Synthesis of natural-product-based compound libraries

Natural products cover a diversity space not yet available from synthetic libraries, with an unrivalled success rate as drug leads. The combinatorial synthesis of non-oligomeric natural-product-based libraries, however, is still limited to few examples because access to easily modified units strongly depends on the availability of a core structure either from a natural source, or through a suitable synthetic route. Only a few resourceful groups have managed the latter approach for more demanding multifunctional natural drug leads, such as epothilones.     

A dual fingerprint-based metric for the design of focused compound libraries and analogs

A computational metric is introduced for the design of combinatorial libraries focused on small molecules with specific activity (e.g., enzyme inhibitors). The method follows a product-based design strategy and uses combinations of two binary molecular fingerprints to create chemical diversity around selected compounds and/or core structures. In the first step, compounds are sampled that are distinct from template molecules but likely to share similar biological activity. In the second step, designed compounds are accepted if they are not too similar to each other, as assessed by calculation of fingerprint overlap. Thus, it is possible to balance molecular "similarity" and "diversity" and control the degree of chemical diversity created in the vicinity of selected template molecules. In essence, the method aims to generate diverse arrays of compounds with a high probability of having activity similar to starting molecule(s) and is therefore well suited for the design of target-focused libraries or series of analogs. As an example, the method is applied to focus libraries on known protein kinase inhibitors.     

Evaluation of storage conditions for refrigerated rabbit skin

An evaluation of various refrigerated (4 °C) storage solutions and conditions was conducted using rabbit skin. Two in vitro methods to assay skin viability are presented: one which directly measures basal cell viability and one which assesses the skin's ability to grow in culture following storage. The superiority of storage in nutrient medium supplemented with fetal bovine serum over conventional storage in saline is clearly demonstrated. Storage in nutrient medium with 10% fetal calf serum resulted in basal cell viabilities which were over 30% higher than viabilities of skin stored by conventional methods in saline. Skin stored in saline failed to grow in culture, while 100% of the cultures of skin stored in medium plus fetal calf serum grew. Although addition of fetal calf serum to the saline improved the basal cell viability, growth in culture occurred only when the skin was stored in a capped tube. Skin stored in medium without serum gave viability results which were not significantly different from the unstored control, but growth rates in culture did differ significantly from the control values. Our study shows that the viability of rabbit skin and its ability to grow in vitro are depressed when the tissue is maintained at 4 °C in saline or in petri dishes, and optimal when refrigerated in nutrient medium supplemented with FBS in a sealed tube.     

草莓贮藏保鲜最佳生态条件及其效果研究

探讨了常温下草莓贮藏保鲜的适宜环境条件及其贮藏过程中草莓的生理生化变化。结果表明,通过改善贮藏的环境因子,保持贮藏库内较稳定的空气湿度、温度(RH为80%左右,T℃为20℃左右)、库内消毒和小盒包装是常温贮藏草莓的关键一步,可使草莓贮藏时间延长到2d.草莓表面保鲜液膜处理使草莓的贮藏时间延长到5d左右,其中LF₁和LF₃处理的草莓在贮藏第5d时好果率为69.27%、69.94%.保鲜液膜能抑制草莓呼吸代谢,提高草莓SOD活性和ASA含量,延缓果实衰老,延长贮藏时间,增加好果率.     

Stable storage conditions of Immobiline chemicals for isoelectric focusing

Most of the problems connected with the use of the Immobiline chemicals (a set of six, non-amphoteric, acrylamido buffers having pK values in the pH 3.5-9.5 interval) can be attributed to the alkaline species (with pK values 6.2, 7.0, 8.5 and 9.3). These compounds, to varying degrees are subjected to two degradation pathways: (a) hydrolysis of the amido bond, producing free acrylic acid and a diamine, the latter unable to be incorporated into the polyacrylamide matrix; (b) spontaneous auto-polymerization, producing a number of oligomers up to n-mers, able to aggregate and precipitate large proteins. Storage of their water solutions as frozen aliquots, a method widely employed, only partially alleviates the problem. Addition of trace-amounts of inhibitors, as lately adopted by the manufacturer, could only reduce the problem of auto-polymerization, but not block the hydrolysis of the amido bond. A new solution has been found, which abolishes both phenomena: storage in n-propanol. As demonstrated by gas chromatography, HPLC analyses and two-dimensional separations of complex samples, storage in organic solvent completely abolishes both hydrolysis and auto-polymerization and allows production of highly reproducible focusing patterns.     

Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors

High-throughput docking is a computational tool frequently used to discover small-molecule inhibitors of enzymes or receptors of known three-dimensional structure. Because of the large number of molecules in chemical libraries, automatic procedures to prune multimillion compound collections are useful for high-throughput docking and necessary for in vitro screening. Here, we propose an anchor-based library tailoring approach (termed ALTA) to focus a chemical library by docking and prioritizing molecular fragments according to their binding energy which includes continuum electrostatics solvation. In principle, ALTA does not require prior knowledge of known inhibitors, but receptor-based pharmacophore information (hydrogen bonds with the hinge region) is additionally used here to identify molecules with optimal anchor fragments for the ATP-binding site of the EphB4 receptor tyrosine kinase. The 21,418 molecules of the focused library (from an initial collection of about 730,000) are docked into EphB4 and ranked by force-field-based energy including electrostatic solvation. Among the 43 compounds tested in vitro, eight molecules originating from two different anchors show low-micromolar activity in a fluorescence-based enzymatic assay. Four of them are active in a cell-based assay and are potential anti-angiogenic compounds.     

医学图书馆馆藏建设的调查分析

探讨了目前医学图书馆馆藏结构的现状和馆藏建设策略的转变,在资金短缺的情况下,医学图书馆要确定有效的采购方案,保质保量,突出重点,加强网络协作,实现资源共享,以满足临床和科研的需要。     

DNA-encoded chemical libraries for the discovery of MMP-3 inhibitors

Encoded self-assembling chemical (ESAC) libraries are characterized by the covalent display of chemical moieties at the extremity of self-assembling oligonucleotides carrying a unique DNA sequence for the identification of the corresponding chemical moiety. We have used ESAC library technology in a two-step selection procedure for the identification of novel inhibitors of stromelysin-1 (MMP-3), a matrix metalloproteinase involved in both physiological and pathological tissue remodeling processes, yielding novel inhibitors with micromolar potency.     

The use of power ultrasound coupled with magnetic separation for the solid phase synthesis of compound libraries

Enhanced reaction rates are observed when power ultrasound is utilized as a substitute for mixing during solid phase organic chemical reactions on a paramagnetic support. Power ultrasound is also used to facilitate the washing of the paramagnetic support as it is magnetically separated from the reaction mixture. Selective examples from a library targeting the kappa-opioid receptor are presented.     

Degradation of biodiesel under different storage conditions

This paper aimed to investigate the biodiesel degradation characteristics under different storage conditions. The qualities of twelve biodiesel samples, which were divided into 3 groups and stored at different temperatures and environments, were monitored at regular interval over a period of 52 weeks. Experimental results demonstrated that the biodiesel under test degraded less than 10% within 52 weeks for those samples stored at 4 and 20 degrees C while nearly 40% degradation was found for those samples stored at a higher temperature, i.e. 40 degrees C. The results suggested that high temperature, together with air exposure, greatly increase the biodiesel degradation rate. The temperature or air exposure alone, however, had little effect on biodiesel degradation. Water content in biodiesel will enhance biodiesel degradation due to hydrolysis but its effect is much less than the above two factors.     

Optimized assay and storage conditions for enzyme activity profiling of ectomycorrhizae

The aim of a joint effort by different research teams was to provide an improved procedure for enzyme activity profiling of field-sampled ectomycorrhizae, including recommendations on the best conditions and maximum duration for storage of ectomycorrhizal samples. A more simplified and efficient protocol compared to formerly published procedures was achieved by using manufactured 96-filter plates in combination with a vacuum manifold and by optimizing incubation times. Major improvements were achieved by performing the series of eight enzyme assays with a single series of root samples instead of two series, reducing the time needed for sample preparation, minimizing error-prone steps such as pipetting and morphotyping, and facilitating subsequent DNA analyses due to the reduced sequencing effort. The best preservation of samples proved to be storage in soil at 4?C6°C in the form of undisturbed soil cores containing roots. Enzyme activities were maintained for up to 4?weeks under these conditions. Short-term storage of washed roots and ectomycorrhizal tips overnight in water did not cause substantial changes in enzyme activity profiles. No optimal means for longer-term storage by freezing at ?20°C or storage in 100% ethanol were recommended.     

Investigation of S-farnesyl transferase substrate specificity with combinatorial tetrapeptide libraries

Using biased tetrapeptide libraries made up of proteinogenic amino acids of the general formula Cys-O2-X3-X4, we searched for new substrates of partly purified rat brain S-farnesyl transferase (FTase). To achieve this task, an assay was developed in which the consumption of the co-substrate (farnesyl pyrophosphate) was measured. After three steps of deconvolution including each synthesis and enzymatic assay, the most efficient substrates found under these particular conditions were Cys-Lys-Gln-Gln (peptide I) and Cys-Lys-Gln-Met (peptide II). As a control, we used another tetrapeptide library (Cys-Val-O3-X4) in which the valine position was arbitrarily fixed, corresponding to Cys-Val-Ile-Met in the CAAX box of K-RasB, although this sublibrary was only marginally active compared with Cys-Lys-X3-X4 in the first round of deconvolution. The best substrate sublibrary was Cys-Val-Thr-X4, threonine being more favourable than the aliphatic amino acids (Val, Ile, Leu, Ala) in this position. Deconvolution finally led to Cys-Val-Thr-Gln, -Met, -Thr and -Ser as the most efficient substrates of FTase. Those tetrapeptides were not substrates of a partly purified geranylgeranyl transferase 1 (GGTase1). We also investigated the influence of the -1 position (at the N-terminus of cysteine) on the specificity of the enzyme, by using a series of pentapeptides constructed on the basis of the best tetrapeptide core (peptide 1). Among this family of analogues, only His-Cys-Lys-Gln-Gln did not behave as a substrate, whereas all the other pentapeptides were measurable substrates, with Gly-, Asn- and Thr-Cys-Lys-Gln-Gln displaying kinetic constants similar to that of Cys-Lys-Gln-Gln. The present work provides strong evidence that the best tetrapeptide substrates of FTase do not necessarily belong to the classical CAAX box, in which A's are lipophilic residues, but rather contain hydrophilic amino acids in the middle of their sequences. Among them, peptides I and II are potent FTase in vitro substrates that are not recognised by GGTase1 and might be new starting points for the design of FTase inhibitors.     

Importance of storage conditions for the stability of zinc- and cadmium-induced metallothionein

We examined the storage stability of metallothionein (MT), a cysteine-rich protein that has diagnostic potential as a cancer marker and in the assessment of Zn status and heavy-metal toxicity. MT was rapidly degraded in samples of rat whole liver at -20 degrees C or -70 degrees C. MT in supernatants from heat-treated rat liver homogenates stored as 1:5 dilutions of liver from Zn- or Cd-induced rats were stable (recovery >98%) for 100 d at temperatures of -70 degrees C and -196 degrees C but not at -20 degrees C, regardless of the presence of dithiothreitol (DTT) or argon. The variability of MT measurement by the 109Cd-hemoglobin affinity assay was however greatest in samples from Zn-induced rats stored without DTT. The integrity of the MT protein in supernatants of heat-treated homogenates stored for 100 d was demonstrated by Sephadex G-75 chromatography. When heat-treated supernatants were stored as dilute solutions (1:125 of liver), MT was unstable regardless of treatment or storage temperature. Our findings show that liver MT is stable for at least 4 mo as a supernatant of a heat-treated homogenate (1:5 dilution of liver) when stored at or below -70 degrees C and in the presence of DTT.     

Effect of storage conditions on function of granulocytes

The effect of collection technique, anticoagulant, pH, glucose, and temperature on in vitro granulocyte function were studied after 24 hr of storage in the liquid state. Collection by CL did not adversely affect granulocyte function, however, cells collected by FL had accelerated loss of bactericidal activity and chemotactic response. Citrate anticoagulants provided better maintenance of bacteridical activity, NBT reduction, and chemotactic response than heparin, EDTA, and ion-exchange anticoagulants. Chemiluminescence was well maintained when the initial pH of the preservative solution (CPD plasma) was between 6.5 and 8.0 but maintenance of chemotaxis required pH of 7.0–7.5. Glucose concentrations of 80–1000 mg/dl provided adequate maintenance of chemiluminescence and chemotaxis. Bacterial killing was well maintained by storage at either 1–6 or 20–24 °C. Storage at 1–6 °C caused decreased chemotaxis, decreased ability of granulocytes to adhere and spread on a foreign surface, and a decreased intravascular recovery and shortened half-life after transfusion. Although short-term liquid storage may be practical, at present, granulocytes should be transfused as soon as possible after collection.