Pharmacophores incorporating numerous excluded volumes defined by X-ray crystallographic structure in three-dimensional database searching: Application to the thyroid hormone receptor

Journal of Medicinal Chemistry

Volumn 41, Issue 14, 1998, Pages 2503-2512

  Greenidge, Paulette A ^a   Carlsson, Bo ^a   Bladh, Lars Göran ^a   Gillner, Mikael ^a  

^a Karo Bio   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DIPHENYL ETHER DERIVATIVE; DRUG CARRIER; HYDROGEN; STEROID; THYROID HORMONE RECEPTOR;

ANIMAL CELL; ARTICLE; BINDING AFFINITY; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DATA BASE; HYDROGEN BOND; HYDROPHOBICITY; LEPIDOPTERA; NONHUMAN; QUANTITATIVE STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

ANIMALS; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; RATS; RECEPTORS, THYROID HORMONE; SOFTWARE; TRIIODOTHYRONINE;

EID: 0032474911     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9708691     Document Type: Article

References (47)

1. Leeson, P. D.; Underwood, A. H. Thyroid Hormone Receptors. In Comprehensive Medicinal Chemistry; Emmet, J. C., Ed.; Pergamon: Oxford, 1991; pp 1145-1173.
2. Yokoyama, N.; Walker, G. N.; Main, A. J.; Stanton, J. L.; Morrissey, M. M.; Boehm, C.; Engle, A.; Neubert, A. D.; Wasvary, J. M.; Stephan, Z. F.; Steele, R. E. Synthesis and Structure-Activity Relationships of Oxamic Acid and Acetic Acid Derivatives Related to L-thyronine. J. Med. Chem. 1995, 38, 695-707.
3. van Beeren, H. C.; Bakker, O.; Wiersinga, W. M. Structure-Function Relationship of the Inhibition of the 3,5,3′-Triiodothyronine Binding to the α1- and β1-Thyroid Hormone Receptor by Amiodarone Analogues. Endocrinology 1996, 137, 2807-2814.
4. Gronemeyer, H.; Laudet, V. Transcription Factors 3: Nuclear Receptors. Protein Profile 1995, 2, 1173-1308.
5. Wagner, R. L.; Apriletti, J. W.; McGrath, M. E.; West, B. L.; Baxter, J. D.; Fletterick, R. J. A Structural Role for Hormone in the Thyroid Hormone Receptor. Nature 1995, 378, 690-697.
6. Leeson, P. D.; Ellis, D.; Emmett, J. C.; Shah, V. P.; Showell, G. A.; Underwood, A. H. Thyroid Hormone Analogues. Synthesis of 3′-Substituted 3,5-Diiodo-L-thyronines and Quantitative Structure-Actvity Studies of in Vitro and in Vivo Thyromimetic Activities in Rat Liver and Heart, J. Med. Chem. 1988, 31, 37-54.
7. Jorgensen, E. C. Thyromimetic and Antithyroid Drugs. In Burger's Medicinal Chemistry, Part 3, 4 ed.; Wolf, M. E., Ed.; Wiley: New York, 1981; Vol. 3, pp 103-145.
8. Cody, V. Thyroid Hormones-Receptor Interactions: Binding Models from Molecular Conformation and Binding Affinity Data. In Computer-Assisted Drug Design; ACS Symposium 112; Olson, E. C., Christoffersen, R. E., Eds.; American Chemical Society: Washington, DC, 1979; pp 281-299.
9. Dietrich, S. W.; Böiger, M. B.; Kollman, P. A.; Jörgensen, E. C. Thyroxine Analogues. 23. Quantitative Structure-Actvity Correlation Studies of In Vivo and In Vitro Thyromimetic Activities. J. Med. Chem. 1977, 20, 863-880.
10. Andrea, T. A.; Dietrich, S. W.; Murray, W. J.; Kollman, P. A.; Jorgensen, E. C.; Rothenberg, S. A Model for Thyroid Hormone-Receptor Interactions. J. Med. Chem. 1979, 22, 221-232.
11. 3 is neutral, especially considering that it is in close proximity to a hydrogen bond-donating group (the backbone amide hydrogen atom of Ser-277). Furthermore, the geometry of this amino-amide hydrogen bond is much more favorable compared to the initially proposed carboxylate-amide hydrogen bond (R. Wagner, personal communication).
12. Gund, P. Three-Dimensional Pharmacophoric Pattern Searching. In Progress in Molecular and Subcellular Biology; Hahn, F. E., Ed.; Springer-Verlag: New York, 1977; Vol. 5, pp 117-143.
13. Greene, J.; Kahn, S.; Savoy, H.; Sprague, P.; Teig, S. Chemical Function Queries for 3D Database Search. J. Chem. Inf. Comput. Sci. 1994, 34, 1297-1308.
14. Pauling, L. The Nature of the Chemical Bond, 3 ed.; Cornell University Press: Ithaca, NY, 1960.
15. Barnum, D.; Greene, J.; Smellie, A.; Sprague, P. Identification of Common Functional Configurations Among Molecules. J. Chem. Inf. Comput. Sci. 1996, 36, 563-571.
16. Catalyst available from Molecular Simulations, Inc., San Diego, CA 92121-3752.
17. Smellie, A.; Kahn, S. D.; Teig, S. L. Analysis of Conformational Coverage. 1. Validation and Estimation of Coverage. J. Chem. Inf. Comput. Sci. 1995, 35, 285-294.
18. Smellie, A.; Teig, S. L.; Towbin, P. Poling: Promoting Conformational Variation. J. Comput. Chem, 1995, 16, 171-187.
19. Barkhem, T.; Carlsson, B.; Simons, J.; Möller, B.; Berkenstam, A.; Gustafsson, J.-Å.; Nilsson, S. High Level Expression of Functional Full Length Human Thyroid Hormone Receptor β1 in Insect Cells Using a Recombinant. Baculovirus. J. Steroid Biochem. Mol. Biol. 1991, 35, 667-675.
20. Sprague, P. W.; Hoffmann, R. Catalyst Pharmacophore Models and Their Utility as Queries for Searching 3D Databases. In Computer-Assisted Lead Finding and Optimization; van de Waterbeemd, H., Testa, B., Folkers, G., Eds.; 1997; pp 223-240.
21. Itai, A.; Tomioka, N.; Kato, Y.; Nishibata, Y.; Saito, S. New Rational in Approaches for Structure-Activity Relationships and Drug Design. In Medicinal Chemistry for the 21st Century; Wermuth, C. G., Koga, N., König, H., Metcalf, B. W., Eds.; Blackwell Scientific Publications: Oxford, 1992; pp 191-212.
22. Finn, P. W.; Snarey, M. Flexible Three-Dimensional Database Searching for the Identification of Novel Lead Compounds. In Design of Bioactive Compounds; Possibilities for Industrial Applications; BIOS Scientific Publishers Ltd.: Oxford, 1996; pp 67-76.
23. Christie, B. D.; Henry, D. R.; Guner, O. F.; Moock, T. E. MACCS-3D: A Tool for Three-Dimensional Drug Design. Online Inf. 1990, 90, 11-13.
24. Guner, O. F.; Hughes, D. W.; Dumont, L. M. An Integrated Approach to Three-Dimensional Information Management with MACCS-3D. J. Chem. Inf. Comput. Sci. 1991, 37, 408-414.
25. Hurst, T. Flexible 3D Searching: the Directed Tweak Technique. J. Chem. Inf. Comput. Sci. 1994, 34, 190-196.
26. Kuntz, I. D.; Meng, E. C.; Shoichet, B. K. Structure-Based Molecular Design. Acc. Chem. Res. 1994, 27, 117-123.
27. Moock, T. E.; Henry, D. R.; Ozkabak, A. G.; Alamgir, M. Conformational Searching in ISIS/3D Databases. J. Chem. Inf. Comput. Sci. 1994, 34, 184-189.
28. Finn, P. W.; Snarey, M. Pharmacophore Searching Using a Conformationally Flexible Database. In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications; Sanz, F., Giraldo, J., Manaut, F., Eds.; Proua Science Publishers: Barcelona, 1995; pp 658-660.
29. Murrall, N. W.; Davies, E. K. Conformational Freedom in 3-D Databases. 1. Techniques. J. Chem. Inf. Comput. Sci. 1990, 30, 312-316.
30. Sprague, P. W. Automated Chemical Hypothesis Generation and Database Searching With Catalyst. Perspect. Drug Discovery Des. 1995, 3, 1-20.
31. Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P.; Miller, M. D. Flexibases: A Way to Enhance the Use of Molecular Docking Methods. J. Comput.-Aided Mol. Des. 1994, 8, 565-582.
32. Ho, C. M. W.; Marshall, G. R. FOUNDATION: A Program to Retrieve All Possible Structures Containing a User-Defined Minimum Number of Matching Query Elements from Three-Dimensional Databases. J. Comput.-Aided Mol. Des. 1993, 7, 3-22.
33. Sheridan, R. P.; Rusinko, A.; Nilakantan, R.; Venkataraghavan, R. Searching for Pharmacophores in Large Coordinate Data Bases and its Use in Drug Design. Proc. Natl. Acad. Sci, U.S.A. 1989, 86, 8165-8169.
34. Böhm, H.-J. On the Use of LUDI to Search the Fine Chemicals Directory for Ligands of Proteins of Known Three-Dimensional Structure. J. Comput.-Aided Mol. Des. 1994, 8, 623-632.
35. 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.
36. Shoichet, B. K.; Bodian, D. L.; Kuntz, I. D. Molecular Docking Using Shape Descriptors. J. Comput. Chem. 1992, 73, 380-397.
37. Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated Docking with Grid-Based Energy Evaluation. J. Comput. Chem. 1992, 13, 505-524.
38. Ewing, T. J.; Kuntz, I. D. Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening. J. Comput. Chem. 1997, 18, 1175-1189.
39. Gschwend, D. A.; Sirawaraporn, W.; Santi, D. V.; Kuntz, I. D. Specificity in Structure-Based Drug Design: Identification of a Novel, Selective Inhibitor of Pneumocystis carinii Dihydrofolate Reductase. Proteins: Struct. Fund. Genet. 1997, 29, 59-67.
40. Lawrence, M. C.; Davis, P. C. CLIX: A Search Algorithm for Finding Novel Ligands Capable of Binding Proteins of Known Three-Dimensional Structure. Proteins: Struct. Funct. Genet. 1992, 12, 31-41.
41. Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: A System to Select 'Quasi-Flexible' Ligands Complementary to a Receptor of Known Three-Dimensional Structure. J. Comput.-Aided. Mol. Des. 1994, 8, 153-174.
42. Miller, M. D.; Sheridan, R. P.; Kearsley, S. K.; Underwood, D. J. Advances in Automated Docking Applied to Human Immunodeficiency Virus Type 1 Protease. Methods Enzymol. 1994, 247, 354-370.
43. Welch, W.; Ruppert, J.; Jain, A. N. Hammerhead: Fast, Fully Automated Docking of Flexible Ligands to Protein Binding Sites. Chem. Biol. 1996, 3, 449-462.
44. Makino, S.; Kuntz, I. D. Automated Flexible Ligand Docking Method and Its Application for Database Search. J. Comput. Chem. 1997, 18, 1812-1825.
45. Bolger, B.; Jorgensen, E. C. Molecular Interactions Between Thyroid Hormone Analogues and the Rat Liver Nuclear Receptor. J. Biol. Chem. 1980, 255, 10271-10277.
46. Parker, M. G.; White, R. Nuclear Receptors Spring Into Action. Nature Struct. Biol. 1996, 3, 113-115.
47. Brzozowski, A. M.; Pike, A. C.; Dauter, Z.; Hubbard, R. E.; Bonn, T.; Engström, O.; Öhman, L.; Greene, G. L.; Gustafsson, J. Å.; Carlquist, M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 1997, 389, 753-758.