Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer

Biochimie

Volumn 93, Issue 6, 2011, Pages 1055-1064

  Chan, Daniel Shiu Hin ^a   Yang, Hui ^a   Kwan, Maria Hiu Tung ^a   Cheng, Zhen ^a   Lee, Paul ^a   Bai, Li Ping ^a   Jiang, Zhi Hong ^a   Wong, Chun Yuen ^b   Fong, Wang Fun ^a   Leung, Chung Hang ^a   Ma, Dik Lung ^a  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

c myc G quadruplex; FDA approved drug; Methylene blue; Repurposing; Structure based optimization

Indexed keywords

3,7 BIS [[3 (4 BROMOPHENYL)PROPYL](METHYL)AMINO]PHENOTHIAZIN 5 IUM IODIDE; 3,7 BIS[(4 BROMOPHENYLETHYL)(METHYL)AMINO]PHENOTHIAZIN 5 IUM IODIDE; CRYSTAL VIOLET; GUANINE QUADRUPLEX; METHYLENE BLUE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CYTOTOXICITY; DRUG APPROVAL; DRUG DESIGN; DRUG SCREENING; DRUG STRUCTURE; FOOD AND DRUG ADMINISTRATION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MASS SPECTROMETRY; MOLECULAR DOCKING; MOLECULAR MODEL; ONCOGENE C MYC; ULTRAVIOLET SPECTROSCOPY;

ANTINEOPLASTIC AGENTS; CELL SURVIVAL; DRUG APPROVAL; G-QUADRUPLEXES; GENE EXPRESSION REGULATION; GENES, MYC; GENES, REPORTER; HELA CELLS; HEP G2 CELLS; HUMANS; LUCIFERASES; METHYLENE BLUE; MOLECULAR DYNAMICS SIMULATION; PROMOTER REGIONS, GENETIC; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79955065928     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2011.02.013     Document Type: Article

References (58)

1. T. Simonsson G-quadruplex DNA structures - variations on a theme Biol. Chem. 382 2001 621 628 (Pubitemid 32472172)
2. J.-L. Mergny, and C. Helene G-quadruplex DNA: a target for drug design Nat. Med 4 1998 1366 1367 (Pubitemid 28553455)
3. J.L. Huppert, and S. Balasubramanian G-quadruplexes in promoters throughout the human genome Nucleic Acids Res. 35 2007 406 413 (Pubitemid 46232058)
4. L.H. Hurley, R.T. Wheelhouse, D. Sun, S.M. Kerwin, M. Salazar, O.Y. Fedoroff, F.X. Han, H. Han, E. Izbicka, and H.D.D. Von G-quadruplexes as targets for drug design Pharmacol. Ther. 85 2000 141 158 (Pubitemid 30160784)
5. S.M. Kerwin G-quadruplex DNA as a target for drug design Curr. Pharm. Des. 6 2000 441 471 (Pubitemid 30396406)
6. T.-M. Ou, Y.-J. Lu, J.-H. Tan, Z.-S. Huang, K.-Y. Wong, and L.-Q. Gu G-quadruplexes: targets in anticancer drug design Chem. Med. Chem. 3 2008 690 713
7. D. Monchaud, and M.-P. Teulade-Fichou A hitchhiker's guide to G-quadruplex ligands Org. Biomol. Chem. 6 2008 627 636 (Pubitemid 351972601)
8. S. Balasubramanian, and S. Neidle G-quadruplex nucleic acids as therapeutic targets Curr. Opin. Chem. Biol. 13 2009 345 353
9. C.A. De, L. Lacroix, C. Douarre, N. Temime-Smaali, C. Trentesaux, J.-F. Riou, and J.-L. Mergny Targeting telomeres and telomerase Biochimie 90 2008 131 155 (Pubitemid 350245369)
10. S. Neidle Human telomeric G-quadruplex: the current status of telomeric G-quadruplexes as therapeutic targets in human cancer FEBS J. 277 2010 1118 1125
11. D. Drygin, A. Siddiqui-Jain, S. O'Brien, M. Schwaebe, A. Lin, J. Bliesath, C.B. Ho, C. Proffitt, K. Trent, J.P. Whitten, J.K.C. Lim, H.D. Von, K. Anderes, and W.G. Rice Anticancer activity of CX-3543: a direct inhibitor of rRNA biogenesis Cancer Res. 69 2009 7653 7661
12. C.V. Dang, K.A. O'Donnell, K.I. Zeller, T. Nguyen, R.C. Osthus, and F. Li The c-Myc target gene network Semin. Cancer Biol. 16 2006 253 264 (Pubitemid 44311039)
13. K.I. Zeller, X. Zhao, C.W.H. Lee, K.P. Chiu, F. Yao, J.T. Yustein, H.S. Ooi, Y.L. Orlov, A. Shahab, H. Choong, Y. Fu, Z. Weng, V.A. Kuznetsov, W.-K. Sung, Y. Ruan, C.V. Dang, and C.-L. Wei Global mapping of c-Myc binding sites and target gene networks in human B cells Proc. Natl. Acad. Sci. U S A 103 2006 17834 17839 (Pubitemid 44852246)
14. E.H. Postel, S.E. Mango, and S.J. Flint A nuclease-hypersensitive element of the human c-myc promoter interacts with a transcription initiation factor Mol. Cell. Biol. 9 1989 5123 5133 (Pubitemid 19275983)
15. T.L. Davis, A.B. Firulli, and A.J. Kinniburgh Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene Proc. Natl. Acad. Sci. U S A 86 1989 9682 9686 (Pubitemid 20030697)
16. A. Siddiqui-Jain, C.L. Grand, D.J. Bearss, and L.H. Hurley Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription Proc. Natl. Acad. Sci. U S A 99 2002 11593 11598 (Pubitemid 34994444)
17. C.L. Grand, H. Han, R.M. Munoz, S. Weitman, H.D.D. Von, L.H. Hurley, and D.J. Bearss The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo Mol. Cancer Ther. 1 2002 565 573
18. J. Seenisamy, S. Bashyam, V. Gokhale, H. Vankayalapati, D. Sun, A. Siddiqui-Jain, N. Streiner, K. Shinya, E. White, W.D. Wilson, and L.H. Hurley Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure J. Am. Chem. Soc. 127 2005 2944 2959 (Pubitemid 40349873)
19. T.-M. Ou, Y.-J. Lu, C. Zhang, Z.-S. Huang, X.-D. Wang, J.-H. Tan, Y. Chen, D.-L. Ma, K.-Y. Wong, J.C.-O. Tang, A.S.-C. Chan, and L.-Q. Gu Stabilization of G-Quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives J. Med. Chem. 50 2007 1465 1474 (Pubitemid 46566333)
20. P. Wu, D.-L. Ma, C.-H. Leung, S.-C. Yan, N. Zhu, R. Abagyan, and C.-M. Che Stabilization of G-Quadruplex DNA with platinum(ii) schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression Chemistry 15 2009 13008 13021
21. H.-M. Lee, D.S.-H. Chan, F. Yang, H.-Y. Lam, S.-C. Yan, C.-M. Che, D.-L. Ma, and C.-H. Leung Identification of natural product fonsecin B as a stabilizing ligand of c-myc G-quadruplex DNA by high-throughput virtual screening Chem. Commun. 46 2010 4680 4682
22. D.W. Carley Drug repurposing: identify, develop and commercialize new uses for existing or abandoned drugs. Part II Idrugs 8 2005 310 313
23. C.R. Chong, and D.J. Sullivan Jr. New uses for old drugs Nature 448 2007 645 646 (Pubitemid 47236844)
24. P. Schneider, Y. Tanrikulu, and G. Schneider Self-organizing maps in drug discovery: compound library design, scaffold-hopping, repurposing Curr. Med. Chem. 16 2009 258 266
25. J.A. DiMasi, R.W. Hansen, and H.G. Grabowski The price of innovation: new estimates of drug development costs J. Health Econ. 22 2003 151 185 (Pubitemid 36279392)
26. I.D. Kuntz Structure-based strategies for drug design and discovery Science 257 1992 1078 1082
27. J. Bajorath Integration of virtual and high-throughput screening Nat. Rev. Drug Discov. 1 2002 882 894 (Pubitemid 37361583)
28. B.K. Shoichet Virtual screening of chemical libraries Nature 432 2004 862 865 (Pubitemid 40037142)
29. D.S.-H. Chan, H.-M. Lee, F. Yang, C.-M. Che, C.C.L. Wong, R. Abagyan, C.-H. Leung, and D.-L. Ma Structure-based discovery of natural product-Like TNF-? inhibitors Angewandte Chemie 49 2010 2860 2864
30. C.-H. Leung, D.S.-H. Chan, H. Yang, R. Abagyan, and D.-L. Ma A natural product-like inhibitor of NEDD8-activating enzyme Chem. Commun 47 2011 2511 2513
31. C.-H. Leung, D.S.-H. Chan, M.H.-T. Kwan, Z. Cheng, D.-L. Ma, Structure-based repurposing of FDA-approved drugs as TNF-α inhibitors, ChemMedChem.,(2011) DOI:10.1002/cmdc.201100016.
32. W.H. Bisson, A.V. Cheltsov, N. Bruey-Sedano, B. Lin, J. Chen, N. Goldberger, L.T. May, A. Christopoulos, J.T. Dalton, P.M. Sexton, X.K. Zhang, and R. Abagyan Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs Proc. Natl. Acad. Sci. U S A 104 2007 11927 11932 (Pubitemid 47185607)
33. J. Sambrook, E.F. Fritsch, and T.E. Maniatis Molecular Cloning, a Laboratory Manual second ed. 1989 E.3 and E.10
34. G. Felsenfeld, and S.Z. Hirschman A neighbor-interaction analysis of the hypochromism and spectra of DNA J. Mol. Biol. 13 1965 407 427
35. K. Suntharalingam, A.J.P. White, and R. Vilar Two metals are better than one: investigations on the interactions between dinuclear metal complexes and quadruplex DNA Inorg. Chem. 49 2010 8371 8380
36. C.V. Kumar, and E.H. Asuncion DNA binding studies and site selective fluorescence sensitization of an anthryl probe J. Am. Chem. Soc. 115 1993 8547 8553
37. O.M. New, and D. Dolphin Design and synthesis of novel phenothiazinium photosensitizer derivatives Eur. J. Org. Chem. 2009 2675 2686
38. T.B. Lanni, K.L. Greene, C.N. Kolz, K.S. Para, M. Visnick, J.L. Mobley, D.T. Dudley, T.J. Baginski, and M.B. Liimatta Design and synthesis of phenethyl benzo[1,4]oxazine-3-ones as potent inhibitors of PI3Kinaseγ Bioorg. Med. Chem. Lett. 17 2007 756 760 (Pubitemid 46108555)
39. A.R. Thornton, V.I. Martin, and S.B. Blakey π-Nucleophile traps for metallonitrene/alkyne cascade reactions: a versatile process for the synthesis of α-aminocyclopropanes and β-aminostyrenes J. Am. Chem. Soc. 131 2009 2434 2435
40. A.H. Lewin, H.A. Navarro, and S.W. Mascarella Structure-activity correlations for β-phenethylamines at human trace amine receptor 1 Bioorg. Med. Chem. 16 2008 7415 7423
41. L. Strekowski, D.F. Hou, R.L. Wydra, and R.F. Schinazi A synthetic route to 3-(dialkylamino)phenothiazin-5-ium salts and 3,7-disubstituted derivatives containing two different amino groups J. Heterocycl. Chem. 30 1993 1693 1695
42. M. Totrov, and R. Abagyan Flexible protein-ligand docking by global energy optimization in internal coordinates Proteins 1997 215 220 Suppl. 1 (Pubitemid 28090502)
43. D.-L. Ma, T.-S. Lai, F.-Y. Chan, W.-H. Chung, R. Abagyan, Y.-C. Leung, and K.-Y. Wong Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking ChemMedChem. 3 2008 881 884
44. G.N. Parkinson, M.P.H. Lee, and S. Neidle Crystal structure of parallel quadruplexes from human telomeric DNA Nature 417 2002 876 880 (Pubitemid 34670337)
45. A. Ambrus, D. Chen, J. Dai, R.A. Jones, and D. Yang Solution structure of the biologically relevant G-quadruplex element in the human c-myc promoter. Implications for G-quadruplex stabilization Biochemistry 44 2005 2048 2058 (Pubitemid 40227475)
46. S.L. Narsapur, and G.J. Naylor Methylene blue. A possible treatment for manic depressive psychosis J. Affect. Disord. 5 1983 155 161 (Pubitemid 13120409)
47. J. Clutton-Brock Two cases of poisoning by contamination of nitrous oxide with higher oxides of nitrogen during anaesthesia Br. J. Anaesth. 39 1967 388 392
48. J. Clifton 2nd, and J.B. Leikin Methylene blue Am. J. Ther. 10 2003 289 291
49. M. Wainwright, and L. Amaral The phenothiazinium chromophore and the evolution of antimalarial drugs Trop. Med. Int. Health 10 2005 501 511 (Pubitemid 40806655)
50. J.P. Tardivo, G.A. Del, d.O.C. Santos, D.S. Gabrielli, H.C. Junqueira, D.B. Tada, D. Severino, R.d.F. Turchiello, and M.S. Baptista Methylene blue in photodynamic therapy: from basic mechanisms to clinical applications Photodiagnosis Photodyn. Ther. 2 2005 175 191 (Pubitemid 41751085)
51. H. Sun, J. Xiang, Y. Zhang, G. Xu, L. Xu, and Y. Tang Spectroscopic studies of the interaction between methylene blue and G-quadruplex Chin. Sci. Bull. 51 2006 1687 1692 (Pubitemid 44432151)
52. P. Ragazzon, and J.B. Chaires Use of competition dialysis in the discovery of G-quadruplex selective ligands Methods 43 2007 313 323 (Pubitemid 47633211)
53. J. Seenisamy, E.M. Rezler, T.J. Powell, D. Tye, V. Gokhale, C.S. Joshi, A. Siddiqui-Jain, and L.H. Hurley The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4 J. Am. Chem. Soc. 126 2004 8702 8709 (Pubitemid 38955732)
54. Y. Wang, and A. Zhou Spectroscopic studies on the binding of methylene blue with DNA by means of cyclodextrin supramolecular systems J. Photochem. Photobiol. A Chem. 190 2007 121 127
55. M. Hossain, P. Giri, and G.S. Kumar DNA intercalation by quinacrine and methylene blue: a comparative binding and thermodynamic characterization study DNA Cell Biol. 27 2008 81 90 (Pubitemid 351271515)
56. L.-P. Bai, M. Hagihara, Z.-H. Jiang, and K. Nakatani Ligand binding to tandem G quadruplexes from human telomeric DNA ChemBioChem 9 2008 2583 2587
57. T.-C. He, A.B. Sparks, C. Rago, H. Hermeking, L. Zawel, C.L.T. Da, P.J. Morin, B. Vogelstein, and K.W. Kinzler Identification of c-MYC as a target of the APC pathway Science (Washington, D. C.) 281 1998 1509 1512 (Pubitemid 28425575)
58. R.K. Thakur, P. Kumar, K. Halder, A. Verma, A. Kar, J.L. Parent, R. Basundra, A. Kumar, and S. Chowdhury Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression Nucleic Acids Res. 37 2009 172 183