Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 7, 2011, Pages 649-662

  Van Deursen, Ruud ^a   Blum, Lorenz C ^a   Reymond, Jean Louis ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

Chemical space; Fragments; PubChem; Virtual screening

Indexed keywords

ATOMS; BIOCHEMISTRY; CHEMICAL ANALYSIS; PRINCIPAL COMPONENT ANALYSIS;

CHEMICAL SPACE; DESCRIPTORS; FRAGMENT; INTEGER VALUES; NON-HYDROGEN ATOMS; ORGANIC MOLECULES; PRINCIPAL-COMPONENT ANALYSIS; PUBCHEM; SIMILARITY SEARCH; VIRTUAL SCREENING;

MOLECULES;

ARTICLE; CHEMICAL STRUCTURE; DATA ANALYSIS; FACTUAL DATABASE; HISTOGRAM; MOLECULAR SIZE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUANTUM CHEMISTRY; STRUCTURE ANALYSIS;

EID: 80955180072     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9437-x     Document Type: Article

References (38)

1. AG Coyne DE Scott C Abell 2010 Drugging challenging targets using fragment-based approaches Curr Opin Chem Biol 14 299 307 10.1016/j.cbpa.2010.02. 010 1:CAS:528:DC%2BC3cXmvVWqs7c%3D
2. MN Schulz RE Hubbard 2009 Recent progress in fragment-based lead discovery Curr Opin Pharmacol 9 615 621 10.1016/j.coph.2009.04.009 1:CAS:528:DC%2BD1MXht1WntLbO
3. M Hartenfeller G Schneider 2011 De novo drug design Methods Mol Biol 672 299 323 10.1007/978-1-60761-839-3-12 1:CAS:528:DC%2BC3cXhtlejsr7L
4. J Venhorst S Nunez CG Kruse 2010 Design of a high fragment efficiency library by molecular graph theory ACS Med Chem Lett 1 499 503 10.1021/ml100163s 1:CAS:528:DC%2BC3cXhtFSnsbbN
5. RA Carr M Congreve CW Murray DC Rees 2005 Fragment-based lead discovery: leads by design Drug Discov Today 10 987 992 10.1016/S1359-6446(05)03511-7 1:CAS:528:DC%2BD2MXmt1Whtr0%3D (Pubitemid 40967047)
6. DC Rees M Congreve CW Murray R Carr 2004 Fragment-based lead discovery Nat Rev Drug Discov 3 660 672 10.1038/nrd1467 1:CAS:528:DC%2BD2cXmtVOht7Y%3D (Pubitemid 39173507)
7. PJ Hajduk J Greer 2007 A decade of fragment-based drug design: strategic advances and lessons learned Nat Rev Drug Discov 6 211 219 10.1038/nrd2220 1:CAS:528:DC%2BD2sXit12rtr4%3D (Pubitemid 46344625)
8. SM Boyd GE de Kloe 2010 Fragment library design: efficiently hunting drugs in chemical space Drug Discov Today 7 e173 e180 10.1016/j.ddtec.2010.11. 010 1:CAS:528:DC%2BC3MXhsVegsLs%3D
9. CM Dobson 2004 Chemical space and biology Nature 432 824 828 10.1038/nature03192 1:CAS:528:DC%2BD2cXhtVOht7jN (Pubitemid 40037137)
10. Y Wang J Xiao TO Suzek J Zhang J Wang SH Bryant 2009 PubChem: a public information system for analyzing bioactivities of small molecules Nucleic Acids Res 37 W623 W633 10.1093/nar/gkp456 1:CAS:528:DC%2BD1MXosFSktL8%3D
11. KT Nguyen LC Blum R van Deursen JL Reymond 2009 Classification of organic molecules by molecular quantum numbers ChemMedChem 4 1803 1805 10.1002/cmdc.200900317 1:CAS:528:DC%2BD1MXhtlagu77M
12. SG Wang WH Schwarz 2009 Icon of chemistry: the periodic system of chemical elements in the new century Angew Chem Int Ed Engl 48 3404 3415 10.1002/anie.200800827 1:CAS:528:DC%2BD1MXltFGht7w%3D
13. RS Pearlman KM Smith 1998 Novel software tools for chemical diversity Perspect Drug Discov Des 9-11 339 353 10.1023/A:1027232610247 (Pubitemid 128491931)
14. H Geppert M Vogt J Bajorath 2010 Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation J Chem Inf Model 50 205 216 10.1021/ci900419k 1:CAS:528:DC%2BC3cXnvFWmsA%3D%3D
15. JL Reymond R Van Deursen LC Blum L Ruddigkeit 2010 Chemical space as a source for new drugs Med Chem Commun 1 30 38 10.1039/c0md00020e 1:CAS:528:DC%2BC3cXhtVeju7rF
16. LB Akella D DeCaprio 2010 Cheminformatics approaches to analyze diversity in compound screening libraries Curr Opin Chem Biol 14 325 330 10.1016/j.cbpa.2010.03.017 1:CAS:528:DC%2BC3cXmvVWqsLw%3D
17. FR Burden 1989 Molecular-Identification Number for Substructure Searches J Chem Inf Comput Sci 29 225 227 1:CAS:528:DyaL1MXkslOis74%3D
18. RS Pearlman KM Smith 1999 Metric validation and the receptor-relevant subspace concept J Chem Inf Comput Sci 39 28 35 1:CAS:528:DyaK1MXos1eh (Pubitemid 129676554)
19. TI Oprea J Gottfries 2001 Chemography: the art of navigating in chemical space J Comb Chem 3 157 166 10.1021/cc0000388 1:CAS:528:DC%2BD3MXhtFams78%3D (Pubitemid 33614499)
20. J Rosen J Gottfries S Muresan A Backlund TI Oprea 2009 Novel chemical space exploration via natural products J Med Chem 52 1953 1962 10.1021/jm801514w 1:CAS:528:DC%2BD1MXislKqu78%3D
21. P Willett 2006 Similarity-based virtual screening using 2D fingerprints Drug Discov Today 11 1046 1053 10.1016/j.drudis.2006.10.005 1:CAS:528: DC%2BD28Xht1eqtb%2FN (Pubitemid 44792477)
22. T Fink H Bruggesser JL Reymond 2005 Virtual exploration of the small-molecule chemical universe below 160 daltons. Angew Chem Int Ed Engl 44 1504 1508 10.1002/anie.200462457 1:CAS:528:DC%2BD2MXit12gs74%3D (Pubitemid 40460043)
23. T Fink JL Reymond 2007 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 47 342 353 10.1021/ci600423u 1:CAS:528:DC%2BD2sXhtVens7k%3D (Pubitemid 46615939)
24. LC Blum JL Reymond 2009 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13 J Am Chem Soc 131 8732 8733 10.1021/ja902302h 1:CAS:528:DC%2BD1MXmvFWru7k%3D
25. Blum LC, van Deursen R, Reymond JL (2011) Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. J Comput Aided Mol Des. doi: 10.1007/s10822-011-9436-y
26. N Huang BK Shoichet JJ Irwin 2006 Benchmarking sets for molecular docking J Med Chem 49 6789 6801 10.1021/jm0608356 1:CAS:528:DC%2BD28XhtFehurzI (Pubitemid 44749746)
27. R van Deursen LC Blum JL Reymond 2010 A searchable map of PubChem J Chem Inf Model 50 1924 1934 10.1021/ci100237q
28. G Siegal E Ab J Schultz 2007 Integration of fragment screening and library design Drug Discov Today 12 1032 1039 10.1016/j.drudis.2007.08.005 1:CAS:528:DC%2BD2sXhsVSmurnI (Pubitemid 350180558)
29. M Congreve G Chessari D Tisi AJ Woodhead 2008 Recent developments in fragment-based drug discovery J Med Chem 51 3661 3680 10.1021/jm8000373 1:CAS:528:DC%2BD1cXotFKisLg%3D (Pubitemid 351956496)
30. CA Lipinski F Lombardo BW Dominy PJ Feeney 1997 Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv Drug Del Rev 23 3 25 10.1016/S0169- 409X(96)00423-1 1:CAS:528:DyaK2sXktlKlsQ%3D%3D (Pubitemid 27046991)
31. SJ Teague AM Davis PD Leeson T Oprea 1999 The Design of Leadlike Combinatorial Libraries Angew Chem Int Ed Engl 38 3743 3748 10.1002/(SICI)1521- 3773(19991216)38:24<3743::AID-ANIE3743>3.0.CO;2-U 1:CAS:528:DC%2BD3cXms12i (Pubitemid 30022004)
32. M Congreve R Carr C Murray H Jhoti 2003 A rule of three for fragment-based lead discovery? Drug Discov Today 8 876 877 10.1016/S1359- 6446(03)02831-9 (Pubitemid 37194496)
33. AA Khalifa M Haranczyk J Holliday 2009 Comparison of nonbinary similarity coefficients for similarity searching, clustering and compound selection J Chem Inf Model 49 1193 1201 10.1021/ci8004644
34. J Overington 2009 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 Aided Mol Des 23 195 198 10.1007/s10822-009-9260-9
35. A Schuffenhauer N Brown P Selzer P Ertl E Jacoby 2005 Relationships between molecular complexity, biological activity, and structural diversity J Chem Inf Model 46 525 535 10.1021/ci0503558
36. M Krier G Bret D Rognan 2006 Assessing the scaffold diversity of screening libraries J Chem Inf Model 46 512 524 10.1021/ci050352v 1:CAS:528:DC%2BD28XlvFSntg%3D%3D
37. D Rogers M Hahn 2010 Extended-Connectivity Fingerprints J Chem Inf Model 50 742 754 10.1021/ci100050t 1:CAS:528:DC%2BC3cXlt1Onsbg%3D
38. P Willett JM Barnard GM Downs 1998 Chemical similarity searching J Chem Inf Comput Sci 38 983 996 1:CAS:528:DyaK1cXks1ynu74%3D (Pubitemid 128591261)