电喷雾质谱法研究防己诺林碱与G-四链体的相互作用

采用电喷雾质谱法研究了防己诺林碱与双链核酸及G-四链体的相互作用. 结果表明, 防己诺林碱可选择性地与G-四链体结合. 利用串联质谱技术对防己诺林碱与核酸的结合模式进行了研究, 结果表明, 防己诺林碱可能通过末端堆积作用与G-四链体结合, 而通过插入作用与双链核酸结合. 结合模式的差异导致防己诺林碱选择性地与G-四链体结合.     

吲哚并喹啉衍生物与G-四链体相互作用的分子模拟研究

G-四链体是富含鸟嘌呤碱基的DNA序列通过氢键相互作用形成的四链螺旋结构. 通过小分子化合物诱导与稳定端粒G-四链体从而抑制端粒酶活性是一种新的抗癌策略. 为了研究一系列吲哚并喹啉衍生物与端粒G-四链体的相互作用, 探究其相互作用模式, 从而为实现基于G-四链体结构的药物合理设计提供依据, 使用分子对接的方法构建了吲哚并喹啉衍生物与G-四链体复合物结构, 在此基础上进行分子动力学模拟, 并使用线性相互作用能(LIE)方法计算了化合物与G-四链体的结合自由能. 结果表明: 化合物与G-四链体的主要相互作用方式由氢键、静电与π-π堆积作用构成, 侧链末端基团类型和侧链的长短是影响相互作用强弱的重要因素. 通过LIE方法计算的结合自由能与实验结果基本吻合, 相关度达到r²＝0.79. 并且, 基于预测的结合模式, 总结了拥有更高活性的新型吲哚并喹啉衍生物应具有的几个结构特征.     

DNA G-四链体识别探针研究进展

G-四链体是一种由富含鸟嘌呤核酸序列形成的独特的二级结构,广泛分布于真核生物基因组,如端粒DNA、r DNA和一系列基因中的启动子区域。G-四链体结构对很多重要的生理过程如基因的转录、复制、重组以及保持染色体的稳定性方面具有重要作用。G-四链体的特异、高灵敏检测将为进一步了解G-四链体结构在人类细胞基因组中的分布、功能和机制奠定基础,也可能为靶向G-四链体的肿瘤治疗方法提供新的思路。因而过去几十年人们一直致力于开发设计具有高选择性和高灵敏度的G-四链体识别探针,这些探针已经广泛应用于溶液中G-四链体的识别,而且具有良好的选择性。目前也有少数探针能够直接用于检测活体G-四链体结构。本文综述了一些常见的靶向G-四链体的小分子配体,以及它们在染色体和活体细胞G-四链体检测中的应用。笔者希冀本文能为设计识别G-四链体的高性能探针,进一步实现活细胞内G-四链体的检测提供借鉴。     

人体端粒中(3+1)混合结构G-四链体稳定性的分子动力学模拟

利用分子动力学模拟方法, 考察了人体端粒中(3+1)混合结构G-四链体的结构及稳定性问题. 讨论了配位K+离子、药物分子(端粒抑素)和溶剂水分子对G-四链体的Hoogsteen氢键结构、π-π堆积作用的影响. 研究表明, K+离子与鸟嘌呤碱基上O6原子的配位作用减弱了对角鸟嘌呤间O6-O6的静电排斥作用, 使得相邻的四个鸟嘌呤能够以Hoogsteen氢键结合的方式形成具有近平面结构的稳定G-四平面. 另一方面, G-四平面间、G-四平面与药物分子间的π-π堆积作用降低了G-四链体复合物的总能, 有利于其稳定存在. 此外, 溶剂水分子主要分布在G-四链体的TTA环、骨架和糖环的周围, 使其位移涨落增大; 然而, 在3 ns动力学模拟中, 由于水分子没有进入到G-四链体的空腔中, 溶剂水对G-四平面的结构影响不明显.     

一种不对称菁染料及其与不同结构DNA的相互作用

为考察小分子配基与不同核酸结构的结合机理,发展新的核酸探针分子,合成了一种新型一次甲基不对称菁染料(MTP).吸收光谱、荧光光谱及圆二色光谱研究结果表明,MTP可与平行和混合平行G-四链体DNA(如c-myc和22AGK+)较强地结合,并引起130~180倍的荧光增强;其与单/双链DNA作用较弱,导致40~60倍荧光增强;而与反平行G-四链体DNA(如TBA和22AGNa+)的作用最弱,只引起15~25倍荧光增强;以上结果表明MTP可作为荧光探针分子用于区别不同结构的核酸分子.结合机理研究表明,平行和混合平行G-四链体DNA优先通过沟槽结合模式结合1分子MTP,再通过末端堆积模式结合另1分子MTP.     

高选择性端粒G-四链体稳定性配体:9-O-多胺取代小檗碱衍生物的合成及活性评价

设计合成了3个多胺取代的小檗碱衍生物5a~5c, 并利用圆二色(CD)光谱、 荧光共振能量转移(FRET)熔点实验、 荧光光谱和聚合酶链反应(PCR)终止实验等手段研究了小檗碱衍生物5a~5c与端粒DNA的相互作用. 结果表明, 小檗碱衍生物5a~5c可以诱导端粒DNA序列形成反平行结构G-四链体, 显著地提高了端粒G-四链体的稳定性, 有效地抑制了端粒的扩增; 而与双链DNA的相互作用则很小, 是高选择性的端粒G-四链体配体.     

核酸G-四链体的识别、复合物结构与细胞内探测的研究进展

富含鸟嘌呤的DNA或RNA序列可以折叠成非典型G-四链体二级结构. G-四链体结构丰富多样,在生物体内动态存在,参与了转录、复制、基因组稳定性和表观遗传调控等关键的基因组功能,与癌症生物学密切相关. G-四链体的结构与功能机制研究促进了以G-四链体为靶点的肿瘤治疗干预.本文综合评述了核酸G-四链体的特异性识别、细胞内探测及生物学功能的调控,总结了识别靶向G-四链体的小分子及复合物结构的研究进展,讨论了以G-四链体为靶点的靶向干预及疾病治疗的可能性,最后展望了G-四链体未来研究所面临的挑战与机遇.     

异核苷G-四链DNA结构与活性的研究

富含鸟嘌呤的核酸序列能形成各种G-四链结构,G-四链结构具有重要的生物功能,在许多细胞内的事件如端粒DNA的保护和延长、复制、重组和转录等事件中有重要作用.一些以G-四链结构为靶点的小分子可抑制端粒酶的活性,使G-四链结构成为抗肿瘤药物设计的重要靶点.同时,某些特定序列的G-四链DNA具有抗肿瘤抗病毒等活性,如其中一个G-四链DNA T30923已经进入抗HIV-1 Ⅱ期临床研究.T30923的改进体T40214,即15聚体5′-(GGGC)4-3′,形成了一个对称而紧凑的分子内G-四链(图1),它的loop区因同时结合了两个K+而大大的增加了结构的稳定性[1].这种分子内的G-四链结构是体外抑制HIV整合酶以及抑制被感染细胞中HIV-1病毒的复制所必需的[2].为了增加T40214在体内的化学及酶稳定性,我们将异核苷分别掺入15聚体中[3],通过CD光谱、电泳等方法研究掺入异核苷的G-四链在结构和活性上的变化.     

人类端粒DNA的分子识别及其作用机制探讨

核酸中富含短的G-碱基重复的序列可以形成一种复杂的高级结构,称为G-四链体（G-quadruplex）.在基因组中,借助生物信息学发现这类富G序列广泛分布在基因的启动子区,特别是那些参与到复制中去的基因,例如癌基因.同时发现这类序列在mRNA的5′非翻译区（5′UTR）也广泛存在.这类序列在染色体末段端粒部位的存在及功能已得到充分阐明.已知端粒富含G-碱基序列,其3′末端以单链状态存在,这使得在一些小分子的选择性作用下端粒序列很容易形成G-四链体结构,进而破坏端粒结构,影响端粒酶活性.已知端粒酶在超过85%的肿瘤中过量表达,因此,端粒酶已经成为抗癌药物设计的特殊靶点,是目前本领域的研究热点之一.已发现系列配体通过有效抑制端粒酶而表现高的抗肿瘤活性.本文主要综述了近年来端粒G-四链体分子识别及其药物靶向的最新进展,并对其作用机理做了进一步的分析和探讨.     

原癌基因c-myc启动区G-四链体结构及靶向小分子配体*

随着DNA G-四链体结构的发现和现代分子生物学技术对其与癌症关系的揭示,DNA G-四链体逐渐成为抗肿瘤药物研究的新靶点。c-myc启动区 G-四链体由于在细胞生长、增殖、凋亡、衰老及肿瘤形成等过程中的重要作用,成为DNA G-四链体中最受关注的序列之一。本文旨在对c-myc启动区 G-四链体的结构及靶向c-myc G-四链体的小分子配体的研究进展进行综述。首先,介绍c-myc G-四链体的生物学意义;其次,对几种常用的c-myc G-四链体的结构进行解析;最后,对以c-myc为靶点的小分子配体的研究进展及其与G-四链体的作用模式进行综述,并对目前以c-myc G-四链体为靶点、已经走向临床实验的CX-3543的开发与作用机制进行介绍。     

Specific recognition of human telomeric G-quadruplex DNA with small molecules and the conformational analysis by ESI mass spectrometry and circular dichroism spectropolarimetry

Electrospray ionization mass spectrometry (ESI-MS) was utilized to investigate the binding affinity and stoichiometry of small molecules with human telomeric G-quadruplex DNA. The binding-affinity order obtained for the (AGGGTT)(4) quadruplex was: Tel01>ImImImbetaDp>PyPyPygammaImImImbetaDp. The specific binding of Tel01 and PyPyPygammaImImImbetaDp in one system consisting of human telomeric G-quadruplex and duplex DNA was observed directly for the first time. This revealed that PyPyPygammaImImImbetaDp has a binding specificity for the duplex DNA, whereas Tel01 selectively recognizes the G-quadruplex DNA. Moreover, both ESI-MS and circular dichroism (CD) spectra indicated that Tel01 favored the formation and stabilization of the antiparallel G-quadruplex, and a structural transition of the (AGGGTT)(4) sequence from a coexistence of parallel and antiparallel G-quadruplexes to a parallel G-quadruplex induced by annealing.     

Cationic metal-corrole complexes: design, synthesis, and properties of guanine-quadruplex stabilizers

A series of pyridinium and quaternary ammonium copper corroles has been designed and synthesized. All new compounds have been fully characterized by NMR spectroscopy, high-resolution mass spectrometry, UV/Vis spectrscopy, and elemental analysis. Biochemical studies have indicated that all of these corrole derivatives can stabilize G-quadruplex structures, with corrole 4 being the most effective according to the results of circular dichroism (CD) melting experiments, polymerase chain reaction (PCR) stop assays, and surface plasmon resonance (SPR) experiments. Moreover, both corroles 3 and 4 tend to induce the human telomeric sequence to form hybrid G-quadruplex structures, whereas corroles 8 and 9 are more inclined to induce the human telomeric sequence to form antiparallel G-quadruplex structures.     

Formation and recognition of G-quadruplex in promoter of c-myb oncogene by electrospray ionization mass spectrometry

In this study, electrospray ionization mass spectrometry (ESI-MS) is used to study the formation of G-quadruplex by d(GGAGGAGGAGGA) which locates at the promoter region of c-myb gene. In addition, a natural small molecule, dehydrocorydaline from a Chinese herb, is found to have the highest binding affinity with the G-quadruplex in nine natural small molecules studied, and the binding selectivity of this natural molecule toward the c-myb G-quadruplex with respect to corresponding duplex DNA is significantly higher than that of the broad-spectrum G-quadruplex-ligand TMPyP4. The result from ESI-MS indicates that the gas-phase kinetic stability of the G-quadruplex can be enhanced by binding of dehydrocorydaline. To further investigate the binding properties of dehydrocorydaline to the G-quadruplex, Autodock3 is used to calculate the docked sites and docked energies of small molecules binding to the G-quadruplex and the result shows that the docked energy of dehydrocorydaline is the biggest in the nine small molecules used, consistent with the result from ESI-MS.     

Telomestatin-induced stabilization of the human telomeric DNA quadruplex monitored by electrospray mass spectrometry

Electrospray mass spectrometry (ESI-MS) was used to monitor the kinetics of duplex formation between the human telomeric DNA quadruplex and its complementary strand; the complexation of telomestatin to the G-quadruplex delays the unwinding of the quadruplex structure and formation of the duplex.     

Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular g-quadruplex

Telomestatin is a natural product isolated from Streptomyces anulatus 3533-SV4 and has been shown to be a very potent telomerase inhibitor. The structural similarity between telomestatin and a G-tetrad suggested to us that the telomerase inhibition might be due to its ability either to facilitate the formation of or trap out preformed G-quadruplex structures, and thereby sequester single-stranded d[T(2)AG(3)](n) primer molecules required for telomerase activity. Significantly, telomestatin appears to be a more potent inhibitor of telomerase (5 nM) than any of the previously described G-quadruplex-interactive molecules. In this communication we provide the first experimental evidence that telomestatin selectively facilitates the formation of or stabilizes intramolecular G-quadruplexes, in particular, that produced from the human telomeric sequence d[T(2)AG(3)](4). A simulated annealing (SA) docking approach was used to study the binding interactions of telomestatin with the intramolecular antiparallel G-quadruplex structure. Each intramolecular G-quadruplex molecule was found to bind two telomestatin molecules (unpublished results). A 2:1 model for the telomestatin bound in the external stacking mode in an energy minimized complex with the human telomeric basket-type G-quadruplex was constructed. Our observation that a G-quadruplex-interactive molecule without significant groove interactions is able to reorient in a G-quadruplex structure proints to the importance of core interaction with an asymmetric G-quadruplex structure in producing selective binding. Furthermore, the G-quadruplex interactions of telomestatin are more selective for the intramolecular structure in contrast to other G-quadruplex-interactive agents, such as TMPyP4.     

Mass spectrometric studies on effects of counter ions of TMPyP4 on binding to human telomeric DNA and RNA G-quadruplexes

A comparative study on human telomeric DNA G-quadruplex binding of meso-5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) between its two salt forms, i.e., tetratosylate and tetrachloride, was conducted by using ESI-TOF-MS, UV-melting measurement, and molecular modeling methods. Besides cation TMPyP4, the tosyl anion was found to bind to human telomeric DNA G-quadruplex with multiple binding stoichiometries from 1:1 to 3:1 observed in ESI-TOF-MS spectra, indicating that the stabilization activity of TMPyP4 tetratosylate on G-quadruplex is derived from a synergetic effect of both TMPyP4 cation and tosyl anion. A molecular modeling study suggests that a tosyl anion fills up the vacant space between TMPyP4 cation and DNA G-quadruplex and thus stabilizes the complex by 3.8 kcal/mol. Therefore, it is estimated that TMPyP4 tetratosylate’s activity might not reflect the real effect of TMPyP4 cation in some bioassays related to G-quadruplex stabilization. This was verified by the results of less binding affinity of TMPyP4 tetrachloride with DNA G-quadruplex obtained from ESI-TOF-MS measurement, and of 2.27 °C less thermal stabilization of TMPyP4 tetrachloride for DNA G-quadruplex, compared to its tetratosylate under the same conditions. Our study demonstrated the influence of counter ions of TMPyP4 on G-quadruplex binding, which sheds light on the proper usage of TMPyP4 salt in the chemical and biological research associated with G-quadruplex binding. Subsequently, the binding of TMPyP4 tetrachloride to human telomeric RNA G-quadruplexes was studied with ESI-TOF-MS technique. The binding constants of TMPyP4 with human telomeric G-quadruplexes indicated that TMPyP4 binds to human telomeric RNA G-quadruplex one order of magnitude stronger than DNA counterpart. This is a comprehensive mass spectrometric report on binding study of TMPyP4 with human telomeric DNA/RNA G-quadruplexes.

?     

Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure

The human telomeric sequence d[T(2)AG(3)](4) has been demonstrated to form different types of G-quadruplex structures, depending upon the incubation conditions. For example, in sodium (Na(+)), a basket-type G-quadruplex structure is formed. In this investigation, using circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and a polymerase stop assay, we have examined how the addition of different G-quadruplex-binding ligands affects the conformation of the telomeric G-quadruplex found in solution. The results show that while telomestatin binds preferentially to the basket-type G-quadruplex structure with a 2:1 stoichiometry, 5,10,15,20-[tetra-(N-methyl-3-pyridyl)]-26-28-diselena sapphyrin chloride (Se2SAP) binds to a different form with a 1:1 stoichiometry in potassium (K(+)). CD studies suggest that Se2SAP binds to a hybrid G-quadruplex that has strong parallel and antiparallel characteristics, suggestive of a structure containing both propeller and lateral, or edgewise, loops. Telomestatin is unique in that it can induce the formation of the basket-type G-quadruplex from a random coil human telomeric oligonucleotide, even in the absence of added monovalent cations such as K(+) or Na(+). In contrast, in the presence of K(+), Se2SAP was found to convert the preformed basket G-quadruplex to the hybrid structure. The significance of these results is that the presence of different ligands can determine the type of telomeric G-quadruplex structures formed in solution. Thus, the biochemical and biological consequences of binding of ligands to G-quadruplex structures found in telomeres and promoter regions of certain important oncogenes go beyond mere stabilization of these structures.     

Investigation of formation,recognition, stabilization,and conversion of dimeric G-quadruplexes of HIV-1 integrase inhibitors by electrospray ionization mass spectrometry

The dimeric G-quadruplex structures of d(GGGTGGGTGGGTGGGT) (S1) and d(GTGGTGGGTGGGTGGGT) (S2), the potent nanomolar HIV-1 integrase inhibitors, were detected by electrospray ionization mass spectrometry (ESI-MS) for the first time. The formation and conversion of the dimers were induced by NH(4)(+), DNA concentration, pH, and the binding molecules. We directly observed the specific binding of a perylene derivative (Tel03) and ImImImbetaDp in one system consisting of the intramolecular and the dimeric G-quadruplexes of the HIV-1 integrase inhibitor, which suggested that Tel03 could shift the equilibrium to the dimeric G-quadruplex formation, while ImImImbetaDp induces preferentially a structural change from the dimer to the intramolecular G-quadruplex. The results of this study indicated that Tel03 and ImImImbetaDp favor the stabilization of the dimeric G-quadruplex structures.     

咪唑修饰萘酰亚胺与DNA的作用及其细胞毒性

设计合成了咪唑及其烷基化咪唑阳离子基团修饰的萘酰亚胺衍生物。利用紫外-可见吸收光谱、荧光光谱、圆二色谱和荧光共振能量转移等方法研究了它们与小牛胸腺DNA(CT DNA)和G-四链体DNA的相互作用。这些化合物对端粒DNA序列的G-四链体有很高的结合能力(K_α4×10~6 L·mol~(-1)),并能够稳定G-四链体。DNA粘度实验结果表明萘酰亚胺衍生物与CT DNA通过插入作用结合。Autodock分子对接模拟结果表明这些化合物通过疏水作用、静电作用或氢键等方式与人体端粒G-四链体的loop和沟槽部分结合。咪唑阳离子基团修饰的萘酰亚胺衍生物4a–c能够定位于细胞核,对肺癌细胞的细胞毒性要高于咪唑基团修饰的萘酰亚胺衍生物3。化合物4a和4b对肺癌细胞A549的细胞毒性明显高于正常人胚肺成纤维细胞MRC-5,表现出良好的抗癌活性。     

Recognize three different human telomeric G-quadruplex conformations by quinacrine

Recognition of different human telomeric G-quadruplex structures has been a very important task for developing anti-cancer drug design. However, it also is a very challenging question since multiple conformational isomers of telomeric G-quadruplexes coexist under some conditions. Here, three different conformations including parallel, antiparallel, and mixed-type telomeric G-quadruplex structures have been well recognized by quinacrine (QNA) through monitoring its absorption, fluorescence, and fluorescence lifetime spectra. The multiple structures of H22 G-quadruplexes under physiological K(+) conditions could also be easily determined to coexist as mixed-type and antiparallel G-quadruplexes. The recognition mechanism based on the different binding affinity and binding sites has been further elucidated by association with the nuclear magnetic resonance (NMR) results.