An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands

Journal of Chemical Information and Modeling

Volumn 46, Issue 6, 2006, Pages 2610-2622

  Fukunishi, Yoshifumi ^a,b   Hojo, Shinichi ^b   Nakamura, Haruki ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b TOKYO METROPOLITAN UNIVERSITY   (Japan)

^c OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; LEARNING SYSTEMS; MOLECULAR STRUCTURE; OPTIMIZATION; PRINCIPAL COMPONENT ANALYSIS; PROTEINS;

CYTOCHROME; DOCKING CALCULATIONS; IN SILICO SCREENING; LIGANDS;

PIGMENTS;

CYTOCHROME P450; LIGAND; PROTEIN;

ARTICLE; ARTIFICIAL INTELLIGENCE; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG INDUSTRY; DRUG SCREENING; GENETIC POLYMORPHISM; HUMAN; METHODOLOGY; PHARMACEUTICS; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL MODEL;

ARTIFICIAL INTELLIGENCE; BINDING SITES; CHEMISTRY, PHARMACEUTICAL; COMBINATORIAL CHEMISTRY TECHNIQUES; CYTOCHROME P-450 ENZYME SYSTEM; DRUG EVALUATION, PRECLINICAL; DRUG INDUSTRY; HUMANS; LIGANDS; MODELS, CHEMICAL; MODELS, STATISTICAL; POLYMORPHISM, GENETIC; PRINCIPAL COMPONENT ANALYSIS; PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; TECHNOLOGY, PHARMACEUTICAL;

EID: 33845790192     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600334u     Document Type: Article

References (48)

1. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A Geometric Approach to Macromolecule-Ligand Interactions. J. Mol. Biol. 1982, 161, 269-288.
2. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A Fast Flexible Docking Method Using an Incremental Construction Algorithm. J. Mol. Biol. 1996, 261, 470-489.
3. Jones, G.; Willet, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking. J. Mol. Biol. 1997, 267, 727-748.
4. Paul, N.; Rognan, D. ConsDock: A New Program for the Consensus Analysis of Protein-Ligand Interactions. Proteins: Struct., Funct., Genet 2002, 47, 521-533.
5. Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity. Proteins: Struct., Funct., Genet. 1998, 33, 367-382.
6. McGann, M. R.; Almond, H. R.; Nicholls, A.; Grant, J. A.; Brown, F. K. Gaussian Docking Functions. Biopolymers 2003, 68, 76-90.
7. Goodsell, D. S.; Olson, A. J. Automated Docking of Substrates to Proteins by Simulated Annealing. Proteins: Struct., Funct., Genet. 1990, 8, 195-202.
8. Taylor, J. S.; Burnett, R. M. DARWIN: A Program for Docking Flexible Molecules. Proteins: Struct., Funct., Genet. 2000, 41, 173-191.
9. Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM: A New Method for Structure Modeling and Design: Application to Docking and Structure Prediction from the Disordered Native Conformation. J. Comput. Chem. 1994, 15, 488-506.
10. Colman, P. M. Structure-Based Drug Design. Curr. Opin. Struct. Biol. 1994, 4, 868-874.
11. Krammer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: A Novel Scoring Function for Predicting Binding Affinities. J. Mol. Graphics Modell. 2005, 23, 395-407.
12. Fukunishi, Y.; Mikami, Y.; Nakamura, H. Similarities among Receptor Pockets and among Compounds: Analysis and Application to in Silico Ligand Screening. J. Mol. Graphics Modell. 2005, 24, 34-45.
13. Orita, M.; Yamamoto, S.; Katayama, N.; Aoki, M.; Takayama, K.; Yamagiwa, Y.; Seki, N.; Suzuki, H.; Kurihara, H.; Sakashita, H.; Takeuchi, M.; Fujita, S.; Yamada, T.; Tanaka, A. Coumarin and Chomen-4-one Analogues as Tautomerase Inhibitors of Macrophage Migration Inhibitory Factor: Discovery and X-ray Crystallography. J. Med. Chem. 2001, 44, 540-547.
14. Cotesta, S.; Giordanetto, F.; Trosset, J. Y.; Crivori, P.; Kroemer, R. T.; Stouten, P. F. W.; Vulpetti, A. Virtual Screening to Enrich a Compound Collection with CDK2 Inhibitors Using Docking, Scoring, and Composite Scoring Models. Proteins: Struct., Funct., Bioinf. 2005, 60, 629-643.
15. Schellhammer, I.; Rarey, M. FlexX-Scan: Fast, Structure-Based Virtual Screening. Proteins: Struct., Funct., Bioinf. 2004, 57, 504-517.
16. Evers, A.; Hessler, G.; Matter, H.; Klabunde, T. Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols. J. Med. Chem. 2005, 48, 5448-5465.
17. Howard, M. H.; Cenizal, T.; Gutteridge, S.; Hanna, W. S.; Tao, Y.; Totrov, M.; Wittenbach, V. A.; Zheng, Y.-J. A Novel Class of Inhibitors of Peptide Deformylase Discovered through High-Through-put Screening and Virtual Ligand Screening. J. Med. Chem. 2004, 47, 6669-6672.
18. Godden, J. W.; Stahura, F. L.; Bajorath, J. POT-DMC: A Virtual Screening Method for the Identification of Potent Hits. J. Med. Chem. 2004, 47, 5608-5611.
19. β-Selective Ligands as Potential Preventative Therapy against Age-Related Neurodegenerative Diseases. J. Med. Chem. 2005, 48, 3463-3466.
20. Mestres, J.; Veeneman, G. H. Identification of "Latent Hits" in Compound Screening Collections. J. Med. Chem. 2003, 46, 3441-3444.
21. Vigers, G. P. A.; Rizzi, J. P. Multiple Active Site Corrections for Docking and Virtual Screening. J. Med. Chem. 2004, 47, 80-89.
22. Fukunishi, Y.; Mikami, Y.; Kubota, S.; Nakamura, H. Multiple Target Screening Method for Robust and Accurate in Silico Ligand Screening. J. Mol. Graphics Modell. 2005, 25, 61-70.
23. Pickett, S. In Protein-Ligand Interactions from Molecular Recognition to Drug Design - Methods and Principles in Medicinal Chemistry; Boehm, H. J., Schneider, G., Mannhold, R., Kubinyi, H., Folkers, G., Eds.; Wiley-VCH: Weinheim, Germany, 2003; pp 88-91.
24. Pearlman, R. S.; Smith, K. M. Metric Validation and the Receptor-Relevant Subspace Concept. J. Chem. Inf. Compt. Sci. 1999, 39, 28-35.
25. 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.
26. Briem, H.; Kuntz, I. D. Molecular Similarity Based on DOCK-Generated Fingerprints. J. Med. Chem. 1996, 39, 3401-3408.
27. 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.
28. Briem, H.; Lessel, U. F. In Vitro and in Silico Affinity Fingerprints; Finding Similarities beyond Structural Classes. Perspect. Drug Discovery Des. 2000, 20, 231-244.
29. 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.
30. Hsu, N.; Cai, D.; Damodaran, K.; Gomez, R. F.; Keck, J. G.; Laborde, E.; Lum, R. T.; Macke, T. J.; Martin, G.; Schow, S. R.; Simon, R. J.; Villar, H. O.; Wick, M. M.; Beroza, P. Novel Cyclooxygenase-1 Inhibitors Discovered Using Affinity Fingerprints. J. Med. Chem. 2004, 47, 4875-4880.
31. Fukunishi, Y.; Mikami, Y.; Takedomi, K.; Yamanouchi, M.; Shima, H.; Nakamura, H. Classification of Chemical Compounds by Protein-Compound Docking for Use in Designing a Focused Library. J. Med. Chem. 2006, 49, 523-533.
32. Kamataki, T. In P450 no Bunshiseibutugaku; Oomura, T., Ishimura, T., Fujii, Y., Eds.; Koudansya: Tokyo, 2005; pp 148-149.
33. Iwasawa, Y. In Medicinal Chemistry; Yamakawa, K., Kanaoka, Y., Iwasawa, Y., Eds.; Koudansya: Tokyo, 2004; pp 73-85.
34. Butina, D.; Segall, M. D.; Frankcombe, K. Predicting ADME Properties in Silico: Methods and Models. Drug Discovery Today 2002, 7, S83-S88.
35. Ekins, S.; Waller, C. L.; Swaan, P. W.; Cruciani, G.; Wrighton, S. A.; Wikel, J. H. Progress in Predicting Human ADME Parameters in Silico. J. Pharmacol. Toxicol. Methods 2000, 251-272.
36. Cattel, R. B. The Scree Test for the Number of Factors. Multivar. Behav. Res. 1966, 1, 245-276.
37. Abdi, H. In Encyclopedia for Research Methods for the Social Science; Lewis-Beck, M., Futing, T., Eds.; Sage; Thousand Oaks, CA, 2003; pp 978-982.
38. Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.: Cole, J. C.; Taylor, R. A New Test Set for Validating Predictions of Protein-Ligand Interaction. Proteins: Struct., Funct., Genet. 2002, 49, 457-471.
39. Watanabe, T.; Fukui, Y. In Saiboumaku no Jyuyoutai; Takayanagi, I., Ed.; Nanzandou: Tokyo, 1998; pp 121-131.
40. Koike, K.; Nagatomo, T. In Saiboumaku no Jyuyoutai; Takayanagi, I., Ed.; Nanzandou; Tokyo, 1998; pp 103-118.
41. Sasa, M.; Ishihara, K. In Saiboumaku no Jyuyoutai; Takayanagi, I., Ed.; Nanzandou; Tokyo, 1998; pp 135-147.
42. Nakata, Y.; Inoue, A. In Saiboumaku no Jyuyoutai; Takayanagi, I., Ed.; Nanzandou: Tokyo, 1998; pp 169-182.
43. Gasteiger, J.; Marsili, M. Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges. Tetrahedron 1980, 36, 3219-3228.
44. Gasteiger, J.; Marsili, M. A New Model for Calculating Atomic Charges in Molecules. Tetrahedron Lett. 1978, 3181-3184.
45. Case, D. A.; Darden, T. A.; Cheatham, T. R., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8; University of California: San Francisco, CA, 2004.
46. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. "Scaffold- Hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. Angew. Chem., Int. Ed. 1999, 38, 2894-2896.
47. Beresford, A. P.; Selick, H. E.; Tarbit, M. H. The Emerging Importance of Predictive ADME Simulation in Drug Discovery. Drug Discovery Today 2002, 7, 109-116.
48. Sugiyama, M. In Mechanisms of Drug Interactions; Sugiyama, M., Kamiya, H., Eds.; Iyakusyuppan: Tokyo, 2004; pp 46-88.