Fragment Database FDB-17

Journal of Chemical Information and Modeling

Volumn 57, Issue 4, 2017, Pages 700-709

  Visini, Ricardo ^a   Awale, Mahendra ^a   Reymond, Jean Louis ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL STABILITY; MOLECULES; NEAREST NEIGHBOR SEARCH; SYNTHESIS (CHEMICAL); VISUALIZATION;

CHEMICAL SPACE; COMBINATORIAL EXPLOSION; COMPLEX MOLECULES; INTERACTIVE VISUALIZATIONS; NEAREST NEIGHBORS; STEREOCHEMICAL COMPLEXITY; SYNTHETIC FEASIBILITY; VIRTUAL SCREENING;

DATABASE SYSTEMS;

ALGORITHM; DRUG DATABASE; DRUG STABILITY; INFORMATION SCIENCE; PRECLINICAL STUDY; PROCEDURES;

ALGORITHMS; DATABASES, PHARMACEUTICAL; DRUG EVALUATION, PRECLINICAL; DRUG STABILITY; INFORMATICS;

EID: 85018531230     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.7b00020     Document Type: Article

References (69)

1. 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 10.1038/nrd1086
2. Cayley, E. Ueber Die Analytischen Figuren, Welche in Der Mathematik Bäume Genannt Werden Und Ihre Anwendung Auf Die Theorie Chemischer Verbindungen Ber. Dtsch. Chem. Ges. 1875, 8, 1056-1059 10.1002/cber.18750080252
3. Schiff, H. Zur Statistik Chemischer Verbindungen Ber. Dtsch. Chem. Ges. 1875, 8, 1542-1547 10.1002/cber.187500802191
4. Henze, H. R.; Blair, C. M. The Number of Isomeric Hydrocarbons of the Methane Series J. Am. Chem. Soc. 1931, 53, 3077-3085 10.1021/ja01359a034
5. 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 10.1016/S0169-409X(96)00423-1
6. 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 10.1002/(SICI)1098-1128(199601)16:1<3::AID-MED1>3.0.CO;2-6
7. Ertl, P. Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-Like Bioisosteric Groups J. Chem. Inf. Comput. Sci. 2003, 43, 374-380 10.1021/ci0255782
8. Kirkpatrick, P.; Ellis, C. Chemical Space Nature 2004, 432, 823-823 10.1038/432823a
9. Weininger, D. Smiles, a Chemical Language and Information-System 0.1. Introduction to Methodology and Encoding Rules J. Chem. Inf. Model. 1988, 28, 31-36 10.1021/ci00057a005
10. Sadowski, J.; Gasteiger, J. From Atoms and Bonds to 3-Dimensional Atomic Coordinates-Automatic Model Builders Chem. Rev. 1993, 93, 2567-2581 10.1021/cr00023a012
11. 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. et al. Molecular Shape and Medicinal Chemistry: A Perspective J. Med. Chem. 2010, 53, 3862-3886 10.1021/jm900818s
12. Danziger, D. J.; Dean, P. M. Automated Site-Directed Drug Design: A General Algorithm for Knowledge Acquisition About Hydrogen-Bonding Regions at Protein Surfaces Proc. R. Soc. London, Ser. B 1989, 236, 101-113 10.1098/rspb.1989.0015
13. Lewell, X. Q.; Judd, D. B.; Watson, S. P.; Hann, M. M. Recap-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry J. Chem. Inf. Comput. Sci. 1998, 38, 511-522 10.1021/ci970429i
14. Leach, A. R.; Hann, M. M. The in Silico World of Virtual Libraries Drug Discovery Today 2000, 5, 326-336 10.1016/S1359-6446(00)01516-6
15. Patel, H.; Bodkin, M. J.; Chen, B.; Gillet, V. J. Knowledge-Based Approach to De Novo Design Using Reaction Vectors J. Chem. Inf. Model. 2009, 49, 1163-1184 10.1021/ci800413m
16. Hu, Q.; Peng, Z.; Kostrowicki, J.; Kuki, A. Leap into the Pfizer Global Virtual Library (Pgvl) Space: Creation of Readily Synthesizable Design Ideas Automatically Methods Mol. Biol. 2011, 685, 253-276 10.1007/978-1-60761-931-4-13
17. Foloppe, N. The Benefits of Constructing Leads from Fragment Hits Future Med. Chem. 2011, 3, 1111-1115 10.4155/fmc.11.46
18. Murray, C. W.; Rees, D. C. The Rise of Fragment-Based Drug Discovery Nat. Chem. 2009, 1, 187-192 10.1038/nchem.217
19. Fink, T.; Bruggesser, H.; Reymond, J. L. Virtual Exploration of the Small-Molecule Chemical Universe Below 160 Da Angew. Chem., Int. Ed. 2005, 44, 1504-1508 10.1002/anie.200462457
20. 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 10.1021/ci600423u
21. Reymond, J. L.; Van Deursen, R.; Blum, L. C.; Ruddigkeit, L. Chemical Space as a Source for New Drugs MedChemComm 2010, 1, 30-38 10.1039/c0md00020e
22. Johansson, E. M. V.; Kadam, R. U.; Rispoli, G.; Crusz, S. A.; Bartels, K.-M.; Diggle, S. P.; Camara, M.; Williams, P.; Jaeger, K.-E.; Darbre, T. et al. Inhibition of Pseudomonas Aeruginosa Biofilms with a Glycopeptide Dendrimer Containing D-Amino Acids MedChemComm 2011, 2, 418-420 10.1039/c0md00270d
23. 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 10.1021/ci300415d
24. Reymond, J. L.; Ruddigkeit, L.; Blum, L. C.; Van Deursen, R. The Enumeration of Chemical Space WIREs comput. Mol. Sci. 2012, 2, 717 10.1002/wcms.1104
25. Reymond, J. L. The Chemical Space Project Acc. Chem. Res. 2015, 48, 722-730 10.1021/ar500432k
26. McKay, B. D. Practical Graph Isomorphism Congressus Numerantium 1981, 30, 45-87
27. 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 10.1002/cmdc.200900317
28. van Deursen, R.; Blum, L. C.; Reymond, J. L. A Searchable Map of Pubchem J. Chem. Inf. Model. 2010, 50, 1924-1934 10.1021/ci100237q
29. 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 10.1007/s10822-011-9436-y
30. Ruddigkeit, L.; Blum, L. C.; Reymond, J.-L. Visualization and Virtual Screening of the Chemical Universe Database Gdb-17 J. Chem. Inf. Model. 2013, 53, 56-65 10.1021/ci300535x
31. Schwartz, J.; Awale, M.; Reymond, J.-L. Smifp (Smiles Fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules J. Chem. Inf. Model. 2013, 53, 1979-1989 10.1021/ci400206h
32. Awale, M.; van Deursen, R.; Reymond, J. L. Mqn-Mapplet: Visualization of Chemical Space with Interactive Maps of Drugbank, Chembl, Pubchem, Gdb-11, and Gdb-13 J. Chem. Inf. Model. 2013, 53, 509-518 10.1021/ci300513m
33. Awale, M.; Reymond, J. L. Atom Pair 2d-Fingerprints Perceive 3d-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of Zinc and Gdb-17 J. Chem. Inf. Model. 2014, 54, 1892-1897 10.1021/ci500232g
34. Ruddigkeit, L.; Awale, M.; Reymond, J. L. Expanding the Fragrance Chemical Space for Virtual Screening J. Cheminf. 2014, 6, 27-39 10.1186/1758-2946-6-27
35. Law, V.; Knox, C.; Djoumbou, Y.; Jewison, T.; Guo, A. C.; Liu, Y.; Maciejewski, A.; Arndt, D.; Wilson, M.; Neveu, V. et al. Drugbank 4.0: Shedding New Light on Drug Metabolism Nucleic Acids Res. 2014, 42, D1091-D1097 10.1093/nar/gkt1068
36. Bento, A. P.; Gaulton, A.; Hersey, A.; Bellis, L. J.; Chambers, J.; Davies, M.; Kruger, F. A.; Light, Y.; Mak, L.; McGlinchey, S. et al. The Chembl Bioactivity Database: An Update Nucleic Acids Res. 2014, 42, D1083-D1090 10.1093/nar/gkt1031
37. Sterling, T.; Irwin, J. J. Zinc 15 - Ligand Discovery for Everyone J. Chem. Inf. Model. 2015, 55, 2324-2337 10.1021/acs.jcim.5b00559
38. Kim, S.; Thiessen, P. A.; Bolton, E. E.; Chen, J.; Fu, G.; Gindulyte, A.; Han, L.; He, J.; He, S.; Shoemaker, B. A. et al. Pubchem Substance and Compound Databases Nucleic Acids Res. 2016, 44, D1202-D1213 10.1093/nar/gkv951
39. 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, 1520-4 10.1002/cmdc.200800198
40. 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 10.1021/jm100959g
41. Garcia-Delgado, N.; Bertrand, S.; Nguyen, K. T.; van Deursen, R.; Bertrand, D.; Reymond, J.-L. Exploring Alpha 7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database Gdb ACS Med. Chem. Lett. 2010, 1, 422-426 10.1021/ml100125f
42. 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 10.1021/jm300030r
43. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A Rule of Three for Fragment-Based Lead Discovery? Drug Discovery Today 2003, 8, 876-877 10.1016/S1359-6446(03)02831-9
44. Klebe, G. Virtual Ligand Screening: Strategies, Perspectives and Limitations Drug Discovery Today 2006, 11, 580-594 10.1016/j.drudis.2006.05.012
45. Scior, T.; Bender, A.; Tresadern, G.; Medina-Franco, J. L.; Martinez-Mayorga, K.; Langer, T.; Cuanalo-Contreras, K.; Agrafiotis, D. K. Recognizing Pitfalls in Virtual Screening: A Critical Review J. Chem. Inf. Model. 2012, 52, 867-881 10.1021/ci200528d
46. Heikamp, K.; Bajorath, J. The Future of Virtual Compound Screening Chem. Biol. Drug Des. 2013, 81, 33-40 10.1111/cbdd.12054
47. 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 10.1016/j.copbio.2009.08.003
48. Forino, M.; Jung, D.; Easton, J. B.; Houghton, P. J.; Pellecchia, M. Virtual Docking Approaches to Protein Kinase B Inhibition J. Med. Chem. 2005, 48, 2278-2281 10.1021/jm048962u
49. 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 10.1021/ci900419k
50. Wieland, T.; Kerber, A.; Laue, R. Principles of the Generation of Constitutional and Configurational Isomers J. Chem. Inf. Comput. Sci. 1996, 36, 413-419 10.1021/ci9502663
51. Buchanan, B. G.; Smith, D. H.; White, W. C.; Gritter, R. J.; Feigenbaum, E. A.; Lederberg, J.; Djerassi, C. Applications of Artificial Intelligence for Chemical Inference. 22. Automatic Rule Formation in Mass Spectrometry by Means of the Meta-Dendral Program J. Am. Chem. Soc. 1976, 98, 6168-6178 10.1021/ja00436a017
52. Gillet, V. J.; Newell, W.; Mata, P.; Myatt, G.; Sike, S.; Zsoldos, Z.; Johnson, A. P. Sprout: Recent Developments in the De Novo Design of Molecules J. Chem. Inf. Model. 1994, 34, 207-217 10.1021/ci00017a027
53. Brown, N.; McKay, B.; Gilardoni, F.; Gasteiger, J. A Graph-Based Genetic Algorithm and Its Application to the Multiobjective Evolution of Median Molecules J. Chem. Inf. Comput. Sci. 2004, 44, 1079-1087 10.1021/ci034290p
54. Brown, N.; McKay, B.; Gasteiger, J. The De Novo Design of Median Molecules within a Property Range of Interest J. Comput.-Aided Mol. Des. 2004, 18, 761-771 10.1007/s10822-004-6986-2
55. Lameijer, E. W.; Kok, J. N.; Back, T.; Ijzerman, A. P. The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules J. Chem. Inf. Model. 2006, 46, 545-552 10.1021/ci050369d
56. van Deursen, R.; Reymond, J. L. Chemical Space Travel ChemMedChem 2007, 2, 636-640 10.1002/cmdc.200700021
57. Virshup, A. M.; Contreras-Garcia, J.; Wipf, P.; Yang, W.; Beratan, D. N. Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds J. Am. Chem. Soc. 2013, 135, 7296-7303 10.1021/ja401184g
58. 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 10.1021/ci025599w
59. Awale, M.; Reymond, J. L. Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and Chembl in High Dimensional Chemical Spaces J. Chem. Inf. Model. 2015, 55, 1509-1516 10.1021/acs.jcim.5b00182
60. Hagadone, T. R. Molecular Substructure Similarity Searching: Efficient Retrieval in Two-Dimensional Structure Databases J. Chem. Inf. Model. 1992, 32, 515-521 10.1021/ci00009a019
61. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754 10.1021/ci100050t
62. ChemAxon Ltd. http:www.chemaxon.com (accessed Feb 20, 2017).
63. Hawkins, P. C.; Skillman, A. G.; Warren, G. L.; Ellingson, B. A.; Stahl, M. T. Conformer Generation with Omega: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database J. Chem. Inf. Model. 2010, 50, 572-584 10.1021/ci100031x
64. Hawkins, P. C.; Nicholls, A. Conformer Generation with Omega: Learning from the Data Set and the Analysis of Failures J. Chem. Inf. Model. 2012, 52, 2919-2936 10.1021/ci300314k
65. Rush, T. S.; Grant, J. A.; Mosyak, A.; 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 10.1021/jm040163o
66. Hawkins, P. C.; Skillman, A. G.; Nicholls, A. Comparison of Shape-Matching and Docking as Virtual Screening Tools J. Med. Chem. 2007, 50, 74-82 10.1021/jm0603365
67. The JSci Science Library. http://jsci.sourceforge.net/ (accessed Feb 20, 2017).
68. University of Otago, New Zealand. http://www.cs.otago.ac.nz/cosc453/student-tutorials/principal-components.pdf (accessed Feb 20, 2017).
69. Awale, M.; Reymond, J. L. A Multi-Fingerprint Browser for the Zinc Database Nucleic Acids Res. 2014, 42, W234-W239 10.1093/nar/gku379