Solution of the conformation and alignment tensors for the binding of trimethoprim and its analogs to dihydrofolate reductase: 3D-quantitative structure-activity relationship study using molecular shape analysis, 3-way partial least-squares regression, and 3-way factor analysis

Journal of Medicinal Chemistry

Volumn 39, Issue 24, 1996, Pages 4825-4832

  Dunn III, William J ^a,b   Hopfinger, Anton J ^a,b   Catana, Cornel ^a   Duraiswami, Chaya ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b Chem21 Group Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE; TRIMETHOPRIM; TRIMETHOPRIM DERIVATIVE;

ARTICLE; CRYSTAL STRUCTURE; DRUG BINDING; DRUG CONFORMATION; ENZYME BINDING; FACTORIAL ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS;

CHEMISTRY; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; ENZYME INHIBITORS; ESCHERICHIA COLI; FOLIC ACID ANTAGONISTS; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; STRUCTURE-ACTIVITY RELATIONSHIP; TETRAHYDROFOLATE DEHYDROGENASE; TRIMETHOPRIM;

EID: 0030461968     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm960491r     Document Type: Article

References (36)

1. Hansch, C. A Quantitative Approach to Biochemical Structure-Activity Relationships. Accts. Chem. Res. 1969, 2, 232.
2. Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959.
3. Hopfinger, A. J.; Burke, B. J. Molecular Shape Analysis: A Formalism to Quantitatively Establish Spatial Molecular Similarity. In Concepts and Applications of Molecular Similarity; Johnson, M. A., Maggiora, G. M., Eds.; Wiley and Sons: New York, 1990; p 173.
4. Srivastava, S.; Richardson, W. W.; Bradley, M. P.; Crippen, G. M. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993; p 409.
5. Good, A. C.; Peterson, S. J.; Richards, W. G. QSAR's from Similarity Matrices. Technique Validation and Application in the Comparison of Different Similarity Evaluation Methods. J. Med. Chem. 1993, 36, 2929.
6. Folkers, G.; Merz, A.; Rognan, D. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993; p 583.
7. 2-Guided Region Selection for Comparative Molecular Field Analysis: A Simple Method to Achieve Consistent Results. J. Med. Chem. 1995, 38, 1060.
8. Marshall, G. R. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993; p 80.
9. Green, S. M.; Marshall, G. R. 3D-QSAR: A Current Perspective. TiPS 1995, 16, 285.
10. Hopfinger, A. J.; Burke, B. J.; Dunn, W. J., III. A Generalized Formalism for Three-Dimensional Quantitative Structure-Property Relationship Analysis for Flexible Molecules Using Tensor Representation. J. Med. Chem. 1994, 37, 3768.
11. Burke, B. J.; Dunn, W. J., III; Hopfinger, A. J. Construction of a Molecular Shape Analysis-Three-Dimensional Quantitative Structure-Analysis Relationship for an Analog Series of Pyridobenzodiazepinone Inhibitors of Muscarinic 2 and 3 Receptors. J. Med. Chem. 1994, 37, 3775.
12. Baker, D. J.; Beddell, C. R.; Champness, J. N.; Goodford, P. J.; Norrington, F. E. A.; Smith, D. R.; Stammers, D. K. The Binding of Trimethoprim to Bacterial Dihydrofolate Reductase. FEBS. Lett. 1981, 126, 49.
13. Dean, P. M. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993.
14. Levin, J. Three-mode Factor Analysis. Psychol. Bull. 1965, 64, 442-452.
15. Apellof, C. J.; Davidson, E. R. Three Dimensional Rank Annihilation for Multicomponent Determinations. Anal. Chim. Acta 1983, 146, 9-14. Sanchez, E.; Kowalski, B. R. Generalized Rank Annihilation Factor Analysis. Anal. Chem. 1986, 58, 496-499.
16. Apellof, C. J.; Davidson, E. R. Three Dimensional Rank Annihilation for Multicomponent Determinations. Anal. Chim. Acta 1983, 146, 9-14. Sanchez, E.; Kowalski, B. R. Generalized Rank Annihilation Factor Analysis. Anal. Chem. 1986, 58, 496-499.
17. Zeng, Y.; Hopke, P. K. The Application of Three-mode Factor Analysis (TMFA) to Receptor Modeling of Scenes Particle Data. Atmosph. Environ. 1992, 26A, 1701-1711.
18. Lohmöller, J.-B.; Wold, H. Three-Mode Path Models with Latent Variables and Partial Least Squares (PLS) Parameter Estimation. Proceedings of the European Meeting of the Psychometric Society; University of Gronigen: The Netherlands, 1980; p 50.
19. Glen, W. G.; Dunn, W. J., III; Scott, D. R. Principal Components Analysis and Partial Least Squares Regression. Tetrahedron Comput. Method 1989, 2, 349.
20. Koetzle, T. F.; Williams, G. J. B. The Crystal and Molecular Structure of the Antifolate Drug Trimethoprim (2,4-Diamino-5-(3,4,5-triemthoxybenzyl)pryrimidme). A Neutron Diffraction Study. J Am. Chem. Soc. 1976, 98, 2074.
21. Mathews, D. A.; Bolin, J. T.; Burridge, J. M.; Filmen, D. J.; Volz, K. W.; Kaufman, B. T.; Beddell, C. R.; Champness, J. N.; Stammers, D. K.; Kraut, J. Refined Crystal Structures of Escherichia coli and Chicken Liver Dihydrofolate Reductase Containing Bound Trimethoprim. J. Biol. Chem. 1985, 260, 381.
22. 50) of enzyme reaction. Biochem. Pharmacol. 1973, 22, 3099-3108.
23. (a) Burke, B. J.; Hopfinger, A. J. 1-(Substituted-benzyl)imidazole-2(3H)-thione Inhibitors of Dopamine-Hydroxylase. J. Med. Chem. 1990, 33, 274.
24. (b) Koehler, M. G.; Rowberg-Schaefer, K.; Hopfinger, A. J. A molecular shape analysis and quantitative structure-activity relationship investigation of some triazine-antifolate inhibitors of leishmania dihydrofolate reductase. Arch. Biochem. Biophys. 1988, 266, 152-161.
25. Mabilia, M.; Pearlstein, R. A.; Hopfinger, A. J. Molecular shape analysis and energetics-based intermolecular modeling of benzylpyrimidine dihydrofolate reductase inhibitors. Eur. J. Med. Chem. - Chim. Ther. 1985, 20, 163-174.
26. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 38. The MNDO method, Approximations and Parameters. J. Am. Chem. Soc. 1977, 99, 4899. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 39. MNDO Results for Molecules Containing Hydrogen, Carbon, Nitrogen and Oxygen. J. Am. Chem. Soc. 1977, 99, 4907.
27. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 38. The MNDO method, Approximations and Parameters. J. Am. Chem. Soc. 1977, 99, 4899. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 39. MNDO Results for Molecules Containing Hydrogen, Carbon, Nitrogen and Oxygen. J. Am. Chem. Soc. 1977, 99, 4907.
28. Hopfinger, A. J.; Perlstein, R. A. Molecular Mechanics Force-Field Parameterization Procedures. J. Comput. Chem. 1985, 5, 486.
29. Koehler, M. G.; Hopfinger, A. J. Molecular Modeling of Polymers: 5. Inclusion of intermolecular energetics in estimating glass and crystal-melt transition temperatures. Polymer 1989, 30, 116-126.
30. Hansch, C.; Leo, A. Substituent Constants for Correlation Analysis in Chemistry and Biology; Wiley-Interscience: New York, 1979.
31. Rogers, D.; Hopfinger, A. J. Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 1994, 34, 854-866.
32. Rogers, D.; Dunn, W. J., III. Genetic Partial Least Squares. J. Comput.-Aided Mol. Des. 1996, in press.
33. Wold, S.; Eriksson, L. Statistical Validation of QSAR Results. In Chemometric Methods in Molecular Design; Waterbeemd, H., Ed.; VCH Publishers, Inc.: New York, 1995; p 311.
34. Li, R.-L.; Poe, M. Quantitative Structure-Activity Relationships for the Inhibition of Escherichia coli Dihydrofolate Reductase by 5-(Substituted benzyl)-2,4-diaminopyrimidines. J. Med. Chem. 1988, 31, 366.
35. Selassie, S. D.; Li, R.-L.; Poe, M.; Hansch, C. On the Optimization of Hydrophobic and Hydrophilic Substituent Interactions of 2,4-Diamino-5-(substituted-benzyl)pyrimidines with Dihydrofolate Reductase. J. Med. Chem. 1991, 34, 46.
36. 31P NMR study. FEBS Lett. 1991, 38, 44.