6-N-benzoyl-2'-O-pixyladenosine | 84315-17-3

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘌呤核苷
• 英文名称: 6-N-benzoyl-2'-O-pixyladenosine
• 英文别名: N-Benzoyl-2'-O-(9-phenyl-9H-xanthen-9-yl)adenosine；N-[9-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-(9-phenylxanthen-9-yl)oxyoxolan-2-yl]purin-6-yl]benzamide
• CAS: 84315-17-3
• 化学式: C₃₆H₂₉N₅O₆
• 分子量: 627.656
• InChiKey: ODJQOAMKFNURON-JYYIKNSZSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  4.7
• 重原子数：
  47
• 可旋转键数：
  7
• 环数：
  8.0
• sp3杂化的碳原子比例：
  0.17
• 拓扑面积：
  141
• 氢给体数：
  3
• 氢受体数：
  9

反应信息

• 作为反应物：
  描述：

  6-N-benzoyl-2'-O-pixyladenosine 在 吡啶 、 四氮唑 、 ammonium hydroxide 、 水 、 碘 、 溶剂黄146 作用下， 反应 25.25h， 生成 Sodium adenosine 3',5'-bis(ethylphosphate)
  参考文献：
  名称：

  通过1 H-和31 P-NMR光谱评估分支RNA溶液结构中竞争性2'«5'与3'«5'堆叠

  摘要：

  制备五种新型腺苷磷酸化衍生物，即腺苷2'，3'-双（磷酸乙酯）（11），腺苷2'，3'-双（磷酸酯（13），腺苷2'，3'，5'-tris据报道有磷酸乙酯（15），腺苷2'，5'-双（乙基磷酸）（17）和腺苷3'，5'-双（乙基磷酸）（19）。这些化合物以及甲基β-D-呋喃呋喃糖基双- 2'，3'-二乙基磷酸酯（9），被用作参考系统31 P和1 H-NMR上的支链的RNA结构的构象研究20 - 30。化合物11，13，15，17和19保留了分支点腺苷的基本结构元素，而分子内碱基堆积的相互作用被除去了。的31的P-NMR的化学位移20 - 30，对引用的9，11，13，或15，示出了图案，其通常与我们先前从可变温辐射结果一致31P-NMR实验。数据表明，对于2'-磷酸基团，P-O3'（ζ）和P-05'（α）键周围的g，g的贡献明显大于对3'-磷酸基团的贡献。这些结果指向套索里亚特所有这些合成

  DOI：

  10.1016/s0040-4020(01)88130-8

文献信息

• A new regiospecific synthesis of “Branched” tetraribonucleotide and its three analogues to delineate the chemospecific role of the “Branch-point” adenine nucleotide in splicing
  作者：N. Balgobin、A. Földesi、G. Remand、J. Chattopadhyaya

  DOI：10.1016/s0040-4020(01)86223-2

  日期：1988.1

  2'-OH protecting groups (9-phenylxanthen-9-yl-), by a mild acid treatment, at the branch-accepting sugar moiety to give the intermediates 23–26 in high yields. These intermediates 23–26 have been subsequently converted to the “branched” tetraribonucleotides 28–31 by reactions with appropriately protected 5'-phosphiteamidite block 27 in the usual manner. The deprotectected “branched” tetraribonucleotides

  使用关键的三聚体结构单元19-22报告了四个“支链”四核糖核苷酸32-35的合成，这些结构单元是通过H-膦酸酯化学方法开发的，通过18与14-17的反应方便地制备的。互补的适当选择2'-OH保护基团的中间体19-22已经允许一个区域选择性除去一个2'-OH保护基团（9- phenylxanthen -9-基 - ），通过温和的酸处理，在分支接受糖部分以高收率得到中间体23–26。这些中间体23-26随后通过与受适当保护的5'-亚磷酰胺嵌段27的反应以常规方式转化为“支链”四核糖核苷酸28-31。1 H-和31 p-NMR光谱。这些分支的四核糖核苷酸的二维1 H / 31 P相关光谱法已明确地确定了3'→5'和2'→5'磷酸二酯键的区域特异性位点。
• Solution conformation of hexameric & heptameric lariat-RNAs and their self-cleavage reactions which give products mimicking those from some catalytic RNAs (ribozymes)
  作者：B. Rousse、N. Puri、G. Viswanadham、P. Agback、C. Glemarec、A. Sandström、C. Sund、J. Chattopadhyaya

  DOI：10.1016/s0040-4020(01)80852-8

  日期：1994.1

  The small ''lariat'' hexameric 1 and heptameric 2 RNAs undergo self-cleavage, whereas the two cyclic A(2'-->5)G and A(3'-->5')G linked tetramers 3 and 4 do not self-cleave. The site of phosphodiester cleavage is specific and occurs at the 3'-phosphate of the guanosine residue to give a guanosine 2',3'-cyclic phosphate and a 5'-hydroxyl termini. At 22 degrees C, the heptamer 2 (k = 0.16 x 10(-3) min(-1)) cleaves ca. six times faster than the hexamer 1 (k = 0.25 x 10(-4) min(-1)). The rare of cleavage is temperature and pH dependent. The addition of Mg2+ ions slightly increases the rate of cleavage, but NMR studies show that it does not produce any changes in the conformation of the ribose rings and of the glycosidic bonds. H-1-NMR shows that the lariat-hexamer 1 exists as two conformers (A and B) in slow exchange on the NMR time scale. The enthalpy term (Delta H = 7.1 kcal mol(-1)) favours the A-form while the entropy term (Delta S = 21 cal mol(-1) K-1) favours the B-form. The energy of activation for the transition between the A- and B-forms is 23 kcal.mol(-1). The loop nucleotides in the B-form of hexamer 1 have ribose, glycosidic bonds and phosphate backbone conformation that are very similar to those of heptamer 2. At low temperature, the conformation of the A(2'-->5)G linked tetramer 3 and A(3'-->5')G linked tetramer 4 is very similar to the conformation of the A-form of hexamer 1. Torsional constraints derived from H-1-H-1, H-1-P-31 and C-13-P-31 coupling constants were used for molecular dynamics simulations in water with sodium counterions for a total of 226 ps. The MD simulations were first carried out with torsional constraints derived from J-couplings (0-96 ps) and then completely without constraints (106-226 ps). No major conformational changes occurred upon the release of the constraints indicating that the ensemble of conformers generated during the MD simulation are not artificially held in these conformations by the NMR constraints and these conformers may be good representatives of the actual NMR observed solution structures. A comparison of the self-cleavage rate between hexamer, heptamer and hammerhead-RNA (k(cat) approximate to 0.5 min(-1) at 37 degrees C) also suggests that the cleavage-site geometry of the hammerhead-RNA should be much closer to the transition state/intermediate geometry than heptamer 2. The pH-dependent study of the self-cleavage reaction of hexamer hexamer 1 has shown that the self-cleavage rate peaks at pH 6 and slows down considerably both above and below this pH. Nonspecific cleavage starts becoming important at a very low pH (less than or equal to 3) and at a high pH (greater than or equal to 10). The structures generated during both NMR constrained and unconstrained MD runs show that the cleavage-site between G(3) and U-7 in heptamer 2 has the following average local conformation: S-sugar for G(3), epsilon(-) (-86 degrees+/-13 degrees), zeta(+) (91 degrees+/-16 degrees),alpha(+) (85 degrees+/-24 degrees), beta(t) (163 degrees+/-13 degrees) and gamma(+) (65 degrees+/-11 degrees). Molecular modelling studies on the MD generated geometry show that a simple rotation of the local phosphate backbone at the cleavage-site from epsilon(-) (d(O2'-3'P) = 3.8 Angstrom) --> epsilon = 120 degrees (d(O2'-3'P) = 2.8 Angstrom) and a rotation of zeta(+) --> zeta(t) would position the leaving 5'-terminus of U-7 for a potential in-line displacement by 2'-OH of G(3) (Note that in the latter geometrical transition, alpha(+), beta(t) and gamma(+) and the South-sugar of U-7 remain unchanged). Such a geometry at the cleavage site would produce an optimal local structure for a neighbouring nucleophilic attack by 2'-OH to give the trigonal-bipyramidal phosphorane transition state/intermediate.
• New regiospecific synthesis of branched tetra-, nona- & deca-RNA modelling the lariat formed in RNA splicing reactions
  作者：C. Sund、A. Földesi、S. Yamakage、P. Agback、J. Chattopadhyaya

  DOI：10.1016/s0040-4020(01)86562-5

  日期：1991.8

  Convergent syntheses of branched tetraribonucleotide 39, nonaribonucleotide 40 and decaribonucleotide 41, modelling the lariat of pre-mRNA processing reaction, are reported. The first key step in the present strategy involves the condensation of the phosphodiester blocks 1, 5 or 15 with the 3',5'-dihydroxy-6-N-benzoyl-2'-O-pixyl(9-phenylxanthen-9-yl)adenosine 29 to give 30a (65%), 31a (63%) or 32a (70%). Chemospecific phosphorylation at 3'-OH of these intermediates afforded the intermediates 30b (92%), 31b (83%) or 32b (80%) which were treated with mild acid to achieve a regiospecific removal of the 2'-O-pixyl group to give compounds 30c (74%), 31c (86%) or 32c (85%). The second key step involved the introduction of biscyanoethylphosphotriester moiety to the 2'-OH of the branch-point adenosine in 30c, 31c or 32c in one single step using (biscyanoethoxy)-(diisopropylamino)phosphine to give the crucial branch-point building blocks 30d (46%), 31d (64%) or 32d (62%) with two dissimilar vicinal phosphates at 2'- and 3'- of the branch-point. These blocks were then converted to the fully protected intermediates 33a (59%) [30d+28 --> 33a], 34a (69%) [31d+19 --> 34a] and 35a (56%) [32d+19 --> 35a], and were subsequently treated with a bulky tertiary amine to give the branch-point 2'-cyanoethylphosphodiester blocks 33b (64%), 34b (67%) and 35b (68%). These were then condensed in the usual way with the appropriate 5'-hydroxy block (27 or 25) to give the fully protected branched oligomers 36 (69%) [33b+27 --> 36], 37 (67%) [34b+25 --> 37] and 38 (63%) [35b+25 --> 38]. These oligomers were then deprotected in the usual manner to give the final branched oligoribonucleotides 39, 40 and 41 in 62%, 21% and 21% yields respectively. Detailed 500 MHz H-1-NMR and 202.4 MHz P-31-NMR studies on 39, 40 and 41 have unequivocally established their purities. Detailed spectroscopic studies such as COSY, HOHAHA & NOESY have also clearly established the structural integrity of the synthetic target compounds.
• Pathak, T.; Chattopadhyaya, J., Acta chemica Scandinavica. Series B: Organic chemistry and biochemistry, 1985, vol. 39, # 10, p. 799 - 806
  作者：Pathak, T.、Chattopadhyaya, J.

  DOI：——

  日期：——
• BALGOBIN, N.;FOLDESI, A.;REMAUD, G.;CHATTOPADHYAYA, J., TETRAHEDRON, 44,(1988) N 22, C. 6929-6939
  作者：BALGOBIN, N.、FOLDESI, A.、REMAUD, G.、CHATTOPADHYAYA, J.

  DOI：——

  日期：——