Library fingerprints: A novel approach to the screening of virtual libraries

Journal of Chemical Information and Modeling

Volumn 47, Issue 4, 2007, Pages 1354-1365

  Klon, Anthony E ^a   Diller, David J ^a  

^a PHARMACOPEIA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATORIAL MATHEMATICS; DIGITAL LIBRARIES; PARAMETER ESTIMATION; PHYSICAL CHEMISTRY; VIRTUAL REALITY;

NONCOMBINATORIAL LIBRARIES; SINGLE-COMPOUND SCREENING; VIRTUAL LIBRARIES;

DATA PRIVACY;

ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; DRUG DESIGN;

BAYES THEOREM; CLUSTER ANALYSIS; DRUG DESIGN;

EID: 34547686017     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci7000204     Document Type: Article

References (55)

1. Lowrie, J. F.; Delisle, R. K.; Hobbs, D. W.; Diller, D. J. The Different Strategies for Designing GPCR and Kinase Targeted Libraries. Comb. Chem. High Throughput Screening 2004, 7, 495-510.
2. Matter, H.; Baringhaus, K.-H.; Naumann, T.; Klabunde, T.; Pirard, B. Computational Approaches Towards the Rational Design of Drug-Like Compounds. Comb. Chem. High Throughput Screening 2001, 4, 453-475.
3. Miller, J, L. Recent Developments in Focused Library Design: Targeting Gene-Families. Curr. Top. Med. Chem. 2006, 6, 19-29.
4. Klabunde, T.; Hessler, G. Drug Design Strategies for Targeting G-Protein-Coupled Receptors. ChemBioChem 2002, 3, 928-944.
5. Crossley, R. The Design of Screening Libraries Targeted at G-Protein Coupled Receptors. Curr. Top. Med. Chem. 2004, 4, 581-588.
6. Orry, A. J.; Abagyan, R. A.; Cavasotto, C. N. Structure-Based Development of Target-Specific Compound Libraries. Drug Discovery Today 2006, 11, 261-266.
7. Lipinski, G A.; Lombardo F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Developmental Settings. Adv. Drug Delivery Rev. 2001, 46, 3-26.
8. Oprea, T. I. Property Distribution of Drug-Related Chemical Databases. J. Comput.-Aided Mol. Des. 2000, 14, 251-264.
9. Delisle, R. K.; Lowrie, J. F.; Hobbs, D. W.; Diller, D. J. Computational ADME/Tox Modeling: Aiding Understanding and Enhancing Decision Making in Drug Design. Curr. Comput.-Aided Drug Des. 2005, 1, 325-345.
10. Cheng, A.; Diller, D. J.; Dixon, S. L.; Egan, W. J.; Lauri, G.; Merz, K. M., Jr. Computation of the Physio-Chemical Properties and Data Mining of Large Molecular Collections. J. Comput. Chem. 2002, 23, 172-183.
11. Glick, M.; Klon, A. E.; Acklin, P.; Davies, J, W. Enriching Extremely Noisy High-Throughput Screening Data Using a Naive Bayes Classifier. J. Biomol. Screening 2004, 9, 32-36.
12. Diller, D. J.; Hobbs, D. W. Deriving Knowledge through Data Mining High-Throughput Screening Data. J. Med. Chem. 2004, 47, 6373-6383.
13. Yan, S. F.; Asatryan, H.; Li, J.; Zhou, Y. Novel Statistical Approach for Primary High-Throughput Screening Hit Selection. J. Chem. Inf. Model. 2005, 45, 1784-1790.
14. Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks. J. Med. Chem. 1996, 39, 2887-2893.
15. Ohlmeyer, M. H.; Swanson, R. N.; Dillard, L. W.; Reader, J. C.; Asouline, G.; Kobayashi, R.; Wigler, M.; Still, W. C. Complex Synthetic Chemical Libraries Indexed with Molecular Tags. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 10922-10926.
16. Stroke, I. L.; Cole, A. G.; Simhadri, S.; Brescia, M. R.; Desai, M.; Zhang, J. J.; Merritt, J. R.; Appell, K. C.; Henderson, I.; Webb, M. L. Identification of CXCR3 Receptor Agonists in Combinatorial Small-Molecule Libraries. Biochem. Biophys. Res. Commun. 2006, 349, 221-228.
17. NIH Roadmap for Medical Research. Molecular Libraries and Imaging Overview, http://nihroadmap.nih.gov/molecularlibraries/index.asp. (accessed August 9, 2006).
18. MDL Drug Data Report; Elsevier MDL: San Leandro, CA, May 25, 2006.
19. Molecular Operating Environment, version 2006.08; Chemical Computing Group, Inc.: Montreal, Quebec, Canada, 2006.
20. Wildman, S. A.; Crippen, G. M. Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
21. Ertl, P.; Rohde, B.; Selzer, P. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties. J. Med. Chem. 2000, 43, 3714-3717.
22. Reference deleted in press.
23. Klon, A. E.; Lowrie, J. F.; Diller, D. J. Improved Naive Bayesian Modeling of Numerical Data for Absorption, Distribution, Metabolism and Excretion (ADME) Property Prediction. J. Chem. Inf. Model. 2006, 46, 1945-1956.
24. 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.
25. Witten, I. H.; Frank, E. ROC Curves. In Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, 1st ed.; Morgan Kaufmann Publishers: New York, 2000; pp 141 - 147.
26. Todeschini, R.; Consonni, V.; Mauri, A.; Pavan, M. DRAGON, version 5.; Talete srl: Milano, Italy, 2004.
27. Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K. Atomic Physicochemical Parameters for Three Dimensional Structure Directed Quantitative Structure-Activity Relationships. 4. Additional Parameters for Hydrophobic and Dispersive Interactions and Their Application for an Automated Superposition of Certain Naturally Occurring Nucleoside Antibiotics. J. Chem. Inf. Comput. Sci. 1989, 29, 163-172.
28. Balaban, A. T. Highly Discriminating Distance-Based Topological Index. Chem. Phys. Lett. 1982, 89, 399-404.
29. Clark, A. M.; Labute, P.; Santavy, M. 2D Structure Depiction. J. Chem. Inf. Model. 2006, 46, 1107-1123.
30. 3 Adenosine Receptors Designed by 3D Database Searching. J /Med. Chem. 2005, 48, 8253-8260.
31. 2A) Antagonists. Bioorg. Med. Chem. Lett. 2005, 15, 1333-1336.
32. Matasi, J. J.; Caldwell, J. P.; Zhang, H.; Fawzi, A.; Cohen-Williams, M. E.; Varty, G. B.; Tulshian, D. B. 2-(2-Furanyl)-7-phenyl[ 1,2,4]-triazolo [l,5-c]pyrimidin-5-amine Analogs: Highly Potent, Orally Active, Adenosine A2A Antagonists. Part 1. Bioorg. Med. Chem. Lett. 2005, 15, 3670-3674.
33. 1 Adenosine Receptors. J. Med. Chem. 2005, 48, 7172-7185.
34. 2A Adenosine Receptor Antagonists. Design, Synthesis, and Pharmacological Characterization. J. Med. Chem. 2005, 48, 6887-6896.
35. 3 Adenosine Receptor Antagonists: Synthesis, Biological Evaluation, and Molecular Modeling Studies of 2-(Hetero)aryl- and 2-Carboxy-substitued derivatives. J. Med. Chem. 2005, 48, 7932-7945.
36. Peng, H.; Kumaravel, G.; Yao, G.; Sha, L.; Wang, J.; Van Vlijmen, H.; Bohnert, T.; Huang, C.; Vu, C. B.; Ensinger, C. L.; Chang, H.; Engber, T. M.; Whalley, E. T.; Petter, R. G Novel Bicyclic Piperazine Derivatives of Triazolotriazine and Triazolopyrimidines as Highly Potent and Selective Adenosine A2A Receptor Antagonists. J. Med. Chem. 2004, 47, 6218-6229.
37. 2A Receptor Antagonists. Bioorg. Med. Chem. Lett. 2004, 14, 817-821.
38. 2A Receptors and Therapeutic Applications. Curr. Top. Med. Chem. 2002, 3, 413-426.
39. Vu, C. B.; Peng, B.; Kumaravel, G.; Smits, G.; Jin, X.; Phadke, D.; Engber, T.; Huang, C.; Reilly, J.; Tam, S.; Grant, D.; Hetu, G.; Chen, L.; Zhang, J.; Petter, R. G Piperazine Derivatives of [1,2,4]Triazolo-[1,5-a] [l,3,5]triazine as Potent and Selective Adenosine A2A Receptor Antagonists. J. Med. Chem. 2004, 47, 4291-4299.
40. Jeong, L. S.; Lee, H. W.; Jacobson, K. A.; Kim, H. O.; Shin, D. H.; Lee, J. A.; Gao, Z. G.; Lu, C.; Duong, H. T.; Guanga, P.; Lee, S. K.; Jin, D. Z.; Chun, M. W.; Moon, H. R. Structure-Activity Relationships of 2-Chloro-N6-substituted-4′-thioadenosine-5′-uronamides as Highly Potent and Selective Agonists at the Human A3 Adenosine Receptor. J. Med. Chem. 2006, 49, 273-281.
41. Jacobson, K. A.; Gao, Z.-G. Adenosine Receptors as Therapeutic Targets. Nat. Rev. Drug Discovery 2006, 5, 247-264.
42. Moro, S.; Gao, Z.-G.; Jacobson, K. A.; Spalluto, G. Progress in the Pursuit of Therapeutic Adenosine Receptor Antagonists. Med. Res. Rev. 2005, 26, 131-159.
43. Palmer, J. T.; Bryant, C.; Wang, D.-X.; Davis, D. E.; Setti, E. L.; Rydzewski, R. M.; Venkatraman, S.; Tian, Z. Q.; Burrill, L. C.; Mendonça, R. V.; Springman, E. McCarter, J.; Chung, T.; Cheung, H.; Jane, J. W.; McGrath, M.; Somoza, J. R.; Enriquez, P.; Yu, Z. W; Strickley, R. M.; Liu, L.; Venuti, M. C.; Percival, M. D.; Falgueyret, J. P.; Prasit, P.; Oballa, R.; Riendeau, D.; Young, R. N.; Wesolowski, G.; Rodan, S. B.; Johnson, C.; Kimmel, D. B.; Rodan, G. Design and Synthesis of Tri-Ring P3 Benzaminde-Containing Aminonitriles as Potent, Selective, Orally Effective Inhibitors of Cathepsin K. J. Med. Chem. 2005, 48, 7520-7534.
44. Marquis, R. W.; Ru, Y.; LoCastro, S. M.; Zeng, J.; Yamashita, D. S.; Oh, H. J.; Erhard, K. F.; Davis, L. D.; Tomaszek, T. A.; Tew, D.; Salyers, K.; Proksch, J.; Ward, K., Smith, B.; Levy, M.; Cummings, M. D., Haltiwanger, R. C.; Trescher, G.; Wang, B.; Hemling, M. E.; Quinn, C. J.; Cheng, H. Y.; Lin, F.; Smith, W. W.; Janson, C. A.; Zhao, B.; McQueney, M. S.; D'Alessio, K.; Lee, C. P.; Marzulli, A.; Dodds, R. A.; Blake, S.; Hwang, S. M.; James, I. E.; Gress, G J.; Bradley, B. R.; Lark, M. W.; Gowen, M.; Veber, D. F. Azepanone-Based Inhibitors of Human and Rat Cathepsin K. J. Med. Chem. 2001, 44, 1380-1395.
45. Marquis, R. W.; Ru, Y.; Zeng, J.; Trout, R. E. L.; LoCastro, S. M.; Gribble, A. D.; Witherington, J.; Fenwick, A. E.; Granier, B.; Tomaszek, T.; Tew, D.; Hemling, M. E.; Quinn, C. J.; Smith, W. W.; Zhao, B.; McQueney, M. S.; Janson, G A.; D'Alessio, K.; Veber, D. F. Cyclic Ketone Inhibitors of the Cysteine Protease Cathepsin K. J. Med. Chem. 2001, 44, 725-736.
46. Altmann, E.; Renaud, J.; Green, J.; Farley, D.; Cutting, B.; Jahnke, W. Arylaminoethyl Amines as Novel Non-Covalent Cathepsin K Inhibitors. J. Med. Chem. 2002, 45, 2352-2354.
47. Altmann, E.; Cowan-Jacob, S. W.; Missbach, M. Novel Purine Nitrile Derived Inhibitors of the Cysteine Protease Cathepsin K. J. Med. Chem. 2004, 47, 5833-5836.
48. Loser, R.; Schilling, K.; Dimmig, E.; Gutschow, M. Interaction of Papain-Like Cysteine Proteases with Dipeptide-Derived Nitriles. J. Med. Chem. 2005, 48, 7688-7707.
49. Tavares, F. X.; Deaton, D. N.; Miller, A. B.; Miller, L. R.; Wright, L. L.; Zhou, H. Q. Potent and Selective Ketoamide-Based Inhibitors of Cystein Protease, Cathepsin K. J. Med. Chem. 2004, 47, 5049-5056.
50. Tavares, F. X.; Boncek, V.; Deaton, D. N.; Hassell, A. M.; Long, S. T.; Miller, A. B.; Payne, A. A.; Miller, L. R.; Shewchuk, L. M.; Wells-Knecht, K.; Willard, D. H., Jr.; Wright, L. L.; Zhou, H. Q. Design of Potent, Selective, and Orally Bioavailable Inhibitors of Cystein Protease Cathepsin K. J. Med. Chem. 2004, 47, 588-599.
51. Falgueyret, J.-P.; Desmarais, S.; Oballa, R.; Black, W. C.; Cromlish, W.; Khougaz, K.; Lamontagne, S.; Masse, F.; Riendeau, D.; Toulmond, S.; Percival, M. D. Lysosomotropism of Basic Cathepsin K Inhibitors Contributes to Increased Cellular Potencies against Off-Target Cathe-psins and Reduced Functional Selectivity. J. Med. Chem. 2005, 48, 7535-7543.
52. Marquis, R. W.; James, I.; Zeng, J.; Trout, R. E. L.; Thompson, S.; Rahman, A.; Yamashita, D. S.; Xie, R.; Ru, Y.; Gress, G J.; Blake, S.; Lark, M. A.; Hwang, S.-M.; Tomaszek, T.; Offen, P.; Head, M. S.; Cummings, M. D.; Veber, D. F. Azepanone-Based Inhibitors of Human Cathepsin L. J. Med. Chem. 2005, 48, 6870-6878.
53. Ng, H. P.; May, K.; Bauman, J. G.; Ghannam, A.; Islam, I.; Liang, M.; Horuk, R.; Hesselgesser, J.; Snider, R. M.; Perez, H. D.; Morrissey, M. M. Discovery of Novel Non-Peptide CCRI Receptor Antagonists. J. Med. Chem. 1999, 42, 4680-4694.
54. Naya, A.; Sagara, Y.; Ohwaki, K.; Saeki, T.; Ichikawa, D.; Iwasawa, Y.; Noguchi, K.; Ohtake, N. Design, Synthesis, and Discovery of a Novel CCRI Antagonist. J. Med. Chem. 2001, 44, 1429-1435.
55. Medina, J. C.; Johnson, M. G.; Collins, T. L. CXCR3 Antagonists. Annu. Rep. Med. Chem. 2005, 40, 215-225.