LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters

Journal of Chemical Information and Modeling

Volumn 45, Issue 1, 2005, Pages 160-169

  Wolber, Gerhard ^a   Langer, Thierry ^b  

^a Inte:Ligand GmbH   (Austria)

^b UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; AUTOMATION; BIOFILTERS; CHELATION; COMPLEXATION; DATA ACQUISITION; DERIVATIVES; ORGANIC COMPOUNDS; PROTEINS; VIRUSES;

LIGANDS; PHARMACOPHORES; RECEPTORS; RHINOVIRUS;

PHARMACODYNAMICS;

ANTINEOPLASTIC AGENT; ANTIVIRUS AGENT; BCR ABL TYROSINE KINASE; BCR-ABL TYROSINE KINASE; LIGAND; PROTEIN TYROSINE KINASE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DRUG ANTAGONISM; DRUG DESIGN; DRUG EFFECT; HYDROGEN BOND; PROTEIN BINDING; RHINOVIRUS;

ANTINEOPLASTIC AGENTS; ANTIVIRAL AGENTS; DRUG DESIGN; HYDROGEN BONDING; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN-TYROSINE KINASES; RHINOVIRUS; SOFTWARE;

EID: 13844320566     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci049885e     Document Type: Article

References (44)

1. Drews, J. Drug Discovery: A Historical Perspective. Science 2000, 287, 1960-1964.
2. Langer, T.; Hoffmann, R.; Bachmair, F.; Begle, S. Chemical function based pharmacophore models as suitable filters for virtual screening. J. Mol. Struct. (THEOCHEM) 2000, 503, 59-72.
3. Walters, W.; Stahl, M.; Murcko, M. Virtual Screening - an overview. Drug Discovery Today 1998, 3, 160-178.
4. SYBYL 6.6/FlexX, Tripos Inc., 1699 South Hanley Road, St. Louis, Missouri, 63144, U.S.A.
5. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 267, 470-489.
6. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. Multiple automatic base selection: Protein - ligand docking based on incremental construction without manual intervention. J. Comput.-Aided Mol. Des. 1997, 11, 369-384.
7. Oshiro, C.; Kuntz, I. Flexible ligand docking using a genetic algorithm. J. Comput.-Aided Mol. Des. 1995, 9, 113-130.
8. Weiner, S.; Kollman, P.; Case, D.; Singh, U.; Ohio, C.; Alagona, G.; Profeta, S.; Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 1984, 106, 765-784.
9. Morris, G. M; Goodsell, D. S.; Halliday, R.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J. Comput. Chem. 1998, 19, 1639-1662.
10. Jones, G.; Willett, P.; Glen, R. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol Biol. 1995, 245, 43-53.
11. Jones, G.; Willett, P.; Glen, R.; Leach, A.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
12. Schrödinger, Portland, OR97201.
13. Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldan, M. Ligand-Fit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graphics Modell. 2003, 21, 289-307.
14. Böhm, H.-J. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput.-Aided Mol Des. 1992, 6, 593-606.
15. Berman, H.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
16. Cambridge Crystallographic Data Centre, Relibase: A program for searching protein - ligand databases, http://relibase.ccdc.cam.ac.uk/, 2003.
17. Hendlich, M.; Rippmann, F.; Barnickel, G. BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank. J. Chem. Inf. Comput. Sci. 1997, 37, 774-778.
18. Sayle, R.; Milner-White, E. RASMOL: Biomolecular graphics for all. TIBS 1995, 20, 374-376.
19. Hooft, R.; Vriend, G.; Sander, C.; Abola, E. Errors in protein structures. Nature 1996, 381, 272-272.
20. PDB File Format Contents Guide, Version 2.2, http://www.rcsb.org/ pdb/docs/format/pdbguide2.2/, 1996.
21. Sayle, R. PDB: Cruft to Content: Perception of Molecular Connectivity from 3D Coordinates, http://www.daylight.com/meetings/mug01/Sayle/m4xbondage. html, 2001.
22. Gasteiger, J.; Jochum, C. An Algorithm for the Perception of Synthetically Important Rings. J. Chem. Inf. Comput. Sci. 1979, 19, 43-48.
23. Wipke, W.; Dyott, T. Use of Ring Assemblies in Ring Perception Algorithm. J. Chem. Inf. Comput. Sci. 1975, 15, 140-147.
24. Hendrickson, J.; Grier, D.; Toczko, A. Condensed structure identification and ring perception. J. Chem. Inf. Comput. Sci. 1984, 24, 195-203.
25. Balducci, R.; Pearlman, R. Efficient exact solution of the ring perception problem. J. Chem. Inf. Comput. Sci. 1994, 34, 822-831.
26. Fan, B.; Panaye, A.; Doucet, J.; Barbu, A. Ring perception. A new algorithm for directly finding the smallest set of smallest rings from a connection table. J. Chem. Inf. Comput. Sci. 1993, 33, 657-662.
27. Downs, G.; Gillet, V.; Holliday, J.; Lynch, M. Review of Ring Perception Algorithms for Chemical Graphs. J. Chem. Inf. Comput. Sci. 1989, 29, 172-187.
28. Figueras, J. Ring Perception using Breadth-First Search. J. Chem. Inf. Comput. Sci. 1996, 36, 986-991.
29. Wolber, G.; Langer, T. CombGen: A novel software package for the rapid generation of virtual combinatorial libraries. In Rational Approaches to drug design; Höltje, H.-D., Sippl, W., Eds.; Prous Science: 2000; pp 390-399.
30. Green, J.; Kahn, S.; Savoj, H.; Sprague, P.; Teig, S. Chemical function queries for 3D database search. J. Chem. Inf. Comput. Sci. 1994, 34, 1297-1308.
31. Krovat, E.; Langer, T. Non-Peptide Angiotensin II Receptor Antagonists: Chemical Feature Based Pharmacophore Identification. J. Med. Chem. 2003, 46, 716-726.
32. Catalyst, Version 4.7, Accelrys Inc., 9685 Scranton Road, San Diego, CA 92121-3752, U.S.A., 2001.
33. Pauling, L. The Nature of the Chemical Bond, 2nd ed; Cornell University Press: New York, 1948.
34. Khan, A. A liquid water model: Density variation from supercooled to superheated states, prediction of H-bonds and temperature limits. J. Phys. Chem. 2000, 104, 11268-11274.
35. Lipinski, 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.
36. Wildman, S. A.; Crippen, G. M. Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39 (5), 868-873.
37. Kabsch, W. A solution for the best rotation to relate to sets of vectors. Acta Crystallogr. 1976, A32, 922-923.
38. Wimmer, E. Genome-linked proteins of viruses. Cell 1982, 28, 199-201.
39. Viropharma, 405 Eagleview Boulevard, Exton, PA 19341.
40. Hadfield, A. T.; Diana, G. T.; Rossmann, M. G. Analysis of three structurally related antiviral compounds in complex with human rhinovirus 16. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14730.
41. Carroll, M.; Ohno-Jones, S.; Tamura, S.; Buchdunger, E.; Zimmermann, J.; Lydon, N. B.; Gilliland, D. G.; Druker, B. J. CGP 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing BCR-ABL, TEL-ABL, and TEL-PDGFR fusion proteins. Blood 1997, 90, 4947.
42. Zimmermann, J.; Buchdunger, E.; Mett, H.; Meyer, T.; Lydon, N. B. Potent and selective inhibitors of the ABL-kinase: phenylaminopyrimidine (PAP) derivatives. Bioorg. Med. Chem. Lett. 1997, 7, 187.
43. Buchdunger, E.; Cioffi, C. L.; Law, N.; Stover, D.; Ohno-Jones, S.; Druker, B. J.; Lydon, N. B. Abl protein-tyrosine kinase inhibitor STI571 inhibits in vitro signal transduction mediated by c-kit and platelet-derived growth factor receptors. J. Pharmacol. Exp. Ther. 2000, 295(1), 139-145.
44. Schindler, T.; Bornmann, W.; Pellicena, P. W.; Miller, W. T.; Clarkson, B.; Kuriyan, J. Structural mechanism for STI-571 inhibition of Abelson Tyrosine Kinase. Science 2000, 289, 1938-1942.