原卟啉原IX的构象分析

在合理药物设计方法中 ,当靶标酶的三维结构未知时 ,对其底物进行构象分析 ,特别是确定其活性构象 ,对阐明靶标酶活性中心的空间形状和作用位点具有十分重要的意义。我们曾利用距离比较法确定了原卟啉原氧化酶的底物—原卟啉原IX的活性构象 ,本文从构象分析的角度对 4种不同构象的原卟啉原IX分子与二苯醚类分子的晶体学构象进行了几何参数的比较和分析 ,结果进一步证实了距离比较法所确定的活性构象更为可靠     

原卟啉原Ⅸ的构象分析

在合理药物设计方法中,当靶标酶的三维结构未知时,对其底物进行构象分析,特别是确定其活性构象,对阐明靶标酶活性中心的空间形状和作用位点具有十分重要的意义.我们曾利用距离比较法确定了原卟啉原氧化酶的底物-原卟啉原Ⅸ的活性构象,本文从构象分析的角度对4种不同构象的原卟啉原Ⅸ分子与二苯醚类分子的晶体学构象进行了几何参数的比较和分析,结果进一步证实了距离比较法所确定的活性构象更为可靠.     

人类免疫缺陷病毒整合酶二酮酸类抑制剂的三维药效团构建

应用遗传算法相似性程序(GASP), 以作用于I型人类免疫缺陷病毒(human immun-odeficiency virus type 1, HIV-1)整合酶(IN)的二酮酸类(diketoacids, DKAs)抑制剂构建药效团模型. 所选训练集分子均具有可靠的类药性特征及DKAs药效团特征. 尝试将抑制剂与药效团叠合后的构象和抑制剂与IN的对接构象进行叠合, 得到药效团模型与分子对接构象中IN残基的相对位置, 并基于抑制剂的药效团模型特征与周围IN氨基酸残基位置的匹配情况进行药效团特征的修改. 所得最优药效团由1个疏水特征、3对氢键特征和1个氢键供体特征组成. 该药效团的命中物质量(goodness of hit, GH)为0.56, 产出率(Y)达63.6%, 假阳性率(FP)为0.41%. 该药效团具有较好的置信度, 产出率较高而假阳性率较低, 可用于数据库搜索发现新的具有DKAs药效团特征的活性化合物, 也可为先导化合物的改造提供帮助.     

距离比较法(DISCO)构建ALS抑制剂药效团模型

在乙酰乳酸合成酶（ALS）三维结构未知的情况下,利用距离比较法（DISCO） ,将10 个结构特征具有代表性的ALS抑制剂的分子构象进行叠合,建立了可能的 药效团模型,并初步验证了模型的可靠性。     

人类谷胱甘肽硫转移酶家族等位基因蛋白B与抑制剂作用模型的理论研究

采用分子动力学模拟方法系统地研究了谷胱甘肽硫转移酶家族(Glutathione S-transferases,GSTs)的等位基因蛋白B(GSTP1*B)与抑制剂利尿酸(EA)以及EA的谷胱甘肽(GSH)共轭物EAG(I),EAG(O)的具体结合方式.抑制剂及其谷胱甘肽共轭物与蛋白的相互作用能计算结果及分子动力学轨迹的统计分析结果表明,GSTP1*B与EA的谷胱甘肽共轭物的结合能力优于其与EA的结合能力,Phe8,Arg13,Trp38和Tyr108是作用过程中的关键残基,对稳定抑制剂及其谷胱甘肽共轭物在GSTP1*B的G和H位点的构象具有重要的作用.通过对构象的统计分析发现,残基Phe8和Tyr108与GSTP1*B酶对抑制剂的选择性密切相关.     

配体活性构象搜寻方法及其应用研究——Ⅰ.搜寻方法及凝血酶抑制剂活性构象的搜寻

在综合系统构象搜寻和配体-生物大分子对接(Dock)方法的基础上,发展了根据受体活性部位三维结构搜寻配体活性构象的搜寻方法BCSPL.用此方法搜寻了凝血酶抑制剂PPACK的活性构象,结果与晶体结构非常吻合,又用此方法搜寻了膦酰肽类和二肽、三肽类凝血酶抑制剂与人体α凝血酶结合时的活性构象,并在此基础上用分子力学计算了抑制剂与凝血酶的结合能,结果表明结合能与活性有很好的相关性,计算结果能合理地解释抑制剂与凝血酶的相互作用方式及结构与活性的关系.     

光系统Ⅱ抑制剂—反式氰基丙烯酸酯比较分子场和电子结构研究

对反式氰基丙烯酸酯系列活性分子采用限制性系统搜索方法确定的药效团模型 ,与 9类不同骨架结构的光系统 抑制剂 DISCO模型中的反式氰基丙烯酸酯分子(M- 2 2 )的活性构象为模板所确定的药效团模型是非常相近的。对两种方法所获得的活性构象分子进行了 Co MFA研究 ,其结果是一致的。采用 PM3方法进行了量子化学计算 ,计算结果表明两种模型的构象分子具有相近的电子结构 ,根据分子静电场、立体场和电子结构探讨了该类抑制剂的构效关系。     

基于配体与受体结构的酪氨酸酶抑制剂定量构效关系分析

酪氨酸酶是细胞内催化合成黑素的关键酶。 理解酪氨酸酶抑制剂结构与活性之间的关系对于设计新药和化妆品具有重要意义。 然而,酪氨酸酶抑制剂的定量构效关系仍不清楚。 本文利用配体和结构描述符构建了隐式和显式模型,阐明了酪氨酸酶抑制剂定量构效关系。 隐式模型的相关系数R高达0.961,显式模型的相关系数为0.775。 两个模型很好地预测了3个茶多酚的酪氨酸酶抑制活性,表儿茶素没食子酸酯(ECG)>表没食子儿茶素没食子酸酯(EGCG)>没食子酸(G)。 相关性分析发现,抑制剂与酪氨酸酶结合引起的构象熵损失与抑制剂的活性密切相关。 具有较少构象熵损失的ECG在4种茶多酚中具有较高酪氨酸酶抑制活性。 结合自由能计算也证实ECG与酪氨酸酶的结合能力最强。 此外,通过分解结合自由能发现,酪氨酸酶活性中心的氨基酸残基(His57、His201、Asn202、His205、Glu192和Val215)与抑制剂形成了较强的范德华和静电相互作用,进而稳定了复合物结构。     

光系统II(PSII)抑制剂的比较分子场研究

以光系统II抑制剂DISCO(DIStance COmparisons)模型的活性构象分子作为模板,利用比较分子场分析方法对三类结构不同的化合物进行了三维构效关系的研究.研究结果有助于对DISCO重叠模型的评估和新型PSII抑制剂的设计与合成.     

石杉碱甲-AChE复合物中石杉碱甲的结构特征: 量子化学研究

在运用量子化学从头计算方法(HF/4-31G)结合点电荷模型方法对AChE-HupA复合物活性位点的410个原子和1929个点电荷进行理论计算的基础上, 比较了石杉碱甲分子在形成复合物前后的结构变化特征。发现复合物中石杉碱甲分子构象并非能量最低构象, 它的能量比HF/4-31G全优化得到的构象的能量高91.8kj/mol。和单分子状态相比, 形成复合物后季铵基和内酰胺基的N-H, C=O键的键长变长、键强减弱, 其总原子净电荷也发生了明显的变化。且这些基团的空间取向都有不同程度的改变, C(8)-N(21)键的旋转达20ⅲ。这些信息将有益于设计新的AChE抑制剂。     

Design,Synthesis, and Herbicidal Evaluation of Novel Uracil Derivatives Containing 1,3,4‐Thiadiazolyl Moiety

Uracil derivatives, such as commercial herbicides butafenacil and benzfendizone, have been identified as inhibitors of protoporphyrinogen oxidase (Protox, EC 1.3.3.4), one of the most important action targets of herbicides. In order to search for novel Protox inhibitors with high efficacy, broad‐spectrum activity, and safety to crops, commercially herbicide butafenacil was used as lead compound for further optimization; a series of title compounds 8a , 8b , 8c , 8d , 8e , 8f , 8g , 8h , 8i , 8j , 8k , 8l , 8m , 8n were designed and synthesized by introducing 1,3,4‐thiadiazole moiety into the uracil skeleton. The preliminary bioassays (in vitro) indicated that most of the target compounds displayed better inhibition against Echinochloa crus‐galli than Brassica campestris. The greenhouse bioassay results indicated that most of the compounds tested exhibited good‐to‐excellent herbicidal activities against B. campestris, A. retroflexus, E. crusgalli, and D. sanguinalis in pre‐emergence treatment at a dose of 1500 g/ha, for example, compound 8d showed 100% inhibition against the four plants tested in pre‐emergence treatment at a dose of 1500 g/ha. So, these types of skeletons can be used as valuable lead compounds for the development of a pre‐emergent herbicide.     

新型原卟啉原氧化酶抑制剂的固相合成及生物活性研究

采用固相有机合成技术,合成了全新结构的新型原卟啉原氧化酶抑制剂化合物.初步建立了针对特殊靶酶PPO的酶生物活性测定方法,对所合成的化合物进行了生物活性测定,初步结果表明预期有活性的化合物显示出一定的PPO酶抑制活性.     

Design,Synthesis and Herbicidal Activity of Novel Sulfonylureas Containing Tetrahydrophthalimide Substructure

To develop novel sulfonylurea herbicides, a series of chlorsulfuron derivatives was designed and synthesized through introducing tetrahydrophthalimide substructure taken from protoporphyrinogen IX oxidase(PPO) inhibitors onto the critical 5-position of the classical benzene ring. The structures of title compounds were confirmed by infrared spectroscopy, ultraviolet spectroscopy, ¹H and ¹³C NMR spectrometry, mass spectrometry and elemental analysis. In addition, the crystal structure of compound II-5 was further determined by X-ray diffraction analysis. Bioassay results showed that individual compounds exhibited good herbicidal activities, especially compound II-8, which displayed 100% inhibition rate against Echinochloa crusgalli at 150 g/ha(1 ha=10⁴ m²) with the method of foliage spray in the pot experiment.     

A selectivity study of benzenesulfonamide derivatives on human carbonic anhydrase II/IX by 3D-QSAR,Molecular Docking and Molecular Dynamics Simulation

Nowadays, different approaches have been pursued with the intent to develop sulfonamide-like carbonic anhydrase inhibitors that possess better selectivity profiles toward the different human isoforms of the enzyme. Here, we used conventional 3D-QSAR methods, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and Topomer CoMFA, to construct three-dimensional quantitative structure-activity relationship (3D-QSAR) models for benzenesulfonamide derivatives as human carbonic anhydrase (hCA) II/IX inhibitors. The theoretical models had good reliability (R²>0.75) and predictability (Q²>0.55), and the contour maps could graphically present the contributions of the force fields for activity and identify the structural divergence between human carbonic anhydrase II inhibitors and human carbonic anhydrase IX inhibitors. Consequently, we explored the selectivity of inhibitor for human carbonic anhydrase II and IX through molecular docking, and the difference of activity coincides with the potential binding mode well. According to the results of the predicted values and the molecule docking, we found that the inhibitors published in the literature had stronger inhibition on the hCA IX; based on the theoretical models, we designed seven new compounds with good potential activity and reasonably good ADMET profile, which could selectively inhibit hCA IX. Molecular Dynamics Simulation showed that newly-designed compound D7 had good selectivity on hCA IX. The findings from 3D-QSAR and docking studies maybe helpful in the rational drug design of isoform-selective inhibitors.     

Effect of metals on herbicides-alpha-synuclein association: a possible factor in neurodegenerative disease studied by capillary electrophoresis

The aggregation of alpha-synuclein in the dopaminergic neurons of the substantia nigra is a critical step in the Parkinson's disease (PD). The etiology of the disease is unknown but recent epidemiological and experimental studies have renewed interest in the hypothesis that environmental factors, especially herbicides and metals, have a role on the pathogenesis of PD. For the first time, the association constants of alpha-synuclein with five herbicides have been calculated using a capillary electrophoresis (CE) method. In addition, the effect of a number of metals on this binding has been investigated. It appears that the herbicides preferentially bind to a partially folded intermediate conformation of alpha-synuclein induced by manganese, aluminium, cadmium, copper and zinc. Then, metal increases the synuclein-herbicide association. However, this study shows contrasting actions with the antibiotic rifampicin and magnesium addition leading to a decrease of the alpha-synuclein-herbicide interaction even if other metals are present in the bulk solvent. Considering epidemiological studies, all these results suggest an underlying molecular basis for PD and related body diseases.     

ALS抑制剂合理分子设计的研究进展

以乙酰乳酸合成酶为靶标合理设计开发新型超高效除草剂是当前除草剂化学研究中的重要领域。结合本课题组的研究工作,从ALS抑制剂的结构特征、分子力学与量子化学研究、定量构效关系(QSAR)与三维定量构效关系(3D-QSAR)研究、非线性QSAR研究以及新型除草剂的分子设计等几个方面对该领域的研究现状进行了总结报道,并对该领域的发展前景及存在的问题进行了展望。     

Synthesis and Herbicidal Evaluation of Novel Uracil Derivatives Containing Benzothiazol‐2‐yl Moiety

In order to search for novel Protox inhibitors with high efficiency, broad‐spectrum activity, and safety to crops, commercially herbicide butafenacil was used as lead compound for further optimization, a series of title compounds 3a , 3b , 3c , 3d , 3e , 3f , 3g , 3h , 3i were designed and synthesized by introducing benzothiazol‐2‐yl moiety into the uracil skeleton. The bioassays indicated that some of the target compounds displayed moderate herbicidal activities in the post‐emergence treatment.     

Rapid and sensitive determination of phosphorus-containing amino acid herbicides in soil samples by capillary zone electrophoresis with diode laser-induced fluorescence detection

A straightforward and sensitive method has been developed for the analysis of phosphorus-containing amino acid herbicides (glufosinate and aminomethylphosphonic acid, the major metabolite of glyphosate) in soil samples. For this purpose, the analytical features of two indocyanine fluorescent dyes, sulfoindocyanine succinimidyl ester (Cy5) and 1-ethyl-1-[5-(N-succinimidyl-oxycarbonyl)pentyl]-3,3,3,3-tetramethyl-indodicarbocyanine chloride, as labeling reagents for the determination of these herbicides by CZE with diode LIF detection were investigated. Practical aspects related to the labeling chemistry and CZE separation showed that the two probes behave similarly, Cy5 being the best choice for the determination of these herbicides on account of its higher sensitivity. The optimum procedure includes a derivatization step of the pesticides at 25 degrees C for 30 min and direct injection to CZE analysis, which is conducted within about 14 min using ACN in the running buffer. The lowest detectable analyte concentration ranged from 0.025 to 0.18 microg/L with a precision of 3.6-5.4%. These results indicate that indocyanine fluorescence dyes are useful as rapid and sensitive labels for the determination of these herbicides when compared with typical fluorescein dyes such as FITC and 5-(4,6-dichloro-s-triazin-2-ylamino) fluorescein, because they provide faster labeling reactions even at room temperature and the excess of reagent practically does not interfere the determination. Finally, the Cy5 method was successfully applied to soil samples without a preliminary clean-up procedure, and the herbicides were measured without any interference from coexisting substances. The recoveries of these compounds in these samples at fortification levels of 100-500 ng/g were 90-93%.