1,5-anhydro-4-O-(tert-butyldimethylsilyl)-2,3-dideoxy-6-O-(4,4'-dimethoxytrityl)-3-fluoro-2-(thymin-1-yl)-D-altritol | 1117903-22-6

• 分子结构分类: 有机化合物 - 苯类化合物 - 三苯基化合物
• 英文名称: 1,5-anhydro-4-O-(tert-butyldimethylsilyl)-2,3-dideoxy-6-O-(4,4'-dimethoxytrityl)-3-fluoro-2-(thymin-1-yl)-D-altritol
• 英文别名: 1-[(3R,4S,5R,6R)-6-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-5-[tert-butyl(dimethyl)silyl]oxy-4-fluorooxan-3-yl]-5-methylpyrimidine-2,4-dione
• CAS: 1117903-22-6
• 化学式: C₃₈H₄₇FN₂O₇Si
• 分子量: 690.884
• InChiKey: LZXKMBFLVVKBIA-YVEASBDZSA-N

物化性质

• 密度：
  1.21±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  6.54
• 重原子数：
  49
• 可旋转键数：
  12
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.42
• 拓扑面积：
  95.6
• 氢给体数：
  1
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  1,5-anhydro-4-O-(tert-butyldimethylsilyl)-2,3-dideoxy-6-O-(4,4'-dimethoxytrityl)-3-fluoro-2-(thymin-1-yl)-D-altritol 在 N-甲基咪唑 、 四氮唑 、 四丁基氟化铵 、 氨 、 三氯氧磷 作用下， 以 四氢呋喃 、 1,4-二氧六环 、 水 、 N,N-二甲基甲酰胺 、 乙腈 为溶剂， 反应 56.67h， 生成 1,5-anhydro-2-(4-N-benzoyl-5-methyl-cytosin-1-yl)-4-O-(cyanoethoxydiisopropylaminophosphinyl)-2,3-dideoxy-6-O-(4,4'-dimethoxytrityl)-3-fluoro-D-altritol
  参考文献：
  名称：

  Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3′-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

  摘要：

  The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F center dot center dot center dot H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonudeotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)center dot center dot center dot H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.

  DOI：

  10.1021/ja207086x
• 作为产物：
  描述：

  1,5-anhydro-4,6-O-benzylidene-2-deoxy-3-O-methanesulfonyl-2-(thymin-1-yl)-D-altritol 在 吡啶 、 咪唑 、 全氟丁基磺酰氟 、 20% palladium hydroxide on charcoal 、 氢气 、 1,8-二氮杂双环[5.4.0]十一碳-7-烯 、 sodium hydroxide 作用下， 以 1,4-二氧六环 、 甲醇 、 N,N-二甲基甲酰胺 为溶剂， 反应 69.0h， 生成 1,5-anhydro-4-O-(tert-butyldimethylsilyl)-2,3-dideoxy-6-O-(4,4'-dimethoxytrityl)-3-fluoro-2-(thymin-1-yl)-D-altritol
  参考文献：
  名称：

  Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3′-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

  摘要：

  The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F center dot center dot center dot H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonudeotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)center dot center dot center dot H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.

  DOI：

  10.1021/ja207086x

文献信息

• TETRAHYDROPYRAN NUCLEIC ACID ANALOGS
  申请人：Swayze Eric E.

  公开号：US20090092981A1

  公开（公告）日：2009-04-09

  The present disclosure describes tetrahydropyran nucleoside analogs, oligomeric compounds prepared therefrom and methods of using the oligomeric compounds. More particularly, tetrahydropyran nucleoside analogs are provided, having one or more chiral substituents, that are useful for enhancing properties of oligomeric compounds including nuclease resistance and binding affinity. In some embodiments, the oligomeric compounds provided herein hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA.

  本公开描述了四氢吡喃核苷类似物，以及由此制备的寡聚合物化合物和使用这些寡聚合物化合物的方法。更具体地说，提供了具有一个或多个手性取代基的四氢吡喃核苷类似物，这些类似物可用于增强包括核酸酶抗性和结合亲和性在内的寡聚合物化合物的性质。在某些实施例中，本文提供的寡聚合物可以与目标RNA的部分杂交，导致目标RNA失去正常功能。
• Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3′-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides
  作者：Martin Egli、Pradeep S. Pallan、Charles R. Allerson、Thazha P. Prakash、Andres Berdeja、Jinghua Yu、Sam Lee、Andrew Watt、Hans Gaus、Balkrishen Bhat、Eric E. Swayze、Punit P. Seth

  DOI：10.1021/ja207086x

  日期：2011.10.19

  The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F center dot center dot center dot H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonudeotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)center dot center dot center dot H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.