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。     

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。     

MOE软件在分子对接教学中的应用*

主要介绍MOE软件在分子对接教学中的应用。详细介绍了MOE用于分子对接的使用流程,并分析了对接的可靠性及小分子与蛋白的连接情况,为后续药物的设计提供参考。本案例既可以用于理论教学也可以设计成计算机辅助药物设计上机实验,增强了学生的学习兴趣,降低了教学的难度,也为涉及到分子对接的大学生创新创业项目提供方法。     

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.     

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.     

HIV蛋白酶抑制剂——利迪链菌素的分子对接研究

用分子对接的方法, 对利迪链菌素的抗HIV蛋白酶活性进行了研究. 为了更准确地反映利迪链菌素分子与酶蛋白结合的情况, 充分考虑受体活性部位的柔性, 采用了FlexX(初步对接)和Flexidock(精确对接)分两步将配体与受体进行对接. 在初步对接中, 设计了不同的受体活性部位来考察是否有结合水分子参与抑制剂与酶的结合. 对一种作用方式已知的非肽类HIV蛋白酶抑制剂Aha006进行的对接研究显示, 分子模拟的结果与实际情况吻合得较好, 证明了本文所采用的方法的可靠性. 利迪链菌素与蛋白酶活性部位的对接结果显示, 配体分子与受体之间的结合没有结合水分子的参与, 两者通过5对氢键作用结合成为稳定的复合物. 利迪链菌素占据结合腔, 覆盖了蛋白酶的活性三联体Asp25-Thr26-Gly27, 从而起到抑制其生物活性的作用.     

基于分子对接的苯丙素甙（PPGs）类化合物的虚拟筛选和合理设计

采用虚拟化合物生成法对抗肿瘤的苯丙素甙(PPGs)类化合物进行了配体受体对 接研究。以三种不同的骨架结构为基础分别生成了五十个虚拟苯丙素甙(PPGs)类化 合物，并将它们与端粒DNA受体进行分子对接，分析已知结构的对接结果，通过虚 拟筛选的方法得到了一批与受体相互作用能较高并且复合物能量较低的新的有潜力 的活性化合物。该方法可以弥补分子对接研究中，只能计算药物与受体的相互作用 ，无法有效设计新化合物的不足。这种方法在基于结构的药物分子设计中具有重要 的意义。     

基于配体、受体和复合物指纹的虚拟筛选方法比较

近年来, 作为基于配体和基于受体两种方法的补充, 以复合物指纹为基础的药物筛选方法相关研究正受到广泛的重视. 那么这种新兴的方法相对于传统方法在筛选结果准确率上是否具有优势? 同时, 由于复合物指纹可以通过复合物结构测定和将相应蛋白和配体进行分子对接两种方式获得, 那么基于这两种方式获得的复合物指纹所得的筛选结果准确率是否有显著性差异呢? 通过对一系列HIV-1蛋白酶复合物晶体结构同时进行基于配体的相似性搜索、分子对接传统的能量打分、基于复合物晶体结构的复合物指纹的相似性搜索和基于分子对接所得复合物结构的复合物指纹的相似性搜索的筛选比较, 结果表明: (1)如果三种方法都是直接基于实验结构, 那么复合物指纹和分子对接两种方法都因为是兼顾了受体和配体两个方面, 准确率都要高于仅仅基于配体的方法|(2)实际运用中, 通过实验测定所有复合物结构并不可行, 因此需要进行分子对接才能大量的获得复合物结构并进一步生成相应的复合物指纹, 令人兴奋的是, 基于此种方式获得的复合物指纹与直接基于实验复合物结构获得的复合物指纹在筛选结果上并无显著性差异, 从而可以作为实验复合物指纹筛选方法的有效补充.     

基于分子对接的6-萘甲基取代HEPT类HIV-1逆转录酶抑制剂构效关系研究

采用分子对接方法得到了一系列6-萘甲基取代HEPT类逆转录酶抑制剂分子与HIV-1逆转录酶复合物模型,从中抽取出抑制剂分子的活性构象,进一步应用CoMFA和CoMSIA方法建立了具有较好预测能力的3D-QSAR模型,深入探讨了这些化合物的定量构效关系,为进一步的药物设计奠定了良好的基础.另外,以化合物13及其相应的β异构体24为代表,结合量子化学从头算分子轨道理论方法考察了它们的前线轨道,为阐明α和β系列化合物的活性差异提供了理论依据.     

Surface Reconstruction by a Coassembly Approach

Materials with switchable surfaces, capable of changing surface properties under external stimuli, are playing a pivotal role in many applications, such as tissue engineering, biosensors, and drug/protein delivery. In this research silica particles with patterned and switchable surfaces are fabricated. Surface micelles on silica particles are formed by coassembly of polymer brushes and “free” block copolymer chains in a selective solvent. The cores of the surface micelles are crosslinked by anthracene photodimerization. After quaternization of the coronae, amphiphilic surface micelles are prepared. The surface micelles are able to rearrange in different media. After treatment with an organic solvent, the surfaces of silica particles are occupied by hydrophobic polymer components; in aqueous solution, the positively charged polymer chains are on the surfaces. The switching of the surface micelles results in changes in surface composition and wetting behaviors.     

Densities,speeds of sound,excess volumes and viscosities of binary mixtures of mtbe with tetralin and decalin at 303.15 k

Measurements of densities, speeds of sound, excess volumes and viscosities of binary mixture of methyl tert-butyl ether with tetralin and decalin are reported at 303.15?K over the entire range of composition. Excess volumes are measured using batch dilatometer technique. Sound speeds are obtained using ultrasonic interferometer. Densities are computed from excess volume data. Isentropic compressibilities are derived from density and sound speed data. Speeds of sound are evaluated on the basis of Jacobson's free length theory and Schaff's collision factor theory. The predicted values are in good agreement with the experimental results. The viscosity data are analysed on the basis of corresponding states approach. Excess volumes and deviation in isentropic compressibilities are negative and deviation in viscosities are positive over the entire composition range. The experimental results are discussed in terms of possible molecular interactions between unlike molecules.     

Characterization of Defects in Glasses and Coatings on Glasses by Microanalytical Techniques

 The most relevant defects in glasses and thin films on glasses are categorized and investigated by the appropriate microanalytical techniques. Knots, which are local glassy inclusions, are described in greater detail. The combination of EPMA/EDX and LA-ICP-MS allow the determination of element concentrations in the defect down into the low ppm range, thus finally enabling the identification of a special source of the defect from otherwise non distinguishable refractories. The results of analysis of stones and striae are reported and defect sources are discussed. Local defects in thin films are characterized which can be explained by high intrinsic compressive stress in the films. Typical glass and thin film defects are used to illustrate the problem-solving process in industrial labs.     

Dielectrophoresis applications in biomedical field and future perspectives in biomedical technology

Dielectrophoresis (DEP) is a technique to manipulate trajectories of polarisable particles in nonuniform electric fields by utilizing unique dielectric properties. The manipulation of a cell using DEP has been demonstrated in various modes, thereby indicating potential applications in the biomedical field. In this review, recent DEP applications in the biomedical field are discussed. This review is intended to highlight research work that shows significant approach related to DEP application in biomedical field reported between 2016 and 2020. First, single-shell model and multiple-shell model of cells are introduced. Current device structures and recently introduced electrode patterns for DEP applications are discussed. Second, the biomedical uses of DEP in liquid biopsies, stem cell-based therapies, and diagnosis of infectious diseases due to bacteria and viruses are presented. Finally, the challenges in DEP research are discussed, and the reported solutions are explained. DEP's potential research directions are mentioned.     

Inorganic electrides

Inorganic electrides are a novel kind of ionic compounds in which the anions are electrons confined in a complex array of cavities or channels and the cations are nanoscale arrays of alkali metal ions that provide charge balance. In electrides the donated electron behaves like a low-density correlated electron gas, whereby the dimensionality of the electron gas and its electronic and magnetic properties are determined by the topology of the cavities in the host matrix. Unlike traditional electrides, in which alkali cations are encapsulated within an organic cage, inorganic electrides are thermally stable. The current inorganic electrides based on alkali metal loaded zeolites can be designed as useful reduced-dimensionality materials. Inorganic electrides are powerful reducing agents, and they are able to reduce small aromatic molecules to the radical anions within the channels of the zeolite.     

油页岩中微量元素赋存形态的研究

通过浮沉实验及脱灰实验对抚顺、龙口、茂名3种油页岩样中部分微量元素进行了赋存形态的研究。结果表明,浮沉实验所得微量元素的赋存状态结果与脱灰实验基本一致,抚顺、龙口、茂名3种油页岩中大部分微量元素以无机态赋存,但也有所区别,抚顺、龙口、茂名油页岩中的元素V、Mn、Zn、Sr、Mo、Ta以及抚顺油页岩中的Cr、Te,龙口油页岩中的Cd、Sn,茂名油页岩中的Cd、Sn、Pb,主要赋存于无机矿物中;茂名油页岩中的Cr、Te,抚顺油页岩中的Cd,龙口油页岩中的Pb有相对较多的比例富集于有机质部分;龙口、茂名油页岩中的元素Co,抚顺油页岩中的Co、Sn、Pb,更多地富集于黏土矿中,但也有少部分富集于有机质中。     

Review of Analytical Methods for Atmospheric Oxidants Measurements

Abstract

Instrumental and manual methods currently available for the measurement of atmospheric oxidants are surveyed. Techniques used in the United States are emphasized and their advantages and disadvantages are discussed. Commercial systems are evaluated in terms of general operating principles rather than of specific instruments. The ability of these techniques to meet the measurement requirements defined by U.S. Federal air quality oxidant criteria are discussed. Alternative chemical techniques that may have some advantages over the neutral, buffered KI procedure are discussed. Also some attractive, alternative instrumental procedures that are ozone-specific are presented. These systems are based on chemiluminescence and ultraviolet absorption photometry. Electrochemical and colorimetric methods for total oxidant measurements are compared. Finally, some data are presented on relationships of ozone and total oxidants.     

纳米氧化锆的制备与应用

综述了纳米ZrO2粉体的制备与应用,展望了其发展前景。目前,纳米ZrO2粉体的制备方法以化学法为主。文章介绍了共沉淀法、金属醇盐法、溶胶-凝胶法、反胶团法、水热法、溶剂蒸发法、共蒸馏法及化学气相法等制备方法,并对上述各种方法作出评价。文章还介绍了纳米ZrO2粉体的应用研究,将其分散于陶瓷基体中以降低陶瓷的烧结温度,提高陶瓷的韧性和强度;将纳米ZrO2用作催化剂,在催化加氢及土壤固氮等方面呈现良好的催化活性和选择性。     

Contactless conductivity detection for microfluidics: designs and applications

Different methods for construction of contactless conductivity detectors (CCD) for microchip electrophoresis device are described in this review. This includes three main schemes of CCD for microchips, such as (i) the detection electrodes are placed along the microchannel from outside of the microchip and they are insulated from the channel by the cover lid of microchip device; (ii) the electrodes are placed across of the microchannel in the same plane and they are insulated by thin separation channel walls and (iii) electrodes are buried in widened part of microchannel and they are insulated from solution by ultrathin layer of silicon carbide. Specific issues related to the CCD on microfluidics are discussed, such as an influence of shape and magnitude of ac voltage and placement of electrodes and their insulation. Various applications for security, pharmacological, bioassays and food analysis purposes are described.     

Transport coefficients of air,argon-air,nitrogen-air,and oxygen-air plasmas

Calculated values of the viscosity, thermal conductivity and electrical conductivity of air and mixtures of air and argon, air and nitrogen, and air and oxygen at high temperatures are presented. In addition, combined ordinary, pressure, and thermal diffusion coefficients are given for the gas mixtures. The calculations, which assione local thermodynamic equilibrium, are performed for atmospheric pressure plasmas in the temperature range from 300 to 30,000 K. The results for air plasmas are compared with those of published theoretical and experimental studies. Significant discrepancies are found with the other theoretical studies; these are attributed to differences in the collision integrals used in calculating the transport coefficients. A number of the collision integrals used here are significantly more accurate than values used previously, resulting in more reliable values of the transport coefficients.