N-磷酰化多巴胺与溶菌酶相互作用的ESI-MS研究

采用电喷雾离子肼-质谱(ESI-MS)研究了一系列结构具有可比性的N-磷酰化多巴胺与溶菌酶的非共价相互作用, 比较了磷上不同取代基对相互作用的影响. 结果表明, 磷上的烷氧取代基上烷基碳原子的个数及排列顺序对二者相互作用有较大影响; 取代基上碳链越长, 溶液中溶菌酶的构象越趋于收缩, 二者之间越容易形成带低电荷和高质核比的复合物, 且其稳定性也随着取代基的增长而增强; 当取代基碳原子数相同时, 直链取代的磷酰化多巴胺与溶菌酶形成的复合物比支链取代的底物与溶菌酶形成的复合物稳定.     

槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点

深入理解药物分子和核酸碱基间的相互作用机制对合理设计研发新型高效药物有重要意义. 本文运用密度泛函理论B3LYP方法对核酸碱基尿嘧啶和胸腺嘧啶与药物分子槲皮素间的氢键相互作用位点进行了研究. 使用B3LYP/6-31G(d)方法优化得到了30个稳定的氢键复合物结构, 使用B3LYP/6-311++G(3df,2p)方法计算了这些复合物的结合能. 研究结果表明, 槲皮素可以使用5个不同的结合位点与尿嘧啶或胸腺嘧啶形成氢键复合物, 尿嘧啶或胸腺嘧啶可以使用3个不同的结合位点与槲皮素形成氢键复合物. 当槲皮素的结合位点固定时, 槲皮素与尿嘧啶的位点u1或胸腺嘧啶的位点t1形成的氢键作用最强, 与位点u2或位点t2形成的氢键强度最弱; 当尿嘧啶或胸腺嘧啶的作用位点固定时, 二者与槲皮素的位点qu1 形成的氢键作用最强, 与位点qu5 作用强度次之, 与位点qu3的作用强度最弱. 分子中原子(AIM)和自然键轨道(NBO)分析计算结果表明, 轨道作用在氢键中起重要作用.     

二元和三元复合物中阳离子硫键与磷键的理论研究

采用MP2/cc-pVDZ和cc-pVTZ基组分别对复合物XH₂S⁺…NCH₂P和NCH₂P…PyX(X=NH₂, CH₃, H, CN, F, Cl, Br)中的硫键和磷键进行了研究, 讨论了键长、 键临界点的电荷密度(ρ)、 拉普拉斯密度(▽²ρ)、 范德华表面穿透距离、 二阶稳定化能和电荷转移量对硫键和磷键相互作用能的影响. 结果表明, 当取代基X为吸电子基团时, 形成的硫键较强. 当X为给电子基团时, 形成的磷键较强. 利用能量分解方法分析了取代基—CN导致硫键稳定性反常的可能原因. 还进一步讨论了三元复合物H₃S⁺…NCH₂P…PyX(X=NH₂, CH₃, H, CN, F, Cl, Br)中硫键和磷键的协同相互作用以及取代基对复合物稳定性的影响. 并通过对比相同的2种单体在三元复合物和二元复合物中的二阶稳定化能和相互作用能的差值, 说明了硫键与磷键起到相互促进的正协同作用, 增强了三元复合物的稳定性.     

金丝桃素分子结构及其与HIV病毒蛋白酶作用的分子动力学研究

采用用计算化学方法研究金丝桃素分子结构特征, 并用分子动力学方法研究其与HIV蛋白酶的相互作用, 探讨其可能的抗HIV病毒作用机理. 结果表明, 金丝桃素分子结构具有刚性特征, 与HIV蛋白酶在酶的催化活性位点与ASP-A25 and ASP-B25以氢键作用相结合.     

过渡金属M (M=Cu,Ag, Au)对X…Cl (X = F,Cl, Br)卤键相互作用强度的影响

采用量子化学方法,通过MCH2X…ClF(M=Cu,Ag,Au;X=F,Cl,Br)和CH3X…ClF两类复合物的对比,探讨了过渡金属对卤键相互作用强度的影响.CH3X…ClF复合物只有卤键相互作用,而优化MCH2X…ClF复合物除了得到一种只含有卤键相互作用的构型外,还得到一种含有过渡金属和Cl原子相互作用的稳定构型.含有过渡金属的复合物稳定性明显增加,Ag取代的复合物稳定性增加最为明显,Cu次之,Au最不明显.X原子最负分子表面静电势(MEP)减小是复合物稳定性增加的根本原因.利用自然键轨道(NBO)及分子中原子(AIM)分析进一步对体系的分子间相互作用进行了探讨.二阶稳定化能与键鞍点处拓扑性质的计算结果与相互作用能符合得很好.     

非肽类SARS冠状病毒3CL蛋白酶抑制剂的设计与活性表征

SARS冠状病毒3CL蛋白酶是SARS病毒复制过程中的主要蛋白酶, 针对其开展药物设计有望得到有效的抗SARS病毒药物. 本文基于SARS冠状病毒3CL蛋白酶的三维结构, 对现有化学试剂及临床用药数据库进行虚拟筛选, 选出可能对SARS冠状病毒3CL蛋白酶有抑制的非肽化合物进行初步活性测试, 并研究了已知的人鼻病毒3C蛋白酶抑制剂对SARS冠状病毒3CL蛋白酶的活性, 合成了两种母环的衍生物, 得到靛红和哌嗪两类SARS冠状病毒3CL蛋白酶的抑制剂, 其中一个靛红类化合物的IC₅₀为0.76 µmol•L^－1; 而抗组胺药哌嗪类化合物对SARS冠状病毒3CL蛋白酶及细胞培育的SARS病毒的抑制作用, 提示了老药可以开发出新的用途.     

拟南芥TIR1与生长素IAA相互作用的分子对接及分子动力学研究

基于最新得到的拟南芥运输抑制剂响应蛋白质1(TIR1)与吲哚乙酸(IAA)复合物的晶体结构, 使用分子对接方法和分子动力学方法对TIR1与生长素IAA相互作用的方式进行了研究. 分子对接结果表明, 通过逐级考察辅酶InsP₆和中心水分子的影响, 发现辅酶InsP₆和中心水分子对生长素IAA正确结合到活性位点有重要作用. 分子动力学结果表明, 复合物体系在整个模拟过程中较为稳定, 2个水分子相继作为中心水分子与生长素IAA形成了稳定的氢键作用, IAA与活性位点处残基的相互作用与晶体结构相比略有差异.     

HXeBr与苯和苯的衍生物弱相互作用的理论研究

采用MP2/aug-cc-pVDZ (对于Xe和I原子采用aug-cc-pVDZ-PP基组)优化了复合物HXeBr…C₆H₅X (X=H, CH₃, NH₂, N(CH₃)₂, NHCH₃, OH, OCH₃, CN, F, Cl, Br, I, COOH, SO₃H, CF₃)及单体的几何构型, 详细分析了π…H键和双齿氢键两种弱相互作用类型的特征, 以及不同的取代基对这两种弱相互作用能的影响. 对14个双齿氢键型复合物, 我们发现复合物的相互作用能与苯环衍生物(C₆H₅X)的偶极矩, 复合物中Xe-Br键键长的变化, H-Xe键键长的变化和H-Xe键振动频率的变化, 以及双齿氢键上Br原子和两个H原子范德华表面相互穿透距离之和均有较好的线性关系. 另外, 我们还发现复合物的相互作用能与双齿氢键上两个键临界点的电子密度之和, 电子密度Laplacian值之和, 静电势之和, 以及双齿氢键和苯环碳原子形成环的环临界点处的电子密度, 电子密度Laplacian值以及静电势均有着较好的线性关系.     

取代基对腺嘌呤与胸腺嘧啶氢键复合物体系结合能的影响

优化得到了17个取代胸腺嘧啶与腺嘌呤形成的氢键复合物的结构, 并计算了这些复合物的结合能, 探讨了胸腺嘧啶上不同取代基对结合能的影响. 结果表明, CF₃取代的胸腺嘧啶与腺嘌呤间的结合能大于胸腺嘧啶与腺嘌呤间的结合能, 这可能是屈氟尿苷具有阻止病毒及肿瘤扩散功能的原因所在. SO₃H, CN和NO₂取代的胸腺嘧啶与腺嘌呤间具有更大的结合能, 表明这3个基团取代的胸腺嘧啶也可能具有潜在的抗肿瘤作用. 分子中原子理论与自然键轨道分析表明, 在所有体系中, 氢键N—H…N最强, N—H…O=C次之, C—H…O=C最弱, 轨道作用在氢键作用中占有重要地位.     

多溴联苯醚与人血清白蛋白相互作用的表面等离子体共振及分子对接

采用表面等离子体共振(SPR)技术,在模拟生理条件下实时动态研究了8种典型多溴联苯醚(PBDEs)与人血清白蛋白(HSA)相互作用的动力学和热力学行为.通过分子对接模拟研究了PBDEs与HSA相互作用的分子机制,探讨了不同PBDEs与蛋白的结合模式及作用力.动力学实验结果表明, PBDEs中溴原子的个数和取代位置对相互作用有规律性的影响.溴原子通过改变PBDEs分子与HSA作用过程中的解离速率来影响其亲和力,溴原子个数越多, PBDEs与HSA作用的亲和力越强;而取代基位置则影响PBDEs与HSA作用结合速率的快慢,同分异构体中间位取代溴的亲和力大于邻位取代溴.分子对接结果显示, 8种PBDEs主要结合于HSA的Site I位点,但结合位点周边氨基酸残基类型的差异影响了结合力.范德华力和氢键对结合能的贡献远大于静电力.     

Discovery of Anti-SARS Coronavirus Drug Based on Molecular Docking and Database Screening

The active site of 3CL proteinase (3CL^por) for coronavirus was identified by comparing the crystal structures of human and porcine coronavirus. The inhibitor of the main protein of rhinovirus (Ag7088) could bind with 3CL^pro of human coronavirus, then it was selected as the reference for molecular docking and database screening. The ligands from two databases were used to search potential lead structures with molecular docking. Several structures from natural products and ACD-SC databases were found to have lower binding free energy with 3CL^pro than that of Ag7088. These structures have similar hydrophobicity to Ag7088. They have complementary electrostatic potential and hydrogen bond aeceptor and donor with 3CL^pro, showing that the strategy of anti-SARS drug design based on molecular docking and database screening is feasible.     

SARS 3CL蛋白酶同源二聚化与底物结合互为别构调控因素

研究了严重急性呼吸系统综合症(SARS)冠状病毒3C-Like蛋白酶(3CLpro)在存在底物或抑制剂时的二聚体形成情况. 通过测定酶活性随酶浓度的变化, 拟合出在底物存在下酶二聚体的解离常数约为0.94 μmol·L-1, 小于纯蛋白酶的二聚体解离常数(14.0 μmol·L-1), 表明底物对二聚体的形成具有增强作用. 选用与底物具有类似结合方式的靛红类抑制剂N-萘甲基靛红-5-甲酰胺(5f), 利用超速离心沉降速率方法定量测定了SARS 3CL蛋白酶单体和二聚体在不同浓度5f时的含量, 发现5f同样具有诱导二聚体形成的能力. 在3 μmol·L-1蛋白酶浓度下测定得到诱导二聚的EC50 值(半数有效浓度)约为1 μmol·L-1, 说明二聚体中只有一个单体与抑制剂结合. 研究结果表明, 随着底物浓度的升高, SARS 3CL蛋白酶会形成更多的二聚体, 而二聚体含量的提高又反过来提高酶的活性, 这种双向别构调控机制有可能是病毒用来调控多聚蛋白水解速率和组装时机的一种方法.     

High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase

The causative agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus, SARS-CoV. The main proteinase of SARS-CoV, 3CLpro, is an attractive target for therapeutics against SARS owing to its fundamental role in viral replication. We sought to identify novel inhibitors of 3CLpro to advance the development of appropriate therapies in the treatment of SARS. 3CLpro was cloned, expressed, and purified from the Tor2 isolate. A quenched fluorescence resonance energy transfer assay was developed for 3CLpro to screen the proteinase against 50,000 drug-like small molecules on a fully automated system. The primary screen identified 572 hits; through a series of virtual and experimental filters, this number was reduced to five novel small molecules that show potent inhibitory activity (IC50 = 0.5-7 microM) toward SARS-CoV 3CLpro.     

A survey of interactions in crystal structures of pyrazine‐based compounds

The important role of pyrazine (pz) and its derivatives in fields such as biochemistry and pharmacology, as well as in the study of magnetic properties, is surveyed. Recognition of these properties without extensive investigations into their structural properties is not possible. This review summarizes interactions that exist between these organic compounds by themselves in the solid state, as well as those in coordination polymers with metal ions and in polyoxometalate‐based hybrids. Complexes based on pyrazine ligands can generate metal–organic framework (MOF) structures that bind polyoxometalates (POMs) through covalent and noncovalent interactions. Some biological and magnetic properties involving these compounds are considered and the effect of hydrogen bonding on their supramolecular architectures is highlighted.     

Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties

By chemically modifying or replacing the backbone of oligonucleotides it is possible to modulate the DNA and RNA recognition properties and fine-tune the physiochemical properties of oligomers. This is important because it challenges our understanding of natural nucleic acid structural and recognition properties and can lead to nucleic acid mimics with a wide range of applications in nucleic acid targeting, analysis or diagnostics. In this paper we describe the solid phase synthesis of pyrrolidine-amide oligonucleotide mimics (POMs) using Fmoc-peptide chemistry. This required the synthesis of adeninyl, cytosinyl, thyminyl and guaninyl pyrrolidine monomers, with Fmoc- and standard acyl-protecting groups on the exocyclic amino groups and nucleobases respectively. These monomers were used to synthesise several thyminyl and adeninyl POM pentamers, with modest coupling efficiency. The pentamers were purified by RP-HPLC, characterised by mass spectrometry and their DNA and RNA binding properties were investigated using UV thermal denaturation/renaturation experiments. This revealed that all the pentamers exhibit strong affinity for complementary nucleic acids. The further evaluation of longer mixed-sequence POMs is described in a second accompanying paper (R. J. Worthington et al., Org. Biomol. Chem., 2006, DOI: 10.1039/b613386j).     

Beyond Charge Balance: Counter‐Cations in Polyoxometalate Chemistry

Polyoxometalates (POMs) are molecular metal‐oxide anions applied in energy conversion and storage, manipulation of biomolecules, catalysis, as well as materials design and assembly. Although often overlooked, the interplay of intrinsically anionic POMs with organic and inorganic cations is crucial to control POM self‐assembly, stabilization, solubility, and function. Beyond simple alkali metals and ammonium, chemically diverse cations including dendrimers, polyvalent metals, metal complexes, amphiphiles, and alkaloids allow tailoring properties for known applications, and those yet to be discovered. This review provides an overview of fundamental POM–cation interactions in solution, the resulting solid‐state compounds, and behavior and properties that emerge from these POM–cation interactions. We will explore how application‐inspired research has exploited cation‐controlled design to discover new POM materials, which in turn has led to the quest for fundamental understanding of POM–cation interactions.     

Recent advances in polyoxometalates acid-catalyzed organic reactions

Polyoxometalates (POMs) have conducive properties such as controlled Brønsted and Lewis acidity, high thermal stability, nontoxic nature, tunable solubility, and less corrosiveness. POMs have been extensively applied in catalytic organic reactions and have an exciting prospect for industrial applications. This review summarized recent progress in the application of POMs as acid catalysts for various organic reactions including CC bond formation, CN bond formation, CO bond formation, heterocyclic synthesis reactions, cyanosilylation and hydrolysis reactions. Various POMs catalysts including heteropoly acids (HPAs) and cationic functionalized HPAs with Brønsted acidity, HPAs supported on non-precious metal support with Brønsted acidity (or both Brønsted and Lewis acidity), transition metal substituted POMs with Lewis acidity were applied in above reactions. This review attempts to provide up-to-date information about POMs acid-catalyzed organic reactions and propose future prospects.