"Bayes affinity fingerprints" Improve retrieval rates in virtual screening and define orthogonal bioactivity space: When are multitarget drugs a feasible concept?

Journal of Chemical Information and Modeling

Volumn 46, Issue 6, 2006, Pages 2445-2456

  Bender, Andreas ^a   Jenkins, Jeremy L ^a   Glick, Meir ^a   Zhan, Deng ^a   Nettles, James H ^a   Davies, John W ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION METHODS; DATABASE SYSTEMS; DRUG PRODUCTS; INFORMATION RETRIEVAL; OPTIMIZATION; VIRTUAL REALITY;

FINGERPRINTS; ORTHOGONAL BIOACTIVITY SPACE; RETRIEVAL RATES; VIRTUAL SCREENING;

PATTERN MATCHING;

DRUG; LIGAND;

ALGORITHM; ANIMAL; ARTICLE; BAYES THEOREM; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COMPUTER PROGRAM; DRUG DESIGN; FACTUAL DATABASE; HUMAN; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS;

ALGORITHMS; ANIMALS; BAYES THEOREM; CHEMISTRY; CHEMISTRY, PHARMACEUTICAL; DATABASES, FACTUAL; DRUG DESIGN; HUMANS; LIGANDS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE;

EID: 33750986884     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600197y     Document Type: Article

References (37)

1. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
2. Johnson, M. A.; Maggiora, G. M. Concepts and Applications of Molecular Similarity; John Wiley & Sons: New York, 1990.
3. Bender, A.; Glen, R. C. Molecular Similarity: A Key Technique in Molecular Informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
4. Bender, A.; Jenkins, J. L.; Li, Q.; Adams, S. E.; Cannon, E. O.; Glen, R. C. Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR. Anna. Rep. Comput. Chem. 2006, in press.
5. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors; Wiley-VCH: Weinheim, Germany, 2000.
6. Willett, P. Textual and Chemical Information Retrieval: Different Applications but Similar Algorithms. Inf. Res. 1999, 5, pp-pp.
7. Stiefl, N.; Baumann, K. Mapping Property Distributions of Molecular Surfaces: Algorithm and Evaluation of a Novel 3D Quantitative Structure-Activity Relationship Technique. J. Med. Chem. 2003, 46, 1390-1407.
8. Jenkins, J. L.; Glick, M.; Davies, J. W. A 3D Similarity Method for Scaffold Hopping from the Known Drugs or Natural Ligands to New Chemotypes. J. Med. Chem. 2004, 47, 6144-6159.
9. Baumann, K. Distance Profiles (DiP): A Translationally and Rotationally Invariant 3D Structure Descriptor Capturing Steric Properties of Molecules. Quant. Struct.-Act. Relat. 2002, 21, 507-519.
10. Bender, A.; Mussa, H. Y.; Gill, G. S.; Glen, R. C. Molecular Surface Point Environments for Virtual Screening and the Elucidation of Binding Patterns (MOLPRINT 3D). J. Med. Chem. 2004, 47, 6569-6583.
11. 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.
12. 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.
13. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOL-PRINT 2D): Evaluation of Performance. J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.
14. Bender, A.; Glen, R. C. A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication. J. Chem. Inf. Model. 2005, 45, 1369-1375.
15. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Enhancing the Effectiveness of Similarity-Based Virtual Screening Using Nearest-Neighbor Information. J. Med. Chem. 2005, 48, 7049-7054.
16. WOMBAT WOrld of Molecular BioAcTivity (WOMBAT); Sunset Molecular Discovery LLC: Santa Fe. NM. http://www.sunsetmolecular.com/ (accessed Jul 2006).
17. Kauvar, L. M.; Higgins, D. L.; Villar. H. O.; Sportsman, J. R.; Engqvist-Goldstein, A.; Bukar, R.; Bauer, K. E.; Dilley, H.; Rocke, D. M. Predicting Ligand Binding to Proteins by Affinity Fingerprinting. Chem. Biol. 1995, 2, 107-118.
18. Beroza, P.; Villar, H. O.; Wick, M. M.; Martin, G. R. Chemoproteomics as a Basis for Post-Genomic Drug Discovery. Drug Discovery Today 2002, 7, 807-814.
19. Briem, H.; Lessel, U. In Vitro and in Silico Affinity Fingerprints: Finding Similarities beyond Structural Classes. Perspect. Drug Discovery Des. 2000, 20, 231-244.
20. Lessel, U. F.; Briem, H. Flexsim-X: A Method for the Detection of Molecules with Similar Biological Activity. J. Chem. Inf. Comput. Sci. 2000, 40, 246-253.
21. Weber, A.; Teckentrup, A.; Briem, H. Flexsim-R: A Virtual Affinity Fingerprint Descriptor To Calculate Similarities of Functional Groups. J. Comput.-Aided Mol. Des. 2002, 16, 903-916.
22. Weinstein, J. N.; Myers, T. G.; Oconnor, P. M.; Friend, S. H.; Fornace, A. J.; Kohn, K. W.; Fojo, T.; Bates, S. E.; Rubinstein, L. V.; Anderson, N. L.; Buolamwini, J. K.; vanOsdol, W. W.; Monks, A. P.; Scudiero, D. A.; Sausville. E. A.; Zaharevitz, D. W.; Bunow, B.; Viswanadhan, V. N.; Johnson, G. S.; Wittes, R. E.; Paull, K. D. An Information-Intensive Approach to the Molecular Pharmacology of Cancer. Science 1997, 275, 343-349.
23. Krejsa, C. M.; Horvath, D.; Rogalski, S. L.; Penzotti, J. E.; Mao, B.; Barbosa, F.; Migeon, J. C. Predicting ADME Properties and Side Effects: The BioPrint Approach. Curr. Opin. Drug Discovery Dev. 2003, 6, 470-480.
24. Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Biospectra Analysis: Model Proteome Characterizations for Linking Molecular Structure and Biological Response. J. Med. Chem. 2005, 48, 6918-6925.
25. Oprea, T. I. Chemical Space Navigation in Lead Discovery. Curr. Opin. Chem. Biol. 2002, 6, 384-389.
26. Karthikeyan, M.; Glen, R. C.; Bender, A. General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks. J. Chem. Inf. Model 2005, 45, 581-590.
27. Givehchi, A.; Bender, A.; Glen, R. C. Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors. J. Chem. Inf. Model. 2006, 46 (3), 1078-1083.
28. Sheridan, R. P.; Shpungin, J. Calculating Similarities between Biological Activities in the MDL Drug Data Report Database. J. Chem. Inf. Comput. Sci. 2004, 44, 727-740.
29. PipelinePilot 5.1; Scitegic: San Diego, CA. http://www.scitegic.com/ (accessed Jul 2006).
30. Nidhi; Glick, M.; Davies, J. W.; Jenkins, J. L. Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases. J. Chem. Inf. Comput. Sci. 2006, 46(3), 1124-1133.
31. Glen, R. C.; Bender, A.; Arnby, C. H.; Carlsson, L.; Boyer, S.; Smith, J. Circular Fingerprints: Flexible Molecular Descriptors with Applications from Physical Chemistry to ADME. IDrugs 2006, 9, 199-204.
32. Statistica 7.0; Statsoft: Tulsa, OK. http://www.statsoft.com (accessed Sept 2006).
33. 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.-Aided Mol. Des. 2004, 18, 529-536.
34. Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks. J. Med. Chem. 1996, 39, 2887-2893.
35. Zhang, Q.; Muegge, I. Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring. J. Med. Chem. 2006, 49, 1536-1548.
36. Morphy, R.; Kay, C.; Rankovic, Z. From Magic Bullets to Designed Multiple Ligands. Drug Discovery Today 2004, 9, 641-651.
37. Hopkins, A. L.; Mason, J. S.; Overington, J. P. Can We Rationally Design Promiscuous Drugs? Curr. Opin. Struct. Biol. 2006, 16, 127-136.