Linear and nonlinear 3D-QSAR approaches in tandem with ligand-based homology modeling as a computational strategy to depict the pyrazolo-triazolo- pyrimidine antagonists binding site of the human adenosine A2A receptor

Journal of Chemical Information and Modeling

Volumn 48, Issue 2, 2008, Pages 350-363

  Michielan, Lisa ^a   Bacilieri, Magdalena ^a   Schiesaro, Andrea ^a   Bolcato, Chiara ^b   Pastorin, Giorgia ^b   Spalluto, Giampiero ^b   Cacciari, Barbara ^c   Klotz, Karl Norbet ^d   Kaseda, Chosei ^e   Moro, Stefano ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF TRIESTE   (Italy)

^c UNIVERSITY OF FERRARA   (Italy)

^d UNIVERSITY OF WÜRZBURG   (Germany)

^e YAMATAKE CORPORATION   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; LIGANDS;

BINDING AFFINITY; COMPUTATIONAL TECHNIQUES;

NUCLEOTIDES;

ADENOSINE A2A RECEPTOR; LIGAND; PYRAZOLE DERIVATIVE; PYRIMIDINE DERIVATIVE; TRIAZOLE DERIVATIVE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; HUMAN; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SEQUENCE HOMOLOGY;

BINDING SITES; HUMANS; LIGANDS; MODELS, MOLECULAR; PYRAZOLES; PYRIMIDINES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTOR, ADENOSINE A2A; SEQUENCE HOMOLOGY, AMINO ACID; TRIAZOLES;

EID: 41549169302     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700300w     Document Type: Article

References (67)

1. Moro, S.; Bacilieri, M.; Deflorian, F. Combining Ligand-Based and Structure-Based Drug Design in the Virtual Screening Arena. Expert Opin. Drug Discovery 2007, 2, 37-49.
2. Fanelli, F.; De Benedetti, P. G. Computational Modeling Approaches to Structure-Function Analysis of G Protein-Coupled Receptors. Chem. Rev. 2005, 105, 3297-3351.
3. 3 Adenosine Receptor as an Example. Trends Pharmacol. Sci. 2005, 26, 44-51.
4. Cramer, R. D. I.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5969-5967.
5. Moro, S.; Bacilieri, M.; Ferrari, C.; Spalluto, G. Autocorrelation of Molecular Electrostatic Potential Surface Properties Combined with Partial Least Squares Analysis as Alternative Attractive Tool to Generate Ligand-Based 3D-QSARs. Curr. Drug Discovery. Technol. 2005, 2, 13-21.
6. 3 Adenosine Receptor Antagonists. J. Med. Chem. 2005, 48, 5698-5704.
7. 3 Adenosine Receptor Antagonist. Bioorg. Med. Chem. 2006, 14, 4923-4932.
8. 3 Adenosine Receptor Antagonists as a Key Study. Lett. Drug Des. Discovery 2007, 4, 122-127.
9. Bacilieri, M.; Varano, F.; Deflorian, F.; Marini, M.; Catarzi, D.; Colotta, V.; Filacchioni, G.; Galli, A.; Costagli, C.; Kaseda, C.; Moro, 5. Tandem 3D-QSARs Approach as Valuable Tool to Predict Binding Affinity Data: Design of New Gly/NMDA Receptor Antagonists as a Key Study. J. Chem. Inf. Model. 2007, in press.
10. Moro, S.; Bacilieri, M.; Deflorian, F.; Spalluto, G. G Protein-Coupled Receptors as Challenging Draggable Targets: Insights from in Silico Studies. New J. Chem. 2006, 30, 301-308.
11. Moro, S.; Deflorian, F.; Bacilieri, M.; Spalluto, G. Ligand-Based Homology Modeling as Attractive Tool to Inspect GPCR Structural Plasticity. Curr. Pharm. Des. 2006, 12, 2175-2185.
12. 3 Adenosine Receptor Antagonists. Synthesis, Pharmacological Evaluation and Ligand-Receptor Modeling Studies. J. Med. Chem. 2007, 50, 4061-4074.
13. Bolcato, C.; Cusan, C.; Pastorin, G.; Spalluto, G.; Cacciari, B.; Klotz, K. N.; Morizzo, E.; Moro, S. Pyrazolo-triazolo-pyrimidines as Adenosine Receptor Antagonists: Effect of the N-5 Bond Type on the Affinity and Selectivity at the Four Adenosine Receptor Subtypes. Purinergic Signalling, 2007, in press, DOI: 10.1007/s11302-007-9058-y.
14. Fredholm, B. B.; Arslan, G.; Halldner, L.; Kull, B.; Schulte, G.; Wasserman, W. Structure and Function of Adenosine Receptors and their Genes. Naunyn-Schmiedeberg's Arch. Pharmacol. 2000, 362, 364-374.
15. Ferre, S.; Von, Euler, G.; Johansson, B.; Fredholm, B. B.; Fuxe, K. Stimulation of High-Affinity Adenosine A2 Receptors Decreases the Affinity of Dopamine D2 Receptors in Rat Striatal Membranes. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 7238-7241.
16. Ribeiro, J. A.; Sebastiao, A. M.; De Mendonca, A. Adenosine Receptors in the Nervous System: Pathophysiological Implications. Prog. Neurobiol. 2002, 68, 377-392.
17. Jacobson, K. A.; Gao, Z. G. Adenosine Receptors as Therapeutic Targets. Nat. Rev. Drug Discovery 2006, 5, 247-264.
18. 2A Receptor Antagonists in Parkinson's Disease. Pharmacol. Ther. 2005, 105, 267-310.
19. 2A Receptor Antagonists: Actions on Parkinson's Disease Models. Eur. J. Pharmacol. 2005, 512, 157-164.
20. Johnston, T. H.; Brotchie, J. M. Drugs in Development for Parkinson's Disease: an Update. Curr. Opin. Invest. Drugs 2006, 7, 25-32.
21. 2A Adenosine Receptor Agonists and Antagonists. Chem. Med. Chem. 2007, 2, 260-281.
22. Baraldi, P. G.; Cacciari, B.; Borea, P. A.; Varani, K.; Pastorin, G.; Da, Ros, T.; Tabrizi, M. A.; Fruttarolo, F.; Spalluto, G. Pyrazolotriazolo- pyrimidine Derivatives as Adenosine Receptor Antagonists: a Possible Template for Adenosine Receptor Subtypes? Curr. Pharm. Des. 2002, 5, 2299-2332.
23. Moro, S.; Gao, Z. G.; Jacobson, K. A.; Spalluto, G. Progress in the Pursuit of Therapeutic Adenosine Receptor Antagonists. Med. Res. Rev. 2006, 26, 131-159.
24. 3 Adenosine Receptor Antagonists. Eur. J. Med. Chem. 2003, 38, 367-382.
25. 2A Adenosine Receptor Antagonists: a Study on the Importance of Modifications at the Side Chain on the Activity and Solubility. J. Med. Chem. 2002, 45, 115-126.
26. 2A Adenosine Receptor Antagonists. J. Med. Chem. 1998, 41, 2126-2133.
27. 3 Adenosine Receptor Antagonists. J. Med. Chem. 2002, 45, 770-780.
28. 3 Adenosine Receptor. Drug Dev. Res. 2001, 52, 406-415.
29. 3 Adenosine Receptors Antagonists. J. Med. Chem. 2003, 46, 1229-1241.
30. Guba, W.; Nettekoven, M.; Pullmann, B.; Riemer, C.; Schmitt, S. Comparison of Inhibitory Activity of Isomeric Triazolopyridine Derivatives towards Adenosine Receptor Subtypes or Do Similar Structures Reveal Similar Bioactivities? Bioorg. Med. Chem. Lett. 2004, 14, 3307-3312.
31. OpenMosix, version 2.4.26; Moshe Bar, Tel Aviv University: Israel, 2004.
32. Adriana, version 2.0; Molecular Networks GmbH: Erlangen, Germany, 2003.
33. The Unscrumbler, version 9.2; CAMO Process AS: Oslo, Norway, 2003.
34. DataFOREST, version 9; Yamatake Corporation: Fujisawa-shi Kanagawa, Japan, 2007.
35. DataNESIA, version 3.2; Yamatake Corporation: Fujisawa-shi Kanagawa, Japan, 2007.
36. Molecular Operating Environment, version 2006.08; Chemical Computing Group: Montreal, Canada, 2006.
37. MOPAC, version 7; J. J. P. Stewart, Fujitsu Limited: Tokyo, Japan, 1993.
38. Gasteiger, J.; Marsili, M. Iterative Partial Equalization of Orbital Electronegativity - a Rapid Access to Atomic Charges. Tetrahedron 1980, 36, 3219-3228.
39. Gasteiger, J.; Saller, H. Calculation of the Charge Distribution in Conjugated Systems by a Quantification of the Resonance Concept. Angew. Chem., Int. Ed. Engl. 1985, 24, 687-689.
40. Moreau, G.; Broto, P. The Autocorrelation of a Topological Structure: a New Molecular Descriptor. Nouv. J. Chim. 1980, 4, 359-360.
41. Moreau, G.; Broto, P. Autocorrelation of Molecular Structures, Application to SAR Studies. Nouv. J. Chim. 1980, 4, 757-764.
42. Gasteiger, J.; Li, X.; Rudolph, C.; Sadovski, J.; Zupan, J. Representation of Molecular Electrostatic Potential by Topological Feature Maps. J. Am. Chem. Soc. 1994, 116, 4608-4620.
43. Wagener, M.; Sadovski, J.; Gasteiger, J. Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks. J. Am. Chem. Soc. 1995, 117, 7769-7778.
44. Bauknecht, H.; Zell, A.; Bayer, H.; Levi, P.; Wagener, M.; Sadowski, J.; Gasteiger, J. Locating Biologically Active Compounds in Medium-Sized Heterogeneous Datasets by Topological Autocorrelation Vectors: Dopamine and Benzodiazepine Agonists. J. Chem. Inf. Comput. Sci. 1996, 36, 1205-1213.
45. Myers, R.; Montgomery, D. C. Response methodology surface; John Wiley, Ed.; Wiley-Interscience: New York, U.S.A., 1995.
46. Kaseda, C. Response Surface Methodology using a spline algorithm; G.d.a.c.S., Ed.; Nashboro Press: Fujisawa-shi Kanagawa, Japan, 2004.
47. 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, 739-745.
48. Cornell, W. D. C. P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5196.
49. Levitt, M. Accurate Modeling of Protein Conformation by Automatic Segment Matching. J. Mol. Biol. 1992, 226, 507-533.
50. Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity. Proteins: Struct., Funct. Genet. 1998, 33, 367-382.
51. Halgren, T. Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
52. 8 Pyrazole Nitrogen, J. Med. Chem. 2000, 43, 4768-4780.
53. 3 Adenosine Receptor Antagonists. Influence of the Heteroaryl Substituent on Binding Affinity and Molecular Modeling Investigation. J. Med. Chem. 2006, 49, 1720-1729.
54. Karaneswsky, C.; Thomson, D.; Michellys, A.; Ruppar, P.; Chen, J. H. PCT Int. Appl. 2005, WO2005009104200-2005009140716.
55. Klotz, K. N.; Hessling, J.; Hegler, J.; Owman, C.; Kull, B.; Fredholm, B. B.; Lohse, M. J. Comparative Pharmacology of Human Adenosine Receptor Subtypes-Characterization of Stably Transfected Receptors in CHO Cells. Naunyn-Schmiedeberg's Arch. Pharmacol. 1998, 357, 1-9.
56. De Lean, A.; Hancock, A. A.; Lefkowitz, R. J. Validation and Statistical Analysis of a Computer Modeling Method for Quantitative Analysis of Radioligand Binding Data for Mixtures of Pharmacological Receptor Subtypes. Mol. Pharmacol. 1982, 21, 5-16.
57. 1 Adenosine Receptors. J. Biol. Chem. 1985, 260, 14659-14664.
58. i) and the Concentration of Inhibitor which Causes 50% Inhibition (IC50) of an Enzymatic Reaction. Biochem. Pharmacol. 1973, 22, 3099-3108.
59. Brown, G.; Wyatt, J.; Harris, R.; Yao, X. Diversity Creation Methods: a Survey and Categorisation. J. Inf. Fusion. 2005, 6, 1-28.
60. Cacciari, B.; Bolcato, C.; Spalluto, G.; Klotz, K.-N.; Bacilieri, M.; Deflorian, F.; Moro, S. Pyrazolo-triazolo-pyrimidines as Adenosine Receptor Antagonists: A Complete Structure-Activity Profile. Purinergic Signalling 2007, 3, 183-193.
61. 3 Adenosine Receptor Antagonists: Synthesis, Pharmacological and Ligand-Receptor Modeling Studies. J. Med. Chem. 2004, 47, 3580-3590.
62. 3 Adenosine Receptor Antagonists. Bioorg. Med. Chem. 2005, 13, 705-715.
63. 3 Adenosine Receptor Antagonists: Synthesis, Biological Evaluation and Molecular Modeling Studies of 2-(hetero)aryl- and 2-carboxy-substituted Derivatives. J. Med. Chem. 2005, 45, 7932-7945.
64. 3 Adenosine Receptor Antagonists. Synthesis, Pharmacological Evaluation and Ligand-Receptor Modeling Studies, J. Med. Chem. 2006, 49, 3916-3925.
65. Moro, S.; Deflorian, F.; Spalluto, G.; Pastorin, G.; Cacciari, B.; Kim, S. K.; Jacobson, K. A. Demystifying the Three Dimensional Structure of G Protein-Coupled Receptors (GPCRs) with the Aid of Molecular Modeling. Chem. Commun. (Cambridge) 2003, 2949-2956.
66. 3 Receptor Antagonists: an Update. Curr. Med. Chem. 2006, 13, 639-645.
67. 3 Adenosine Receptor. J. Biol. Chem. 2002, 277, 19056-19063.