Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns

Journal of Chemical Information and Modeling

Volumn 48, Issue 9, 2008, Pages 1747-1753

  Auer, Jens ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; FILTRATION; PATTERN RECOGNITION;

BINDING CONFORMATIONS; BIOACTIVE CONFORMATION; CHEMICAL PATTERN; CONFORMATIONAL ENSEMBLE; ENERGY CONFORMERS; PROTEIN-LIGAND COMPLEXES; SMALL MOLECULES; X-RAY STRUCTURE;

CONFORMATIONS;

ENZYME; ENZYME INHIBITOR; LIGAND;

ARTICLE; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; STRUCTURE ACTIVITY RELATION;

BINDING SITES; ENZYME INHIBITORS; ENZYMES; LIGANDS; MODELS, BIOLOGICAL; MOLECULAR CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 54249157493     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci8001793     Document Type: Article

References (21)

1. Diller, D. J.; Merz, K. M. Can we separate active from inactive conformations? J. Comput.-Aided Mol. Des. 2002, 16, 105-112.
2. Perola, E.; Charifson, P. S. Conformational analysis of druglike molecules bound to proteins: An extensive study of ligand reorganization upon binding. J. Med. Chem. 2004, 47, 2499-2510.
3. Agrafiotis, D. K.; Gibbs, A. C.; Zhu, F.; Izrailev, S.; Martin, E. Conformational sampling of bioactive molecules: A comparative study. J. Chem. Inf. Mod. 2007, 47, 1067-1086.
4. Stockwell, G. R.; Thornton, J. M. Conformational diversity of ligands bound to proteins. J. Mol. Biol. 2006, 356, 928-44.
5. Boström, J.; Norrby, P.-O.; Liljefors, T. Conformational energy penalties of protein-bound ligands. J. Comput.-Aided Mol. Des. 1998, 12, 383-396.
6. Nicklaus, M. C.; Wang, S.; Driscoll, J. S.; Milne, G. W. A. Conformational changes of small molecules binding to proteins. Bioorg. Med. Chem. 1995, 3, 411-428.
7. Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 2004, 47, 2977-2980.
8. Wang, R.; Fang, X.; Lu, Y.; Yang, C. Y.; Wang, S. The PDBbind database: methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119.
9. Molecular Operating Environment, 2007.09; Chemical Computing Group Inc.: Montreal, Quebec, Canada, 2007.
10. Stewart, J. J. P. MOPAC: A semiempirical molecular orbital program. J. Comput.-Aided Mol. Des. 1990, 4, 1-103.
11. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM 1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
12. Dewar, M. J. S.; Thiel, W. Ground states of molecules. 38. The MNDO method. Approximations and parameters. J. Am. Chem. Soc. 1977, 99, 4899-4907.
13. Stewart, J. J. P. Optimization of parameters for semiempirical methods I. Method. J. Comput. Chem. 1989, 10, 209-220.
14. Fayyad, U.; Irani, K. On the handling of continuous-valued attributes in decision tree generation. Machine Learn. 1992, 8, 87-102.
15. Auer, J.; Bajorath, J. Emerging chemical patterns: a new methodology for molecular classification and compound selection. J. Chem. Inf. Mod. 2006, 46, 2502-2514.
16. Dong, G.; Li, J.; Chaudhuri, S.; Madigan, D.; Fayyad, U. Efficient mining of emerging patterns: Discovering trends and differences. In KDD-99: The Fifth ACM SIGKDD International Conference; Proceedings of the Fifth ACM SIGKDD International Conference, San Diego, California, 1999; Chaudhuri, S., Madigan, D., Eds.; ACM Press: New York, 1999; pp 43-52.
17. Auer, J.; Bajorath, J. Simulation of sequential screening experiments using emerging chemical patterns. Med. Chem. 2008, 4, 80-90.
18. Clark, A.; Labute, P. 2D depiction of protein-ligand complexes. J. Chem. Inf. Model. 2007, 47, 1933-1944.
19. Cristalli, G.; Costanzi, S.; Lambertucci, C.; Lupidi, G.; Vittori, S.; Volpini, R.; Camaioni, E. Adenosine deaminase: Functional implications and different classes of inhibitors. Med Res. Rev. 2001, 21, 105-128.
20. Terasaka, T.; Kinoshita, T.; Kuno, M.; Nakanishi, I. A highly potent non-nucleoside adenosine deaminase inhibitor: Efficient drug discovery by intentional lead hybridization. J. Am. Chem. Soc. 2004, 126, 34-35.
21. Yakovlev, G.; Mitkevich, V.; Makarov, A. Ribonuclease inhibitors. Mol. Biol. 2006, 40, 867-874.