Discovery of α7-nicotinic receptor ligands by virtual screening of the chemical universe database GDB-13

Journal of Chemical Information and Modeling

Volumn 51, Issue 12, 2011, Pages 3105-3112

  Blum, Lorenz C ^a   Van Deursen, Ruud ^a   Bertrand, Sonia ^b   Mayer, Milena ^b   Bürgi, Justus J ^a   Bertrand, Daniel ^b   Reymond, Jean Louis ^a  

^a UNIVERSITY OF BERN   (Switzerland)

^b HiQscreen   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL STABILITY; NICOTINE;

CITY-BLOCK DISTANCES; NICOTINIC RECEPTOR LIGANDS; ORGANIC MOLECULES; SIMILARITY MEASURE; STRUCTURAL ELEMENTS; SYNTHETIC FEASIBILITY; VIRTUAL SCREENING; XENOPUS OOCYTE;

LIGANDS;

BUNGAROTOXIN RECEPTOR; LIGAND; MOLECULAR MOTOR; NICOTINIC RECEPTOR;

ANIMAL; ARTICLE; CHEMISTRY; DRUG DEVELOPMENT; FACTUAL DATABASE; GENE EXPRESSION; GENETICS; HUMAN; METABOLISM; MOLECULAR LIBRARY; XENOPUS;

ANIMALS; DATABASES, FACTUAL; DRUG DISCOVERY; GENE EXPRESSION; HUMANS; LIGANDS; MOLECULAR MOTOR PROTEINS; RECEPTORS, NICOTINIC; SMALL MOLECULE LIBRARIES; XENOPUS;

EID: 84555220598     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200410u     Document Type: Article

References (35)

1. Bohacek, R. S.; McMartin, C.; Guida, W. C. The art and practice of structure-based drug design: a molecular modeling perspective Med. Res. Rev. 1996, 16, 3-50
2. Pearlman, R. S.; Smith, K. M. Novel software tools for chemical diversity Perspect. Drug Discovery Des. 1998, 9-11, 339-353
3. Oprea, T. I.; Gottfries, J. Chemography: The art of navigating in chemical space J. Comb. Chem. 2001, 3, 157-166
4. Dobson, C. M. Chemical space and biology Nature 2004, 432, 824-828
5. Schneider, G.; Fechner, U. Computer-based de novo design of drug-like molecules Nat. Rev. Drug Discovery 2005, 4, 649-63
6. Geppert, H.; Vogt, M.; Bajorath, J. Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation J. Chem. Inf. Model. 2010, 50, 205-216
7. Reymond, J. L.; Van Deursen, R.; Blum, L. C.; Ruddigkeit, L. Chemical space as a source for new drugs Med. Chem. Commun. 2010, 1, 30-38
8. Hartenfeller, M.; Schneider, G. De novo drug design Methods Mol. Biol. 2011, 672, 299-323
9. Fink, T.; Bruggesser, H.; Reymond, J. L. Virtual exploration of the small-molecule chemical universe below 160 Da Angew. Chem., Int. Ed. Engl. 2005, 44, 1504-1508
10. Fink, T.; Reymond, J. L. 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. Inf. Model. 2007, 47, 342-353
11. Blum, L. C.; Reymond, J. L. 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13 J. Am. Chem. Soc. 2009, 131, 8732-8733
12. Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discovery Today 2006, 11, 580-94
13. Kolb, P.; Ferreira, R. S.; Irwin, J. J.; Shoichet, B. K. Docking and chemoinformatic screens for new ligands and targets Curr. Opin. Biotechnol. 2009, 20, 429-436
14. Nguyen, K. T.; Syed, S.; Urwyler, S.; Bertrand, S.; Bertrand, D.; Reymond, J. L. Discovery of NMDA glycine site inhibitors from the chemical universe database GDB ChemMedChem 2008, 3, 1520-1524
15. Nguyen, K. T.; Luethi, E.; Syed, S.; Urwyler, S.; Bertrand, S.; Bertrand, D.; Reymond, J. L. 3-(aminomethyl)piperazine-2,5-dione as a novel NMDA glycine site inhibitor from the chemical universe database GDB Bioorg. Med. Chem. Lett. 2009, 19, 3832-3835
16. Garcia-Delgado, N.; Bertrand, S.; Nguyen, K. T.; van Deursen, R.; Bertrand, D.; Reymond, J.-L. Exploring a7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB ACS Med. Chem. Lett. 2010, 1, 422-426
17. Luethi, E.; Nguyen, K. T.; Burzle, M.; Blum, L. C.; Suzuki, Y.; Hediger, M.; Reymond, J. L. 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. 2010, 53, 7236-7250
18. Nguyen, K. T.; Blum, L. C.; van Deursen, R.; Reymond, J. L. Classification of organic molecules by molecular quantum numbers ChemMedChem 2009, 4, 1803-1805
19. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching J. Chem. Inf. Comput. Sci. 1998, 38, 983-996
20. Khalifa, A. A.; Haranczyk, M.; Holliday, J. Comparison of Nonbinary Similarity Coefficients for Similarity Searching, Clustering and Compound Selection J. Chem. Inf. Model. 2009, 49, 1193-1201
21. van Deursen, R.; Blum, L. C.; Reymond, J. L. A searchable map of PubChem J. Chem. Inf. Model. 2010, 50, 1924-1934
22. van Deursen, R.; Blum, L. C.; Reymond, J. L. Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem J. Comput.-Aided Mol. Des. 2011, 25, 649-662
23. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. 'Scaffold-Hopping' by Topological Pharmacophore Search: A Contribution to Virtual Screening Angew. Chem., Int. Ed. Engl. 1999, 38, 2894-2896
24. Blum, L. C.; van Deursen, R.; Reymond, J. L. Visualisation and subsets of the chemical universe database GDB-13 for virtual screening J. Comput.-Aided Mol. Des. 2011, 25, 637-647
25. Warr, W. A. ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI) J. Comput.-Aided Mol. Des. 2009, 23, 195-198
26. Hogg, R. C.; Bandelier, F.; Benoit, A.; Dosch, R.; Bertrand, D. An automated system for intracellular and intranuclear injection J. Neurosci. Methods 2008, 169, 65-75
27. Taly, A.; Corringer, P. J.; Guedin, D.; Lestage, P.; Changeux, J. P. Nicotinic receptors: allosteric transitions and therapeutic targets in the nervous system Nat. Rev. Drug Discovery 2009, 8, 733-750
28. Paleari, L.; Cesario, A.; Fini, M.; Russo, P. alpha7-Nicotinic receptor antagonists at the beginning of a clinical era for NSCLC and Mesothelioma? Drug Discovery Today 2009, 14, 822-836
29. Tocris Bioscience; http://www.tocris.com (accessed October 17, 2011).
30. Rush, T. S., III; Grant, J. A.; Mosyak, L.; Nicholls, A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction J. Med. Chem. 2005, 48, 1489-1495
31. Irwin, J. J.; Shoichet, B. K. ZINC-A free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45, 177-182
32. Celie, P. H.; van Rossum-Fikkert, S. E.; van Dijk, W. J.; Brejc, K.; Smit, A. B.; Sixma, T. K. Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures Neuron 2004, 41, 907-914
33. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662
34. Hansen, S. B.; Sulzenbacher, G.; Huxford, T.; Marchot, P.; Taylor, P.; Bourne, Y. Structures of Aplysia AChBP complexes with nicotinic agonists and antagonists reveal distinctive binding interfaces and conformations Embo J. 2005, 24, 3635-3646
35. Reymond, J. L.; van Deursen, R.; Bertrand, D. What we have learned from crystal structures of proteins to receptor function. Biochem. Pharmacol. 2011, 82, 1521-1527.