Molecular modeling approaches to study the binding mode on tubulin of microtubule destabilizing and stabilizing agents

Topics in Current Chemistry

Volumn 286, Issue , 2009, Pages 279-328

  Botta, Maurizio ^a   Forli, Stefano ^b   Magnani, Matteo ^c   Manetti, Fabrizio ^a  

^a UNIVERSITY OF SIENA   (Italy)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c Siena Biotech SpA   (Italy)

Author keywords

Microtubule targeting agents; Molecular docking; Molecular modeling; Pharmacophore; Quantitative structure activity relationships; Tubulin

Indexed keywords

EID: 69249114865     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128_2008_20     Document Type: Article

References (135)

1. Jordan MA, Wilson L (2004) Nat Rev Cancer 4:253
2. Ravelli RB, Gigant B, Curmi PA, Jourdain I, Lachkar S, Sobel A, Knossow M (2004) Nature 428:198
3. Gigant B, Wang C, Ravelli RB, Roussi F, Steinmetz MO, Curmi PA, Sobel A, Knossow M (2005) Nature 435 : 519
4. Downing KH, Nogales E (1998) Curr Opin Cell Biol 10:16
5. Prinz H (2002) Exp Rev Anticancer Ther 2:695
6. Li Q, Sham HL (2002) Exp Opin Ther Patents 12:1663
7. Checchi PM, Nettles JH, Zhou J, Snyder JP, Joshi HC (2003) Trends Pharmacol Sci 24:361
8. Gupta S, Bhattacharyya B (2003) Mol Cell Biochem 253:41
9. Hastie SB (1991) Pharmacol Ther 51:377
10. Bhattacharyya B, Panda P, Gupta S, Banerjee M (2008) Med Res Rev 28:155
11. Nakagawa-Goto K, Chen CX, Hamel E, Wu CC, Bastow KF, Brossi A, Lee KH (2005) Bioorg Med Chem Lett 15 : 235
12. Beckers T, Mahboobi S (2003) Drugs Fut 28 : 767
13. Pettit GR, Singh SB, Hamel E, Lin CM, Alberts DS, Garcia-Kendall D (1989) Experientia 45 : 680
14. Pettit GR, Cragg GM, Singh SB (1987) J Nat Prod 50:386
15. Pettit GR, Cragg GM, Herald DL, Schmidt JM, Lohavanijaya P (1982) Can J Chem 60:1374
16. Lin CM, Ho HH, Pettit GR, Hamel E (1989) Biochemistry 28:6984
17. Jordan A, Hadfield JA, Lawrence NJ, McGown AT (1998) Med Res Rev 18:259
18. Nam NH (2003) Curr Med Chem 10:1697
19. Ohsumi K, Nakagawa R, Fukuda Y, Hatanaka T, Morinaga Y, Nihei Y, Ohishi K, Suga Y, Akiyama Y, Tsuji T (1998) J Med Chem 41:3022
20. Pettit GR, Temple C Jr, Narayanan VL, Varma R, Simpson MJ, Boyd MR, Rener GA, Bansal N (1995) Anticancer Drug Res 10:299
21. Nihei Y, Suzuki M, Okano A, Tsuji T, Akiyama Y, Tsuruo T, Saito S, Hori K, Sato Y (1999) Jpn J Cancer Res 90:1387
22. Wang L, Woods KW, Li Q, Barr KJ, McCroskey RW, Hannick SM, Gherke L, Credo RB, Hui YH, Marsh K, Warner R, Lee JY, Zielinski-Mozng N, Frost D, Rosenberg SH, Sham HL (2002) J Med Chem 45:1697
23. Lin CM, Singh SB, Chu PS, Dempcy RO, Schmidt JM, Pettit GR, Hamel E (1988) Mol Pharmacol 34 : 200
24. Tron GC, Pirali T, Sorba G, Pagliai F, Busacca S, Genazzani AA (2006) J Med Chem 49 : 3033
25. Ter Haar E, Rosekranz HS, Hamel E, Day BW (1996) Bioorg Med Chem 4:1659
26. Brown ML, Rieger JM, Macdonald TL (2000) Bioorg Med Chem 8 : 1433
27. Weigt M, Weise M (2000) QSAR J 19:142
28. Zhang SX, Feng J, Kuo SC, Brossi A, Hamel E, Tropsha A, Lee KH (2000) J Med Chem 43 : 167
29. Berg U, Bladh H (1999) Helv Chim Acta 82:323
30. Brossi A, Lee KH, Yeh HJC (1999) Helv Chim Acta 82:1223
31. Ducki S, Mackenzie G, Lawrence NJ, Snyder JP (2005) J Med Chem 48:457
32. Vedani A, Dobler M (2002) J Med Chem 45:2139
33. Feher M, Schmidt JM (2000) J Chem Inf Comput Sci 40:495
34. Kearsley SK, Smith GM (1990) Tetrahedron Comput Methods 3:615
35. De Martino G, Edler MC, La Regina G, Coluccia A, Barbera MC, Barrow D, Nicholson RI, Chiosis G, Brancale A, Hamel E, Artico M, Silvestri R (2006) J Med Chem 49:947
36. Rappl C, Barbier P, Bourgarel-Rey V, Gregoire C, Gilli R, Manon C, Combes S, Finet JP, Peyrot V (2006) Biochemistry 45 : 9210
37. Kong Y, Grembecka J, Edler MC, Hamel E, Mooberry SL, Sabat M, Rieger J, Brown ML (2005) Chem Biol 12:1007
38. Nguyen TL, McGrath C, Hermone AR, Burnett JC, Zaharevitz DW, Day BW, Wipf P, Hamel E, Gussio R (2005) J Med Chem 48:6107
39. Kim DY, Kim KH, Kim ND, Lee KY, Han CK, Yoon JH, Moon SK, Lee SS, Seong BL (2006) J Med Chem 49:5564
40. Bellina F, Cauteruccio S, Monti S, Rossi R (2006) Bioorg Med Chem Lett 16:5757
41. Zhang Q, Peng Y, Wang XI, Keenan SM, Arora S, Welsh WJ (2007) J Med Chem 50:749
42. De Martino G, La Regina G, Coluccia A, Edler MC, Barbera MC, Brancale A, Wilcox E, Hamel E, Artico M, Silvestri R (2004) J Med Chem 47:6120
43. La Regina G, Edler MC, Brancale A, Kandil S, Coluccia A, Piscitelli F, Hamel E, De Martino G, Matesanz R, Diaz JF, Scovassi AI, Prosperi E, Lavecchia A, Novellino E, Artico M, Silvestri R (2007) J Med Chem 50:2865
44. Romagnoli R, Baraldi PG, Pavani MG, Tabrizi MA, Preti D, Fruttarolo F, Piccagli L, Jung MK, Hamel E, Borgatti M, Gambari R (2006) J Med Chem 49:3906
45. Bai R, Covell DG, Pei XF, Ewell JB, Nguyen NY, Brossi A, Hamel E (2000) J Biol Chem 275 : 40443
46. Nogales E, Wolf SG, Downing KH (1998) Nature 391:199
47. Bai R, Pettit GR, Hamel E (1990) J Biol Chem 265:17141
48. Mitra A, Sept D (2004) Biochemistry 43:13955
49. Löwe J, Li H, Downing KH, Nogales E (2001) J Mol Biol 313:1045
50. Barbier P, Gregoire C, Devred F, Sarrazin M, Peyrot V (2001) Biochemistry 40:13510
51. Ojima I, Chakravarty S, Inoue T, Lin S, He L, Horwitz SB, Kuduk SD, Danishefsky SJ (1999) Proc Natl Acad Sci U S A 96:4256
52. Suffness M, Wall ME Suffness M(ed.) Taxol: science and applications. CRC Press, Boca Ranton, FL, (1995)In:pp 3-25.
53. Schiff PB, Fant J, Horwitz SB (1979) Nature 277:665
54. Höfle G, Bedorf N, Gerth K, Reichenbach H (1993), (GBF) DE-4138042 1993; Chem Abstr
55. Bollag DM, McQueney PA, Zhu J, Hensens O, Koupal L, Liesch J, Goetz M, Lazarides E, Woods CM (1995) Cancer Res 55:2325
56. Hung DT, Chen J, Schreiber SL (1996) Chem Biol 3:287
57. Longley RE, Gunasekera SP, Faherty D, McLane J, Dumont F (1993) Ann NY Acad Sci 696 : 94
58. Long BH, Carboni JM, Wasserman AJ, Cornell LA, Casazza AM, Jensen PR, Lindel T, Fenical W, Fairchild CR (1998) Cancer Res 58:1111-1115
59. Hamel E, Sackett DL, Vourloumis D, Nicolaou KC (1999) Biochemistry 38:5490
60. He L, Jagtap PG, Kingston DG, Shen HJ, Orr GA, Horwitz SB (2000) Biochemistry 39 : 3972
61. Wilson L, Jordan MA (2004) Chemotherapy 16:83
62. Jordan MA, Wendell K, Gardiner S, Derry WB, Copp H, Wilson L (1996) Cancer Res 56 : 816
63. Nuijen B, Bouma M, Schellens JH, Beijnen JH (2001) Invest New Drugs 19:143
64. Aversa SM, Cattelan AM, Salvagno L, Crivellari G, Banna G, Trevenzoli M, Chiarion-Sileni V, Monfardini S (2005) Crit Rev Oncol Hematol 53:235
65. Mekhail TM, Markman M (2002) Exp Opin Pharmacother 3:755
66. Zhao J, Kim JE, Reed E, Li QQ (2005) Int J Oncol 27 : 247
67. Ballone P, Marchi M (1993) J Phys Chem 103:3097
68. Milanesio M, Ugliengo P, Viterbo D (1999) J Med Chem 42:291
69. Guéritte-Voegelein F, Guénard D, Mangatal K, Poitier P, Guilhem J, Cesario M, Pascard C (1990) Acta Crystallogr Sect C 46 : 781
70. Jiménez-Barbero J, Amat-Guerri F, Snyder JP (2002) Curr Med Chem Anticancer Agents 2 : 91
71. Brünger AT, Karplus M (1991) Acc Chem Res 24:54
72. Leach AR (1996) Molecular modelling, principles and applications. Longman, London, pp 436 - 442
73. Mastropaolo D, Camerman A, Luo Y, Brayer GD, Camerman N (1995) Proc Natl Acad Sci U S A 92:6920
74. Vander Velde DG, Georg GI, Grunewald GL, Gunn CW, Mitscher LA (1993) J Am Chem Soc 115 : 11650
75. Williams HJ, Scott AI, Dieden RA, Swindell CS, Chirlian LE, Francl MM, Heerding JM, Krauss NE (1993) Tetrahedron 49:6545
76. Boge TC, Wu ZJ, Himes RH, Vander Velde DG, Georg GI (1999) Bioorg Med Chem Lett 9 : 3047
77. Dubois J, Guénard D, Guéritte-Voegelein F, Guedira N, Potier P, Gillet B, Beloeil JC (1993) Tetrahedron 49 : 6533
78. Snyder JP, Nevins N, Cicero DO, Jansen JJ (2000) Am Chem Soc 122:724
79. Snyder JP, Nettles JH, Cornett B, Downing KH, Nogales E (2001) Proc Natl Acad Sci USA 98 : 5312
80. Cachau RR, Gussio R, Beutler JA, Chmurny GN, Hilton BD, Muschik GM, Erickson JW (1994) Supercomput Appl High Performance Comput 8 : 24
81. Discovery/InsightII was a software formerly distributed by Accelrys Inc.: San Diege, CA.
82. Wang M, Xia X, Kim Y, Hwang D, Jansen JM, Botta M, Liotta DC, Snyder JP (1999) Org Lett 15:43-46
83. Zbinden P, Max D, Folkers G, Vedani A (1998) QSAR 17:112
84. Rao S, Krauss NE, Heerding JM, Swindell CS, Ringel I, Orr GA, Horwitz SB (1994) J Biol Chem 269 : 3132
85. Rao S, Orr GA, Chaudray AG, Kingston DGI, Horwitz SB (1995) J Biol Chem 35:20235
86. Giannakakou P, Gussio R, Nogales E, Downing KH, Zaharevitz D, Bollbuck B, Poy G, Sacket D, Nicolaou KC, Fojo T (2000) Proc Natl Acad Sci USA 6:2904
87. He L, Jagtap PG, Kingston DG, Shen HJ, Orr GA, Horwitz SB (2000) Biochemistry 39 : 3972
88. Barboni L, Lambertucci C, Appendino G, Vander Velde DG, Himes RH, Bombardelli E, Wang M, Snyder JP (2001) J Med Chem 44:1576
89. Querolle O, Dubois J, Thoret S, Roussi F, Montiel-Smith S, Gueritte F, Guenard D (2003) J Med Chem 46 : 3623
90. Ganesh T, Guza RC, Bane S, Ravindra R, Shanker N, Lakdawala AS, Snyder JP, Kingston DG (2004) Proc Natl Acad Sci USA 101:10006
91. Shanker N, Kingston DG, Ganesh T, Yang C, Alcaraz AA, Geballe MT, Banerjee A, McGee D, Snyder JP, Bane S (2007) Biochemistry 46 : 11514
92. Gao Q, Wei JM, Chen SH (1995) Pharm Res 12:337
93. Gao Q, Chen SH (1996) Tetrahedron Lett 37:3425
94. Paloma LG, Guy RK, Wrasidlo W, Nicolaou KC (1994) Chem Biol 1:107
95. Ojima I, Kuduk SD, Chakravarty S, Ourevitch M, Begue JP (1997) J Am Chem Soc 119 : 5519
96. Jimenez-Barbero J, Souto AA, Abal M, Barasoain I, Evangelio JA, Acuna AU, Andreu JM, Amat-Guerri F (1998) Biorg Med Chem 6:1857
97. Ewing TJA, Kuntz ED (1997) J Comp Chem 18:1175
98. Barboni L, Datta A, Dutta D, Georg G, Velde DG, Himes RH, Wang M, Snyder JP (2001) J Org Chem 66 : 3321
99. Wang M, Cornett B, Nettles J, Liotta DC, Snyder JP (2000) J Org Chem 65:1059
100. Gueritte F (2001) Curr Pharm Des 7:1229
101. Barboni L, Giarlo G, Riccutelli M, Ballini R, Georg G, VanderVelde DG, Himes RH, Wang M, Lakdawala A, Snyder JP (2004) Org Lett 6 : 461
102. Wu JH, Zamir LO (2000) Anticancer Drug Des 15 : 73
103. Nogales E, Whittaler M, Milligan RA, Downing KH (1999) Cell 96:79
104. Buey RM, Díaz FJ, Andreu JM, O'Brate A, Giannakakou P, Nicolaou KC, Sasmal PK, Ritzén A, Namoto K (2004) Chem Biol 11:225
105. Nogales E (1999) Cel Mol Life Sci 56:133
106. Miller ML, Ojima I (2001) Chem Rec 1:195
107. Mastalerz H, Zhang G, Kadow J, Fairchild C, Long B, Vyas DM (2001) Org Lett 3:1613
108. Lee KW, Briggs JM (2001) J Comput Aided Mol Des 15:41
109. Nicolaou KC, Vourloumis D, Li T, Pastor J, Wissinger N, He Y, Ninkovic S, Sarabaia F, Vallberg H, Roschangar F, King NP, Finlay MRV, Giannakakou P, Verdier-Pinard P, Hamel E (1997) Angew Chem Int Ed Engl 36:2093
110. Nicolaou KC, Roschangar F, Vourloumis D (1998) Angew Chem Int Ed Engl 37:2014
111. Winkler JD, Axelsen PH (1996) Bioorg Med Chem Lett 6:2963
112. Chou T, Zhang X, Balog A, Su D, Meng D, Savin K, Bertino JR, Danishefsky SJ (1997) Proc Natl Acad Sci U S A 95 : 9642
113. Rao S, Krauss NE, Heerding JM, Swindell CS, Ringel I, Orr GA, Horwitz SB (1994) J Biol Chem 269 : 3132
114. Manetti F, Forli S, Maccari L, Corelli F, Botta M (2001) Il Farmaco 58:375
115. Manetti F, Maccari L, Corelli F, Botta M (2004) Curr Topics Med Chem 4 : 203
116. Nettles JH, Li H, Cornett B, Krahn JM, Snyder JP, Downing KH (2004) Science 305:866
117. Carlomagno T, Blommers MJ, Meiler J, Jahnke W, Schupp T, Petersen F, Schinzer D, Altmann KH, Griesinger C (2007) Angew Chem 115:2615
118. Reese M, Sänchez-Pedregal VM, Kubicek K, Meiler J, Blommers MJ, Griesinger C, Carlomagno T (1997) Angew Chem Int Ed Engl 46:1864
119. Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJ, Griesinger C, Carlomagno T (2005) Angew Chem Intl Ed Engl 44 : 4172
120. Botta M, Forli S, Altmann K-H (unpublished results)
121. Bold G, Wojeik S, Caravatti G, Lindauer R, Stierlin C, Gertsch J, Wartmann M, Altmann KH (2006) Chem Med Chem 1:37
122. Zhan W, Jiang Y, Brodie PJ, Kingston DI, Liotta DC, Snyder JP (2008) Org Lett 10:1565
123. Martello L, LaMarche MJ, He L, Beauchamp TJ, Smith AB, Hotwitz SB (2001) Chem Biol 8 : 843
124. Sánchez-Pedregal VM, Kubicek K, Meiler J, Lyothier I, Paterson I, Carlomagno T (2006) Angew Chem Int Ed Engl 45 : 7388
125. Smith ABI, LaMarche MJ, Falcone-Hindley M (2001) Org Lett 5:695
126. Petitt GR, Chichacz ZA, Gao F, Boyd MR, Schmidt JM (1994) J Chem Soc Chem Commun 1 : 1111
127. Madiraju C, Edker MC, Hamel E, Raccor BS, Balachandran R, Zhu G, Giuliano KA, Vogt A, Shin Y, Fournier JH, Fukui Y, Bruckner AM, Curran DP, Day BW (2005) Biochemistry 44 : 15053
128. Mooberry SL, Tien G Hernandez AH, Plubrukar A, Davidson BS (1999) Cancer Res 59 : 653
129. Pryor DE, O'Brate A, Bilcer G, Diaz JF, Wang Y, Wang Y, Kabaki M, Jung MK, Andreu JM, Ghosh AK, Giannakakou P, Hamel E (2002) Biochemistry 41:9109
130. Gapud EJ, Bai R, Ghosh AK, Hamel E (2004) Mol Pharmacol 66:113
131. Gaitanos TN, Buey RM, Diaz JF, Northcote PT, Teesdale-Spittle P, Andreu JM, Miller JH (2004) Cancer Res 64 : 5063
132. Miller JH, Rouwe B, Gaitanos TN, Hood KA, Crume KP, Backstrom BT, La Flamme AC, Berridge MV, Northcote PT (2004) Apoptosis 9 : 785
133. Pineda O, Farràs J, Maccari L, Manetti F, Botta M, Vilarrasa J (2004) Bioorg Med Chem Lett 14 : 4825
134. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) J Comput Chem 19:1639
135. Jones G, Willet P, Glen RC, Leach AR, Taylor J (1997) J Mol Biol 267:727