Docking study of cistanoside C to telomeric DNA fragment

Experiments show that the natural products phenyl propanoid glycosides (PPGs) extracted from the plant Pedicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecule Cistanoside C and telomeric DNA fragment has been carried out. The docking calculations performed using JUMNA software showed that the Cistanoside C could be docked into the minor groove of telomeric DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the saccharide side-groups.     

Dinuclear Ruthenium(II) Complexes That Induce and Stabilise G‐Quadruplex DNA

A series of dinuclear ruthenium(II) complexes were synthesised, and the complexes were determined to be new highly selective compounds for binding to telomeric G‐quadruplex DNA. The interactions of these complexes with telomeric G‐quadruplex DNA were studied by using circular dichroism (CD) spectroscopy, fluorescence resonance energy transfer (FRET) melting assays, isothermal titration calorimetry (ITC) and molecular modelling. The results showed that the complexes 1 , 2 and 4 induced and stabilised the formation of antiparallel G‐quadruplexes of telomeric DNA in the absence of salt or in the presence of 100 mM K⁺‐containing buffer. Furthermore, complexes 1 and 2 strongly bind to and effectively stabilise the telomeric G‐quadruplex structure and have significant selectivity for G‐quadruplex over duplex DNA. In comparison, complex 3 had a much lesser effect on the G‐quadruplex, suggesting that possession of a suitably sized plane for good π–π stacking with the G‐quadruplets is essential for the interaction of the dinuclear ruthenium(II) complexes with the G‐quadruplex. Moreover, telomerase inhibition by the four complexes and their cellular effects were studied, and complex 1 was determined to be the most promising inhibitor of both telomerase and HeLa cell proliferation.     

Photo-Oxidizing Ruthenium(II) Complexes with Enhanced Visible-Light Absorption and G-quadruplex DNA Binding Abilities

Photosensitizers that gather high photo-oxidizing power and strong visible-light absorption are of great interest in the development of new photo-chemotherapeutics. Indeed, such compounds constitute attractive candidates for the design of type I photosensitizers that are not dependent on the presence of oxygen. In this paper, we report on the synthesis and studies of new ruthenium(II) complexes that display strong visible-light absorption and can oxidize guanine residues under visible-light irradiation, as evidenced by nanosecond transient absorption spectroscopy. The reported compounds also tightly bind to G-quadruplex DNA structures from the human telomeric sequence (TTAGGG repeat). The kinetic and thermodynamic parameters of the interaction of these Ru(II) complexes with G-quadruplex and duplex DNA were studied thanks to luminescence titrations and bio-layer interferometry measurements, which revealed higher affinities towards the non-canonical G-quadruplex architecture. Docking experiments and non-covalent ionic analysis allowed us to gain information on the mode and the strength of the interaction of the compounds towards G-quadruplex and duplex DNA. The different studies emphasize the substantial influence of the position and the number of non-chelating nitrogen atoms on the interaction with both types of DNA secondary structures.     

电喷雾质谱法研究天然产物小分子识别人类端粒G-四链体及复合物的热稳定性

利用电喷雾质谱(ESI-MS)研究了12种天然产物小分子与人类端粒G-四链体结构的非共价相互作用和识别功能, 比较了不同小分子与人类端粒G-四链体的结合强弱, 发现了一种新的识别小分子——防己诺林碱对人类端粒G-四链体有很好的结合. 通过质谱升温实验比较了小分子结合对G-四链体热稳定性的影响, 防己诺林碱的结合使G-四链体的离子的解离温度(T1/2)上升到200 ℃. 利用分子模拟对G-四链体DNA与小分子结合的模式以及稳定性进行了探讨, 给出了防己诺林碱可能的结合位点和结合模式, Autodock计算出来的结合能约为-31.5 kJ·mol-1. 同原来的平面型分子不同, 防己诺林碱是一类新型结构的分子, 为设计合成新型G-四链体识别分子提供了新的结构模型.     

Decompaction of cationic gemini surfactant-induced DNA condensates by beta-cyclodextrin or anionic surfactant

Compaction of DNA by cationic gemini surfactant hexamethylene-1,6-bis-(dodecyldimethylammoniumbromide) (C12C6C12Br2) and the subsequent decompaction of the DNA-C12C6C12Br2 complexes by beta-cyclodextrin (beta-CD) or sodium dodecyl sulfate (SDS) have been studied by using zeta potential and particle size measurements, atomic force microscopy (AFM), isothermal titration microcalorimetry (ITC), and circular dichroism. The results show that C12C6C12Br2 can induce the collapse of DNA into densely packed bead-like structures with smaller size in an all-or-none manner, accompanied by the increase of zeta potential from highly negative values to highly positive values. In the decompaction of the DNA-C12C6C12Br2 complexes, beta-CD and SDS exhibit different behaviors. For beta-CD, the experimental results suggest that it can remove the outlayer hydrophobically bound C12C6C12Br2 molecules from the DNA-C12C6C12Br2 complexes by inclusion interaction, and the excess beta-CD may attach on the complexes by forming inclusion complexes with the hydrocarbon chains of the electrostatically bound C12C6C12Br2 that cannot be removed. The increase of steric hindrance due to the attachment of beta-CD molecules results in the decompaction of the DNA condensates though the true release of DNA cannot be attained. However, for SDS, the experimental results suggest that it can realize the decompaction and release of DNA from its complexes with C12C6C12Br2 due to both ion-pairing and hydrophobic interaction between SDS and C12C6C12Br2.     

Targeting G-Rich DNA Structures with Photoreactive Bis-Cyclometallated Iridium(III) Complexes

The synthesis and characterisation of three novel iridium(III) bis-cyclometallated complexes is reported. Their photophysics have been fully characterised by classical methods and revealed charge-transfer (CT) and ligand-centred (LC) transitions. Their ability to selectively interact with G-quadruplex telomeric DNA over duplex DNA has been studied by circular dichroism (CD), bio-layer interferometry (BLI) and surface plasmon resonance (SPR) analyses. Interestingly, one of the complexes was able to promote photoinduced electron transfer (PET) with the guanine DNA base, which in turn led to oxidative damage (such as the formation of 8-oxoguanine) to the telomeric sequence. To the best of our knowledge, this is the first study of highly photo-oxidising bis-cyclometallated iridium(III) complexes with G-quadruplex telomeric DNA.     

Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking

Experiments show that the natural substances phenylpropanoid glycosides (PPGs) extracted from pelicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecules and isolated DNA bases, as well as a DNA fragment has been performed. An interaction mechanism reported early has been refined. The docking calculations performed using junction minimization of nucleic acids (JUMNA) software showed that the PPG molecules can be docked into the minor groove of DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the rhamnosyl side-groups.     

Theoretical study of fast repair of DNA damage by cistanoside C and analogs: Mechanism and docking

Experiments show that the natural substances phenylpropanoid glycosides (PPGs) extracted from pelicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecules and isolated DNA bases, as well as a DNA fragment has been performed. An interaction mechanism reported early has been refined. The docking calculations performed using junction minimization of nucleic acids (JUMNA) software showed that the PPG molecules can be docked into the minor groove of DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the rhamnosyl side-groups.     

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.     

Induced-fit recognition of DNA by small circular oligonucleotides

We have investigated the molecular interaction between cyclic and linear oligonucleotides. We have found that short cyclic oligonucleotides can induce hairpinlike structures in linear DNA fragments. By using NMR and CD spectroscopy we have studied the interaction of the cyclic oligonucleotide d with d, as well as with its two linear analogs d(GTCCCTCA) and d(CTCAGTCC). Here we report the NMR structural study of these complexes. Recognition between these oligonucleotides occurs through formation of four intermolecular Watson-Crick base pairs. The three-dimensional structure is stabilized by two tetrads, formed by facing the minor-groove side of the Watson-Crick base pairs. Overall, the structure is similar to those observed previously in other quadruplexes formed by minor-groove alignment of Watson-Crick base pairs. However, in this case the complexes are heterodimeric and are formed by two different tetrads (G:C:A:T and G:C:G:C). These complexes represent a new model of DNA recognition by small cyclic oligonucleotides, increasing the number of potential applications of these interesting molecules.     

Interaction of DNA/polycation complexes with phospholipids: stabilizing strategy for gene delivery

The interaction between negatively charged lipid vesicles and positively charged DNA/polylysine complexes was studied. The interaction does not lead to release of DNA from the initial complexes. The particles formed are easy to prepare, they have slight negative charge, small dimensions and show good stability in physiological NaCl solution. Such properties might indicate that stabilization of the particles by lipid coating might be a potent strategy, alternative to PEGylation of DNA/polycation complexes. Interaction of DNA/polycation complex particles with lipid vesicles.     

Selective G-quadruplex DNA stabilizing agents based on bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine

Various biologically relevant G-quadruplex DNA structures offer a platform for therapeutic intervention for altering the gene expression or by halting the function of proteins associated with telomeres. One of the prominent strategies to explore the therapeutic potential of quadruplex DNA structures is by stabilizing them with small molecule ligands. Here we report the synthesis of bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine and their interaction with human telomeric DNA and promoter G-quadruplex forming DNAs. The interactions of ligands with quadruplex forming DNAs were studied by various biophysical, biochemical, and computational methods. Results indicated that bisquinolinium ligands bind tightly and selectively to quadruplex DNAs at low ligand concentration (～0.2-0.4 μM). Furthermore, thermal melting studies revealed that ligands imparted higher stabilization for quadruplex DNA (an increase in the T(m) of up to 21 °C for human telomeric G-quadruplex DNA and >25 °C for promoter G-quadruplex DNAs) than duplex DNA (ΔT(m) ≤ 1.6 °C). Molecular dynamics simulations revealed that the end-stacking binding mode was favored for ligands with low binding free energy. Taken together, the results indicate that the naphthyridine-based ligands with quinolinium and pyridinium side chains form a promising class of quadruplex DNA stabilizing agents having high selectivity for quadruplex DNA structures over duplex DNA structures.     

C_（12）C_6C_（12）Br_2/C_（12）E_（10）混合表面活性剂与DNA之间的相互作用

本文以构建有效的非病毒基因载体为目的,研究了C12C6C12Br2/C12E10混合表面活性剂组成对其与DNA之间相互作用的影响,并对混合表面活性剂与DNA形成的聚集体结构和形貌进行了表征。结果表明,当固定混合表面活性剂的总浓度为1.0 mmol/L时,混合表面活性剂组成的改变会引起混合体系浊度、聚集体表面电荷和聚集体...     

Structural basis for telomeric G-quadruplex targeting by naphthalene diimide ligands

The folding of the single-stranded 3' end of the human telomere into G-quadruplex arrangements inhibits the overhang from hybridizing with the RNA template of telomerase and halts telomere maintenance in cancer cells. The ability to thermally stabilize human telomeric DNA as a four-stranded G-quadruplex structure by developing selective small molecule compounds is a therapeutic path to regulating telomerase activity and thereby selectively inhibit cancer cell growth. The development of compounds with the necessary selectivity and affinity to target parallel-stranded G-quadruplex structures has proved particularly challenging to date, relying heavily upon limited structural data. We report here on a structure-based approach to the design of quadruplex-binding ligands to enhance affinity and selectivity for human telomeric DNA. Crystal structures have been determined of complexes between a 22-mer intramolecular human telomeric quadruplex and two potent tetra-substituted naphthalene diimide compounds, functionalized with positively charged N-methyl-piperazine side-chains. These compounds promote parallel-stranded quadruplex topology, binding exclusively to the 3' surface of each quadruplex. There are significant differences between the complexes in terms of ligand mobility and in the interactions with quadruplex grooves. One of the two ligands is markedly less mobile in the crystal complex and is more quadruplex-stabilizing, forming multiple electrostatic/hydrogen bond contacts with quadruplex phosphate groups. The data presented here provides a structural rationale for the biophysical (effects on quadruplex thermal stabilization) and biological data (inhibition of proliferation in cancer cell lines and evidence of in vivo antitumor activity) on compounds in this series and, thus, for the concept of telomere targeting with DNA quadruplex-binding small molecules.     

Disubstituted 2-phenyl-benzopyranopyrimidine derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA

A series of 2-phenyl-benzopyranopyrimidine (PBPP) derivatives with alkylamino side chains were synthesized and found to be a new type of highly selective ligand to bind with telomeric G-quadruplex DNA, and their biological properties were reported for the first time. Their interactions with telomeric G-quadruplex DNA were studied with FRET melting, surface plasmon resonance, CD spectroscopy, and molecular modeling. Our results showed that the disubstituted PBPP derivatives could strongly bind to and effectively stabilize the telomeric G-quadruplex structure, and had significant selectivity for G-quadruplex over duplex DNA. In comparison, the mono substituted derivatives had much less effect on the G-quadruplex, suggesting that the disubstitution of PBPP is essential for its interaction with the G-quadruplex. Furthermore, telomerase inhibition of the PBPP derivatives and their cellular effects were studied, and compound 11b was found to be the most promising compound as a telomerase inhibitor and telomeric G-quadruplex binding ligand for further development for cancer treatment.     

基于酰腙配体的双锡核二(2,4-二氯苄基)锡配合物的合成、结构及生物活性

二(2,4-二氯苄基)二氯化锡分别与对甲氧基苯甲酰肼缩2-丁酮酸或2-噻吩酰肼缩2-丁酮酸酸反应,合成了两个二(2,4-二氯苄基)锡配合物(C1、C2),通过傅里叶变换红外光谱仪(FTIR)、核磁共振波谱仪(NMR)、高分辨质谱仪(HRMS)以及X射线单晶衍射(SCXRD)等表征了配合物结构。 两个配合物分子均为双锡核分子,以Sn₂O₂四元环为中心对称,且锡原子与配位原子形成七配位畸变五角双锥构型。 配合物C1、C2在空气氛围,120 ℃以下可稳定存在。 配合物C1、C2对人肺癌细胞(NCI-H460)、人肝癌细胞(HepG2)和人乳腺癌细胞(MCF7)均有较好的抑制作用,配合物C1略优于C2。 配合物C1、C2通过插入结合方式与小牛胸腺DNA相互作用,并且配合物C1与DNA的作用略强于C2。     

基于取代苯甲酰肼缩丙酮酸配体的二苄基锡配合物的合成、晶体结构及生物活性

二苄基二氯化锡分别与对甲氧基苯甲酰肼缩丙酮酸及对硝基苯甲酰肼缩丙酮酸反应,合成了2个二苄基锡配合物(C1、C2),通过元素分析、IR、~1H NMR、~(13)C NMR、~(119)Sn NMR、HRMS以及X射线单晶衍射等表征了配合物结构。测试了配合物C1、C2的热稳定性以及配合物对癌细胞H460、HepG2、MCF7的体外抑制活性;在Tris-HCl缓冲溶液中,以EB做为荧光探针,用荧光光谱法初步研究了配合物C1与小牛胸腺DNA的相互作用;并且用凝胶电泳法研究了配合物C1切割质粒DNA pBR322的能力。结果表明:配合物C1、C2对3种癌细胞都有较好的抑制作用,但是C1更优于C2;配合物C1与小牛胸腺DNA作用是插入结合作用所致,能有效的将超螺旋DNA pBR322切割成缺刻型DNA。     

Synthesis, spectroscopic characterization and DNA nuclease activity of Cu(II) complexes derived from pyrazolone based NSO-donor Schiff base ligands

Two neutral mononuclear Cu(II) complexes have been prepared in EtOH using Schiff bases derived from 4-toluoyl pyrazolone and thiosemicarbazide. Both the ligands have been characterized on the basis of elemental analysis, IR, (1)H NMR, (13)C NMR and mass spectral data. The molecular geometry of one of these ligands has been determined by single crystal X-ray study. It reveals that these ligands exist in amine-one tautomeric form in the solid state. Microanalytical data, Cu-estimation, molar conductivity, magnetic measurements, IR, UV-Visible, FAB-Mass, TG-DTA data and ESR spectral studies were used to confirm the structures of the complexes. Electronic absorption and IR spectra of the complexes suggest a square-planar geometry around the central metal ion. The interaction of complexes with pET30a plasmid DNA was investigated by spectroscopic measurements. Results suggest that the copper complexes bind to DNA via an intercalative mode and can quench the fluorescence intensity of EB bound to DNA. The interaction between the complexes and DNA has also been investigated by agarose gel electrophoresis, interestingly, we found that the copper(II) complexes can cleave circular plasmid DNA to nicked and linear forms.     

The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality?

Human telomeric DNA with hundreds of repeats of the 5’-TTAGGG-3’ motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.