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。     

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.     

Determination of heats of detonation and influence of components of composite explosives on heats of detonation of high explosives

The heats of detonation of 20 simple high explosives and explosive mixtures were determined by means of an adiabatic detonation calorimeter designed by the authors. The results indicated that the performance of the instrument was reliable and the experimental data were very accurate. For explosive mixtures, there was a linear accumulative relationship between the heats of detonation of the explosive mixture and its components. Accordingly, the heats of detonation of explosive mixtures could be calculated directly from the heats of detonation of simple explosives and the characteristic heats of other components. The experiments showed that the gold or brass shell of the cylindrical charge could be substituted by a thick-walled porcelain shell, which had the advantage of cheapness.

     

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。     

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.     

恶臭嗅辨实验室建设探讨

针对恶臭测试的环境影响问题,提出了解决的实例方案,并对方案的要点及优缺点进行讨论,此方案在实际操作中具有较好的效果。     

Summary of development of the theory of stability of colloids and thin films

In this review, the research of the author in the field of colloidal systems is summarized. The factors influencing colloidal stability are systematized and analyzed. Examples are presented to illustrate the practical utilization of the theory of stability of colloids and thin films.This review was prepared on the basis of the works of the author, which were awarded the State Premium for 1991 in the field of science and technology, chemistry section.Institute of Physical Chemistry, Russian Academy of Sciences, 117915 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 8, pp. 1708–1717, August, 1992.     

Study of hydration of two cements of different strengths

Main hydration products of two cement pastes, i.e. CSH-gel, portlandite (P) (and specific surface S) were studied by static heating, and by SEM, TEM and XRD, as a function of cement strength (C-33 and C-43) hydration time (th) and subsequent hydration in water vapour.Total change in mass on hydration and air drying, M_o, increased with strength of cement paste and with hydration time. Content of water escaping at 110 to 220°C, defined as water bound with low energy, mainly interlayer and hydrate water, was independent on cement strength but its content increased with (th). Content of chemically bound (zeolitic) water in CSH-gel, escaping at 220-400°C, was slightly dependent on strength and increased with (th). It was possibly derived from the dehydroxylation of CSH-gel and AFm phase. Portlandite water, escaping at 400-500°C, was independent on cement strength and was higher on longer hydration. Large P crystals were formed in the weaker cement paste C-33. Smaller crystals were formed in C-43 but they increased with (th). Carbonate formated on contact with air (calcite, vaterite and aragonite), decomposed in cement at 600-700^oC. It was high in pastes C-33(1 month) and C-43(1 month), i.e. 5.7 and 3.3%, respectively; it was less than 1% after 6 hydration months (low sensitivity to carbonation) in agreement with the XRD study showing carbonates in the air dry paste (1month), and its absence on prolonged hydration (6 months) and on acetone treatment. Water vapour treatment of (6 months) pastes or wetting-drying increased this sensitivity.Nanosized P-crystals, detected by TEM, could contribute to the cement strength; carbonate was observed on the rims of gel clusters.This revised version was published online in November 2005 with corrections to the Cover Date.     

解决能源问题的新途径——光解水制氢的研究

面对日益枯竭的能源危机,氢能是一种洁净、最有前景的替代能源。目前在各种制氢的方法中光催化分解水制氢的研究最多,光解水过程中催化剂最关键,本文对利用太阳能光解水的途径、提高光催化反应效率以及光催化剂的开发研究进行了综述。     

黄酮化合物的合成研究进展

黄酮化合物是一类具有多种生物活性的天然产物,其经典的合成方法主要为查耳酮路线和β-丙二酮路线.近年来出现了许多新技术、新方法.本文介绍了2'-羟基查尔酮的氧化关环法、黄烷酮氧化法、改进的Baker-Venkataraman法及其他合成黄酮化合物的方法.