Synthesis of bicyclic 2′-deoxynucleosides with α-L-ribo- And β-D-xylo-configurations and restricted S- and N-type conformations

Journal of Organic Chemistry

Volumn 74, Issue 4, 2009, Pages 1557-1566

  Shaikh, Khalil I ^a   Kumar, Surender ^a,b   Lundhus, Lene ^a   Bond, Andrew D ^b   Sharma, Pawan K ^b   Nielsen, Poul ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b KURUKSHETRA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYNUCLEOSIDES; OLIGODEOXYNUCLEOTIDES; PHOSPHORAMIDITE; SIX-MEMBERED RINGS; X-RAY CRYSTALLOGRAPHIES;

CONFORMATIONS; NUCLEIC ACIDS; RNA; SYNTHESIS (CHEMICAL);

X RAY CRYSTALLOGRAPHY;

6 HYDROXY 1 HYDROXYMETHYL 8 (THYMIN 1 YL) 3,9 DIOXABICYCLO[4.3.0]NONANE; BICYCLIC 2' DEOXYNUCLEOSIDE; COMPLEMENTARY DNA; COMPLEMENTARY RNA; DNA; NUCLEOSIDE; OLIGODEOXYNUCLEOTIDE; RNA; UNCLASSIFIED DRUG;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CHEMICAL STRUCTURE; CONFORMATION; CRYSTAL STRUCTURE; NUCLEIC ACID ANALYSIS; PROTON NUCLEAR MAGNETIC RESONANCE; STEREOCHEMISTRY; SYNTHESIS; THERMOSTABILITY; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; BICYCLO COMPOUNDS, HETEROCYCLIC; BIOMIMETICS; CARBOHYDRATE CONFORMATION; CRYSTALLOGRAPHY, X-RAY; DNA; NUCLEIC ACID DENATURATION; NUCLEOSIDES; OLIGONUCLEOTIDES; RIBOSE; RNA; STEREOISOMERISM; SUBSTRATE SPECIFICITY; TRANSITION TEMPERATURE; XYLOSE;

EID: 64349112164     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo8023472     Document Type: Article

References (64)

1. (a) Kool, E. T. Chem. Rev. 1997, 97, 1473-1487.
2. (b) Kurreck, J. Eur. J. Biochem. 2003, 270, 1628-1644.
3. (a) Meldgaard, M.; Wengel, J. J. Chem. Soc, Perkin Trans. 2000,1, 35393554.
4. (b) Leumann, C. J. Bioorg. Med. Chem. 2002, 10, 841-854.
5. (a) Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. Chem. Commun. 1998, 455-456.
6. (b) Koshkin, A. A.; Singh, S. K.; Nielsen, P.; Rajwanshi, V. K.; Kumar, R.; Meldgaard, M.; Olsen, C. E.; Wengel, J. Tetrahedron 1998, 54, 3607-3630.
7. (c) Obika, S.; Nanbu, D.; Hari, Y.; Andoh, J.; Morio, K.; Doi, T.; Imanishi, T. Tetrahedron Lett. 1998, 39, 5401-5404.
8. (d) Koshkin, A. A.; Nielsen, P.; Meldgaard, M.; Rajwanshi, V. K.; Singh, S. K.; Wengel, J. J. Am. Chem. Soc. 1998, 120, 13252-13253.
9. (a) Bondensgaard, K.; Petersen, M.; Singh, S. K.; Rajwanshi, V. K.;
10. Kumar, R.; Wengel, J.; Jacobsen, J. P. Chem. Eur. J. 2000, 6, 2687-2695.
11. (b) Nielsen, K. E.; Rasmussen, J.; Kumar, R.; Wengel, J.; Jacobsen, J. P. Bioconjugate Chem. 2004, 15, 449-457.
12. (c) Petersen, M.; Bondensgaard, K.;Wengel, J.; Jacobsen, J. P. J. Am. Chem. Soc. 2002, 124, 5974-5982.
13. (a) Petersen, M.; Wengel, J. Trends Biotechnol. 2003, 21, 74-81.
14. (b) Jepsen, J. S.; Wengel, J. Curr. Opin. Drug Discovery Dev. 2004, 7, 188-194.
15. (c) Kaur, H.; Babu, B. R.; Maiti, S. Chem. Rev. 2007, 107, 4672-4697.
16. (a) Rajwanshi, V. K.; Håkansson, A. E.; Sørensen, M. D.; Pitsch, S.; Singh, S. K.; Kumar, R.; Nielsen, P.; Wengel, J. Angew. Chem., Int. Ed. 2000, 39, 1656-1659.
17. (b) Christensen, N. K.; Bryld, T.; S0rensen, M. D.; Arar, K.; Wengel, J.; Nielsen, P. Chem. Commun. 2004, 282-283.
18. Sørensen, M. D.; Kvasrnø, L.; Bryld, T.; Håkansson, A. E.; Verbeure, B.; Gaubert, G.; Herdewijn, P.; Wengel, J. J. Am. Chem. Soc. 2002, 124, 2164-2176.
19. Petersen, M.; Håkansson, A. E.; Wengel, J.; Jacobsen, J. P. J. Am. Chem. Soc. 2001, 123, 7431-7432.
20. (a) Rajwanshi, V. K.; Håkansson, A. E.; Dahl, B. M.; Wengel, J. Chem. Commun. 1999, 1395-1396.
21. (b) Rajwanshi, V. K.; Hakansson, A. E.; Kumar, R.; Wengel, J. Chem. Commun. 1999, 2073-2074.
22. (a) Nielsen, P.; Dalskov, J. K. Chem. Commun. 2000, 1179-1180.
23. (b) Nielsen, P.; Christensen, N. K.; Dalskov, J. K. Chem. Eur. J. 2002, 8, 712-722.
24. (a) Morvan, F.; Rayner, B.; Imbach, J.-L.; Thenet, S.; Bertrand, J.-R.; Paoletti, J.; Malvy, C.; Paoletti, C. Nucleic Acids Res. 1987, 15, 3421-3437.
25. (b) Thuong, N. T.; Asseline, U.; Roig, V.; Takasugi, M.; Helene, C. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 5129-5133.
26. (c) Gagnor, C.; Bertrand, J.-R.; Thenet, S.; Lemaître, M.; Morvan, F.; Rayner, B.; Malvy, C.; Lebleu, B.; Imbach, J.-L.; Paoletti, C. Nucleic Acid Res. 1987, 15, 10419-10436.
27. (d) Gagnor, C.; Rayner, B.; Leonetti, J.-P.; Imbach, J.-L.; Lebleu, B. Nucleic Acid Res. 1989, 17, 5107-5114.
28. The N-type conformation is defined as the conformation with the 3'′- carbon puckering to the same side as the 5'′-carbon. Therefore, we define 1, 2, and 8 as N-type mimics, whereas 4-7 are defined as S-type mimics.
29. For definitions and nomenclature regarding nucleoside and nucleic acid structure and conformations, see: Saenger, W. Principles of Nucleic Acid Structure; Springer: New York, 1984.
30. (a) Christensen, N. K.; Petersen, M.; Nielsen, P.; Jacobsen, J. P.; Olsen, C. E.; Wengel, J. J. Am. Chem. Soc. 1998, 120, 5458-5463.
31. (b) Højland, T.; Kumar, S.; Babu, B. R.; Umemoto, T.; Albsk, N.; Sharma, P. K.; Nielsen, P.; Wengel, J. Org. Biomol. Chem. 2007, 5, 2375-2379.
32. Sharma, P. K.; Petersen, M.; Nielsen, P. J. Org. Chem. 2005, 70, 4918-4928.
33. (a) Tarköy, M.; Bolli, M.; Schweizer, B.; Leumann, C. Helv. Chim. Acta 1993, 76, 481-510.
34. (b) Altmann, K.-H.; Imwinkelried, R.; Kesselring, R.; Rihs, G. Tetrahedron Lett. 1994, 35, 7625-7628.
35. (c) Nielsen, P.; Pfundheller, H. M.; Olsen, C. E.; Wengel, J. J. Chem. Soc., Perkin Trans. 1997, 1, 3423-3433.
36. (d) Ravn, J.; Thorup, N.; Nielsen, P. J. Chem. Soc., Perkin Trans. 2001, 1, 1855-1861.
37. (e) Renneberg, D.; Leumann, C. J. J. Am. Chem. Soc. 2002, 124, 5993-6002.
38. (f) Albaek, N.; Ravn, J.; Freitag, M.; Thomasen, H.; Christensen, N. K.; Petersen, M.; Nielsen, P. Nucleosides, Nucleotides Nucleic Acids 2003, 22, 723-725.
39. (g) Freitag, M.; Thomasen, H.; Christensen, N. K.; Petersen, M.; Nielsen, P. Tetrahedron 2004, 60, 3775-3786.
40. (h) Obika, S.; Osaki, T.; Sekiguchi, M.; Somjing, R.; Harada, Y.; Imanishi, T. Tetrahedron Lett. 2004, 45, 4801-4804.
41. (i) Obika, S.; Sekiguchi, M.; Somjing, R.; Imanishi, T. Angew. Chem., Int. Ed. 2005, 44, 1944-1947.
42. (j) Stauffiger, A.; Leumann, C. Nucleic Acids Symp. Ser. 2008, 52, 267-268.
43. Also an α-D-ribo-configured S-type mimic has been studied: Keller, B. M.; Leumann, C. J. Synthesis 2002, 789-796.
44. (a) Sugaya, K.; Harada, Y.; Mitsuoka, Y.; Osaki, T.; Obika, S.; Kodama, T.; Imanishi, T. Nucleic Acid Symp. Ser. 2007, 51, 155-156.
45. (b) Osaki, T.; Obika, S.; Harada, Y.; Mitsuoka, Y.; Sugaya, K.; Sekiguchi, M.; Roonjang, S.; Imanishi, T. Tetrahedron 2007, 63, 8977-8986.
46. (a) Obika, S.; Sekiguchi, M.; Osaki, T.; Shibata, N.; Masaki, M.; Hari, Y.; Imanishi, T. Tetrahedron Lett. 2002, 43, 4365-4368.
47. (b) Sekiguchi, M.; Obika, S.; Harada, Y.; Osaki, T.; Somjing, R.; Mitsuoka, Y.; Shibata, N.; Masaki, M.; Imanishi, T. J. Org. Chem. 2006, 71, 1306-1316.
48. Thomasen, H.; Meldgaard, M.; Freitag, M.; Petersen, M.; Wengel, J.; Nielsen, P. Chem. Commun. 2002, 1888-1889.
49. (a) Koole, L. H.; Buck, H. M.; Vial, J.-M.; Chattopadhyaya, J. Acta Chem. Scand. 1989, 43, 665-669.
50. (b) Webb, T. R. Tetrahedron Lett. 1988, 29, 3769-3772.
51. (c) Huss, S.; De las Heras, F. G.; Camarasa, M. J. Tetrahedron 1991, 47, 1727-1736.
52. (d) Dupouy, C.; Lavedan, P.; Escudier, J.-M. Tetrahedron 2007, 63, 11235-11243.
53. (a) Bender, S. L.; Moffett, K. K. J. Org. Chem. 1992, 57, 1646-1647.
54. (b) Jung, P. M. J.; Burger, A.; Biellmann, J.-F. Tetrahedron Lett. 1995, 36, 1031-1034.
55. (c) Nielsen, P.; Larsen, K.; Wengel, J. Acta Chem. Scand. 1996, 50, 1030-1035.
56. (d) Jung, P. M. J.; Burger, A.; Biellmann, J.-F. J. Org. Chem. 1997, 62,8309-8314.
57. The cleavage of an N3-benzylthymine-bond has been reported before using Na-naphthalate as the active reagent: Philips, K. D.; Horwitz, J. P. J. Org. Chem. 1975, 40, 1856-1858. Therefore, the synthesis of the bicyclic nucleoside target has also been approached using the N3-benzylated compound 12 in order to remove both benzyl groups in the last step. All steps were prepared in similar yields giving finally the N3-benzyl derivative of 8. However, efficient removal of the N3-benzyl group was not accomplished. See Supporting Information for details.
58. (a) O-Yang, C.; Wu, H. Y.; Fraser-Smith, E. B.; Walker, K. A. M. Tetrahedron Lett. 1992, 33, 37-40.
59. (b) Thrane, H.; Fensholdt, J.; Regner, M.; Wengel, J. Tetrahedron 1995, 51, 10389-10402.
60. (a) Montembault, M.; Bourgougnon, N.; Lebreton, J. Tetrahedron Lett. 2002, 43, 8091-8094.
61. (b) Le Clézio, I.; Gornitzka, H.; Escudier, J.-M.; Vigroux, A. J. Org. Chem. 2005, 70, 1620-1629.
62. Albffik, N.; Petersen, M.; Nielsen, P. J. Org. Chem. 2006, 71, 7731-7740.
63. Håkansson, A. E.; Koshkin, A. A.; Sørensen, M. D.; Wengel, J. J. Org. Chem. 2000, 65, 5161-5166.
64. Babu, B. R.; Raunak; Poopeiko, N. E.; Juhl, M.; Bond, A. D.; Parmar, V. S.; Wengel, J. Eur. J. Org. Chem. 2005, 2297-2321.