High resolution mass spectrometry based profiling of diet-related deoxyribonucleic acid adducts

Exposure of DNA to endo- and exogenous DNA binding chemicals can result in the formation of DNA adducts and is believed to be the first step in chemically induced carcinogenesis. DNA adductomics is a relatively new field of research which studies the formation of known and unknown DNA adducts in DNA due to exposure to genotoxic chemicals. In this study, a new UHPLC-HRMS(/MS)-based DNA adduct detection method was developed and validated. Four targeted DNA adducts, which all have been linked to dietary genotoxicity, were included in the described method; O⁶-methylguanine (O⁶-MeG), O⁶-carboxymethylguanine (O⁶-CMG), pyrimidopurinone (M1G) and methylhydroxypropanoguanine (CroG). As a supplementary tool for DNA adductomics, a DNA adduct database, which currently contains 123 different diet-related DNA adducts, was constructed. By means of the newly developed method and database, all 4 targeted DNA adducts and 32 untargeted DNA adducts could be detected in different DNA samples. The obtained results clearly demonstrate the merit of the described method for both targeted and untargeted DNA adduct detection in vitro and in vivo, whilst the diet-related DNA adduct database can distinctly facilitate data interpretation.     

Crystal structures of four δ‐keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ‐keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2‐cyano‐5‐oxo‐5‐phenyl‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₂N₂O₃, (1), ethyl 2‐cyano‐5‐(4‐methoxyphenyl)‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₂₀H₂₄N₂O₄, (2), ethyl 5‐(4‐chlorophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁ClN₂O₃, (3), and the previously published ethyl 5‐(4‐bromophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁BrN₂O₃, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3 , 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53 , 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple‐bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C—X...N and C—N...X angles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.     

色谱柱分类数据库用于指导天然药物化学对照品色谱纯度测定时色谱柱理性选择

由于中药化学对照品多数来源于动植物药材,很容易混有结构类似物,故有机杂质测定是可能影响其化学对照品赋值准确性的关键风险因素。中药化学对照品的有机杂质测定通常采用药典收载或文献报道的高效液相色谱法,这些方法通常仅规定“以十八烷基硅烷键合硅胶为填充剂”,无适宜色谱柱的品牌信息,或者实验室无文献所用的色谱柱品牌,而目前市场上已有800多种品牌的C₁₈柱,生产工艺的不同导致不同品牌C₁₈柱的选择性有差异,甚至差异显著。这很容易出现由于色谱柱选择不适宜而导致测定结果不准确的风险。该文采用国外色谱柱分类数据库指导对照品纯度考察时色谱柱的理性选择,尽可能减少色谱柱盲选可能导致的纯度结果不准确的风险。首先,用数据库挑选2根选择性差异显著的色谱柱（选择性因子F≥6）进行平行实验,以尽可能反映采用不同品牌色谱柱可能出现的分离效果差异。如果这2根色谱柱的分离效果及纯度测定结果无显著性差异,则可以交叉验证该对照品纯度测定的准确性。否则需要从数据库中选择另外1根与之前试验中分离效果更好、选择性相似的色谱柱进行纯度结果验证。在N-反式-p-对香豆酰基酪胺和表儿茶素没食子酸酯首批对照品的纯度考察中,使用了上述策略并验证了其有效性和科学性,计划推广应用至更多的中药化学对照品,特别当其可能含碱性或弱酸性化合物时,更应该尝试采用本文推荐的色谱柱选择策略交叉验证其纯度测定结果的准确性。     

Identification of a Prenyl Chalcone as a Competitive Lipoxygenase Inhibitor: Screening,Biochemical Evaluation and Molecular Modeling Studies

Cyclooxygenase (COX) and lipoxygenase (LOX) are key targets for the development of new anti-inflammatory agents. LOX, which is involved in the biosynthesis of mediators in inflammation and allergic reactions, was selected for a biochemical screening campaign to identify LOX inhibitors by employing the main natural product library of Brazilian biodiversity. Two prenyl chalcones were identified as potent inhibitors of LOX-1 in the screening. The most active compound, (E)-2-O-farnesyl chalcone, decreased the rate of oxygen consumption to an extent similar to that of the positive control, nordihydroguaiaretic acid. Additionally, studies on the mechanism of the action indicated that (E)-2-O-farnesyl chalcone is a competitive LOX-1 inhibitor. Molecular modeling studies indicated the importance of the prenyl moieties for the binding of the inhibitors to the LOX binding site, which is related to their pharmacological properties.     

民用船舶数据库管理系统

对民用船舶信息的管理是一项重要的工作,实现船舶信息管理的电子化,既减轻了管理人员的负担,又可以避免由于误操作而引起的错误。因此,对民用船舶数据库管理系统的开发和功能加以介绍,有助于其推广应用。     

Integrated Access to Genomic and Other Bioinformation: An Essential Ingredient of the Drug Discovery Process

Abstract

Due to the high rate of data production and the need of researchers to have rapid access to new data, public databases have become the major medium through which genome mapping and sequencing data as well as macromolecular structural data are published. There are now more than 250 databases of biomolecular, structural, genetic, or phenotypic data, many of which are doubling in size annually. These databases, many of which were created and are maintained by experimentalists for their own research use, provide valuable collections of organized, validated data. However, the very number and diversity of databases now make efficient data resource discovery as important as effective data resource use. Existing autonomous biological databases contain related data which are more valuable when interconnected than when isolated. Political and scientific realities dictate that these databases will be built by different teams, in different locations, for different purposes, and using different data models and supporting DBMSs. As a consequence, connecting the related data they contain is not straightforward. Experience with existing biological databases indicates that it is possible to form useful queries across these databases, but that doing so usually requires expertise in the semantic structure of each source database. Advancing to the next level of integration among biological information resources poses significant technical and sociological challenges.     

The Cambridge Structural Database in Retrospect and Prospect

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal–organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small‐molecule crystallography. Nearly 40 000 new structures are added each year. As X‐ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self‐financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC’s funding model in relation to open access and open data paradigms.     

地球化学模拟在高放废物地质处置中的应用与发展

随着核能事业的发展,高放废物的处理和处置问题日益突出.其中,研究高放废物在环境介质中的吸附、扩散和迁移行为是获取放射性核素对周围环境和人群健康影响的基础参数的最重要和最直接的途径.近年来,人们利用已有的实验数据及核素的基础热力学和动力学数据,附以相应的数学模型,建立了一些地球化学模拟软件,用于分析核素在地质介质中可能发生的连续性和长期性变化.目前,国内外常用的地球化学模拟软件有十多种.本文从热力学平衡计算原理、种态分布计算方法和表面配位模型假设等几个方面对地球化学模拟软件进行了简要介绍,对近年来地球化学模拟软件在核素种态分布计算和表面配位模型模拟两方面的应用进行了举例分析,并以Ca-U-CO3配合物为例,说明完备的热力学数据对地球化学模拟软件发展的重要性,以期促进我国地球化学模型的应用和发展.