Dissimilarity-based approaches to compound acquisition

The concept of molecular diversity has been integrated in drug discovery efforts for many years. Applications of molecular diversity have been used to identify compounds for screening and to select compounds to augment proprietary collections. These early efforts were crude and suffered from a number of faults, but their evolution has, over the years, led to an improvement in the computational procedures used to identify new commercial compounds for acquisition. Although not much has recently been written about modern methods for augmenting compound collections, this activity is still a very relevant and important task to those involved with the development of compound collections. This review focuses on the process and software used to identify compounds deemed worthy of acquisition.     

Quantification of polyacetylenes in apiaceous plants by high-performance liquid chromatography coupled with diode array detection

Polyacetylenes are known for their biofunctional properties in a wide range of organisms. In the present study, the most frequently occurring polyacetylenes, i.e. falcarinol, falcarindiol, and falcarindiol-3-acetate, were determined in six genera of the Apiaceae family. For this purpose, a straightforward and reliable method for the screening and quantification of the polyacetylenes using high-performance liquid chromatography coupled with diode array and mass spectrometric detection without tedious sample clean-up has been developed. Peak assignment was based on retention times, UV spectra, and mass spectral data. Quantification was carried out using calibration curves of authentic standards isolated from turnip-rooted parsley and Ligusticum mutellina, respectively. The references were unambiguously identified by Fourier transform-IR (FT-IR) spectroscopy, GC-MS, HPLC-MSn in the positive ionization mode, and 1H NMR and 13C NMR spectroscopy. To the best of our knowledge, the occurrence of falcarindiol-3-acetate in Anthriscus sylvestris and Pastinaca sativa has been reported for the first time. The data revealed great differences in the polyacetylene contents and varying proportions of individual compounds in the storage roots of Apiaceous plants. The results of the present study may be used as a suitable tool for authenticity control and applied to identify novel sources devoid or particularly rich in polyacetylenes, thus facilitating breeding programs for the selective enrichment and depletion of these plant secondary metabolites, respectively.     

Field studies on the potential of butanone, carbon dioxide, honey extract, 1-octen-3-ol, L-lactic acid and phenols as attractants for mosquitoes

Various combinations of six candidate attractants--butanone, carbon dioxide (CO2), honey, octenol, lactic acid and mixed phenols--were tested against natural populations of mosquitoes in Everglades National Park, Florida, U.S.A., using unlighted CDC-baited traps. With few exceptions, the attractancy of these candidate compounds to mosquitoes, when used alone, was less than that of CO2 alone. The exceptions were that octenol and honey extract alone attracted larger numbers of Coquillettidia perturbans (Walker). Addition of lactic acid and/or octenol to CO2 increased trap collections of Aedes taeniorhynchus (Wiedemann), Anopheles atropos D. & K., and An. crucians Wiedemann by 1.4-13.8 times. Culex nigripalpus Theobald collections were increased 2.7 times by the addition of lactic acid, while the addition of octenol produced mixed results. Whereas the addition of lactic acid reduced collections of Cx (Melanoconion) spp., the addition of octenol generally increased collections. The opposite happened for Wyeomyia mitchellii (Theobald). For the biting midge, Culicoides furens (poey), octenol (1.6-23.4 x ) and phenol (2.7 x ) alone attracted larger numbers, and lactic acid alone attracted approximately the same numbers as CO2 alone. The combinations octenol + phenol and octenol + 200 ml/min CO2 increased C. furens collections c. 100 times over CO2 alone. The combination of octenol + CO2 increased (1.6 x ) collections of the tabanid Diachlorus ferrugatus (Fabricius). Butanone appeared to decrease the trap collections of all species when combined with CO2 or octenol + CO2.     

Production of antibacterial compounds by phylloplane-inhabiting yeasts and yeastlike fungi.

The production of antibacterial compounds by yeasts and yeastlike fungi isolated from the phylloplane is reported. Aureobasidium pullulans, Citeromyces matritensis, Cryptococcus laurentii, Rhodotorula glutinis, and Sporobolomyces roseus produced antibacterial compounds inhibitory to both Pseudomonas fluorescens and Staphylococcus aureus in an overlay bioassay. In contrast, isolates of Candida albicans, Filobasidium uniguttulatum, Saccharomyces cerevisiae, Torulaspora delbruckii, Tremella foliacea, Trichosporon beigelii, and Trichosporon dulcitum obtained from soil or from culture collections did not produce inhibitory compounds when screened by the same procedure. The production of antibacterial compounds was examined in more detail, using several isolates of A. pullulans distinguished by cluster analysis on the basis of biochemical and physiological tests. They were found to produce a range of antibacterial compounds with different activities. Two distinct antibiotics were produced by an isolate of A. pullulans in liquid culture during both the logarithmic and the stationary phases of growth.     

Fragrance chemistry and pollinator affinities in Nyctaginaceae

We present results of dynamic head-space collections and GC-MS analyses of floral and vegetative fragrances for 20 species in three genera of Nyctaginaceae: Acleisanthes, Mirabilis and Selinocarpus. Most of the species included in this study are either hawkmoth or noctuid moth-pollinated. A wide variety of compounds were observed, including mono- and sesquiterpenoids, aromatics (both benzenoids and phenylpropanoids), aliphatic compounds, lactones, and nitrogen-bearing compounds. Intraspecific variation in fragrance profiles was significantly lower than interspecific variation. Each species had a unique blend of volatiles, and the fragrance of many species contained species-specific compounds. The fragrance profiles presented here are generally consistent with previous studies of fragrance in a variety of moth-pollinated angiosperms.     

Further acetogenins from Tasmanian collections of Caulocystis cephalornithos demonstrating chemical variability

Samples of the brown alga Caulocystis cephalornithos, from five locations in southern and southeastern Tasmania, were investigated for comparison of their acetogenin content. In contrast with previously studied brown algae, including mainland Australian collections of C. cephalornithos, Tasmanian collections of C. cephalornithos were found to contain unusually high levels of tridec-1-ene, a hydrocarbon not previously reported from a marine alga. The novel metabolite (E)-nonadec-3-en-2-one was also isolated. Compounds previously described from this alga were present, together with a suite of homologues not previously observed in this species. The compounds present suggested that the alkyl chain of the orsellinic acid derivatives was present prior to cyclisation. Large variations in relative metabolite content were observed both within and between collection sites.     

High-throughput bioluminescence screening of ubiquitin-proteasome pathway inhibitors from chemical and natural sources

To discover original inhibitors of the ubiquitin-proteasome pathway, the authors have developed a cell-based bioluminescent assay and used it to screen collections of plant extracts and chemical compounds. They first established a DLD-1 human colon cancer cell line that stably expresses a 4Ubiquitin-Luciferase (4Ub-Luc) reporter protein, efficiently targeted to the ubiquitin-proteasome degradation pathway. The assay was then adapted to 96- and 384-well plate formats and calibrated with reference proteasome inhibitors. Assay robustness was carefully assessed, particularly cell toxicity, and the statistical Z factor value was calculated to 0.83, demonstrating a good performance level of the assay. A total of 18,239 molecules and 15,744 plant extracts and fractions thereof were screened for their capacity to increase the luciferase activity in DLD-1 4Ub-Luc cells, and 21 molecules and 66 extracts inhibiting the ubiquitin-proteasome pathway were identified. The fractionation of an active methanol extract of Physalis angulata L. aerial parts was performed to isolate 2 secosteroids known as physalin B and C. In a cell-based Western blot assay, the ubiquitinated protein accumulation was confirmed after a physalin treatment confirming the accuracy of the screening process. The method reported here thus provides a robust approach to identify novel ubiquitin-proteasome pathway inhibitors in large collections of chemical compounds and natural products.     

Antitumor activity and distribution of pyrroloiminoquinones in the sponge genus Zyzzya

A detailed analysis of four different collections of the sponge genus Zyzzya yielded nine pyrroloiminoquinones of the makaluvamine, batzelline, and isobatzelline/damirone classes. Dereplication analyses of additional Zyzzya extracts did not disclose more potent or additional new compounds. Comparative testing of these compounds in the National Cancer Institute's 60 cell line human tumor screen revealed varying levels of potency and differential cytotoxicity, apparently related to the unsaturation levels in and substitution patterns on the core ring system. Further studies on the topoisomerase II-mediated DNA cleavage were conducted. Reductive activation of the pyrroloiminoquinones led to DNA damage in vitro, which correlated with half wave potentials and reversibility parameters. DNA damage could be abrogated by ascorbate. Fluorescence displacement was used to measure intercalation with DNA; intercalation efficiency did not correlate with DNA-damaging proficiency. Makaluvamine H (5) emerged as the most potent and differential of our isolates, roughly comparable to makaluvamines C (in vitro) and I (in vivo). 3,7-Dimethyl guanine was isolated from one of the Zyzzya collections and from the sponge Latrunculia purpurea.     

Involvement of volatile compounds of Artemisia in browse preference by mule deer

Twelve collections of sagebrush, representing eight taxa at an unfenced plot near Price, Utah, were investigated to determine if the relative levels of eight major volatile compounds in the leaves influenced mule deer utilization of the various taxa during the winter. The compounds investigated were methacrolein, -pinene, camphene, β-pinene, arthole, 1,8-cineole, p-cymene, and camphor. Stepwise regression analysis indicated that one-fifth or less of the variability in utilization could be attributed to the relative percentages of the volatile constituents in the leaves. Oxygenated compounds (especially methacrolein and arthole) seemed to be more highly correlated with sagebrush utilization than hydrocarbons, and this correlation appeared to be inverse.     

Homogeranyl nerol derivatives and a melampolide from Smallanthus glabratus

The investigation of the aerial parts of Smallanthus glabratus from two locations afforded the same known compounds but some additional new compounds which were not present in both collections. From the first location typical melampolides, one of them not isolated previously, and two homoditerpenes were isolated. The material from the second location gave four closely related homoditerpenes and two geranyl nerol derivatives from which the homoditerpenes were derived. The structures were elucidated by high field ¹H NMR spectroscopy. Chemotaxonomic aspects are discussed briefly.     

Baseline susceptibility to bacterial insecticides in populations of Culex pipiens complex (Diptera: Culicidae) from California and from the Mediterranean Island of Cyprus

Bacterial insecticides play an increasingly important role in mosquito control. To establish guidelines for detecting resistance at an early stage, information on natural variation in susceptibility of insect populations to these insecticides is needed. Between 1990 and 1993, the susceptibility of Culex pipiens L. complex to Bacillus thuringiensis subsp. israelensis de Barjac and/or Bacillus sphaericus Neide was determined in 31 collections from California. These collections were undertaken before the widespread use of B. thuringiensis subsp. israelensis and before the registration of B. sphaericus in California. Seven collections from the Mediterranean island of Cyprus, where no microbial insecticides have been used, also were tested. The 1990-1991 California collections exhibited limited variation in susceptibility to B. thuringiensis subsp. israelensis. LC50 and LC95 values spanned about a three-fold and four-fold range, respectively. The 1993 Cyprus collections exhibited both higher mean LC values, and greater variability in those values, than the California collections. The LC50s for the Cyprus collections varied over a 10-fold range, whereas the LC50s varied over a 12.5-fold range. Variation in susceptibility to B. sphaericus among the 1991 California collections was about five-fold at the LC50 and LC95. No significant geographic variation in susceptibility to B. thuringiensis subsp. israelensis was observed among regions within California. Although variation in susceptibility was limited among California collections, the greater variability observed among the Cyprus collections and between the Cyprus and California collections illustrates the importance of establishing regional baselines to monitor accurately for changes in susceptibility.     

Mapping the history of botanical collectors: spatial patterns,diversity, and uniqueness through time

This study examines changing spatial patterns of botanical collections over a 400 year time frame, focussing on the collections at the Natural History Museum (BM) in comparison with global patterns. The Plant Collector Resource Database, which contains 68,000 collector records was used to generate 250,667 unique collector × country × date records. We observe an exponential increase in the number of collectors over time. The activities of collectors were investigated in 50-year time-slices from 1650–2000. We specifically considered the geographic scope of collections (i.e., countries in which collections were made), the depth of collections (i.e., the number of collectors per country) and the uniqueness of collections (i.e., the proportion not duplicated in other herbaria). Uniqueness was highest for the earliest time-slice. Collector activity is shown to be strongly influenced by extrinsic factors such as the development of trade and empire, which allowed for collections to expand in scope and depth, and conflicts, which reduced collecting activity. A striking finding concerns the uniqueness of collections through time. The considerable unique element of the collections in herbaria highlighted by this study provides a strong motivation for digitization efforts to ensure that collections are accessible to address key questions in systematics, biogeography, and ecology.     

Neuropeptidomics strategies for specific and sensitive identification of endogenous peptides

A new approach using targeted sequence collections has been developed for identifying endogenous peptides. This approach enables a fast, specific, and sensitive identification of endogenous peptides. Three different sequence collections were constituted in this study to mimic the peptidomic samples: SwePep precursors, SwePep peptides, and SwePep predicted. The searches for neuropeptides performed against these three sequence collections were compared with searches performed against the entire mouse proteome, which is commonly used to identify neuropeptides. These four sequence collections were searched with both Mascot and X! Tandem. Evaluation of the sequence collections was achieved using a set of manually identified and previously verified peptides. By using the three new sequence collections, which more accurately mimic the sample, 3 times as many peptides were significantly identified, with a false-positive rate below 1%, in comparison with the mouse proteome. The new sequence collections were also used to identify previously uncharacterized peptides from brain tissue; 27 previously uncharacterized peptides and potentially bioactive neuropeptides were identified. These novel peptides are cleaved from the peptide precursors at sites that are characteristic for prohormone convertases, and some of them have post-translational modifications that are characteristic for neuropeptides. The targeted protein sequence collections for different species are publicly available for download from SwePep.     

Prediction Errors in Learning Drug Response from Gene Expression Data – Influence of Labeling,Sample Size,and Machine Learning Algorithm

Model-based prediction is dependent on many choices ranging from the sample collection and prediction endpoint to the choice of algorithm and its parameters. Here we studied the effects of such choices, exemplified by predicting sensitivity (as IC50) of cancer cell lines towards a variety of compounds. For this, we used three independent sample collections and applied several machine learning algorithms for predicting a variety of endpoints for drug response. We compared all possible models for combinations of sample collections, algorithm, drug, and labeling to an identically generated null model. The predictability of treatment effects varies among compounds, i.e. response could be predicted for some but not for all. The choice of sample collection plays a major role towards lowering the prediction error, as does sample size. However, we found that no algorithm was able to consistently outperform the other and there was no significant difference between regression and two- or three class predictors in this experimental setting. These results indicate that response-modeling projects should direct efforts mainly towards sample collection and data quality, rather than method adjustment.     

中国普通小麦初选核心种质的产生

对中国普通小麦种质资源构建了初选核心种质。地方品种和选育品种分别构建。按栽培区(地理生态区)分组。地方品种按亚区分为28组,选育品种按大区分为10组。各组内在21个表型性状聚类的基础上,按平方根法取样,并依遗传多样性指数与遗传丰富度加以调整。提出在生产上或育种中起过重要作用的品种为必选材料。初步选定的材料经种植核对,淘汰错杂后,产生初选核心种质。地方品种全部供试材料11694份,初选核心种质3283份,取样比例为28．18％。选育品种全部11441份,初选核心种质1684份,取样比例为14．9％。计划经分子标记分析,最后核心种质的比例占全部种质的10％左右。根据全部材料21个性状遗传多样性指数测验,初选核心种质,除芒和壳两性状外,与全部种质的遗传差异均未达到显水平。讨论了初选核心种质的构建方法。指出陕南部西山地和汾渭谷地是中国小麦地方品种遗传变异多样性的富集地。育成品种多样性程度以西南冬麦区和黄淮冬麦区为最高。     

Lead compounds discovered from libraries: part 2

Many lead compounds with the potential to progress to viable drug candidates have been identified from libraries during the past two years. There are two key strategies most often employed to find leads from libraries: first, high-throughput biological screening of corporate compound collections; and second, synthesis and screening of project-directed libraries (i.e. target-based libraries). Numerous success stories, including the discovery of several clinical candidates, testify to the utility of chemical library collections as proven sources of new leads for drug development.     

Aggregation pheromone of Metamasius spinolae (Coleoptera: Curculionidae): chemical analysis and field test

Male Metamasius spinolae (Gylh.) produce several volatile compounds that are likely constituents of its aggregation pheromone. These compounds were identified by volatile collections and gas chromatography (GC), followed by coupled gas chromatography-mass spectrometry (GC-MS), as 2-methyl-4-heptanone [1], 6-methyl-2hepten-4-one [2], and 2-hydroxy-2-methyl-4-heptanone [3]. Preliminary field experiments using synthetic racemates of these compounds showed that significantly more adult cactus weevils were caught in traps baited with the major single compound three or the 2 + 3 binary combination than in unbaited control traps. However, highest trap efficacy occurred with the 1 + 2 binary combination and a blend of all three synthetic compounds plus prickly pear. Potential uses for the cactus weevil pheromone and possible ways to increase trap captures are discussed.     

The sesquiterpene hydrocarbons of maize (Zea mays) form five groups with distinct developmental and organ-specific distributions

The sesquiterpene hydrocarbon chemistry of maize (Zea mays) inbred line B73 was analyzed by both direct solvent extraction and headspace sampling. In seedlings, 15 olefinic compounds were identified, and 21 olefins were detected in mature plants after anthesis. Both solvent extracts and collections of headspace terpenes were found to contain the same compounds in the same relative proportions suggesting that there is no selective barrier to release from plants. Approximately 25% of the stored pool was found to be released from young seedlings per hour. The individual sesquiterpenes varied extensively in their abundance among different organs and developmental stages. Compounds could be divided into five different groups such that the members of each group always occur together in the same constant ratios to one another. Each group has a distinct distribution pattern. Group A includes the two dominant compounds, (E)-beta-farnesene and alpha-bergamotene, and appears only after herbivore damage in seedlings, but is constitutively present in the leaves and husks after anthesis. The major compounds of group B, including alpha-copaene, germacrene D and delta-cadinene, were present throughout the seedling but found only in husks of mature plants. The group C compounds, beta-bisabolene and an unknown sesquiterpene olefin, are restricted to the roots. The presence of group D and E compounds was confined to the leaves and husk of mature plants. The complex sesquiterpene mixture of group D is identical to the products formed by the previously identified terpene synthase TPS4, suggesting that each of the four other sesquiterpene hydrocarbon mixtures may also represent the products of a single terpene synthase.     

Volatiles from apple (Malus domestica) eliciting antennal responses in female codling moth Cydia pomonella (L.) (Lepidoptera: Tortricidae): effect of plant injury and sampling technique

The antennal responses of codling moth females, Cydia pomonella, to volatiles from apple branches with green fruits were recorded by electroantennography coupled to gas chromatography. The antennae strongly responded to 4,8-dimethyl-1,3(E),7-nonatriene, linalool, beta-caryophyllene, (E)-beta-farnesene, germacrene D, (Z,E)-alpha-farnesene, (E,E)-alpha-farnesene and methyl salicylate. These compounds were all present in volatile collections on Porapak Q from both living and cut branches. Analysis by the solid phase microextraction technique (SPME) showed that the emission of some electrophysiologically active compounds increased after branches had been cut, especially 4,8-dimethyl-1,3(E),7-nonatriene, linalool and (E,E)-alpha-farnesene. The identification of apple volatiles eliciting antennal responses is the first step towards the identification of compounds mediating host-finding and oviposition in codling moth females.