Modelling of full-length human α4β2 nicotinic receptor by fragmental approach and analysis of its binding modes

Biochemical and Biophysical Research Communications

Volumn 369, Issue 2, 2008, Pages 648-653

  Pedretti, Alessandro ^a   Marconi, Cristina ^a   Bolchi, Cristiano ^a   Fumagalli, Laura ^a   Ferrara, Rossana ^a   Pallavicini, Marco ^a   Valoti, Ermanno ^a   Vistoli, Giulio ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

Fragmental modelling; Homology modelling; Molecular docking; Nicotine; Nicotinic receptors

Indexed keywords

3 (2 AZETIDINYLMETHOXY)PYRIDINE; 3 METHYL 5 (1 METHYL 2 PYRROLIDINYL)ISOXAZOLE; CITISINE; EPIBATIDINE; HERBACEOUS AGENT; NICOTINE; NICOTINIC RECEPTOR; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BETA CHAIN; BINDING AFFINITY; DRUG RECEPTOR BINDING; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; RECEPTOR BINDING;

BINDING SITES; COMPUTER SIMULATION; HUMANS; MODELS, CHEMICAL; MODELS, MOLECULAR; NICOTINE; PROTEIN BINDING; PROTEIN CONFORMATION; RECEPTORS, NICOTINIC;

EID: 40849137551     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.02.080     Document Type: Article

References (22)

1. Sine S.M., and Engel A.G. Recent advances in Cys-loop receptor structure and function. Nature 440 (2006) 448-455
2. Jensen A.A., Frølund B., Liljefors T., and Krogsgaard-Larsen P. Neuronal nicotinic acetylcholine receptors: structural revelations, target identifications, and therapeutic inspirations. J. Med. Chem. 48 (2005) 4705-4745
3. Romanelli M.N., Gratteri P., Guandalini L., Martini E., Bonaccini C., and Gualtieri F. Central nicotinic receptors: structure, function, ligands, and therapeutic potential. ChemMedChem 2 (2007) 746-767
4. Sixma T.K., and Smit A.B. Acetylcholine binding protein (AChBP): a secreted glial protein that provides a high-resolution model for the extracellular domain of pentameric ligand-gated ion channels. Annu. Rev. Biophys. Biomol. Struct. 32 (2003) 311-334
5. Miyazawa A., Fujiyoshi Y., and Unwin N. Structure and gating mechanism of the acetylcholine receptor pore. Nature 423 (2003) 949-955
6. Unwin N. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. J. Mol. Biol. 346 (2005) 967-989
7. Suto M.J., and Zacharias N. Neuronal nicotinic acetylcholine receptors as drug targets. Expert Opin. Ther. Targets 8 (2004) 61-64
8. Cheng X., Wang H., Grant B., Sine S.M., and McCammon J.A. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput. Biol. 2 (2006) e134
9. Bisson W.H., Scapozza L., Westera G., Mu L., and Schubiger P.A. Ligand selectivity for the acetylcholine binding site of the rat alpha4beta2 and alpha3beta4 nicotinic subtypes investigated by molecular docking. J. Med. Chem. 48 (2005) 5123-5130
10. Mazurov A., Hauser T., and Miller C.H. Selective alpha7 nicotinic acetylcholine receptor ligands. Curr. Med. Chem. 13 (2006) 1567-1584
11. Glennon R.A. Medicinal chemistry of alpha4beta2 nicotinic cholinergic receptor ligands. Prog. Med. Chem. 42 (2004) 55-123
12. Pedretti A., Villa M., Pallavicini M., Valoti E., and Vistoli G. Construction of human ghrelin receptor (hGHS-R1a) model using a fragmental prediction approach and validation through docking analysis. J. Med. Chem. 49 (2006) 3077-3085
13. Pedretti A., and Vistoli G. Modeling of human ghrelin receptor (hGHS-R1a) in its close state and validation by molecular docking. Bioorg. Med. Chem. 15 (2007) 3054-3064
14. Pedretti A., De Luca L., Sciarrillo C., and Vistoli G. Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping. ChemMedChem 3 (2008) 79-90
15. Shi J., Blundell T.L., and Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310 (2001) 243-257
16. De Luca L., Pedretti A., Vistoli G., Barreca M.L., Villa L., Monforte P., and Chimirri A. Analysis of the full-length integrase-DNA complex by a modified approach for DNA docking. Biochem. Biophys. Res. Commun. 310 (2003) 1083-1088
17. Pedretti A., Villa L., and Vistoli G. VEGA: a versatile program to convert, handle and visualize molecular structure on windows-based PCs. J. Mol. Graph. 21 (2002) 47-49
18. Kalé L., Skeel R., Bhandarkar M., Brunner R., Gursoy A., Krawetz N., Phillips J., Shinozaki A., Varadarajan K., and Schulten K. NAMD2: greater scalability for parallel molecular dynamics. J. Comp. Physiol. 151 (1999) 283-312
19. Hashimoto H. Recent structural studies of carbohydrate-binding modules. Cell. Mol. Life Sci. 63 (2006) 2954-2967
20. Sansom M.S., and Weinstein H. Hinges, swivels and switches: the role of prolines in signalling via transmembrane alpha-helices. Trends Pharmacol. Sci. 21 (2000) 445-451
21. Hales T.G., Dunlop J.I., Deeb T.Z., Carland J.E., Kelley S.P., Lambert J.J., and Peters J.A. Common determinants of single channel conductance within the large cytoplasmic loop of 5-hydroxytryptamine type 3 and alpha4beta2 nicotinic acetylcholine receptors. J. Biol. Chem. 281 (2006) 8062-8071
22. Cashin A.L., Petersson E.J., Lester H.A., and Dougherty D.A. Using physical chemistry to differentiate nicotinic from cholinergic agonists at the nicotinic acetylcholine receptor. J. Am. Chem. Soc. 127 (2005) 350-356