Quantitative structure-activity relationship studies of RAR α, β, γ retinoid agonists

Quantitative Structure-Activity Relationships

Volumn 18, Issue 2, 1999, Pages 107-123

  Douguet, Dominique ^a   Thoreau, Etienne ^a   Grassy, Gérard ^b  

^a Galderma R and D   (France)

^b CNRS   (France)

Author keywords

Molecular modeling; PCA; QSAR; Retinoids; Variable mapping

Indexed keywords

COMPUTATIONAL CHEMISTRY; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR GRAPHICS; MOLECULAR MODELING; MULTIVARIANT ANALYSIS; QUANTUM THEORY; SEARCH ENGINES;

AMINO-ACIDS; NATURAL ANALOG; PCA; QSAR; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP STUDIES; RETINOIDS; STRUCTURE-ACTIVITY RELATIONSHIPS; SYNTHETIC ANALOGUES; VARIABLE MAPPING; VITAMIN A;

AMINO ACIDS;

RETINOIC ACID RECEPTOR AGONIST; RETINOID; UNCLASSIFIED DRUG;

AGONIST; ARTICLE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM MECHANICS; RECEPTOR AFFINITY;

EID: 0033049676     PISSN: 09318771     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-3838(199906)18:2<107::AID-QSAR107>3.0.CO;2-3     Document Type: Article

References (77)

1. Gudas, L. J., Sporn, M. B. and Roberts, A. B., Cellular biology and biology and biochemistry of the retinoids, in: Sporn, M. B., Roberts, A. B., Goodman, D. S., The Retinoids Biology, Chemistry and Medicine, Raven Press, New York, 1994, pp 443-520.
2. Pawson, B. A., Ehmann, C. W., Itri, L. M. and Sherman, M. I., Retinoids at the threshold: Their biological significance and therapeutic potential, J. Med. Chem. 25, 1269-1277 (1982).
3. Boyd, A. S., An overview of retinoids, Am. J. Med. 86, 568-574 (1989).
4. Hong, W. K. and Itri, L. M., Retinoids and human cancer, in: Sporn, M. B., Roberts, A. B., Goodman, D. S., The Retinoids Biology, Chemistry and Medicine, Raven Press, New York, 1994, pp 597-630.
5. Amstrong, R. B., Ashenfelter, K. O., Eckhoff, C., Levin, A. A. and Shapiro, S. S., General and reproductive toxicology of retinoids, in: Sporn, M. B., Roberts, A. B., Goodman, D. S., The Retinoids Biology, Chemistry and Medicine, Raven Press, New York, 1994, pp 545-572.
6. Moras, D. and Gronemeyer, H., The nuclear receptor ligand-binding domain: structure and function, Current Opinion in Cell Biology, 10, 384-391 (1998).
7. Glass, C. K., Differential recognition of target genes by nuclear receptor monomers, dimers, and heterodimers, Endocr. Rev. 15, 391-407 (1994).
8. Petkovich, M., Brand, N. J., Krust, A. and Chambon, P., A human retinoic acid receptor which belongs to the family of nuclear receptors, Nature, 330, 444-450 (1987).
9. Rosen, J., Day, A., Jones, T. K., Turner Jones, E. T., Nadzan, A. M. and Stein, R. B., Intracellular Receptors and signal Transducers and Activators of Transcription Superfamilies: Novel Targets for Small-Molecule Drug Discovery, J. Med. Chem. 38, 25, 4855-4874 (1995).
10. Chambon, P., A decade of molecular biology of retinoic acid receptors, The Faseb J. 10, 940-954 (1996).
11. Renaud, J-P., Rochel, N., Ruff, M., Vivat, V., Chambon, P., Gronemeyer, H. and Moras, D., Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid, Nature, 378, 681-689 (1995). Crystallographic coordinates are available in the PDB (accession code 21bd).
12. Martin, B., Bernardon, J.-M., Cavey, M. T., Bernard, B., Carlavan, I., Charpentier, B., Pilgrim, W. R., Shroot, B. and Reichert, U., Selective synthetic ligands for human nuclear retinoic acid receptors, Skin Pharmacol. 5, 57-65 (1992).
13. Cavey, M. T., Martin, B., Carlavan, I. and Shroot, B., In vitro binding of retinoids to the nuclear retinoic acid receptor α, Anal. Biochem. 186, 19-23 (1990).
14. VAMP, Oxford Molecular Ltd, The Magdalen Centre, Oxford Science Park, Sandford-on-Thames, Oxford OX4 4GA, United Kingdom.
15. InsightII, Molecular Simulations Incorporated, San Diego.
16. ASP, Automated Similarity Package, Oxford Molecular Ltd, The Magdalen Centre, Oxford Science Park, Sandford-on-Thames, Oxford OX4 4GA, United Kingdom.
17. Carbo, R., Leyda, L. and Arnau, M., An Electron Density Measure of the Similarity Between Two Compounds, Int. J. Quantum Chem. 17, 1185-1189 (1980).
18. Carbo, R. and Domingo, L., LCAO-MO Similarity Measures and Taxonomy, Int. J. Quantum Chem. 32, 517-545 (1987).
19. Good, A. C. and Richards, W. G., Rapid Evaluation of Shape Similarity Using Gaussian Functions, J. Chem. Inf Comput. Sci. 33, 112-116 (1993).
20. Good, A. C., Hodgkin, E. E. and Richards, W. G., Utilization of Gaussian Functions for the Rapid Evaluation of Molecular Similarity, J. Chem. Inf Comput. Sci. 32, 188-191 (1992).
21. Abraham, R. J. and Smith, P.E., 'charge calculations in molecular mechanics', J. Computer Aided Mol. Design, 3, 175 (1989).
22. TSAR , Oxford Molecular Ltd, The Magdalen Centre, Oxford Science Park, Sandford-on-Thames, Oxford OX4 4GA, United Kingdom.
23. Viswanadhan, V. N., Ghose, A. K., Revankar, G. R. and Robins, R. K., Atomic Physicochemical Parameters for Three Dimensional Structure Directed Quantitative Structure-Activity Relationships, J. Chem. Inf Comput. Sci. 29, 163-172 (1989).
24. Gaillard, P., Carrupt, P.-A., Testa, B. and Boudon, A., Molecular Lipophilicity Potential, a tool in 3D QSAR: Method and applications, J. Comput.-Aided Mol. Design. 8, 83-96 (1994).
25. Karelson, M., Lobanov, V.S. and Katritzky, A.R., Quantum-chemical Descriptors in QSAR/QSPR Studies, Chem. Rev. 96, 1027-1043 (1996).
26. Silla, E., Tunon, I. and Pascual-Ahuir, J. L., GEPOL: An improved description of molecular surfaces. II. Computing the molecular area and volume, J. Comput. Chem. 12, 1077-1088 (1991). QCPE #554.
27. Hall, L. H. and Kier, L.B., The molecular connectivity chi indexes and kappa shape indexes in structure-properties modelling. Rev. Comput. Chem. 9, 367 (1992).
28. Grassy, G., Fagart, J., Calas, B., Adenot, M., Rafestin-Obelin, M. E. and Auzou, G., Structure-activity relationships of steroids with mineralocorticoid activity, Eur. J. Med. Chem. 32, 869-879 (1997).
29. Grassy, G., Trappe, P., Bompart, J., Calas, B. and Auzou, G., Variable mapping of structure-activity relationships: Application to 17-spirolactone derivatives with mineralocorticoid activity, J. Mol. Graphics. 13, 356-367 (1995).
30. Grassy, G., Yasri, A., Buelow, R., Kaczorek, M. and Calas, B, Indirect Molecular Recognition: 'in silico screening' applied to the rational design of novel immunosuppressive compounds, Actualités de Chimie Thérapeutique, 24 (1998).
31. Grassy, G., Calas, B, Yasri, A., Lahana, R., Woo, J., Lyer, S., Kaczorek, M., Floc'h, R. and Buelow, R., Computer-assisted rational design of immunosuppressive compounds, Nature Biotech. 16, 748-752 (1998).
32. Waterbeemd, H. V. D., Carter, R. E., Grassy, G., Kubinyi, H., Martin, Y. C., Tute, M. S. and Willett, P., Glossary of Terms used in Computationnal Drug Design, Pure & Appl. Chem. 69, 5, 1137-1152 (1997).
33. McFarland, J. W. and Gans, D. J., On the Significance of Clusters in the graphical Display of Structure-Activity Data, J. Med. Chem. 29, 505-514 (1986).
34. Bonchev, D., Seitz, W. A., Mountain, C. F. and Balaban, A. T., Modelling the Anticarcinogenic Action of Retinoids by Making Use of OASIS Method. Inhibition of the Induction of Ornithine Decarboxylase by Arotinoids, J. Med. Chem. 37, 2300-2307 (1994).
35. Bonchev, D., Mountain, C. F., Seitz, W. A. and Balaban, A. T., Modelling the Anticancer Action of some Retinoid Compounds by Making Use of OASIS Method, J. Med. Chem. 36, 1562-1569 (1993).
36. Jaeger, E. P., Jurs, P. C. and Stouch, T. R., Structure-activity relationships studies of retinoid cancer inhibition, Eur. J. Med. Chem. 28, 275-290 (1993).
37. Charpentier, B., Bernardon, J.-M., Eustache, J., Millois, C., Martin, B., Michel, S. and Shroot, B., Synthesis, Structure-Affinity Relationships, and Biological Activities of Ligands Binding to Retinoic Acid Receptor Subtypes, J. Med. Chem. 38, 4993-5006 (1995).
38. Klaholz, B. P., Renaud, J. P., Mitschler, A., Zusi, C., Chambon, P., Gronemeyer, H. and Moras, D., Conformational adaptation of agonists to the human nuclear receptor RARγ, Nature Structural Biology, 5, 199-202 (1998).
39. Shroot, B., Eustache, J. and Bouclier, M., DE 34 43 230, November 28 (1996).
40. Shroot, B., Eustache, J. and Bernardon, J.-M., FR 2 570 377, September 17 (1985).
41. Eustache, J., Watts, O., Bernardon, J.-M. and Nédoncelle, Ph., EP 0 210 929, July 25 (1986).
42. Shroot, B., Eustache, J., Bernardon, J.-M. and Nédoncelle, Ph., FR 2 614 618, April 30 (1987).
43. Maignan, J., Lang, G., Malle, G., Restle, S. and Shroot, B., EP 0 220 118, October 10 (1986).
44. Maignan, J., Lang, G., Malle, G., Restle, S. and Shroot, B., FR 26 01 670, July 17 (1986).
45. Bernardon, J.-M. and Pilgrim, W., WO 92/06948, October 11 (1991).
46. Bernardon, J.-M, EP 0 661 260 A1, November 10 (1994).
47. Rocher, J.-P. and Bernardon, J.-M, EP 0 514 269 A1, May 14 (1992).
48. Shroot, B., Eustache, J. and Bernardon, J.-M, EP 0 199 636, May 11 (1986).
49. Shroot, B., Eustache, J. and Bernardon, J.-M, EP 0 232 199, January 20 (1987).
50. Maignan, J., US 5,023,363, June 11 (1991).
51. Shroot, B., Eustache, J. and Bernardon, J.-M, EP 0 325 540, January 19 (1989).
52. Charpentier, B., WO 92/19583, May 4 (1992).
53. Bernardon, J.-M. and Charpentier, B., EP 0 679 631 A1, May 3 (1995).
54. Bernardon, J.-M., EP 0 722 928 A1, December 19 (1995).
55. Charpentier, B. and Bernardon, J.-M., EP 0 658 553 A1, November 10 (1994).
56. Bernardon, J.-M., EP O 661 258 A1, November 10 (1994).
57. Bernardon, J.-M., WO 97/33881, March 5 (1997).
58. Bernardon, J.-M., Charpentier B., EP 0 776 881 A1, November 13 (1996).
59. Bernardon, J.-M., WO 97/33856, March 5 (1997).
60. Charpentier, B. and Nédoncelle, Ph., EP 0 732 328 A1, March 1 (1996).
61. Bernardon, J.-M, EP 0 679 630 A1, March 29 (1995).
62. Dawson, M.I., Chan, R.L., Derdzinski, K., Hobbs, P.D., Chao, W.R., Schiff, and L.J., Synthesis and Pharmacological Activity of 6-[(E)-2-(2,6,6-Trimethyl-lcyclohexen-1-yl) ethen-1-yl]-and 6-(1,2,3,4-Tetrahydro-1,1,4,4-Tetramethyl-6-naphthyl)-2-naphthalene carboxylic Acids, J. Med. Chem. 26, 1653-1656 (1983).
63. Loeliger, P., Bollag, W. and Mayer, H., Arotinoids, a new class of highly active retinoids, Eur. J. Med. Chem. Chim. Ther. 15, 9-15 (1980).
64. Swann, R. T., Smith, D., Tramposch, K. M. and Zussi, F. C., Eur. Pat. Appl., 0747347A1, May 20 (1996).
65. Kagechika, H., Kawachi, E., Hashimoto, Y. and Shudo, K., New type inducers of differenciation of human HL60 promyelocitic leukemia cells. Terephtalic anilides, Chem. Pharm. Bull. (Tokyo), 32, 4209-4219 (1984).
66. Chugoku, Igakukagakuin, yakubutsu, kenkyush, JP 06 072 866.
67. Kagechika, H., Kawachi, E., Hashimoto, Y. and Shudo, K., Retinobenzoic Acids. 2_Structure-Activity Relationships of chalcone-4-carboxylic Acids and Flavone-4′-carboxylic Acids, J. Med. Chem. 32, 834-840 (1989).
68. Chandraratna, R. A. S. and Weinkam, R. J., EP 0 337 689, April 10 (1989).
69. Janssen, B. and Wüst, H.-H., EP 0 386 452, February 1 (1990).
70. Janssen, B. and Wüst, H.-H., EP 0 386 451, February 1 (1990).
71. Pfahl, M., Lu, X.-P., Rideout, D. and Zhang, H., WO 98/01132, July 8 (1996).
72. Shudo, K., Sugioka, T., Inazu, M., Tanaka, H., Inoue, T. and Kitamura, K., EP 0 619 116, March 30 (1994).
73. Bernardon, J.-M., Patent deposed (1998).
74. Dawson, M., Cameron, J. F., Hobbs, P. D., Jong, L., Pfahl, M., Zhang. X.-K. and Lehmann, J.M., US 5,466,861, November 14 (1995).
75. Chandraratna, R. A. S., EP 0 284 288, March 17 (1988).
76. Boehm, M. F., Zhang, E., Badea, B. A., White, S. K., Mais, D. E., Berger, E., Suto, C. M., Goldman, M. E. and Heyman, R. A., Synthesis and Structure-Activity Relationships of novel retinoid X Receptor selective Retinoids, J. Med. Chem. 37, 2930-41 (1994).
77. Chandraratna, R., US 5,602,130, March 8 (1993)