Web search and data mining of natural products and their bioactivities in PubChem

Natural products,as major resources for drug discovery historically,are gaining more attentions recently due to the advancement in genomic sequencing and other technologies,which makes them attractive and amenable to drug candidate screening.Collecting and mining the bioactivity information of natural products are extremely important for accelerating drug development process by reducing cost.Lately,a number of publicly accessible databases have been established to facilitate the access to the chemical biology data for small molecules including natural products.Thus,it is imperative for scientists in related fields to exploit these resources in order to expedite their researches on natural products as drug leads/candidates for disease treatment.PubChem,as a public database,contains large amounts of natural products associated with bioactivity data.In this review,we introduce the information system provided at PubChem,and systematically describe the applications for a set of PubChem web services for rapid data retrieval,analysis,and downloading of natural products.We hope this work can serve as a starting point for the researchers to perform data mining on natural products using PubChem.     

Performance of (consensus) kNN QSAR for predicting estrogenic activity in a large diverse set of organic compounds

A novel method (in the context of quantitative structure–activity relationship (QSAR)) based on the k nearest neighbour (kNN) principle, has recently been introduced for the derivation of predictive structure–activity relationships. Its performance has been tested for estimating the estrogen binding affinity of a diverse set of 142 organic molecules. Highly predictive models have been obtained. Moreover, it has been demonstrated that consensus-type kNN QSAR models, derived from the arithmetic mean of individual QSAR models were statistically robust and provided more accurate predictions than the great majority of the individual QSAR models. Finally, the consensus QSAR method was tested with 3D QSAR and log?P data from a widely used steroid benchmark data set.     

Performance of (consensus) kNN QSAR for predicting estrogenic activity in a large diverse set of organic compounds

A novel method (in the context of quantitative structure-activity relationship (QSAR)) based on the k nearest neighbour (kNN) principle, has recently been introduced for the derivation of predictive structure-activity relationships. Its performance has been tested for estimating the estrogen binding affinity of a diverse set of 142 organic molecules. Highly predictive models have been obtained. Moreover, it has been demonstrated that consensus-type kNN QSAR models, derived from the arithmetic mean of individual QSAR models were statistically robust and provided more accurate predictions than the great majority of the individual QSAR models. Finally, the consensus QSAR method was tested with 3D QSAR and log P data from a widely used steroid benchmark data set.     

Molecular iodine catalyzed synthesis of tetrazolo[1,5-a]-quinoline based imidazoles as a new class of antimicrobial and antituberculosis agents

A series of some new tetrazolo[1,5-a]quinoline based tetrasubstituted imidazole derivatives 6a-1 have been synthesized by a reaction of tetrazolo[1,5-a]quinoline-4-carbaldehyde 3a-d,benzil 4,aromatic amine 5a-c and ammonium acetate in the presence of iodine through one-pot multi-component reaction(MCR) approach.All the derivatives were screened for antimicrobial and antituberculosis activities and results worth further investigations.     

Heat-treated magnesia as an adsorbent for the class separation of aliphatic monocarbonyl compounds

In order to control the activity of magnesia as an adsorbent, the effect of temperature was studied. The activity of various temperature of treatment showed two regions. During the first, in the range 106–320°, the activity increased with increasing temperature, whereas at temperatures above 320° the activity decreased with increasing temperature.The iodine number of heat-treated magnesia correlated well with its affinity for 2,4-dinitrophenylhydrazones of carbonyls.By heating several batches of magnesia at graphically determined temperatures. it was possible to obtain adsorbents with the same activity for class separation.     

Palladium catalyzed Suzuki C-C couplings in an ionic liquid: nanoparticles responsible for the catalytic activity

A new family of functionalized ligands derived from norborn-5-ene-2,3-dicarboxylic anhydride has been used in Suzuki C-C cross-couplings between aryl boronic acids and aryl bromide derivatives in [BMI][PF(6)] (BMI=1-n-butyl-3-methyl-imidazolium), using palladium acetate as catalytic precursor. High conversions and yields are obtained when amine ligands containing hydroxy groups are involved. TEM analyses after catalysis show the formation of small nanoparticles, in contrast to the agglomerates observed when nanoparticles are intentionally preformed, with a consequent decrease in the catalytic activity in the latter case. Some tests, including the correlation effect between solvent and ligand, are carried out to try to identify the true nature of the catalyst. All the results obtained suggest that formation of nanoparticles is required to lead to a catalytically active system.     

Ultrasound-assisted emulsification-microextraction for the sensitive determination of Brett character responsible compounds in wines

In this study, a method based on ultrasound-assisted emulsification-microextraction (USAEME) was optimised for the determination of Brett character responsible compounds (4-ethylguaiacol (EG), 4-ethylphenol (EP), 4-vinylguaiacol (VG) and 4-vinylphenol (VP)) in wines. For this purpose, once the extraction solvent had been selected, the influence on the extraction efficiency of ratio between extraction solvent and sample volumes, temperature, ionic strength and time was studied using experimental design methodology. The optimum conditions found for USAEME of 5mL of wine were 160μL of chlorobenzene at 60°C during 5min without salt addition. Then, the analytical performance of the optimised USAEME procedure was evaluated. For all the studied compounds, the proposed method showed correlation coefficients over 0.984. Satisfactory repeatability (below 10%) and inter-day repeatability (below 11%) were obtained at different concentration levels and the method achieved detection limits similar or even lower than previously reported for these compounds in wines. Moreover, the applicability of the method was evaluated by the analysis of real samples. To our knowledge, this is the first time that USAEME has been applied to the determination of Brett character responsible compounds in wine.     

Synthesis of novel selenium and tellurium-containing tetrazoles: a class of chalcogen compounds with antifungal activity

We describe herein the synthesis and antifungal activity of new 5-arylchalcogenoalkyl-1H-tetrazoles 4. Arylchalcogenoalkyl-1H-tetrazoles 4 have been synthesized in high yields by reaction of arylchalcogenolate anions with chloronitriles 2, and subsequent [2+3] cycloaddition of resulting arylchalcogenoalkylnitriles 3 with sodium azide by zinc catalysis in aqueous solution. The obtained compound 4a was screened for antifungal activity and presented inhibitory property against seven fungal strains. This protocol is an efficient method to produce new selenium–nitrogen compounds with antifungal activity.     

Aminopyrrolic synthetic receptors for monosaccharides: a class of carbohydrate-binding agents endowed with antibiotic activity versus pathogenic yeasts

The biological activity of a set of structurally related aminopyrrolic synthetic receptors for monosaccharides has been tested versus yeast and yeast-like microorganisms and compared to their binding affinity toward mannosides. Antibiotic activity comparable to that of well-known polyene (amphotericin B) or azole (ketoconazole) drugs has been found for some members of the family, along with a general correlation with binding abilities. A systematic structure-activity-affinity investigation shed light on the structural and functional requirements necessary for antibiotic activity and identified the tripodal compound 1 as the most potent compound of the set. Together with toxicity tests and inhibitor localization experiments performed through fluorescence microscopy, these studies led to the characterization of a new class of carbohydrate binding agents possessing antibiotic activity, in which pyrrolic groups precisely structured on a tripodal architecture appear to be responsible for permeability through the cell wall of pathogens, as well as for antibiotic activity inside the cytoplasm.     

Evaluation of a two-stage screening procedure in the combinatorial search for serine protease-like activity

A series of peptidosteroid derivatives containing two independent peptide chains in which Ser and His are incorporated were synthesized by solid-phase peptide synthesis. The activity of the different compounds in the hydrolysis of the activated substrate NF31 was assessed in a stepwise fashion. First, the different resin-bound derivatives 6a-l and 6x-z were individually assayed for serine esterification in the absence of water. The use of a colored substrate allowed for a visual identification of the most active compounds. Through the inclusion of control substances, the involvement of histidine in the mechanism for serine acylation was shown. Second, the hydrolysis and methanolysis of the different acylated derivatives 8a-l and 8x were evaluated using UV spectroscopy, again indicating the involvement of histidine. The feasibility of applying the above procedures in a combinatorial context was proven via the screening of artificial libraries, created by mixing the different resin-bound peptidosteroid compounds. In this respect, the use of a photocleavable linker allowed for the unambiguous structural characterization of the selected members via application of single-bead electrospray tandem mass spectrometry.     

Formation of pyranoanthocyanins in red wines: a new and diverse class of anthocyanin derivatives

Pyranoanthocyanins constitute one of the most important classes of anthocyanin-derived pigments occurring naturally in red wine. Nonetheless, correct assignment of their structures and pathways of formation in red wine has been relatively recent—less than two decades. Study of these newly discovered pigments is progressively unfolding the chemical pathways that drive the evolution of red wine colour during ageing. The objective of this paper is to review current knowledge regarding the pathway of formation in red wine of a great variety of pyranoanthocyanin structures, namely carboxypyranoanthocyanins, methylpyranoanthocyanins, pyranoanthocyanin-flavanols, pyranoanthocyanin-phenols, portisins, oxovitisins, and pyranoanthocyanin dimers. The chromatic features of some of the compounds, for example their colour expression and acid–base equilibria in aqueous media, are also discussed.     

Formation of pyranoanthocyanins in red wines: a new and diverse class of anthocyanin derivatives

Pyranoanthocyanins constitute one of the most important classes of anthocyanin-derived pigments occurring naturally in red wine. Nonetheless, correct assignment of their structures and pathways of formation in red wine has been relatively recent—less than two decades. Study of these newly discovered pigments is progressively unfolding the chemical pathways that drive the evolution of red wine colour during ageing. The objective of this paper is to review current knowledge regarding the pathway of formation in red wine of a great variety of pyranoanthocyanin structures, namely carboxypyranoanthocyanins, methylpyranoanthocyanins, pyranoanthocyanin-flavanols, pyranoanthocyanin-phenols, portisins, oxovitisins, and pyranoanthocyanin dimers. The chromatic features of some of the compounds, for example their colour expression and acid–base equilibria in aqueous media, are also discussed.     

Soluble molecular compounds with the Mg-O-Al structural motif: a model approach for the fixation of organometallics on a MgO surface

We report a facile route to the molecular compounds with the Mg-O-Al structural motif. The reaction of Mg[N(SiMe3)2]2 (1) with a stoichiometric amount of LAlOH(Me) (2) [L = CH{(CMe)(2,6-iPr2C6H3N)}2] in THF/n-hexane at 0 degrees C results in the formation of the heterobimetallic compound (Me3Si)2NMg(THF)2-O-Al(Me)L (3) in high yield. The similar reaction of 1 equiv of Mg[N(SiMe3)2]2 and 2 equiv of LAlOH(Me) results in the formation of trimetallic compound L(Me)Al-O-Mg(THF)2-O-Al(Me)L (4). Structural analyses of 3 and 4 have been carried out, revealing the presence of the Mg-O-Al motif. A tentative assignment of the Mg-O-Al vibrations has been made and was supported by calculations.