基于MOE软件的虚拟仿真实验*——多奈哌齐与乙酰胆碱酯酶的分子对接

基于MOE软件设计了多奈哌齐与乙酰胆碱酯酶的分子对接虚拟仿真实验。通过分子结构预处理、分子对接以及数据分析等内容,帮助学生掌握分子对接的基本技能,深入理解立体化学结构对药物-靶分子相互作用的影响。本实验可以作为药物化学、生物化学等基础课的扩展内容,提高学生研究式学习的兴趣和能力。     

分子对接在药物虚拟筛选中的应用进展

虚拟筛选是药物设计的重要手段之一,利用小分子化合物与药物靶标间的分子对接运算,研究人员可以准确地获取两者之间的相互作用情况,从候选化合物库中快速筛选出潜在的药物或药物前体,从而加速药物开发过程。介绍了虚拟筛选与分子对接的相关原理与流程,主要综述了对药物进行虚拟筛选时所涉及的分子对接技术类型、常见的分子对接软件以及分子对接典型样例。分子对接对提高虚拟筛选的效率、降低药物开发的成本具有重要的现实意义。     

基于MOE软件的本科生专业综合实验项目设计——耐药性金黄色葡萄球菌FtsZ抑制剂的虚拟筛选与验证

以耐药性金黄色葡萄球菌细丝温度敏感蛋白Z(FtsZ)抑制剂的虚拟筛选为例，在食品类专业综合实验课程教学中借助MOE软件，基于分子对接原理方法从花椒活性小分子库中筛选细菌FtsZ蛋白靶向抑制剂。通过配体小分子数据库的建立、受体蛋白质处理、对接参数设置、筛选结果评价和活性验证等内容，帮助学生系统掌握基于分子对接的活性分子虚拟初筛和活性验证工作流程，降低学生理解分子抑菌机制的难度，增强对跨学科交叉研究新手段的认识，拓展研究方法和创新能力。     

人类蛋白激酶组的多靶点分子对接系统

蛋白激酶在信号转导、基因转录和蛋白翻译等生物过程起关键性作用,因而与大量人类疾病密切相关。所以,蛋白激酶的抑制剂筛选是抗肿瘤药物开发的热点,正在向基于全激酶组的高通量多靶点筛选模式发展。为了降低大规模实验筛选的成本,提高成功率,本文构建人类蛋白激酶组的多靶点分子对接系统,对抑制剂-激酶组的相互作用进行预测。我们首先利用同源模建方法,对人类激酶组约500个激酶变异体的催化域进行结构建模;接着以催化域结构模型为受体,用已知激酶抑制剂进行分子对接,对抑制剂与各激酶变异体的结合亲和力进行了定量计算。结果显示,本文所建立的多靶点分子对接系统可以准确预测抑制剂与激酶变异体的相互作用,结合自由能的计算值与实验值有很强的相关性。所以,该分子对接系统可用于多靶点激酶抑制剂的计算筛选,为激酶抑制剂开发与抗肿瘤药物设计提供理论依据。     

遗传算法与药物分子设计

本文对遗传算法及其近年来在药物设计中的应用进行了较为系统的介绍。遗传算法非常适合解决组合优化问题, 它在柔性分子构象搜寻、药效基团推测、蛋白质结构预测、分子对接、全新药物设计以及组合合成中都具有很大的应用潜力。     

分子对接方法的应用与发展

分子对接方法加快了药物开发周期,具有快速、准确度高等优点.本文详述了分子对接方法的基本原理,及分子对接空间和能量的匹配要求和优化时的各种方法.综述了该方法在药物设计、药理分析和探测生命体系等方面的应用.     

R基团筛选技术用于吡啶杂环类mTOR抑制剂的分子设计研究

针对27个吡啶杂环类抑制剂采用Topomer COMFA方法进行了三维定量构效关系分析,新建模型的拟合、交互验证及外部验证的复相关系数分别为r2=0.982,q2=0.857,r2pred=0.829,结果表明模型具有良好的预测能力和可信度.采用基于R基团搜索Topomer Search技术对ZINC数据库进行R基团的虚拟筛选,获得了6个高活性的新抑制剂分子,其预测活性均优于训练集中活性最高分子.运用Surflex-dock分子对接法研究吡啶杂环类抑制剂与mTOR靶点的作用模式.研究结果表明,Topomer search可有效地用于分子设计,结合分子对接结果,新抑制剂分子为mTOR靶向药物设计提供参考.     

基于Discovery Studio软件的本科生创新实验项目设计*——卡托普利与血管紧张素转化酶的分子对接

基于Discovery Studio软件高质量的分子三维结构可视化功能和分子对接模拟模块,设计了卡托普利与血管紧张素转化酶的分子对接实验,让学生通过分子对接模拟过程,掌握药物分子结构特征,理解构效关系特征,认识酶抑制剂和靶蛋白的作用机制,了解药物研究新手段。     

吲哚衍生物类VEGFR-2酪氨酸激酶抑制剂的从头设计

以血管内皮生长因子受体-2(VEGFR-2)酪氨酸激酶的晶体结构为基础, 采用从头药物设计方法, 设计了一系列吲哚类化合物, 并用类药性和分子对接进行了筛选, 最后得到10个对接能量较低的化合物分子, 对具有最低结合能的化合物与VEGFR-2酪氨酸激酶的复合物进行了10 ns的分子动力学模拟, 并对其结合模式进行了分析. 这些化合物结构新颖, 可能作为抗肿瘤的先导化合物或候选药物. 本文结果为VEGFR-2酪氨酸激酶抑制剂的进一步改造、 设计及合成提供了理论基础, 并有助于开发高活性和高选择性的抗肿瘤药物.     

中药有效成分三维结构数据库的开发和研究

介绍了北京大学中药有效成分三维结构数据库软件系统的结构、功能及开发步骤。该数据库系统不仅仅提供6500个中草药有效成分的二维和三维结构以及其它各类相关信息,同时拥有功能强大的数据库查询、维护及分子表达系统。在该系统中,用户可以交互式地实现多种分子特征的查询以及二维子结构的查询。查询得到的分子可以直接在北京大学药物设计系统(PKUDDS)中进行三维结构的显示和分析。该数据库系统和我们科研组开发的北京大学药物设计系统以及中草药信息系统构成了完整的基于中药的药物设计系统。该系统已经用于NS3-NS4A蛋白酶抑制剂以及其它体系的研究并取得了很好的结果。     

非那雄胺合成工艺改进

非那雄胺能抑制5α-还原酶的活性,明显降低二氢睾酮水平,是一种治疗良性前列腺增生的有效药品。该合成工艺以甾烯酮酸为原料,将其与氯化亚砜反应,无须分离即与叔丁胺反应得17β-酰胺化合物,再氧化开环,环合,氢化,脱氢合成了非那雄胺。经元素分析、IR、1HNMR、13CNMR、MS分析表征了其结构。该法无须使用昂贵的2,2-二吡啶二硫化物和剧毒药品苯亚硒酸酐,且以乙酸铵代替氨气,降低了对设备的要求和腐蚀,更适用于工业生产。     

Dichroism of absorption and polarization of phosphorescence of molecules of the closed form of nitrobenzospirothiopyran

The spectral-polarization characteristics of absorption and phosphorescence of molecules of the initial form of nitro-substituted indolinospirobenzothiopyran were studied in oriented polyethylene films and in solutions with different polarity. An oscillator model of the electron transitions responsible for the formation of absorption and luminescence spectra was suggested. It was established that the principal differences in the spectral and photophysical properties of the compound studied and its oxygen-containing analog are associated with the fact that the electronegativity of the S atom is lower than that of the O atom. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1143–1146, June, 1997.     

Acid hydrolysis of carboxymethylcellulose of low degree of substitution

Cotton cellulose was swollen in a sodium hydroxide solution and carboxymethylated by a two-bath method for different periods of time for each process. The kinetics of acid hydrolysis and the crystallinity of the swollen and carboxymethylated samples were measured. The proportion of broken bonds, rate constants for hydrolysis, and permeability of cellulose to hydrolyzing agents were calculated. The susceptibility of glycosidic linkages to acid hydrolysis was improved by carboxymethylation more than by swelling in alkali. The increased accessibility of carboxymethylcellulose to acid was regarded as a consequence of increased intra-and intercrystalline swelling and of the glycosidic bonds' weakness caused by the electron-attracting carboxymethyl group on the C-6 position.     

Estimation of Kinetic Parameters of Thermal Oxidation of Ilmenite

The aim of the presented work was the investigation of thermal oxidation of ilmenite in static air atmosphere. The investigations were carried out by use of a derivatograph (MOM, Hungary). The changes of crystallographic structure of investigated samples were identified by X-ray diffractometry on Philips PW-1710 diffractometer. In temperature above 500°C appears structure of hematite Fe₂O₃. On the basis of the thermogravimetric measurements, the contracting area and contracting volume models were found as the best fitting experimental data. This revised version was published online in August 2006 with corrections to the Cover Date.     

Mechanism of action of base-catalyzed oxygenation of phenol derivatives

Cyclopropyl derivative of 2,6-di-tert-butylphenol is synthesized as a probe to investigate the mechanism of base-catalyzed autooxidation of phenol derivatives. Our study indicates that one electron reduction of molecular oxygen from phenolate gives phenoxyl radical 3, a key intermediate of autooxidation. The coupling of phenoxyl radical and superoxide radical gives peroxylate anion 4 and produces the final epoxy alcohol adduct 6.     

氯氧化镁生成热的研究

用氧化镁氯化镁水溶液制备了8水合氯氧化镁[nMg(OH)2·MgCl2·8H2O], 并测定了其在盐酸中的溶解热, 实验结果表明, 氯氧化镁溶解热与n值呈线性关系, 根据溶解热求出5Mg(OH)2·MgCl2·8H2O和3Mg(OH)2·MgCl2·8H2O的生成热分别为-7727.1和5888.1kJ·mol^1^-。     

化学计量中不确定度评定研究进展

测量不确定度是表征合理地赋予被测量之值的分散性的参数。本文针对化学计量不确定度评定基础模型仅适用于线性模型、概率分布为正态分布或缩放位移t分布等局限,介绍了近年来不确定度评定的研究热点:蒙特卡罗方法(Monte Carlo Method,MCM),不确定度评定的来源、评定概念、评估方法及其发展过程,扩大了测量不确定度评定与表示的适用范围。     

微量钙的测定方法研究进展

介绍了1995-2006年期间测定微量和痕量钙的方法,如电感耦合等离子体-原子发射光谱法、原子吸收光谱法以及离子色谱法等的工作原理和特点,并说明了其测定微量钙的应用领域。并对微量钙的测定技术进行了展望(引用文献55篇)。     

Stages of thermal decomposition of sodium oxo-salts of sulphur

Thermal behaviour of sodium oxo-salts of sulphur: Na₂SO₄, Na₂S₂O₇, Na₂S₂O₆, Na₂SO₃, Na₂S₂O₅, Na₂S₂O₄, Na₂S₂O₃, Na₂S₃O₆ and of sulphides Na₂S and Na₂S₂ was studied on heating up to 1000°C. The experiments were performed with anhydrous compounds obtained from commercial products by recrystallisation and dehydration. The stage mechanisms of decomposition of anionic sub-lattices of the salts have been proposed basing on the Górski’s morphological classification of simple species. The thermal stability and the stage decomposition mechanisms were correlated with the structure and the potential chemical properties of the salt anions. The thermal decomposition processes were studied by means of thermal analysis, and the decomposition products were identified by means of X-ray phase analysis.     

Synthesis of phenolic components of Grains of Paradise

Two vanilloids, (5E)-8-(4-hydroxy-3-methoxyphenyl)oct-5-en-4-one (1) and 4-[3-hydroxydecyl]-2-methoxyphenol (2), isolated from the dried seeds of Grains of Paradise (Aframomum melegueta), were synthesized; the latter compound was made as the S-enantiomer and the material derived from the seeds was found to be a 1:1.7 mixture of the R and S isomers. The synthetic route used should allow the preparation of analogs having extended alkyl chains and consequently different lipophilicity, and 3, a homolog of 2, was also prepared.