Virtual screening against p50 NF-κB transcription factor for the identification of inhibitors of the NF-κB-DNA interaction and expression of NF-κB upregulated genes

ChemMedChem

Volumn 4, Issue 12, 2009, Pages 2024-2033

  Piccagli, Laura ^a   Fabbri, Enrica ^a   Borgatti, Monica ^a   Bianchi, Nicoletta ^a   Bezzerri, Valentino ^b   Mancini, Irene ^a   Nicolis, Elena ^b   Dechecchi, Cristina M ^b   Lampronti, Ilaria ^a   Cabrini, Giulio ^b   Gambari, Roberto ^a  

^a UNIVERSITY OF FERRARA   (Italy)

^b UNIVERSITY HOSPITAL OF VERONA   (Italy)

Author keywords

Drug discovery; Molecular docking; NF B inhibitors; Virtual screening

Indexed keywords

5,7 DIHYDROXY 4 METHYLCOUMARIN; 7,8 DIHYDROXY 4 METHYLCOUMARIN; BROMOPYROGALLOL; CATECHOL; COUMARIN DERIVATIVE; EMBLICA OFFICINALIS EXTRACT; GALLIC ACID; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PROTEIN P50; PYROGALLOL; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; CYSTIC FIBROSIS; GEL MOBILITY SHIFT ASSAY; GENETIC SCREENING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; INHIBITION KINETICS; MOLECULAR DOCKING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN TARGETING; PSEUDOMONAS AERUGINOSA;

ANIMALS; CELL LINE; DNA; GENE EXPRESSION REGULATION; HUMANS; INTERLEUKIN-8; MICE; MODELS, MOLECULAR; NF-KAPPA B P50 SUBUNIT; PROTEIN BINDING; PROTEIN MULTIMERIZATION; RNA, MESSENGER; SMALL MOLECULE LIBRARIES; TRANSCRIPTION FACTOR RELB;

EID: 73449147352     PISSN: 18607179     EISSN: 18607187     Source Type: Journal    
DOI: 10.1002/cmdc.200900362     Document Type: Article

References (52)

1. R. Sen, D. Baltimore, Cell. 1986, 47, 921-928.
2. a) S. Aradhya, D. L. Nelson, Curr. Opin. Genet. Dev. 2001, 11, 300-306;
3. b) A. Kumar, Y. Takada, A. M. Boriek, B. B. Aggarwal, J. Mol. Med. 2004, 82, 434-448;
4. c) A. S. Baldwin, Jr., J. Clin. Invest. 2001, 107, 3-6;
5. d) E. Voskaridouand, E. Terpos, Br. J. Haematol. 2004, 127, 127-139.
6. a) T. Gilmore, M. E. Gapuzan, D. Kalaitzidis, D. Starczynowski, Cancer Lett. 2002, 8, 181,1-9;
7. b) M. Rottner, C. Kunzelmann, M. Mergey, J. M. Freyssinet, M. C. MartÍnez, FASEB J. 2007, 21, 2939-2948;
8. c) T. Okamoto, Endocr. Metab. Immune Disord. Drug Targets 2006, 6, 359-372;
9. d) I. Atreya, R. Atreya, M. F. Neurath, J. Intern. Med. 2008, 263, 591-596;
10. e) C. H. Lee, Y. T. Jeon, S. H. Kim, Y. S. Song, BioFactors 2007, 29, 19-35.
11. a) C. W. Muller, F. A. Rey, M. Sodeoka, G. L. Verdine, S. C. Harrison, Nature 1995, 373, 311-317;
12. b) F. E. Chen, D. B. Huang, Y. Q. Chen, G. Ghosh, Nature 1998, 391, 410-413;
13. c) Y. Q. Chen, S. Ghosh, G. A. Ghosh, Nat. Struct. Biol. 1998, 5, 67-73;
14. d) D. B. Huang, Y. Q. Chen, M. Ruetsche, C. B. Phelps, G. Ghosh, Structure 2001, 9, 669-678.
15. a) J. Hiscott, H. Kwon, P. Genin, J. Clin. Invest. 2001, 107, 143-151;
16. b) L. A. Dickinson, J. W. Trauger, E. E. Baird, P. B. Dervan, B. J. Graves, J. M. Gottesfeld, J. Biol. Chem. 1999, 274, 12765-12773.
17. a) Y. F. Xia, B. Q. Ye, Y. D. Li, J. G. Wang, X. J. He, X. Lin, X. Yao, D. Ma, A. Slungaard, R. Hebbel, N. S. Key, J. G. Geng, J. Immunol. 2004, 173, 4207-4217;
18. b) Y. J. Wang, J. T. Wang, Q. X. Fan, J. G. Geng, Cell. Physiol. Biochem. Cell. Res. 2007, 17, 933-941;
19. c) K. M. Chen, T. E. Spratt, B. A. Stanley, D. A. De Cotiis, M. C. Bewley, J. M. Flanagan, D. Desai, A. Das, E. S. Fiala, S. Amin, K. El-Bayoumy, Cancer Res. 2007, 67, 10475-10483;
20. d) V. Chandrasekaran, E. W. Taylor, J. Mol. Graph. Model. 2008, 26, 861-867;
21. e) H. J. Park, S. H. Lee, D. J. Son, K. W. Oh, K. H. Kim, H. S. Song, G. J. Kim, G. T. Oh, D. Y. Yoon, J. T. Hong, Arthritis Rheum. 2004, 47, 3504-3515;
22. f) H. M. Kim, S. J. Bae, D. W. Kim, B. K. Kim, S. B. Lee, U. S. Lee, C. H. Kim, S. K. Moon, Int. Immunopharmacol. 2007, 7, 1083-1091.
23. a) M. Borgatti, I. Lampronti, A. Romanelli, C. Pedone, M. Saviano, N. Bianchi, C. Mischiati, R. Gambari, J. Biol. Chem. 2003, 278, 7500-7509;
24. b) M. Borgatti, L. Breda, R. Cortesi, C. Nastruzzi, A. Romanelli, M. Saviano, N. Bianchi, C. Mischiati, C. Pedone, R. Gambari, Biochem. Pharmacol. 2002, 64, 609-616;
25. c) M. Borgatti, V. Bezzerri, I. Mancini, E. Nicolis, M. C. Dechecchi, I. Lampronti, P. Rizzotti, G. Cabrini, R. Gambari, Biochem. Biophys. Res. Commun. 2007, 357, 977-983;
26. d) V. Bezzerri, M. Borgatti, E. Nicolis, I. Lampronti, M. C. Dechecchi, I. Mancini, P. Rizzotti, R. Gambari, G. Cabrini, Am. J. Respir. Cell Mol. Biol. 2008, 39, 86-96;
27. e) E. Nicolis, I. Lampronti, M. C. Dechecchi, M. Borgatti, A. Tamanini, N. Bianchi, V. Bezzerri, I. Mancini, M. G. Giri, P. Rizzotti, R. Gambari, G. Cabrini, Int. Immunopharmacol. 2008, 8, 1672-1680;
28. f) I. Lampronti, M. T. Khan, M. Borgatti, N. Bianchi, R. Gambari, Evid. Based Complement. Alternat. Med. 2008, 5, 303-312.
29. a) R. K. Sharma, V. Pande, M. J. Ramos, H. K. Rajor, S. Chopra, K. Meguro, J. Inoue, M. Otsuka, Bioorg. Chem. 2005, 34, 67-81;
30. b) R. K. Sharma, S. Chopra, S. D. Sharma, V. Pande, M. J. Ramos, K. Meguro, J. Inoue, M. Otsuka, J. Med. Chem. 2006, 49, 3595-3601.
31. a) B. Shoichet, Nature 2004, 432, 862-865;
32. b) S. Ghosh, A. Nie, J. An, Z. Huang, Curr. Opin. Chem. Biol. 2006, 10, 194-202;
33. c) G. Klebe, Drug Discovery Today 2006, 11, 580-594.
34. L. Piccagli, E. Fabbri, M. Borgatti, V. Bezzerri, I. Mancini, E. Nicolis, M. C. Dechecchi, I. Lampronti, G. Cabrini, R. Gambari, BMC Struct. Biol. 2008, 8, 38.
35. J. J. Irwin, B. K. Shoichet, J. Chem. Inf. Model. 2005, 45, 177-182.
36. a) T. A. Halgren, R. B. Murphy, R. A. Friesner, H. S. Beard, L. L. Frye, W. T. Pollard, J. L. Banks, J. Med. Chem. 2004, 47, 1750-1759;
37. b) R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis, P. S. Shenkin, J. Med. Chem. 2004, 47, 1739-1749.
38. D. A. Pearlman, P. S. Charifson, J. Med. Chem. 2001, 44, 502-511.
39. a) G. Piani, M. Pasquini, G. Pietraperzia, M. Becucci, A. Armentano, E. Castellucci, Chem. Phys. Lett. 2007, 434, 25-30;
40. b) M. Becucci, G. Pietraperzia, M. Pasquini, G. Piani, A. Zoppi, R. Chelli, E. Castellucci, W. Demtroeder, J. Chem. Phys. 2004, 120, 5601;
41. c) B. M. Giuliano, W. Caminati, Angew. Chem. 2005, 117, 609; Angew. Chem. Int. Ed. 2005, 44, 603.
42. a) M. Stevens, C. Pannecouque, E. De Clercq, J. Balzarini, Biochem. Pharmacol. 2006, 71, 1122-1135;
43. b) O. A. Olajide, E. H. Heiss, D. Schachner, C. W. Wright, A. M. Vollmar, V. M. Dirsch, Bioorg. Med. Chem. 2007, 5, 43-49.
44. C. A. Lipinski, J. Pharmacol. Toxicol. Methods 2000, 44, 235-249.
45. W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11225-11236.
46. F. Mohamadi, M. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, G. Caufield, G. Chang, T. W. Hendrickson, C. Still, J. Comput. Chem. 1990, 11, 440-467.
47. Maestro version 7.0.113: A unified interface for all Schrödinger products, developed and marketed by Schrödinger, LLC, New York, NY (USA), 2005, http://www.schrodinger.com (accessed September 18, 2009).
48. M. D. Eldridge, C. W. Murray, T. R. Auton, G. V. Paolini, R. P. Mee, J. Comput.-Aided. Mol. Des. 1997, 11, 425-445.
49. R. A. Friesner, R. B. Murphy, M. P. Repasky, L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz, J. Med. Chem. 2006, 49, 6177-6196.
50. M. Dewar, G. Zoebish, E. Healy, J. Am. Chem. Soc. 1985, 107, 3902-3909.
51. MOPAC2007: J. J. P. Stewart, Stewart Computational Chemistry, Colorado Springs, CO (USA), 2007, http://openmopac.net (accessed September 18, 2009).
52. E. Fibach, N. Bianchi, M. Borgatti, E. Prus, R. Gambari, Blood 2003, 102, 1276-1281.