Psoralen derivatives as inhibitors of NF-κB/DNA interaction: Synthesis, molecular modeling, 3D-QSAR, and biological evaluation

Journal of Medicinal Chemistry

Volumn 56, Issue 5, 2013, Pages 1830-1842

  Marzaro, Giovanni ^a   Guiotto, Adriano ^a   Borgatti, Monica ^b   Finotti, Alessia ^b   Gambari, Roberto ^b   Breveglieri, Giulia ^b   Chilin, Adriana ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF FERRARA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

I KAPPA B; PSORALEN DERIVATIVE;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DRUG DNA INTERACTION; DRUG SCREENING; DRUG SYNTHESIS; MOLECULAR DOCKING; MOLECULAR MODEL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ANTI-INFLAMMATORY AGENTS; BINDING SITES; CYSTIC FIBROSIS; DNA; INHIBITORY CONCENTRATION 50; MOLECULAR DYNAMICS SIMULATION; NF-KAPPA B; PROTEIN BINDING; PSORALENS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SURFACE PLASMON RESONANCE;

EID: 84875144080     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm3009647     Document Type: Article

References (56)

1. Hayden, M. S.; Ghosh, S. NF-kappaB, the first quarter-century: remarkable progress and outstanding questions Genes Dev. 2012, 26, 203-234
2. Brown, K. D.; Claudio, E.; Siebenlist, U. The roles of the classical and alternative nuclear factor-kappaB pathways: potential implications for autoimmunity and rheumatoid arthritis Arthritis Res. Ther. 2008, 10, 212
3. Siebenlist, U.; Franzoso, G.; Brown, K. Structure, regulation and function of NF-kappa B Annu. Rev. Cell Biol. 1994, 10, 405-455
4. Perkins, N. D. The diverse and complex roles of NF-kappaB subunits in cancer Nat. Rev. Cancer 2012, 12, 121-132
5. Victoriano, A. F.; Okamoto, T. Transcriptional control of HIV replication by multiple modulators and their implication for a novel antiviral therapy AIDS Res. Hum. Retroviruses 2012, 28, 125-138
6. Batra, S.; Balamayooran, G.; Sahoo, M. K. Nuclear factor-kappaB: a key regulator in health and disease of lungs Arch. Immunol. Ther. Exp. 2011, 59, 335-351
7. Ben-Neriah, Y.; Karin, M. Inflammation meets cancer, with NF-kappaB as the matchmaker Nat. Immunol. 2011, 12, 715-723
8. Black, H. R.; Yankaskas, J. R.; Johnson, L. G.; Noah, T. L. Interleukin-8 production by cystic fibrosis nasal epithelial cells after tumor necrosis factor-alpha and respiratory syncytial virus stimulation Am. J. Respir. Cell Mol. Biol. 1998, 19, 210-215 (Pubitemid 128354183)
9. Jones, A. M.; Martin, L.; Bright-Thomas, R. J.; Dodd, M. E.; McDowell, A.; Moffitt, K. L.; Elborn, J. S.; Webb, A. K. Inflammatory markers in cystic fibrosis patients with transmissible Pseudomonas aeruginosa Eur. Respir. J. 2003, 22, 503-506 (Pubitemid 37098933)
10. Bezzerri, V.; Borgatti, M.; Nicolis, E.; Lampronti, I.; Dechecchi, M. C.; Mancini, I.; Rizzotti, P.; Gambari, R.; Cabrini, G. Transcription factor oligodeoxynucleotides to NF-kappaB inhibit transcription of IL-8 in bronchial cells Am. J. Respir. Cell Mol. Biol. 2008, 39, 86-96 (Pubitemid 351883962)
11. Sadikot, R. T.; Zeng, H.; Joo, M.; Everhart, M. B.; Sherrill, T. P.; Li, B.; Cheng, D. S.; Yull, F. E.; Christman, J. W.; Blackwell, T. S. Targeted immunomodulation of the NF-kappaB pathway in airway epithelium impacts host defense against Pseudomonas aeruginosa J. Immunol. 2006, 176, 4923-4930
12. Bezzerri, V.; Borgatti, M.; Finotti, A.; Tamanini, A.; Gambari, R.; Cabrini, G. Mapping the transcriptional machinery of the IL-8 gene in human bronchial epithelial cells J. Immunol. 2011, 187, 6069-6081
13. Tamanini, A.; Borgatti, M.; Finotti, A.; Piccagli, L.; Bezzerri, V.; Favia, M.; Guerra, L.; Lampronti, I.; Bianchi, N.; Dall'Acqua, F.; Vedaldi, D.; Salvador, A.; Fabbri, E.; Mancini, I.; Nicolis, E.; Casavola, V.; Cabrini, G.; Gambari, R. Trimethylangelicin reduces IL-8 transcription and potentiates CFTR function Am. J. Physiol.: Lung Cell. Mol. Physiol. 2011, 300, L380-L390
14. Nicolis, E.; Lampronti, I.; Dechecchi, M. C.; Borgatti, M.; Tamanini, A.; Bianchi, N.; Bezzerri, V.; Mancini, I.; Giri, M. G.; Rizzotti, P.; Gambari, R.; Cabrini, G. Pyrogallol, an active compound from the medicinal plant Emblica officinalis, regulates expression of pro-inflammatory genes in bronchial epithelial cells Int. Immunopharmacol. 2008, 8, 1672-1680
15. Piccagli, L.; Fabbri, E.; Borgatti, M.; Bezzerri, V.; Mancini, I.; Nicolis, E.; Dechecchi, M. C.; Lampronti, I.; Cabrini, G.; Gambari, R. Docking of molecules identified in bioactive medicinal plants extracts into the p50 NF-kappaB transcription factor: correlation with inhibition of NF-kappaB/DNA interactions and inhibitory effects on IL-8 gene expression BMC Struct. Biol. 2008, 8, 38
16. Nicolis, E.; Lampronti, I.; Dechecchi, M. C.; Borgatti, M.; Tamanini, A.; Bezzerri, V.; Bianchi, N.; Mazzon, M.; Mancini, I.; Giri, M. G.; Rizzotti, P.; Gambari, R.; Cabrini, G. Modulation of expression of IL-8 gene in bronchial epithelial cells by 5-methoxypsoralen Int. Immunopharmacol. 2009, 9, 1411-1422
17. Piccagli, L.; Fabbri, E.; Borgatti, M.; Bianchi, N.; Bezzerri, V.; Mancini, I.; Nicolis, E.; Dechecchi, C. M.; Lampronti, I.; Cabrini, G.; Gambari, R. Virtual screening against p50 NF-kappaB transcription factor for the identification of inhibitors of the NF-kappaB-DNA interaction and expression of NF-kappaB upregulated genes ChemMedChem 2009, 4, 2024-2033
18. Piccagli, L.; Borgatti, M.; Nicolis, E.; Bianchi, N.; Mancini, I.; Lampronti, I.; Vevaldi, D.; Dall'Acqua, F.; Cabrini, G.; Gambari, R. Virtual screening against nuclear factor kappaB (NF-kappaB) of a focus library: identification of bioactive furocoumarin derivatives inhibiting NF-kappaB dependent biological functions involved in cystic fibrosis Bioorg. Med. Chem. 2010, 18, 8341-8349
19. Borgatti, M.; Chilin, A.; Piccagli, L.; Lampronti, I.; Bianchi, N.; Mancini, I.; Marzaro, G.; dall'Acqua, F.; Guiotto, A.; Gambari, R. Development of a novel furocoumarin derivative inhibiting NF-kappaB dependent biological functions: design, synthesis and biological effects Eur. J. Med. Chem. 2011, 46, 4870-4877
20. Ghosh, G.; van Duyne, G.; Ghosh, S.; Sigler, P. B. Structure of NF-kappa B p50 homodimer bound to a kappa B site Nature 1995, 373, 303-310
21. Iwai, H.; Zuger, S. Protein ligation: applications in NMR studies of proteins Biotechnol. Genet. Eng. Rev. 2007, 24, 129-145 (Pubitemid 350032946)
22. Hetenyi, C.; van der Spoel, D. Efficient docking of peptides to proteins without prior knowledge of the binding site Protein Sci. 2002, 11, 1729-1737 (Pubitemid 34663553)
23. Hetenyi, C.; van der Spoel, D. Blind docking of drug-sized compounds to proteins with up to a thousand residues FEBS Lett. 2006, 580, 1447-1450 (Pubitemid 43222013)
24. Verma, J.; Khedkar, V. M.; Coutinho, E. C. 3D-QSAR in drug design-a review Curr. Top. Med. Chem. 2010, 10, 95-115
25. Talele, T. T.; Kulkarni, V. M. Three-dimensional quantitative structure-activity relationship (QSAR) and receptor mapping of cytochrome P-450(14 alpha DM) inhibiting azole antifungal agents J. Chem. Inf. Comput. Sci. 1999, 39, 204-210 (Pubitemid 129538905)
26. Walter, D. E.; Muhammad, T. D. Genetically Evolved Receptor Models (GERM): A Procedure for Construction of Atomic-Level Receptor Site Models in the Absence of a Receptor Crystal Structure. In Genetic Algorithms in Molecular Modeling; Devillers, J., Ed.; Academic Press: London, 1996; pp 193-210.
27. Veselovskaya, M. V.; Shilin, S. V.; Garazd, M. M.; Khilya, V. P. Modified coumarins. 9. Synthesis of amino-acid derivatives of 3-(2,3,5-trimethyl-7- oxofuro[3,2- g ]chromen-6-yl)propanoic acid Chem. Nat. Compd. 2003, 39, 177-181
28. Nagorichna, I. V.; Dubovik, I. P.; Garazd, M. M.; Khilya, V. P. Modified coumarins. 10. Synthesis of substituted 2-(7-oxofuro[3,2- g ]chromen-6-yl)acetic acids Chem. Nat. Compd. 2003, 39, 253-261
29. Sharma, R. K.; Chopra, S.; Sharma, S. D.; Pande, V.; Ramos, M. J.; Meguro, K.; Inoue, J.; Otsuka, M. Biological evaluation, chelation, and molecular modeling studies of novel metal-chelating inhibitors of NF-kappaB-DNA binding: structure activity relationships J. Med. Chem. 2006, 49, 3595-3601 (Pubitemid 43902464)
30. Hearst, J. E. Psoralen photochemistry and nucleic acid structure J. Invest. Dermatol. 1981, 77, 39-44 (Pubitemid 12229298)
31. Nurminen, E. M.; Pihlavisto, M.; Lazar, L.; Szakonyi, Z.; Pentikainen, U.; Fulop, F.; Pentikainen, O. T. Synthesis, in vitro activity, and three-dimensional quantitative structure-activity relationship of novel hydrazine inhibitors of human vascular adhesion protein-1 J. Med. Chem. 2010, 53, 6301-6315
32. Discovery Studio Modeling Environment, release 3.1; Accelrys Software Inc.: San Diego, CA, 2005-2011.
33. Tosco, P.; Balle, T. Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields J. Mol. Model. 2011, 17, 201-208
34. Lipkowitz, K. B.; Boyd, D. B. Reviews in Computational Chemistry; John Wiley & Sons, Hoboken, NJ, 1997.
35. Gramatica, P. Principles of QSAR models validation: internal and external QSAR Comb. Sci. 2007, 26, 794-801
36. Borgatti, M.; Mancini, I.; Bianchi, N.; Guerrini, A.; Lampronti, I.; Rossi, D.; Sacchetti, G.; Gambari, R. Bergamot (Citrus bergamia Risso) fruit extracts and identified components alter expression of interleukin 8 gene in cystic fibrosis bronchial epithelial cell lines BMC Biochem. 2011, 12, 15
37. Boyce, B. F.; Yao, Z.; Xing, L. Functions of nuclear factor kappaB in bone Ann. N.Y. Acad. Sci. 2010, 1192, 367-375
38. Piva, R.; Penolazzi, L.; Borgatti, M.; Lampronti, I.; Lambertini, E.; Torreggiani, E.; Gambari, R. Apoptosis of human primary osteoclasts treated with molecules targeting nuclear factor-kappaB Ann. N.Y. Acad. Sci. 2009, 1171, 448-456
39. Atkinson, G. P.; Nozell, S. E.; Benveniste, E. T. NF-kappaB and STAT3 signaling in glioma: targets for future therapies Expert Rev. Neurother. 2010, 10, 575-586
40. Wong, K. K.; Jacks, T.; Dranoff, G. NF-kappaB fans the flames of lung carcinogenesis Cancer Prev. Res. 2010, 3, 403-405
41. Saadane, A.; Masters, S.; DiDonato, J.; Li, J.; Berger, M. Parthenolide inhibits IkappaB kinase, NF-kappaB activation, and inflammatory response in cystic fibrosis cells and mice Am. J. Respir. Cell Mol. Biol. 2007, 36, 728-736 (Pubitemid 46871428)
42. Cigana, C.; Nicolis, E.; Pasetto, M.; Assael, B. M.; Melotti, P. Anti-inflammatory effects of azithromycin in cystic fibrosis airway epithelial cells Biochem. Biophys. Res. Commun. 2006, 350, 977-982 (Pubitemid 44584188)
43. Garazd, M. M.; Garazd, Ia, L.; Ogorodniichuk, A. S.; Khilia, V. P. Synthesis of modified psoralen analogues Bioorg. Khim. 2004, 30, 324-333
44. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25, 1605-1612
45. Marvin, version 5.5.0.1, Program B; ChemAxon: Budapest, Hungary; www.chemaxon.com/products.
46. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: an open chemical toolbox J. Cheminf. 2011, 3, 33
47. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility J. Comput. Chem. 2009, 30, 2785-2791
48. Granovsky, A. A. Firefly, version 7.1.G; http://classic.chem.msu.su/gran/ firefly/index.html.
49. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. General atomic and molecular electronic structure system J. Comput. Chem. 1993, 14, 1347-1363
50. Pastor, M.; Cruciani, G.; Clementi, S. Smart region definition: a new way to improve the predictive ability and interpretability of three-dimensional quantitative structure-activity relationships J. Med. Chem. 1997, 40, 1455-1464 (Pubitemid 27200762)
51. Baroni, M.; Clementi, S.; Cruciani, G.; Costantino, G.; Riganelli, D.; Oberrauch, E. Predictive ability of regression models. Part II: Selection of the best predictive PLS model J. Chemom. 1992, 6, 347-356
52. Borgatti, M.; Bezzerri, V.; Mancini, I.; Nicolis, E.; Dechecchi, M. C.; Lampronti, I.; Rizzotti, P.; Cabrini, G.; Gambari, R. Induction of IL-6 gene expression in a CF bronchial epithelial cell line by Pseudomonas aeruginosa is dependent on transcription factors belonging to the Sp1 superfamily Biochem. Biophys. Res. Commun. 2007, 357, 977-983 (Pubitemid 46693668)
53. Gambari, R.; Feriotto, G.; Rutigliano, C.; Bianchi, N.; Mischiati, C. Biospecific interaction analysis (BIA) of low-molecular weight DNA-binding drugs J. Pharmacol. Exp. Ther. 2000, 294, 370-377 (Pubitemid 30434710)
54. Feriotto, G.; Corradini, R.; Sforza, S.; Bianchi, N.; Mischiati, C.; Marchelli, R.; Gambari, R. Peptide nucleic acids and biosensor technology for real-time detection of the cystic fibrosis W1282X mutation by surface plasmon resonance Lab. Invest. 2001, 81, 1415-1427 (Pubitemid 32980164)
55. Dechecchi, M. C.; Nicolis, E.; Bezzerri, V.; Vella, A.; Colombatti, M.; Assael, B. M.; Mettey, Y.; Borgatti, M.; Mancini, I.; Gambari, R.; Becq, F.; Cabrini, G. MPB-07 reduces the inflammatory response to Pseudomonas aeruginosa in cystic fibrosis bronchial cells Am. J. Respir. Cell Mol. Biol. 2007, 36, 615-624 (Pubitemid 46676721)
56. Borgatti, M.; Mazzitelli, S.; Breveglieri, G.; Gambari, R.; Nastruzzi, C. Induction by TNF-alpha of IL-6 and IL-8 in cystic fibrosis bronchial IB3-1 epithelial cells encapsulated in alginate microbeads J. Biomed. Biotechnol. 2010, 2010