Five- and six-membered conformationally locked 2′,4′- carbocyclic ribo-thymidines: Synthesis, structure, and biochemical studies

Journal of the American Chemical Society

Volumn 129, Issue 26, 2007, Pages 8362-8379

  Srivastava, Puneet ^a   Barman, Jharna ^a   Pathmasiri, Wimal ^a   Plashkevych, Oleksandr ^a   Wenska, Małgorzata ^a   Chattopadhyaya, Jyoti ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BLOOD; CONFORMATIONS; CYCLIZATION; DEGRADATION; NUCLEAR MAGNETIC RESONANCE; PHARMACOKINETICS;

CARBOCYCLIC ANALOGUES; HETERODUPLEXES; THYMIDINES;

NUCLEOTIDES;

ANTISENSE OLIGONUCLEOTIDE; BICYCLO COMPOUND; DOUBLE STRANDED RNA; NUCLEASE; RADICAL; THYMIDINE DERIVATIVE;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CHEMICAL STRUCTURE; CYCLIZATION; ENZYME STABILITY; GENE TARGETING; NUCLEAR OVERHAUSER EFFECT; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTUM YIELD; SERUM; SYNTHESIS;

BASE SEQUENCE; CARBOHYDRATES; HUMANS; MOLECULAR STRUCTURE; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDES, ANTISENSE; ORGANOPHOSPHORUS COMPOUNDS; RIBONUCLEASES; SERUM; THYMIDINE;

EID: 34447129727     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja071106y     Document Type: Article

References (90)

1. Zamecnik, P. C.; Stephenson, M. L. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 280-284.
2. Crooke, S. T. Annu. Rev. Med. 2004, 55, 61-95.
3. Buchini, S.; Leumann, C. J. Curr. Opin. Chem. Biol. 2003, 7 (6), 717-726.
4. Montgomery, M. K.; Xu, S.; Fire, A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95 (26), 15502-15507.
5. Kurreck, J. Eur. J. Biochem. 2003, 270, 1628-1644.
6. Freier, S. M.; Altmann, K. H. Nucleic Acids Res. 1997, 25, 4429-4443.
7. Eckstein, F. Annu. Rev. Biochem. 1985, 54, 367-402.
8. Holmlund, J. T. Ann. N.Y. Acad. Sci. 2003, 1002 (Therapeutic Oligonucleotides), 244-251.
9. Leumann, C. J. Bioorg. Med. Chem. 2002, 10, 841-854.
10. Steffens, R.; Leumann, C. Helv. Chim. Acta 1997, 80, 2426-2439.
11. Wengel, J. Acc. Chem. Res 1999, 32, 301-310.
12. Koshkin, A. A.; Singh, S. K.; Nielsen, P.; Rajwanshi, V. K.; Kumar, R.; Meldgaard, M.; Olsen, C. E.; Wengel, J. Tetrahedron 1998, 54 (14), 3607-3630.
13. Morita, K.; Takagi, M.; Hasegawa, C.; Kaneko, M.; Tsutsumi, S.; Sone, J.; Ishikawa, T.; Imanishi, T.; Koizumi, M. Bioorg. Med. Chem. 2003, 11 (10), 2211-2226.
14. Obika, S.; Nanbu, D.; Hari, Y.; Morio, K.-I.; In, Y.; Ishida, T.; Imanishi, T. Tetrahedron Lett. 1997, 38 (50), 8735-8738.
15. Petersen, M.; Nielsen, C. B.; Nielsen, K. E.; Jensen, G. A.; Bondensgaard, K.; Singh, S. K.; Rajwanshi, V. K.; Koshkin, A. A.; Dahl, B. M.; Wengel, J.; Jacobsen, J. P. J. Mol. Recognit. 2000, 13 (1), 44-53.
16. Singh, S. K.; Kumar, R.; Wengel, J. J. Org. Chem. 1998, 63 (26), 10035-10039.
17. Pradeepkumar, P. I.; Cheruku, P.; Plashkevych, O.; Acharya, P.; Gohil, S.; Chattopadhyaya, J. J. Am. Chem. Soc. 2004, 126, 11484-11499.
18. Honcharenko, D.; Varghese, O. P.; Plashkevych, O.; Barman, J.; Chattopadhyaya, J. J. Org. Chem. 2006, 71, 299-314.
19. Koizumi, M. Curr. Opin. Mol. Ther. 2006, 8, 144-149.
20. Varghese, O. P.; Barman, J.; Pathmasiri, W.; Plashkevych, O.; Honcharenko, D.; Chattopadhyaya, J. J. Am. Chem. Soc. 2006, 128 (47), 15173-15187.
21. Babu, B. R.; Raunak; Poopeiko, N. E.; Juhl, M.; Bond, A. D.; Parmar, V. S.; Wengel, J. Eur. J. Org. Chem. 2005, 11, 2297-2321.
22. Rajwanshi, V. K.; Hakansson, A. E.; Sorensen, M. D.; Pitsch, S.; Singh, S. K.; Kumar, R.; Nielsen, P.; Wengel, J. Angew. Chem., Int. Ed. 2000, 39 (9), 1656-1659.
23. Wang, G.; Giradet, J. L.; Gunic, E. Tetrahedron 1999, 55, 7707-7724.
24. Morita, K.; Hasegawa, C.; Kaneko, M.; Tsutsumi, S.; Sone, J.; Ishikawa, T.; Imanishi, T.; Koizumi, M. Bioorg. Med. Chem. Lett. 2001, 12 (1), 73-76.
25. Morita, K.; Yamate, K.; Kurakata, S.; Abe, K.; Imanishi, T.; Koizumi, M. Nucleic Acids Res. Sup. 2002, 2, 99-100.
26. Morita, K.; Yamate, K.; Kurakata, S.-I.; Watanabe, K.; Imanishi, T.; Koizumi, M. Nucleosides, Nucleotides Nucleic Acids 2003, 22, 1619-1621.
27. Albaek, N.; Petersen, M.; Nielsen, P. J. Org. Chem. 2006, 71 (20), 7731-7740.
28. Teplova, M.; Minasov, G.; Tereshko, V.; Inamati, G. B.; Cook, P. D.; Manoharan, M.; Egli, M. Nat. Struct. Mol. Biol. 1999, 6 (6), 535-539.
29. Prakash, T. P.; Pueschl, A. P.; Lesnik, E.; Mohan, V.; Tereshko, V.; Egli, M.; Manoharan, M. Org. Lett. 2004, 6 (12), 1971-1974.
30. Kanazaki, M.; Ueno, Y.; Shuto, S.; Matsuda, A. J. Am. Chem. Soc. 2000, 122 (11), 2422-2432.
31. Monia, B. P.; Johnston, J. F.; Sasmor, H.; Cummins, L. L. J. Biol. Chem. 1996, 271 (24), 14533-14540.
32. Prhavc, M.; Prakash, T. P.; Minasov, G.; Cook, P. D.; Egli, M.; Manoharan, M. Org. Lett. 2003, 5 (12), 2017-2020.
33. Hanessian, S.; Dhanoa, D. S.; Beaulieu, P. L. Can. J. Chem. 1987, 65 (8), 1859-1866.
34. Beckwith, A. L. J. Tetrahedron 1981, 37 (18), 3073-3100.
35. Beckwith, A. L. J.; Phillipou, G.; Serelis, A. K. Tetrahedron Lett. 1981, 29, 2811-2814.
36. Baldwin, J. E. J. Chem. Soc. Chem. Commun. 1976, 18, 738-741.
37. Baldwin, J. E. J. Chem. Soc. Chem. Commun. 1976, 18, 734-736.
38. Baldwin, J. E.; Cutting, J.; Dupont, W.; Kruse, L.; Silberman, L.; Thomas, R. C. J. Chem. Soc. Chem. Commun. 1976, 18, 736-738.
39. Giese, B. Angew. Chem. 1983, 95 (10), 771-782.
40. Curran, D. P. Synthesis 1988, 6, 417-439.
41. Curran, D. P. Synthesis 1988, 7, 489-513.
42. Stork, G.; Baine, N. H. J. Am. Chem. Soc. 1982, 104 (8), 2321-2323.
43. RajanBabu, T. V. J. Org. Chem. 1988, 53 (19), 4522-4530.
44. RajanBabu, T. V. Acc. Chem. Res. 1991, 24 (5), 139-145.
45. RajanBabu, T. V.; Fukunaga, T. J. Am. Chem. Soc. 1989, 111 (1), 296-300.
46. RajanBabu, T. V.; Fukunaga, T.; Reddy, G. S. J. Am. Chem. Soc. 1989, 111 (5), 1759-1769.
47. Beckwith, A. L. J.; Schiesser, C. H. Tetrahedron 1985, 41 (19), 3925-3941.
48. Motherwell, W. B.; Crich, D. Free radical chain reactions in organic synthesis; Academic Press: New York, 1992, 0-12-508760-8.
49. Beckwith, A. L. J.; Page, D. M. Tetrahedron 1999, 55 (11), 3245-3254.
50. Bakuzis, P.; Campos, O. O. S.; Bakuzis, M. L. F. J. Org. Chem. 1976, 41 (20), 3261-3264.
51. Lopez, J. C.; Fraser-Reid, B. J. Am. Chem. Soc. 1989, 111 (9), 3450-3452.
52. Lopez, J. C.; Gomez, A. M.; Fraser-Reid, B. J. Chem. Soc. Chem. Commun. 1993, 9, 762-764.
53. Lopez, J. C.; Gomez, A. M.; Fraser-Reid, B. J. Chem. Soc Chem. Commun. 1994, 13, 1533-1534.
54. Lopez, J. C.; Gomez, A. M.; Fraser-Reid, B. J. Org. Chem. 1995, 60 (12), 3871-3878.
55. Xi, Z.; Agback, P.; Plavec, J.; Sandstroem, A.; Chattopadhyaya, J. Tetrahedron 1992, 48 (2), 349-370.
56. Xi, Z.; Agback, P.; Sandstroem, A.; Chattopadhyaya, J. Tetrahedron 1991, 47 (46), 9675-9690.
57. Xi, Z.; Glemarec, C.; Chattopadhyaya, J. Tetrahedron 1993, 49 (34), 7525-7546.
58. Xi, Z.; Rong, J.; Chattopadhyaya, J. Tetrahedron 1994, 50 (17), 5255-5272.
59. Thibaudeau, C.; Acharya, P.; Chattopadhyaya, J. Stereoelectronic Effects in Nucleosides & Nucleotides and their Structural Implications; Uppsala University Press: Uppsala, 1999, 91-506-1351-0.
60. Mancuso, A. J.; Brownfain, D. S.; Swern, D. J. Org. Chem. 1979, 44 (23), 4148-4150.
61. Wittig, G.; Schlosser, M. Angew. Chem. 1960, 72, 324.
62. Vorbrüggen, H.; Höfle, G. Chem. Ber 1981, 114, 1256-1258.
63. Bax, A.; Summers, M. J. Am. Chem. Soc. 1986, 108, 2093-2094.
64. Bax, A.; Davis, D. G. J. Magn. Reson. 1985, 65, 355-360.
65. Barton D, H. R.; Mccombie, S. W. J. Chem Soc., Perkin Trans. 1 1975, 1574.
66. Haasnoot, C. A. G.; de Leeuw, F. A. A. M.; Altona, C. Tetrahedron 1980, 36, 2783-2792.
67. Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94 (23), 8205-1822.
68. Graessmann, M.; Michaels, G.; Berg, B.; Graessmann, A. Nucleic Acids Res. 1991, 19 (1), 53-9.
69. Wagner, R. W.; Matteucci, M. D.; Lewis, J. G.; Gutierrez, A. J.; Moulds, C.; Froehler, B. C. Science 1993, 260 (5113), 1510-13.
70. Marquez, V. E.; Siddiqui, M. A.; Ezzitouni, A.; Russ, P.; Wang, J.; Wagner, R. W.; Matteucci, M. D. J. Med. Chem. 1996, 39 (19), 3739-3747.
71. Pradeepkumar, P. I.; Chattopadhyaya, J. J. Chem. Soc., Perkin Trans. 2 2001, 2074-2083.
72. Grunweller, A.; Wyszko, E.; Bieber, B.; Jahnel, R.; Erdmann Volker, A.; Kurreck, J. Nucleic Acids Res. 2003, 31 (12), 3185-3193.
73. Ambros, V. Cell (Cambridge, MA, U.S.) 2001, 107 (7), 823-826.
74. Ruvkun, G. Science (Washington, DC, U.S.) 2001, 294 (5543), 797-799.
75. Braasch, D. A.; Jensen, S.; Liu, Y.; Kaur, K.; Arar, K.; White, M. A.; Corey, D. R. Biochemistry 2003, 42 (26), 7967-7975.
76. Elmen, J.; Thonberg, H.; Ljungberg, K.; Frieden, M.; Westergaard, M.; Xu, Y.; Wahren, B.; Liang, Z.; Orum, H.; Koch, T.; Wahlestedt, C. Nucleic Acids Res. 2005, 33 (1), 439-447.
77. Kurreck, J.; Wyszko, E.; Gillen, C.; Erdmann, V. A. Nucleic Acids Res. 2002, 30 (9), 1911-1918.
78. Steffens, R.; Leumann, C. J. J. Am. Chem. Soc. 1999, 121 (14), 3249-3255.
79. Egli, M.; Minasov, G.; Tereshko, V.; Pallan, P. S.; Teplova, M.; Inamati, G. B.; Lesnik, E. A.; Owens, S. R.; Ross, B. S.; Prakash, T. P.; Manoharan, M. Biochemistry 2005, 44 (25), 9045-9057.
80. Renneberg, D.; Bouliong, E.; Reber, U.; Schumperli, D.; Leumann Christian, J. Nucleic Acids Res. 2002, 30 (13), 2751-2757.
81. Bolli, M.; Trafelet, H. U.; Leumann, C. Nucleic Acids Res. 1996, 24 (23), 4660-4667.
82. Perbost, M.; Lucas, M.; Chavis, C.; Pompon, A.; Baumgartner, H.; Rayner, B.; Griengl, H.; Imbach, J. L. Biochem. Biophys. Res. Commun. 1989, 165 (2), 742-747.
83. Altmann, K.-H.; Bevierre, M.-O.; De Mesmaeker, A.; Moser, H. E. Bioorg. Med. Chem. Lett. 1995, 5 (5), 431-436.
84. Teplova, M.; Wallace, S. T.; Tereshko, V.; Minasov, G.; Symons, A. M.; Cook, P. D.; Manoharan, M.; Egli, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (25), 14240-14245.
85. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102 (11), 1995-2001.
86. Frisch, M. J., et al. Gaussian 98 (Revision A.6). Gaussian, Inc.: Pittsburgh, PA, 1998.
87. Case, D. A., et al. AMBER 7. University of California: San Francisco, 2002.
88. Cheatham, T. E., III; Kollman, P. A. J. Am. Chem. Soc. 1997, 119, 4805-4825.
89. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
90. Huggins, M. L. J. Am. Chem. Soc. 1953, 75, 4123-4126.