Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid)

Journal of Organic Chemistry

Volumn 79, Issue 11, 2014, Pages 5047-5061

  Kumar, Pawan ^a,b   Østergaard, Michael E ^a   Baral, Bharat ^a   Anderson, Brooke A ^a   Guenther, Dale C ^a   Kaura, Mamta ^a   Raible, Daniel J ^a   Sharma, Pawan K ^b   Hrdlicka, Patrick J ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b KURUKSHETRA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; FLUORESCENCE; GENE EXPRESSION; HYDROCARBONS; LOCKS (FASTENERS); MOLECULAR BIOLOGY; OLIGONUCLEOTIDES; RNA;

BINDING SPECIFICITIES; BIOPHYSICAL PROPERTIES; FLUORESCENCE PROPERTIES; LOCKED NUCLEIC ACID; MEDICINAL CHEMISTRY; PHARMACOKINETIC PROFILES; SINGLE NUCLEOTIDE POLYMORPHISMS; THERMAL DENATURATIONS;

MONOMERS;

ALKYNE; LOCKED NUCLEIC ACID; MONOMER; NUCLEIC ACID BASE; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHORAMIDOUS ACID; SPLEEN EXONUCLEASE; URIDINE; NUCLEIC ACID; OLIGONUCLEOTIDE; ORGANOPHOSPHORUS COMPOUND; RNA; URIDINE PHOSPHORAMIDITE;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; DENATURATION; ENZYME STABILITY; FUNCTIONAL ASSESSMENT; HYDROPHOBICITY; MODULATION; PHYSICAL CHEMISTRY; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTHESIS; THERMAL ANALYSIS; ANALOGS AND DERIVATIVES; CHEMISTRY; CONFORMATION;

MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; OLIGODEOXYRIBONUCLEOTIDES; OLIGONUCLEOTIDES; ORGANOPHOSPHORUS COMPOUNDS; RNA; URIDINE;

EID: 84902095856     PISSN: 00223263     EISSN: 15206904     Source Type: Journal    
DOI: 10.1021/jo500614a     Document Type: Article

References (111)

1. Herdewijn, P. Chem. Biodiv. 2010, 7, 1-59
2. Obika, S.; Abdur Rahman, S. M.; Fujisaka, A.; Kawada, Y.; Baba, T.; Imanishi, T. Heterocycles 2010, 81, 1347-1392
3. Prakash, T. P. Chem. Biodiv. 2011, 8, 1616-1641
4. Zhou, C.; Chattopadhyaya, J. Chem. Rev. 2012, 112, 3808-3832
5. Seth, P. P.; Vasquez, G.; Allerson, C. A.; Berdeja, A.; Gaus, H.; Kinberger, G. A.; Prakash, T. P.; Migawa, M. T.; Bhat, B.; Swayze, E. E. J. Org. Chem. 2010, 75, 1569-1581
6. Li, Q.; Yuan, F.; Zhou, C.; Plashkevych, O.; Chattopadhyaya, J. J. Org. Chem. 2010, 75, 6122-6140
7. Liu, Y.; Xu, J.; Karimiahmadabadi, M.; Zhou, C.; Chattopadhyaya, J. J. Org. Chem. 2010, 75, 7112-7128
8. Upadhayaya, R.; Deshpande, S. A.; Li, Q.; Kardile, R. A.; Sayyed, A. Y.; Kshirsagar, E. K.; Salunke, R. V.; Dixit, S. S.; Zhou, C.; Foldesi, A.; Chattopadhyaya, J. J. Org. Chem. 2011, 76, 4408-4431
9. Shrestha, A. R.; Hari, Y.; Yahara, A.; Osawa, T.; Obika, S. J. Org. Chem. 2011, 76, 9891-9899
10. Hanessian, S.; Schroeder, B. R.; Giacometti, R. D.; Merner, B. L.; Østergaard, M. E.; Swayze, E. E.; Seth, P. P. Angew. Chem., Int. Ed. 2012, 51, 11242-11245
11. Madsen, A. S.; Wengel, J. J. Org. Chem. 2012, 77, 3878-3886
12. Haziri, A. I.; Leumann, C. J. J. Org. Chem. 2012, 77, 5861-5869
13. Gerber, A.-B.; Leumann, C. J. Chem. Eur. J. 2013, 19, 6990-7006
14. Morihiro, K.; Kodama, T.; Kentefu; Moai, Y.; Veedu, R. N.; Obika, S. Angew. Chem., Int. Ed. 2013, 52, 5074-5078
15. Hari, Y.; Osawa, T.; Kotobuki, Y.; Yahara, A.; Shrestha, A. R.; Obika, S. Bioorg. Med. Chem. 2013, 21, 4405-4412
16. Hari, Y.; Morikawa, T.; Osawa, T.; Obika, S. Org. Lett. 2013, 15, 3702-3705
17. Migawa, M. T.; Prakash, T. P.; Vasquez, G.; Seth, P. P.; Swayze, E. E. Org. Lett. 2013, 15, 4316-4319
18. Hanessian, S.; Schroeder, B. R.; Merner, B. L.; Chen, B.; Swayze, E. E.; Seth, P. P. J. Org. Chem. 2013, 78, 9051-9063
19. Hanessian, S.; Wagger, J.; Merner, B. L.; Giacometti, R. D.; Østergaard, M. E.; Swayze, E. E.; Seth, P. P. J. Org. Chem. 2013, 78, 9064-9075
20. Eschenmoser, A. Science 1999, 284, 2118-2124
21. Hendrix, C.; Rosemeyer, H.; Verheggen, I.; Van Aerschot, A.; Seela, F.; Herdewijn, P. Chem. Eur. J. 1997, 3, 110-120
22. Wang, J.; Verbeure, B.; Luyten, I.; Lescrinier, E.; Froeyen, M.; Hendrix, C.; Rosemeyer, H.; Seela, F.; Van Aerschot, A.; Herdewijn, P. J. Am. Chem. Soc. 2000, 122, 8595-8602
23. Bolli, M.; Trafelet, H. U.; Leumann, C. Nucleic Acids Res. 1996, 24, 4660-4667
24. Renneberg, D.; Leumann, C. J. J. Am. Chem. Soc. 2002, 124, 5993-6002
25. Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. Chem. Commun. 1998, 455-456
26. Kaur, H.; Babu, B. R.; Maiti, S. Chem. Rev. 2007, 107, 4672-4697
27. Obika, S.; Nanbu, D.; Hari, Y.; Andoh, J.-I.; Morio, K.-I.; Doi, T.; Imanishi, T. Tetrahedron Lett. 1998, 39, 5401-5404
28. Kool, E. T. Chem. Rev. 1997, 97, 1473-1487
29. Duca, M.; Vekhoff, P.; Oussedik, K.; Halby, L.; Arimondo, P. B. Nucleic Acids Res. 2008, 36, 5123-5138
30. Bennett, C. F.; Swayze, E. E. Annu. Rev. Pharmacol. Toxicol. 2010, 50, 259-293
31. Østergaard, M. E.; Hrdlicka, P. J. Chem. Soc. Rev. 2011, 40, 5771-5788
32. Watts, J. K.; Corey, D. R. J. Pathol. 2012, 226, 365-379
33. Matsui, M.; Corey, D. R. Drug Discuss. Today 2012, 17, 443-450
34. Dong, H.; Lei, J.; Ding, L.; Wen, Y.; Ju, H.; Zhang, X. Chem. Rev. 2013, 113, 6207-6233
35. Wahlestedt, C.; Salmi, P.; Good, L.; Kela, J.; Johnsson, T.; Hokfelt, T.; Broberger, C.; Porreca, F.; Lai, J.; Ren, K. K.; Ossipov, M.; Koshkin, A.; Jacobsen, N.; Skouv, J.; Oerum, H.; Jacobsen, M. H.; Wengel, J. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5633-5638
36. Graziewicz, M. A.; Tarrant, T. K.; Buckley, B.; Roberts, J.; Fulton, L.; Hansen, H.; Ørum, H.; Kole, R.; Sazani, P. Mol. Ther. 2008, 16, 1316-1322
37. Straarup, E. M.; Fisker, N.; Hedtjarn, M.; Lindholm, M. W.; Rosenbohm, C.; Aarup, V.; Hansen, H. F.; Ørum, H.; Hansen, J. B.; Koch, T. Nucleic Acids Res. 2010, 38, 7100-7111
38. Lanford, R. E.; Hildebrandt-Eriksen, E. S.; Petri, A.; Persson, R.; Lindow, M.; Munk, M. E.; Kauppinen, S.; Ørum, H. Science 2010, 327, 198-201
39. Obad, S.; Dos Santos, C. O.; Petri, A.; Heidenblad, M.; Broom, O.; Ruse, C.; Fu, C.; Lindow, M.; Stenvang, J.; Straarup, E. M.; Hansen, H. F.; Koch, T.; Pappin, D.; Hannon, G. J.; Kauppinen, S. Nat. Genet. 2011, 43, 371-378
40. For an updated clinical status of LNA, see: http://www.santaris.com/ product-pipeline.
41. Wienholds, E.; Kloostermann, W. P.; Misk, W. P.; Alvarez-Saavedra, E.; Berezikov, E.; Bruijn, E.; Horvitz, H. R.; Kauppinen, S.; Plasterk, R. H. A. Nature 2005, 309, 310-311
42. Sørensen, M. D.; Kværnø, L.; Bryld, T.; Håkansson, A. E.; Verbeure, B.; Gaubert, G.; Herdewijn, P.; Wengel, J. J. Am. Chem. Soc. 2002, 124, 2164-2176
43. Sørensen, M. D.; Petersen, M.; Wengel, J. Chem. Commun. 2003, 2130-2131
44. Morita, K.; Takagi, M.; Hasegawa, C.; Kaneko, M.; Tsutsumi, S.; Sone, J.; Ishikawa, T.; Imanishi, T.; Koizumi, M. Bioorg. Med. Chem. 2003, 11, 2211-2226
45. Fluiter, K.; Frieden, M.; Vreijling, J.; Rosenbohm, C.; De Wissel, M. B.; Christensen, S. M.; Koch, T.; Ørum, H.; Baas, F. ChemBioChem 2005, 6, 1104-1109
46. Albæk, N.; Petersen, M.; Nielsen, P. J. Org. Chem. 2006, 71, 7731-7740
47. Varghese, O. P.; Barman, J.; Pathmasiri, W.; Plashkevych, O.; Honcharenko, D.; Chattopadhyaya, J. J. Am. Chem. Soc. 2006, 128, 15173-15187
48. Abdur Rahman, S. M.; Seki, S.; Obika, S.; Yoshikawa, H.; Miyashita, K.; Imanishi, T. J. Am. Chem. Soc. 2008, 130, 4886-4896
49. Mitsuoka, Y.; Kodama, T.; Ohnishi, R.; Hari, Y.; Imanishi, T.; Obika, S. Nucleic Acids Res. 2009, 37, 1225-1238
50. Zhou, C.; Liu, Y.; Andaloussi, M.; Badgujar, N.; Plashkevych, O.; Chattopadyaya, J. J. Org. Chem. 2009, 74, 118-134
51. Seth, P. P.; Siwkowski, A.; Allerson, C. R.; Vasquez, G.; Lee, S.; Prakash, T. P.; Wancewicz, E. V.; Witchell, D.; Swayze, E. E. J. Med. Chem. 2009, 52, 10-13
52. Luyten, I.; Herdewijn, P. Eur. J. Med. Chem. 1998, 33, 515-576
53. Ahmadian, M.; Bergstrom, D. E. In Modified Nucleotides in Biochemistry, Biotechnology and Medicine, 1 st ed.; Herdewijn, P., Ed.; Wiley-VCH: Weinheim, Germany, 2008; pp 251-276.
54. Wagner, R. W.; Matteucci, M. D.; Lewis, J. G.; Gutierrez, A. J.; Moulds, C.; Froehler, B. C. Science 1993, 260, 1510-1513
55. Hashimoto, H.; Nelson, M. G.; Switzer, C. J. Am. Chem. Soc. 1993, 115, 7128-7134
56. Sagi, J.; Szemzo, A.; Ebinger, K.; Szabolcs, A.; Sagi, G.; Ruff, E.; Otvos, L. Tetrahedron Lett. 1993, 34, 2191-2194
57. Ahmadian, M.; Zhang, P. M.; Bergstrom, D. E. Nucleic Acids Res. 1998, 26, 3127-3135
58. Heystek, L. E.; Zhou, H. Q.; Dande, P.; Gold, B. J. Am. Chem. Soc. 1998, 120, 12165-12166
59. Kottysch, T.; Ahlborn, C.; Brotzel, F.; Richert, C. Chem. Eur. J. 2004, 10, 4017-4028
60. Okamoto, A.; Kanatani, K.; Saito, I. J. Am. Chem. Soc. 2004, 126, 4820-4827
61. Booth, J.; Brown, T.; Vadhia, S. J.; Lack, O.; Cummins, W. J.; Trent, J. O.; Lane, A. N. Biochemistry 2005, 44, 4710-4719
62. Skorobogatyi, M. V.; Malakhov, A. D.; Pchelintseva, A. A.; Turban, A. A.; Bondarev, S. L.; Korshun, V. A. ChemBioChem 2006, 7, 810-816
63. Østergaard, M. E.; Guenther, D. C.; Kumar, P.; Baral, B.; Deobald, L.; Paszczynski, A. J.; Sharma, P. K.; Hrdlicka, P. J. Chem. Commun. 2010, 4929-4931
64. Barbaric, J.; Wagenknecht, H. A. Org. Biomol. Chem. 2006, 4, 2088-2090
65. Kocalka, P.; Andersen, N. K.; Jensen, F.; Nielsen, P. ChemBioChem 2007, 8, 2106-2116
66. Nguyen, T. N.; Brewer, A.; Stulz, E. Angew. Chem., Int. Ed. 2009, 48, 1974-1977
67. Kaura, M.; Kumar, P.; Hrdlicka, P. J. Org. Biomol. Chem. 2012, 10, 8575-8578
68. Sinkeldam, R. W.; Greco, N. J.; Tor, Y. Chem. Rev. 2010, 110, 2579-2619
69. For a recent example, see: Andersen, N. K.; Anderson, B. A.; Wengel, J.; Hrdlicka, P. J. J. Org. Chem. 2013, 78, 12690-12702
70. Østergaard, M. E.; Kumar, P.; Baral, B.; Raible, D. J.; Kumar, T. S.; Anderson, B. A.; Guenther, D. C.; Deobald, L.; Paszczynski, A. J.; Sharma, P. K.; Hrdlicka, P. J. ChemBioChem 2009, 10, 2740-2743
71. Kumar, P.; Østerggard, M. E.; Hrdlicka, P. J. Curr. Protocols Nucleic Acid Chem. 2011, 44, 4.43.1-4.43.22
72. Sonogashira, K.; Tohda, Y.; Hagihara, N. Tetrahedron Lett. 1975, 50, 4467-4470
73. Agrofoglio, L. A.; Gillaizeau, I.; Saito, Y. Chem. Rev. 2003, 103, 1875-1916
74. Schrock, A. K.; Schuster, G. B. J. Am. Chem. Soc. 1984, 106, 5234-5240
75. Park, S. Y.; Yoon, J. H.; Hong, C. S.; Souane, R.; Kim, J. S.; Mathews, S. E.; Vicens, J. J. Org. Chem. 2008, 73, 8212-8218
76. Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. Angew. Chem., Int. Ed. 2002, 41, 2596-2599
77. Bryld, T.; Lomholt, C. Nucleosides Nucleotides Nucleic Acids 2007, 26, 1645-1647
78. Mergny, J. L.; Lacroix, L. Oligonucleotides 2003, 13, 515-537
79. Gyi, J. I.; Gao, D.; Conn, G. L.; Trent, J. O.; Brown, T.; Lane, A. N. Nucleic Acids Res. 2003, 31, 2683-2693
80. Demidov, V. V.; Frank-Kamenetskii, M. D. Trends Biochem. Sci. 2004, 29, 62-71
81. Korshun, V. A.; Stetsenko, D. A.; Gait, M. J. J. Chem. Soc., Perkin Trans. 1 2002, 1092-1104
82. Dohno, C.; Saito, I. ChemBioChem 2005, 6, 1075-1081
83. Kumar, T. S.; Madsen, A. S.; Østergaard, M. E.; Sau, S. P.; Wengel, J.; Hrdlicka, P. J. J. Org. Chem. 2009, 74, 1070-1081
84. Marin, V.; Hansen, H. F.; Koch, T. R.; Armitage, B. A. J. Biomol. Struct. Dyn. 2004, 21, 841-850
85. Mayer, E.; Valis, L.; Wagner, C.; Rist, M.; Amann, N.; Wagenknecht, H.-A. ChemBioChem 2004, 5, 865-868
86. Hwang, G. T.; Seo, Y. J.; Kim, S. J.; Kim, B. H. Tetrahedron Lett. 2004, 45, 3543-3546
87. Dougherty, G.; Pilbrow, J. R. Int. J. Biochem. 1984, 16, 1179-1192
88. Manoharan, M.; Tivel, K. L.; Zhao, M.; Nafisi, K.; Netzel, T. L. J. Phys. Chem. 1995, 99, 17461-17472
89. Seo, Y. J.; Ryu, J. H.; Kim, B. H. Org. Lett. 2005, 7, 4931-4933
90. Østergaard, M. E.; Kumar, P.; Baral, B.; Guenther, D. C.; Anderson, B. A.; Ytreberg, F. M.; Deobald, L.; Paszczynski, A. J.; Sharma, P. K.; Hrdlicka, P. J. Chem. Eur. J. 2011, 17, 3157-3165
91. Seitz, O.; Schmuck, E. C.; Wennemers, H. Homogeneous DNA Detection. In Highlights in Bioorganic Chemistry; Wiley-VCH: Weinheim, Germany, 2004; pp 311-328.
92. Yamana, K.; Iwase, R.; Furutani, S.; Tsuchida, H.; Zako, H.; Yamaoka, T.; Murakami, A. Nucleic Acids Res. 1999, 27, 2387-2392
93. Yamana, K.; Zako, H.; Asazuma, K.; Iwase, R.; Nakano, H.; Murakami, A. Angew. Chem., Int. Ed. 2001, 40, 1104-1106
94. Mahara, A.; Iwase, R.; Sakamoto, T.; Yamana, K.; Yamaoka, T.; Murakami, A. Angew. Chem., Int. Ed. 2002, 41, 3648-3650
95. Hrdlicka, P. J.; Babu, B. R.; Sørensen, M. D.; Harrit, N.; Wengel, J. J. Am. Chem. Soc. 2005, 127, 13293-13299
96. Astakhova, I. V.; Korshun, V. A.; Wengel, J. Chem. Eur. J. 2008, 14, 11010-11026
97. Wang, G.; Bobkov, G. V.; Mikhailov, S. N.; Schepers, G.; van Aerschot, A.; Rozenski, J.; van der Auweraer, M.; Herdewijn, P.; Feyter, S. D. ChemBioChem 2009, 10, 1175-1185
98. Østergaard, M. E.; Cheguru, P.; Papasani, M. R.; Hill, R. A.; Hrdlicka, P. J. J. Am. Chem. Soc. 2010, 132, 14221-14228
99. Astakhova, I. V.; Lindegaard, D.; Korshun, V. A.; Wengel, J. Chem. Commun. 2010, 46, 8362-8364
100. Förster, U.; Lommel, K.; Sauter, D.; Grünewald, C.; Engels, J. W.; Wachtveitl, J. ChemBioChem 2010, 11, 664-672
101. Mansawat, W.; Boonlua, C.; Siriwong, K.; Vilaivan, T. Tetrahedron 2012, 68, 3988-3995
102. Shen, L.; Siwkowski, A.; Wancewicz, E. V.; Lesnik, E.; Butler, M.; Witchell, D.; Vasquez, G.; Ross, B.; Acevedo, O.; Inamati, G.; Sasmor, H.; Manoharan, M.; Monia, B. P. Antisense Nucleic Acid Drug Dev. 2003, 13, 129-142
103. Kumar, P.; Baral, B.; Anderson, B. A.; Guenther, D. C.; Østergaard, M. E.; Sharma, P. K.; Hrdlicka, P. J. J. Org. Chem. 2014, 10.1021/jo5006153
104. Suenaga, M.; Kaneko, Y.; Kadokawa, J.; Nishikawa, T.; Mori, H.; Tabata, M. Macromol. Biosci. 2006, 6, 1009-1018
105. Godeau, G.; Barthélémy, P. Langmuir 2009, 25, 8447-8450
106. Ott, K.; Schmidt, K.; Kircher, B.; Schumacher, P.; Wiglenda, T.; Gust, R. J. Med. Chem. 2005, 48, 622-629
107. Trybulski, E.; Zhang, J.; Kramss, R. H.; Mangano, R. M. J. Med. Chem. 1993, 36, 3533-3541
108. Gottlieb, H. E.; Kotlyar, V.; Nudelman, A. J. Org. Chem. 1997, 62, 7512-7515
109. Qu, J.; Shiotsuki, M.; Sanda, F.; Masuda, T. Macromol. Chem. Phys. 2007, 208, 823-832
110. Wenting, W.; Wanhua, W.; Shaomin, J.; Hunin, G.; Jiazhang, Z. Eur. J. Inorg. Chem. 2010, 4470-4482
111. Andronova, V. L.; Skorobogtyi, M. V.; Manasova, E. V.; Berlin, Y. A.; Korshun, V. A.; Galegov, G. A. Russ. J. Bioorg. Chem. 2003, 29, 262-266