From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems

Biologically active small molecules have a central role in drug development, and as chemical probes and tool compounds to perturb and elucidate biological processes. Small molecules can be rationally designed for a given target, or a library of molecules can be screened against a target or phenotype of interest. Especially in the case of phenotypic screening approaches, a major challenge is to translate the compound-induced phenotype into a well-defined cellular target and mode of action of the hit compound. There is no “one size fits all” approach, and recent years have seen an increase in available target deconvolution strategies, rooted in organic chemistry, proteomics, and genetics. This review provides an overview of advances in target identification and mechanism of action studies, describes the strengths and weaknesses of the different approaches, and illustrates the need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes.     

Synthesis and X-ray structure of cationic methallyl palladium complexes supported by unsymmetrical β-diimine ligands

Treatment of the unsymmetrical β-iminoamine ligands [PhCN(Ar)CHCNH(Ar)Me] with the zerovalent complex Pd(dba)₂ in the presence of the methallyloxyphosphonium salt, gives high yields of the cationic β-diimine complexes [PhCN(Ar)CH₂CN(Ar)(Me)Pd(η³-C₄H₇)]⁺[PF₆]⁻ (Ar = 2-Me-C₆H₄ (7); 2-MeO-C₆H₄ (8); 2,6-Me₂-C₆H₃ (9); 2,6-iPr₂-C₆H₃ (10)). All the new complexes have been characterised by NMR and IR spectroscopy. The structure of the cationic methallyl palladium complex (10) has been solved by X-ray crystallography.     

新型阳离子聚丙烯酰胺离解行为的研究

前文曾报导,以聚丙烯酰胺为母体,通过甲醛为桥梁引入二氰二胺可合成一种新型阳离子聚电解质,简称PAm·MG,它是一种弱聚碱的盐酸盐,结构式如下(S 为取代度):PAm·MG 对含活性艳红染料的废水有明显的絮凝脱色作用,其絮凝效果受聚合物的取代度、介质的pH 以及外加盐浓度的影响,而这些影响因素又直接与聚碱的离解行为或胺基离子化度(指已离子化的胺基占全部胺基的分数)密切相关.为此,本文对影响PAm·MG 离解行为和离子化度的一些因素作进一步探讨,并通过粘度测定考察离解行为对聚合物在水中形态的影响,为PAm·MG 的实际应用提供理论根据.     

Development of highly cytotoxic and actin-depolymerizing biotin derivatives of aplyronine a

Tied up: A PEG-linked biotin derivative of marine macrolide aplyronine?A (ApA; see scheme) is shown to exhibit potent cytotoxicity and cause actin disassembly in tumor cells. This method of introducing a PEG linker at the end of the aliphatic tail should offer perspectives for developing and using versatile actin-targeting molecular probes. PEG=poly(ethylene glycol).     

Graft copolymer composed of cationic backbone and bottle brush-like side chains as a physically adsorbed coating for protein separation by capillary electrophoresis

To stabilize electroosmotic flow (EOF) and suppress protein adsorption onto the silica capillary inner wall, a cationic hydroxyethylcellulose-graft-poly (poly(ethylene glycol) methyl ether methacrylate) (cat-HEC-g-PPEGMA) graft copolymer composed of cationic backbone and bottle brush-like side chains was synthesized for the first time and used as a novel physically adsorbed coating for protein separation by capillary electrophoresis. Reversed (anodal) and very stable EOF was obtained in cat-HEC-g-PPEGMA-coated capillary at pH 2.2-7.8. The effects of degree of cationization, PEGMA grafting ratio, PEGMA molecular mass, and buffer pH on the separation of basic proteins were investigated. A systematic comparative study of protein separation in bare and HEC-coated capillaries and in cat-HEC-g-PPEGMA-coated capillary was also performed. The basic proteins can be well separated in cat-HEC-g-PPEGMA-coated capillary over the pH range of 2.8-6.8 with good repeatability and high separation efficiency, because the coating combines good protein-resistant property of bottle brush-like PPEGMA side chains with excellent coating ability of cat-HEC backbone. Besides its success in separation of basic proteins, the cat-HEC-g-PPEGMA coating was also superior in the fast separation of other protein samples, such as protein mixture, egg white, and saliva, which indicates that it is a promising coating for further proteomics analysis.     

Two successive reactions on a DNA template: a strategy for improving background fluorescence and specificity in nucleic acid detection

We report a new strategy for template-mediated fluorogenic chemistry that results in enhanced performance for the fluorescence detection of nucleic acids. In this approach, two successive templated reactions are required to induce a fluorescence signal, rather than only one. These novel fluorescein-labeled oligonucleotide probes, termed 2-STAR (STAR = Staudinger-triggered α-azidoether release) probes, contain two quencher groups tethered by separate reductively cleavable linkers. When a 2-STAR quenched probe successively binds adjacent to two mono-triphenylphosphine-(TPP)-DNAs or one dual-TPP-DNA, the two quenchers are released, resulting in a fluorescence signal. Because of the requirement for two consecutive reactions, 2-STAR probes display an unprecedented level of sequence specificity for template-mediated probe designs. At the same time, background emission generated by off-template reactions or incomplete quenching is among the lowest of any fluorogenic reactive probes for the detection of DNA or RNA.     

Synthesis and photophysical properties of novel succinimidyl benzazole derivatives, evaluated by Candida albicans ATCC 10231 fluorescent staining

New fluorescent succinimidyl benzazole derivatives were synthesised and successfully used to stain Candida albicans ATCC 10231 cells. The dyes were characterised by means of infrared, ¹³C and ¹H NMR spectroscopies and elemental analysis. UV-Vis and steady-state fluorescence in solution were also applied to characterise their photophysical behaviour. The novel dyes were fluorescent in the yellow-green region by a phototautomerism in the excited state (ESIPT) with a large Stokes shift (9065-10962 cm⁻¹). Dual fluorescence could also be observed depending on the solvent polarity. The present dyes were used as new probes by means of culture methodology or direct staining to study the micromorphology of Candida albicans.     

Site-specific DNA-programmed growth of fluorescent and functional silver nanoclusters

Precise organization of metallic nanoclusters on DNA scaffolds holds great interest for nanopatterned materials that may find uses in electronics, sensors, medicine, and many other fields. Herein, we report the site-specific growth of fluorescent silver nanoclusters by using a mismatched double-stranded DNA template. Few-atom, molecular-scale Ag clusters are found to localize at the mismatched site and the metallized DNA retains its integrity. The DNA-encapsulated nanoclusters can be utilized as functional biological probes to identify single-nucleotide polymorphisms by taking advantage of the very bright fluorescence and excellent photostability of the nanoclusters. This approach offers the possibility of constructing novel DNA-based nanomaterials and nanomechanical devices with more sophisticated functions and will be highly beneficial in future biochemical, pharmaceutical, nanomechanical, and electronic applications.     

ZrO_2酸碱性质的TPD表征Ⅰ.单组分吸附研究

以NH3、吡啶、Et3N、CO2和苯酚为探针，用TPD－MS方法对ZrO2催化剂的酸碱性质进行了表征．ZrO2上碱性探针（NH3、吡啶和Et3N）的脱附温度远低于在强酸性SiO2－Al2O3上；而酸性探针CO2的脱附温度远低于在强碱性MgO上的结果．为ZrO2的弱酸弱碱性质提供了证明．NH3吸附IR结果表明ZrO2表面配位不饱合Zr4＋为酸（Lewis酸）中心．NH3、吡啶和Et3N与这些酸中心作用的方式和能量分布相似．NH3和CO2的TPD谱图均存在三个脱附峰，且相应脱附峰的温度范围相近．表明ZrO2的酸中心和碱中心具有匹配相当的酸、碱强度，ZrO2为典型的酸－碱双功能催化剂，在苯酚的TPD过程中，ZrO2的特征表现为对苯酚的强吸附和对苯酚分解的高活性．文中结合IR结果，对与NH3和CO2的脱附相联系的表面吸附物种分别进行了讨论．     

Sensing of Fe(III) ion via turn-on fluorescence by fluorescence probes derived from 1-naphthylamine

Fluorescence probes NA1 and NA2 derived from 1-naphthylamine (NA) as fluorophore have been synthesized and characterized by different spectroscopic studies. Identification behaviour of these probes towards various metal ions has been investigated. Both the fluorescent probes are selective as well as sensitive towards Fe(III) ion. Novel fluorescence probe NA2 afforded turn-on fluorescence behaviour for Fe(III) ion over other metal ions such as Ca(II), Mg(II), Mn(II), Fe(II), Co(II), Fe(III), Ni(II), Cu(II), Zn(II) and Hg(II).