Assessing the chemical and biological diversity of an ion channels knowledge database

Channels

Volumn 1, Issue 4, 2007, Pages 291-299

  Ijjaali, Ismaïl ^a   Dubus, Elodie ^a   Bourinet, Emmanuel ^b,c,d   Petitet, François ^a  

^a Aureus Pharma   (France)

^b INSTITUT DE GÉNOMIQUE FONCTIONNELLE   (France)

^c CNRS UMR5203   (France)

^d UNIV MONTPELLIER   (France)

Author keywords

Biological space; Chemical diversity; Drug design; Ion channel; Structure activity relationships (SAR)

Indexed keywords

AGENTS AFFECTING WATER, MOLECULE OR ION TRANSPORT; ION CHANNEL; LIGAND;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; DOSE RESPONSE; DRUG DESIGN; DRUG EFFECT; FACTUAL DATABASE; HUMAN; PRINCIPAL COMPONENT ANALYSIS; STRUCTURE ACTIVITY RELATION;

ANIMALS; CLUSTER ANALYSIS; DATABASES, FACTUAL; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG DESIGN; HUMANS; ION CHANNELS; LIGANDS; MEMBRANE TRANSPORT MODULATORS; MOLECULAR STRUCTURE; PRINCIPAL COMPONENT ANALYSIS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 53049108850     PISSN: 19336950     EISSN: 19336969     Source Type: Journal    
DOI: 10.4161/chan.5099     Document Type: Article

References (71)

1. Duan DY, Liu LL, Bozeat N, Huang ZM, Xiang SY, Wang GL, Ye L, Hume JR. Functional role of anion channels in cardiac diseases. Acta Pharmacol Sin 2005; 26: 265-78.
2. Warnock DG. Liddle syndrome: Genetics and mechanisms of Na+ channel defects. Am J Med Sci 2001; 322: 302-7.
3. Shieh CC, Coghlan M, Sullivan JP, Gopalakrishnan M. Potassium channels: Molecular defects, diseases, and therapeutic opportunities. Pharmacol Rev 2000; 52: 557-94.
4. Pardo LA, Contreras-Jurado C, Zientkowska M, Alves F, Stuhmer W. Role of voltage-gated potassium channels in cancer. J Membr Biol 2005; 205: 115-24.
5. Li S, Gosling M, Poll CT, Westwick J, Cox B. Therapeutic scope of modulation of nonvoltage-gated cation channels. Drug Design Technology 2005; 10: 129-37.
6. Jensen AA, Frølund B, Liljefors T, Krogsgaard-Larsen P. Neuronal nicotinic acetylcholine receptors: Structural revelations, target identifications, and therapeutic inspirations. J Med Chem 2005; 48: 4705-45.
7. Kalso E. Sodium channel blockers in neuropathic pain. Curr Pharm Des 2005; 11: 3005-11.
8. Modest VK, Steger M. GPCR-Tailored pharmacophore pattern recognition of small molecular ligands. J Chem Inf Comput Sci 2004; 44: 1137-47.
9. Balakin KV, Lang SA, Skorenko AV, Tkachenko SE, Ivashchenko AA, Savchuk NP. Structure-based versus property-based approaches in the design of G-protein coupled receptor-targeted libraries. J Chem Inf Comput Sci 2003; 43: 1553-62.
10. Aureus Pharma, Paris, France, www.aureus-pharma.com.
11. Dobson CM. Chemical space and biology. Nature 2004; 432: 824-8.
12. Lipinski C, Hopkins A. Navigating chemical space for biology and medicine. Nature 2004; 432: 855-61.
13. Stockwell BR. Exploring biology with small organic molecules. Nature 2004; 432: 846-54.
14. J Chem. version 3.5.2, ChemAxon, Budapest, Hungary, www.chemaxon.com.
15. MOE (Molecular Operating Environment), version 2005.06, Chemical Computing Group Inc., Montreal, Canada, Hhttp://www.chemcomp.comH.
16. Labute PA. Widely applicable set of descriptors. J Mol Graph Model 2000; 18: 464-77.
17. Doman TN, Cibulskis JM, Cibulskis MJ, McCray PD, Spangler DP. Algorithm5: A technique for fuzzy similarity clustering of chemical inventories. J Chem Inf Comput Sci 1996; 36: 1195-204.
18. Downs GM, Barnard JM. Clustering methods and their uses in computational chemistry. Rev Comput Chem 2004; 18: 1-40.
19. Stanton DT, Morris TW, Roychoudhury S, Parker CN. Application of nearest-neighbor and cluster analyses in pharmaceutical lead discovery. J Chem Inf Comput Sci 1999; 39: 21-7.
20. Ijjaali I, Dubus E, Bourinet E, Petitet F. Ligand-based virtual screening to identify new T-type calcium channel blockers. Channels 2007; 1: 291-5.
21. Jarvis RA, Patrick EA. Clustering using a similarity measure based on shared near neighbors. IEEE T Comput 1973; C22: 1025-34.
22. McGregor MJ, Pallai PV. Clustering of large databases of compounds: Using the MDL keys as structural descriptors. J Chem Inf Comput Sci 1997; 37: 443-8.
23. Bayada DM, Hamersma H, van Geerestein VJ. Molecular diversity and representativity in chemical databases. J Chem Inf Comput Sci 1999; 39: 1-10.
24. Natarajan R, Nirdosh I, Basak SC, Mills DR. QSAR modeling of flotation collectors using principal components extracted from topological indices. J Chem Inf Comput Sci 2002; 42: 1425-30.
25. Pathirathna S, Brimelow BC, Jagodic MM, Krishnan K, Jiang X, Zorumski CF, Mennerick S, Covey DF, Todorovic SM, Jevtovic-Todorovic V. New evidence that both T-type calcium channels and GABAA channels are responsible for the potent peripheral analgesic effects of 5alpha-reduced neuroactive steroids. Pain 2005; 114: 429-43.
26. Russell MG, Carling RW, Atack JR, Bromidge FA, Cook SM, Hunt P, Isted C, Lucas M, McKernan RM, Mitchinson A, Moore KW, Narquizian R, Macaulay AJ, Thomas D, Thompson SA, Wafford KA, Castro JL. Discovery of functionally selective 7,8,9,10-tetrahydro-7,10-ethano-1,2,4-triazolo[ 3,4-a]phthalazines as GABA A receptor agonists at the alpha3 subunit. J Med Chem 2005; 48: 1367-83.
27. Lin NH, Gunn DE, Li Y, He Y, Bai H, Ryther KB, Kuntzweiler T, Donnelly-Roberts DL, Anderson DJ, Campbell JE, Sullivan JP, Arneric SP, Holladay MW. Synthesis and structureactivity relationships of pyridine-modified analogs of 3-[2-((S)-pyrrolidinyl)methoxy]pyri dine, A-84543, a potent nicotinic acetylcholine receptor agonist. Bioorg Med Chem Lett 1998; 8: 249-54.
28. Maryanoff BE, Nortey SO, McNally JJ, Sanfilippo PJ, McComsey DF, Dubinsky B, Shank RP, Reitz AB. Potential anxiolytic agents. III. Novel A-ring modified pyrido[1,2-a]benzimi dazoles. Bioorg Med Chem Lett 1999; 9: 1547-52.
29. Schrimpf MR, Tietje KR, Toupence RB, Ji J, Basha A, Bunnelle WH, Daanen JF, Pace JM, Sippy KB. Diazabicyclic central nervous system active agents. Abbott Laboratories, 2001: WO 0181347.
30. Kazunori O, Osamu O, Kaoru M, Kiyoshi F, Makoto O. 5-substituted-3- oxadiazolyl-1, 6-naphthyridin-2(1H)-one derivatives. Dainippon Pharmaceutical, 2001: US 6172079.
31. Carotti A, Altomare C, Savini L, Chiasserini L, Pellerano C, Mascia MP, Maciocco E, Busonero F, Mameli M, Biggio G, Sanna E. High affinity central benzodiazepine receptor ligands. Part 3: Insights into the pharmacophore and pattern recognition study of intrinsic activities of pyrazolo[4,3-c]quinolin-3- ones. Bioorg Med Chem 2003; 11: 5259-72.
32. Chambers MS, Goodacre SC, Hallett DJ, Jennings A, Jones P, Lewis RT, Moore KW, Russel MG, Street LJ, Szekeres HJ. Imidazo-pyrimidine derivatives as ligands for GABA receptors. Merck Sharp & Dohme, 2002: WO 02074773.
33. Siegel PKS, Goldberg AI, Goldberg MR, Chang PI. Preparation of benzodiazepines for treating Meniere's disease. Merck & Co., Inc, 1997: WO 9749690.
34. Chambers MS, Jones P, MacLeod AM, Maxey RJ, Szekeres HJ. Nitrogen substituted 1,2,4-triazolo[3,4-A]phthalazine derivatives for enhancing condition. Merck & Co., Inc, 2004: US 043982.
35. Lopez-Tudanca PL, Labeaga L, Innerarity A, Alonso-Cires L, Tapia I, Mosquera R, Orjales A. Synthesis and pharmacological characterization of a new benzoxazole derivative as a potent 5-HT3 receptor agonist. Bioorg Med Chem 2003; 11: 2709-14.
36. Wang DX, Booth H, Lerner-Marmarosh N, Osdene TS, Abood LG. Structure-activity relationships for nicotine analogs comparing competition for [3H]nicotine binding and psychotropic potency. Drug Develop Res 1998; 45: 10-6.
37. Wong G, Koehler KF, Skolnick P, Gu ZQ, Ananthan S, Schonholzer P, Hunkeler W, Zhang W, Cook JM. Synthetic and computer-assisted analysis of the structural requirements for selective, high-affinity ligand binding to diazepam-insensitive benzodiazepine receptors. J Med Chem 1993; 36: 1820-30.
38. Crawforth J, Atack JR, Cook SM, Gibson KR, Nadin A, Owens AP, Pike A, Rowley M, Smith AJ, Sohal B, Sternfeld F, Wafford K, Street LJ. Tricyclic pyridones as functionally selective human GABAA alpha 2/3 receptor-ion channel ligands. Bioorg Med Chem Lett 2004; 14: 1679-82.
39. Dodd JH, Bullington JL, Hall DA, Henry JR, Rupert KC. Preparation of dihydropyridine derivatives as inhibitors of calcium-dependent smooth muscle contraction. Ortho-McNeil Pharmaceutical, 2001: WO 0192267.
40. Lewis RT, Blackaby WP, Blackburn T, Jennings AS, Pike A, Wilson RA, Hallett DJ, Cook SM, Ferris P, Marshall GR, Reynolds DS, Sheppard WF, Smith AJ, Sohal B, Stanley J, Tye SJ, Wafford KA, Atack JR. A pyridazine series of alpha2/alpha3 subtype selective GABA A agonists for the treatment of anxiety. J Med Chem 2006; 49: 2600-10.
41. Paolini GV, Shapland RHB, van Hoorn WP, Mason JS, Hopkins AL. Global mapping of the pharmacological space. Nature Biotechnology 2006; 24: 805-15.
42. Weerapura M, Nattel S, Chartier D, Caballero R, Hebert TE. A comparison of currents carried by HERG, with and without coexpression of MiRP1, and the native rapid delayed rectifier current: Is MiRP1 the missing link? J Physiol 2002; 540: 15-27.
43. Kornick CA, Kilborn MJ, Santiago-Palma J, Schulman G, Thaler HT, Keefe DL, Katchman AN, Pezzullo JC, Ebert SN, Woosley RL, Payne R, Manfredi PL. QTc interval prolongation associated with intravenous methadone. Pain 2003; 105: 499-506.
44. Gessner G, Zacharias M, Bechstedt S, Schonherr R, Heinemann SH. Molecular determinants for high-affinity block of human EAG potassium channels by antiarrhythmic agents. Mol Pharmacol 2004; 65: 1120.
45. John G Ondeyka, Richard G Ball, Maria L Garcia, Anne W Dombrowski, Gloria Sabnis, Gregory J Kaczorowski, Deborah L Zink, Gerald F Bills, Michael A Goetz, William A, Schmalhofer, Sheo B Singh. A carotane sesquiterpene as a potent modulator of the Maxi-K channel from Arthrinium phaesospermum. Bioorg Med Chem Lett 1995; 5: 733-4.
46. Selnick HG, Liverton NJ, Baldwin JJ, Butcher JW, Claremon DA, Elliott JM, Freidinger RM, King SA, Libby BE, McIntyre CJ, Pribush DA, Remy DC, Smith GR, Tebben AJ, Jurkiewicz NK, Lynch JJ, Salata JJ, Sanguinetti MC, Siegl PK, Slaughter DE, Vyas K. Class III antiarrhythmic activity in vivo by selective blockade of the slowly activating cardiac delayed rectifier potassium current IKs by (R)-2-(2,4-trifluoromethyl)-N-[2-oxo-5-pheny l-1-(2,2,2-trifluoroethyl)- 2, 3-dihydro-1H-benzo[e][1,4]diazepin-3-yl]acetamide. J Med Chem 1997; 40: 3865-8.
47. Wang J, Salata JJ, Bennett PB. Saxitoxin is a gating modifier of HERG K+ channels. J Gen Physiol 2003; 121: 583-98.
48. Kim YC, Brown SG, Harden TK, Boyer JL, Dubyak G, King BF, Burnstock G, Jacobson KA. Structure-activity relationships of pyridoxal phosphate derivatives as potent and selective antagonists of P2X1 receptors. J Med Chem 2001; 44: 340-349.
49. Bo X, Fischer B, Maillard M, Jacobson KA, Burnstock G. Comparative studies on the affinities of ATP derivatives for P2x-purinoceptors in rat urinary bladder. Br J Pharmacol 1994; 112: 1151-9.
50. Michel AD, Lundstrom K, Buell GN, Surprenant A, Valera S, Humphrey PP. A comparison of the binding characteristics of recombinant P2X1 and P2X2 purinoceptors. Br J Pharmacol 1996; 118: 1806-12.
51. Steward LJ, Boess FG, Steele JA, Liu D, Wong N, Martin IL. Importance of phenylalanine 107 in agonist recognition by the 5-hydroxytryptamine(3A) receptor. Mol Pharmacol 2000; 57: 1249-55.
52. Reeves DC, Goren EN, Akabas MH, Lummis SC. Structural and electrostatic properties of the 5-HT3 receptor pore revealed by substituted cysteine accessibility mutagenesis. J Biol Chem 2001; 276: 42035-42.
53. Werner P, Kawashima E, Reid J, Hussy N, Lundstrom K, Buell G, Humbert Y, Jones KA. Organisation of the mouse 5-HT3 receptor gene and functional expression of two splice variants. Brain Res Mol Brain Res 1994; 26: 233-41.
54. Macor JE, Gurley D, Lanthorn T, Loch J, Mack RA, Mullen G, Tran O, Wright N, Gordon JC. The 5-HT3 antagonist tropisetron (ICS 205-930) is a potent and selective alpha7 nicotinic receptor partial agonist. Bioorg Med Chem Lett 2001; 11: 319-21.
55. Yan D, White MM. Interaction of D-tubocurarine analogs with mutant 5-HT(3) receptors. Neuropharmacology 2002; 43: 367-73.
56. Baker SR, Boots J, Brunavs M, Dobson D, Green R, Hayhurst L, Keenan M, Wallace L. High affinity ligands for the alpha7 nicotinic receptor that show no cross-reactivity with the 5-HT3 receptor. Bioorg Med Chem Lett 2005; 15: 4727-30.
57. Hashimoto K, Fujita Y, Hagiwara H, Iyo M. Phencyclidine-induced cognitive deficits in mice are improved by subsequent subchronic administration of tropisetron: Role of alpha7 nicotinic receptors. Eur J Pharmacol 2006; 553: 191-5.
58. IUPHAR compendium of voltage-gated ion channels. http://www.iuphar-db. org/iuphar-ic/index.html.
59. Carroll FI, Ware R, Brieaddy LE, Navarro HA, Damaj MI, Martin BR. Synthesis, nicotinic acetylcholine receptor binding, and antinociceptive properties of 2'-fluoro-3'-(substituted phenyl)deschloroepibatidine analogues: Novel nicotinic antagonist. J Med Chem 2004; 47: 4588-94.
60. Lee J, Davis CB, Riviero RA, Reitz AB, Shank RP. Synthesis and structure-activity relationship of novel pyridyl ethers for the nicotinic acetylcholine receptor. Bioorg Med Chem Lett 2000; 10: 1063-6.
61. Lin NH, Li Y, He Y, Holladay MW, Kuntzweiler T, Anderson DJ, Campbell JE, Arneric SP. Synthesis and structure-activity relationships of 5-substituted pyridine analogues of 3-[2-((S)-pyrrolidinyl)methoxy]pyridine, A-84543, a potent nicotinic receptor Ligand. Bioorg Med Chem Lett 2001; 11: 631-3.
62. Koren AO, Horti AG, Mukhin AG, Guendisch D, Kimes AS, Dannals RF, London ED. 2-, 5-, and 6-Halo-3-(2(S)-azetidinylmethoxy)pyridines: Synthesis, affinity for nicotinic receptors, and molecular modeling. J Med Chem 1998; 41: 3690-8.
63. Zhang Y, Pavlova OA, Chefer SI, Hall AW, Kurian V, Brown LaVerne L, Kimes AS, Mukhin AG, Horti AG. 5-Substituted derivatives of 6-halogeno-3-((2-(S) azetidinyl)methoxy)pyridi ne and 6-halogeno-3-((2-(S)-pyrrolidinyl)methoxy) pyridine with low picomolar affinity for A4B2 nicotinic acetylcholine receptor and wide range of lipophilicity: Potential probes for imaging with positron emission tomography. J Med Chem 2004; 47: 2453-65.
64. Lin NH, Dong L, Bunnelle WH, Anderson DJ, Meyer MD. Synthesis and biological evaluation of puridine-modified analogues of 3-(2-aminoethoxy) pyridine as novel nicotinic receptor ligands. Bioorg Med Chem Lett 2002; 12: 3321-4.
65. Simsek R, Chang-Fong J, Lee M, Dukat M, Damaj MI, Martin BR, Glennon RA. Quaternary ammonium 3-(aminoethoxy)pyridines as antinociceptive agents. Bioorg Med Chem Lett 2003; 13: 2917-20.
66. Ernst G, Phillips E, Schmiesing R. Preparation of N-pyridylpiperazines and analogs as nicotinic receptor ligands. Astrazeneca, 2004: WO04016616.
67. Hendrix M, Boess FG, Erb C, Flessner T, Van Kampen M, Luithle J, Methfessel C, Wiese WB. Preparation of 2-heteroarylcarboxylic acid amides for therapeutic use as nicotinic acetylcholine receptor agonists. Bayer Aktiengesellschaft, 2003: WO03055878.
68. Nielsen SF, Nielsen EO, Olsen GM, Liljefors T, Peters D. Novel potent ligands for the central nicotinic acetylcholine receptor: Synthesis, receptor binding, and 3D-QSAR analysis. J Med Chem 2000; 43: 2217-26.
69. Balboni G, Marastoni M, Merighi S, Andrea Borea P, Tomatis R. Synthesis and activity of 3-pyridylamine ligands at central nicotinic receptors. Eur J Med Chem 2000; 35: 979-88.
70. Peters D, Olsen GM, Nielsen EO, Ahring PK, Nielsen SF, Jorgensen TD. Aryl-and heteroaryl-substituted diazabicycloalkanes as cholinergic ligands for the nicotinic acetylcholine receptor. Neurosearch A/S, 2002: WO0202564.
71. Peters D, Olsen GM, Nielsen SF, Nielsen EO. Preparation of N-pyridylpiperazines and analogs as nicotinic receptor ligands. Neurosearch A/S, 1999: WO9921834.