Specific alkylation of human telomere repeat sequences by a tandem-hairpin motif of pyrrole-imidazole polyamides with indole-seco-CBI

Bioconjugate Chemistry

Volumn 25, Issue 3, 2014, Pages 552-559

  Yamamoto, Makoto ^a   Bando, Toshikazu ^a   Kawamoto, Yusuke ^a   Taylor, Rhys Dylan ^a   Hashiya, Kaori ^a   Sugiyama, Hiroshi ^a,b,c  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; CELL CULTURE; CELL DEATH; CHROMOSOMES; DNA SEQUENCES; ELECTROPHORESIS;

CHLOROMETHYL; DNA FRAGMENT; HIGH RESOLUTION; HUMAN TELOMERE; IMIDAZOL; POLYACRYLAMIDE GEL ELECTROPHORESIS; PYRROLE-IMIDAZOLE POLYAMIDES; REPEAT SEQUENCES; SEQUENCE SELECTIVITY; SYNTHESISED;

POLYCYCLIC AROMATIC HYDROCARBONS;

DNA; DNA FRAGMENT; IMIDAZOLE; INDOLE; POLYAMIDE; PYRROLE; ALKYLATING AGENT; ANTINEOPLASTIC AGENT; IMIDAZOLE DERIVATIVE; INDOLE DERIVATIVE; POLYAMIDE 1-(CHLOROMETHYL)-5-HYDROXYL-1,2-DIHYDRO--3H-BENZ(E)INDOLE CONJUGATE; PYRROLE DERIVATIVE;

ALKYLATION; APOPTOSIS; ARTICLE; CANCER CELL CULTURE; CONTROLLED STUDY; CYTOTOXICITY; DNA DAMAGE; GENETIC PARAMETERS; HUMAN CELL CULTURE; POLYACRYLAMIDE GEL ELECTROPHORESIS; SYNTHESIS; TELOMERE REPEAT SEQUENCE; CELL DEATH; CELL PROLIFERATION; CHEMISTRY; CONFORMATION; DOSE RESPONSE; DRUG EFFECTS; DRUG SCREENING; HUMAN; LONG TERMINAL REPEAT; STRUCTURE ACTIVITY RELATION; TELOMERE; TUMOR CELL CULTURE;

ALKYLATING AGENTS; ALKYLATION; ANTINEOPLASTIC AGENTS; CELL DEATH; CELL PROLIFERATION; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG SCREENING ASSAYS, ANTITUMOR; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; IMIDAZOLES; INDOLES; MOLECULAR CONFORMATION; PYRROLES; STRUCTURE-ACTIVITY RELATIONSHIP; TELOMERE; TERMINAL REPEAT SEQUENCES; TUMOR CELLS, CULTURED;

EID: 84896537117     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc400567m     Document Type: Article

References (51)

1. Olaussen, K. A., Dubrana, K., Domont, J., Spano, J., Sabatier, L., and Soria, J. (2009) Telomeres and telomerase as targets for anticancer drug development Crit. Rev. Oncol. Hematol. 57, 191-214
2. Aubert, G. and Lansdorp, P. M. (2008) Telomere and aging Physiol. Rev. 88, 557-579
3. Lansdorp, P. M. (2009) Telomeres and disease EMBO J. 28, 2532-2540
4. Blackburn, E. H. (2001) Switching and signaling at the telomere Cell 106, 661-673
5. Zakian, V. A. (2012) Telomeres: the beginnings and ends of eukaryotic chromosomes Exp. Cell Res. 318, 1456-1460
6. Smogorzewska, A. and Lange, T. d. (2004) Regulation of telomerase by telomeric proteins Annu. Rev. Biochem. 73, 177-208
7. Dong, C. K., Masutomi, K., and Hahn, W. C. (2005) Telomerase: regulation, function and transformation Crit. Rev. Oncol. Hematol. 54, 85-93
8. Blackburn, E. H. (2010) Telomeres and telomerase: the means to the end Angew. Chem., Int. Ed. 49, 7405-7421
9. Shin-ya, K., Wierzda, K., Matsuo, K., Ohtani, T., Yamada, Y., Furihara, K., Hayakawa, Y., and Seto, H. (2001) Telomestatin, a novel telomerase inhibitor from Streptomyces anulatus J. Am. Chem. Soc. 123, 1262-1263
10. Burger, A. M., Dai, F., Schultes, C. M., Reszka, A. P., Moore, M. J., Double, J. A., and Neidle, S. (2005) The G-quadruplex-interactive molecule BRACO-19 inhibits tumor growth, consistent with telomere targeting and interference with telomerase function Cancer Res. 65, 1489-1496
11. Wheelhouse, R. T., Sun, D., Han, H., Han, F. X., and Hurley, L. H. (1998) Cationic porphyrins as telomerase inhibitors: the interaction of tetra-(N-methyl-4-pyridyl)porphine with quadruplex DNA J. Am. Chem. Soc. 120, 3261-3262
12. Trauger, J. W., Baird, E. E., and Dervan, P. B. (1996) Recognition of DNA by designed ligands at subnanomolar concentrations Nature 382, 559-561
13. Geierstanger, B. H., Mrksich, M., Dervan, P. B., and Wemmer, D. E. (1994) Design of a G.C-specific DNA minor groove-binding peptide Science 266, 646-650
14. Mrksich, M. and Dervan, P. B. (1995) Recognition in the minor groove of DNA at 5′-(A,T)GCGC(A,T)-3′ by a four ring tripeptide dimer. reversal of the specificity of the natural product distamycin J. Am. Chem. Soc. 117, 3325-3332
15. White, S., Szewczyk, J. W., Turner, J. M., Baird, E. E., and Dervan, P. B. (1998) Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands Nature 391, 468-471
16. Dervan, P. B. (2001) Molecular recognition of DNA by small molecules Bioorg. Med. Chem. 9, 2215-2235
17. Dervan, P. B. and Edelson, B. S. (2003) Recognition of the DNA minor groove by pyrrole-imidazole polyamides Curr. Opin. Struct. Biol. 13, 284-299
18. Dervan, P. B., Doss, R. M., and Marques, M. A. (2005) Programmable DNA binding oligomers for control of transcription Curr. Med. Chem. Anti-Cancer Agents 5, 373-387
19. Blackledge, M. S. and Melander, C. (2013) Programmable DNA-binding small molecules Bioorg. Med. Chem. 21, 6101-6114
20. Minoshima, M., Bando, T., Sasaki, S., Shinohara, K., Shimizu, T., Fujimoto, J., and Sugiyama, H. (2007) DNA alkylation by pyrrole-imidazole seco-CBI conjugates with an indole linker: sequence-specific DNA alkylation with 10-base-pair recognition through heterodimer formation J. Am. Chem. Soc. 129, 5384-5390
21. Bando, T., Narita, A., Sasaki, S., and Sugiyama, H. (2005) Specific adenine alkylation by pyrrole-imidazole CBI conjugates J. Am. Chem. Soc. 127, 13890-13895
22. Bando, T., Sasaki, S., Minoshima, M., Dohno, C., Shinohara, K., Narita, A., and Sugiyama, H. (2006) Efficient DNA alkylation by a pyrrole-imidazole CBI conjugate with an indole linker: sequence-specific alkylation with nine-base-pair recognition Bioconjugate Chem. 17, 715-720
23. Minoshima, M., Chou, J. C., Lefebvre, S., Bando, T., Shinohara, K., Gottesfeld, J. M., and Sugiyama, H. (2010) Potent activity against K562 cells by polyamide-seco-CBI conjugates targeting histone H4 genes Bioorg. Med. Chem. 18, 168-174
24. Takagaki, T., Bando, T., Kitano, M., Hashiya, K., Kashiwazaki, G., and Sugiyama, H. (2011) Evaluation of PI polyamide conjugates with eight-base pair recognition and improvement of the aqueous solubility by PEGylation Bioorg. Med. Chem. 19, 5896-5902
25. Kashiwazaki, G., Bando, T., Yoshidome, T., Masui, S., Takagaki, T., Hashiya, K., Pandian, G. N., Yasuoka, J., Akiyoshi, K., and Sugiyama, H. (2012) Synthesis and biological properties of highly sequence-specific-alkylating N-methylpyrrole-N-methylimidazole polyamide conjugates J. Med. Chem. 55, 2057-2066
26. Yoshidome, T., Endo, M., Kashiwazaki, G., Hidaka, K., Bando, T., and Sugiyama, H. (2012) Sequence-selective single-molecule alkylation with a pyrrole-imidazole polyamide visualized in a DNA nanoscaffold J. Am. Chem. Soc. 134, 4654-4660
27. Takagaki, T., Bando, T., and Sugiyama, H. (2012) Synthesis of pyrrole-imidazole polyamide seco-1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e] indole conjugates with a vinyl linker recognizing a 7 bp DNA sequence J. Am. Chem. Soc. 134, 13074-13081
28. Taylor, R. D., Asamitsu, S., Takenaka, T., Yamamoto, M., Hashiya, K., Kawamoto, Y., Bando, T., Nagase, H., and Sugiyama, H. (2014) Sequence-specific DNA Alkylation targeting for Kras codon 13 mutation by pyrrole-imidazole polyamide seco -CBI conjugates Chem.-Eur. J. 20, 1310-1317
29. Sasaki, S., Minoshima, M., Fujimoto, J., Shinohara, K., Bando, T., and Sugiyama, H. (2007) Sequence-specific alkylation by a tandem motif of pyrrole-imidazole CBI conjugate Nucleic Acids Symp. Ser. 51, 265-266
30. Sasaki, S., Bando, T., Minoshima, M., Shinohara, K., and Sugiyama, H. (2008) Sequence-specific alkylation by Y-shaped and tandem hairpin pyrrole-imidazole polyamides Chem.-Eur. J. 14, 864-870
31. Takahashi, R., Bando, T., and Sugiyama, H. (2003) Specific alkylation of human telomere repeats by hairpin pyrrole-imidazole polyamide Bioorg. Med. Chem. 11, 2503-2509
32. Sasaki, S., Bando, T., Minoshima, M., Shimizu, T., Shinohara, K., Takaoka, T., and Sugiyama, H. (2006) Sequence-specific alkylation of double-strand human telomere repeat sequence by pyrrole-imidazole polyamides with indole linkers J. Am. Chem. Soc. 128, 12162-12168
33. Kashiwazaki, G., Bando, T., Shinohara, K., Minoshima, M., Nishijima, S., and Sugiyama, H. (2009) Cooperative alkylation of double-strand human telomere repeat sequences by PI polyamides with 11-base-pair recognition based on a heterotrimeric design Bioorg. Med. Chem. 17, 1393-1397
34. Kashiwazaki, G., Bando, T., Shinohara, K., Minoshima, M., Kumamoto, H., Nishijima, S., and Sugiyama, H. (2010) Alkylation of a human telomere sequence by heterotrimeric chlorambucil PI polyamide conjugates Bioorg. Med. Chem. 18, 2887-2893
35. Herman, D. M., Baird, E. E., and Dervan, P. B. (1999) Tandem hairpin motif for recognition in the minor groove of DNA by pyrrole-imidazole polyamides Chem.-Eur. J. 5, 975-983
36. Kers, I. and Dervan, P. B. (2002) Search for the optimal linker in tandem hairpin polyamides Bioorg. Med. Chem. 10, 3339-3349
37. Schaal, T. D., Mallet, W. G., McMinn, D. L., Nguyen, N. V., Sopko, M. M., Jhon, S., and Parekh, B. S. (2003) Inhibition of human papilloma virus E2 DNA binding protein by covalently linked polyamides Nucleic Acids Res. 31, 1282-91
38. Maeshima, K., Janssen, S., and Laemmli, U. K. (2001) Specific targeting of insect and vertebrate telomeres with pyrrole and imidazole polyamides EMBO J. 20, 3218-3228
39. Kawamoto, Y., Bando, T., Kamada, F., Li, Y., Hashiya, K., Maeshima, K., and Sugiyama, H. (2013) Development of a new method for synthesis of tandem hairpin pyrrole-imidazole polyamide probes targeting human telomeres J. Am. Chem. Soc. 135, 16468-16477
40. Boger, D. L., Ishizaki, T., Kitos, P. A., and Suntornwat, O. (1990) Synthesis of N-(tert-butyloxycarbonyl)-CBI, CBI, CBI-CDPI1, and CBI-CDPI2: enhanced functional analogs of CC-1065 incorporating the 1,2,9,9a- tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI) left-hand subunit J. Org. Chem. 55, 5823-5832
41. Boger, D. L., Yun, W. Y., and Teegarden, B. R. (1992) An improved synthesis of 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI): a simplified analog of the CC-1065 alkylation subunit J. Org. Chem. 57, 2873-2876
42. Boger, D. L. and McKie, J. A. (1995) An efficient synthesis of 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one CBI: An enhanced and simplified analog of the CC-1065 and duocarmycin alkylation subunits J. Org. Chem. 60, 1271-1275
43. Kastrinsky, D. B. and Boger, D. L. (2004) Effective asymmetric synthesis of 1,2,9,9a-tetrahydrocyclopropa[c]benzo[e]indol-4-one (CBI) J. Org. Chem. 69, 2284-2289
44. Bando, T. and Sugiyama, H. (2006) Synthesis and biological properties of sequence-specific DNA-alkylating pyrrole-imidazole polyamides Acc. Chem. Res. 39, 935-944
45. Promokine; Apoptotic/Necrotic/Healthy Cells Detection Kit (http://www.promokine.info/fileadmin/PDFs/All-PDFs/PK-CA707-30018.pdf)
46. Janssen, S., Cuvier, O., Muller, M., and Laemmli, U. K. (2000) Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster Mol. Cell 6, 1013-1024
47. Belitsky, J. M., Nguyen, D. H., Wurtz, N. R., and Dervan, P. B. (2002) Solid-phase synthesis of DNA binding polyamides on oxime resin Bioorg. Med. Chem. 10, 2767-2774
48. Sugiyama, H., Hosoda, M., Saito, I., Asai, A., and Saito, H. (1990) Covalent alkylation of DNA with Duocarmycin A. Identification of abasic site structure Tetrahedron Lett. 31, 7179-7200
49. Boger, D. L. and Munk, S. A. (1992) DNA alkylation properties of enhanced functional analogs of CC-1065 incorporating the 1,2,9,9a- tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) alkylation subunit J. Am. Chem. Soc. 114, 5487-5496
50. Boger, D. L., Johnson, D. S., and Yun, W. (1994) (+)- and ent-(-)-Duocarmycin SA and (+)- and ent-(-)-N-BOC-DSA DNA alkylation properties. Alkylation site models that accommodate the offset AT-rich adenine N3 alkylation selectivity of the enantiomeric agents J. Am. Chem. Soc. 116, 1635-1656
51. Boger, D. L. and Johnson, D. S. (1996) CC-1065 and the duocarmycins: Understanding their biological function through mechanistic studies Angew. Chem., Int. Ed. Engl. 35, 1438-1474