Correlation between the genetic diversity and variation of total phenolic acids contents in Fructus Xanthii from different populations in China

Fructus Xanthii (Cang-Er-Zi) is a traditional Chinese medicine that is used in curing nasal diseases and headache according to the Chinese Pharmacopoeia. For the effective quality control of its medicinal values, reflected by chemical variation patterns, in addition to the relationship with genetic diversity, analyses based on UV spectrophotometry, HPLC fingerprinting and inter-simple sequence repeat (ISSR) molecular markers were carried out, involving 16 Xanthium populations from different locations in China. The HPLC data showed considerable variation of chemical constituents among the 16 Xanthium populations, and they were classified to three chemotypes by hierarchical clustering analysis. Abundant genetic diversity was detected among the Xanthium populations, which were also clustered into three groups based on their ISSR data and varied according to different species. Combining the genetic divergence and chemical differences showed an important result that, in the two chemotypes, the higher contents of total phenolic acids (TPA) in Fructus Xanthii showed greater genetic diversity (I). We suggest that genetic diversity affects the contents of TPA. Since variable phenolic acid contents may affect therapeutic efficacy, it is important to point out that combining the use of genetic base with chemotype will help control the favourable chemotypes and breed new cultivars with more desirable chemical constituents.     

Association between chemical and genetic variation of Vitex rotundifolia populations from different locations in China: its implication for quality control of medicinal plants

Vitex rotundifolia is a widely distributed plant species that has been extensively used in traditional Chinese medicine. Its fruits, Fructus Viticis, are recorded as Manjingzi in the Pharmacopoeia of the People's Republic of China. For the effective quality control of its medicinal values reflected by chemical variation patterns, in addition to the relationship with genetic diversity, analyses based on high-performance liquid chromatographic (HPLC) fingerprinting and inter simple sequence repeat (ISSR) molecular markers were carried out, involving 14 V. rotundifolia populations from different locations in China. The HPLC data showed considerable variation of chemical constituents among the V. rotundifolia populations. The hierarchical clustering analysis further revealed four major groups based on their chemotype variation. Abundant genetic diversity was detected among the V. rotundifolia populations that also were clustered into four groups based on their ISSR data. It is important to point out that the genetic variation pattern revealed by molecular markers was closely associated with that indicated by chemical constitutes in the fruits of V. rotundifolia. This finding provides a solid basis for the combined use of chemical and genetic fingerprints in efficiently evaluating qualities and choosing favourable chemotypes with appropriate pharmacological properties of V. rotundifolia, in addition to establishing good agricultural practices for medicinal plants.     

Application and exploration of fast gas chromatography-surface acoustic wave sensor to the analysis of thymus species

Fast gas chromatography combined with surface acoustic wave sensor (GC/SAW) has been applied for the detection of volatile aroma compounds emanated from thymus medicinal plants such as T. quinquecostotus (Jeju and Mt. Gaya in South Korea), T. quinquecostotus var. japonica (Ulreung island in South Korea), T. mongolicus (Northeastern Asia), and T. serpyllum (Europe). The GC/SAW involving the fragrance pattern analysis provides a novel analytical method with a very fast separation and characterization of aromas caused by the delicate difference of chemical composition according to botanical and geographical origin. On the comparison of experiments, the characteristic components and analytical tendency for air-dried thymus species detected by GC/SAW appear to be quite similar to those obtained by headspace solid-phase microextraction (HS-SPME)-GC-MS, but the abundance ratios between these two methods are different. In addition to that, the discrimination of various thymus species by using VaporPrint image based on GC/SAW provides a quite reliable result. On the basis of principal component analysis (PCA) results, the ability for classification among species of completely different chemotypes by HS-SPME-GC-MS is good enough, but the classification of same chemotypes species which are from different geographical origin in same country, original species and its variety, an air-drying term for 13 days and 16 months appear much lower than GC/SAW. Interestingly, the present experiment reveals that the air-drying term influences the aroma composition: the concentration of the pharmacologically active species, monoterpene phenol (thymol), reaches its highest concentrations after it was dried for 5 days or 13 days, which is much higher than in fresh or over-dried for a long times.     

A scent of therapy: pharmacological implications of natural products containing redox-active sulfur atoms

A range of sulfur-containing natural products from plants, fungi, bacteria and animals have recently been investigated to determine their therapeutic potential. Preliminary in vitro and in vivo studies of compounds such as ergothioneine, ovothiols, allicin, leinamycin, varacin, lenthionine and diallyltetrasulfide have provided evidence for antioxidant, antibacterial, antimicrobial, antifungal and anticancer properties. The biological activity of these compounds is the result of specific chemical properties which converge in chemotypes such as thiols, disulfides, sulfenic and sulfinic acids,thiosulfinates, sulfoxides, sulfones and polysulfides. Redox-activity, catalysis, metal binding, enzyme inhibition and radical generation allow reactive sulfur species to interact with oxidative stressors, to affect the function of redox-sensitive cysteine proteins and to disrupt the integrity of DNA and cellular membranes. In some cases, the biological activity of sulfur-containing plant products depends on initial enzymatic activation, which allows thiosulfinates and isothiocyanates to be generated with high target selectivity. Not surprisingly, research into the biochemical and pharmacological properties of the lesser known sulfur chemotypes is rapidly gathering momentum.     

Small molecules from spiders used as chemical probes

Spiders are important species in ecological systems and as major predators of insects they are endowed with a plethora of low-molecular-weight natural products having intriguing biological activities. The isolation and biological characterization of these entities are well established, however, only very recently have these compounds been used as templates for the design, synthesis, and biological evaluation of synthetic analogues. In contrast, the investigation of compounds responsible for chemical communication between spiders is far less developed, but recently new light has been shed onto the area of pheromones and allomones from spiders. Herein, we recapitulate these recent results, put them into perspective with previous findings, and provide an outlook for future studies of these chemotypes.     

Activity-aware clustering of high throughput screening data and elucidation of orthogonal structure-activity relationships

From a medicinal chemistry point of view, one of the primary goals of high throughput screening (HTS) hit list assessment is the identification of chemotypes with an informative structure-activity relationship (SAR). Such chemotypes may enable optimization of the primary potency, as well as selectivity and phamacokinetic properties. A common way to prioritize them is molecular clustering of the hits. Typical clustering techniques, however, rely on a general notion of chemical similarity or standard rules of scaffold decomposition and are thus insensitive to molecular features that are enriched in biologically active compounds. This hinders SAR analysis, because compounds sharing the same pharmacophore might not end up in the same cluster and thus are not directly compared to each other by the medicinal chemist. Similarly, common chemotypes that are not related to activity may contaminate clusters, distracting from important chemical motifs. We combined molecular similarity and Bayesian models and introduce (I) a robust, activity-aware clustering approach and (II) a feature mapping method for the elucidation of distinct SAR determinants in polypharmacologic compounds. We evaluated the method on 462 dose-response assays from the Pubchem Bioassay repository. Activity-aware clustering grouped compounds sharing molecular cores that were specific for the target or pathway at hand, rather than grouping inactive scaffolds commonly found in compound series. Many of these core structures we also found in literature that discussed SARs of the respective targets. A numerical comparison of cores allowed for identification of the structural prerequisites for polypharmacology, i.e., distinct bioactive regions within a single compound, and pointed toward selectivity-conferring medchem strategies. The method presented here is generally applicable to any type of activity data and may help bridge the gap between hit list assessment and designing a medchem strategy.     

Chemical Fingerprinting and Hierarchical Clustering Analysis of Centella asiatica from Different Locations in China

Centella asiatica (L.) Urban is a widely distributed herbaceous plant with great medicinal value that has been extensively used in traditional Chinese medicine. For effective quality control of C. asiatica, a feasible approach and control system is necessary. In this paper, a chemical fingerprint method (column liquid chromatography) was developed for investigating and demonstrating the variance of chemical components among different populations of C. asiatica, from 14 locations in China. The LC data showed considerable variation of chemical constituents among C. asiatica populations. Four chemotypes were visually developed from the chromatographic profiles. The hierarchical clustering analysis further suggested that the samples were divided into four major groups. The grouping of 14 C. asiatica populations in hierarchical clustering analysis was in good agreement with the visual comparison of their chromatograms, as demonstrated by chemotypes. In addition, the bioactive compound asiaticoside in this herb was quantitatively determined by a validated reversed-phase liquid chromatography analysis. Chemotype I was identified as asiaticoside-rich chemotype and exhibited significantly higher amounts of asiaticoside. These findings and results provide a solid basis to establish good agriculture practice and select geo-authentic crude drug for C. asiatica. The established method was considered to be suitable for fingerprint analysis for the quality control of C. asiatica.     

Spectroelectrochemical and computational studies on the mechanism of hypoxia selectivity of copper radiopharmaceuticals

Detailed chemical, spectroelectrochemical and computational studies have been used to investigate the mechanism of hypoxia selectivity of a range of copper radiopharmaceuticals. A revised mechanism involving a delicate balance between cellular uptake, intracellular reduction, reoxidation, protonation and ligand dissociation is proposed. This mechanism accounts for observed differences in the reported cellular uptake and washout of related copper bis(thiosemicarbazonato) complexes. Three copper and zinc complexes have been characterised by X-ray crystallography and the redox chemistry of a series of copper complexes has been investigated by using electronic absorption and EPR spectroelectrochemistry. Time-dependent density functional theory (TD-DFT) calculations have also been used to probe the electronic structures of intermediate species and assign the electronic absorption spectra. DFT calculations also show that one-electron oxidation is ligand-based, leading to the formation of cationic triplet species. In the absence of protons, metal-centred one-electron reduction gives the reduced anionic copper(I) species, [CuIATSM](-), and for the first time it is shown that molecular oxygen can reoxidise this anion to give the neutral, lipophilic parent complexes, which can wash out of cells. The electrochemistry is pH dependent and in the presence of stronger acids both chemical and electrochemical reduction leads to quantitative and rapid dissociation of copper(I) ions from the mono- or diprotonated complexes, [CuIATSMH] and [Cu(I)ATSMH2]+. In addition, a range of protonated intermediate species have been identified at lower acid concentrations. The one-electron reduction potential, rate of reoxidation of the copper(I) anionic species and ease of protonation are dependent on the structure of the ligand, which also governs their observed behaviour in vivo.     

Turning the Light on Phenols: New Opportunities in Organic Synthesis

Phenols ( I ) are extremely relevant chemical functionalities in natural, synthetic and industrial chemistry. Their corresponding electron-rich anions, namely phenolates ( I ), are characterized by interesting physicochemical properties that can be drastically altered upon light excitation. Specifically, phenolates ( I ) become strong reducing agents in the excited state and are able to generate reactive radicals from suitable precursors via single-electron transfer processes. Thus, these species can photochemically trigger strategic bond-forming reactions, including their direct aromatic C−H functionalization. Moreover, substituted phenolate anions can act as photocatalysts to enable synthetically useful organic transformations. An alternative mechanistic manifold is represented by the ability of phenolate derivatives I to form ground state electron donor-acceptor (EDA) complexes with electron-poor radical sources. These complementary scenarios have paved the way for the development of a wide range of relevant organic reactions. In this Minireview, we present the main examples of this research field, and give insight on emerging trends in phenols photocatalysis towards richer organic synthesis.     

The isolation and structure elucidation of new cassane diterpene-acids from Caesalpinia crista L. (Fabaceae), and review on the nomenclature of some Caesalpinia species

New cassane diterpene-acids, neocaesalpins H and I, were isolated from the leaves of Caesalpinia crista (Fabaceae), and their structures were deduced on the basis of the spectroscopic and chemical basis. These compounds were characterized as having an alpha,beta-butenolide hemiacetal ring that is rare in nature. The lacking of 5-hydroxy group also distinguished neocaesalpins H and I from cassane diterpenes (caesalpins) occurring in other Caesalpinia species from the phytochemical viewpoint. The nomenclature of three Caesalpinia species was also reviewed, and it was found that some species belonging to the genus Caesalpinia are improperly named and should be changed to valid names.     

Aromatic gold and silver "rings": hydrosilver(I) and hydrogold(I) analogues of aromatic hydrocarbons

Quantum chemical calculations suggest that a series of molecules with the general formula cyclo-Mn(mu-H)n (M = Ag, Au; n = 3-6) are stable. All cyclo-MnHn species, except cyclo-Au(3)H(3), have the same symmetry with the respective aromatic hydrocarbons but differ in that the hydrogen atoms are in bridging positions between the metal atoms and not in terminal positions. The aromaticity of the hydrosilver(I) and hydrogold(I) analogues of aromatic hydrocarbons was verified by a number of established criteria of aromaticity, such as structural, energetic, magnetic, and chemical criteria. In particular, the nucleus-independent chemical shift, the relative hardness, Deltaeta, the electrophilicity index, omega, and the chemical reactivity toward electrophiles are indicative for the aromaticity of the hydrosilvers(I) and hydrogolds(I). A comprehensive study of the structural, energetic, spectroscopic (IR, NMR, electronic, and photoelectron spectra), and bonding properties of the novel classes of inorganic compounds containing bonds that are characterized by a common ring-shaped electron density, more commonly seen in organic molecules, is presented.     

Electronic structure and spectra of linkage isomers of bis(bipyridine)(1,2-dihydroxy-9,10-anthraquinonato)ruthenium(ii) and their redox series

Linkage isomers of bis(bipyridine)(1,2-dihydroxy-9,10-anthraquinonato)ruthenium(II), 1,2- and 1,9-coordinated complexes, and several of their oxidation products have been prepared chemically and/or electrochemically. For the 1,2-coordinated complex, the one- and two-electron oxidized species have been characterized, and for the 1,9-coordinated complex, the one-electron oxidized species has been characterized. The rich redox activity of these complexes leads to ambiguity in assessing the electronic structure. This paper reports EPR spectra of odd-electron species and detailed analyses of electronic spectra and structure of the complexes, based on INDO molecular orbital calculations. Results of calculations on the related 1-hydroxyanthraquinone complex and the free ligands,1,2-dihydroxy-9,10-anthraquinone (alizarin) and 1-hydroxyanthraquinone, are also briefly discussed.     

Three unusual 22-beta-O-23-hydroxy-(5 alpha)-spirostanol glycosides from the fruits of Solanum torvum

Three novel 22-beta-O-spirostanol oligoglycosides, torvosides J (1), K (2) and L (3) have been isolated from the fruits of Solanum torvum SWARTZ and their chemical structures have been characterized based on the spectroscopic means. They are worth of note as rare 22-beta-O-spirostanol glycosides.     

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of sufficiently high quality are available.     

Optimal descriptor as a translator of eclectic information into the prediction of thermal conductivity of micro-electro-mechanical systems

Micro-electro-mechanical systems (MEMS) are involved in various fields of nanotechnology. MEMS are characterized by complex and unclear molecular architecture. However, in most cases information about chemical composition and conditions of synthesis is available. One-variable models for thermal conductivity of MEMS are suggested. These models are based on the representation of MEMS by their chemical composition and technological attributes. We have examined three random splits of available data into the training set and validation set. The average statistical characteristics of these models are quite good. Development of suggested here models is carried out without information on molecular architecture of MEMS.     

Characterizing the diversity and biological relevance of the MLPCN assay manifold and screening set

The NIH Molecular Libraries Initiative (MLI), launched in 2004 with initial goals of identifying chemical probes for characterizing gene function and druggability, has produced PubChem, a chemical genomics knowledgebase for fostering translation of basic research into new therapeutic strategies. This paper assesses progress toward these goals by evaluating MLI target novelty and propensity for undergoing biochemically or therapeutically relevant modulations and the degree of chemical diversity and biogenic bias inherent in the MLI screening set. Our analyses suggest that while MLI target selection has not yet been fully optimized for biochemical diversity, it covers biologically interesting pathway space that complements established drug targets. We find the MLI screening set to be chemically diverse and to have greater biogenic bias than comparable collections of commercially available compounds. Biogenic enhancements such as incorporation of more metabolite-like chemotypes are suggested.     

Volatile Profiling of Magnolia champaca Accessions by Gas Chromatography Mass Spectrometry Coupled with Chemometrics

Magnolia champaca (L.) Baill. ex Pierre of family Magnoliaceae, is a perennial tree with aromatic, ethnobotanical, and medicinal uses. The M. champaca leaf is reported to have a myriad of therapeutic activities, however, there are limited reports available on the chemical composition of the leaf essential oil of M. champaca. The present study explored the variation in the yield and chemical composition of leaf essential oil isolated from 52 accessions of M. champaca. Through hydrodistillation, essential oil yield was obtained, varied in the range of 0.06 ± 0.003% and 0.31 ± 0.015% (v/w) on a fresh weight basis. GC-MS analysis identified a total of 65 phytoconstituents accounting for 90.23 to 98.90% of the total oil. Sesquiterpene hydrocarbons (52.83 to 65.63%) constituted the major fraction followed by sesquiterpene alcohols (14.71 to 22.45%). The essential oils were found to be rich in β-elemene (6.64 to 38.80%), γ-muurolene (4.63 to 22.50%), and β-caryophyllene (1.10 to 20.74%). Chemometrics analyses such as PCA, PLS-DA, sPLS-DA, and cluster analyses such as hierarchical clustering, i.e., dendrogram and partitional clustering, i.e., K-means classified the essential oils of M. champaca populations into three different chemotypes: chemotype I (β-elemene), chemotype II (γ-muurolene) and chemotype III (β-caryophyllene). The chemical polymorphism analyzed in the studied populations would facilitate the selection of chemotypes with specific compounds. The chemotypes identified in the M. champaca populations could be developed as promising bio-resources for conservation and pharmaceutical application and further improvement of the taxa.     

Analyses of lepidopteran sex pheromones by mass spectrometry

Lepidoptera, including about 150,000 species in the world, comprise the second largest insect group, and sex pheromones have been identified from virgin female moths of more than 600 species. The chemical structures are simple, but diverse, because species-specific pheromones play an important role in the reproductive isolation of each species. The pheromone content in each female is quite low, and gas chromatography coupled to mass spectrometry (GC-MS) is most frequently utilized to reveal the chemical structure. Almost all pheromone components are straight-chain compounds and are classified into two major groups [i.e. unsaturated C₁₀-C₁₈ fatty alcohols and their derivatives (Type I) and C₁₇-C₂₃ polyenyl hydrocarbons and their epoxides (Type II)]. In addition to the unbranched compounds, some species secrete methyl-branched compounds (e.g., 2-ketones). For the identification of these compounds, determining the positions of the double bond, the epoxy ring, and the methyl group is an important key step. Copious spectral information measured by electron-impact ionization (70 eV) has been accumulated for these compounds. This review therefore deals with their spectral characteristics, namely, diagnostic ions, to apply them to pheromone studies on new target insects.