N-(5-((3-(dimethylamino)propyl)carbamoyl)-1-methyl-1H-pyrrol-3-yl)-1-methyl-4-(1-methyl-4-(1-methyl-1H-pyrrole-2-carboxamido)-1H-pyrrole-2-carboxamido)-1H-imidazole-2-carboxamide | 1289633-11-9

• 分子结构分类: 有机化合物 - 有机杂环化合物
• 英文名称: N-(5-((3-(dimethylamino)propyl)carbamoyl)-1-methyl-1H-pyrrol-3-yl)-1-methyl-4-(1-methyl-4-(1-methyl-1H-pyrrole-2-carboxamido)-1H-pyrrole-2-carboxamido)-1H-imidazole-2-carboxamide
• CAS: 1289633-11-9
• 化学式: C₂₈H₃₆N₁₀O₄
• 分子量: 576.658
• InChiKey: GQSVNNGNFSLWCF-UHFFFAOYSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  1.87
• 重原子数：
  42.0
• 可旋转键数：
  11.0
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.32
• 拓扑面积：
  152.25
• 氢给体数：
  4.0
• 氢受体数：
  10.0

反应信息

• 作为产物：
  描述：

  1H-咪唑-2-甲酰胺,N-[5-[[[3-(二甲氨基)丙基]氨基]羰基]-1-甲基-1H-吡咯-3-基]-1-甲基-4-[[(1-甲基-4-硝基-1H-吡咯-2-基)羰基]氨基]- 在 5%-palladium/activated carbon 、 氢气 、 三乙胺 作用下， 以 甲醇 、 二氯甲烷 为溶剂， 反应 24.0h， 生成 N-(5-((3-(dimethylamino)propyl)carbamoyl)-1-methyl-1H-pyrrol-3-yl)-1-methyl-4-(1-methyl-4-(1-methyl-1H-pyrrole-2-carboxamido)-1H-pyrrole-2-carboxamido)-1H-imidazole-2-carboxamide
  参考文献：
  名称：

  Hx, a Novel Fluorescent, Minor Groove and Sequence Specific Recognition Element: Design, Synthesis, and DNA Binding Properties of p-Anisylbenzimidazole-imidazole/pyrrole-Containing Polyamides

  摘要：

  With the aim of incorporating a recognition element that acts as a fluorescent probe upon binding to DNA, three novel pyrrole (P) and imidazole (I)-containing polyamides were synthesized. The compounds contain a p-anisylbenzimidazolecarboxamido (Hx) moiety attached to a PP, IP, or PI unit, giving compounds HxPP (2), HxIP (3), and HxPI (4), respectively. These fluorescent hybrids were tested against their complementary nonfluorescent, non-formamido tetraamide counterparts, namely, PPPP (5), PPIP (6), and PPPI (7) (cognate sequences 5'-AAATTT-3', 5'-ATCGAT-3', and 5'-ACATGT-3', respectively). The binding affinities for both series of polyamides for their cognate and noncognate sequences were ascertained by surface plasmon resonance (SPR) studies, which revealed that the Fix-containing polyamides gave binding constants in the 10(6) M-1 range while little binding was observed for the noncognates. The binding data were further compared to the corresponding and previously reported formainido-triamides f-PPP (8), f-PIP (9), and f-PPI (10). DNase I footprinting studies provided additional evidence that the Fix moiety behaved similarly to two consecutive pyrroles (PP found in 5-7), which also behaved like a formamido-pyrrole (f-P) unit found in distamycin and many formamido-triamides, including 8-10. The biophysical characterization of polyamides 2-7 on their binding to the abovementioned DNA sequences was determined using thermal melts (Delta T-M), circular dichroism (CD), and isothermal titration calorimetry (ITC) studies. Density functional calculations (B3LYP) provided a theoretical framework that explains the similarity between PP and Hx on the basis of molecular electrostatic surfaces and dipole moments. Furthermore, emission studies on polyamides 2 and 3 showed that upon excitation at 322 nm binding to their respective cognate sequences resulted in an increase in fluorescence at 370 nm. These low molecular weight polyamides show promise for use as probes for monitoring DNA recognition processes in cells.

  DOI：

  10.1021/bi102028a