Biosynthesis-Assisted Structural Elucidation of the Bartolosides, Chlorinated Aromatic Glycolipids from Cyanobacteria

The isolation of the bartolosides, unprecedented cyanobacterial glycolipids featuring aliphatic chains with chlorine substituents and C-glycosyl moieties, is reported. Their chlorinated dialkylresorcinol (DAR) core presented a major structural-elucidation challenge. To overcome this, we discovered the bartoloside (brt) biosynthetic gene cluster and linked it to the natural products through in vitro characterization of the DAR-forming ketosynthase and aromatase. Bioinformatic analysis also revealed a novel potential halogenase. Knowledge of the bartoloside biosynthesis constrained the DAR core structure by defining key pathway intermediates, ultimately allowing us to determine the full structures of the bartolosides. This work illustrates the power of genomics to enable the use of biosynthetic information for structure elucidation.

In situ analysis and structural elucidation of sainfoin (Onobrychis viciifolia) tannins for high-throughput germplasm screening

A rapid thiolytic degradation and cleanup procedure was developed for analyzing tannins directly in chlorophyll-containing sainfoin (Onobrychis viciifolia) plants. The technique proved suitable for complex tannin mixtures containing catechin, epicatechin, gallocatechin, and epigallocatechin flavan-3-ol units. The reaction time was standardized at 60 min to minimize the loss of structural information as a result of epimerization and degradation of terminal flavan-3-ol units. The results were evaluated by separate analysis of extractable and unextractable tannins, which accounted for 63.6−113.7% of the in situ plant tannins. It is of note that 70% aqueous acetone extracted tannins with a lower mean degree of polymerization (mDP) than was found for tannins analyzed in situ. Extractable tannins had between 4 and 29 lower mDP values. The method was validated by comparing results from individual and mixed sample sets. The tannin composition of different sainfoin accessions covered a range of mDP values from 16 to 83, procyanidin/prodelphinidin (PC/PD) ratios from 19.2/80.8 to 45.6/54.4, and cis/trans ratios from 74.1/25.9 to 88.0/12.0. This is the first high-throughput screening method that is suitable for analyzing condensed tannin contents and structural composition directly in green plant tissue.

Computer-Assisted Approach to Structural Elucidation of Lignans

This paper reports an expert system (SISTEMAT) developed for structural determination of diverse chemical classes of natural products, including lignans, based mainly on 13C NMR and 1H NMR data of these compounds. The system is composed of five programs that analyze specific data of a lignan and shows a skeleton probability for the compound. At the end of analyses, the results are grouped, the global probability is computed, and the most probable skeleton is exhibited to the user. SISTEMAT was able to properly predict the skeletons of 80% of the 30 lignans tested, demonstrating its advantage during the structural elucidation course in a short period of time.

HPLC-ESIMSn Profiling, Isolation, Structural Elucidation, and Evaluation of the Antioxidant Potential of Phenolics from Paepalanthus geniculatus

The methanol extract of the flowers of Paepalanthus geniculatus Kunth. showed radical-scavenging activity in the TEAC assay. An analytical approach based on HPLC:ESIMSn was applied to obtain the metabolite profile of this extract and led to the rapid identification of 19 polyphenolic compounds comprising flavonoids and naphthopyranones. The new naphthopyranone (10, 16), quercetagetin (1, 5, 7, 13), and galetine derivatives (9, 11, 17, 19), and a flavonol glucoside cyclodimer in the truxillate form (12), were identified. Compounds 2, 6, and 7 showed the highest antioxidant capacity and ability to affect the levels of intracellular ROS in human prostate cancer cells (PC3).

Dihydroflavonols from the leaves of Derris urucu (Leguminosae): structural elucidation and DPPH radical-scavenging activity

Derris urucu é uma planta da Amazônia com propriedades inseticida e ictiotóxica. Estudos com esta espécie reportam a presença de flavonóides, principalmente rotenóides, bem como de estilbenos. A partir do extrato etanólico das folhas de Derris urucu (Leguminosae), três novos diidroflavonóides, denominados urucuol A (1), B (2) e C (3) e o diidroflavonol isotirumalina (4), foram isolados e identificados. As estruturas destes compostos foram elucidadas por uma extensiva análise espectroscópica de RMN uni e bidimensional, UV, IV e dados de EM, além de comparação com dados da literatura. Os compostos isolados (1-4) foram avaliados quanto ao seu potencial sequestrador do radical DPPH• e apresentaram baixo poder antioxidante quando comparados ao antioxidante comercial trans-resveratrol.

Flavonoids from the leaves of Deguelia utilis (Leguminosae): structural elucidation and neuroprotective properties

Das folhas de Deguelia utilis foram isolados cinco flavonoides: 5,3'-di-hidróxi-4'-metóxi2'',2''-dimetilcromeno-(5'',6'':6,7)-di-hidroflavonol (1), 5,3'-di-hidróxi-7,4'-dimetóxi-6,8dimetilalil-di-hidroflavonol (2), 5,3'-di-hidróxi-4'-metóxi-8-prenil-2'',2''-dimetilcromeno(5'',6'':6,7)-flavanona (3), 5,3'-di-hidróxi-7,4'-dimetóxi-6,8-dimetilalil-flavanona (4), 3,5,3'-tri-hidróxi-7,4'-dimetóxi-6,8-dimetilalil-flavanol (5), juntamente com os estilbenos: 4-metoxilonchocarpeno (6) e lonchocarpeno (7). Suas estruturas químicas foram elucidadas com base nos seus dados de NMR (ressonância magnética nuclear) e HRESITOF-MS (espectrometria de massas de alta resolução por tempo de vôo, com ionização por eletrospray). Além disso, a fim de investigar o potencial efeito citoprotetor desses flavonoides, foi utilizada uma fração eluída com hexano:AcOEt contendo os sete flavonoides, em um modelo in vitro de neurodegeneração, utilizando culturas primárias do hipocampo de ratos neonatal (PND2-P3) expostos à rotenona, um inibidor mitocondrial do complexo I. Houve uma redução significativa da viabilidade celular (19,4 ± 1,6%), quando as culturas foram expostas à rotenona 30 nmol L^-1 por 72 h. A exposição concomitante das culturas a FR3 (5 µg mL^-1) e rotenona 30 nmol L^-1 resultou em valores de viabilidade celular semelhante ao grupo controle (99,6 ± 4,8%), sugerindo um efeito citoprotetor para essa fração.

Synthesis and Structural Elucidation of Triazolylmolybdenum(VI) Oxide Hybrids and Their Behavior as Oxidation Catalysts

A large family of bifunctional 1,2,4-triazole molecular tectons (tr) has been explored for engineering molybdenum(VI) oxide hybrid solids. Specifically, tr ligands bearing auxiliary basic or acidic groups were of the type amine, pyrazole, 1H-tetrazole, and 1,2,4-triazole. The organically templated molybdenum(VI) oxide solids with the general compositions [MoO3(tr)], [Mo2O6(tr)], and [Mo2O6(tr)(H2O)2] were prepared under mild hydrothermal conditions or by refluxing in water. Their crystal structures consist of zigzag chains, ribbons, or helixes of alternating cis-{MoO4N2} or {MoO5N} polyhedra stapled by short [N–N]-tr bridges that for bitriazole ligands convert the motifs into 2D or 3D frameworks. The high thermal (235–350 °C) and chemical stability observed for the materials makes them promising for catalytic applications. The molybdenum(VI) oxide hybrids were successfully explored as versatile oxidation catalysts with tert-butyl hydroperoxide (TBHP) or aqueous H2O2 as an oxygen source, at 70 °C. Catalytic performances were influenced by the different acidic–basic properties and steric hindrances of coordinating organic ligands as well as the structural dimensionality of the hybrid.

Structural elucidation and antisense properties of a sugar-modified DNA analogue

Antisense oligonucleotides deserve great attention as potential drug candidates for the treatment of genetic disorders. For example, muscle dystrophy can be treated successfully in mice by antisense-induced exon skipping in the pre-mRNA coding for the structural protein dystrophin in muscle cells. For this purpose a sugar- and backbone-modified DNA analogue was designed, in which a tricyclic ring system substitutes the deoxyribose. These chemical modifications stabilize the dimers formed with the targeted RNA relative to native nucleic acid duplexes and increase the biostability of the antisense oligonucleotide. While evading enzymatic degradation constitutes an essential property of antisense oligonucleotides for therapeutic application, it renders the oligonucleotide inaccessible to biochemical sequencing techniques and requires the development of alternative methods based on mass spectrometry. The set of sequences studied includes tcDNA oligonucleotides ranging from 10 to 15 nucleotides in length as well as their hybrid duplexes with DNA and RNA complements. All samples were analyzed on a LTQ Orbitrap XL instrument equipped with a nano-electrospray source. For tandem mass spectrometric experiments collision-induced dissociation was performed, using helium as collision gas. Mass spectrometric sequencing of tcDNA oligomers manifests the applicability of the technique to substrates beyond the scope of enzyme-based methods. Sequencing requires the formation of characteristic backbone fragments, which take the form of a-B- and w-ions in the product ion spectra of tcDNA. These types of product ions are typically associated with unmodified DNA, which suggests a DNA-like fragmentation mechanism in tcDNA. The loss of nucleobases constitutes the second prevalent dissociation pathway observed in tcDNA. Comparison of partially and fully modified oligonucleotides indicates a pronounced impact of the sugar-moiety on the base loss. As this event initiates cleavage of the backbone, the presented results provide new mechanistic insights into the fragmentation of DNA in the gas-phase. The influence of the sugar-moiety on the dissociation extends to tcDNA:DNA and tcDNA:RNA hybrid duplexes, where base loss was found to be much more prominent from sugar-modified oligonucleotides than from their natural complements. Further prominent dissociation channels are strand separation and backbone cleavage of the single strands, as well as the ejection of backbone fragments from the intact duplex. The latter pathway depends noticeably on the base sequence. Moreover, it gives evidence of the high stability of the hybrid dimers, and thus directly reflects the affinity of tcDNA for its target in the cell. As the cellular target of tcDNA is a pre-mRNA, the structure was designed to discriminate RNA from DNA complements, which could be demonstrated by mass spectrometric experiments.

Synthesis of novel O-acylated-D-ribono-1,5-lactones and structural assignment supported by conventional NOESY-NMR and x-ray analysis

A practical method for the structural assignment of 3,4-O-benzylidene-D-ribono-1,5-lactones and analogues using conventional NMR techniques and NOESY measurements in solution is described. 2-O-Acyl-3,4-O-benzylidene-D-ribono-1,5-lactones were prepared in good yields by acylation of Zinner’s lactone with acyl chlorides under mildly basic conditions. Structural determination of 2-O-(4-nitrobenzoyl)-3,4-O-benzylidene-D-ribono-1,5-lactone was achieved by single crystal x-ray diffraction, which supports the results based on spectroscopic data.

Computer-aided Structure Elucidation of Neolignans

This paper describes a new module of the expert system SISTEMAT used for the prediction of the skeletons of neolignans by (13)C NMR, (1)H NMR and botanical data obtained from the literature. SISTEMAT is composed of MACRONO, SISCONST, C13MACH, H1MACH and SISOCBOT programs, each analyzing data of the neolignan in question to predict the carbon skeleton of the compound. From these results, the global probability is computed and the most probable skeleton predicted. SISTEMAT predicted the skeletons of 75% of the 20 neolignans tested, in a rapid and simple procedure demonstrating its advantage for the structural elucidation of new compounds.

Molecular approaches for structural characterization of Bothrops L-amino acid oxidases with antiprotozoal activity: cDNA cloning, comparative sequence analysis, and molecular modeling

Two L-amino acid oxidases (LAAOs) were identified by random sequencing of cDNA libraries from the venom glands of Bothrops moojeni (BmooLAAO) and Bothrops jararacussu (Bjussu LAAO). Phylogenetic analysis involving other SV-LAAOs showed sequence identities within the range 83-87% being closely related to those from Agkistrodon and Trimeresurus. Molecular modeling experiments indicated the FAD-binding, substrate-binding, and helical domains of Bmoo and Bjussu LAAOs. The RMS deviations obtained by the superposition of those domains and that from Calloselasma rhodostoma LAAO crystal structure confirm the high degree of structural similarity between these enzymes. Purified BjussuLAAO-I and BmooLAAO-I exhibited antiprotozoal activities which were demonstrated to be hydrogen-peroxide mediated. This is the first report on the isolation and identification of cDNAs encoding LAAOs from Bothrops venom. The findings here reported contribute to the overall structural elucidation of SV-LAAOs and will advance the understanding on their mode of action. (c) 2006 Elsevier B.V. All rights reserved.

Structural characterization of a new acylpolyaminetoxin from the venom of Brazilian garden spider Nephilengys cruentata

Mario Sergio Palma, Yasuhiro Itagaki, Tsuyoshi Fujita, Hideo Naoki and Terumi Nakajima. Structural characterization of a new acylpolpaminetoxin from the venom of Brazilian garden spider Nephilengys: cruentata. Toxicon 36, 455-493, 1998.-The use of mass spectrometry, in which high-energy CID and charge remote fragmentation both of protonated and sodium-attached molecular ions was applied, afforded the structural elucidation of a new acylgolyaminetoxin with M-W= 801 da from the venom of the Brazilian garden spider Nephilengys cruentata. In spite of having the same M-W of the NPTX-2, previously described in the venom of the Joro spider Nephila clavata, neither toxins are isomers. In order to differentiate them by using the most usual nomenclature, the new toxin was named NPTX-801C and the NPTX-2 was renamed to NPTX-801E. Both toxins have as common structure the 4-hydroxyindole-3-acetyl-asparaginyl-cadaveryl moiety in their molecules and their structure may be represented in a simplified way: NPTX-801E is HO-indole-Asn-Cad-Pta-Orn-Arg and NPTX-801C is HO-indole-Asn-Cad-Gly-Put-Pta-Pta. (C) 1998 Elsevier B.V. Ltd. All rights reserved.

Structural and Interaction Studies of Bacterial Polysaccharides by NMR Spectroscopy

An introduction to bacterial polysaccharides and the methods for structural determination are described in the first two parts of the thesis. In a structural elucidation of bacterial polysaccharides NMR experiments are important as is component analysis. A short description of immunochemical methods such as enzyme immunoassays is included. Two NMR techniques used for interaction studies, trNOE and STD NMR, are also discussed. The third part of the thesis discusses and summarizes the results from the included papers. The structures of the exopolysaccharides produced by two lactic acid bacteria are determined by one- and two dimensional NMR experiments. One is a heteropolysaccharide produced by Streptococcus thermophilus and the other a homopolysaccharide produced by Propionibacterium freudenreichii. The structure of an acidic polysaccharide from a marine bacterium with two serine residues in the repeating unit is also investigated. The structural and immunological relationship between two O-antigenic polysaccharides from Escherichia coli strain 180/C3 and O5 is discussed and investigated. Finally, interaction studies of an octasaccharide derived from the Salmonella enteritidis O-antigen and a bacteriophage are described which were performed with NMR experiments.

Further sesquiterpene lactones from viguiera robusta and the potential anti-inflammatory activity of a heliangolide: Inhibition of human neutrophil elastase release

In addition to known heliangolides, a new eudesmanolide was isolated from the leaf rinse extract of Viguiera robusta (Asteraceae). Structural elucidation was based oil spectral analysis. It is the first report on eudesmanolides in members of the subgenus Calanticaria of Viguiera. In this work, the main isolated compound, the furanoheliangolide budlein A, besides its previously, reported in vitro and in vivo anti-inflammatory activities, inhibited human neutrophil elastase release. The inhibition was at the concentration of (16.83 +/- 1.96) mu M for formylated bacterial tripeptide (fMLP) stimulation and (11.84 +/- 1.62) mu M for platelet aggregation factor (PAF) stimulation, being slightly less active than the reference drug parthenolide. The results are important to demonstrate the potential anti-inflammatory activities of sesquiterpene lactones and corroborate the previous studies using other targets.