Selective recognition of uracil and its derivatives using a DNA repair enzyme structural mimic

Journal of Organic Chemistry

Volumn 75, Issue 2, 2010, Pages 324-333

  Jiang, Yu Lin ^a   Gao, Xiaonan ^a   Zhou, Guannan ^a   Patel, Arpit ^a   Javer, Avani ^a  

^a EAST TENNESSEE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5-FLUOROURACIL; ACTIVE SITE; AMINO ACID RESIDUES; AROMATIC GROUP; BINDING CONSTANT; CHEMICAL EQUATIONS; DNA REPAIR; DNA-REPAIR ENZYMES; FLUORESCENT PROBES; HYDROGEN BONDING NETWORK; HYDROGEN BONDINGS; NEGATIVE SLOPE; SELECTIVE RECOGNITION; SOLUBLE RECEPTOR; STACKING INTERACTION; URACIL-DNA GLYCOSYLASE;

AMINO ACIDS; COMPLEXATION; DNA; ENZYMES; FLUORESCENCE; GENES; HYDROGEN; ORGANIC ACIDS; REPAIR; RNA;

HYDROGEN BONDS;

4 BROMO 2,6 DIAMINOPYRIDINE; 5 FORMYLURACIL; 5 NITROURACIL; AMINOPYRIDINE DERIVATIVE; FLUORESCENT DYE; FLUOROURACIL; NUCLEOSIDE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; THYMINE; UNCLASSIFIED DRUG; URACIL; URACIL DERIVATIVE; URACIL DNA GLYCOSIDASE;

ACIDITY; ARTICLE; COMPLEX FORMATION; DNA REPAIR; ENZYME ACTIVE SITE; ENZYME STRUCTURE; HYDROGEN BOND; MOLECULAR INTERACTION; NONHUMAN;

AMINO ACID SEQUENCE; BINDING SITES; DNA REPAIR ENZYMES; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN BINDING; SPECTROMETRY, FLUORESCENCE; URACIL; URACIL-DNA GLYCOSIDASE;

EID: 75349108273     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo901862x     Document Type: Article

References (57)

1. (a) Klimasauskas, S.; Kumar, S.; Roberts, R. J.; Cheng, X. Cell 1994, 76, 357-369.
2. (b) Parker, J. B.; Bianchet, M. A.; Krosky, D. J.; Friedman, J. I.; Amzel, L. M.; Stivers, J. T. Nature 2007, 449, 433-437.
3. (c) Stivers, J. T.; Jiang, Y. L. Chem. Rev. 2003, 103, 2729-2759.
4. (d) Jiang, Y. L.; Stivers, J. T. Biochemistry 2001, 40, 7710-7719.
5. Jiang, Y. L.; Stivers, J. T. Biochemistry 2002, 41, 11236-11247.
6. Xiao, G.; Tordova, M.; Jagadeesh, J.; Drohat, A. C.; Stivers, J. T.; Gilliland, G. L. Protein Struct. Funct. Genet. 1999, 35, 13-24.
7. Jiang, Y. L.; McDowell, L. M.; Poliks, B.; Studelska, D. R.; Cao, C.; Potter, G. S.; Schaefer, J.; Song, F.; Stivers, J. T. Biochemistry 2004, 43, 15429-15438.
8. Mol, C. D.; Arvai,A. S.; Slupphaug, G.; Kavli, B.; Alseth, I.; Krokan, H. E.; Tainer, J. A. Cell 1995, 80, 869-878.
9. Bennett, M. T.; Rodgers, M. T.; Hebert, A. S.; Ruslander, L. E.; Eisele, L.; Drohat, A. C. J. Am. Chem. Soc. 2006, 128, 12510-12519.
10. (a) Teplova, M.; Yuan, Y. R.; Phan, A. T.; Malinina, L.; Ilin, S.; Teplov, A.; Patel, D. J. Mol. Cell 2006, 21, 75-85.
11. (b) Turner, D. P.; Cortellino, S.; Schupp, J. E.; Caretti, E.; Loh, T.; Kinsella, T. J.; Bellacosa, A. Cancer Res. 2006, 66, 7686-7693.
12. (a) Visnes, T.; Akbari, M.; Hagen, L.; Slupphaug, G.; Krokan, H. E. DNA Repair 2008, 7, 1869-1881.
13. (b) Eot-Houllier, G.; Eon-Marchais, S.; Gasparutto, D.; Sage, E. Nucleic Acids Res. 2005, 33, 260-271.
14. (a) Seiple, L.; Jaruga, P.; Dizdaroglu, M.; Stivers, J. T. Nucleic Acids Res. 2006, 34, 140-151.
15. (b) Lee, J.-H; Park, J.-H.; Jung, Y.; Kim, J.-H.; Jong, H.-S.; Kim, T.-Y.; Bang, Y.-J. Mol. Cancer Therap. 2006, 5, 3085-3095.
16. De Clercq, E; Descamps, J; Huang, G. F.; Torrence, P. Mol. Pharmacol. 1978, 14, 422-430.
17. (a) Kyogoku, Y.; Lord, R. C.; Rich, A. Science 1966, 154, 518-520.
18. (b) Mathews, F. S.; Rich, A. J. Mol. Biol. 1964, 8, 89-95.
19. (c) Kyogoku, Y.; Lord, R. C.; Rich, A. Proc. Natl. Acad. Sci. U.S.A. 1967, 57, 250-257.
20. Muehldorf, A. V.; Engen, D. V.; Warner, J. C.; Hamilton, A. D. J. Am. Chem. Soc. 1988, 110, 6561-6562.
21. (a) Zimmerman, S. C. Top. Curr. Chem. 1993, 165, 71-102.
22. (b) Ong, H. C.; Arambula, J. F.; Ramisetty, R. S.; Baranger, A. M.; Zimmerman, S. C. Chem. Commun. 2009, 668-670.
23. (c) Gray, M.; Goodman, A. J.; Carrol, J. B.; Bardon, K.; Markey, M.; Coohke, G.; Rotello, V. M. Org. Lett. 2004, 6, 385-388.
24. (a) Park, T. K.; Schroeder, J.; Rebek, J., Jr. J. Am. Chem. Soc. 1991, 113, 5125-5127.
25. (b) Murata, H.; Lahti, P. M.; Aboaku, S. Chem. Commun. 2008, 3441-3443.
26. (c) Manesiotis, P.; Hall, A. J.; Sellergren, B. J. Org. Chem. 2005, 70, 2729-2738.
27. (d) Takase, M.; Inouye, M. J. Org. Chem. 2003, 68, 1134-1137.
28. (e) Pauvert, M.; Laine, P.; Jonas, M.; Wiest, O. J. Am. Chem. Soc. 2004, 69, 543-548.
29. (f) Chattopadhyay, P.; Pandey, P. S. Bioorg. Med. Chem. Lett. 2007, 17, 1553-1557.
30. Lamale, B.; Henry, W. P.; Daniels, L. M.; Zhang, C.; Klein, S. M.; Jiang, Y. L. Tetrahedron 2009, 65, 62-69.
31. Klein, S. M.; Zhang, C.; Jiang, Y. L. Tetrahedron Lett. 2008, 49, 2638-2641.
32. (a) Matray, T. J.; Kool, E. T. Nature 1999, 399, 704-708.
33. (b) Jiang,Y. L.; Kwon, K.; Stivers, J. T. J. Biol. Chem. 2001, 276, 42347-42354.
34. (c) Kwon, K.; Jiang, Y. L.; Stivers, J. T. Chem. Biol. 2003, 10, 351-359.
35. Nettekoven, M. Synlett 2001, 1917-1920.
36. Nettekoven, M.; Jenny, C. Org. Proc. Res. Dev. 2003, 7, 38-43.
37. (a) Masciadri, R.; Kamer, M.; Nock, N. Eur. J. Org. Chem. 2003, 4286-4291.
38. (b) Amann, N.; Pandurski, E.; Fiebig, T.; Wagenknecht, H.-A. Chem.-Eur. J. 2002, 8, 4877-4883.
39. Minetti, P.; Tinti, M. O.; Carminati, P.; Castorina, M.; Di Cesare, M. A.; Di Serio, S.; Gallo, G.; Ghirardi, O.; Giorgi, F.; Giorgi, L.; Piersanti, G.; Bartoccini, F.; Tarzia, G. J. Med. Chem. 2005, 48, 6887-6896.
40. Smith, D. K.; Diederich, F. Chem. Commun. 1998, 2501-2502.
41. Brady, S. F.; Varga, S. L.; Freidinger, R. M.; Schwenk, D. A.; Mendlowski, M.; Holly, F. W.; Veber, D. F. J. Org. Chem. 1979, 44, 3101-3105.
42. All dilution experiments and binding constant measurements were performed in water without using any buffer, because receptor 1 became cloudy and precipitated in phosphate buffer at pH 7.
43. (a) McMurry, J. Organic Chemistry, 7th ed.; Thomson, Brooks/Cole: Belmont (CA), 2008; pp 921-924.
44. a for 2,6-diacetamidopyridine was calculated to be 3.68 using Advanced Chemistry Development (ACD/Labs) Software V8.14 for Solaris in Scifinder Scholar.
45. Corbin, P. S.; Zimmerman, S. C.; Thiessen, P. A.; Hawryluk, N. A.; Murray, T. J. J. Am. Chem. Soc. 2001, 123, 10475-10488.
46. Inouye, M.; Hyodo, Y.; Nakazumi, H. J. Org. Chem. 1999, 64, 2704-2710.
47. a (3.68) of 1b and the concentrations of 1a and 1b (both 0.435 μM). At these concentrations, 99.8% of 1b will dissociate to form 1a. Because the proton was not involved in the binding, the concentration of protons from 1b should remain constant. Although the most acidic uracil derivative that we investigated (5-nitrouracil) would decrease the pH of the solution to a calculated value of pH 5.4 during the measurement, the concentration of 1a would barely change because of the decrease in pH.
48. Jiang, Y. L.; Cao, C.; Stivers, J. T.; Song, F.; Ichikawa, Y. Bioorg. Chem. 2004, 32, 244-262.
49. Cao, C.; Jiang, Y. L.; Krosky, D. J.; Stivers, J. T. J. Am. Chem. Soc. 2006, 128, 13034-13035.
50. (a) Parikn, S. S.; Walcher, G.; Jones, G. D.; Slupphaug, G.; Krokan, H. E.; Blackburn,G. M.; Tainer, J. A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5083-5088.
51. (b) Krosky, D. J.; Song, F.; Stivers, J. T. Biochemistry 2005, 44, 5949-5959.
52. Jang, Y. H.; Sowers, L. C.; Cagin, T.; Goddard, W. A., III. J. Phys. Chem. A 2001, 105, 274-280.
53. Shao, Y.; Fusti-Molnar, L.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; Distasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran, G. J. O.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F. C.; Daschel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C.-P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L.; Zhang, W.; Bell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F.; Kong, J.; Krylov, A. I.; Gill, P. M. W.; Head-Gordon, M. Phys. Chem. Chem. Phys. 2006, 8, 3172-3191.
54. Zhao, J.; Khalizov, A.; Zhang, R.; McGraw, R. J. Org. Chem. 2009, 113, 680-689.
55. (a) Palde, P. B.; Gareiss, P. C.; Miller, B. L. J. Am. Chem. Soc. 2008, 130, 9566-9573.
56. (b) Ojida, A.; Takashima, I.; Kohira, T.; Nonaka, H.; Hamachi, I. J. Am. Chem. Soc. 2008, 130, 12095-12101.
57. (c) Butterfield, S. M.; Goodman, C. M.; Rotello, V. M.; Waters, M. L. Angew. Chem., Int. Ed. 2004, 43, 724-727.