOLO[2,3 C]QUINAZOLINE; ADENOSINE A3 RECEPTOR; ADENOSINE A3 RECEPTOR ANTAGONIST; ADENOSINE RECEPTOR; FA 385; G PROTEIN COUPLED RECEPTOR; MRS 1041; MRS 1334; MRS 1505; PURINE P2Y1 RECEPTOR; PURINERGIC RECEPTOR BLOCKING AGENT; PYRAZOLOTRIAZOLOPYRIMIDINE DERIVATIVE; RHODOPSIN; UNCLASSIFIED DRUG; VUF 8504;

AMINO ACID SEQUENCE; ARTICLE; DRUG DESIGN; DRUG RECEPTOR BINDING; DRUG RESEARCH; DRUG SELECTIVITY; DRUG STRUCTURE; DRUG SYNTHESIS; DRUG TARGETING; HIGH THROUGHPUT SCREENING; HUMAN; LIGAND BINDING; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; STRUCTURE ACTIVITY RELATION;

COMPUTER SIMULATION; COMPUTER-AIDED DESIGN; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; PYRIMIDINES; RECEPTOR, ADENOSINE A3; RECEPTORS, G-PROTEIN-COUPLED; RHODOPSIN; STRUCTURAL HOMOLOGY, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; TRIAZOLES;

EID: 33745178449     PISSN: 13816128     EISSN: None     Source Type: Journal    
DOI: 10.2174/138161206777585265     Document Type: Article

References (44)

1. Lefkowitz RJ. Historical review: A brief history and personal retrospective of seven-transmembrane receptors. Trends Pharmacol Sci 2004; 25: 413-22.
2. 3 adenosine receptor as an example. Trends Pharmacol Sci 2005; 26: 413-22.
3. Patel TB. Single transmembrane spanning heterotrimeric G protein-coupled receptors and their signaling cascades. Pharmacol Rev 2004; 56: 371-85.
4. McDonald PH, Lefkowitz RJ. Beta-arrestins: new roles in regulating heptahelical receptors' functions. Cell Signal 2001; 13: 683-9.
5. El Far O, Betz H. G-protein-coupled receptors for neurotransmitter amino acids: C-terminal tails, crowded signalosomes. Biochem J 2002; 365: 329-36.
6. Milligan G. G protein-coupled receptor dimerization: function and ligand pharmacology. Mol Pharmacol 2004; 66: 1-7.
7. Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HBl. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 2003; 63: 1256-72.
8. Filipek S, Teller DC, 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; 2: 375-97.
9. Becker OM, Marantz Y, Sacham S, Inbal B, Heifetz A, Kalid O, et al. G protein-coupled receptors: in silico drug discovery in 3D. Proc Natl Acad Sci USA 2004; 101: 11304-9.
10. Klabunde T, Hessler G. Drug design strategies for targeting G-protein-coupled receptors. Chembiochem 2002; 3: 928-44.
11. May L, Avlani VA, Sexton PM, Christopoulos A. Allosteric modulation of G protein-coupled receptors. Curr Pharm Des 2004; 10: 2003-13.
12. Muller CE. Medicinal chemistry of adenosine A3 receptor ligands. Curr Top Med Chem 2003; 3: 445-62.
13. Moro S, Deflorian F, Spalluto G, Pastorin G, Cacciari G, Kim SK, et al. Demystifying the three dimensional structure of G protein-coupled receptors (GPCRs) with the aid of molecular modeling. Chem Commun (Camb) 2003; 21: 2949-56.
14. Gershengorn MC, Osman R. Minireview: Insights into G protein-coupled receptor function using molecular models. Endocrinology 2001; 142: 2-10.
15. Filipek S, Teller DC, Palczewski K, Hofmann KP, Ernst OP. The crystallographic model of rhodopsin and its use in studies of other G protein-coupled receptors. Annu Rev Biophys Biomol Struct 2003; 32: 375-97.
16. Archer E, Maigret B, Escrieut C, Pradayrol L, Fourmy D. Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? Trends Pharmacol Sci 2003; 24: 36-40.
17. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, et al. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 2000; 289: 739-45.
18. Gutierrez-de-Teran H, Pastor M, Centeno NB, Aqvist J, Sanz F. Novel approaches for modeling of the A1 adenosine receptor and its agonist binding site. Proteins 2004; 54: 705-15.
19. Bissantz C, Logean A, Rognan D. High-throughput modeling of human G-protein coupled receptors: amino acid sequence alignment, three-dimensional model building, and receptor library screening. J Chem Inf Comput Sci 2004; 1162-76.
20. Vermeulen ES, Schmidt AW, Sprouse JS, Wikstrom HV, Grol CJ. Characterization of the 5-HT(7) receptor. Determination of the pharmacophore for 5-HT(7) receptor agonism and CoMFA-based modeling of the agonist binding site. J Med Chem 2003; 46: 5365-74.
21. 2A agonists and antagonists. J Med Chem 2003; 46: 4847-59.
22. Kobilka BK. The role of cytosolic and membrane factors in processing of the human beta-2-adrenergic receptor following translocation and glycosylation in a cell-free system. J Biol Chem 1990; 265: 7610-8.
23. 1 receptor: molecular modeling and site-directed mutagenesis as tools to identify agonist and antagonist recognition sites. J Med Chem 1998; 41: 1456-66.
24. 3 adenosine antagonists: structural homology and receptor docking. J Chem Inf Comput Sci 1998; 38: 1239-48.
25. Moro S, Jacobson KA. Molecular Modeling as a Tool to Investigate Molecular Recognition in P2Y Receptors. Curr Pharm Design 2002; 8: 99-110.
26. Maconi A, Pastorin G, Da Ros T, Spalluto G, Gao ZG, Jacobson KA, et al. Synthesis, biological properties, and molecular modeling investigation of the first potent, selective, and water-soluble human A(3) adenosine receptor antagonist. J Med Chem 2002; 45: 3579-82.
27. Pastorin G, Da Ros T, Spalluto G, Deflorian F, Moro S, Cacciari B, et al. Pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine derivatives as adenosine receptor antagonists. Influence of the N5 substituent on the affinity at the human A3 and A2B adenosine receptor subtypes: a molecular modeling investigation. J Med Chem 2003; 46: 4287-96.
28. Colotta V, Catarzi D, Varano F, Calabri FR, Lenzi O, Filacchini G, et al. 1,2,4-triazolo[4,3-a]quinoxalin-1-one moiety as an attractive scaffold to develop new potent and selective human A3 adenosine receptor antagonists: synthesis, pharmacological, and ligand-receptor modeling studies. J Med Chem 2004; 47: 3580-90.
29. 3 adenosine receptor antagonists: pyrazolo[4,3-e]1,2,4-Triazolo[1,5-c]pyrimidine derivatives as a key study. J Med Chem 2005; 48: 152-62.
30. Fishman P, Bar-Yehuda S. Pharmacology and therapeutic applications of A3 receptor subtype. Curr Top Med Chem 2003; 3: 463-9.
31. Fredholm BB, Arslan G, Halldner BK, Schutle G, Wasserman W. Structure and function of adenosine receptors and their genes. Naunyn Schmiedebergs Arch Pharmacol 2000; 362: 364-74.
32. Parsons M, Young L, Lee IE, Jacobson KA, Liang BT. Distinct cardioprotective effects of adenosine mediated by differential coupling of receptor subtypes to phospholipases C and D. FASEB J 2000; 14: 1423-31.
33. Ferguson G, Watterson KR, Palmer TM. Subtype-specific kinetics of inhibitory adenosine receptor internalization are determined by sensitivity to phosphorylation by G protein-coupled receptor kinases. Mol Pharmacol 2000; 57: 546-52.
34. Palmer TM, Stiles GL. Identification of threonine residues controlling the agonist-dependent phosphorylation and desensitization of the rat A(3) adenosine receptor. Mol Pharmacol 2000; 57: 539-45.
35. Rorke S, Holgate ST. Targeting adenosine receptors: novel therapeutic targets in asthma and chronic obstructive pulmonary disease. Am J Respir Med 2002; 1: 99-105.
36. Jacobson KA. Adenosine A3 receptors: novel ligands and paradoxical effects. Trends Pharmacol Sci 1998; 19: 184-91.
37. Stone TW. Purines and neuroprotection. Adv Exp Med Biol 2002; 513: 249-80.
38. Molecular Operating Environment (MOE 2004.03), C. C. G., Inc, 1255 University St., Suite 1600, Montreal, Quebec, Canada, H3B 3X3.
39. Olah ME, Jacobson KA, Stiles GL. Role of the second extracellular loop of adenosine receptors in agonist and antagonist binding. Analysis of chimeric A1/A3 adenosine receptors. J Biol Chem 1994; 269: 24692-8.
40. Gao ZG, Van Muijwijk-Koezen JE, Chen A, Muller CE, Ijzerman AP, Jacobson KA. Allosteric modulation of A(3) adenosine receptors by a series of 3-(2-pyridinyl)isoquinoline derivatives. Mol Pharmacol 2001; 60: 1057-63.
41. Gao ZG, Chen A, Barak D, Kim SK, Muller CA, Jacobson KA. Identification by site-directed mutagenesis of residues involved in ligand recognition and activation of the human A3 adenosine receptor. J Biol Chem 2002; 277: 19056-63.
42. May LT, Avlani VA, Sexton PM, Christopoulos A. Allosteric modulation of G protein-coupled receptors. Curr Pharm Des 2004; 10(17): 2003-13.
43. Messer WS. Jr. Bivalent ligands for G protein-coupled receptors. Curr Pharm Des 2004; 10(17): 2015-20.
44. Piiper A, Zeuzem S. Receptor tyrosine kinases are signaling intermediates of G protein-coupled receptors. Curr Pharm Des 2004; 10(28): 3539-45.