精制透骨消痛颗粒防治骨性关节炎的计算机药理学

采用分子相似性分析、化学空间、分子对接、生物网络技术和药代动力学性质预测等计算机药理学方法研究中药精制透骨消痛颗粒中514个化合物的药理学机制. 结果表明: 该复方所含化合物在化学结构上具有多样性及大部分化合物在化学空间上具有类药性质; 通过514 与35个骨性关节炎疾病相关的公认靶标的相互作用及它们在靶空间的分布上阐明了精制透骨消痛颗粒防治骨性关节炎的可能作用机理, 发现了一些潜在的活性分子; 通过分析药物库中骨性关节炎的药物-靶点的作用网络及精制透骨消痛颗粒中分子-靶点的作用网络的异质性值、特征路径长度等特征, 揭示精制透骨消痛颗粒的多药物、多靶点、多途径分子作用机制. 结果有助于理解中药精制透骨消痛颗粒的复杂作用机制.     

极化中子衍射及在电子自旋密度研究中的应用

极化中子衍射方法常用于研究含未配对电子化合物中电子自旋密度的分布．分子中电子自旋密度分布从一个独特的角度反映化合物的磁性质．本文介绍极化中子衍射方法的背景知识和基本原理．包括中子源、中子和X射线衍射、极化中子衍射,以及一些常用的实验数据处理方法．选用几个实例总结了用极化中子衍射方法得到的电子自旋密度分布在无机和有机化学中的应用．通过单分子磁体[Fe8O2（OH）12（tacn）6]^8＋和氰基桥联化合物K2[Mn（H2O）2]3[Mo（CN）7]2·6H2O,说明如何用该方法研究金属原子间的磁相互作用;并通过Ru（acac）3这个只含一个未配对电子的化合物来说明如何获得化合物中金属和配体上小的自旋密度;最后介绍了该方法在nitronylnitroxide自由基研究中的应用．     

酪氨酸激酶抑制剂的比较分子场分析

采用比较分子场分析(CoMFA)方法研究了一组嘧啶类衍生物酪氨酸激酶抑制剂活性与结构的关系.所得模型不仅能够很好地预报训练集中的化合物的活性,而且还可以准确地预报预报集中的化合物活性.通过分析分子场等值面图在空间的分布,可以观察到叠加分子周围的立体和静电特征对化合物活性的影响.     

雪花胺类化合物的三维构效关系研究

雪花胺是一类重要的乙酰胆碱脂酶抑制剂，有可能发展成治疗阿尔茨海默病的药物. 利用分子力学计算得到了这类化合物的优势构象，并对这些化合物进行了CoMFA研究．发现，对于雪花胺类化合物，影响其药效的主要因素是空间结构，电荷作用力的影响较小．对空间因素的进一步分析发现，对于该类分子，不宜用空阻较大的基团进行取代．由电荷影响的分析得到了在不同位置上取代基所应有的电荷性质．三维定量构效关系研究为基于雪花胺的抑制剂设计提供了方案．     

空间距离在三维分子相似度计算中的应用

采用Tripos公司的MOPAC模块计算分子的空间距离,所得距离矩阵用带有约束条件的空间距离方法计算分子的相似度,同时通过4组化合物的计算,与纯空间距离方法进行比较,得到了较为满意的结果。     

光诱导下卟啉蒽醌分子内电子转移过程的研究(Ⅰ)──荧光法

利用荧光手段对自制的3种卟啉蒽醌化合物及其锌配合物与母体卟啉进行了研究，计算了各种化合物单重激发态的能量Es、荧光量子产率及荧光猝灭百分率．从荧光猝灭的角度证明它们确实能在光激发下进行分子内电子转移，形成分子内电荷分离态．同时探讨了有机碱的轴向配位及溶剂对PAQ化合物荧光性质的影响．     

固态类杂芪分子一阶超极化率测定及溶剂效应

用溶致变色法研究溶剂对反式 (4 N ,N 二甲氨基 ) (4 N 甲基吡啶基 )杂芪碘 (DAPSI) ,反式 (2 N 甲基吡咯基 ) (4 N 甲基吡啶基 )杂芪碘 (MPPSI) ,反式 (2 吡咯基 ) (4 N 甲基吡啶基 )杂芪碘 (PPSI)、反式 (2 呋喃基 ) (4 N 甲基吡啶基 )杂芪碘 (FPSI)、反式 (2 噻吩基 ) (4 N 甲基吡啶基 )杂芪碘 (TPSI)和反式 (4 N 甲基吡啶基 )杂芪碘 (PSI)的分子一阶超极化率 (βxxx)的影响 ,揭示了溶剂极性 (ET(30 ) )与类杂芪染料的 βxxx值间很好的线性关系和影响规律 ,引入了溶剂化效应对待测化合物分子能级的影响与待测化合物分子间相互作用能级间存在等效能级的概念 ,从溶剂极性 (ET(30 )值 )与 βxxx值间的线性关系求出了在纯固态下类杂芪染料的 βsxxx值 ,及基态与第一激发态间跃迁能和最大吸收波长 .证明了MPPSI、PPSI、FPSI、TPSI和PSI在纯固态下的 βsxxx值与给电子取代基的富电子性间有很好的线性关系     

外电场作用下寡聚苯分子导线的性质

利用Hartree-Fock 方法在6-31G*水平上对聚苯分子进行了计算研究. 分别从几何构型、分子轨道空间分布和分子轨道能级三个方面讨论了外电场对寡聚苯分子导线的影响, 给出了分子导线的性质与外电场的关系. 进一步, 连接硫原子于聚苯分子的两端, 并共价结合在金电极上. 利用非平衡格林函数方法对其在0-2.0 V 偏压下电子输运特征进行了深入研究.     

褪黑激素受体拮抗剂的三维定量构效关系研究

采用两种分子场分析方法即比较分子场分析法（CoMFA）和比较分子相似因子分析法（CoMSIA）进行了37个褪黑激素受体拮抗剂的构效关系研究.计算结果表明，两种方法得到的构效关系模型都具有较好的预测能力.在计算中，还考察了不同格点距离和电荷计算方法对构效关系模型的影响.通过分析分子场等值面图在空间的分布，可以观察到叠合分子周围分子场特征对化合物活性的影响，为设计新的褪黑激素拮抗剂提供了一些理论依据.     

化合物分子表面积计算方法的研究

化合物的分子表面积是重要的物理化学性质参数．根据不同的应用领域及数学方法,提出了多种分子表面积算法[1-10],由此产生了“分子表面积法”,各方法的有效性在各具体应用领域都已被验证．本文将统计方法中的随机变量引入计算化合物分子表面积体系,由分子模型化技术得到化合物分子的原子坐标,不考虑化合物分子中原子的相互作用及分子间近似,直接计算分子表面积．使用该方法可以计算“净”分子表面积、“溶剂可及表面积”、甚至分子结构片段,分子结构中有交叉重叠片段及存在“空洞”的各种分子表面积,该算法及程序较简捷,适应范围广,计算结果较为满意．     

Computational pharmacological studies on cardiovascular disease by Qishen Yiqi Diwan

Computational pharmacological methods were used to study the distribution of 1729 compounds contained in a Chinese medicine, Qishen Yiqi Diwan, in chemical space. The results show that most of these compounds have good drug-like properties. Molecular docking was used to study the interactions between 1729 compounds of Qishen Yiqi Diwan and 26 drug targets related to cardiovascular disease and the distribution of 1729 compounds in drug-target space. The results may shed light on the action mechanism and the search for the active compounds in Qishen Yiqi Diwan.     

An integrated approach of high-performance liquid chromatography–mass spectrometry-based chemical profiling,network pharmacology,and molecular docking to reveal the potential mechanisms of Qishen Gubiao granules for treating coronavirus disease 2019

Qishen Gubiao granules, a traditional Chinese medicine preparation composed of nine herbs, have been widely used to prevent and treat coronavirus disease 2019 with good clinical efficacy. In the present study, an integrated strategy based on chemical profiling followed by network pharmacology and molecular docking was employed, to explore the active components and potential molecular mechanisms of Qishen Gubiao granules in the therapy of coronavirus disease 2019. Using the ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry technique, a total of 186 ingredients corresponding to eight structure types in Qishen Gubiao preparation were identified or structurally annotated with the elucidation of the fragmentation pathways in the typical compounds. The network pharmacology analysis screened 28 key compounds including quercetin, apigenin, scutellarein, luteolin and naringenin acting on 31 key targets, which possibly modulated signal pathways associated with immune and inflammatory responses in the treatment of coronavirus disease 2019. The molecular docking results observed that the top 5 core compounds had a high affinity for angiotensin-converting enzyme 2 and 3-chymotrypsin-like protease. This study proposed a reliable and feasible approach for elucidating the multi-components, multi-targets, and multi-pathways intervention mechanism of Qishen Gubiao granules against coronavirus disease 2019, providing a scientific basis for its further quality evaluation and clinical application.     

Thermal desorption gas chromatography with mass spectrometry study of outgassing from polymethacrylimide foam (Rohacell®)

Polymethacrylimide foams are used as light structural materials in outer‐space devices; however, the foam closed cells contain volatile compounds that are outgassed even at low temperatures. These compounds ignite as plasmas under outer‐space radiation and the intense radio‐frequency fields used in communications. Since plasmas may cause spacecraft fatal events, the conditions in which they are ignited should be investigated. Therefore, qualitative and quantitative knowledge about polymethacrylimide foam outgassing should be established. Using thermogravimetric analysis, weight losses reached 3% at ca. 200°C. Thermal desorption gas chromatography with mass spectrometry detection was used to study the offgassed compounds. Using successive 4 min heating cycles at 125°C, each one corresponding to an injection, significant amounts of nitrogen (25.3%), water (2.6%), isobutylene (11.3%), tert‐butanol (2.9%), 1‐propanol (11.9%), hexane (25.3%), propyl methacrylate (1.4%), higher hydrocarbons (11.3%), fatty acids (2.2%) and their esters (1.3%), and other compounds were outgassed. Other compounds were observed during the main stage of thermal destruction (220–280°C). A similar study at 175°C revealed the extreme difficulty in fully outgassing polar compounds from polymethacrylimide foams by baking and showed the different compositions of the offgassed atmosphere that can be expected in the long term.     

Chemical Variations among Shengmaisan-Based TCM Patent Drugs by Ultra-High Performance Liquid Chromatography Coupled with Hybrid Quadrupole Orbitrap Mass Spectrometry

Shengmaisan (SMS) is a famous traditional Chinese medicine (TCM) formula to treat coronary heart diseases. It has been developed into several TCM patent drugs to meet the demands of different patients. In this study, a research strategy was proposed to reveal the chemical variations among four SMS-based patent drugs, including Shengmai Oral Solution (Shengmaiyin, SMY), Shengmai Capsule (Shengmai Jiaonang, SMJN), Yiqi Fumai Injection (YQFMI), and Yiqi Fumai Capsule (Yiqi Fumai Jiaonang, YQJN). Firstly, 227 compounds were tentatively identified using an Orbitrap-MS in the full scan/dd-MS² mode. Secondly, untargeted metabolomics analysis suggested that ginsenosides, steroidal saponins, and lignans were the main types of differential compounds for the four patent drugs. Finally, the contents of 25 compounds were simultaneously determined in 30 batches of samples in the parallel reaction monitoring (PRM) mode. Partial least squares discriminant analysis (PLS-DA) revealed the contents of ginsenosides Re, Rg1, Rb1, Ro, and Rg3, and schisandrin showed the highest intergroup variations. These compounds were chemical markers to differentiate the SMS-based patent drugs.     

Simultaneous determination of eight bioactive components of Qishen Yiqi dripping pills in rat plasma using UFLC–MS/MS and its application to a pharmacokinetic study

In this study, a rapid and reliable ultra‐fast liquid chromatography–tandem mass spectrometry method was developed and validated for the simultaneous determination of eight active ingredients, including astragaloside IV, ononin, tanshinol, protocatechualdehyde, protocatechuic acid, salvianolic acid D, rosmarinic acid and ginsenoside Rg₁, in rat plasma. The plasma samples were pretreated by protein precipitation with acetonitrile. Chromatographic separation was performed on a Waters Acquity UPLC® BEH C₁₈ column (1.7 μm particles, 2.1 × 100 mm). The mobile phase consisted of 0.1% aqueous formic acid (A)–acetonitrile with 0.1% formic acid (B) at a flow rate of 0.4 mL/min. Quantification was performed on a triple quadruple tandem mass spectrometry with electrospray ionization by multiple reaction monitoring both in the negative and in the positive ion mode. The lower limit of quantification of tanshinol was 2.0 ng/mL and the others were 5.0 ng/mL. The extraction recoveries, matrix effects, intra‐ and inter‐day precision and accuracy of eight tested components were all within acceptable limits. The validated method was successfully applied to the pharmacokinetic study of the eight active constituents after intragastric administration of three doses (1.0, 3.0, 6.0 g/kg body weight) of Qishen Yiqi Dripping Pills to rats.     

A Chemometric Analysis of Compounds from Native New Zealand Medicinal Flora

Several hundred (396) compounds from New Zealand flora with medicinal properties were analyzed for their physicochemical properties. It was found that approximately 10 % fulfilled all the requirements to be considered to be lead‐like, over half of the compounds were deemed to be in the drug‐like space and ≈75 % were in the known drug space. These results indicate the presence of a significant proportion of compounds that are of particular interest to pursue as potential lead compounds or therapeutics. Additionally, compound classes were analyzed separately—most carbonyl‐containing compounds (aldehydes, ketones, esters and lactones), along with phenols were the most lead‐like compounds, which also displayed very good proportions in the drug‐like and known drug space. The information presented herein can be harnessed and utilized in future work, through focussing on the compounds and compound classes that exhibit high‐levels of lead‐likeness for further development.     

气相色谱法测定密闭空间空气中7种苯系物

建立气相色谱法测定密闭空间空气中异丙苯等7种苯系物的方法。采用活性炭富集采样,二硫化碳解吸样品,DB-624毛细管柱分离,实现了对异丙苯、正丙苯、特丁苯、正丁苯、仲丁基苯、1,3,5-三甲苯、1,2,4-三甲苯等7种苯系物完全分离并准确测定,特别是可以将难分离的1,3,5-三甲苯和仲丁基苯完全分离。建立的7种苯系物工作曲线线性良好,相关系数r^2≥0.997,加标回收率在83.2%~111.0%之间,测定结果的相对标准偏差不大于6.3%(n=6),方法检出限为0.02~0.06 mg/m^3。该方法选择性好,测量范围宽,方法检出限低,可用于密闭空间空气中异丙苯等7种苯系物的测定。     

药物发现中常用化合物库特征描述与对比分析

随着计算技术的发展和分子模拟软件的日趋成熟, 虚拟筛选已经在药物发现过程中发挥着越来越重要的作用. 在虚拟筛选过程中, 所使用化合物库的质量对先导化合物发现的成功率起着至关重要的作用. 本文通过对已知药物库、天然产物库、中药原植物化学成分库、筛选常用商业化合物库以及研究者所在实验室建立的化合物库的分析比较, 从化合物库的分子多样性、化学空间和分子骨架等多个方面提取并对比每一种化合物库的特征, 发现了已知药物库与中药原植物化学成分库的特征相似性, 揭示了中药原植物化学成分库作为筛选库的类药性优势, 并且深化了对几种筛选用化合物库特征的认识和理解.