Pharmacophore mapping and in silico screening to identify new potent leads for A 2A adenosine receptor as antagonists

Journal of Receptors and Signal Transduction

Volumn 32, Issue 2, 2012, Pages 102-113

  Mustyala, Kiran Kumar ^a   Chitturi, Annapurna Renee ^a   Naikal James, Prameela Subhashini ^a   Vuruputuri, Uma ^a  

^a OSMANIA UNIVERSITY   (India)

Author keywords

3D QSAR; A 2A adenosine receptor; Docking; Pharmacophore mapping; PHASE; Virtual screening

Indexed keywords

ADENOSINE A2 RECEPTOR; ADENOSINE A2 RECEPTOR ANTAGONIST;

COMPUTER MODEL; DATA BASE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; PHARMACOPHORE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW;

BINDING SITES; COMPUTER SIMULATION; DATABASES, FACTUAL; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PURINERGIC P1 RECEPTOR ANTAGONISTS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTOR, ADENOSINE A2A; SMALL MOLECULE LIBRARIES;

EID: 84858176208     PISSN: 10799893     EISSN: 15324281     Source Type: Journal    
DOI: 10.3109/10799893.2012.660532     Document Type: Review

References (65)

1. Jacobson KA, Gao ZG. Adenosine receptors as therapeutic targets. Nat Rev Drug Discov 2006, 5, 247-264. (Pubitemid 43336037)
2. Abbracchio MP, Burnstock G, Verkhratsky A, Zimmermann H. Purinergic signalling in the nervous system: an overview. Trends Neurosci 2009, 32, 19-29.
3. Fredholm BB, IJzerman AP, Jacobson KA, Klotz KN, Linden J. International Union of Pharmacology. XXV. Nomenclature and classifcation of adenosine receptors. Pharmacol Rev 2001, 53, 527-552. (Pubitemid 33136237)
4. Fredholm BB, Arslan G, Halldner L, Kull B, Schulte G, Wasserman W. Structure and function of adenosine receptors and their genes. Naunyn Schmiedebergs Arch Pharmacol 2000, 362, 364-374.
5. Dunwiddie T V, Masino SA. The role and regulation of adenosine in the central nervous system. Annu Rev Neurosci 2001, 24, 31-55. (Pubitemid 32695222)
6. Sawynok J, Liu XJ. Adenosine in the spinal cord and periphery: release and regulation of pain. Prog Neurobiol 2003, 69, 313-340. (Pubitemid 36645052)
7. Shi Y, Liu X, Gebremedhin D, Falck JR, Harder DR, Koehler RC. Interaction of mechanisms involving epoxyeicosatrienoic acids, adenosine receptors, and metabotropic glutamate receptors in neurovascular coupling in rat whisker barrel cortex. J Cereb Blood Flow Metab 2008, 28, 111-125.
8. Schwarzschild MA, Agnati L, Fuxe K, Chen JF, Morelli M. Targeting adenosine A2A receptors in Parkinson's disease. Trends Neurosci 2006, 29, 647-654. (Pubitemid 44602262)
9. Lahiri S, Mitchell CH, Reigada D, Roy A, Cherniack NS. Purines, the carotid body and respiration. Respir Physiol Neurobiol 2007, 157, 123-129. (Pubitemid 46621170)
10. Basheer R, Strecker RE, Takkar MM, McCarley RW. Adenosine and sleep-wake regulation. Prog Neurobiol 2004, 73, 379-396. (Pubitemid 39094087)
11. Meng F, Xie GX, Chalmers D, Morgan C, Watson SJ Jr, Akil H. Cloning and expression of the A2a adenosine receptor from guinea pig brain. Neurochem Res 1994, 19, 613-621. (Pubitemid 24139256)
12. Peterfreund RA, MacCollin M, Gusella J, Fink JS. Characterization and expression of the human A2a adenosine receptor gene. J Neurochem 1996, 66, 362-368. (Pubitemid 26010801)
13. Jaakola VP, Grifth MT, Hanson MA, Cherezov V, Chien EY, Lane JR, Ijzerman AP, Stevens RC. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 2008, 322, 1211-1217.
14. Fredholm BB. Adenosine, an endogenous distress signal, modulates tissue damage and repair. Cell Death Difer 2007, 14, 1315-1323. (Pubitemid 46965261)
15. Schapira AH, Bezard E, Brotchie J, Calon F, Collingridge GL, Ferger B, Hengerer B, Hirsch E, Jenner P, Le Novère N, Obeso JA, Schwarzschild MA, Spampinato U, Davidai G. Novel pharmacological targets for the treatment of Parkinson's disease. Nat Rev Drug Discov 2006, 5, 845-854. (Pubitemid 44480538)
16. Blum D, Hourez R, Galas MC, Popoli P, Schifmann SN. Adenosine receptors and Huntington's disease: implications for pathogenesis and therapeutics. Lancet Neurol 2003, 2, 366-374. (Pubitemid 38352564)
17. Satoh S, Matsumura H, Hayaishi O. Involvement of adenosine A2A receptor in sleep promotion. Eur J Pharmacol 1998, 351, 155-162. (Pubitemid 28312926)
18. Yao L, Arolfo MP, Dohrman DP, Jiang Z, Fan P, Fuchs S, Janak PH, Gordon AS, Diamond I. betagamma Dimers mediate synergy of dopamine D2 and adenosine A2 receptor-stimulated PKA signaling and regulate ethanol consumption. Cell 2002, 109, 733-743. (Pubitemid 34722269)
19. El Yacoubi M, Ledent C, Parmentier M, Daoust M, Costentin J, Vaugeois J. Absence of the adenosine A(2A) receptor or its chronic blockade decrease ethanol withdrawal-induced seizures in mice. Neuropharmacology 2001, 40, 424-432. (Pubitemid 32144720)
20. Okusa MD, Linden J, Huang L, Rieger JM, Macdonald TL, Huynh L P. A(2A) adenosine receptor-mediated inhibition of renal injury and neutrophil adhesion. Am J Physiol Renal Physiol 2000, 279, F809-F818.
21. Gao Z, Li Z, Baker SP, Lasley RD, Meyer S, Elzein E, Palle V, Zablocki JA, Blackburn B, Belardinelli L. Novel short-acting A2A adenosine receptor agonists for coronary vasodilation: inverse relationship between afnity and duration of action of A2A agonists. J Pharmacol Exp Ter 2001, 298, 209-218. (Pubitemid 32574529)
22. Schindler CW, Karcz-Kubicha M, Torndike EB, Müller CE, Tella SR, Ferré S, Goldberg SR. Role of central and peripheral adenosine receptors in the cardiovascular responses to intraperitoneal injections of adenosine A1 and A2A subtype receptor agonists. Br J Pharmacol 2005, 144, 642-650. (Pubitemid 40445612)
23. Varani K, Portaluppi F, Gessi S, Merighi S, Ongini E, Belardinelli L, Borea PA. Dose and time efects of cafeine intake on human platelet adenosine A(2A) receptors: functional and biochemical aspects. Circulation 2000, 102, 285-289. (Pubitemid 30457577)
24. Peirce SM, Skalak TC, Rieger JM, Macdonald TL, Linden J. Selective A(2A) adenosine receptor activation reduces skin pressure ulcer formation and infammation. Am J Physiol Heart Circ Physiol 2001, 281, H67-H74.
25. Brown RA, Spina D, Page CP. Adenosine receptors and asthma. Br J Pharmacol 2008, 153 Suppl 1, S446-S456. (Pubitemid 351341018)
26. Fozard JR, Ellis KM, Villela Dantas MF, Tigani B, Mazzoni L. Efects of CGS 21680, a selective adenosine A2A receptor agonist, on allergic airways infammation in the rat. Eur J Pharmacol 2002, 438, 183-188. (Pubitemid 34241507)
27. Montesinos MC, Desai A, Delano D, Chen JF, Fink JS, Jacobson MA, Cronstein BN. Adenosine A2A or A3 receptors are required for inhibition of infammation by methotrexate and its analog MX-68. Arthritis Rheum 2003, 48, 240-247. (Pubitemid 36091669)
28. Sullivan GW, Fang G, Linden J, Scheld WM. A2A adenosine receptor activation improves survival in mouse models of endotoxemia and sepsis. J Infect Dis 2004, 189, 1897-1904. (Pubitemid 38657226)
29. Odashima M, Bamias G, Rivera-Nieves J, Linden J, Nast CC, Moskaluk CA, Marini M, Sugawara K, Kozaiwa K, Otaka M, Watanabe S, Cominelli F. Activation of A2A adenosine receptor attenuates intestinal infammation in animal models of infammatory bowel disease. Gastroenterology 2005, 129, 26-33. (Pubitemid 41002039)
30. Montesinos MC, Gadangi P, Longaker M, Sung J, Levine J, Nilsen D, Reibman J, Li M, Jiang CK, Hirschhorn R, Recht PA, Ostad E, Levin RI, Cronstein BN. Wound healing is accelerated by agonists of adenosine A2 (G alpha s-linked) receptors. J Exp Med 1997, 186, 1615-1620. (Pubitemid 27479823)
31. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. Binding DB: a web-accessible database of experimentally determined protein-ligand binding afnities. Nucleic Acids Res 2007, 35, D198-D201. (Pubitemid 46056198)
32. Okamura T, Kurogi Y, Hashimoto K, Sato S, Nishikawa H, Kiryu K, Nagao Y. Structure-activity relationships of adenosine A3 receptor ligands: new potential therapy for the treatment of glaucoma. Bioorg Med Chem Lett 2004, 14, 3775-3779. (Pubitemid 38765172)
33. Okamura T, Kurogi Y, Nishikawa H, Hashimoto K, Fujiwara H, Nagao Y. 1,2,4-Triazolo5,1-ipurine derivatives as highly potent and selective human adenosine A(3) receptor ligands. J Med Chem 2002, 45, 3703-3708. (Pubitemid 34856110)
34. Minetti P, Tinti MO, Carminati P, Castorina M, Di Cesare MA, Di Serio S, Gallo G, Ghirardi O, Giorgi F, Giorgi L, Piersanti G, Bartoccini F, Tarzia G. 2-n-Butyl-9-methyl-8-1,2,3triazol-2-yl-9H-purin-6-ylamine and analogues as A2A adenosine receptor antagonists. Design, synthesis, and pharmacological characterization. J Med Chem 2005, 48, 6887-6896. (Pubitemid 41533110)
35. Baraldi PG, Fruttarolo F, Tabrizi MA, Preti D, Romagnoli R, El-Kashef H, Moorman A, Varani K, Gessi S, Merighi S, Borea PA. Design, synthesis, and biological evaluation of C9-and C2-substituted pyrazolo4,3-e-1,2,4-triazolo1,5- cpyrimidines as new A2A and A3 adenosine receptors antagonists. J Med Chem 2003, 46, 1229-1241. (Pubitemid 36428228)
36. Michielan L, Bolcato C, Federico S, Cacciari B, Bacilieri M, Klotz KN, Kachler S, Pastorin G, Cardin R, Sperduti A, Spalluto G, Moro S. Combining selectivity and afnity predictions using an integrated Support Vector Machine (SVM) approach: An alternative tool to discriminate between the human adenosine A(2A) and A(3) receptor pyrazolo-triazolo-pyrimidine antagonists binding sites. Bioorg Med Chem 2009, 17, 5259-5274.
37. Campbell RM, Cartwright C, Chen W, Chen Y, Duzic E, Fu JM, Loveland M, Manning R, McKibben B, Pleiman CM, Silverman L, Trueheart J, Webb DR, Wilkinson V, Witter DJ, Xie X, Castelhano AL. Selective A1-adenosine receptor antagonists identifed using yeast Saccharomyces cerevisiae functional assays. Bioorg Med Chem Lett 1999, 9, 2413-2418. (Pubitemid 29391532)
38. Mantri M, de Graaf O, van Veldhoven J, Göblyös A, von Frijtag Drabbe Künzel JK, Mulder-Krieger T, Link R, de Vries H, Beukers MW, Brussee J, Ijzerman AP. 2-Amino-6-furan-2-yl-4-substituted nicotinonitriles as A2A adenosine receptor antagonists. J Med Chem 2008, 51, 4449-4455.
39. Beattie D, Brearley A, Brown Z, Charlton SJ, Cox B, Fairhurst RA, Fozard JR, Gedeck P, Kirkham P, Meja K, Nanson L, Neef J, Oakman H, Spooner G, Taylor RJ, Turner RJ, West R, Woodward H. Synthesis and evaluation of two series of 4'-aza-carbocyclic nucleosides as adenosine A2A receptor agonists. Bioorg Med Chem Lett 2010, 20, 1219-1224.
40. Duplantier AJ, Bachert EL, Cheng JB, Cohan VL, Jenkinson TH, Kraus KG, McKechney MW, Pillar JD, Watson JW. SAR of a series of 5,6-dihydro-(9H)- pyrazolo3,4-c-1,2,4-triazolo4,3-alphapyridines as potent inhibitors of human eosinophil phosphodiesterase. J Med Chem 2007, 50, 344-349. (Pubitemid 46147713)
41. Lanier MC, Moorjani M, Luo Z, Chen Y, Lin E, Tellew JE, Zhang X, Williams J P, Gross RS, Lechner SM, Markison S, Joswig T, Kargo W, Piercey J, Santos M, Malany S, Zhao M, Petroski R, Crespo MI, Díaz JL, Saunders J, Wen J, O'Brien Z, Jalali K, Madan A, Slee DH. N-6-amino-2-(heteroaryl)pyrimidin-4- ylacetamides as A2A receptor antagonists with improved drug like properties and in vivo efcacy. J Med Chem 2009, 52, 709-717.
42. Zhang X, Tellew JE, Luo Z, Moorjani M, Lin E, Lanier MC, Chen Y, Williams JP, Saunders J, Lechner SM, Markison S, Joswig T, Petroski R, Piercey J, Kargo W, Malany S, Santos M, Gross RS, Wen J, Jalali K, O'Brien Z, Stotz CE, Crespo MI, Díaz JL, Slee DH. Lead optimization of 4-acetylamino-2-(3,5- dimethylpyrazol-1-yl)-6-pyridylpyrimidines as A2A adenosine receptor antagonists for the treatment of Parkinson's disease. J Med Chem 2008, 51, 7099-7110.
43. Dixon SL, Smondyrev AM, Rao SN. PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Des 2006, 67, 370-372.
44. Brooks WH, Daniel KG, Sung SS, Guida WC. Computational validation of the importance of absolute stereochemistry in virtual screening. J Chem Inf Model 2008, 48, 639-645. (Pubitemid 351535431)
45. Mohamadi F, Richards NGJ, Guida WC, Liskamp R, Lipton M, Caufeld C, et al. Macromodel-an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J Computational Chemistry 1990, 11, 440-467.
46. Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field. J Chemical Teory and Computation 2010, 6, 1509-1519.
47. Chang G, Guida WC, Still WC. An internal-coordinate Monte Carlo method for searching conformational space. J American Chemical Society 1989, 111, 4379-4386.
48. Goodman JM, Still WC. An unbounded systematic search of conformational space. Journal of Computational Chemistry. 1991, 12, 1110-1117.
49. Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 2006, 20, 647-671. (Pubitemid 46023928)
50. Chen X, Rusinko A, Young SS. Recursive Partitioning Analysis of a Large Structureâ̂'Activity Data Set Using Tree-Dimensional Descriptors1. J Chem Inf Comput Sci 1998, 38, 1054-1062. (Pubitemid 128591268)
51. Chen X, Rusinko A 3rd, Tropsha A, Young SS. Automated pharmacophore identifcation for large chemical data sets. J Chem Inf Comput Sci 1999, 39, 887-896.
52. Lather V, Kristam R, Saini JS, Karthikeyan NA, Balaji VN. QSAR Models for Prediction of Glycogen Synthase Kinase-3β Inhibitory Activity of Indirubin Derivatives. QSAR & Combinatorial Science 2008, 27, 718-728.
53. Hansch C, Muir R, Fujita T, Maloney P, Geiger F, Streich M. The Correlation of Biological Activity of Plant Growth Regulators and Chloromycetin Derivatives with Hammett Constants and Partition Coefcients. J American Chemical Society 1963, 85, 2817-2824.
54. Narkhede SS, Degani MS. Pharmacophore Refnement and 3D-QSAR Studies of Histamine H3 Antagonists. QSAR & Combinatorial Science 2007, 26, 744-753. (Pubitemid 46984720)
55. Telvekar VN, Kundaikar HS, Patel KN, Chaudhari HK. 3-D QSAR and Molecular Docking Studies on Aryl Benzofuran-2-yl Ketoxime Derivatives as Candida albicans N-myristoyl transferase Inhibitors. QSAR & Combinatorial Science 2008, 27, 1193-1203.
56. Bag S, Tawari NR, Degani MS. Insight into Inhibitory Activity of Mycobacterial Dihydrofolate Reductase Inhibitors by In-silico Molecular Modeling Approaches. QSAR & Combinatorial Science 2009, 28, 296-311.
57. Shoichet BK. Virtual screening of chemical libraries. Nature 2004, 432, 862-865. (Pubitemid 40037142)
58. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004, 47, 1739-1749. (Pubitemid 38380917)
59. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard W T, Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004, 47, 1750-1759. (Pubitemid 38380918)
60. Almerico AM, Tutone M, Lauria A. 3D-QSAR pharmacophore modeling and in silico screening of new Bcl-xl inhibitors. Eur J Med Chem 2010, 45, 4774-4782.
61. Tawari NR, Degani MS. Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity. J Comput Chem 2010, 31, 739-751.
62. Rajender PS, Vasavi M, Vuruputuri U. Identifcation of novel selective antagonists for cyclin C by homology modeling and virtual screening. Int J Biol Macromol 2011, 48, 292-300.
63. Pawar V, Lokwani D, Bhandari S, Mitra D, Sabde S, Bothara K, Madgulkar A. Design of potential reverse transcriptase inhibitor containing Isatin nucleus using molecular modeling studies. Bioorg Med Chem 2010, 18, 3198-3211.
64. Reddy AS, Pati SP, Kumar PP, Pradeep HN, Sastry GN. Virtual screening in drug discovery-a computational perspective. Curr Protein Pept Sci 2007, 8, 329-351. (Pubitemid 47317040)
65. Yang SY. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov Today 2010, 15, 444-450.