Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors

Bioorganic and Medicinal Chemistry

Volumn 14, Issue 17, 2006, Pages 6001-6011

  Oliveira, Fernanda G ^a   Sant'Anna, Carlos M R ^b   Caffarena, Ernesto R ^c   Dardenne, Laurent E ^d   Barreiro, Eliezer J ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b FEDERAL RURAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c INSTITUTO OSWALDO CRUZ   (Brazil)

^d LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

Author keywords

Empirical free energy model; Molecular docking; Molecular modeling; Phosphodiesterases; Semiempirical calculations

Indexed keywords

PHOSPHODIESTERASE IV; PHOSPHODIESTERASE IV INHIBITOR; ROLIPRAM;

ARTICLE; EMPIRICISM; ENERGY TRANSFER; ENTHALPY; ENTROPY; ENZYME ACTIVATION; ENZYME ACTIVITY; LIGAND BINDING; MATHEMATICAL COMPUTING; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PREDICTION; SOLVATION;

3',5'-CYCLIC-NUCLEOTIDE PHOSPHODIESTERASE; COMBINATORIAL CHEMISTRY TECHNIQUES; ENZYME INHIBITORS; HETEROCYCLIC COMPOUNDS, 3-RING; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 33746263844     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2006.05.017     Document Type: Article

References (66)

1. Conti M., and Jin S.L.C. Prog. Nucleic Acid Res. Mol. Biol. 63 (1999) 1-38
2. Houslay M.D., Sullivan M., and Bolger G.B. Adv. Pharmacol. 44 (1998) 225-342
3. Huai Q., Wang H., Sun Y., Kim H.Y., Liu Y., and Ke H. Structure 11 (2003) 865-873
4. Torphy T.J. Am. J. Respir. Crit. Care Med. 157 (1998) 351-370
5. Torphy T.J., Stadel J.M., Burman M., Cieslinski L.B., McLaughlin M.M., White J.R., and Livi G.P. J. Biol. Chem. 267 (1992) 1798-1804
6. Jacobitz S., McLaughlin M.M., Livi G.P., Burman M., and Torphy T.J. Mol. Pharmacol. 50 (1996) 891-899
7. Owens R.J., Catterall C., Batty D., Jappy J., Russell A., Smith B., O'Connell J., and Perry M.J. Biochem. J. 326 (1997) 53-60
8. Rocque W.J., Tian G., Wiseman J.S., Holmes W.D., Zajac-Thompson I., Willard D.H., Patel I.R., Wisely B., Clay W.C., Kadwell S.H., Hoffman C.R., and Luther M.Z. Biochemistry 36 (1997) 14250-14261
9. Carpenter D.O., Briggs D.B., Knox A.P., and Strominger N. J. Neurophys. 59 (1988) 358-369
10. Eben E., and Rüther E. Pharmacopsychiatry 18 (1985) 69-70
11. Horowski R., and Sastre-y-Hernandez M. Curr. Ther. Res. 38 (1985) 23-29
12. Wxkman F., Fichte K., Meya U., and Sastre-y-Hernandez M. Curr. Ther. Res. 43 (1988) 195-291
13. Wachtel H. Neuropharmacology 22 (1983) 267-272
14. Zeller E., Stief H.-J., Pflug B., and Sastre-y-Hernandez M. Pharmacopsychiatry 17 (1984) 188-190
15. Sette C., and Conti M. J. Biol. Chem. 271 28 (1996) 16526-16534
16. Alvarez R., Sette C., Yang D., Eglen R.M., Wilhelm R., Shelton E.R., and Conti M. Mol. Pharmacol. 48 (1995) 616-622
17. Huston E., Pooley L., Julien P., Scotland G., McPhee I., Sullivan M., Bolger G., and Houslay M. J. Biol. Chem. 271 (1997) 31334-31344
18. Xu R.X., Hassel A.M., Vanderwall S., Lambert M.H., Holmes W.D., Luther M.A., Rocque W.J., Milburn M.V., Zharo Y., Ke H., and Nolte R.T. Science 288 (2000) 1822-1825
19. Xu R.X., Rocque W.J., Lambert M.H., Vanderwall D.E., Luther M.A., and Nolte R.T. J. Mol. Biol. 337 (2004) 355-365
20. Laliberté F., Han Y., Govindarajan A., Giroux A., Liu S., Bobechko B., Lario P., Bartlett A., Gorseth E., Gresser M., and Huang Z. Biochemistry 39 (2000) 6449-6458
21. Liu S., Laliberté F., Bobechko B., Bartlett A., Lario P., Gorseth E., Van Hamme J., Gresser M.J., and Huang Z. Biochemistry 40 (2001) 10179-10186
22. Wu G., and Vieth M. J. Med. Chem. 47 (2004) 3142-3148
23. Alcaro A., Gasparrini F., Incani O., Medduci S., Misiti D., Pierini M., and Villani C. J. Comput. Chem. 21 (2000) 515-530
24. Brooks III C.L., Karplus M., and Pettitt B.M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. Advances in Chemical Physics Vol. LXXI (1988), John Wiley & Sons, New York
25. VanGunsteren W.F., King P.M., and Mark A.E. Q. Rev. Biophys. 27 4 (1994) 435-481
26. Hansson T., Marelius J., and Åqvist J. J. Comput. Aided Mol. Des. 12 (1998) 27-35
27. Åqvist J., Luzhkov V.B., and Brandsdal B.O. Acc. Chem. Res. 35 (2002) 358-365
28. Asi A.M., Rahman N.A., and Merican A.F. J. Mol. Graphics Modell. 22 (2004) 249-262
29. Raha K., and Merz Jr. K.M. J. Am. Chem. Soc. 126 (2004) 1020-1021
30. Böhm H.J. J. Comput. Aided Mol. Des. 8 (1994) 243-256
31. Rarey M., Kramer B., Lengauer T., and Klebe G. J. Mol. Biol. 261 (1996) 470-489
32. Eldridge M.D., Murray C.W., Auton T.R., Paolini G.V., and Mee R.P. J. Comput. Aided Mol. Des. 11 (1997) 425-445
33. Williams D.H., and Westwell M.S. Chem. Soc. Rev. 27 (1998) 57-63
34. Wang S., Milne G.W.A., Nicklaus M.C., Marquez V.E., Lee J., and Blumberg P.M. J. Med. Chem. 37 (1994) 1326-1338
35. Searle M.S., Williams D.H., and Gerhard U. J. Am. Chem. Soc. 114 (1992) 10697-10704
36. Searle M.S., and Williams D.H. J. Am. Chem. Soc. 114 (1992) 10690-10697
37. Dal Piaz V., Giovannoni M.P., Castellana C., Palacios J.M., Beleta J., Doménech T., and Segarra V. Eur. J. Med. Chem. 33 (1998) 789-797
38. Sinnokrot M.A., Valeev E.F., and Sherrill C.D. J. Am. Chem. Soc. 124 (2002) 10887-10893
39. Mannargudi S.S., Sasidhar Y.U., and Balaji P.V. Protein Sci. 13 (2004) 2502-2514
40. Fernandez-Alonso M.C., Cañada F.J., Jimenez-Barbero J., and Cuevas G. J. Am. Chem. Soc. 127 (2005) 7379-7386
41. Sujatha M.S., Sasidhar Y.U., and Balaji P.V. Biochemistry 44 (2005) 8554-8562
42. Tauer T.P., and Sherrill C.D. J. Phys. Chem. A 109 (2005) 10475-10478
43. Saldou N., Obernolte R., Huber A., Baecker P.A., Wilhelm R., Alvarez R., Li B., Xia L., Callan O., Su C., Jarnagin K., and Shelton E.R. Cell. Signal. 10 (1998) 427-440
44. Gratteri P., Bonaccini C., and Milani F. J. Med. Chem. 48 (2005) 1657-1665
45. Houslay M.D., Schafer P., and Zhang K.Y.J. Drug Discovery Today 10 (2005) 1503-1519
46. Garmer D.R., Gresh N., and Roque B. Proteins 31 (1998) 42-60
47. Antony J., Piquemal J.H., and Gresh N. J. Comput. Chem. 26 (2005) 1131-1147
48. Donchev A.G., Ozrin V.D., Subbotin M.V., Tarasov O.V., and Tarasov V.I. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 7829-7834
49. Tait A., Luppi A., Hatzelmann A., Fossa P., and Mosti L. Bioorg. Med. Chem. 13 (2005) 1393-1402
50. Card G.L., England B.P., Suzuki Y., Fong D., Powell B., Lee B., Luu C., Tabrizizad M., Gillette S., Ibrahim P.N., Artis D.R., Bollag G., Milburn M.V., Kim S.H., Schlessinger J., and Zhang K.Y.J. Structure 12 (2004) 2233-2247
51. Berendsen H.J.C., Vanderspoel D., and Vandrunen R. Comput. Phys. Commun. 91 (1995) 43-56
52. Lindahl E., Hess B., and van der Spoel D. J. Mol. Model. 7 (2001) 306-317
53. Jorgensen W.L., and Tirado-Rives J. J. Am. Chem. Soc. 110 (1988) 1657-1666
54. Jorgensen W.L.J., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926-935
55. Ryckaert J.P., and Bellemans A. Faraday Discuss. Chem. Soc. 66 (1978) 95-106
56. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. J. Comput. Chem. 18 (1997) 1463-1472
57. Hockney R.W., Goel S.P., and Eastwood J.W. J. Comput. Phys. 14 (1974) 148-158
58. Morris G.M., Goddsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. J. Comput. Chem. 19 (1998) 1639-1662
59. Halgren T. J. Comput. Chem. 17 (1996) 490-519
60. Sinnokrot M.O., and Sherrill C.D. J. Chem. Phys. Chem. A 107 (2003) 8377-8379
61. Stewart, J. J. P. QCPE 455, available from Indiana University, Bloomington, USA, 1992.
62. Stewart J.J.P. J. Comput. Chem. 10 (1989) 209-220
63. Stewart J.J.P. J. Comput. Chem. 10 (1989) 221-264
64. Baker J. J. Comput. Chem. 7 (1986) 385-395
65. Cheng Y., and Prusoff W.H. Biochem. Pharm. 22 (1973) 3099-3108
66. Chambers C.C., Hawkins G.D., Cramer C.J., and Truhlar D.G. J. Phys. Chem. 100 (1996) 16385-16398