J. L. M. Tributino et al. / Bioorg. Med. Chem. 17 (2009) 1125–1131
1131
3. (a) Smith, W. L.; Meade, E. A.; DeWitt, D. L. Ann. N.Y. Acad. Sci. 1994, 714, 136;
(b) Vane, J.; Bakhle, Y. S.; Botting, R. M. Ann. Rev. Pharmacol. Toxicol. 1998, 38,
97.
4. For a recent review, see: Fraga, C. A. M.; Barreiro, E. J. Curr. Med. Chem. 2006, 13,
167.
mice spent licking or biting the injected paw or leg was recorded.
Two distinct periods of intensive licking activity were identified
and scored separately unless otherwise stated. The first period
(earlier or neurogenic phase) was recorded 0–5 min after formalin
injection and the second period (later or inflammatory phase) was
recorded 15–30 min after injection.
5. For recent examples, see: (a) Lima, P. C.; Lima, L. M.; da-Silva, K. C. M.; Léda, P.
H. O.; Miranda, A. L. P.; Fraga, C. A. M.; Barreiro, E. J. Eur. J. Med. Chem. 2000, 35,
187; (b) Cunha, A. C.; Figueiredo, J. M.; Tributino, J. L. M.; Miranda, A. L. P.;
Castro, H. C.; Zingali, R. B.; Fraga, C. A. M.; de-Souza, M. C. B. V.; Ferreira, V. F.;
Barreiro, E. J. Bioorg. Med. Chem. 2003, 11, 2051; (c) Silva, G. A.; Costa, L. M. M.;
Brito, F. C. F.; Miranda, A. L. P.; Barreiro, E. J.; Fraga, C. A. M. Bioorg. Med. Chem.
2004, 12, 3149; (d) Silva, A. G.; Zapata-Sudo, G.; Kummerle, A. E.; Fraga, C. A.
M.; Barreiro, E. J.; Sudo, R. T. Bioorg. Med. Chem. 2005, 13, 3431; (e) Bezerra-
Netto, H. J. C.; Lacerda, D. I.; Miranda, A. L. P.; Alves, H. M.; Barreiro, E. J.; Fraga,
C. A. M. Bioorg. Med. Chem. 2006, 14, 7924; (f) Duarte, C. D.; Tributino, J. L. M.;
Lacerda, D. I.; Martins, M. V.; Alexandre-Moreira, M. S.; Dutra, F.; Bechara, E. J.
H.; De-Paula, F. S.; Goulart, M. O. F.; Ferreira, J.; Calixto, J. B.; Nunes, M. P.;
Bertho, A. L.; Miranda, A. L. P.; Barreiro, E. J.; Fraga, C. A. M. Bioorg. Med. Chem.
2007, 15, 2421.
4.5. Molecular modeling
4.5.1. Selection of protein crystal structures
Ligand-bound crystal structures of COX-1 and COX-2 were re-
trieved from RCSB Protein Data Bank.37 In this study, COX-1 crystal
structure 1PXX and COX-2 crystal structure 1CX2 were evaluated
and selected for docking.24,25
6. (a) Barreiro, E. J.; Fraga, C. A. M.; Miranda, A. L. P.; Rodrigues, C. R. Quím. Nova
2002, 25, 129; (b) Mahy, J. P.; Gaspard, S.; Mansuy, D. Biochemistry 1993, 32, 4014.
7. Lages, A. S.; Silva, K. C. M.; Miranda, A. L. P.; Fraga, C. A. M.; Barreiro, E. J. Bioorg.
Med. Chem. Lett. 1998, 8, 183.
8. (a) Khanapure, S. P.; Garvey, D. S.; Young, D. V.; Ezawa, M.; Earl, R. A.; Gaston, R.
D.; Fang, X.; Murty, M.; Martino, A.; Shumway, M.; Trocha, M.; Marek, P.; Tam,
S. W.; Janero, D. R.; Letts, L. G. J. Med. Chem. 2003, 46, 5484; (b) Khanapure, S. P.;
Augustyniak, M. E.; Earl, R. A.; Garvey, D. S.; Letts, L. G.; Martino, A. M.; Murty,
M. G.; Schwalb, D. J.; Shumway, M. J.; Trocha, A. M.; Young, D. V.; Zemtseva, I.
S.; Janero, D. R. J. Med. Chem. 2005, 48, 3930.
9. Duarte, C. D.; Barreiro, E. J.; Fraga, C. A. M. Mini-Rev. Med. Chem. 2007, 7, 1108.
10. Miranda, A. L. P; Lima, P. C.; Tributino, J. L. M.; Melo, P. A.; Fernandes, P. D.;
Cintra, W. M.; Fraga, C. A. M.; Barreiro, E. J. Abstracts of Papers, 6ème Congrès
Annuel de la Société Française de Pharmacologie, Rennes, France, 2002; P296.
11. Lima, L. M.; Barreiro, E. J. Curr. Med. Chem. 2005, 12, 23.
12. Barreiro, E. J.; Fraga, C. A. M. Quím. Nova 1999, 22, 744.
13. (a) Barreiro, E. J.; Lima, M. E. F. J. Pharm. Sci. 1992, 81, 1219; (b) Barreiro, E. J.;
Costa, P. R. R.; Coelho, F. A. S.; De-Farias, F. M. C. J. Chem. Res. (S) 1985, 220.
14. Ekeley, J. B.; Klemme, M. J. Am. Chem. Soc. 1928, 50, 2711.
15. Yamada, S.; Morizono, D.; Yamamoto, K. Tetrahedron Lett. 1992, 33, 4329.
16. Farrugia, L. J. J. Appl. Crystallogr. 1997, 30, 565.
4.5.2. Preparation of the ligands
The preparation of the ligands for docking with GOLD was per-
formed using SYBYL version 8.0.38 First, the ligand coordinates
were generated using the program SKETCHER, available in SYBYL ver-
sion 8.0. Next, the correct atom types (including hybridization
states) and correct bond types were defined and hydrogen atoms
were added. The energies of ligand structures were further min-
imized using the semiempirical AM1 method in SYBYL 8.0. PM3,
AM1, MMFF94 and Gasteiger-Hückel charges were assigned to
the ligand database.38
4.5.3. Preparation of protein structures
Proteins were prepared for the docking studies using the Bio-
polymer module of SYBYL 8.0. AMBER7 FF99 charges were attributed
to the protein atoms.38 Biopolymer protein analysis tool was used,
in a stepwise process of analysis and correction of geometry
parameters. The assignment of hydrogen positions has been made
on the basis of default rules. The side chains of lysine, arginine and
the carboxylate groups of aspartic and glutamic acid have been
modeled in their ionized states. Water molecules contained in
the PDB file have been removed. Finally, the active site of the
ensemble has been defined as the collection of residues within
20.0 Å of the hydroxyl oxygen atom of Tyr385.
17. Ferreira, S. H. J. Pharm. Pharmacol. 1979, 31, 648.
18. Rabasseda, X. Drugs Today 1996, 32, 365.
19. Seibert, K.; Zhang, Y.; Leahy, K.; Hauser, S.; Masferrer, J. L.; Perkins, W.; Lee, L.;
Isakson, P. C. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 12013.
20. Smith, C. J.; Zhang, Y.; Koboldt, C. M.; Muhammad, J.; Zweifel, B. S.; Shaffer, A.;
Talley, J. J.; Masferrer, J. L.; Seibert, K.; Isakson, P. C. Proc. Natl. Acad. Sci. U.S.A.
1998, 95, 13313.
21. Patrignani, P.; Panara, M. R.; Greco, A.; Fusco, O.; Natoli, C.; Iacobelli, S.;
Cipollone, F.; Ganci, A.; Creminon, C.; MacLouf, J.; Patrono, C. J. Pharmacol. Exp.
Ther. 1994, 271, 1705.
22. Young, J. M.; Panah, S.; Satchawatcharaphong, C.; Cheung, P. S. Inflamm. Res.
1996, 45, 246.
23. Rodrigues, C. R.; Veloso, M. P.; Verli, H.; Fraga, C. A. M.; Miranda, A. L. P.;
Barreiro, E. J. Curr. Med. Chem. 2002, 9, 849.
24. Kiefer, J. R.; Pawlitz, J. L.; Moreland, K. T.; Stegeman, R. A.; Hood, W. F.; Gierse, J.
K.; Stevens, A. M.; Goodwin, D. C.; Rowlinson, S. W.; Marnett, L. J.; Stallings, W.
C.; Kurumbail, R. G. Nature 2000, 405, 97.
25. Kurumbail, R. G.; Stevens, A. M.; Gierse, J. K.; McDonald, J. J.; Stegeman, R. A.;
Pak, J. Y.; Gildehaus, D.; Miyashiro, J. M.; Penning, T. D.; Seibert, K.; Isakson, P.
C.; Stallings, W. C. Nature 1996, 384, 644.
4.5.4. ChemScore fitness function
ChemScore is an empirical scoring function to estimate the
free energy of ligand binding to protein. It uses simple contact
terms to estimate lipophilic and metal–ligand binding contribu-
tions, including hydrogen bonding interactions. The detailed
methodology by which ChemScore calculates the free energy of
binding between protein and ligands has been described some-
where else.27
26. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J. Mol. Biol. 1997, 267,
727.
27. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. J. Comp.-
Aided Mol. Des. 1997, 11, 425.
Acknowledgements
28. Enraf-Nonius COLLECT. Nonius BV, Delft, The Netherlands, 1997–2000.
29. Otwinowski, Z.; Minor, W.. In Methods in Enzymology; Carter, C. W., Jr., Sweet, R.
M., Eds.; Academic Press: New York, 1997; Vol. 276, pp 307–326.
30. Sheldrick, G. M., SHELXS-97 Program for Crystal Structure Resolution; University of
Göttingen: Germany, 1997.
The authors thank Central Analítica (IQ-UFRJ) for technical facil-
ities and CAPES (BR), CNPq (BR), FAPERJ (BR), PRONEX (BR) and IM-
INOFAR (BR, #420.015/05-1) for financial support and fellowships.
31. Sheldrick, G. M., SHELXL-97 Program for Crystal Structure Refinement; University
of Göttingen: Germany, 1997.
32. Farrugia, L. J. J. Appl. Crystallogr. 1999, 32, 837.
Supplementary data
33. Bruno, I. J.; Cole, J. C.; Edgington, P. R.; Kessler, M. K.; Macrae, C. F.; McCabe, P.;
Pearson, J.; Taylor, R. Acta Crystallogr. Sect. B: Struct. Sci. 2002, 58, 389.
34. Ribeiro, I. G.; Silva, K. C. M.; Parrini, S. C.; Miranda, A. L. P.; Fraga, C. A. M.;
Barreiro, E. J. Eur. J. Med. Chem. 1998, 33, 225.
35. Lavich, T. R.; Cordeiro, R. S. B.; Silva, P. M. R.; Martins, M. A. Braz. J. Med. Biol.
Res. 2005, 38, 445.
Supplementary data associated with this article can be found, in
36. Hunskaar, S.; Berge, O.; Hole, K. Pain 1987, 30, 103.
References and notes
37. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.;
Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235.
38. SYBYL 8.0 ed., Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA;
1. Nathan, C. Nature 2002, 420, 846.
2. Williams, M.; Kowaluk, E. A.; Arneric, S. P. J. Med. Chem. 1999, 42, 1481.