Investigation of the relative cellular permeability of DNA-binding pyrrole-imidazole polyamides

Journal of Medicinal Chemistry

Volumn 52, Issue 15, 2009, Pages 4604-4612

  Liu, Bo ^a   Kodadek, Thomas ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ALANINE 3,3' DIAMINO N METHYLDIPROPYLAMINE; DEXAMETHASONE DERIVATIVE; DNA; ETHYLENEDIAMINE; GLUCOCORTICOID RECEPTOR; HEAT SHOCK PROTEIN 90; HYBRID PROTEIN; IMIDAZOLE DERIVATIVE; ISOTHIOCYANIC ACID DERIVATIVE; LUCIFERASE; POLYAMIDE; PROPYLAMINE; PYRROLE DERIVATIVE; TRANSCRIPTION FACTOR GAL4; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CARBON NUCLEAR MAGNETIC RESONANCE; CELL MEMBRANE PERMEABILITY; CHEMICAL STRUCTURE; CONTROLLED STUDY; DNA BINDING; ELECTROSPRAY MASS SPECTROMETRY; ENZYME ASSAY; HELA CELL; HERPES SIMPLEX VIRUS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; LIGAND BINDING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PROTEIN DNA INTERACTION; PROTON NUCLEAR MAGNETIC RESONANCE; RECEPTOR BINDING; YEAST;

DEXAMETHASONE; DNA; FEMALE; HELA CELLS; HUMANS; IMIDAZOLES; NYLONS; PERMEABILITY; PYRROLES; RECEPTORS, GLUCOCORTICOID; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 68549098042     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9002999     Document Type: Article

References (29)

1. Ptashne, M.; Gann, A. Transcriptional activation by recruitment. Nature 1997, 386, 569-577.
2. Denison, C.; Kodadek, T. Small-molecule-based strategies for controlling gene expression. Chem. Biol. 1998, 5, R129-145.
3. Koh, J. T.; Zheng, J. The new biomimetic chemistry: artificial transcription factors. ACS Chem. Biol. 2007, 2, 599-601.
4. Majmudar, C. Y.; Mapp, A. K. Chemical approaches to transcriptional regulation. Curr. Opin. Chem. Biol. 2005, 9, 467-474.
5. Ansari, A. Z.; Mapp, A. K. Modular design of artificial transcription factors. Curr. Opin. Chem. Biol. 2002, 6, 765-772.
6. Dervan, P. B. Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 2001, 9, 2215-2235.
7. Mrksich, M.; Wade, W. S.; Dwyer, T. J.; Geierstanger, B. H.; Wemmer, D. E.; Dervan, P. B. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 7586-7590.
8. Wade, W. S.; Mrksich, M.; Dervan, P. B. Design of peptides that bind in the minor groove of DNA at 5′-(a,T)G(a,T)C(a,T)-3′ sequences by a dimeric side-by-side motif. J. Am. Chem. Soc. 1992, 114, 8783-8794.
9. Mrksich, M.; Parks, M. E.; Dervan, P. B. Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA. J. Am. Chem. Soc. 1994, 116, 7983-7988.
10. White, S.; Szewczyk, J. W.; Turner, J. M.; Baird, E. E.; Dervan, P. B. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 1998, 391, 468-471.
11. Melander, C.; Burnett, R.; Gottesfeld, J. M. Regulation of gene expression with pyrrole-imidazole polyamides. J. Biotechnol. 2004, 112, 195-220.
12. Edelson, B. S.; Best, T. P.; Olenyuk, B.; Nickols, N. G.; Doss, R. M.; Foister, S.; Heckel, A.; Dervan, P. B. Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates. Nucleic Acids Res. 2004, 32, 2802-2818.
13. Best, T. P.; Edelson, B. S.; Nickols, N. G.; Dervan, P. B. Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12063-12068.
14. Hsu, C. F.; Dervan, P. B. Quantitating the concentration of Py-Im polyamide-fluorescein conjugates in live cells. Bioorg. Med. Chem. Lett. 2008, 18, 5851-5855.
15. Yu, P.; Liu, B.; Kodadek, T. A high-throughput assay for assessing the cell permeability of combinatorial libraries. Nat. Biotechnol. 2005, 23, 746-751.
16. Pratt, W. B.; Toft, D. O. Steroid receptor interactions with heat shock protein and immunophilin chaperones. Endocr. Rev. 1997, 18, 306-360.
17. Govindan, M. V.; Manz, B. Three-step purification of glucocorticoid receptors from rat liver. Eur. J. Biochem. 1980, 108, 47-53.
18. Lopez, S.; Simons, J.; Stoney, S. Dexamethasone 21-(β- isothiocyanatoethyl) thioether: a new affinity label for glucocorticoid receptors. J. Med. Chem. 1991, 34, 1762-1767.
19. Simons, J.; Stoney, S.; Pons, M.; Johnson, D. F. α-Keto mesylate: a reactive, thiol-specific functional group. J. Org. Chem. 1980, 45, 3084-3088.
20. Liu, B.; Yu, P.; Alluri, P. G.; Kodadek, T. Simple reporter gene-based assays for hairpin poly(amide) conjugate permeability and DNA-binding activity in living cells. Mol. BioSyst. 2005, 1, 307-317.
21. Mapp, A. K.; Ansari, A. Z.; Ptashne, M.; Dervan, P. B. Activation of gene expression by small molecule transcription factors. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 3930-3935.
22. Baird, E. E.; Dervan, P. B. Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am. Chem. Soc. 1996, 118, 6141-6146.
23. Nickols, N. G.; Jacobs, C. S.; Farkas, M. E.; Dervan, P. B. Improved nuclear localization of DNA-binding polyamides. Nucleic Acids Res. 2007, 35, 363-370.
24. Kwon, Y.; Arndt, H. D.; Mao, Q.; Choi, Y.; Kawazoe, Y.; Dervan, P. B.; Uesugi, M. Small molecule transcription factor mimic. J. Am. Chem. Soc. 2004, 126, 15940-15941.
25. Xiao, X.; Yu, P.; Lim, H. S.; Sikder, D.; Kodadek, T. A cell-permeable synthetic transcription factor mimic. Angew. Chem., Int. Ed. 2007, 46, 2865-2868.
26. Nickols, N. G.; Dervan, P. B. Suppression of androgen receptor-mediated gene expression by a sequence-specific DNA-binding polyamide. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 10418-10423.
27. Kelly, J. J.; Baird, E. E.; Dervan, P. B. Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 6981-6985.
28. Aponte, J. C.; Verastegui, M.; Zimic, M.; Quiliano, M.; Vaisberg, A. J.; Gilman, R. H.; Hammond, G. B. Synthesis, cytotoxicity, and anti-Trypanosoma cruzi activity of new chalcones. J. Med. Chem. 2008, 51, 6230-6234.
29. Poulin-Kerstien, A. T.; Dervan, P. B. DNA-templated dimerization of hairpin polyamides. J. Am. Chem. Soc. 2003, 125, 15811-15821.