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.     

应用超滤液相色谱和电喷雾质谱技术筛选MMP-2活性成分

采用超滤液相色谱和电喷雾质谱技术,结合基质金属蛋白酶-2体外抑制实验,对葛根素、大豆苷和大豆苷元3种异黄酮类化合物抑制基质金属蛋白酶-2抑制活性进行了研究.研究结果表明,3种异黄酮类化合物均可抑制基质金属蛋白酶-2活性,其中葛根素抑制基质金属蛋白酶-2活性最强,其次为大豆苷和大豆苷元.     

新型SARS-CoⅤ 3CL蛋白酶荧光多肽底物的设计、制备及其酶动力学研究

以邻氨基苯甲酸(Abz)为荧光发射基团、2,4-二硝基苯基乙二胺(Eddnp)为荧光猝灭基团,设计合成了SARS-CoⅤ3CL蛋白酶的新型荧光多肽底物:H2N-E(Eddnp)STLQSGLK(Abz)-CONH2.用液相色谱-质谱(LC-MS)联用技术进行了表征,表明该多肽底物能被SARS-CoⅤ3CL蛋白酶识别,并在QS之间被专一性酶解.另外,利用该多肽底物的荧光共振能量转移(FRET)特性,对SARS-CoⅤ3CL蛋白酶的酶解动力学性质进行了研究,结果表明,此荧光多肽底物可以作为荧光探针,应用于SARS-CoⅤ3CL蛋白酶活性的测定及其抑制剂的筛选.     

SARS冠状病毒主要蛋白酶二聚体静电和疏水效应的研究

从三种冠状病毒主要蛋白酶SARS 3CL, HCoV 3CL和TGEC 3CL蛋白酶结构出发,着重研究了三种蛋白酶二聚体单体之间的静电和疏水相互作用.用连续介质模型有限差分方法计算得到三种蛋白二聚体界面处的静电势,发现三种蛋白酶单体和单体之间静电势分布具有明显的互补性,三种蛋白酶二聚体单体之间具有相同的静电相互作用能.用溶剂可及表面积模型分析了分子表面积及疏水性,发现三种蛋白酶具有相同的疏水分布,其中SARS 3CL蛋白酶疏水率为74%,驱动其单体聚合成二聚体.对三种蛋白酶的去溶剂化能疏水项的计算表明,三种蛋白酶二聚体单体之间具有相似的疏水相互作用能.     

新型SARS-CoV 3CL蛋白酶荧光多肽底物的设计、制备及其酶动力学研究

以邻氨基苯甲酸（Abz）为荧光发射基团、2，4-二硝基苯基乙二胺（rdanp）为荧光猝灭基团，设计合成了SARS，CoV3CL蛋白酶的新型荧光多肽底物：H2N-E（Eddnp）STLQSGLK（Abz）-CONH2．用液相色谱-质谱（LC—MS）联用技术进行了表征，表明该多肽底物能被SAILS-CoV 3CL蛋白酶识别，并在QS之间被专一性酶解．另外，利用该多肽底物的荧光共振能量转移（FRET）特性，对SARS—CoV 3CL蛋白酶的酶解动力学性质进行了研究，结果表明，此荧光多肽底物可以作为荧光探针，应用于SARS—CoV 3CL蛋白酶活性的测定及其抑制剂的筛选．     

静电和疏水效应对SARS冠状病毒3CL蛋白酶二聚体稳定性的影响

从TGEV3CL蛋白酶二聚体结构出发,研究了TGEV3CL蛋白酶二聚体单体之间的静电和疏水相互作用.蛋白质的静电相互作用通过有限差分方法求解Poisson-Boltzmann方程得到,疏水相互作用通过分析溶剂可及性表面模型得到.考察了不同pH值对SARS3CL蛋白酶二聚体静电和疏水相互作用的影响,在pH=5.5～8.5时,二聚体静电相互作用能、静电去溶剂化能和疏水自由能都具有较小的数值,表明在该条件下静电和疏水相互作用有利于二聚体的稳定存在.由于SARS3CL蛋白酶活性模式为二聚体,因此,在该pH值范围内,有利于蛋白酶保持活性.在pH=7.0条件下,蛋白酶单体之间具有最强的静电和疏水相互作用,从而使蛋白酶具有最强的活性,这与实验结果相一致.pH值对静电去溶剂化能的影响大于疏水自由能,表明静电作用是造成强酸或强碱条件下二聚体不能稳定存在的主要原因.     

壳聚糖固定化总状毛霉MR137-3蛋白酶的性质

以壳聚糖为载体，戊二醛作交联剂，将总状毛霉MR137—3蛋白酶固定在壳聚糖上。研究了戊二醛浓度，给酶量，处理时间对MR137—3蛋白酶固定化的影响。同时对固定化酶与游离酶的热稳定性、最适pH、最适温度以及脲、有机溶剂、金属离子的影响等理化性质进行了探讨。     

多光谱法与分子对接模型研究西维来司钠与弹性蛋白酶的相互作用

采用多种光谱法及分子对接技术对西维来司钠（ONO-5046）与弹性蛋白酶的相互作用进行研究,利用荧光光谱法判断出ONO-5046的加入对弹性蛋白酶产生荧光猝灭作用,与弹性蛋白酶相互作用的猝灭类型为静态猝灭,ONO-5046与弹性蛋白酶以结合比为1∶1的比例构成复合物。经计算,ONO-5046与弹性蛋白酶体系的ΔH<0和ΔS<0,判断出氢键与范德华力为其主要结合作用力,由ΔG<0可知该反应可以自发进行。同步荧光光谱法、紫外-可见分光光谱法和圆二色光谱法探讨了ONO-5046的加入使弹性蛋白酶中氨基酸残基周围环境的疏水性降低,二级结构发生改变,α-螺旋结构的比例减少,无规则卷曲的比例增多;分子对接模拟结果表明：在与弹性蛋白酶相互作用过程中,ONO-5046分子骨架上的多个酰基结构、2个苯环以及较长的共轭结构能提供氢键与范德华力的作用位点,同时,端碳上的3个甲基结构有利于疏水作用,ONO-5046上的氧负离子与弹性蛋白酶的精氨酸存在盐桥作用。以上结果表明,ONO-5046与弹性蛋白酶的结合存在多种作用力,能形成稳定的复合物,从而抑制了弹性蛋白酶的活性。     

离子液体预处理对羊毛蛋白酶水解性能的影响

利用一种新型绿色溶剂--离子液体1-丁基-3-甲基咪唑氯盐(1-butyl-3-methylimidazolium chloride,[BMIM]Cl)对羊毛进行预处理,从而提高蛋白酶对羊毛的水解效率.系统研究了[BMIM]Cl预处理对蛋白酶处理后羊毛减量率、碱溶解度、蛋白质释放速率、氨基酸组成的影响,并从表面形态、表面润湿性能和纤维晶体结构等方面探讨了[BMIM]Cl对蛋白酶水解的促进作用机理.结果表明:羊毛经过[BMIM]Cl处理后,纤维减量率从2.68%提高到4.47%,碱溶解度达到11.6%,水解液中蛋白质浓度的变化显示[BMIM]Cl预处理使得蛋白质释放速率快速增加;羊毛纤维中低硫和部分高硫氨基酸百分比的降低进一步证实[BMIM]Cl预处理对蛋白酶水解起到了全面促进作用.SEM、润湿接触角以及WAXD测试结果显示预处理破坏了纤维鳞片层,增加了表面润湿性能,并且使得纤维结晶度下降,从而提高了蛋白酶对纤维的可及度,有利于酶解速率的提高.     

ApIV 3C蛋白酶抑制剂的虚拟筛选及活性测定

运用Discovery Studio 4.5软件,通过同源建模及分子动力学优化获得柞蚕小吐白水软化病毒(Ap IV)3C蛋白酶的3D结构;通过分子对接对天然产物库进行虚拟筛选,得到1个Ap IV 3C蛋白酶的有效抑制剂3',4',5,7-四羟基异黄酮(Orobol).分子对接和分子动力学(MD)模拟结果进一步证明Orobol能稳定结合于Ap IV 3C蛋白酶的结合口袋处.体内外的Ap IV病毒抑制实验结果表明,Orobol具有良好的抗病毒活性.     

SARS病毒蛋白水解酶的三维结构模建及可能的小肽抑制剂研究

SARS病毒作为一种正链病毒 (Positive stranded RNA virus) ,其传播复制起重要作用的是其内部的 E蛋白、S蛋白、M蛋白、N蛋白、RNA聚合蛋白和蛋白水解酶 (Proteinase)等 6种蛋白质 .其中蛋白水解酶与 SARS病毒的复制密切相关 ,是抗 SARS病毒药物筛选的理想靶点 ,而它的三级结构则是研究病毒机理和进行药物设计的基础 .我们采用生物信息学的方法 ,利用 NCBI和 EBI提供在线蛋白质序列相似搜索工具 Blast和 FASTA3 ,找到同源性为 43 .791 %的 1 L VO(PDB编号 ) [1] ,并在 SiliconGranphics工作站上利用 Insight 的 Homology…     

基于机器学习方法的丙型肝炎病毒非结构蛋白5B聚合酶抑制剂活性预测

在丙型肝炎病毒(HCV)的基因复制和蛋白质成熟的过程中, 非结构蛋白5B(NS5B)作为RNA依赖的RNA聚合酶起到了重要的作用. 抑制NS5B聚合酶可以阻止丙型肝炎病毒的RNA复制, 因此成为一种治疗丙型肝炎的有效方法. 通过计算机方法进行虚拟筛选和预测NS5B聚合酶抑制剂已经变得越来越重要. 本文主要采用机器学习方法(支持向量机(SVM)、k-最近相邻法(k-NN)和C4.5决策树(C4.5 DT))对已知的丙型肝炎病毒NS5B蛋白酶抑制剂与非抑制剂建立分类预测模型. 1248个结构多样性化合物(552个NS5B抑制剂与696个非NS5B抑制剂)被用于测试分类预测系统, 并用递归变量消除法选择与NS5B抑制剂相关的性质描述符以提高预测精度. 独立验证集的总预测精度为84.1%-85.0%, NS5B抑制剂的预测精度为81.4%-91.7%, 非NS5B抑制剂的预测精度为78.2%-87.2%. 其中支持向量机给出最好的NS5B抑制剂预测精度(91.7%); C4.5决策树给出最好的非NS5B抑制剂预测精度(87.2%); k-最近相邻法给出最好的总预测精度(85.0%). 研究表明机器学习方法可以有效预测未知数据集中潜在的NS5B抑制剂, 并有助于发现与其相关的分子描述符.     

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.     

Cordycepin Inhibits Virus Replication in Dengue Virus-Infected Vero Cells

Dengue virus (DENV) infection causes mild to severe illness in humans that can lead to fatality in severe cases. Currently, no specific drug is available for the treatment of DENV infection. Thus, the development of an anti-DENV drug is urgently required. Cordycepin (3′-deoxyadenosine), which is a major bioactive compound in Cordyceps (ascomycete) fungus that has been used for centuries in Chinese traditional medicine, was reported to exhibit antiviral activity. However, the anti-DENV activity of cordycepin is unknown. We hypothesized that cordycepin exerts anti-DENV activity and that, as an adenosine derivative, it inhibits DENV replication. To test this hypothesis, we investigated the anti-DENV activity of cordycepin in DENV-infected Vero cells. Cordycepin treatment significantly decreased DENV protein at a half-maximal effective concentration (EC50) of 26.94 μM. Moreover, DENV RNA was dramatically decreased in cordycepin-treated Vero cells, indicating its effectiveness in inhibiting viral RNA replication. Via in silico molecular docking, the binding of cordycepin to DENV non-structural protein 5 (NS5), which is an important enzyme for RNA synthesis, at both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, was predicted. The results of this study demonstrate that cordycepin is able to inhibit DENV replication, which portends its potential as an anti-dengue therapy.     

Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase

The SARS coronavirus 3C-like proteinase is considered as a potential drug design target for the treatment of severe acute respiratory syndrome (SARS). Owing to the lack of available drugs for the treatment of SARS, the discovery of inhibitors for SARS coronavirus 3C-like proteinase that can potentially be optimized as drugs appears to be highly desirable. We have built a "flexible" three-dimensional model for SARS 3C-like proteinase by homology modeling and multicanonical molecular dynamics method and used the model for virtual screening of chemical databases. After Dock procedures, strategies including pharmocophore model, consensus scoring, and "drug-like" filters were applied in order to accelerate the process and improve the success rate of virtual docking screening hit lists. Forty compounds were purchased and tested by HPLC and colorimetric assay against SARS 3C-like proteinase. Three of them including calmidazolium, a well-known antagonist of calmodulin, were found to inhibit the enzyme with an apparent K(i) from 61 to 178 microM. These active compounds and their binding modes provide useful information for understanding the binding sites and for further selective drug design against SARS and other coronavirus.     

Secondary Structure and Membrane Topology of the Full‐Length Dengue Virus NS4B in Micelles

Dengue virus nonstructural protein 4B (NS4B) is a membrane protein consisting of 248 residues with a crucial role in virus replication and interference with the host innate immunity. The dengue virus serotype 3 NS4B was reconstituted into lyso‐myristoyl phosphatidylglycerol (LMPG) micelles. Backbone resonance assignment of NS4B was obtained using conventional solution NMR experiments. Further studies suggested that NS4B contained eleven helices and six of them form five potential transmembrane regions. This study provides atomic level information for an important drug target to control flavivirus infections.     

Protein-RNA interactions during TMV assembly.

A review of the structural studies of tobacco mosaic virus (TMV) is given. TMV is essentially a flat helical microcrystal with 16 1/3 subunits per turn. A single strand of RNA runs along the helix and is deeply embedded in the protein. The virus particles form oriented gels from which high-resolution X-ray fiber diffraction data can be obtained. This may be interpreted by the use of six heavy-chain derivatives to give an electron density map at 0.4 nm resolution from which the RNA configuration and the form of the inner part of the protein subunit may be determined. In addition, the protein subunits form a stable 17-fold two-layered disk which is involved in virus assembly and which crystallizes. By the use of noncrystallographic symmetry and a single heavy-atom derivative, it has been possible to solve the structure of the double disk to 0.28 nm resolution. In this structure one sees that an important structural role is played by four alpha-helices, one of which (the LR helix) appears to form the main binding site for the RNA. The main components of the binding site appear to be hydrophobic interactions with the bases, hydrogen bonds between aspartate groups and the sugars, and arginine salt bridges to the phosphate groups. The binding site is between two turns of the virus helix or between the turns of the double disk. In the disk, the region proximal to the RNA binding site is in a random coil until the RNA binds, whereupon the 24 residues involved build a well-defined structure, thereby encapsulating the RNA.     

VIRUS RESISTANCE OF TRANSGENIC TOBACCO PLANTS EXPRESSING TOBACCO MOSAIC VIRUS COAT PROTEIN GENE

An intermediate expressing vector carrying the tobacco mosaic virus (TMV, Chinese common strain) coat protein (CP) gene was constructed by recombinant DNA techniques. The TMV-CP gene was transferred into the tobacco genome via Ti plasmid and a large number of regenerated plants, including both systemic and local lesion hosts for TMV, were obtained. Southern blot analysis revealed that 1-5 copies of the CP gene were integrated into the tobacco genome. RNA and protein analysis demonstrated that the TMV-CP gene was correctly expressed in the transgenic plants. The abundance of TMV-CP mRNA in total leaf RNA accounted for 0.005-0.01%, while the amount of coat proteins reached 0.05-0.2% of the total leaf soluble proteins. Virus challenge experiments showed that the symptom development of virus infection was markedly delayed and the replication as well as the spread of the virus was significantly inhibited in the transgenic plants expressing the TMV-CP gene. Three of these plants were completely protected afte