Visualization and virtual screening of the chemical universe database GDB-17

Journal of Chemical Information and Modeling

Volumn 53, Issue 1, 2013, Pages 56-65

  Ruddigkeit, Lars ^a   Blum, Lorenz C ^a   Reymond, Jean Louis ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL STABILITY; QUANTUM THEORY; SCAFFOLDS;

CHEMICAL SPACE; CITY-BLOCK DISTANCES; MEDICINAL CHEMISTRY; QUANTUM NUMBERS; SCAFFOLD HOPPING; SIMILARITY SEARCH; SYNTHETIC FEASIBILITY; VIRTUAL SCREENING;

CHEMICAL ANALYSIS;

DRUG; LIGAND;

ARTICLE; CHEMICAL DATABASE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER INTERFACE; DRUG DATABASE; DRUG SCREENING; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS;

COMPUTER GRAPHICS; DATABASES, CHEMICAL; DATABASES, PHARMACEUTICAL; DRUG EVALUATION, PRECLINICAL; LIGANDS; PHARMACEUTICAL PREPARATIONS; PRINCIPAL COMPONENT ANALYSIS; USER-COMPUTER INTERFACE;

MLCS; MLOWN;

EID: 84873036431     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300535x     Document Type: Article

References (56)

1. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 1997, 23, 3-25
2. 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
3. Dobson, C. M. Chemical space and biology Nature 2004, 432, 824-828
4. Schneider, G.; Fechner, U. Computer-based de novo design of drug-like molecules Nat. Rev. Drug Discovery 2005, 4, 649-663
5. Jorgensen, W. L. Efficient drug lead discovery and optimization Acc. Chem. Res. 2009, 42, 724-733
6. Reymond, J. L.; Van Deursen, R.; Blum, L. C.; Ruddigkeit, L. Chemical space as a source for new drugs MedChemComm 2010, 1, 30-38
7. Hartenfeller, M.; Schneider, G. De novo drug design Methods Mol. Biol. 2011, 672, 299-323
8. Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discovery Today 2006, 11, 580-594
9. 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, 429-36
10. 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
11. Bleicher, K. H.; Bohm, H. J.; Muller, K.; Alanine, A. I. Hit and lead generation: Beyond high-throughput screening Nat. Rev. Drug Discovery 2003, 2, 369-378
12. Schreiber, S. L. Small molecules: the missing link in the central dogma Nat. Chem. Biol. 2005, 1, 64-66
13. Mayr, L. M.; Bojanic, D. Novel trends in high-throughput screening Curr. Opin. Pharmacol. 2009, 9, 580-588
14. Hann, M. M. Molecular obesity, potency and other addictions in drug discovery MedChemComm 2011, 2, 349-355
15. Renner, S.; Popov, M.; Schuffenhauer, A.; Roth, H. J.; Breitenstein, W.; Marzinzik, A.; Lewis, I.; Krastel, P.; Nigsch, F.; Jenkins, J.; Jacoby, E. Recent trends and observations in the design of high-quality screening collections Future Med. Chem. 2011, 3, 751-766
16. 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
17. 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
18. 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
19. Foloppe, N. The benefits of constructing leads from fragment hits Future Med. Chem. 2011, 3, 1111-1115
20. 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
21. 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
22. 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
23. 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
24. Blum, L. C.; van Deursen, R.; Bertrand, S.; Mayer, M.; Burgi, J. J.; Bertrand, D.; Reymond, J. L. Discovery of alpha7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13 J. Chem. Inf. Model. 2011, 51, 3105-3112
25. Brethous, L.; Garcia-Delgado, N.; Schwartz, J.; Bertrand, S.; Bertrand, D.; Reymond, J. L. Synthesis and Nicotinic Receptor Activity of Chemical Space Analogues of N-(3R)-1-Azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) and 1,4-Diazabicyclo[3.2.2]nonane-4-carboxylic Acid 4-Bromophenyl Ester (SSR180711) J. Med. Chem. 2012, 55, 4605-4618
26. Reymond, J. L.; Awale, M. Exploring Chemical Space for Drug Discovery Using the Chemical Universe Database ACS Chem. Neurosci. 2012, 3, 649-657
27. Ruddigkeit, L.; Van Deursen, R.; Blum, L. C.; Reymond, J. L. Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17 J. Chem. Inf. Model. 2012, 52, 2864-2875
28. Teague, S. J.; Davis, A. M.; Leeson, P. D.; Oprea, T. The Design of Leadlike Combinatorial Libraries Angew. Chem., Int. Ed. Engl. 1999, 38, 3743-3748
29. Wang, Y.; Xiao, J.; Suzek, T. O.; Zhang, J.; Wang, J.; Bryant, S. H. PubChem: a public information system for analyzing bioactivities of small molecules Nucleic Acids Res. 2009, 37, W623-W633
30. Sauer, W. H.; Schwarz, M. K. Molecular shape diversity of combinatorial libraries: a prerequisite for broad bioactivity J. Chem. Inf. Comput. Sci. 2003, 43, 987-1003
31. Lovering, F.; Bikker, J.; Humblet, C. Escape from flatland: increasing saturation as an approach to improving clinical success J. Med. Chem. 2009, 52, 6752-6756
32. Ritchie, T. J.; Macdonald, S. J.; Young, R. J.; Pickett, S. D. The impact of aromatic ring count on compound developability: further insights by examining carbo- and hetero-aromatic and -aliphatic ring types Drug Discovery Today 2011, 16, 164-171
33. Pearlman, R. S.; Smith, K. M. Novel software tools for chemical diversity Persp. Drug Discovery Des. 1998, 9-11, 339-353
34. 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
35. van Deursen, R.; Blum, L. C.; Reymond, J. L. A searchable map of PubChem J. Chem. Inf. Model. 2010, 50, 1924-1934
36. 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
37. Reymond, J. L.; Blum, L. C.; Van Deursen, R. Exploring the Chemical Space of Known and Unknown Organic Small Molecules at www.gdb.unibe.ch. Chimia 2011, 65, 863-867.
38. 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
39. Awale, M.; Reymond, J. L. Cluster analysis of the DrugBank chemical space using molecular quantum numbers Bioorg. Med. Chem. 2012, 20, 5372-5378
40. Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: a large-scale bioactivity database for drug discovery Nucleic Acids Res. 2012, 40, D1100-D1107
41. Knox, C.; Law, V.; Jewison, T.; Liu, P.; Ly, S.; Frolkis, A.; Pon, A.; Banco, K.; Mak, C.; Neveu, V.; Djoumbou, Y.; Eisner, R.; Guo, A. C.; Wishart, D. S. DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs Nucleic Acids Res. 2011, 39, D1035-D1041
42. Wang, X.; Wang, J. T. L. Fast Similarity Search in Three-Dimensional Structure Databases J. Chem. Inf. Comput. Sci. 2000, 40, 442-451
43. Dutta, D.; Guha, R.; Jurs, P. C.; Chen, T. Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing J. Chem. Inf. Model. 2005, 46, 321-333
44. Swamidass, S. J.; Baldi, P. Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval J. Chem. Inf. Model. 2007, 47, 952-964
45. Baldi, P.; Benz, R. W.; Hirschberg, D. S.; Swamidass, S. J. Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval J. Chem. Inf. Model. 2007, 47, 2098-2109
46. Nisius, B.; Vogt, M.; Bajorath, J. r. Development of a Fingerprint Reduction Approach for Bayesian Similarity Searching Based on Kullback-Leibler Divergence Analysis J. Chem. Inf. Model. 2009, 49, 1347-1358
47. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
48. Nasr, R.; Hirschberg, D. S.; Baldi, P. Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors J. Chem. Inf. Model. 2010, 50, 1358-1368
49. Nasr, R.; Vernica, R.; Li, C.; Baldi, P. Speeding Up Chemical Searches Using the Inverted Index: The Convergence of Chemoinformatics and Text Search Methods J. Chem. Inf. Model. 2012, 52, 891-900
50. 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
51. Rush, T. S., 3rd; 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
52. 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
53. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A rule of three for fragment-based lead discovery? Drug Discovery Today 2003, 8, 876-877
54. Nicholls, A.; McGaughey, G. B.; Sheridan, R. P.; Good, A. C.; Warren, G.; Mathieu, M.; Muchmore, S. W.; Brown, S. P.; Grant, J. A.; Haigh, J. A.; Nevins, N.; Jain, A. N.; Kelley, B. Molecular Shape and Medicinal Chemistry: A Perspective J. Med. Chem. 2010, 53, 3862-3886
55. Willett, P. Similarity-based virtual screening using 2D fingerprints Drug Discovery Today 2006, 11, 1046-1053
56. AbdulHameed, M. D.; Chaudhury, S.; Singh, N.; Sun, H.; Wallqvist, A.; Tawa, G. J. Exploring polypharmacology using a ROCS-based target fishing approach J. Chem. Inf. Model. 2012, 52, 492-505