Homology model directed alignment selection for comparative molecular field analysis: Application to photosystem II inhibitors

Journal of Computer-Aided Molecular Design

Volumn 14, Issue 2, 2000, Pages 181-197

  Jalaie, Mehran ^a,b   Erickson, Jon A ^a,c  

^a DOW AGROSCIENCES LLC   (United States)

^b INDIANA UNIVERSITY   (United States)

^c ELI LILLY AND COMPANY   (United States)

Author keywords

3D QSAR; Herbicide; Inhibitor scoring; Protein modeling; Structure based design; SYBYL

Indexed keywords

COMPUTATIONAL CHEMISTRY; DOCKING; DOCKS; HYDRAULIC STRUCTURES; MOLECULAR GRAPHICS; PROTEINS; THREE DIMENSIONAL COMPUTER GRAPHICS;

3D-QSAR; ANALYSIS MODELS; COMPARATIVE MOLECULAR FIELD ANALYSIS; HOMOLOGY MODELING; INHIBITOR SCORING; PHOTOSYSTEM II INHIBITOR; PHOTOSYSTEM-II; PROTEIN MODELS; STRUCTURE-BASED DESIGNS; SYBYL;

CRYSTAL STRUCTURE;

BUTENANILIDE; HERBICIDE; NAPHTHOQUINONE; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; CRYSTAL STRUCTURE; MOLECULAR MODEL; PHOTOSYSTEM II; PREDICTION; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE HOMOLOGY; SPINACH; STRUCTURE ACTIVITY RELATION;

EID: 0033955361     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008198211292     Document Type: Article

References (79)

1. Cramer, R.D. III, DePriest, S.A., Patterson, D.E. and Hecht, P., In Kubinyi, H. (Ed.), 3D QSAR Drug Design: Theory, Methods and Applications, ESCOM, Leiden, 1993, pp. 443-485.
2. Folkers, G., Merz, A. and Rognan, D., In Kubinyi, H. (Ed.), 3D QSAR in Drug Design: Theory, Methods and Applications, ESCOM, Leiden, 1993, pp. 583-618.
3. Hopfinger, A.J. and Tokarski, J.S., In Charifson, P.S. (Ed.), Pract. Appl. Comput.-Aided Drug Des., Dekker, New York, NY, 1997, pp. 105-164.
4. Martin, Y.C., Kim, K-H. and Lin, C.T., Adv. Quart. Struct.-Prop. Relat, 1 (1996) 1.
5. Davis, A., In van de Waterbeemd, H. (Ed.), Adv. Comp.-Ass. Tech. Drug Discovery, VCH, New York, NY, 1994, pp. 39-60.
6. Cramer, R.D. III, Patterson, D. and Bunce, B., J. Am. Chem. Soc., 110 (1988) 5959.
7. Lindberg, W., Persson, J.A. and Wold, S., Anal. Chem., 55 (1983) 643.
8. Dunn, W.J., III, Wold, S., Edlund, U., Hellberg, S. and Gasteiger, J., Quant. Struct.Act. Relat. Pharmacol., Chem. Biol., 3 (1984) 131.
9. For a recent example of this approach see: Cho, S.J., Serrano G.M.L., Bier, J. and Tropsha, A., J. Med. Chem., 39 (1996) 5064.
10. Marshall, G.R., Barry, C.D., Bossghard, H.E., Dammkoehler, R.A. and Dun, D.A., In Olson, E.C. and Christoffersen, R.E. (Eds), Computer-Assisted Drug Design, ACS Symp. Series, Vol. 112, American Chemical Society, Washington, DC, 1979, 205-226.
11. Mayer, D., Naylor, C.B., Motoc, I. and Marshall, G.R., J. Comput.-Aided Mol. Design, 1 (1987) 3.
12. Dammkoehler, R.A., Karasek, S.F., Shands, E.F.B. and Marshall, G.R., J. Comput-Aided Mol. Design, 3 (1989) 3.
13. For an example see: DePriest, S.A., Mayer, D., Naylor, C.B. and Marshall, G.R., J. Am. Chem. Soc., 115 (1993) 5372.
14. Martin, Y.C., Bures, M.G., Danaher, E.A, DeLazzer, J., Lico, I. and Pavelik, P.A., J. Comput.-Aided Mol. Design, 7 (1993) 83.
15. Myers, A.M., Charfison, P.S., Owens, C.E., Kula, N.S., McPhail, A.T., Baldessarini, R.J., Booth, R.G. and Wyrick, S.D., J. Med. Chem., 37 (1994) 4109.
16. Barnum, D., Greene, J., Smellie, A. and Sprague, P., J. Chem. Inf. Comput. Sci., 36 (1996) 563.
17. Smellie, A., Teig, S.L. and Towbin, P., J. Comput. Chem., 16 (1995) 171.
18. Langer, T. and Hoffman, R.D., J. Chem. Inf. Comput. Sci., 38 (1998) 325.
19. Bargar, T.M., Secor, J., Markley, L.D., Shaw, B.A. and Erickson, J.A., Pest. Sci., 55 (1999) 1059.
20. SYBYL, version 6.4, 1997, Tripos Inc, St. Louis, MO.
21. Clark, M., Cramer, R.D. III, Jones, D.M., Patterson, D.E. and Simeroth, P.E., Tet. Comput. Meth., 3 (1990) 47.
22. Rault, S., Bureau, R., Pilo, J.C. and Robba, M., J. Comput.-Aided Mol. Design, 6 (1992) 553.
23. Klebe, G. and Abraham, U., J. Med. Chem., 36 (1993) 70.
24. Kearsley, S.K. and Smith, G.M., Tet. Comput. Meth., 3 (1990) 615.
25. Horowitz, J.P., Massova, I., Wiese, T.E., Besler, B.H. and Corbett, T.H., J. Med. Chem., 37 (1994) 781.
26. Tafi, A., Anasttassopoulou, J., Theophanides, T., Botta, M., Corelli, F., Massa, S., Artico, M., Costi, R., Di Santo, R. and Rango, R., J. Med. Chem., 39 (1996) 1227.
27. Carrigan, S.W., Fox, P.C., Wall, M.E., Wan, M.C. and Bowen, J.P., J. Comput.-Aided Mol. Design, 11 (1997) 71.
28. Clark, R.D., Parlow, J.J., Brannigan, L.H., Schnur, D.M. and Duewer, D.L., In Hansch, C. and Fujita, T. (Eds), Classical and Three-Dimensional QSAR in Agrochemistry, ACS Symp. Series, Vol. 606, American Chemical Society, Washington, DC, 1995, pp. 264-281.
29. Folkers, G., Merz, A. and Rognan, D., In Wermuth, C.G. (Ed.), Trends in QSAR and Molecular Modeling 92, ESCOM, Leiden, 1993, pp. 233-244.
30. Ortiz, A.R., Pastor, M., Palomer, A., Cruciani, U., Gago, F. and Wade, R.C., J. Med. Chem., 40 (1997) 1136.
31. Waller, C.L., Oprea, T.I., Giolitti, A. and Marshall, G.R., J. Med. Chem., 36 (1993) 4152.
32. Oprea, T.I., Waller, C.L. and Marshall, G.R., J. Med. Chem., 37 (1994) 2206.
33. Schmetzer, S., Greenidge, P., Kovar, K.-A., Meike, S.-A. and Folkers, G., J. Comput.-Aided Mol. Design, 11 (1997) 278.
34. Vedani, A., Zbinden, P., Snyder, J.P. and Greenidge, P.A., J. Am. Chem. Soc., 117 (1995) 4987.
35. Zbinden, P., Dobler, M., Folkers, G. and Vedani, A., Quant. Struct.-Act. Relat., 17 (1998) 122.
36. Sanchez, R. and Sali, A., Curr. Opin. Struct. Biol., 7 (1997) 206.
37. Boehm, G., Biophys. Chem., 59 (1996) 1.
38. Johnson, M.S., Srinivasan, N., Sowdhamini, R. and Blundell, T.L., Crit. Rev. Biochem. Mol. Biol., 29 (1994) 1.
39. Ortiz, A.R., Pisabarro, M.T., Gago, F. and Wade, R.C., J. Med. Chem., 38 (1995) 2681.
40. Tokarski, J.S. and Hopfinger, A.J., J. Chem. Inf. Comput. Sci., 37 (1997) 779, 792.
41. Artico, M., Botta, M., Corelli, F., Mai, A., Massa, S. and Ragno, R., Bioorg. Med. Chem., 4 (1996) 1715.
42. Carrieri, A., Altomare, C., Barreca, M.L., Contento, A., Carotti, A. and Hansch, C., Il Farmaco, 49 (1994) 573.
43. Gainper, A.M., Winger, R.H., Liedl, K.R., Sotriffer, C.A., Varga, J.M., Kroemer, R.T. and Rode, B.M., J. Med. Chem., 39 (1996) 2882.
44. Goodsell, D.S. and Olsen, A.J., Proteins Struct. Funct. Genet., 8 (1990) 195.
45. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
46. Shoichet, B.K., Bodian, D.L. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 380.
47. Meng, E.C., Shoichet, B.K. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 505.
48. Meng, E.C., Gschweng, D.A., Blaney, J.M. and Kuntz, I.D., Proteins Struct. Funct. Genet., 17 (1993) 266.
49. Leach, A.R. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 730.
50. Ewing, T.J.A. and Kuntz, I.D., J. Comput. Chem., 18 (1997) 1175.
51. Bowyer, J., Hilton, M., Whitelegge, J., Jewess, P., Camilleri, P., Crofts, A. and Robinson, H., Z. Naturforsch., 45c (1990) 379.
52. Tietjen, K.G., Kluth, J.F., Anfree, R., Haug, M., Lindig, M., Muller, K.H., Wroblowsky, H.J. and Trebst, A., Pest. Sci., 31 (1991) 65.
53. Ruffle, S.V., Donnelly, D., Blundell, T.L. and Nugent, J.H.A., Photosynthesis Res., 34 (1992) 287.
54. Egner, U., Hoyer, G.-A. and Saenger, W., Eur. J. Biochem., 206 (1992) 685.
55. Egner, U., Hoyer, G.-A. and Saenger, W., Biochim. Biophys. Acta, 1142 (1993) 106.
56. Mackay, S.P. and O'Malley, P.J., Z. Naturforsch., 48c (1993), 773.
57. Sobolev, V. and Edelman M., Proteins Struct. Funct. Genet., 21 (1995) 214.
58. Svensson, B., Etchebest, C., Tuffery, P., van Kan, P., Smith, J. and Styring, S., Biochemistry, 35 (1996) 14486.
59. Egner, U., Gerbling, K.P., Hoyer, G.-A., Kruger, G. and Wegner, P., Pest. Sci., 47 (1996) 145.
60. Deisenhofer, J., Epp, O., Miki, K., Huber, R. and Michel, H., Nature, 318 (1985) 618.
61. Michel, H. and Deisenhofer, J., Biochemistry, 27 (1988) 1.
62. Draber, W., Tietjen, K., Kluth, J.F. and Trebst, A., Angew. Chem. Int. Ed. Engl., 30 (1991) 1621.
63. Huppazt, J.L., Weed Sci., 44 (1996) 743.
64. Vaz, R., Weed Sci., 44 (1996) 718.
65. Draber, W., Trebst, A. and Oettmeier, W., In Hansch, C. and Fujita, T. (Eds), Classical and Three-Dimensional QSAR in Agrochemistry, ACS Symp. Series, Vol. 606, American Chemical Society, Washington, DC, 1995, pp. 186-198.
66. Eilers, R.J., Crouse, G.D., Durst, G.L., Manly, C.J., Webster, J.D. and Streusand, V.J., Pest. Biochem. Phys., 43 (1992) 162.
67. QUANTA, 1997, Molecular Simulations Inc., San Diego, CA.
68. Zurawksi, G., Bohnert, H.J., Whitfeld, P.R. and Bottomley, W., Proc. Natl. Acad. Sci. USA, 79 (1982) 7699.
69. CHARMm, 1997, Molecular Simulations Inc., San Diego, CA.
70. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.
71. DOCK version 4.0, University of California, 1997, San Fransisco, CA.
72. CONCORD 4.0, 1998, University of Texas, Austin, TX.
73. Gasteiger, J. and Marsili, M., Tetrahedron, 36 (1980) 3219.
74. Marsili, M. and Gasteiger, J., Croat. Chem. Acta, 53 (1980) 601.
75. Cho, S.J. and Tropsha, A., J. Med. Chem., 38 (1995) 1060.
76. Sulea, T., Oprea, T.I., Muresan, S. and Chan, S.L., J. Chem. Inf. Comput. Sci., 3 (1997) 1162.
77. Bush, B.L. and Nachbar, R.B., J. Comput.-Aided Mol. Design, 7 (1993) 587.
78. Lindgren, F., Geladi, P., Ranner, S. and Wold, S., J. Chemometrics, 8 (1994) 349.
79. Verloop, A., Hoogenstraaten, W. and Tipker, J., Med. Chem., 11 (1976) 165.