规则溶液理论应用于bola/SDS混合体系的研究

以规则溶液理论研究了bola型阳离子两亲分子与十二烷基硫酸钠（SDS）混合体系的表面和胶团相互作用.相互作用参数的数值表明, bola分子与SDS在胶团中和溶液表面都发生了强烈的相互作用,这种相互作用的强度与普通季铵盐/烷基硫酸钠混合体系相当.这说明bola分子与SDS混合体系中的协同作用主要是由亲水基之间的静电相互作用产生的, 而bola分子结构中疏水部分对相互作用没有显著影响.     

二芳基甲烷衍生物保留因子与分离因子的神经网络理论研究

为了研究手性二芳基甲烷衍生物的保留因子和分离因子,基于分子结构及邻接矩阵,计算了63个手性二芳基甲烷衍生物的分子连接性指数和电性拓扑状态指数。建立了这些分子保留因子、分离因子与优化得到的结构指数之间的相关性模型,并将筛选的结构参数作为BP神经网络的输入层变量,采用不同的网络结构,获得了令人较为满意的三个预测模型,模型的总相关系数R分别为0.981、0.972和0.992。利用模型计算得到的保留因子和分离因子预测值与实验值的平均误差分别为0.041、0.042和0.010,吻合度较好。结果表明手性二芳基甲烷衍生物的保留因子及分离因子与分子结构参数之间有良好的非线性关系。     

计算机辅助筛选酪氨酸激酶相关蛋白TRP-2 CTL模拟表位

运用多项式方案、量化基序方案等经典的CTL表位筛选方案, 初步筛选了酪氨酸激酶相关蛋白TRP-2 CTL表位TRP-2_180～188 (SVYDFFVWL)的模拟表位, 以通过表位改造提高其与HLA-A2.1分子结合的能力, 从而提高其免疫原性. 根据打分结果, 合成了4个得分较高的九肽序列, 亲和力实验结果表明所筛选的4个序列较原序列均有较高的亲和力, 但对2位的单突变结果较1和2位双突变结果理想, 进一步运用分子模拟方法对4个序列与HLA-A2.1分子间的相互作用进行了分子模拟分析, 分子模拟结果较好地解释了上述实验现象, 从而为进一步的结构改造提供了理论依据. 本研究提供了一个合理高效的模拟表位筛选方法.     

4-硝基-1,3-丁二烯基胺分子的氢键效应

在从头计算的水平上, 利用杂化密度泛函理论研究了溶剂对4-硝基-1,3-丁二烯基胺分子的几何结构、分子内的电荷分布和电荷转移态的能量漂移的影响. 在四种极性溶剂中, 我们构造了包括氢键作用的超分子结构. 分别研究了由极化连续模型模拟的溶剂和溶质分子的长程相互作用, 溶剂和溶质分子的氢键作用, 以及溶剂和溶质分子的整体作用对分子结构和性质的影响. 研究结果表明氢键作用引起了溶质分子结构和性质的较大变化, 从而将明显地影响该类分子的非线性光学性质. 因此, 在模拟溶剂效应时需要考虑氢键作用.     

分子全息QSAR预测环境污染物的雌激素活性

某些天然和人工合成有机化学物质能够干扰人类和野生动物内分泌系统的正常功能(一般称为“内分泌干扰物质”, EDCs), 从而对人类和野生动物种群的生存和持续繁衍造成严重威胁. 鉴于人工合成化学品种类繁多、结构复杂, 发展基于结构的快速筛选方法, 对环境中污染物进行筛选和评价, 具有重要的实际意义. 应用一种新的分子结构表征方法——分子全息, 利用多变量统计方法——偏最小二乘分析(PLS), 以105种典型的环境雌激素类化合物为研究对象, 发展了完全基于分子结构的定量预测模型, 可以对环境中有机污染物的雌激素活性进行比较准确的预测和快速筛选.     

基于DFT和分子连接性指数方法研究醇类化合物的水溶解度和分配系数

将DFT方法计算得到的量化参数和分子连接性指数联合应用到60个醇类化合物的溶解度和辛醇/水分配系数的QSPR研究中,分别通过逐步回归得到具有显著统计意义的4个参数和5个参数的QSPR方程.以此4个参数和5个参数分别作为输入参数,采用BPNN,RBFNN方法建立了QSPR预测模型,使用Latin-partition交叉验证方法评价模型的预测能力.BPNN,RBFNN模型对溶解度预测的相关系数分别为0.993和0.994,而对辛醇/水分配系数预测的相关系数分别0.990和0.997,结果令人满意.     

吲哚酚衍生物的结构——式电位关系及电氧化机理

以半经验分子轨道方法计算吲哚酚衍生物的分子结构参数.以主因子分析法和多元线性回归法研究了吲哚酚衍生物的式电位与其分子结构参数间的关系.研究发现,在所选择的19个分子结构参数中,双中心电子交换能(E     

β-联碳酰基类衍生物有序自组装膜的STM研究

在大气条件下, 利用扫描隧道显微镜研究了四个β-联碳酰基类衍生物在高定向裂解石墨(HOPG)表面的自组装结构. 研究分子的结构中均包含π电子共轭体系和烷基链. 实验研究了分子结构对自组装结构的影响, 并利用分子结构的变化实现了自组装膜结构的调控. 结果表明, 在甲苯溶剂中制备的这些自组装结构均长程有序, 分子间氢键和偶极相互作用是影响自组装膜结构变化的重要因素.     

N-磷酰化肽酯及小肽与溶菌酶相互作用的ESI-MS研究

用ESI-MS研究了一系列结构具有可比性的N-磷酰化肽酯及小肽和溶菌酶的非共价相互作用, 比较了磷酰化肽酯及小肽分子中的不同基团对相互作用的影响. 结果表明—OH对其与溶菌酶的相互作用有较大贡献; 芳香环由于位阻原因, 对相互作用有促进和阻碍双重效应; 当—OH与芳香环相连时会发生协同效应, 可使相互作用显著增强. 磷酰化肽酯及小肽的体积大小、空间位阻对相互作用亦有显著影响. 磷酰化二肽中氨基酸残基的构型、顺序、碳链长短的变化(增加1～2个C)对其与蛋白溶菌酶之间的相互作用在质谱中没有表现出影响. 分子结构较为伸展、分子柔顺性好、空间位阻较小的磷酰化小肽更容易使蛋白在溶液中的构象趋于收缩, 而构象较为收缩的蛋白分子更易结合空间位阻较小的磷酰化小肽分子.     

结合三维静电势参数研究二取代苯的定量结构－疏水性关系

对含有常见取代基的92个二取代苯化合物进行了结构优化和静电势及其导出参数的计算,运用多元线性回归方法对化合物的疏水常数与分子的结构参数进行了关联.结果表明,分子表面负静电势的加和ΣV－S、分子空间内最负的静电势Vmin、表面最大静电势Vs,max以及分子体积V、极性表面积APS和分子的偶极密度μ/V这六个参数,可以很好地用于表达这些化合物疏水性与分子结构间的定量关系,而不用具体考虑分子中极性基团间的相互作用.用建立起来的QSPR(quantitative structure-property relationship)关系式对111个类似化合物的疏水性进行了预测,获得了满意的结果.     

On the magnitude of the chelate effect for the recognition of proteins by pharmacophores scaffolded by self-assembling oligonucleotides

The simultaneous interaction of the binding moieties of a bidentate ligand on adjacent epitopes of a target protein represents an attractive avenue for the discovery of specific, high-affinity binders. We used short DNA fragments in heteroduplex format to scaffold pairs of binding molecules with defined spatial arrangements. Iminobiotin derivates were coupled either via bifunctional linkers or by using various oligonucleotides, thus allowing monovalent or bivalent binding to streptavidin. We determined the binding affinities of the synthesized constructs in solution. We also investigated the efficiency of recovery of superior bidentate ligands in affinity capture experiments, by using both radioactive counts and DNA microarrays as readouts. This analysis confirmed the suitability of the DNA heteroduplex as a scaffold for the identification of synergistic pairs of binding moieties, capable of a high-affinity interaction with protein targets by virtue of the chelate effect.     

Sliding on DNA: From Peptides to Small Molecules

Many DNA binding proteins utilize one‐dimensional (1D) diffusion along DNA to accelerate their DNA target recognition. Although 1D diffusion of proteins along DNA has been studied for decades, a quantitative understanding is only beginning to emerge and few chemical tools are available to apply 1D diffusion as a design principle. Recently, we discovered that peptides can bind and slide along DNA—even transporting cargo along DNA. Such molecules are known as molecular sleds. Here, to advance our understanding of structure–function relationships governing sequence nonspecific DNA interaction of natural molecular sleds and to explore the potential for controlling sliding activity, we test the DNA binding and sliding activities of chemically modified peptides and analogs, and show that synthetic small molecules can slide on DNA. We found new ways to control molecular sled activity, novel small‐molecule synthetic sleds, and molecular sled activity in N‐methylpyrrole/N‐methylimidazole polyamides that helps explain how these molecules locate rare target sites.     

Morindone, an Anthraquinone, Intercalates DNA Sans Toxicity: a Spectroscopic and Molecular Modeling Perspective

For the first time, interaction between non-toxic anthraquinone morindone with both natural and synthetic DNA duplexes has been demonstrated in this paper. Detailed analyses of the binding of morindone with DNA via UV?Cvis, FTIR, and circular dichroism spectroscopies were carried out. In addition, bioinformatics tools have been employed to scrutinize the binding of the dye with DNA in silico. Results represent morindone to be a better binder with a score of ?5.79 compared to EtBr (known mutagenic intercalator) recorded at ?5.02. Further interaction is accentuated by the microscope-assisted evidence of nuclear specific staining of tissues by morindone. The electrophoretic analysis reveals the efficacy endowed within morindone dye in rendering protection to DNA exposed to H₂O₂ damage and thereby conferring it safe to the nucleic acid. As DNA is often the target for majority of anticancer and antibiotic drugs, study on the interaction between molecules like morindone and DNA has relevance and implications in several biological applications including cancer therapy. Thus, we propose that morindone can also be harnessed as a diagnostic probe for DNA structure in addition to DNA-directed therapeutics.     

Mapping Polyamide–DNA Interactions in Human Cells Reveals a New Design Strategy for Effective Targeting of Genomic Sites

Targeting the genome with sequence‐specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole‐based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide–DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high‐affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in vivo.     

毛细管电泳结合电喷雾质谱分析人类癌基因c-myb四链体核酸与活性天然产物的相互作用

药物与靶点间的作用关系直接影响到药理和药效。药物-靶点结合能力、结合计量关系等信息是药物研发过程中必需的表征数据。人类癌基因c-myb在结直肠癌等多种癌症组织中存在过度表达,目前已成为结直肠癌、白血病等癌症疾病潜在的治疗靶点。位于癌基因c-myb启动子区的一段富含鸟嘌呤（G）的DNA序列,通过阳离子的诱导可自发折叠形成分子内G-四链体,而小分子的特异性识别可以稳定该G-四链体,进而调节基因的转录和表达过程。该文采用压力辅助毛细管电泳前沿分析（PACE-FA）结合电喷雾质谱（ESI-MS）研究人类癌基因c-myb启动子G-四链体（G4）与天然产物分子间的相互作用。PACE-FA法在毛细管电泳前沿分析（CE-FA）过程中施加一个与分析物迁移同向的压力,在保证结果准确度的前提下,能够大大加快分析速度。同时结合ESI-MS,可快速解析结合分子与靶点的亲合力和化学计量关系。首先,利用ESI-MS快速筛选出3种有亲合力的天然产物,亲合力大小依次为：土荆皮乙酸>丁溴东莨菪碱>荷叶碱。考虑到溶液相中存在特异性与非特异性结合,接着用PACE-FA法准确分析溶液相中结合的特异性和结合常数。结果发现：丁溴东莨菪碱能够特异性结合靶点G4 DNA,结合比为1：1,结合常数为1.18×10⁵ L/mol;荷叶碱属于非特异性结合,而土荆皮乙酸并未与靶点G4 DNA形成复合物。该组合方法不仅分析速度快,而且能够提高亲和分析的准确度和特异性,有望应用于靶向药物先导结构的发现和作用机制评价。     

Noncovalent attachment of psoralen derivatives with DNA: Hartree-Fock and density functional studies on the probes

Two psoralen derivatives (probes) were prepared. Their geometries were optimized at the Hartree-Fock (HF) and Density Functional (B3LYP) levels employing 6-31G** and cc-pVDZ basis sets. Their interaction with DNA was investigated using spectrophotometric and computational techniques. Both of them have shown strong binding to calf thymus DNA. The red-shift and hypochromism that detected in the spectrum were taken as an evidence for the strong interaction between these probes and DNA. The spectrophotometric DNA titration data were treated by two different methodologies to calculate the intercalation affinity. Half-reciprocal plots gave binding constants of 5.5065 x 10(4) and 6.4727 x 10(4) for 8-butoxypsoralen (8-BOP) and 8-hexoxypsoralen (8-HOP), respectively. Schatchard plots gave a comparable intercalation binding constants and also the surface binding constants along with the number of intercalated probe molecules per base pair. The interaction between these probes and DNA were studied theoretically. The energy of interaction was computed using molecular mechanics method. Strength of interaction of these probes with different types of DNA was computed and compared. Calculated energies of interaction were compared with the observed intercalation affinities. HOMO and LUMO energies were computed and used to account for the strength of interaction.     

Regulation of singlet oxygen generation using single-walled carbon nanotubes

We have designed a novel photodynamic therapy (PDT) agent using protein binding aptamer, photosensitizer, and single-walled carbon nanotube (SWNT). The PDT is based on covalently linking a photosensitizer with an aptamer then wrapping onto the surface of SWNTs, such that the photosensitizer can only be activated by light upon target binding. We have chosen the human alpha-thrombin aptamer and covalently linked it with Chlorin e6 (Ce6), which is a second generation photosensitizer. Our results showed that SWNTs are great quenchers to singlet oxygen generation (SOG). In the presence of its target, the binding of target thrombin will disturb the DNA interaction with the SWNTs and cause the DNA aptamer to fall off the SWNT surface, resulting in the restoration of SOG. This study validated the potential of our design as a novel PDT agent with regulation by target molecules, enhanced specificity, and efficacy of therapeutic function, which directs the development of photodynamic therapy to be safer and more selective.     

Fluorescence images of DNA-bound YOYO between coupled silver particles

Oligonucleotide-bound silver particles were coupled through hybridization with target complementary oligonucleotides. YOYO molecules were intercalated into DNA duplexes bound between the coupled metal particles. Fluorescence images of YOYO molecules were monitored by scanning confocal microscopy. Relative to the free single YOYO, the emission brightness of the image was enhanced 80-fold after intercalating the fluorophores into the DNA duplexes between the coupled silver particles. Some images of the labeled metal particle dimers were observed to be dumbbell-shaped, suggesting that the stretching of intercalated YOYO molecules was restricted because of the orientation effect of fluorophores. The shortened lifetime of YOYO molecules between the coupled metal particles indicated that the fluorescence was enhanced via a near-field interaction mechanism between the fluorophore and the metal nanoparticle.     

Novel virtual screening protocol based on the combined use of molecular modeling and electron-ion interaction potential techniques to design HIV-1 integrase inhibitors

HIV-1 integrase (IN) is an essential enzyme for viral replication and represents an intriguing target for the development of new drugs. Although a large number of compounds have been reported to inhibit IN in biochemical assays, no drug active against this enzyme has been approved by the FDA so far. In this study, we report, for the first time, the use of the electron-ion interaction potential (EIIP) technique in combination with molecular modeling approaches for the identification of new IN inhibitors. An innovative virtual screening approach, based on the determination of both short- and long-range interactions between interacting molecules, was employed with the aim of identifying molecules able to inhibit the binding of IN to viral DNA. Moreover, results from a database screening on the commercial Asinex Gold Collection led to the selection of several compounds. One of them showed a significant inhibitory potency toward IN in the overall integration assay. Biological investigations also showed, in agreement with modeling studies, that these compounds prevent recognition of DNA by IN in a fluorescence fluctuation assay, probably by interacting with the DNA binding domain of IN.