Assessing the geometric diversity of cytochrome P450 ligand conformers by hierarchical clustering with a stop criterion

Journal of Chemical Information and Modeling

Volumn 49, Issue 2, 2009, Pages 330-337

  Meslamani, Jamel Eddine ^a,b   André, François ^a   Petitjean, Michel ^a  

^a DIF   (France)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING ALGORITHMS; LIGANDS; MOLECULES;

AGGLOMERATIVE HIERARCHICAL CLUSTERING; CONFORMATIONAL SPACE; CYTOCHROME P450; NUMBER OF CLASS; RIGID CONFORMERS; SMALL MOLECULES; STRUCTURAL FLEXIBILITIES; STRUCTURAL REDUNDANCY;

HIERARCHICAL CLUSTERING;

CYTOCHROME P450; LIGAND;

ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; CONFORMATION; METABOLISM;

CLUSTER ANALYSIS; CYTOCHROME P-450 ENZYME SYSTEM; LIGANDS; MOLECULAR CONFORMATION;

EID: 65249106631     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800275k     Document Type: Article

References (38)

1. Guengerich, F. P. Human Cytochrome P450 Enzymes. In Cytochrome P450, Structure, Mechanism, and Biochemistry, third ed.; Ortiz de Montellano, P. R., Ed.; Kluwer/Plenum: New York, 2005; Chapter 10, section 6.20.3, pp 425-426.
2. Lewis, D. F. V. Criteria Governing Substrate Selectivity for Human Hepatic P450s. In Guide to Cytochromes P450, Structure and Function; Taylor & Francis: London, UK, 2001; Chapter 4.4, pp 102-109.
3. Nguyen, T. A.; Tychopoulos, M.; Bichat, F.; Zimmermann, C.; Flinois, J. P.; Diry, M.; Ahlberg, E.; Delaforge, M.; Corcos, L.; Beaune, P.; Dansette, P.; Andre, F.; de Waziers, I. Improvement of Cyclophosphamide Activation by CYP2B6 Mutants: from in Silico to ex Vivo. Mol. Pharmacol. 2008, 73, 1122-1133.
4. Lafite, P.; André, F.; Zeldin, D. C.; Dansette, P. M.; Mansuy, D. Unusual Regioselectivity and Active Site Topology of Human Cytochrome P450 2J2. Biochemistry 2007, 46, 10237-10247.
5. Terfloth, L.; Bienfait, B.; Gasteiger, J. Ligand-Based Models for the Isoform Specificity of Cytochrome P450 3A4, 2D6, and 2C9 Substrates. J. Chem. Inf. Model. 2007, 47, 1688-1701.
6. Good, A. C.; Cheney, D. L. Analysis and Optimization of Structure-Based Virtual Screening Protocols (1): Exploration of Ligand Conformational Sampling Techniques. J. Mol. Gr. Model. 2003, 22, 23-30.
7. Montes, M.; Braud, E.; Miteva, M. A.; Goddard, M.-L.; Mondesert, O.; Kolb, S.; Brun, M.-P.; Ducommun, B.; Garbay, C.; Villoutreix, B. O. Receptor-Based Virtual Ligand Screening for the Identification of Novel CDC25 Phosphatase Inhibitors. J. Chem. Inf. Model. 2008, 48, 157-165.
8. Kenworthy, K. E.; Bloomer, J. C.; Clarke, S. E.; Houston, J. B. A. CYP 3A4 drug interactions: correlation of 10 in vitro probe substrates. Br. J. Clin. Pharmacol. 1999, 48, 716-727.
9. Lill, M. A.; Dobler, M.; Vedani, A. Prediction of small-molecule binding to cytochrome P450 3A4: flexible docking combined with multidimensional QSAR. ChemMedChem 2006, 1, 73-81.
10. SYBYL 7.2; Tripos International: St Louis, Mo, 2006.
11. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and use of quantum mechanical molecular models. 76. AMI: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
12. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03w; revision C.02, Gaussian, Inc.; Wallingford, CT, 2004.
13. Loriot, S.; Sachdeva, S.; Bastard, K.; Prevost, C.; Cazals, F. On the Characterization and Selection of Diverse Conformational Ensembles; INRIA Research Report 6503, April 2008; https://hal.inria.fr/inria-00252046 (accessed Sep 16, 2008).
14. Borodina, Y. V.; Bolton, E.; Fontaine, F.; Bryant, S. H. Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space. J. Chem. Inf. Model. 2007, 47, 1428-1437.
15. Boström, J. Reproducing the Conformations of Protein-Bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools. J. Comput.-Aided Mol. Des. 2001, 15, 1137-1152.
16. Bohme Leite, T.; Gomes, D.; Miteva, M. A.; Chomilier, J.; Villoutreix, B. O.; Tufféry, P. Frog: a FRee Online druG 3D Conformation Generator. Nucleic Acids Res. 2007, 35, 568-572.
17. Ghose, A. K.; Jaeger, E. P.; Kowalczyk, P. J.; Peterson, M. L.; Treasurywala, A. M. Conformational Searching Methods for Small Molecules. I. Study of the SYBYL SEARCH Method. J. Comput. Chem. 1993, 14, 1050-1065.
18. Petitjean, M. http://petitjeanmichel.free.fr/itoweb.petitjean.freeware. html#ARMS (accessed Sep 16, 2008).
19. Petitjean, M. On the Root Mean Square Quantitative Chirality and Quantitative Symmetry Measures. J. Math. Phys. 1999, 40, 4587-4595; see the Appendix.
20. Petitjean, M. Chiral Mixtures. J. Math. Phys. 2002, 43, 4147-4157; Appendix A.5.
21. Petitjean, M. Three-Dimensional Pattern Recognition from Molecular Distance Minimization. J. Chem. Inf. Comput. Sci. 1996, 36, 1038-1049.
22. Petitjean, M. Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm. Comp. Chem. 1998, 22, 463-465.
23. Nakache, P.; Confais, J. Algorithmes d'agrégation fondés surun lien métrique. In Approche Pragmatique de la Classification; Technip: Paris, France, 2005; Chapter 1.8, pp 35-43.
24. Shenkin, P. S.; McDonald, D. Q. Cluster Analysis of Molecular Conformations. J. Comput. Chem. 1994, 15, 899-916.
25. Vesterman, B.; Golender, V.; Golender, L.; Fuchs, B. Conformer Clustering Algorithm and its Application for Crown-Type Macrocycles. J. Mol. Struct. 1996, 368, 145-151.
26. Mirkin, B. Validity and Reliability. In Clustering for Data Mining, A Data Recovery Approach; Chapman & Hall/CRC: Boca Raton, FL, 2005; Chapter 7.5, pp 232-243.
27. Nakache, P.; Confais, J. Nombre de classes a retenir. In Approche Pragmatique de la Classification; Technip: Paris, France, 2005; Chapter 7, pp 189-205.
28. Milligan, G. W.; Cooper, M. C. An Examination of Procedures for Determining the Number of Clusters in a Data Set. Psychometrika 1985, 50, 159-179.
29. Dubes, R. C. How Many Clusters are Best? - An Experiment. Pattern Rec. 1987, 20, 645-663.
30. Jain, A. K.; Dubes, R. C. Cluster Validity. In Algorithms for Clustering Data; Prentice Hall: Englewood Cliffs, NJ, 1988; Chapter 4, pp 143-222.
31. Atlas, R. S.; Overall, J. E. Comparative Evaluation of Two Superior Stopping Rules for Hierarchical Cluster Analysis. Psychometrika 1994, 59, 581-591.
32. Bezdek, J. C.; Pal, N. R. Some New Indexes of Cluster Validity. IEEE Trans. Syst. Man Cyber. 1998, 28, 301-315.
33. Günter, S.; Bunke, H. Validation Indices for Graph Clustering. Pattern Rec. Lett. 2003, 24, 1107-1113.
34. Bolshakova, N.; Azuaje, F. Cluster Validation techniques for Genome Expression Data. Signal Process. 2003, 83, 825-833.
35. Mojena, R. Hierarchical Grouping Methods and Stopping Rules: An Evaluation. Comput. J. 1977, 20, 359-363.
36. Jung, Y.; Park, H.; Du, D.-Z.; Drake, B. L. A Decision Criterion for the Optimal Number of Clusters in Hierarchical Clustering. J. Global Optim. 2006, 25, 91-111.
37. O'Donohue, M. F.; Burgess, A. W.; Walkinshaw, M. D.; Treutlein, H. R. Modeling Conformational Changes in Cyclosporin A. Protein Sci. 1995, 4, 2191-2202.
38. Verheyden, P.; Jaspers, H.; De Wolf, E.; van Binst, G. Conformational Study of Cyclosporin A in Acetone at Low Temperature. Int. J. Pept. Protein Res. 1994, 44, 364-371.