Enhancing the effectiveness of similarity-based virtual screening using nearest-neighbor information

Journal of Medicinal Chemistry

Volumn 48, Issue 22, 2005, Pages 7049-7054

  Hert, Jérôme ^a   Willett, Peter ^a   Wilton, David J ^a   Acklin, Pierre ^b   Azzaoui, Kamal ^b   Jacoby, Edgar ^b   Schuffenhauer, Ansgar ^b  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOTENSIN RECEPTOR ANTAGONIST; DOPAMINE 2 RECEPTOR BLOCKING AGENT; PROSTAGLANDIN SYNTHASE INHIBITOR; PROTEIN KINASE C INHIBITOR; PROTEINASE INHIBITOR; RENIN INHIBITOR; SEROTONIN 1A AGONIST; SEROTONIN 3 ANTAGONIST; SEROTONIN UPTAKE INHIBITOR; SUBSTANCE P ANTAGONIST; THROMBIN INHIBITOR;

ARTICLE; DATA BASE; DRUG SCREENING; DRUG STRUCTURE; DRUG SYNTHESIS; HIGH THROUGHPUT SCREENING; HYPOTHESIS; VIRTUAL REALITY;

COMPUTING METHODOLOGIES; DATABASES, FACTUAL; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 27544441634     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm050316n     Document Type: Article

References (48)

1. Bohm, H.-J., Schneider, G., Eds. Virtual Screening for Bioactive Molecules; Wiley-VCH: Weinheim, Germany, 2000.
2. Klebe, G., Ed. Virtual Screening: An Alternative or Complement to High Throughput Screening; Kluwer: Dordrecht, The Netherlands, 2000.
3. Bajorath, J. Integration of Virtual and High-Throughput Screening. Nat. Rev. Drug Discovery 2002, 1, 882-894.
4. Lyne, P. D. Structure-Based Virtual Screening: An Overview. Drug Discovery Today 2002, 7, 1047-1055.
5. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. A Review of Protein-Small Molecule Docking Methods. J. Coraput.-Aided Mol. Des. 2002, 16, 151-166.
6. Warr, W. A.; Willett, P. The Principles and Practice of 3D Database Searching. Designing Bioactive Molecules: Three-Dimensional Techniques and Applications; American Chemical Society: Washington, DC, 1997; pp 73-95.
7. Cramer, R. D.; Redl, G.; Berkoff, C. E. Substructural Analysis. A Novel Approach to the Problem of Drug Design. J. Med. Chem. 1974, 17, 533-538.
8. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci 1998, 38, 983-996.
9. Dean, P. M., Ed. Molecular Similarity in Drug Design; Chapman and Hall: Glasgow, U.K., 1994.
10. Sheridan, R. P.; Kearsley, S. K. Why Do We Need So Many Chemical Similarity Search Methods? Drug Discovery Today 2002, 7, 903-911.
11. Bender, A.; Glen, R. C. Molecular Similarity: A Key Technique in Molecular Informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
12. Nikolova, N.; Jaworska, J. Approaches To Measure Chemical Similarity. A Review. Quant. Struct.-Act. Relat. Comb. Sci. 2003, 22, 1006-1026.
13. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
14. Willett, P.; Winterman, V.; Bawden, D. Implementation of Nearest Neighbour Searching in an Online Chemical Structure Search System. J. Chem. Inf. Comput. Sci. 1986, 26, 36-41.
15. Shemetulskis, N. E.; Dunbar, J. B.; Dunbar, B. W.; Moreland, D. W.; Humblet, C. Enhancing the Diversity of a Corporate Database Using Chemical Database Clustering and Analysis. J. Comput.-Aided Mol. Des. 1995, 9, 407-416.
16. Ginn, C. M. R.; Willett, P.; Bradshaw, J. Combination of Molecular Similarity Measures Using Data Fusion. Perspect. Drug Discovery Des. 2000, 20, 1-16.
17. Fligner, M. A.; Verducci, J. S.; Blower, P. E. A Modification of the Jaccard-Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings. Technometrics 2002, 44, 110-119.
18. Holliday, J. D.; Salim, N.; Whittle, M.; Willett, P. Analysis and Display of the Size Dependence of Chemical Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2003, 43, 819-828.
19. Chen, X.; Reynolds, C. H. Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2002, 42, 1407-1414.
20. Sheridan, R. P.; Feuston, B. P.; Maiorov, V. N.; Kearsley, S. K. Similarity to Molecules in the Training Set Is a Good Discriminator for Prediction Accuracy in QSAR. J. Chem. Inf. Comput. Sci. 2004, 44, 1912-1928.
21. Xue, L.; Stahura, F. L.; Bajorath, J. Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening. J. Chem. Inf. Comput. Sci. 2004, 2032-2039.
22. Shanmugasundaram, V.; Maggiora, G. M.; Lajiness, M. S. Hit-Directed Nearest-Neighbor Searching. J. Med. Chem. 2005, 48, 240-248.
23. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures. J. Chem. Inf. Comput. Sci. 2004, 44, 1177-1185.
24. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of Topological Descriptors for Similarity-Based Virtual Screening Using Multiple Bioactive Reference Structures. Org. Biomol. Chem. 2004, 2, 3256-3266.
25. Whittle, M.; Gillet, V. J.; Willett, P.; Alex, A.; Losel, J. Enhancing the Effectiveness of Virtual Screening by Fusing Nearest-Neighbour Lists: A Comparison of Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2004, 44, 1840-1848.
26. Johnson, M. A., Maggiora, G. M., Eds. Concepts and Applications of Molecular Similarity; John Wiley: New York, 1990.
27. Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighbourhood Behaviour: A Useful Concept for Validation of "Molecular Diversity" Descriptors. J. Med. Chem. 1996, 39, 3049-3059.
28. Schuffenhauer, A.; Jacoby, E. Annotating and Mining the Ligand-Target Chemogenomics Knowledge Space. BIOSILICO 2004, 2, 190-200.
29. Kubinyi, H. Similarity and Dissimilarity: A Medicinal Chemist's View. Perspect. Drug Discovery Des. 1998, 9-11, 225-252.
30. Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
31. Brown, R. D.; Martin, Y. C. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding. J. Chem. Inf. Comput. Sci. 1997, 37, 1-9.
32. Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do Structurally Similar Molecules Have Similar Biological Activities? J. Med. Chem. 2002, 45, 4350-4358.
33. Xue, L.; Stahura, F. L.; Godden, J. W.; Bajorath, J. Fingerprint Scaling Increases the Probability of Identifying Molecules with Similar Activity in Virtual Screening Calculations. J. Chem. Inf. Comput. Sci. 2001, 41, 746-753.
34. Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins. J. Chem. Inf. Comput. Sci. 2003, 43, 391-405.
35. Kearsley, S. K.; Sallamack, S.; Fluder, E. M.; Andose, J. D.; Mosley, R. T.; Sheridan, R. P. Chemical Similarity Using Physicochemical Property Descriptors. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127.
36. Salim, N.; Holliday, J. D.; Willett, P. Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion. J. Chem. Inf. Comput. Sci. 2003, 43, 435-442.
37. Delaney, J. Assessing the Ability of Chemical Similarity Measures To Discriminate between Active and Inactive Compounds. Mol. Diversity 1995, 1, 217-222.
38. Matter, H. Selecting Optimally Diverse Compounds from Structure Databases: A Validation Study of Two-Dimensional and Three-Dimensional Molecular Descriptors. J. Med. Chem. 1997, 40, 1219-1229.
39. Klon, A. E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J. W. Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results. J. Med. Chem. 2004, 47, 2743-2749.
40. van Rijsbergen, C. J. Information Retrieval; Butterworth: London, 1979.
41. Siegal, S.; Castellan, N. J. Nonparametric Statistics for the Behavioral Sciences; McGraw-Hill: New York, 1988.
42. Oprea, T. I. Chemical Space Navigation in Lead Discovery. Curr. Opin. Chem. Biol. 2002, 6, 384-389.
43. Jacoby, E.; Davies, J.; Blommers, M. J. J. Design of Small Molecule Libraries for NMR Screening and Other Applications in Drug Discovery. Curr. Top. Med. Chem. 2003, 3, 11-23.
44. Dobson, C. M. Chemical Space and Biology. Nature 2004, 432, 824-828.
45. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Manuscript in preparation.
46. Croft, W. B.; Lucia, T. J.; Cringean, J. K.; Willett, P. Retrieving Documents by Plausible Inference: An Experimental Study. Inf. Process. Manage. 1989, 25, 599-614.
47. Good, A. C.; Hermsmeier, M. A.; Hindle, S. A. Measuring CAMD Technique Performance: A Virtual Screening Case Study in the Design of Validation Experiments. J. Comput.-Aid. Mol. Des. 2004, 18, 529-536.
48. Harper, G.; Bravi, G. S.; Pickett, S. D.; Hussain, J.; Green, D. V. S. The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data. J. Chem. Inf. Comput. Sci. 2004, 44, 2145-2156.