A Method for Clustering and Screening of Long-dimensional Chemical Data Based on Fingerprints and Similarity Measurements

A method for the treatment of long-dimensional chemical data arrays is presented in this work with the aim of maximising classification models. The method is based on the construction of fingerprints and the subsequent generation of a similarity matrix. The similarity calculation has been modified through a scaling process to take into account different significance shown by the variables. The method was applied to spectral measurements of wines and several aspects were studied, namely: threshold considered in the construction of fingerprints and patterns, weighting factor used for scaling, normalisation method, etc. The application of both Principal Components Analysis and Soft-Independent Modelling of Class Analogies to the similarity matrices gave better classifications of the information than those obtained using original data.     

淫羊藿根与叶活性成分的分析和比较

采用细胞膜色谱法（ＣＭＣ）筛选，并结合离体药理实验确定主要活性成分，利用高效液相色谱法分析比较了淫羊藿根与叶中的活性成分及其差异性．色谱条件为Ｋｒｏｍａｓｉｌ ＯＤＳ 柱（１５０ ｍｍ× ４．６ ｍｍ．Ｉ．Ｄ ）流动相甲醇－水（７０：３０，Ｖ：Ｖ）；检测波长２７０ｎｍ。筛选发现淫羊藿根中的两个有效成分ＹＹＨ－２１４和ＹＹＨ－２１６对血管有较强的舒张作用，表明活性成分在ＣＭＣ模型体系中的保留特性与药理作用之间存在良好的相关性。在此色谱条件下淫羊藿叶未检测到这两种活性成分．     

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Summary An extensive crystal survey of the Cambridge Structural Database has been carried out to provide hydrogen-bond data for use in drug-design strategies. Previous crystal surveys have generated 1D frequency distributions of hydrogen-bond distances and angles, which are not sufficient to model the hydrogen bond as a ligand-receptor interaction. For each hydrogen-bonding group of interest to the drug designer, geometric hydrogen-bond criteria have been derived. The 3D distribution of complementary atoms about each hydrogen-bonding group has been ascertained by dividing the space about each group into bins of equal volume and counting the number of observed hydrogen-bonding contacts in each bin. Finally, the propensity of each group to form a hydrogen bond has been calculated. Together, these data can be used to predict the potential site points with which a ligand could interact and there-fore could be used in molecular-similarity studies, pharmacophore query searching of databases, or de novo design algorithms.     

A microtiter plate assay for the detection of inhibitors of the Na +, K + -ATpase

A rapid microtiter plate assay for the detection of inhibitors of the Na⁺, K⁺-ATPase has been developed. The assay is based on the measurement of inorganic phosphate released from the substrate, ATP, and has been designed to be carried out in the individual wells of a microtiter plate. Since the production of inorganic phosphate is determined colorimetrically, multiple samples can be tested simultaneously using a microtiter plate reader. This microtiter plate assay is particularly useful for screening large numbers of samples, such as microbial culture supernatants.     

Spectroscopic and biological studies on newly synthesized nickel(II) complexes of semicarbazones and thiosemicarbazones

Nickel(II) complexes, having the general composition Ni(L)2X2, have been synthesized [where L: isopropyl methyl ketone semicarbazone (LLA), isopropyl methyl ketone thiosemicarbazone (LLB), 4-aminoacetophenone semicarbazone (LLC) and 4-aminoacetophenone thiosemicarbazone (LLD) and X=Cl-, 1/2SO(4)2-]. All the Ni(II) complexes reported here have been characterized by elemental analyses, magnetic moments, IR, electronic and mass spectral studies. All the complexes were found to have magnetic moments corresponding to two unpaired electrons. The possible geometries of the complexes were assigned on the basis of electronic and infrared spectral studies. Newly synthesized ligand and its nickel(II) complexes have been screened against different bacterial and fungal growth.     

Cross-linking chemistry and biology: development of multifunctional photoaffinity probes

An efficient method of photoaffinity labeling has been developed based on rationally designed multifunctional photoprobes. Photoaffinity techniques have been used to elucidate the protein structure at the interface of biomolecules by the photochemical labeling of interacting sites. However, the identification of labeled sites within target proteins is often difficult. Novel biotinyl bioprobes bearing a diazirine photophore have contributed significantly to the rapid elucidation of ligand binding sites within proteins, thereby extending conventional photoaffinity methods. This article discusses the synthesis and applications of various photoprobes bearing a biotin, including strategies using cleavable linkages between photophores. The combination of photoaffinity methods with chip technology is also described as a novel entry to rapid affinity-based screening of inhibitors. This review focuses on a rapid and reliable photoaffinity method utilizing diazirine-based multifunctional photoprobes with numerous potential applications in functional proteomics of biomolecular interactions.     

NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

High throughput screening of O-glycosylation conditions

We report a novel methodology for rapid and quantitative screening of O-glycosylation reactions of application to the analysis of parallel reaction systems. Our system exploits perdeuterated benzyl (Bn-d₇) ether, and stereoselectivity and yield are evaluated by ¹H NMR and MALDI-TOF MS, respectively. This paper summarizes over 240 screenings of 1 → 3 linkage formation between glucose residues targeting the α-isomer in high yield.     

Functionalized Self-Assembled Monolayers on Gold as Binding Matrices for the Screening of Antibody-Antigen Interactions

Two different types of -substituted alkanethiol/disulfide compounds have been used to prepare monolayer architectures on gold serving as platforms for the immobilization of receptor probe molecules – antibodies. These are: (i) carboxylic acid alkanethiols post-reacted with amino biotin to generate streptavidin surfaces, and (ii) N-hydroxysuccinimide-terminated disulfide surfaces. The properties of the monolayers, with and without attached receptor probe molecules, were analysed using infrared spectroscopy, ellipsometry, fluorescence scanning and atomic force microscopy. Several experimental parameters, such as condensation reagents, additives, probe and target concentrations and immobilization time, were systematically varied to determine the dynamic range and to optimize the sensitivity and signal-to-noise ratio of the biochip platforms. Fluorescence screening using Cy5-labelled antigens finally demonstrated that both surfaces could be successfully employed to immobilize the antibodies. The pros and cons of the two approaches are also discussed.Received November 15, 2002; accepted March 25, 2003 Published online July 28, 2003