5-[(benzyloxy)methyl]uridine | 24751-66-4

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘧啶核苷
• 英文名称: 5-[(benzyloxy)methyl]uridine
• 英文别名: 5-Benzyloxymethyl-uridin；1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(phenylmethoxymethyl)pyrimidine-2,4-dione
• CAS: 24751-66-4
• 化学式: C₁₇H₂₀N₂O₇
• 分子量: 364.355
• InChiKey: GTEHVOGHMYRBQM-IXYNUQLISA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -0.8
• 重原子数：
  26
• 可旋转键数：
  6
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.41
• 拓扑面积：
  129
• 氢给体数：
  4
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  5-[(benzyloxy)methyl]uridine 在 4-二甲氨基吡啶 、 偶氮二异丁腈 、 四丁基氟化铵 、 三正丁基氢锡 作用下， 以 四氢呋喃 、 吡啶 、 甲苯 、 乙腈 为溶剂， 反应 42.0h， 生成 5-(benzyloxy)methyl-2′-deoxyuridine
  参考文献：
  名称：

  Aromaticvs. Carbohydrate Residues in the Major Groove: Synthesis of 5-[(Benzyloxy)methyl]pyrimidine Nucleosides and Their Incorporation into Oligonucleotides

  摘要：

  The synthesis of 5-[(benzyloxy)methyl]-substituted pyrimidine 2'-deoxynucleosides 14 and 15 starting from the uracil derivative 6 and tetra-O-acetyl-D-ribose is described (Schemes 1-3). These nucleosides were converted to the corresponding cyanoethyl phosphoramidites 18 and 19, respectively, and incorporated into oligodeoxynucleotide decamers. The 5-[(benzyloxy)methyl]-nucleoside building blocks T-bo(d) and C-bom(d) (bo = benzyloxy, bom = (benzyloxy)methyl) - shape analogs of the naturally occurring glucosylated nucleosides 1 and 2 (see Fig. 1) - lead to weaker binding affinities of oligodeoxynucleotides pairing to DNA as well as RNA complements. The modification is more destabilizing in the case of T-bo(d) than C-bom(d). Analysis of the thermodynamics of duplex formation shows that T-bo(d) and C-bom(d), incorporation leads to a smaller entropy change in duplex formation that is, however, overcompensated by a less Favorable enthalpy term. Molecular-modeling studies suggest that the benzyl groups reside in the major groove which would explain the improved pairing entropy as a result of the exclusion of ordered H2O.

  DOI：

  10.1002/1522-2675(20000809)83:8<1962::aid-hlca1962>3.0.co;2-8
• 作为产物：
  描述：

  四乙酰核糖 在 sodium hydroxide 、 N,O-双三甲硅基乙酰胺 、 三氟甲磺酸三甲基硅酯 作用下， 以 四氢呋喃 、 甲醇 、 水 、 乙腈 为溶剂， 反应 18.58h， 生成 5-[(benzyloxy)methyl]uridine
  参考文献：
  名称：

  Aromaticvs. Carbohydrate Residues in the Major Groove: Synthesis of 5-[(Benzyloxy)methyl]pyrimidine Nucleosides and Their Incorporation into Oligonucleotides

  摘要：

  The synthesis of 5-[(benzyloxy)methyl]-substituted pyrimidine 2'-deoxynucleosides 14 and 15 starting from the uracil derivative 6 and tetra-O-acetyl-D-ribose is described (Schemes 1-3). These nucleosides were converted to the corresponding cyanoethyl phosphoramidites 18 and 19, respectively, and incorporated into oligodeoxynucleotide decamers. The 5-[(benzyloxy)methyl]-nucleoside building blocks T-bo(d) and C-bom(d) (bo = benzyloxy, bom = (benzyloxy)methyl) - shape analogs of the naturally occurring glucosylated nucleosides 1 and 2 (see Fig. 1) - lead to weaker binding affinities of oligodeoxynucleotides pairing to DNA as well as RNA complements. The modification is more destabilizing in the case of T-bo(d) than C-bom(d). Analysis of the thermodynamics of duplex formation shows that T-bo(d) and C-bom(d), incorporation leads to a smaller entropy change in duplex formation that is, however, overcompensated by a less Favorable enthalpy term. Molecular-modeling studies suggest that the benzyl groups reside in the major groove which would explain the improved pairing entropy as a result of the exclusion of ordered H2O.

  DOI：

  10.1002/1522-2675(20000809)83:8<1962::aid-hlca1962>3.0.co;2-8

文献信息

• NUCLEOTIDES AND NUCLEOSIDES AND METHODS FOR THEIR USE IN DNA SEQUENCING
  申请人：LITOSH Vladislav A.

  公开号：US20100041041A1

  公开（公告）日：2010-02-18

  The present invention relates generally to labeled and unlabled cleavable terminating groups and methods for DNA sequencing and other types of DNA analysis. More particularly, the invention relates in part to nucleotides and nucleosides with chemically cleavable, photocleavable, enzymatically cleavable, or non-photocleavable groups and methods for their use in DNA sequencing and its application in biomedical research.

  本发明涉及标记和未标记的可断裂终止基团以及用于DNA测序和其他类型的DNA分析的方法。更具体地，本发明部分涉及具有化学可断裂、光解、酶解或非光解基团的核苷酸和核苷以及它们在DNA测序中的使用及其在生物医学研究中的应用。
• Nucleotides and Nucleosides and Methods for their Use in DNA Sequencing
  申请人：Litosh Vladislav A.

  公开号：US20130035237A1

  公开（公告）日：2013-02-07

  The present invention relates generally to labeled and unlabled cleavable terminating groups and methods for DNA sequencing and other types of DNA analysis. More particularly, the invention relates in part to nucleotides and nucleosides with chemically cleavable, photocleavable, enzymatically cleavable, or non-photocleavable groups and methods for their use in DNA sequencing and its application in biomedical research.

  本发明通常涉及带有标记和未标记的可断裂终止基团及其在DNA测序和其他类型的DNA分析中的方法。更具体地，本发明部分涉及具有化学可断裂、光解、酶解或非光解基团的核苷酸和核苷以及它们在DNA测序中的应用及其在生物医学研究中的应用方法。
• Modification of N-hydroxycytidine yields a novel lead compound exhibiting activity against the Venezuelan equine encephalitis virus
  作者：Isaac L. Downs、A. David Ordonez Luna、Krishna P. Kota、Sarah K. Rubin、Serena S. Shirsekar、Michael D. Ward、Rekha G. Panchal、Vladislav A. Litosh

  DOI：10.1016/j.bmcl.2023.129432

  日期：2023.10

  antiviral compounds with diminished side effects. This presumption is due to the substantial structural difference with natural cytidine leading to less recognizability by host cell enzymes. Among the 42 antimetabolite species that have been synthesized and screened against VEEV, one hit compound was identified. The structural features of the modifying moiety were similar to those of the anticancer lead

  能够干扰核酸合成的核苷和核碱基类似物在对抗传染病方面发挥了重要作用。然而，这些药物中的许多都与重要且可能致命的脱靶细胞内效应有关，从而限制了它们的使用。基于之前发现的碱基修饰的 2'-脱氧尿苷，与抗代谢化疗药物相比，它表现出高抗癌活性，同时对快速分裂的正常人类细胞表现出较低的毒性，我们假设N 4 -羟基胞苷 (NHC) 分子的类似修饰将提供副作用减少的新型抗病毒化合物。这一推测是由于与天然胞苷的显着结构差异导致宿主细胞酶的识别能力较低。在针对 VEEV 合成和筛选的 42 种抗代谢药物中，鉴定出一种有效化合物。该修饰部分的结构特征与之前报道的抗癌先导2′-脱氧尿苷衍生物的结构特征相似，为进一步进行针对先导改进的构效关系（SAR）研究提供了机会，并深入了解作用机制，这可以导致识别针对广谱 RNA 病毒感染的候选药物。
• US8148503B2
  申请人：——

  公开号：US8148503B2

  公开（公告）日：2012-04-03
• US8497360B2
  申请人：——

  公开号：US8497360B2

  公开（公告）日：2013-07-30