What we have learned from crystal structures of proteins to receptor function

Biochemical Pharmacology

Volumn 82, Issue 11, 2011, Pages 1521-1527

  Reymond, J L ^a   Van Deursen, Ruud ^a   Bertrand, D ^b  

^a UNIVERSITY OF BERN   (Switzerland)

^b HiQScreen   (Switzerland)

Author keywords

Function; Ligand gated channel; Pharmacology; Structure

Indexed keywords

1,4 DIAZABICYCLO[3.2.2]NONANE 4 CARBOXYLIC ACID 4 BROMOPHENYL ESTER; 4 AMINOBUTYRIC ACID A RECEPTOR; 4 CHLORO N (3 QUINUCLIDINYL)BENZAMIDE; ACETYLCHOLINE BINDING PROTEIN; AGENTS INTERACTING WITH TRANSMITTER, HORMONE OR DRUG RECEPTORS; AZETIDINE DERIVATIVE; BINDING PROTEIN; CARBON; CYTISINE; EPIBATIDINE; FLUORINE; GLYCINE RECEPTOR; LIGAND GATED ION CHANNEL; METABOTROPIC RECEPTOR; NEUROTRANSMITTER; NGB 5 5; NICOTINE; NICOTINIC AGENT; NICOTINIC RECEPTOR; NICOTINIC RECEPTOR BLOCKING AGENT; NITROGEN; OXYGEN; PROTEIN; PURINERGIC P2X RECEPTOR; RECEPTOR; SAZETIDINE A; SEROTONIN 3 RECEPTOR; TROPISETRON; UNCLASSIFIED DRUG; UNINDEXED DRUG; VARENICLINE;

ALLOSTERISM; BINDING AFFINITY; COMPUTER AIDED DESIGN; COMPUTER MODEL; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DRUG DESIGN; DRUG RESEARCH; DRUG SCREENING; DRUG STRUCTURE; DRUG SYNTHESIS; LIGAND BINDING; MOLECULAR BIOLOGY; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; RECEPTOR BINDING; RECEPTOR FUNCTION; REVIEW; STRUCTURAL HOMOLOGY;

EID: 80255135633     PISSN: 00062952     EISSN: 18732968     Source Type: Journal    
DOI: 10.1016/j.bcp.2011.07.061     Document Type: Note

References (54)

1. N. Unwin Refined structure of the nicotinic acetylcholine receptor at 4A resolution J Mol Biol 346 2005 967 989 (Pubitemid 40215523)
2. R.E. Hibbs, and E. Gouaux Principles of activation and permeation in an anion-selective Cys-loop receptor Nature 2011
3. D. Bertrand, J.L. Galzi, A. Devillers-Thiéry, S. Bertrand, and J.P. Changeux Stratification of the channel domain in neurotransmitter receptors Curr Opin Cell Biol 5 1993 688 693 (Pubitemid 23266344)
4. A. Devillers-Thiéry, J.L. Galzi, J.L. Eiselé, S. Bertrand, D. Bertrand, and J.P. Changeux Functional architecture of the nicotinic acetylcholine receptor: a prototype of ligand-gated ion channels J Membr Biol 136 1993 97 112 (Pubitemid 23353232)
5. B. Laube, H. Hirai, M. Sturgess, H. Betz, and J. Kuhse Molecular determinants of agonist discrimination by NMDA receptor subunits: analysis of the glutamate binding site on the NR2B subunit Neuron 18 1997 493 503 (Pubitemid 27138796)
6. R.A. North Molecular physiology of P2X receptors Physiol Rev 82 2002 1013 1067
7. T. Kawate, J.C. Michel, W.T. Birdsong, and E. Gouaux Crystal structure of the ATP-gated P2X(4) ion channel in the closed state Nature 460 2009 592 598
8. A.I. Sobolevsky, M.P. Rosconi, and E. Gouaux X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor Nature 462 2009 745 756
9. M. Gopalakrishnan, L.M. Monteggia, D.J. Anderson, E.J. Molinari, M. Piattoni-Kaplan, and D. Donnelly-Roberts Stable expression, pharmacologic properties and regulation of the human neuronal nicotinic acetylcholine alpha 4 beta 2 receptor J Pharmacol Exp Ther 276 1996 289 297 (Pubitemid 26150970)
10. B. Buisson, M. Gopalakrishnan, S.P. Arneric, J.P. Sullivan, and D. Bertrand Human alpha4beta2 neuronal nicotinic acetylcholine receptor in HEK 293 cells: a patch-clamp study J Neurosci 16 1996 7880 7891 (Pubitemid 26405051)
11. Y.F. Vallejo, B. Buisson, D. Bertrand, and W.N. Green Chronic nicotine exposure upregulates nicotinic receptors by a novel mechanism J Neurosci 25 2005 5563 5572 (Pubitemid 40800648)
12. J.P. Changeux The TiPS lecture. The nicotinic acetylcholine receptor: an allosteric protein prototype of ligand-gated ion channels Trends Pharmacol Sci 11 1990 485 492
13. J.P. Changeux, and S.J. Edelstein Allosteric mechanisms of signal transduction Science 308 2005 1424 1428 (Pubitemid 40791288)
14. R.C. Hogg, and D. Bertrand Partial agonists as therapeutic agents at neuronal nicotinic acetylcholine receptors Biochem Pharmacol 73 2007 459 468 (Pubitemid 46043572)
15. R.M. Krause, B. Buisson, S. Bertrand, P.J. Corringer, J.L. Galzi, and J.P. Changeux Ivermectin: a positive allosteric effector of the alpha7 neuronal nicotinic acetylcholine receptor Mol Pharmacol 53 1998 283 294 (Pubitemid 28099739)
16. D.F. Cully, D.K. Vassilatis, K.K. Liu, P.S. Paress, L.H. Van der Ploeg, and J.M. Schaeffer Cloning of an avermectin-sensitive glutamate-gated chloride channel from Caenorhabditis elegans Nature 371 1994 707 711 (Pubitemid 24327331)
17. T. Collins, and N.S. Millar Nicotinic acetylcholine receptor transmembrane mutations convert ivermectin from a positive to a negative allosteric modulator Mol Pharmacol 78 2010 198 204
18. S.D. Silberberg, M. Li, and K.J. Swartz Ivermectin interaction with transmembrane helices reveals widespread rearrangements during opening of P2X receptor channels Neuron 54 2007 263 274 (Pubitemid 46561201)
19. G. Schneider, and U. Fechner Computer-based de novo design of drug-like molecules Nat Rev Drug Discov 4 2005 649 663 (Pubitemid 41149759)
20. G. Klebe Virtual ligand screening: strategies, perspectives and limitations Drug Discov Today 11 2006 580 594
21. J.L. Reymond, R. Van Deursen, L.C. Blum, and L. Ruddigkeit Chemical space as a source for new drugs Med Chem Commun 1 2010 30 38
22. H. Geppert, M. Vogt, and J. Bajorath Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation J Chem Inform Model 50 2010 205 216
23. P. Kolb, R.S. Ferreira, J.J. Irwin, and B.K. Shoichet Docking and chemoinformatic screens for new ligands and targets Curr Opin Biotechnol 20 2009 429 436
24. D. Rogers, and M. Hahn Extended-connectivity fingerprints J Chem Inform Model 50 2010 742 754
25. A. Nicholls, G.B. McGaughey, R.P. Sheridan, A.C. Good, G. Warren, and M. Mathieu Molecular shape and medicinal chemistry: a perspective J Med Chem 53 2010 3862 3886
26. N. Huang, B.K. Shoichet, and J.J. Irwin Benchmarking sets for molecular docking J Med Chem 49 2006 6789 6801 (Pubitemid 44749746)
27. Y. Wang, J. Xiao, T.O. Suzek, J. Zhang, J. Wang, and S.H. Bryant PubChem: a public information system for analyzing bioactivities of small molecules Nucl Acids Res 37 2009 W623 W633
28. A.J. Williams Public chemical compound databases Curr Opin Drug Discov Dev 11 2008 393 404 (Pubitemid 351572450)
29. J. Overington ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr J Comput Aid Mol Des 23 2009 195 198
30. A. Bender, J.L. Jenkins, J. Scheiber, S.C. Sukuru, M. Glick, and J.W. Davies How similar are similarity searching methods? A principal component analysis of molecular descriptor space J Chem Inform Model 49 2009 108 119
31. R. van Deursen, L.C. Blum, and J.L. Reymond A searchable map of PubChem J Chem Inform Model 50 2010 1924 1934
32. R. van Deursen, L.C. Blum, and J.L. Reymond Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem J Comput Aided Mol Des 2011
33. H. Koeppen Virtual screening - what does it give us? Curr Opin Drug Discov Dev 12 2009 397 407
34. B.K. Cassels, I. Bermudez, F. Dajas, J.A. Abin-Carriquiry, and S. Wonnacott From ligand design to therapeutic efficacy: the challenge for nicotinic receptor research Drug Discov Today 10 2005 1657 1665 (Pubitemid 41817614)
35. J.W. Daly Nicotinic agonists, antagonists, and modulators from natural sources Cell Mol Neurobiol 25 2005 513 552 (Pubitemid 41199710)
36. P.H. Celie, S.E. van Rossum-Fikkert, W.J. van Dijk, K. Brejc, A.B. Smit, and T.K. Sixma Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures Neuron 41 2004 907 914 (Pubitemid 38429734)
37. S.B. Hansen, G. Sulzenbacher, T. Huxford, P. Marchot, P. Taylor, and Y. Bourne Structures of Aplysia AChBP complexes with nicotinic agonists and antagonists reveal distinctive binding interfaces and conformations EMBO J 24 2005 3635 3646 (Pubitemid 41509370)
38. N. Armstrong, and E. Gouaux Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core Neuron 28 2000 165 181
39. C. Ulens, A. Akdemir, A. Jongejan, R. van Elk, S. Bertrand, and A. Perrakis Use of acetylcholine binding protein in the search for novel alpha7 nicotinic receptor ligands. In silico docking, pharmacological screening, and X-ray analysis J Med Chem 52 2009 2372 2383
40. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J Mol Biol 267 1997 727 748 (Pubitemid 27170693)
41. F. Picard, S. Bertrand, O.K. Steinlein, and D. Bertrand Mutated nicotinic receptors responsible for autosomal dominant nocturnal frontal lobe epilepsy are more sensitive to carbamazepine Epilepsia 40 1999 1198 1209 (Pubitemid 29416388)
42. B. Buisson, and D. Bertrand Open-channel blockers at the human alpha4beta2 neuronal nicotinic acetylcholine receptor Mol Pharmacol 53 1998 555 563 (Pubitemid 28162880)
43. N. Garcia-Delgado, S. Bertrand, K.T. Nguyen, R. van Deursen, D. Bertrand, and J-L. Reymond Exploring a7-nicotinic receptor ligand diversity by scaffold enumeration from the chemical universe database GDB ACS Med Chem Lett 1 2010 422 426
44. A.L. Bodnar, L.A. Cortes-Burgos, K.K. Cook, D.M. Dinh, V.E. Groppi, and M. Hajos Discovery and structure-activity relationship of quinuclidine benzamides as agonists of alpha7 nicotinic acetylcholine receptors J Med Chem 48 2005 905 908 (Pubitemid 40270435)
45. B. Biton, O.E. Bergis, F. Galli, A. Nedelec, A.W. Lochead, and S. Jegham SSR180711, a novel selective alpha7 nicotinic receptor partial agonist: (1) binding and functional profile Neuropsychopharmacology 32 2007 1 16 (Pubitemid 44967780)
46. L.C. Blum, and J.L. Reymond 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13 J Am Chem Soc 131 2009 8732 8733
47. T. Fink, and J.L. Reymond Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery J Chem Inform Model 47 2007 342 353 (Pubitemid 46615939)
48. T. Fink, H. Bruggesser, and J.L. Reymond Virtual exploration of the small-molecule chemical universe below 160 daltons Angew Chem Int Ed Engl 44 2005 1504 1508 (Pubitemid 40460043)
49. E. Luethi, K.T. Nguyen, M. Burzle, L.C. Blum, Y. Suzuki, and M. Hediger Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB) J Med Chem 53 2010 7236 7250
50. K.T. Nguyen, E. Luethi, S. Syed, S. Urwyler, S. Bertrand, and D. Bertrand 3-(aminomethyl)piperazine-2,5-dione as a novel NMDA glycine site inhibitor from the chemical universe database GDB Bioorg Med Chem Lett 19 2009 3832 3835
51. K.T. Nguyen, S. Syed, S. Urwyler, S. Bertrand, D. Bertrand, and J.L. Reymond Discovery of NMDA glycine site inhibitors from the chemical universe database GDB ChemMedChem 3 2008 1520 1524
52. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, and R.K. Belew AJ Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J Comput Chem 19 1998 1639 1662 (Pubitemid 128590223)
53. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, and D.T. Mainz Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J Med Chem 47 2004 1739 1749 (Pubitemid 38380917)
54. D. Bertrand, and M. Gopalakrishnan Allosteric modulation of nicotinic acetylcholine receptors Biochem Pharmacol 74 2007 1155 1163 (Pubitemid 47417931)