Attack of radicals and protons on ladderane lipids: quantum chemical calculations and biological implications

Quantum chemical calculations on possible decomposition processes for ladderane lipids are described. Based on the results of these calculations, it is proposed that hydrogen atom abstraction next to the ladderane core can lead to opening of the cyclobutane rings comprising the ladderane substructure, and protonation leads directly to fragmentation. Potential biological implications of these processes are discussed.     

基于分子指纹对黄酮类化合物及其抗DPPH自由基活性的QSAR分析

应用定量构效关系（Quantitative structure activity relationship, QSAR）研究阐明黄酮类化合物（Flavonoid compounds, FCs）的子结构指纹（Substructure fingerprint）与1,1-二苯基-2-三硝基苯肼（1,1-Diphenyl-2-picrylhydrazyl, DPPH）自由基清除能力之间的关系,从而指导高效抗氧化物质的设计和发现。在PubMed数据库中收集77个具有明确抗氧化活性的黄酮类化合物,而在ChEMBL数据库中收集86个无抗DPPH活性的黄酮类化合物。这163个黄酮类化合物的子结构指纹由PubChem系统生成,然后通过卡方检验筛选出与黄酮类化合物的抗氧化活性显著相关的分子指纹,最后通过判别分析建立预测QSAR模型,并采用回代法和交叉验证法对已建立的模型进行准确性和稳健性的验证。结果表明,黄酮类化合物抗DPPH自由基活性与ESSSR环的计数、简单相邻原子的类型和简单的SMARTS模式等因素有关。此外,所建立的QSAR模型能较好地预测黄酮类化合物的DPPH自由基清除活性,可用于评价候选抗氧化剂的潜力。     

Registry and search of chemical compounds on graphics display

The registry and substructure search component of in-house system SPHINCS (Structure /Property Handling Information Network for Chemical Substances) has been developed. For registry, a chemical structure is constructed on a graphics display by use of templates (e.g., 6N for pyridine, NH2 for amino group) and commands (e.g., BOND, EXCHANGE, DELETE). The generated connection table and atom coordinates are stored in a file. In a search, a query substructure is drawn on a graphics display. Special atom symbols (e.g., A for any atoms but hydrogen, HT for hetero atoms) can be used to represent the generic nature of a search. More than 1000 fragment codes (elements, rings, chains and augmented atoms), generated by computer analysis of connection tables, are used as primary search screens. An atom—bond—atom search program removes false drop structures. The structures retrieved are displayed in forms familiar to chemists with use of templates.     

Models of steroid binding based on the minimum deviation of structurally assigned 13C NMR spectra analysis (MiDSASA)

This paper develops a quantitative k-nearest neighbors modeling technique. The technique is used to demonstrate that a compound's biological binding activity to a receptor can be calculated from the minimum of the square root of the sum of squared deviations (SSSD) of a structurally assigned chemical shift on a template between the unknown compound to be predicted and a set of known compounds with known activities. When building models of biological activity, nonlinear relationships are built into the input training data. If a model is developed by selecting only compounds with minimum structurally assigned chemical shift deviations from the unknown compound, some of the nonlinear relationships can be removed. The smaller the total chemical shift deviation between a compound with known activity and another compound with unknown activity, the more likely it will have similar biological, chemical, and physical properties. This means that a model can be produced without rigorous statistics or neural networks. This technique is similar to structure-activity relationship (SAR) modeling, but instead of relying on substructure fragments to produce a model, this new model is based on minimum chemical shift differences on those substructure fragments. We refer to this method as minimum deviation of structurally assigned spectra analysis (MiDSASA) modeling. Modeling by the minimum deviation concept can be applied to other chemoinformatic data analyses such as metabolite concentrations in metabolic pathways for metabolomics research. A MiDSASA template model for 30 steroids binding the corticosterone binding globulin based on the activity factors of the two nearest compounds had a correlation of 0.88. A MiDSASA template model for 50 steroids binding the aromatse enzyme based on the average activity of the four nearest compounds had a correlation of 0.71.     

Biologically active azolo-1,2,4-triazines and azolopyrimidines

The review presents current data on the methods of synthesis and biological activity of purine-isosteric azolo-annulated 1,2,4-triazines and pyrimidines with a bridgehead nitrogen atom, which are among the most promising classes of biologically active compounds.     

Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion

Ab initio HF and MP2 calculations on prototype model linkages of phosphorothioate DNA backbones illuminate the effects of phosphorothioation on electronic and structural properties of DNA backbone. The replacement of a bridging oxygen atom by sulfur in the phosphodiester linkage is energetically favored over that of replacement of a non-bridging oxygen atom. In phosphorothioate derivatives containing the P(OS)_nb moiety, the non-bridging oxygen atom always bears a higher negative charge than the non-bridging sulfur. Additional calculations on protonated (neutral) adducts suggest that phosphorothioation of the phosphodiester linkage lowers its proton affinity. Moreover, protonation of the non-bridging oxygen atom at phosphorous is favored over the protonation of the non-bridging sulfur atom for linkages containing the P(OS)_nb moiety. The ab initio calculated structural parameters are compared to the available crystallographic data of small phosphorothioate molecules and phosphorothioate oligodeoxynucleotides. These results have implications upon the biological activity of phosphorothioate DNA analogs.     

Combining horizontal and vertical substructure relationships in scaffold hierarchies for activity prediction

For a systematic exploration of structural relationships between molecular scaffolds, ～24,000 unique scaffolds were extracted from 458 different target sets. Substructure relationships between these scaffolds were systematically determined. The scaffold tree data structure was utilized to study structural relationships between original scaffolds and derivative scaffolds obtained by rule-based decomposition. Leaf-to-root substructure relationships that resulted from rule-based decomposition were compared to leaf-to-leaf relationships between original scaffolds most of which were not part of the scaffold tree hierarchy. Decomposed scaffolds not contained in active target set compounds were prioritized on the basis of hierarchical scaffold patterns and additional substructure relationships. For high-priority virtual scaffolds, activity predictions were carried out, and these scaffolds were often found in external test compounds having the predicted activity. Taken together, our results suggest that leaf-to-root substructure relationships in scaffold trees should best be complemented with additional substructure relationships to determine high-priority virtual scaffolds for activity prediction.     

HAD: an automated database tool for analyzing screening hits in drug discovery

Collecting, organizing, and reviewing chemical information associated with screening hits are human time-consuming. The task depends highly on the individual, and human errors may result in missing leads or wasting resources. To overcome these hurdles, we have developed a decision support system, Hits Analysis Database (HAD). HAD is a software tool that automatically generates an ISIS database file containing compound structures, biological activities, calculated properties such as clogP, hazard fragment labels, structure classifications, etc. All data are processed by available software and packed into a single SD file. In addition to search capabilities, HAD provides an overview of structural classes and associated activity statistics. Chemical structures can be organized by maximum common substructure clustering. The ease of use and customized features make HAD a chief tool in lead selection processes.     

CCBF--A system for the computer processing of chemical and biological facts

A computer-based system for the documentation of company research results in drug research is described. The system stores the numerous results of standardized biological tests and processes chemical formulas by topological techniques. The stored material is processed to provide computer-printed card indexes and lists on chemical and/or biological topics. The programs enable searches to be made for any desired substructure and for pharmacophoric groups, thus providing highly effective assistance in the search for structure-activity relationships.     

三苯基锡芳氧乙酸酯的合成和表征

三苯基锡芳氧乙酸酯的合成和表征刘宝殿，包明，张景萍（东北师范大学化学系、东北师范大学分析测试中心，长春，１３００２４）关键词芳氧乙酸，三苯基锡芳氧乙酸酯，合成，生物活性三苯基醋酸锡和三苯基氢氧化锡是防治甜菜褐斑病的有效药剂［１］．芳氧乙酸及其酯也具有...     

Identification of maximal common substructures in structure/activity studies

A new approach is described for the identification of the two-dimensional maximum common substructure (MCS) in studies of structure/activity relationships. The structures of compounds are converted to superatom trees by division into three categories: ring systems, functional groups and chains. The MCS can be identified more efficiently by comparison of such trees than by the usual comparison at the atom/bond level, because there are fewer nodes. The algorithm used is based on a compatibility table.     

Molecular Property eXplorer: a novel approach to visualizing SAR using tree-maps and heatmaps

The tremendous increase in chemical structure and biological activity data brought about through combinatorial chemistry and high-throughput screening technologies has created the need for sophisticated graphical tools for visualizing and exploring structure-activity data. Visualization plays an important role in exploring and understanding relationships within such multidimensional data sets. Many chemoinformatics software applications apply standard clustering techniques to organize structure-activity data, but they differ significantly in their approaches to visualizing clustered data. Molecular Property eXplorer (MPX) is unique in its presentation of clustered data in the form of heatmaps and tree-maps. MPX employs agglomerative hierarchical clustering to organize data on the basis of the similarity between 2D chemical structures or similarity across a predefined profile of biological assay values. Visualization of hierarchical clusters as tree-maps and heatmaps provides simultaneous representation of cluster members along with their associated assay values. Tree-maps convey both the spatial relationship among cluster members and the value of a single property (activity) associated with each member. Heatmaps provide visualization of the cluster members across an activity profile. Unlike a tree-map, however, a heatmap does not convey the spatial relationship between cluster members. MPX seamlessly integrates tree-maps and heatmaps to represent multidimensional structure-activity data in a visually intuitive manner. In addition, MPX provides tools for clustering data on the basis of chemical structure or activity profile, displaying 2D chemical structures, and querying the data based over a specified activity range, or set of chemical structure criteria (e.g., Tanimoto similarity, substructure match, and "R-group" analysis).     

Phosphorus-containing Derivatives of Indole and Pyrrole. (Review)

Data on the synthesis and chemical properties of the phosphorus-containing derivatives of indoles and pyrroles, published in 1976-1998, are reviewed. The introduction of substituents containing tri- and tetracoordinated phosphorus atom into the heterocycle and the side chain is discussed. Information on the biological activity is presented.     

Computer-aided elucidation of structures by carbon-13 nuclear magnetic resonance The DARC-EPIOS Method: Characterization of Ordered Substructures by Correlating the Chemical Shifts of Their Bonded Carbon Atoms

A reference substructure (SS) for which all spectral information (I) associated with each carbon atom is expressed as a function of the molecular environment is proposed. This information is expressed by topological relations, within this substructure, for which the spectral responses of its “bonded atoms” are linearly related to external alkyl effects. A correlation space (SS/I) is built with these topological relations (1–4 per carbon substructure). The resolving capacity of this SS/I space is greatly enhanced by introducing, in addition to all the reference substructures, some functions such as heteroatoms, cyclic structures, and stereochemical situations. The action of these functions is estimated by a statistical study of a large population of compounds from the DARC-PLURIDATA ¹³C-n.m.r. bank. This work introduces the notion of multiatom-centered substructure/multi-chemical shift relations, the discriminating ability of which compares very favorably to that of the notion of atom-centered substructure/monochemical shift relations. The generic reference subtructure defined as ELCO_b with its multichemical shifts constitutes a simple structural whole which is useful for critical improvement of the experimental reference data (distribution of spectral information and medium effects) and has proved to be excellent for the elucidation of new structures.     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Different synthetic routes to 4-(1H-benzo[d]imidazol-2-yl)aniline

The benzimidazole nucleus is an important pharmacophore in drug discovery, being a good bioisostere of naturally occurring nucleotides. This heterocycle may represent a type of privileged substructure which can interact with proteins and enzymes; it has, hence, been extensively utilized as a drug scaffold in medicinal chemistry. The connection between wide ranging biological activity and compounds containing the benzimidazole nucleus is known, and well documented in the literature. Benzimidazole derivatives have a multitude of interesting pharmacological activity, including antiviral, antitumor, antihypertensive, proton pump inhibitory, anthelmintic, antimicrobial, and anti-inflammatory activity. Accordingly, a brief survey is given below covering the synthesis of 2-phenybenzimidazole derivatives and their biological importance.     

Substructure mining using elaborate chemical representation

Substructure mining algorithms are important drug discovery tools since they can find substructures that affect physicochemical and biological properties. Current methods, however, only consider a part of all chemical information that is present within a data set of compounds. Therefore, the overall aim of our study was to enable more exhaustive data mining by designing methods that detect all substructures of any size, shape, and level of chemical detail. A means of chemical representation was developed that uses atomic hierarchies, thus enabling substructure mining to consider general and/or highly specific features. As a proof-of-concept, the efficient, multipurpose graph mining system Gaston learned substructures of any size and shape from a mutagenicity data set that was represented in this manner. From these substructures, we extracted a set of only six nonredundant, discriminative substructures that represent relevant biochemical knowledge. Our results demonstrate the individual and synergistic importance of elaborate chemical representation and mining for nonlinear substructures. We conclude that the combination of elaborate chemical representation and Gaston provides an excellent method for 2D substructure mining as this recipe systematically explores all substructures in different levels of chemical detail.