Advertisement

2′,4′-Bridged Nucleic Acids Containing Plural Heteroatoms in the Bridge Moiety

  • Yoshiyuki Hari
  • Satoshi Obika
Chapter

Abstract

Bridge modifications between the 2′- and 4′-positions of a nucleoside have attracted much attention for improving properties of nucleic acid drugs, and many classes of 2′,4′-bridged nucleic acids have been developed to date. Evaluation of oligonucleotides containing 2′,4′-bridged nucleic acids suggests that, in addition to the bridge size, the number, type, and position of atoms composing the bridge unit affect (i) the binding affinity to target nucleic acid, (ii) resistance against nuclease degradation, and other factors. The addition of plural heteroatoms is an attractive bridge modification because interaction of the heteroatom with water can affect the properties of the oligonucleotides. In this chapter, focusing on 2′,4′-bridged nucleic acids containing plural heteroatoms in the bridge moiety, we mainly describe the design concept and synthesis. In addition, properties of 2′,4′-bridged nucleic acids are briefly explained.

Keywords

2′,4′-Bridged nucleic acid Modified oligonucleotide Oligonucleotide synthesis Duplex-forming ability Nuclease resistance 

References

  1. 1.
    Singh SK, Koshkin AA, Wengel J, Nielsen P (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem Commun: 455–456Google Scholar
  2. 2.
    Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J (1998) LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54:3607–3630CrossRefGoogle Scholar
  3. 3.
    Obika S, Nanbu D, Hari Y, Morio K, In Y, Ishida T, Imanishi T (1997) Synthesis of 2′-Ο,4′-C-methyleneuridine and – cytidine. Novel bicyclic nucleosides having a fixed C3′-endo sugar puckering. Tetrahedron Lett 38:8735–8738CrossRefGoogle Scholar
  4. 4.
    Obika S, Nanbu D, Hari Y, Ando J, Morio K, Doi T, Imanishi T (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O,4′-C-methyleneribonucleosides. Tetrahedron Lett 39:5401–5404CrossRefGoogle Scholar
  5. 5.
    Petersen M, Wengel J (2003) LNA: a versatile tool for therapeutics and genomics. Trends Biotech 21:74–81CrossRefGoogle Scholar
  6. 6.
    Koch T (2003) Locked nucleic acids: a family of high affinity nucleic acid probes. J Phys Condens Matter 15:S1861–S1871CrossRefGoogle Scholar
  7. 7.
    Vester B, Wengel J (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43:13233–13241CrossRefPubMedGoogle Scholar
  8. 8.
    Jepsen JS, Sørensen MD, Wengel J (2004) Locked nucleic acid: a potent nucleic acid analog in therapeutics and biotechnology. Oligonucleotides 14:130–146CrossRefPubMedGoogle Scholar
  9. 9.
    Kaur H, Babu R, Maiti S (2007) Perspectives on chemistry and therapeutic applications of locked nucleic acid (LNA). Chem Rev 107:4672–4697CrossRefPubMedGoogle Scholar
  10. 10.
    Veedu RN, Wengel J (2009) Locked nucleic acid as a novel class of therapeutic agents. RNA Biol 6:321–323CrossRefPubMedGoogle Scholar
  11. 11.
    Campbell MA, Wengel J (2011) Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 40:5680–5689CrossRefPubMedGoogle Scholar
  12. 12.
    Zhou C, Chattopadhyaya J (2009) The synthesis of therapeutic locked nucleos(t)ides. Curr Opin Drug Discov Dev 12:876–898Google Scholar
  13. 13.
    Rahman SMA, Imanishi T, Obika S (2009) Synthesis of several types of bridged nucleic acids. Chem Lett 38:512–517CrossRefGoogle Scholar
  14. 14.
    Obika S, Rahman SMA, Fujisaka A, Kawada Y, Baba T, Imanishi T (2010) Bridged nucleic acids: development, synthesis and properties. Heterocycles 81:1347–1392CrossRefGoogle Scholar
  15. 15.
    Yamamoto T, Nakatani M, Narukawa K, Obika S (2011) Antisense drug discovery and development. Fut Med Chem 3:339–365CrossRefGoogle Scholar
  16. 16.
    Zhou C, Chattopadhyaya J (2012) Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 112:3808–3832CrossRefPubMedGoogle Scholar
  17. 17.
    Astakhova IK, Wengel J (2014) Scaffolding along nucleic acid duplexes using 2′-amino-locked nucleic acids. Acc Chem Res 47:1768–1777CrossRefPubMedGoogle Scholar
  18. 18.
    Morita K, Hasegawa C, Kaneko M, Tsutsumi S, Sone J, Ishikawa T, Imanishi T, Koizumi M (2002) 2′-O,4′-C-Ethylene-bridged nucleic acids (ENA): high-nuclease-resistant and thermodynamically stable oligonucleotides for antisense drug. Bioorg Med Chem Lett 12:73–76CrossRefPubMedGoogle Scholar
  19. 19.
    Morita K, Takagi M, Hasegawa C, Kaneko M, Tsutsumi S, Sone J, Ishikawa T, Imanishi T, Koizumi M (2003) Synthesis and properties of 2′-O,4′-C-ethylene-bridged nucleic acids (ENA) as effective antisense oligonucleotides. Bioorg Med Chem 11:2211–2226CrossRefPubMedGoogle Scholar
  20. 20.
    Wang G, Gunic E, Girardet J-L, Stoisavljevic V (1999) Conformationally locked nucleosides. Synthesis and hybridization properties of oligodeoxynucleotides containing 2′,4′-C-bridged 2′-deoxynucleosides. Bioorg Med Chem Lett 9:1147–1150CrossRefPubMedGoogle Scholar
  21. 21.
    Wang G, Girardet J-L, Gunic E (1999) Conformationally locked nucleosides. Synthesis and stereochemical assignments of 2′-C,4′-C-bridged bicyclonucleosides. Tetrahedron 55:7707–7724CrossRefGoogle Scholar
  22. 22.
    Singh SK, Kumar R, Wengel J (1998) Synthesis of novel bicycle[2.2.1] ribonucleosides: 2′-amino- and 2′-thio-LNA monomeric nucleosides. J Org Chem 63:6078–6079CrossRefPubMedGoogle Scholar
  23. 23.
    Singh SK, Kumar R, Wengel J (1998) Synthesis of 2′-amino-LNA: a novel conformationally restricted high-affinity oligonucleotide analogue with a handle. J Org Chem 63:10035–10039CrossRefGoogle Scholar
  24. 24.
    Kumar R, Singh SK, Koshkin AA, Rajwanshi VK, Meldgaard M, Wengel J (1998) The first analogues of LNA (locked nucleic acids): phosphorothioate-LNA and 2′-thio-LNA. Bioorg Med Chem Lett 8:2219–2222CrossRefPubMedGoogle Scholar
  25. 25.
    Morihiro K, Kodama T, Kentefu, Moai Y, Veedu RN, Obika S (2013) Selenomethylene locked nucleic acid enables reversible hybridization in response to redox changes. Angew Chem Int Ed 52:5074–5078CrossRefGoogle Scholar
  26. 26.
    Xu J, Liu Y, Dupouy C, Chattopadhyaya J (2009) Synthesis of conformationally locked carba-LNAs through intramolecular free-radical addition to C=N. Electrostatic and steric implication of the carba-LNA substituents in the modified oligos for nuclease and thermodynamic stabilities. J Org Chem 74:6534–6554CrossRefPubMedGoogle Scholar
  27. 27.
    Sørensen MD, Petersen M, Wengel J (2003) Functionalized LNA (locked nucleic acid): high-affinity hybridization of oligonucleotides containing N-acylated and N-alkylated 2′-amino-LNA monomers. Chem Commun: 2130–2131Google Scholar
  28. 28.
    Varghese OP, Barman J, Pathmasiri W, Plashkevych O, Honcharenko D, Chattopadhyaya J (2006) Conformationally constrained 2′-N,4′-C-ethylene-bridged thymidine (aza-ENA-T): Synthesis, structure, physical, and biochemical studies of aza-ENA-T-modified oligonucleotides. J Am Chem Soc 128:15173–15187CrossRefPubMedGoogle Scholar
  29. 29.
    Albæk N, Petersen M, Nielsen P (2006) Analogues of a locked nucleic acid with three-carbon 2′,4′-linkages: synthesis by ring-closing metathesis and influence on nucleic acid duplex stability and structure. J Org Chem 71:7731–7740CrossRefPubMedGoogle Scholar
  30. 30.
    Srivastava P, Barman J, Pathmasiri W, Plashkevych O, Wenska M, Chattopadhyaya J (2007) Five- and six-membered conformationally locked 2′,4′-carbocyclic ribo-thymidines: synthesis, structure, and biochemical studies. J Am Chem Soc 129:8362–8379CrossRefPubMedGoogle Scholar
  31. 31.
    Zhou C, Liu Y, Andaloussi M, Badgujar N, Plashkevych O, Chattopadhyaya J (2009) Fine tuning of electrostatics around the internucleotidic phosphate through incorporation of modified 2′,4′-carbocyclic-LNAs and – ENAs leads to significant modulation of antisense properties. J Org Chem 74:118–134CrossRefPubMedGoogle Scholar
  32. 32.
    Zhou C, Plashkevych O, Chattopadhyaya J (2009) Double sugar and phosphate backbone-constrained nucleotides: synthesis, structure, stability, and their incorporation into oligodeoxynucleotides. J Org Chem 74:3248–3265CrossRefPubMedGoogle Scholar
  33. 33.
    Kumar S, Hansen MH, Albæk N, Steffansen SI, Petersen M, Nielsen P (2009) Synthesis of functionalized carbocyclic locked nucleic acid analogues by ring-closing diene and enyne metathesis and their influence on nucleic acid stability and structure. J Org Chem 74:6756–6769CrossRefPubMedGoogle Scholar
  34. 34.
    Seth PP, Vasquez G, Allerson CA, Berdeja A, Gaus H, Kinberger GA, Prakash TP, Migawa MT, Bhat B, Swayze EE (2010) Synthesis and biophysical evaluation of 2′,4′-constrained 2′O-methoxyethyl and 2′,4′-constrained 2′O-ethyl nucleic acid analogues. J Org Chem 75:1569–1581CrossRefPubMedGoogle Scholar
  35. 35.
    Liu Y, Xu J, Karimiahmadabadi M, Zhou C, Chattopadhyaya J (2010) Synthesis of 2′,4′-propylene-bridged (carba-ENA) thymidine and its analogues: the engineering of electrostatic and steric effects at the bottom of the minor groove for nucleobase and thermodynamic stabilities and elicitation of RNase H. J Org Chem 75:7112–7128CrossRefPubMedGoogle Scholar
  36. 36.
    Johannsen MW, Crispino L, Wamberg MC, Kalra N, Wengel J (2011) Amino acids attached to 2′-amino-LNA: synthesis and excellent duplex stability. Org Biomol Chem 9:243–252CrossRefPubMedGoogle Scholar
  37. 37.
    Seth PP, Allerson CA, Berdeja A, Siwkowski A, Pallan PS, Gaus H, Prakash TP, Watt AT, Egli M, Swayze EE (2010) An exocyclic methylene group acts as a bioisostere of the 2′-oxygen atom in LNA. J Am Chem Soc 132:14942–14950CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Upadhayaya RS, Deshpande SG, Li Q, Kardile RA, Sayyed AY, Kshirsagar EK, Salunke RV, Dixit SS, Zhou C, Földesi A, Chattopadhyaya J (2011) Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3′-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry. J Org Chem 76:4408–4431CrossRefPubMedGoogle Scholar
  39. 39.
    Yamaguchi T, Horiba M, Obika S (2015) Synthesis and properties of 2′-O,4′-C-spirocyclopropylene bridged nucleic acid (scpBNA), an analogue of 2′,4′-BNA/LNA bearing a cyclopropane ring. Chem Commun 51:9737–9740CrossRefGoogle Scholar
  40. 40.
    Yahara A, Shrestha AR, Yamamoto T, Hari Y, Osawa T, Yamaguchi M, Nishida M, Kodama T, Obika S (2012) Amido-bridged nucleic acids (AmNAs): synthesis, duplex stability, nuclease resistance, and in vitro antisense potency. ChemBioChem 13:2513–2516CrossRefPubMedGoogle Scholar
  41. 41.
    Yamamoto T, Yahara A, Waki R, Yasuhara H, Wada F, Harada-Shiba M, Obika S (2015) Amido-bridged nucleic acids with small hydrophobic residues enhance hepatic tropism of antisense oligonucleotides in vivo. Org Biomol Chem 13:3757–3765CrossRefPubMedGoogle Scholar
  42. 42.
    Martin P (1995) Ein neuer zugang zu 2′-O-alkylribonucleosiden und eigenschaften deren oligonucleotide. Helv Chim Acta 78:486–504CrossRefGoogle Scholar
  43. 43.
    Baker BF, Lot SS, Condon TP, Cheng-Flournoy S, Lesnik EA, Sasmor HM, Bennett (1997) 2′-O-(2-methoxy)ethyl-modified anti-intercellular adhesion molecule 1(ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells. J Biol Chem 272:11994–12000CrossRefPubMedGoogle Scholar
  44. 44.
    Seth PP, Siwkowski A, Allerson CA, Vasquez G, Lee S, Prakash TP, Wancewicz EV, Witchell D, Swayze EE (2009) Short antisense oligonucleotides with novel 2′-4′ conformationally restricted nucleoside analogues show improved potency without increased toxicity in animals. J Med Chem 52:10–13CrossRefPubMedGoogle Scholar
  45. 45.
    Prakash TP, Siwkowski A, Allerson CR, Migawa MT, Lee S, Gaus HJ, Black C, Seth PP, Swayze EE, Bhat B (2010) Antisense oligonucleotides containing conformationally constrained 2′,4′-(N-methoxy)aminomethylene and 2′,4′-aminooxymethylene and 2′-Ο,4′-C-aminomethylene bridged nucleoside analogues show improved potency in animal models. J Med Chem 53:1636–1650CrossRefPubMedGoogle Scholar
  46. 46.
    Mori K, Kodama T, Baba T, Obika S (2011) Bridged nucleic acid conjugates at 6′-thiol: synthesis, hybridization properties and nuclease resistances. Org Biomol Chem 9:5272–5279CrossRefPubMedGoogle Scholar
  47. 47.
    Baba T, Kodama T, Mori K, Imanishi T, Obika S (2010) A novel bridged nucleoside bearing a conformationally switchable sugar moiety in response to redox changes. Chem Commun 46:8058–8060CrossRefGoogle Scholar
  48. 48.
    Barrón LB, Waterman KC, Filipiak P, Hug GL, Nauser T, Schöneich C (2004) Mechanism and kinetics of photoisomerization of a cyclic disulfide, trans-4,5-dihydroxy-1,2-dithiacyclohexane. J Phys Chem A 108:2247–2255CrossRefGoogle Scholar
  49. 49.
    Barrón LB, Waterman KC, Offerdahl TJ, Munson E, Schöneich C (2005) Reactions of aliphatic thiyl radicals in the solid state: photoisomerization of trans-4,5-dihydroxy-1,2-dithiacyclohexane and oxidation of dithiothreitol. J Phys Chem A 109:9241–9248CrossRefPubMedGoogle Scholar
  50. 50.
    Shrestha AR, Kotobuki Y, Hari Y, Obika S (2014) Guanidine bridged nucleic acid (GuNA): an effect of a cationic bridged nucleic acid on DNA binding affinity. Chem Commun 50:575–577CrossRefGoogle Scholar
  51. 51.
    Rahman SMA, Seki S, Obika S, Yoshikawa H, Miyashita K, Imanishi T (2008) Design, synthesis, and properties of 2′,4′-BNANC: a bridged nucleic acid analogue. J Am Chem Soc 130:4886–4896CrossRefPubMedGoogle Scholar
  52. 52.
    Miyashita K, Rahman SMA, Seki S, Obika S, Imanishi T (2007) N-methyl substituted 2′,4′-BNANC: a highly nuclease-resistant nucleic acid analogue with high-affinity RNA selective hybridization. Chem Commun: 3765–3767Google Scholar
  53. 53.
    Rahman SMA, Seki S, Obika S, Haitani S, Miyashita K, Imanishi T (2007) Highly stable pyrimidine-motif triplex formation at physiological pH values by a bridged nucleic acid analogue. Angew Chem Int Ed 46:4306–4309CrossRefGoogle Scholar
  54. 54.
    Yamamoto T, Yasuhara H, Wada F, Harada-Shiba M, Imanishi T, Obika S (2012) Superior silencing by 2′,4′-BNANC-based short antisense oligonucleotides compared to 2′,4′-BNA/LNA-based apolipoprotein B antisense inhibitors. J Nucleic Acids 2012:707323CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Yamamoto T, Harada-Shiba M, Nakatani M, Wada S, Yasuhara H, Narukawa K, Sasaki K, Shibata M, Torigoe H, Yamaoka T, Imanishi T, Obika S (2012) Cholesterol-lowering action of BNA-based antisense oligonucleotides targeting PCSK9 in atherogenic diet-induced hypercholesterolemic mice. Mol Ther Nucleic Acids 1:e22CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Kondo J, Nomura Y, Kitahara Y, Obika S, Torigoe H (2016) The crystal structure of 2′,4′-BNANC[N-Me]-modified antisense gapmer in complex with the target RNA. Chem Commun 52:2354–2357CrossRefGoogle Scholar
  57. 57.
    Torigoe H, Rahman SM, Takuma H, Sato N, Imanishi T, Obika S, Sasaki K (2011) Interrupted 2′-O,4′-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition. Nucleosides Nucleotides Nucleic Acids 30:63–81CrossRefPubMedGoogle Scholar
  58. 58.
    Shrestha AR, Hari Y, Yahara A, Osawa T, Obika S (2011) Synthesis and properties of a bridged nucleic acid with a perhydro-1,2-oxazin-3-one ring. J Org Chem 76:9891–9899CrossRefPubMedGoogle Scholar
  59. 59.
    Hari Y, Osawa T, Kotobuki Y, Yahara A, Shrestha AR, Obika S (2013) Synthesis and properties of thymidines with six-membered amide bridge. Bioorg Med Chem 21:4405–4412CrossRefPubMedGoogle Scholar
  60. 60.
    Mitsuoka Y, Fujimura Y, Waki R, Kugimiya A, Yamamoto T, Hari Y, Obika S (2014) Sulfonamide-bridged nucleic acid: synthesis, high RNA selective hybridization, and high nuclease resistance. Org Lett 16:5640–5643CrossRefPubMedGoogle Scholar
  61. 61.
    Mitsuoka Y, Aoyama H, Kugimiya A, Fujimura Y, Yamamoto T, Waki R, Wada F, Tahara S, Sawamura M, Noda M, Hari Y, Obika S (2016) Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure. Org Biomol Chem.  https://doi.org/10.1039/c6ob01051b
  62. 62.
    Gryaznov SM, Letsinger RL (1992) Selective O-phophitilation with nucleoside phosphoramidite reagents. Nucleic Acids Res 20:1879–1882Google Scholar
  63. 63.
    Barman J, Gurav D, Oommen OP, Varghese OP (2015) 2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability. RSC Adv 5:12257–12260Google Scholar
  64. 64.
    Hari Y, Obika S, Ohnishi R, Eguchi K, Osaki T, Ohishi H, Imanishi T (2006) Synthesis and properties of 2′-O,4′-C-methyleneoxymethylene bridged nucleic acid. Bioorg Med Chem 14:1029–1038CrossRefPubMedGoogle Scholar
  65. 65.
    Mitsuoka Y, Kodama T, Ohnishi R, Hari Y, Imanishi T, Obika S (2009) A bridged nucleic acid, 2′,4′-BNACOC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2′,4′-BNACOC monomers and RNA-selective nucleic-acid recognition. Nucleic Acids Res 37:1225–1238CrossRefPubMedPubMedCentralGoogle Scholar
  66. 66.
    Morihiro K, Kodama T, Nishida M, Imanishi T, Obika S (2009) Synthesis of light-responsive bridged nucleic acid and changes in affinity with complementary ssRNA. ChemBioChem 10:1784–1788CrossRefPubMedGoogle Scholar
  67. 67.
    Morihiro K, Kodama T, Obika S (2011) Benzylidene acetal type bridged nucleic acids: changes in properties upon cleavage of the bridge triggered by external stimuli. Chem Eur J 17:7918–7926CrossRefPubMedGoogle Scholar
  68. 68.
    Kasahara Y, Kitadume S, Morihiro K, Kuwahara M, Ozaki H, Sawai H, Imanishi T, Obika S (2010) Effect of 3′-end capping of aptamer with various 2′,4′-bridged nucleotides: enzymatic post-modification toward a practical use of polyclonal aptamers. Bioorg Med Chem Lett 20:1626–1629CrossRefPubMedGoogle Scholar
  69. 69.
    Nishida M, Baba T, Kodama T, Yahara A, Imanishi T, Obika S (2010) Synthesis, RNA selective hybridization and high nuclease resistance of an oligonucleotide containing novel bridged nucleic acid with cyclic urea structure. Chem Commun 46:5283–5285CrossRefGoogle Scholar
  70. 70.
    Hari Y, Morikawa T, Osawa T, Obika S (2013) Synthesis and properties of 2′-O, 4′-C-ethyleneoxy bridged 5-methyluridine. Org Lett 15:3702–3705CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Faculty of Pharmaceutical SciencesTokushima Bunri UniversityTokushimaJapan
  2. 2.Osaka UniversitySuitaJapan

Personalised recommendations