Reliability of comparative molecular field analysis models: Effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors

Journal of Medicinal Chemistry

Volumn 40, Issue 7, 1997, Pages 1136-1148

  Ortiz, Angel R ^a,b   Pastor, Manuel ^b,d   Palomer, Albert ^c   Cruciani, Gabriele ^d   Gago, Federico ^b   Wade, Rebecca C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF ALCALÁ   (Spain)

^c Laboratorios Menarini   (Spain)

^d UNIVERSITY OF PERUGIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOLIPASE A2 INHIBITOR;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DRUG CONFORMATION; DRUG RECEPTOR BINDING; ENZYME INHIBITION; HUMAN; MOLECULAR MODEL; PEPTIDE MAPPING; RECEPTOR AFFINITY; STRUCTURE ACTIVITY RELATION; SYNOVIAL FLUID;

ENZYME INHIBITORS; HUMANS; MODELS, CHEMICAL; PHOSPHOLIPASES A; STRUCTURE-ACTIVITY RELATIONSHIP; SYNOVIAL FLUID;

EID: 0030892498     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9601617     Document Type: Article

References (41)

1. (a) Jolles, G., Wooldridge, K. R. H., Eds. Drug Design: Fact or Fantasy? Academic Press: London, 1984.
2. (b) Dean, P. M. Molecular Foundations of Drug-Receptor Interactions; Cambridge University Press: Cambridge, 1987.
3. (c) Hansch, C., Sammcs, P. G., Taylor, J. B., Eds. Comprehensive Medicinal Chemistry. Vol. IV: Quantitative Drug Design; Pergamon Press: New York, 1990.
4. Kubinyi, H., Ed. 3D-QSAR in Drug Design. Theory, Methods and Applications; ESCOM Science Publishers B.V.: Leiden, The Netherlands, 1993.
5. 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, 5959-5967.
6. (a) Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of drug binding affinities by Comparative Binding Energy Analysis: Application to Human Synovial Fluid Phospholipase A2 Inhibitors. In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications; Sanz, F., Giraldo, J., Manaut, F., Eds.; J. R. Prous Science Publishers: Barcelona, 1995; pp 439-443.
7. (b) Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of drug binding affinities by Comparative Binding Energy Analysis. J. Med. Chem. 1995, 38, 2681-2691.
8. Cramer, R. D., III. Partial Least Squares (PLS): Its strengths and limitations. Perspect. Drug Discovery Des. 1993, 1, 269-278.
9. (a) Cruciani, G.; Clementi, S.; Baroni, M. Variable selection in PLS analysis. In 3D-QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM Science Publishers B.V.: Leiden, The Netherlands, 1993; pp 551-564.
10. (b) Wold, S.; Johansson, E.; Cocchi, M. PLS - Partial least-squares projections to latent structures. In 3D-QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed., ESCOM Science Publishers B.V.: Leiden, The Netherlands, 1993; pp 523-550.
11. (a) Baroni, M.; Constantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Generating Optimal Linear PLS Estimations (GOLPE): An advanced chemometric tool for handling 3D-QSAR problems. Quant. Struct.-Act. Relat. 1993, 12, 9-20.
12. (b) GOLPE 3.0, Multivariate Infometric Analysis, Perugia, Italy, 1995.
13. 2-guided region selection for comparative molecular field analysis: a simple method to achieve consistent results. J. Med. Chem. 1995, 38, 1060-1066.
14. Cruciani, G.; Watson, K. A. Comparative molecular field analysis using GRID force-field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b. J. Med. Chem. 1994, 37, 2589-2601.
15. Greco, G.; Novellino, E.; Pellecchia, M.; Silipo, C.; Vittoria, A. Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR. J. Comput. Aid. Mol. Des. 1994, 8, 97-112.
16. Davis, A. M.; Gensmentel, N. P.; Johansson, E.; Marriott, D. P. The use of the GRID program in the 3D-QSAR analysis of a series of calcium-channel agonists. J. Med. Chem. 1994, 37, 963-972.
17. (a) Kubinyi, H. Variable selection in QSAR studies. I. An evolutionary algorithm. Quant. Struct.-Act. Relat. 1994, 13, 285-294.
18. (b) Kubinyi, H. Variable selection in QSAR studies. II. A highly efficient combination of systematic search and evolution. Quant. Struct. Act. Relat. 1994, 13, 393-401.
19. (a) Garcia, M. L. Manuscript in preparation.
20. (b) Cabre, F.; Carabaza, A.; Garcìa, A. M.; Gomez, M.; Garcìa, L.; Mauleon, D.; Carganico, G. Presentation at the VIIIth International Congress on Prostaglandins and Related Compounds, Montreal, Canada, 1992.
21. (c) Carganico, G.; Mauleon, D.; GarcÌa, M. L. Spanish Patent WO-94/28004, 1994.
22. Wery, J.-P.; Schevitz, R. W.; Clawson, D. K.; Bobbitt, J. L.; Dow, E. R.; Gamboa, G.; Goodson, T.; Hermann, R. B.; Kramer, R. M.; McClure, D. B.; Mihelich, E. D.; Putname, J. E.; Sharp, J. D.; Stark, D. H.; Teater, C.; Warrick, M. W.; Jones, N. D. Structure of a recombinant human rheumatoid arthritic synovial fluid phospholipase A2 at 2.2 Å resolution. Nature 1991, 352, 79-82.
23. 2 from inflammatory exudate. Science 1991, 254, 1007-1010.
24. 2 inhibitors. J. Med. Chem. 1994, 37, 337-341.
25. (a) GRIN, GRID and GRAB (version 11), 1994, Molecular Discovery Ltd., West Way House, Elms Parade, Oxford OX2 9LL, England.
26. (b) Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important molecules. J. Med. Chem. 1985, 28, 849-857.
27. (c) Boobbyer, D. N. A.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J. Med. Chem. 1989, 32, 1083-1094.
28. (d) Wade, R. C.; Clark, K. J.; Goodford, P. J. Further development of hydrogen-bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J. Med Chem. 1993, 36, 140-147.
29. (e) Wade, R. C.; Goodford, P. J. Further development of hydrogen-bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J. Med. Chem. 1993, 36, 148-156.
30. Sharp, K. A.; Honig, B. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301.
31. Tripos Associates, 1699 S. Hanley Rd, St. Louis, MO.
32. Warshel, A.; Russell, S. T. Calculations of electrostatic interactions in biological systems and in solution. Quart. Rev. Biophys. 1984, 17, 283-422.
33. Hingerty, B. E.; Ritchie, R. H.; Ferrell, T. L.; Turner, J. E. Dielectric effect in biopolymers: the theory of ionic saturation revisited. Biopolymers 1985, 24, 427-439.
34. Friedman, R.; Honig, B. The electrostatic contribution to DNA base-stacking interactions. Biopolymers 1992, 32, 145.
35. Box, G. E. P.; Hunter, W. G.; Hunter, J. S. Statistics for Experimenters; John Wiley and Sons: New York, 1978; Chapter 12.
36. Mitchell, T. J. An algorithm for the construction of "D-optimal" experimental designs. Technometrics 1974, 16, 203.
37. De Priest, S. A.; Mayer, D.; Naylor, C. B.; Marshall, G. R. 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: a comparison of CoMFA models based on deduced and experimentally determined active site geometries. J. Am. Chem. Soc. 1993, 115, 5372-5384.
38. 2. Nature Struct. Biol. 1995, 2, 458-465.
39. 2. J. Med. Chem. 1994, 37, 4118-4129.
40. Verlinde, C. L. M. J.; Dijkstra, B. W. Drug or tool, design or serendipity? Nature Struct. Biol. 1995, 2, 429-432.
41. Kraulis, P. J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 1991, 24, 946-950.