A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: Analysis of a "highly twisted" benzimidazole-diamidine

Journal of the American Chemical Society

Volumn 128, Issue 24, 2006, Pages 7846-7854

  Goodwin, Kristie D ^a   Lewis, Mark A ^b   Tanious, Farial A ^c   Tidwell, Richard R ^d   Wilson, W David ^c   Georgiadis, Millie M ^a   Long, Eric C ^b  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b INDIANA UNIVERSITY   (United States)

^c GEORGIA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; CRYSTAL STRUCTURE; CRYSTALLINE MATERIALS; CRYSTALLOGRAPHY; ETHERS; FLUORESCENCE;

BINDING LIGANDS; HIGH-RESOLUTION STRATEGY; INTERCALATOR DISPLACEMENT; WATER-MEDIATED INTERACTIONS;

DNA;

BENZIMIDAZOLE; BENZIMIDAZOLEDIAMIDINE; CYTOSINE; DIAMIDINE DERIVATIVE; DIPHENYL ETHER; DNA BINDING AGENT; GUANINE; LIGAND; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG; WATER;

ARTICLE; AT RICH SEQUENCE; BINDING AFFINITY; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DIFFRACTION; DNA BINDING; FLUORESCENCE ANALYSIS; HIGH RESOLUTION HOST GUEST CRYSTALLOGRAPHIC TECHNIQUE; HIGH THROUGHPUT FLUORESCENT INTERCALATOR DISPLACEMENT ASSAY; HIGH THROUGHPUT SCREENING; MOLECULAR INTERACTION; STRUCTURE ANALYSIS; TECHNIQUE;

BASE PAIRING; BASE SEQUENCE; BENZIMIDAZOLES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; FLUORESCENT DYES; HYDROGEN BONDING; INTERCALATING AGENTS; LIGANDS; NUCLEIC ACID CONFORMATION; PENTAMIDINE; PHENYL ETHERS; TIME FACTORS;

EID: 33745422093     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0600936     Document Type: Article

References (37)

1. Neidle, S. Nat. Prod. Rep. 2001, 18, 291-309.
2. Zimmer, C.; Wahnert, U. Prog. Biophys. Mol. Biol. 1986, 47, 31-112.
3. Bailly, C.; Chaires, J. B. Bioconjugate Chem. 1998, 9, 513-538.
4. Waring, M. J. In Molecular Aspects of Anticancer Drug-DNA Interactions; Neidle, S., Waring, M. J., Eds.; Macmillan: London, UK, 1993; Vol. 1, pp 212-242.
5. Claussen, C. A.; Long, E. C. Chem. Rev. 1999, 99, 2797-2816.
6. Dervan, P. B.; Burli, R. W. Curr. Opin. Chem. Biol. 1999, 3, 688-693.
7. Reddy, B. S.; Sondhi, S. M.; Lown, J. W. Pharmacol. Ther. 1999, 84, 1-111.
8. Tidwell, R. R.; Boykin, D. W. In DNA and RNA Binders: From small molecules to drugs; Demeunynck, M., Bailly, C., Wilson, D. D., Eds.; Wiley-VCH: Weinheim, 2003; Vol. 2, pp 414-460.
9. Thurston, D. E. Br. J. Cancer 1999, 80 Suppl. 1, 65-85.
10. Browne, M. J., Thurlbey, P. L., Eds. In Genomes, Molecular Biology and Drug Discovery; Academic Press: London, 1996.
11. Huang, X.; Pieczko, M. E.; Long, E. C. Biochemistry 1999, 38, 2160-2166.
12. Boger, D. L.; Fink, B. E.; Hedrick, M. P. J. Am. Chem. Soc. 2000, 122, 6382-6394.
13. Boger, D. L.; Dechantsreiter, M. A.; Ishii, T.; Fink, B. E.; Hedrick, M. P. Bioorg. Med. Chem. 2000, 8, 2049-2057.
14. Hecht, S. M. Eur. J. Cancer 2002, 38, S13-S14.
15. Tse, W.; Boger, D. L. Acc. Chem. Res. 2004, 37, 61-69.
16. Fox, K. R., Ed. Methods in Molecular Biology; Humana Press: Totowa, NJ, 1997; Vol. 90.
17. Goodwin, K. D.; Long, E. C.; Georgiadis, M. M. Nucleic Acids Res. 2005, 33, 4106-4116.
18. Cote, M. L.; Yohannan, S. J.; Georgiadis, M. M. Acta Crystallogr., Sect. D 2000, 56 (Pt 9), 1120-1131.
19. Cote, M. L.; Georgiadis, M. M. Acta Crystallogr., Sect. D 2001, 57, 1238-1250.
20. Cote, M. L.; Pflomm, M.; Georgiadis, M. M. J. Mol. Biol. 2003, 330, 57-74.
21. Najmudin, S.; Cote, M. L.; Sun, D.; Yohannan, S.; Montano, S. P.; Gu, J.; Georgiadis, M. M. J. Mol. Biol. 2000, 296, 613-632.
22. Sun, D.; Jessen, S.; Liu, C.; Liu, X.; Najmudin, S.; Georgiadis, M. M. Protein Sci. 1998, 7, 1575-1582.
23. Ferre-D'Amare, A. R.; Zhou, K.; Doudna, J. A. J. Mol. Biol. 1998, 279, 621-631.
24. Ferre-D'Amare, A. R.; Doudna, J. A. J. Mol. Biol. 2000, 295, 541-556.
25. The H-G method does not include any time advantage for completion of the crystallographic refinement, which takes approximately 2 weeks.
26. Lewis, M. A.; Long, E. C. Bioorg. Med. Chem. 2006, 14, 3481-3490.
27. -1. Additional information and SPR sensorgrams are provided in Supporting Information.
28. Lu, X. J.; Olson, W. K. Nucleic Acids Res. 2003, 31, 5108-5121.
29. Geometry-optimized structures were obtained by means of ab initio calculations with the Hartree-Fock approximation at the 321G* basis set level. Calculations were performed with the Spartan '04 software package (Wavefunction, Inc.).
30. Bostock-Smith, C. E.; Harris, S. A.; Laughton, C. A.; Searle, M. S. Nucleic-Acids Res. 2001, 29, 693-702.
31. Bailly, C.; Chessari, G.; Carrasco, C.; Joubert, A.; Mann, J.; Wilson, W. D.; Neidle, S. Nucleic Acids Res. 2003, 31, 1514-1524.
32. Tidwell, R. R.; Geratz, J. D.; Dann, O.; Volz, O.; Zeh, D.; Loewe, H. J. Med. Chem. 1978, 21, 613-623.
33. Otwinowski, Z.; Minor, W. In Macromolecular Crystallography, part A, Carter, J., C. W.; Sweet, R. M., (eds) Academic Press: New York, 1997; Vol. 276, pp 307-326.
34. Navaza, J. Acta Crystallogr., Sect. A 1994, 50, 157-163.
35. Macke, T.; Case, D. A. In Molecular Modeling of Nucleic Acids, Leontes, N. B., SantaLucia, J. J., Eds.; American Chemical Society: Washington, D.C., 1998; Vol. 1, pp 379-393.
36. Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M. Acta Crystallogr., Sect. A 1991, 47, 110-119.
37. Brunger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr., Sect. D 1998, 54, 905-921.