脂肪链在吡咯-咪唑聚酰胺及其结合物与B-DNA键合中的作用

吡咯-咪唑聚酰胺是一类人工合成的能够在B-DNA小沟特异性识别碱基序列的有机小分子,并且能通过细胞膜进入细胞,调控基因的表达。它主要由五元杂环化合物N-甲基吡咯(Py)、N-甲基咪唑(Im)、N-甲基-3-羟基吡咯(Hp)芳香氨基酸及脂肪链氨基酸组成。在这种小分子对生物大分子识别事件中, 脂肪链^作为构建聚酰胺及其结合物的一部分, 在聚酰胺特异性识别DNA、延长DNA识别序列、连接分子荧光标记、对DNA指定位点的烷基化及基因调控等方面都起着非常重要的作用。本文阐述了脂肪链在上述诸方面应用的研究进展,并简要地分析了存在的问题和应用前景。     

新型的DNA切割试剂制备与应用

将具有DNA选择性识别的小分子与具有DNA切割活性的小分子缀合,合成对DNA具有定点切割效果的试剂是化学生物学研究领域具有挑战性的研究之一,它为化学、药学和生物学在生命科学中的相互渗透开辟了又一个广阔的空间.设计了具有切割系统和识别系统的定点切割试剂,识别系统由寡聚酰胺组成,含有N-甲基吡咯的寡聚酰胺能够穿透细胞膜与特定的碱基序列高亲和力地结合,并控制基因表达,是一类十分重要的化学物质;切割系统由大环多胺和它的金属配合物构成,大环多胺的金属配合物可作为仿酶催化剂.化合物1的锌配合物对pBR322DNA的切割见下图,此结果为进一步研究DNA特异识别及切割分子提供一个良好的基础.     

N-甲基吡咯类聚酰胺的合成及其与DNA的相互作用

本研究主要是设计并合成了3个含有4个N-甲基吡咯的聚酰胺化合物(PyPyPyPyβDp,PyPyPyPyγDp, NO₂PyPyPyPyβDp),并使用ESI-MS法研究了其与DNA的相互作用.     

聚酰胺类DNA识别分子质谱的碎裂机理

采用ESI-MS法研究了8个含有N-甲基吡咯(Py)和N-甲基咪唑(Im)杂环的聚酰胺质谱的特征和碎裂机理. MSⁿ数据表明, 聚酰胺化合物的主要碎裂路径是环与环间化学键的断裂, 即C—CO键、CO—NH键、HN—C键的断裂, 同时伴随着H原子的重排. 利用这些碎裂特征, 可以得到聚酰胺丰富的结构信息和区分它们的两种同分异构体.     

新型吡咯类衍生物的合成

2,5-己二酮和胺(氨基硫脲、硫脲、苯胺、氨基酸)经过Paal-Knorr反应合成6个2,5-二甲基-N-取代吡咯衍生物;分别以新合成的N-吡咯甘氨酸、N-苯基吡咯化合物为原料,进行酯化反应和Mannich,Friedel-Craft反应,合成3个N-(2,5-二甲基吡咯)甘氨酸酯类化合物和2个N-苯基-2,5-二甲基吡咯衍生物.所有化合物都通过IR,1HNMR,13CNMR,HRMS波谱方法对其结构进行了确证.     

二[1-甲基-4-(1-甲基-4-硝基吡咯-2-酰胺基)吡咯-2-酰胺基乙基]胺的合成与表征

报道了一种对称平行的多酰胺分子——二[1-甲基-4-(1-甲基-4-硝基吡咯-2-酰胺基)吡咯-2-酰胺基乙基]胺的合成方法, 以期对DNA序列进行新的特异性识别和切割, 从而研制新型有效的工具酶或抗癌药物. 合成方法简便易行、耗时短、不需过柱分离, 每步合成都有较高产率.     

喹啉季铵盐和1,3-茚满二酮及2-芳亚甲基1,3-茚满二酮的环加成反应合成茚满酮类含氮杂环化合物（英文）

在三乙胺存在下, N-苯甲酰基甲基喹啉溴化物和1,3-茚满二酮在乙醇中于室温反应,主要产物为多取代二氢吡咯[1,2-a]喹啉,次要产物为2-(1-苯甲酰基甲基)喹啉-4-亚基)-1,3-茚满二酮.在相同条件下,N-苄基喹啉溴化物和1,3-茚满二酮在乙醇中于室温反应,主要产物则为2-(1-苯甲酰基甲基)喹啉-4-亚基)-1,3-茚满二酮.另一方面, N-苯甲酰基甲基和N-乙氧羰基甲基以及N-(对硝基苄基)喹啉溴化物和芳香醛,1,3-茚满二酮的三组分反应,在三乙胺存在下在乙醇中高效地生成螺[茚满-2,3'-吡咯[1,2-a]喹啉]衍生物,反应具有很好的非对映选择性.     

1,2-二甲基咪唑啉的合成及表征

对1,2-二甲基咪唑啉的合成进行了详细研究. 以甲胺水溶液和2-溴乙胺氢溴酸盐(1)为原料进行反应, 在两种原料物质的量之比为5∶1, 缓缓回流12 h的条件下, 得到N-甲基乙二胺(2), N-甲基乙二胺经过乙酸化得到N-甲基-N,N′-二乙酰基乙二胺(3), 然后, N-甲基-N,N′-二乙酰基乙二胺和氧化钙在高温下关环得到1,2-二甲基咪唑啉(4). 并对所得到的产物1,2-二甲基咪唑啉经元素分析, 1H NMR, IR和GC-MS得到了表征.     

不同支化结构的聚酰胺胺的合成、活性及其在基因载体中的应用（英文）

具有不同拓扑结构的聚酰胺胺是基因载体和药物传递的理想选择.报道了一系列具有相同重复单元,但是支化度不同的聚酰胺胺.通过N,N-亚甲基二(丙烯酰胺)(MBA)和L-半胱氨酸甲酯盐酸盐(CYS)在水/二甲基亚砜的共溶剂中的Michael加成缩聚反应,成功地制备出了不同支化度的聚酰胺胺.制备的阳离子聚酰胺胺(PAAs)具有良好的DNA复合能力.     

钯催化的酰胺羰化反应研究-溶剂的影响

考察了不同溶剂(如N-甲基吡咯烷酮、乙腈、聚乙二醇、1-甲基-3-己基咪唑六氟磷酸盐)以及不同共催化剂(如十六烷基三甲基溴化铵、四丁基溴化铵、溴化锂)对苯甲醛酰胺羰化反应的影响.与使用高沸点的有机溶剂N-甲基吡咯烷酮相比,使用乙腈、聚乙二醇和1-甲基-3-己基咪唑六氟磷酸盐作溶剂,反应后处理过程大大简化,反应界面更加友好.聚乙二醇作溶剂首次应用于酰胺羰化反应.     

Sequence‐Specific DNA Recognition by Cyclic Pyrrole–Imidazole Cysteine‐Derived Polyamide Dimers

Pyrrole–imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence‐specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence‐specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β‐alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA.     

Alternative heterocycles for DNA recognition: the benzimidazole/imidazole pair

Boc-protected benzimidazole-pyrrole, benzimidazole-imidazole, and benzimidazole-methoxypyrrole amino acids were synthesized and incorporated into DNA binding polyamides, comprised of N-methyl pyrrole and N-methyl imidazole amino acids, by means of solid-phase synthesis on an oxime resin. These hairpin polyamides were designed to determine the DNA recognition profile of a side-by-side benzimidazole/imidazole pair for the designated six base pair recognition sequence. Equilibrium association constants of the polyamide-DNA complexes were determined at two of the six base pair positions of the recognition sequence by quantitative DNase I footprinting titrations on DNA fragments each containing matched and single base pair mismatched binding sites. The results indicate that the benzimidazole-heterocycle building blocks can replace pyrrole-pyrrole, pyrrole-imidazole, and pyrrole-hydroxypyrrole constructs while retaining relative site specifities and subnanomolar match site affinities. The benzimidazole-containing hairpin polyamides represent a novel class of DNA binding ligands featuring tunable target recognition sequences combined with the favorable properties of the benzimidazole type DNA minor groove binders.     

Fmoc solid phase synthesis of polyamides containing pyrrole and imidazole amino acids

[structure: see text]. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids are synthetic ligands that have an affinity and specificity for DNA comparable to those of many naturally occurring DNA binding proteins. A machine-assisted Fmoc solid phase synthesis of polyamides has been optimized to afford high stepwise coupling yields (>99%). Two monomer building blocks, Fmoc-Py acid and Fmoc-Im acid, were prepared in multigram scale. Cleavage by aminolysis followed by HPLC purification affords up to 200 mg quantities of polyamide with purities and yields greater than or equal to those reported using Boc chemistry. A broader set of reaction conditions will increase the number and complexity of minor groove binding polyamides which may be prepared and help ensure compatibility with many commercially available peptide synthesizers.     

Electrospray ionization mass spectrometric analysis of noncovalent complexes between DNA and polyamides containing N-methylpyrrole and N-methylimidazole

Electrospray ionization mass spectrometry was utilized to investigate the noncovalent complexes between novel polyamides and DNA containing the TCCT sequence. We analyzed the noncovalent binding of the polyamides with the DNA and assessed their relative affinities and stoichiometry. The results confirm that hairpin polyamides have higher binding affinities than three-ring polyamides. The hairpin polyamide (PyPyPyPygammaPyImImPybetaDp) has the highest affinity, and the beta-linked polyamide (PyPyPybetaImImImbetaDp) shows a dominant 1:2 binding stoichiometry. Two groups of competition experiments were undertaken to compare the binding affinities of the duplex DNA with different polyamides directly. The affinity scale thus obtained for the group-1 polyamides is PyPyPyPygammaPyImImPybetaDp > PyPyPybetaImImImbetaDp approximately PyPyPygammaImImImbetaDp > PyPyPybetaDp > PyImImbetaDp approximately ImImPybetaDp, and the order for the group-2 polyamides is PyPyPygammaImImImbetaDp > PyPyPygammaImImImbetaOEt > PyPyPygammaImImImbetaCOOH.     

Sequence-specific trapping of topoisomerase I by DNA binding polyamide-camptothecin conjugates

Hairpin pyrrole-imidazole polyamides are synthetic ligands that bind in the minor groove of DNA with affinities and specificities comparable to those of DNA binding proteins. Three polyamide-camptothecin conjugates 1-3 with linkers varying in length between 7, 13, and 18 atoms were synthesized to trap the enzyme Topoisomerase I and induce cleavage at predetermined DNA sites. One of these, polyamide-camptothecin conjugate 3 at nanomolar concentration (50 nM) in the presence of Topo I (37 degrees C), induces DNA cleavage between three and four base pairs from the polyamide binding site in high yield (77%).     

Investigation of non-covalent complexes of HIV-1 promoter DNA and polyamides containing N-methylpyrrole by electrospray ionization mass spectrometry

Eight novel polyamides containing N-methylpyrrole were designed to target the sequence (5'-CTGCATATAAGCAG-3'/5'-CTGCTTATATGCAG-3') of the TATA box element of the HIV-1 promoter DNA. The non-covalent complexes of the promoter DNA and the polyamides were investigated by electrospray ionization (ESI) mass spectrometry, which provided strong evidence for the binding of the novel polyamides to the sequence of the TATA box element. It also revealed that polyamide 2 (PyPyPyPybetaDp), a potent binder of HIV-1 promoter DNA and a lead molecule for the design of new anti-HIV-1 drugs, had the highest binding affinity with the TATA box element DNA among these polyamides by examining the stoichiometry and the selectivity.     

Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues

A combined structural and quantitative biophysical profile of the DNA binding affinity, kinetics and sequence-selectivity of hairpin polyamide analogues is described. DNA duplexes containing either target polyamide binding sites or mismatch sequences are immobilized on a microelectrode surface. Quantitation of the DNA binding profile of polyamides containing N-terminal 1-alkylimidazole (Im) units exhibit picomolar binding affinities for their target sequences, whereas 5-alkylthiazole (Nt) units are an order of magnitude lower (low nanomolar). Comparative NMR structural analyses of the polyamide series shows that the steric bulk distal to the DNA-binding face of the hairpin iPr-Nt polyamide plays an influential role in the allosteric modulation of the overall DNA duplex structure. This combined kinetic and structural study provides a foundation to develop next-generation hairpin designs where the DNA-binding profile of polyamides is reconciled with their physicochemical properties.