Overcoming the inadequacies or limitations of experimental structures as drug targets by using computational modeling tools and molecular dynamics simulations

ChemMedChem

Volumn 2, Issue 10, 2007, Pages 1388-1401

  Marco, Esther ^a   Gago, Federico ^b  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b UNIVERSITY OF ALCALÁ   (Spain)

Author keywords

Ligand docking; Molecular dynamics; Normal mode analysis; Quantitative structure activity relationships; Virtual screening

Indexed keywords

LIGAND;

CHEMICAL STRUCTURE; COMPUTER SIMULATION; PHARMACOLOGY; PROTEIN FOLDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW;

COMPUTER SIMULATION; LIGANDS; MOLECULAR STRUCTURE; PHARMACOLOGY; PROTEIN FOLDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 41949132326     PISSN: 18607179     EISSN: 18607187     Source Type: Journal    
DOI: 10.1002/cmdc.200700087     Document Type: Review

References (151)

1. R. E. Dickerson, Present at the flood: How structural biology came about, Sinauer Associates, Sunderland, MA, 2005.
2. J. M. Chandonia, S. Brenner, Science 2006, 311, 347-351.
3. E. Abola, P. Kuhn, T. Earnest, R. C. Stevens, Nat. Struct. Biol. 2000, Suppl. 7, 973-977.
4. T. L. Sorensen, K. E. McAuley, R. Flaig, E. M. Duke, Trends Biotechnol. 2006, 24, 500-508.
5. T. L. Blundell, H. Jhoti, C. Abell, Nat. Rev. Drug Discovery 2002, 1, 45-54.
6. A. Chien, I. Foster, D. Goddette, Drug Discovery Today 2002, 7, S176-S180.
7. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucleic Acids Res. 2000, 28, 235-242.
8. D. Bailey, E. Zanders, P. Dean, Nat. Biotechnol. 2001, 19, 207-209.
9. a) J. Dundas, Z. Ouyang, J. Tseng, A. Binkowski, Y. Turpaz, J. Liang, Nucleic Acids Res. 2006, 34 (Web Server issue), W116-118;
10. b) URL: http://cast.engr.uic.edu.
11. a) P. Goodford, J. Med. Chem. 1985, 28, 849-857;
12. b) URL: http://www.moldiscovery.com.
13. D. C. Phillips in Biomolecular Stereodynamics II (Ed.: R. H. Sarma), Adenine Press, Guilderland, NY, 1981, p. 497.
14. B. Halle, Proc. Natl. Acad. Sci. USA 2002, 99, 1274-1279.
15. Z. Yuan, T. L. Bailey, R. D. Teasdale, Proteins 2005, 58, 905-912.
16. K. U. Linderstrom-Lang, J. A. Schellman in The Enzymes, Vol. 1 (Eds.: P. D. Boyer, A. Lardy, K. Myrbick), Academic Press, New York, 1959, p. 443.
17. J. A. Schellman, C. G. Schellman, Protein Sci. 1997, 6, 1092-1100.
18. M. Gerstein, W. A. Krebs, Nucleic Acids Res. 1998, 26, 4280-4290.
19. M. G. Bursavich, D. H. Rich, J. Med. Chem. 2002, 45, 541-558.
20. E. Fischer, Ber. Dtsch. Chem. Ges. 1894, 27, 2985-2993.
21. D. E. Koshland, Proc. Natl. Acad. Sci. USA 1958, 44, 98-104.
22. F. Schotte, M. Lim, T. A. Jackson, A. V. Smirnov, J. Soman, J. S. Olson, G. N. Phillips, Jr., M. Wulff, P. A. Anfinrud, Science 2003, 300, 1944-1947.
23. K. Moffat, Acta Crystallogr. Sect. A 1998, 54, 833-841.
24. M. Schmidt, H. Ihee, R. Pahl, V. Srajer, Methods Mol. Biol. 2005, 305, 115-154.
25. S. Flores, N. Echols, D. Milburn, B. Hespenheide, K. Keating, J. Lu, S. Wells, E. Z. Yu, M. Thorpe, M. Gerstein, Nucleic Acids Res. 2006, 34(Database issue), D296-D301.
26. W. G. Krebs, M. Gerstein, Nucleic Acids Res. 2000, 28, 1665-1675.
27. N. Echols, D. Milburn, M. Gerstein, Nucleic Acids Res. 2003, 31, 478-482.
28. a) R. Maiti, G. H. van Domselaar, D. S. Wishart, Nucleic Acids Res. 2005, 33(Web Server issue), W358-W362;
29. b) URL: http://wishart.biology.ualberta.ca/moviemaker.
30. a) H. Frauenfelder, S. G. Sligar, P. G. Wolynes, Science 1991, 254, 1598-1603;
31. b) M. K. Hong, D. Braunstein, B. R. Cowen, H. Frauenfelder, I. E. Iben, J. R. Mourant, P. Ormos, R. Scholl, A. Schulte, P. J. Steinbach, Biophys. J. 1990, 58, 429-436.
32. F. Karush, J. Am. Chem. Soc. 1950, 72, 2705-2713.
33. J. Foote, C. Milstein, Proc. Natl. Acad. Sci. USA 1994, 91, 10370-10374.
34. G. Weber, Biochemistry 1972, 11, 864-878.
35. K. A. Dill, Protein Sci. 1999, 8, 1166-1180.
36. D. W. Miller, K. A. Dill, Protein Sci. 1997, 6, 2166-2179.
37. C. J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 1999, 8, 1181-1190.
38. C. J. Tsai, D. Xu, R. Nussinov, Folding Des. 1998, 3, R71-R80.
39. K. A. Dill, H. S. Chan, Nat. Struct. Biol. 1997, 4, 10-19.
40. H. A. Carlson, Curr. Opin. Chem. Biol. 2002, 6, 447-452.
41. T. Kenakin, Annu. Rev. Pharmacol. Toxicol. 2002, 42, 349-379.
42. P. A. Lochhead, G. Sibbet, N. Morrice, V. Cleghon, Cell 2005, 121, 925-936.
43. P. A. Lochhead, R. Kinstrie, G. Sibbet, T. Rawjee, N. Morrice, V. Cleghon, Mol. Cell 2006, 24, 627-633.
44. J. Monod, J. Wyman, J. P. Changeux, J. Mol. Biol. 1965, 12, 88-118.
45. D. E. Koshland, Jr., G. Nemethy, D. Filmer, Biochemistry 1966, 5, 365-385.
46. E. Freire, Proc. Natl. Acad. Sci. USA 1999, 96, 10118-10122.
47. K. Gunasekaran, B. Ma, R. Nussinov, Proteins Struct. Funct. Bioinf. 2004, 57, 433-443.
48. V. J. Hilser, E. Freire, J. Mol. Biol. 1996, 262, 756-772.
49. a) J. Vertrees, P. Barritt, S. Whitten, V. J. Hilser, Bioinformatics 2005, 21, 3318-3319;
50. b) URL: http://best.utmb.edu/BEST/.
51. I. Luque, E. Freire, Proteins 2000, 41, 63-71.
52. For a review, see: I. Luque, S. A. Leavitt, E. Freire, Annu. Rev. Biophys. Biomol. Struct. 2002, 31, 235-256.
53. S. A. Leavitt, A. Schon, J. C. Klein, U. Manjappara, I. M. Chaiken, E. Freire, Curr. Protein Pept. Sci. 2004, 5, 1-8.
54. G. Tachedjian, M. Orlova, S. G. Sarafianos, E. Arnold, S. P. Goff, Proc. Natl. Acad. Sci. USA 2001, 98, 7188-7193.
55. a) A. Christopoulos, T. Kenakin, Pharmacol. Rev. 2002, 54, 323-374;
56. b) C. J. Langmead, A. Christopoulos, Trends Pharmacol. Sci. 2006, 27, 475-481.
57. M. Chebib, G. A. R. Johnston, J. Med. Chem. 2000, 43, 1427-1447.
58. a) W. Wriggers, K. Schulten, Proteins Struct. Funct. Bioinf. 1997, 29, 1-14;
59. b) URL: http://biomachina.org/disseminate/hingefind/hingefind.html.
60. a) V. Hayward, V. , H. J. C. Berendsen, Proteins Struct. Funct. Bioinf. 1998, 30, 144-154;
61. b) S. Hayward, R. Lee, J. Mol. Graph. Model. 2002, 21, 181-183;
62. c) URL: http://www.cmp.uea.ac.uk/dyndom.
63. a) B. Brooks, M. Karplus, Proc. Natl. Acad. Sci. USA 1983, 80, 6571-6575;
64. b) N. Go, T. Noguti, T. Nishikawa, Proc. Natl. Acad. Sci. USA 1983, 80, 3696-3700.
65. M. M. Tirion, Phys. Rev. Lett. 1996, 77, 1905-1908.
66. K. Hinsen, Proteins Struct. Funct. Bioinf. 1998, 33, 417-429.
67. I. Bahar, A. R. Atligan, B. Erman, Folding Des. 1997, 2, 173-181.
68. a) F. Tama, Y. H. Sanejouand, Protein Eng. 2001, 14, 1-6;
69. b) M. Delarue, Y.-H. Sanejouand, J. Mol. Biol. 2002, 320, 1011-1024.
70. W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, M. Gerstein, Proteins Struct. Funct. Bioinf. 2002, 48, 682-695.
71. a) E. Lindahl, C. Azuara, P. Koehl, M. Delarue, Nucleic Acids Res. 2006, 34(Web Server issue), W52-W56;
72. b) URL: http://lorentz.immstr.pasteur.fr/nma/index.php.
73. a) K. Suhre, Y. H. Sanejouand, Nucleic Acids Res. 2004, 32(Web Server issue), W610-W614;
74. b) URL: http://www.igs.cnrs-mrs.fr/elnemo/.
75. a) P. J. Kraulis, J. Appl. Crystallogr. 1991, 24, 946-950;
76. b) URL: http://www.avatar.se/molscript/.
77. W. L. DeLano, The PyMOL Molecular Graphics System, 2002; URL: http://pymol.sourceforge.net/.
78. F. Tama, F. X. Gadea, O. Marques, Y. H. Sanejouand, Proteins Struct. Funct. Bioinf. 2000, 41, 1-7.
79. A. Taly, M. Delarue, T. Grutter, M. Nilges, N. Le Novere, P. J. Corringer, J. P. Changeux, Biophys. J. 2005, 88, 3954-3965.
80. H. Valadie, J. J. Lacapcre, Y. H. Sanejouand, C. Etchebest, J. Mol. Biol. 2003, 332, 657-674.
81. G. M. Keseru, I. Kolossvary, J. Am. Chem. Soc. 2001, 123, 12708-12709.
82. C. N. Cavasotto, J. A. Kovacs, R. A. Abagyan, J. Am. Chem. Soc. 2005, 127, 9632-9640.
83. L. W. Yang, X. Liu, C. J. Jursa, M. Holliman, A. J. Rader, H. A. Karimi, I. Bahar, Bioinformatics 2005, 21, 2978-2987.
84. L. W. Yang, A. J. Rader, X. Liu, C. J. Jursa, S. C. Chen, H. A. Karimi, I. Bahar, Nucleic Acids Res. 2006, 34(Web Server issue), W24-W31.
85. a) D. J. Jacobs, A. J. Rader, L. A. Kuhn, M. F. Thorpe, Proteins 2001, 44, 150-165;
86. b) M. I. Zavodszky, M. Lei, M. F. Thorpe, A. R. Day, L. A. Kuhn, Proteins 2004, 57, 243-261.
87. A. Ahmed, H. Gohlke, Proteins 2006, 63, 1038-1051.
88. a) J. A. McCammon, M. Karplus, Nat. Struct. Biol. 2002, 9, 646-652;
89. b) T. E. Cheatham III, P. A. Kollman, Annu. Rev. Phys. Chem. 2000, 51, 435-471.
90. J. A. McCammon, B. R. Gelin, M. Karplus, Nature 1977, 267, 585-590.
91. R. Elber, M. Karplus, Science 1987, 235, 318-321.
92. M. Rueda, C. Ferrer-Costa, T. Meyer, A. Pérez, J. Camps, A. Hospital, J. L. Gelpí, M. Orozco, Proc. Natl. Acad. Sci. USA 2007, 104, 796-801.
93. For reviews, see: a) A. Kitao, N. Go, Curr. Opin. Struct. Biol. 1999, 9, 164-169;
94. b) H. J. C. Berendsen, S. Hayward, Curr. Opin. Struct. Biol. 2000, 10, 165-169.
95. M. Rueda, P. Chacón, M. Orozco, Structure 2007, 15, 565-575.
96. H. Alonso, A. A. Bliznyuk, J. E. Gready, Med. Res. Rev. 2006, 26, 531-568.
97. a) B. J. Berne, J. E. Straub, Curr. Opin. Struct. Biol. 1997, 7, 181-189;
98. b) A. Mitsutake, Y. Sugita, Y. Okamoto, Biopolymers 2001, 60, 96-123;
99. c) D. Hamelberg, J. Mongan, J. A. McCammon, J. Chem. Phys. 2004, 120, 11919-11929.
100. Ajay, M. A. Murcko, J. Med. Chem. 1995, 38, 4953-4967.
101. B. Honig, A. Nicholls, Science 1995, 268, 1144-1149.
102. T. Rodinger, R. Pomès, Curr. Opin. Struct. Biol. 2005, 15, 164-170.
103. T. P. Straatsma, J. A. McCammon, Annu. Rev. Phys. Chem. 1992, 43, 407-435.
104. M. K. Gilson, H. X. Zhou, Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42.
105. J. Åqvist, V. B. Luzhkov, B. O. Brandsdal, Acc. Chem. Res. 2002, 35, 358-365.
106. N. Foloppe, R. Hubbard, Curr. Med. Chem. 2006, 13, 3583-3608.
107. P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, T. E. Cheatham III, Acc. Chem. Res. 2000, 33, 889-897.
108. A. Checa, A. R. Ortiz, B. de Pascual-Teresa, F. Gago, J. Med. Chem. 1997, 40, 4136-4145.
109. S. Wold, E. Johansson, M. Cocchi in 3D QSAR in Drug Design. Theory, Methods and Applications (Ed.: H. Kubinyi), ESCOM Science Publishers B.V., Leiden, 1993, pp. 523-550.
110. R. D. Cramer III, D. E. Patterson, J. D. Bunce, J. Am. Chem. Soc. 1988, 110, 5959-5967.
111. For reviews, see: a) R. C. Wade, A. R. Ortiz, F. Gago, Perspect. Drug Discovery Des. 1998, 9/10/11, 19-34;
112. b) R. C. Wade, A. R. Ortiz, F. Gago in 3D QSAR in Drug Design, Vol. 2 (Eds.: H. Kubinyi, G. Folkers, Y. C. Martin), Kluwer Academic, Dordrecht, 1998, pp. 19-34;
113. c) J. Damborský, J. Kmuníèek, T. Jedlièka, S. Luengo, F. Gago, A. R. Ortiz, R. C. Wade, Enzyme Functionality: Design, Engineering and Screening (Ed.: A. Svendsen), Marcel Dekker, New York • Basel, 2004, pp. 79-96.
114. F. Rodríguez-Barrios, F. Gago, J. Am. Chem. Soc. 2004, 126, 2718-2719.
115. M. Murcia, A. R. Ortiz, J. Med. Chem. 2004, 47, 805-820.
116. M. Murcia, A. Morreale, A. R. Ortiz, J. Med. Chem. 2006, 49, 6241-6253.
117. D. González-Ruiz, H. Gohlke, Curr. Med. Chem. 2006, 13, 2607-2625.
118. S. F. Sousa, P. A. Fernandes, M. J. Ramos, Proteins 2006, 65, 15-26.
119. R. M. Knegtel, I. D. Kuntz, C. M. Oshiro, J. Mol. Biol. 1997, 266, 424-440.
120. M. Gerstein, A. M. Lesk, C. Chothia, Biochemistry 1994, 33, 6739-6749.
121. J. Schlitter, M. Engels, P. Krüger, J. Mol. Graph. 1994, 12, 84-89.
122. J. Mendieta, G. Ramírez, F. Gago, Proteins Struct. Funct. Bioinf. 2001, 44, 460-469.
123. J. Mendieta, F. Gago, G. Ramírez, Biochemistry 2005, 44, 14470-14476.
124. F. Rodríguez-Barrios, J. Balzarini, F. Gago, J. Am. Chem. Soc. 2004, 126, 15386-15387.
125. F. Rodríguez-Barrios, J. Balzarini, F. Gago, J. Am. Chem. Soc. 2005, 127, 7570-7578.
126. D. M. Lorber, M. K. Udo, B. K. Shoichet, Protein Sci. 2002, 11, 1393-1408.
127. C. M. Crews, J. L. Collins, W. S. Lane, M. L. Snapper, S. L. Schreiber, J. Biol. Chem. 1994, 269, 15411-15414.
128. E. Marco, S. Martín-Santamaría, C. Cuevas, F. Gago, J. Med. Chem. 2004, 47, 4439-4452.
129. M. R. Walter, W. J. Cook, L. B. Cole, S. A. Short, G. W. Koszalka, T. A. Krenitsky, S. Ealick, J. Biol. Chem. 1990, 265, 14016-14022.
130. V. L. Schramm, Curr. Opin. Struct. Biol. 2005, 15, 604-613.
131. J. Mendieta, S. Martín-Santamaría, E. M. Priego, J. Balzarini, M. J. Camarasa, M. J. Pérez-Pérez, F. Gago, Biochemistry 2004, 43, 405-414.
132. a) J. Damborsky, M. Prokop, J. Koca, Trends Biochem. Sci. 2001, 26, 71-73;
133. b) URL: http://ncbr.chemi.muni.cz/triton/triton.html.
134. a) O. Poirot, K. Suhre, C. Abergel, E. O'Toole, C. Notredame, Nucleic Acids Res. 2004, 32(Web Server issue), W37-W40;
135. b) URL: http://www.igs.cnrs-mrs.fr/Tcoffee/.
136. a) D. Lupyan, A. Leo-Macias, A. R. Ortiz, Bioinformatics 2005, 21, 3255-3263;
137. b) URL: http://ub.cbm.uam.es/mammoth/mult/.
138. J. Chen, C. L. Brooks III, Proteins Struct. Funct. Bioinf. 2007, 67, 922-930.
139. R. Sánchez, U. Pieper, F. Melo, N. Eswar, M. A. Marti-Renom, M. S. Madhusudhan, N. Mirkovic, A. Sali, Nat. Struct. Biol. 2000, Suppl. 7, 986-990.
140. K. Ginalski, Curr. Opin. Struct. Biol. 2006, 16, 172-177.
141. a) U. Pieper, N. Eswar, F. P. Davis, H. Braberg, M. S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B. M. Webb, D. Eramian, M. Y. Shen, L. Kelly, F. Melo, A. Sali, Nucleic Acids Res. 2006, 34(Database issue), D291-D295;
142. b) URL: http://salilab.org/modbase/.
143. P. J. O'Hara, P. O. Sheppard, H. Thogersen, D. Venezia, B. A. Haldeman, V. McGrane, K. M. Houamed, C. Thomsen, T. L. Gilbert, E. R. Mulvihill, Neuron 1993, 11, 41-52.
144. a) L. Holm, C. Sander, Nucleic Acids Res. 1997, 25, 231-234;
145. b) URL: http://ekhidna.biocenter.helsinki.fi/dali/.
146. A. I. Hernández, O. Familiar, A. Negri, F. Rodríguez- Barrios, F. Gago, A. Karlsson, M. J. Camarasa, J. Balzarini, M. J. Pérez-Pérez, J. Med. Chem. 2006, 49, 7766-7773.
147. a) M. Petrek, M. Otyepka, P. Banas, P. Kosinova, J. Koca, J. Damborsky, BMC Bioinf. 2006, 7, 316;
148. b) URL: http://loschmidt.chemi.muni.cz/caver.
149. S. J. Teague, Nat. Rev. Drug Discovery 2003, 2, 527-541.
150. The Institute for Genomic Research; URL: http://www.tigr.org/tdb/.
151. T. Kenakin, Trends Pharmacol. Sci. 2004, 25, 186-192.