Pharmacokinetically based mapping device for chemical space navigation

Journal of Combinatorial Chemistry

Volumn 4, Issue 4, 2002, Pages 258-266

  Oprea, Tudor I ^a   Zamora, Ismael ^a,b   Ungell, Anna Lena ^a  

^a ASTRAZENECA R AND D   (Sweden)

^b Lead Molec Discov Slt Francesc C   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE;

EID: 0012286670     PISSN: 15204766     EISSN: None     Source Type: Journal    
DOI: 10.1021/cc010093w     Document Type: Article

References (57)

1. Lehn, J. M. Dynamic combinatorial chemistry and virtual combinatorial libraries. Chem. - Eur. J. 1999, 5, 2455-2463.
2. Lipinski, C. A. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods 2000, 44, 235-249.
3. Lipinski, C. A.; Lombarde, 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.
4. Artursson, P.; Karlsson, J. Correlation between oral drug absoprtion in humans and apparent drug permeability coefficients in human intestinal epithelial (Caco-2 cells). Biochem. Biophys. Commun. 1991, 175, 880-885.
5. Warr, W. A. Combinatorial chemistry and molecular diversity. An overview. J. Chem. Inf. Comput. Sci. 1997, 37, 132-140.
6. Martin, Y. C.; Brown, D.; Bures, M. G. Quantifying diversity. In Combinatorial chemsitry and molecular diversity in drug discovery; Gordon, E. M., Kerwin, J. F., Eds.; Wiley-Liss: New York, 1998; pp 369-385.
7. Pearlman, R. S.; Smith, K. M. Novel Software Tools for Chemical Diversity. Perspect. Drug Discovery Des. 1998, 9-11, 339-353.
8. Pickett, S. D.; McLay, I. M.; Clark, D. E. Enhancing the hit-to-lead properties of lead optimization libraries. J. Chem. Inf. Comput. Sci. 2000, 40, 263-272.
9. Darvas, F.; Dorman, G. Early integration of ADME/Tox parameters into the design process of combinattorial libraries. Chim. Oggi 1999, 17, 10-13.
10. Oprea, T. I.; Zamora, I.; Svensson, P. Quo Vadis, scoring functions? Toward an integrated pharmacokinetic and binding affinity prediction framework. In Combinatorial library design and evaluation for drug design; Ghose, A. K., Viswanadhan, V. N., Eds.; Marcel Dekker, Inc.: New York, 2001; pp 233-266.
11. Willett, P. Chemoinformatics - similarity and diversity in chemical libraries. Curr. Opin. Biotechnol. 2000, 11, 85-88.
12. Livingstone, D. J. The characterization of chemical structures using molecular properties. A survey. J. Chem. Inf. Comput. Sci. 2000, 40, 195-209.
13. Jamois, E. A.; Hassan, M.; Waldman, M. Evaluation of reagent-based and product-based strategies in the design of combinatorial library subsets. J. Chem. Inf. Comput. Sci. 2000, 40, 63-70.
14. Leach, A. R.; Bradshaw, J.; Green, D. V. S.; Hann, M. M. Implementation of a system for reagent selection and library enumeration, profiling, and design. J. Chem. Inf. Comput. Sci. 1999, 39, 1161-1172.
15. Lobanov, V. S.; Agrafiotis, D. K. Stochastic similarity selections from large combinatorial libraries. J. Chem. Inf. Comput. Sci. 2000, 40, 460-470.
16. Oprea, T. I. Rapid estimation of hydrophobicity for virtual combinatorial library analysis. SAR QSAR Environ. Res. 2001, 12, 129-141.
17. Shi, S.; Peng, Z.; Kostrowicki, J.; Paderes, G.; Kuki, A Efficient combinatorial filtering for desired molecular properties of reaction products, J. Mol. Graphics Modell. 2000, 18, 478-496.
18. Sadowski, J.; Kubinyi, H. A Scoring Scheme for discriminating between drugs and nondrugs J. Med. Chem. 1998, 41, 3325-3329.
19. Ajay; Walters, W. P.; Murcko, M. A. Can we learn to distinguish between "Drug-like" and "Nondrug-like" molecules? J. Med. Chem. 1998, 41, 3314-3324.
20. Teague, S. J.; Davis, A. M.; Leeson, P. D.; Oprea, T. I. The design of leadlike combinatorial libraries. Angew. Chem., Int. Ed. Engl. 1985, 24, 3743-3748.
21. Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. Is There a Difference between Leads and Drugs? A Historical Perspective. J. Chem. Inf. Comput. Sci. 2001, 41, 1308-1315.
22. Jackson, J. E. A Users Guide to Principal Components; Wiley: New York, 1991.
23. Austel, V. A manual method for systematic drug design. Eur. J. Med. Chem. 1982, 17, 9-16.
24. Johnson, M. E.; Nachtsheim, C. J. Some guidelines for constructing exact D-optimal designs on convex design spaces. Technometrics 1983, 25, 271-277.
25. Oprea, T. I.; Gottfries, J.; Sherbukhin, V.; Svensson, P.; Kühler, T. C. Chemical information management in drug discovery: Optimizing the computational and combinatorial chemistry interfaces. J. Mol. Graphics Modell. 2000, 18, 512-524.
26. Oprea, T. I.; Gottfries, J. Chemography: The Art of Chemical Space Navigation. J. Comb. Chem. 2001, 3, 157-446.
27. Oprea, T. I.; Gottfries, J. ChemGPS: A chemical space navigation tool. In Rational Approaches to Drug Design; Höltje, H.-D., Sippl, W., Eds.; Prous Science Press: Barcelona, Spain 2001; pp 437-446.
28. Goodford, P. J. Computational procedure for determining energetically favourable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857.
29. Clementi, S.; Cruciani, G.; Fifi, P.; Riganelli, D.; Valigi, R.; Musumarra, G. A new set of principal properties for heteroaromatics obtained by GRID. Quant. Struct. - Act. Relat. 1996, 15, 108-120.
30. Sandberg, M.; Eriksson, L.; Jonsson, J.; Sjöström, M.; Wold, S. New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J. Med. Chem. 1998, 41, 2481-2491.
31. Olsson, T.; Sherbukhin, V. Synthesis and Structure Administration (SaSA), 1997-2001. AstraZeneca. http://www.ast-razeneca.com.
32. Raevsky, O. A.; Grigor'ev, V. Yu.; Kireev, D.; Zefirov, N. S. Complete thermodynamic description of H-Bonding in the framework of multiplicative approach. Quant. Struct. - Act. Relat. 1992, 11, 49-64. HYBOT is available from Pion Inc., Cambridge, Massachussets, http://www.pion-inc.com.
33. Waiver of in vivo bioavailability and bioequivalence studies for immediate-release solid oral dosage forms based on a biopharmaceutics classification system. U.S. Department of Health and Human Services, Food and Drug Administration. http://www.fda.gov/cder/OPS/BCS_guidance.htm (accessed 2000).
34. Cruciani, G.; Crivori, P.; Carrupt, P.-A.; Testa, B. Molecular fields in quantitative structure - permeation relationships: the VolSurf approach. J. Mol. Struct.: THEOCHEM 2000, 503, 17-30. VolSurf is available from Molecular Discovery Ltd., http://www.moldiscovery.com.
35. Cruciani, G.; Pastor, M.; Guba, W. VolSurf: A new tool for pharmacokinetic optimization of lead compounds. Eur. J. Pharm. Sci. 2000, 11 (Suppl. 2), S29-S39.
36. Guba, W.; Cruciani, G. Molecular field-derived descriptors for the multivariate modeling of pharmacokinetic data. In Molecular Modeling and Prediction of Bioactivity; Gundertofte, K., Jørgensen, F. S., Eds.; Kluwer Academic/Plenum Publishers: New York, 2000; pp 89-94.
37. Crivori, P.; Cruciani, G.; Carrupt, P. A.; Testa, B. Predicting blood-brain barrier permeation from three-dimensional molecular structure. J. Med. Chem. 2000, 43 (11), 2204-2216.
38. Zamora, I.; Oprea, T. I.; Ungell, A.-L. Prediction of oral drug permeability. In Rational Approaches to Drug Design; Höltje, H.-D., Sippl, W., Eds.; Prous Science Press: Barcelona, Spain, 2001; pp 271-280.
39. The Pomona Masterfile is an extensive collection of experimental log P values, available from Albert Leo, Pomona College, California, http://clogp.pomona.edu.
40. Abraham, M. H.; Le, J. The correlation and prediction of the solubility of compounds in water using an amended solvation energy relationship. J. Pharm. Sci. 1999, 88, 868-880.
41. CONCORD; Tripos, Inc.: St. Louis, MO, 2000; http://www.tripos.com.
42. SYBYL, version 6.2; Tripos, Inc.; St. Louis, MO, 2000.
43. Bobbyer, D. N. A.; Goodford, P. J.; McWhinnie, P. M. New hydrogen-bond potential for use in determining energically favourable binding sites of molecules of known structure. J. Med. Chem. 1989, 32, 1083-1094.
44. Leo, A.; Weininger, A. CMR3 Reference Manual; Daylight Chemical Information Systems: Santa Fe, NM, 1995; http://www.daylight.com/.
45. Glen, R. C. A Fast Empirical Method for the Calculation of Molecular Polarizability. J. Comput.-Aided Mol. Des. 1994, 8, 457-466.
46. Oprea, T. I. Property Distribution of Drug-related Chemical Databases. J. Comput.-Aided Mol. Des. 2000, 14, 251-264.
47. Basak, S. C.; Balaban, A. T.; Grunwald, G. D.; Gute, B. D. Topological indices: Their nature and mutual relatedness. J. Chem. Inf. Comput. Sci. 2000, 40, 891-898.
48. Balaban, A. T. Topological and Stereochemical Molecular Descriptors for Databases Useful in QSAR Similarity/Dissimilarity and Drug Design. SAR QSAR Environ. Res. 1998, 8, 1-21.
49. Van de Waterbeemd, H.; Camenisch, G.; Folkers, G.; Raevsky, O. A. Estimation of Caco-2 Cell Permeability Using Calculated Molecular Descriptors. Quant. Struct. - Act. Relat. 1996, 15, 480-490.
50. Gasteiger, J.; Marsili, M. Iterative Partial Equalization of Orbital Electronegativity: A Rapid Access to Atomic Charges. Tetrahedron 1980, 36, 3219-3222.
51. CLOGP; Biobyte, Inc.: Claremont, CA; http://clogp.pomona.edu/.
52. ACDLogP; ACD Labs: Toronto, Canada; http://www.acd-labs.com/.
53. oct from Structures. Chem. Rev. 1993, 5, 1281-1306.
54. Wold, S.; Ruhe, A.; Wold, H.; Dunn, W. J., III The collinearity problem in linear regression. The partial least squares approach to generalised inverses. J. Sci. Stat. Comput. 1984, 5, 735-743.
55. Höskuldsson, A. PLS regression methods. J. Chemom. 1988, 2, 211-228.
56. SIMCA-P, version 8.0; Umetrics: Umeå, Sweden; http://www.umetrics.com/.
57. Wold, S.; Albano, C.; Dunn, W. J., III; Edlund, U.; Esvense, K.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjöström, M. Multivariate Data Analysis in Chemistry. In Chemometrics, Mathematics and Statistics in Chemistry; Kowalski, B., Ed.; D. Reidel Publishing Company: Dordrecht. The Netherlands, 1983; pp 17-96.