Computational analysis of the binding ability of heterocyclic and conformationally constrained epibatidine analogs in the neuronal nicotinic acetylcholine receptor

Molecular Diversity

Volumn 14, Issue 2, 2010, Pages 201-211

  Soriano, Elena ^a   Marco Contelles, José ^a   Colmena, Inés ^b   Gandía, Luis ^b  

^a INSTITUTO DE QUÍMICA ORGÁNICA GENERAL   (Spain)

^b INSTITUTO TEÓFILO HERNANDO   (Spain)

Author keywords

Epibatidine; Epibatidine analogs; Molecular docking; Nicotinic acetylcholine receptor (nAChR; Pharmacophore

Indexed keywords

DRUG ANALOG; EPIBATIDINE; FREE RADICAL; NICOTINIC RECEPTOR ALPHA4BETA2; OXADIAZOLE DERIVATIVE; FUSED HETEROCYCLIC RINGS; NICOTINIC RECEPTOR; PYRIDINE DERIVATIVE;

ARTICLE; DRUG ANALYSIS; DRUG BINDING; DRUG CONFORMATION; DRUG SYNTHESIS; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL; ANIMAL; BINDING SITE; BIOLOGY; CALCIUM SIGNALING; CATTLE; CELL CULTURE; CHEMISTRY; CHROMAFFIN CELL; CONFORMATION; METABOLISM; METHODOLOGY; MOLECULAR DYNAMICS; PROTEIN BINDING;

ANIMALS; BICYCLO COMPOUNDS, HETEROCYCLIC; BINDING SITES; CALCIUM SIGNALING; CATTLE; CELLS, CULTURED; CHROMAFFIN CELLS; COMPUTATIONAL BIOLOGY; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PYRIDINES; RECEPTORS, NICOTINIC;

EID: 77954662702     PISSN: 13811991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11030-009-9161-9     Document Type: Article

References (34)

1. Gotti C, Riganti L, Vailati S, Clementi F (2006) Brain neuronal nicotinic receptors as new targets for drug discovery. Curr Pharm Des 12:407-428. doi:10.2174/138161206775474486
2. Unwin N (2005) Refined structure of nicotinic receptors at 4ANG resolution. J Mol Biol 346:967-989. doi:10.1016/j.jmb.2004.12. 031 (Pubitemid 40215523)
3. Sine SM (2002) The nicotinic receptor ligand binding domain. J Neurobiol 53:431-446. doi:10.1002/neu.10139 (Pubitemid 35375577)
4. Brejc K, van Dijk WJ, Klaassen RV, Schuurmans M, van Der Oost J, Smit AB, Sixma TK (2001) Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 411:269-276. doi:10.1038/35077011 (Pubitemid 32467026)
5. Schapira M, Abagyan R, TotrovM(2002) Structural model of nicotinic acetylcholine receptor subtypes bound to a acetylcholine and nicotine. BMC Struct Biol 2:1-8. doi:10.1186/1472-6807-2-1
6. BeersWH, Reich E (1970) Structure and activity of acetylcholine. Nature 228:917-922. doi:10.1038/228917a0
7. Sheridan RP, Nilakantan R, Dixon JS, Venkataraghavan R (1986) The ensemble approach to distance geometry: Application to the nicotinic pharmacophore. J Med Chem 29:899-906. doi:10.1021/ jm00156a005
8. Tønder JE, Olesen PH, Hansen JB, Begtrup M, Pettersson I (2001) An improved nicotinic pharmacophore and a stereoselective CoMFA-model for nicotinic agonists acting at the central nicotinic acetylcholine receptors labeled by [H-3]-N-methylcarbamylcholine. J Comput Aided Mol Des 15:247-258. doi:10. 1023/A:1008140021426
9. Wei ZL, Petukhov PA, Xiao Y, Tuckmantel W, George C, Kellar KJ, Kozikowski AP (2003) Synthesis, nicotinic acetylcholine receptor binding affinities, and molecular modeling of constrained epibatidine analogues. J Med Chem 46:921-924. doi:10. 1021/jm025613w (Pubitemid 36423139)
10. Romanelli MN, Gratteri P, Guandalini L, Martini E, Bonaccini C, Gualtieri F (2007) Central nicotinic receptors: structure, function, ligands, and therapeutic potential. ChemMedChem 2:746-767. doi:10.1002/cmdc.200600207
11. Dart MJ, Wasicak JT, Ryther KB, Schrimpf MR, Kim KH, Anderson DJ, Sullivan JP, Meyer MD (2000) Structural aspects of high affinity ligands for the a4β2 neuronal nicotinic receptor. Pharm Acta Helv 74:115-123. doi:10.1016/ S0031-6865(99)00023-30
12. Whiting P, Lindstrom J (1987) Purification and characterization of a nicotinic acetycholine receptor from rat brain. Proc Natl Acad Sci USA 84:595-599. doi:10.1073/pnas.84.2.595 (Pubitemid 17006242)
13. Flores CM, Rogers SW, Pabreza LA, Wolfe BB, Kellar KJ (1992) A subtype of nicotinic cholinergic receptor in rat brain is composed of a4β2 subunits and is up-regulated by chronic nicotinic treatment. Mol Pharmacol 41:31-37
14. Corringer PJ, Le Novere N, Changeux JP (2000) Nicotinic receptors at the amino acid level. Annu Rev Pharmacol Toxicol 40:431-458. doi:10.1146/annurev. pharmtox.40.1.431 (Pubitemid 30340689)
15. Sine SM, Wang HL, Bren N (2002) Lysine scanning mutagenesis delineates structural model of the nicotinic receptor ligand binding domain. J Biol Chem 277:29210-29223. doi:10.1074/jbc. M203396200
16. Figl A, Cohen BN, Quick MW, Davidson N, Lester HA (1992) Regions of the a4β2 subunit chimeras that contribute to the agonist selectivity of the neural nicotinic receptors. FEBS Lett 308:245-248. doi:10.1016/0014-5793(92) 81284-S
17. Gómez-Sánchez E, Soriano E, Marco-Contelles J (2007) Synthesis of 7-Azabicyclo[2.2.1]heptane and 2-Oxa-4-azabicyclo[3.3.1]non- 3-ene derivatives by base-promoted heterocyclizationof alkyl N-(cis(trans)-3, trans(cis)-4-dibromo-cyclohex-1-yl)carbamates, and N-(cis(trans)-3, trans(cis)-4-dibromo-cyclohex-1-yl)-2,2,2- trifluoroacetamides. J Org Chem 72:8656-8670. doi:10.1021/ jo701625a (Pubitemid 350071690)
18. Gómez-Sánchez E, Soriano E, Marco-Contelles J (2008) The synthesis of heterocyclic analogues of epibatidine via 7-azabicyclo[ 2.2.1]hept-2-yl radical intermediates. I. Intermolecular reactions. J Org Chem 73:6784-6792. doi:10.1021/jo8011094
19. Armstrong A, Bhonoah Y, Shanahan SE (2007) Aza-Prins-pinacol approach to 7-azabicyclo[2.2.1]heptanes. Syntheses of ±-epibatidine and ±-epiboxidine. J Org Chem 72:8019-8024. doi:10. 1021/jo701536a
20. Morris GM (1998) Automated docking using lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 19:1639-1662. doi:10.1002/ (SICI)1096-987X(19981115)19:143.0. CO;2-B
21. Le Novere N, Grutter T, Changeux JP (2002) Models of the extracellular domain of the nicotinic receptors and agonist- and Ca2+ binding sites. Proc Natl Acad Sci USA 99:3210-3215. doi:10. 1073/pnas.042699699 (Pubitemid 34240611)
22. Frisch M J, Trucks G W, Schlegel H B, Scuseria G E, Robb M A, Cheeseman J R, Montgomery Jr J A, Vreven T, Kudin K N, Burant J C, Millam J M, Iyengar S S, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson G A, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox J E, Hratchian H P, Cross J B, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann R E, Yazyev O, Austin A J, Cammi R, Pomelli C, Ochterski J W, Ayala P Y, Morokuma K, Voth G A, Salvador P, Dannenberg J J, Zakrzewski V G, Dapprich S, Daniels A D, Strain MC, Farkas O,Malick D K, Rabuck A D, Raghavachari K, Foresman J B, Ortiz J V, Cui Q, Baboul A G, Clifford S, Cioslowski J, Stefanov B B, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin R L, Fox D J, Keith T, Al-Laham M A, Peng C Y, Nanayakkara A, Challacombe M, Gill P MW, Johnson B, ChenW,Wong MW, Gonzalez C, Pople J A, Gaussian Inc, Wallingford, CT.
23. Bayly CI, Cieplack P, Kollman PA (1993) A well-behaved electrostatic potential basic method using charge restraints for deriving atomic-charges. The RESP model. J Phys Chem 97:10269-10280. doi:10.1021/j100142a004
24. Halgren TA (1996) Merck molecular force field. I. Basis, form, scope, parameterization and performance of MMFF94. J Comput Chem 17:490-519 and following papers in this issue. doi:10.1002/ (SICI)1096-987X(199604)17:5/63.0. CO;2-P
25. SpartanPro (v. 1.0.5) (2000) Wavefunction, Irvine, CA
26. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489. doi:10.1006/jmbi.1996.0477 (Pubitemid 26335901)
27. Livett BG (1984) Adrenal medullary chromaffin cells in vitro. Physiol Rev 64:1103-1161
28. Moro MA, López MG, Gandía L, Michelena P, García AG (1990) Separation and culture of living adrenaline- and noradrenalinecontaining cells from bovine adrenal medullae. Anal Biochem 185:243-248. doi:10.1016/0003-2697(90)90287-J
29. Brieaddy LE, Mascarella SW, Navarro HA, Atkinson RN, Damaj MI, Martin BR, Carroll FI (2001) Synthesis of bridged analogs of epibatidine. 3-Chloro-5,7,8,9,9a,10-hexahydro-7,10-metahnopyrrolo[ 1,2-b]-2,6-naphthyridine and 2-chloro-5,5a,6,7,8,9,10-hexahydro- 5,8-metahnopyrrolo[2,1-b]-1,7- naphthyridine. Tetrahedron Lett 42:3795-3797. doi:10.1016/S0040-4039(01)00575-5 (Pubitemid 32493755)
30. Carroll FI (2004) Epibatidine structure-activity relationships. Bioorg Med Chem Lett 14:1889-1896. doi:10.1016/j.bmcl.2004.02. 007
31. Glennon RA, Herndon JA, Dukat M (1994) Epibatidine-aided studies toward definition of a nicotinic receptor pharmacophore. Med Chem Res 4:461-473
32. T?nder JE, Olesen PH (2001) Agonists at the a4β2 nicotinic acetylcholine receptors: structure-activity relationships andmolecular modeling. Curr Med Chem 8:651-674
33. Tønder JE, Hansen JB, Begtrup M, Pettersson I, Rimvall K, Christensen B, Ehrbar U, Olesen PH (1999) Improving the nicotinic pharmacophore with a series of (isoxazole)methylene-1-azacyclic compounds: synthesis, structure-activity relationship, andmolecularmodeling. JMedChem42:4970-4980. doi:10.1021/jm9910627
34. Glennon RA, Dukat M, Liao L (2004) Musings on a4β2 nicotinic acetylcholine (nACh) receptor pharmacophore models. Curr Top Med Chem 4:631-644. doi:10.2174/1568026043451122 (Pubitemid 38842581)