RESUMO
In nature, the vast majority of sesquiterpenes are produced by type I mechanisms, and glycosylated sesquiterpenes are rare in actinobacteria. Streptomyces olindensis DAUFPE 5622 produces the sesquiterpenes olindenones A-G, a new class of rearranged drimane sesquiterpenes. Olindenones B-D are oxygenated derivatives of olindenone A, while olindenones E-G are analogs glycosylated with dideoxysugars. 13C-isotope labeling studies demonstrated olindenone A biosynthesis occurs via the methylerythritol phosphate (MEP) pathway and suggested the rearrangement is only partially concerted. Based on the structures, one potential mechanism of olindenone A formation proceeds by cyclization of the linear terpenoid precursor, likely occurring via a terpene cyclase-mediated type II mechanism whereby the terminal alkene of the precursor is protonated, triggering carbocation-driven cyclization followed by rearrangement. Diphosphate hydrolysis may occur either before or after cyclization. Although a biosynthetic route is proposed, the terpene cyclase gene responsible for producing olindenones currently remains unidentified.
Assuntos
Sesquiterpenos , Streptomyces , Sesquiterpenos/química , Terpenos/metabolismo , Streptomyces/metabolismo , CiclizaçãoRESUMO
INTRODUCTION: We developed Data Base similarity (DBsimilarity), a user-friendly tool designed to organize structure databases into similarity networks, with the goal of facilitating the visualization of information primarily for natural product chemists who may not have coding experience. METHOD: DBsimilarity, written in Jupyter Notebooks, converts Structure Data File (SDF) files into Comma-Separated Values (CSV) files, adds chemoinformatics data, constructs an MZMine custom database file and an NMRfilter candidate list of compounds for rapid dereplication of MS and 2D NMR data, calculates similarities between compounds, and constructs CSV files formatted into similarity networks for Cytoscape. RESULTS: The Lotus database was used as a source for Ginkgo biloba compounds, and DBsimilarity was used to create similarity networks including NPClassifier classification to indicate biosynthesis pathways. Subsequently, a database of validated antibiotics from natural products was combined with the G. biloba compounds to identify promising compounds. The presence of 11 compounds in both datasets points to possible antibiotic properties of G. biloba, and 122 compounds similar to these known antibiotics were highlighted. Next, DBsimilarity was used to filter the NPAtlas database (selecting only those with MIBiG reference) to identify potential antibacterial compounds using the ChEMBL database as a reference. It was possible to promptly identify five compounds found in both databases and 167 others worthy of further investigation. CONCLUSION: Chemical and biological properties are determined by molecular structures. DBsimilarity enables the creation of interactive similarity networks using Cytoscape. It is also in line with a recent review that highlights poor biological plausibility and unrealistic chromatographic behaviors as significant sources of errors in compound identification.
Assuntos
Produtos Biológicos , Produtos Biológicos/química , Espectroscopia de Ressonância Magnética/métodos , Bases de Dados Factuais , Extratos Vegetais/química , AntibacterianosRESUMO
Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether they can prevent mortality and the underlying host response mechanisms remains elusive. Here, we conducted omics analyses on the coral Mussismilia hispida exposed to bleaching conditions in a long-term mesocosm experiment and inoculated with a selected BMC consortium or a saline solution placebo. All corals were affected by heat stress, but the observed "post-heat stress disorder" was mitigated by BMCs, signified by patterns of dimethylsulfoniopropionate degradation, lipid maintenance, and coral host transcriptional reprogramming of cellular restructuration, repair, stress protection, and immune genes, concomitant with a 40% survival rate increase and stable photosynthetic performance by the endosymbiotic algae. This study provides insights into the responses that underlie probiotic host manipulation. We demonstrate that BMCs trigger a dynamic microbiome restructuring process that instigates genetic and metabolic alterations in the coral host that eventually mitigate coral bleaching and mortality.
Assuntos
Antozoários , Transtornos de Estresse por Calor , Microbiota , Animais , Antozoários/genética , Recifes de Corais , Resposta ao Choque Térmico/genética , SimbioseRESUMO
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
Assuntos
Metabolômica , Teoria QuânticaRESUMO
Fermented aqueous extracts of Viscum album L. are widely used for cancer treatment in complementary medicine. The high molecular weight compounds viscotoxins and lectins are considered to be the main active substances in the extracts. However, a vast number of small molecules (≤1500 Da) is also expected to be present, and few studies have investigated their identities. In this study, a comprehensive metabolome analysis of samples of fermented aqueous extracts of V. album from two host tree species (Malus domestica and Pinus sylvestris), both prepared by two pharmaceutical manufacturing processes, was performed by liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS). A total of 212 metabolites were putatively annotated, including primary metabolites (e.g., amino acids, organic acids, etc.) and secondary metabolites (mostly phenolic compounds). A clear separation between V. album samples according to the host tree species, but not due to manufacturing processes, was observed by principal component analysis. The biomarkers responsible for this discrimination were assessed by partial least squares-discriminant analysis. Because V. album extracts from different host trees have different clinical applications, the present work highlights the possibility of characterizing the metabolome for identification and traceability of V. album fermented aqueous extracts.
Assuntos
Fermentação , Metaboloma , Metabolômica , Extratos Vegetais/metabolismo , Espectrometria de Massas em Tandem , Viscum album/metabolismo , Cromatografia Líquida , Análise Discriminante , Análise dos Mínimos Quadrados , Análise Multivariada , Análise de Componente PrincipalRESUMO
INTRODUCTION: Molecular networks are now established as the method of choice for tandem mass spectrometry dereplication and similarity-based structure elucidation. Node identification can be used to start the propagation of the structure elucidation of unknown compounds progressively. OBJECTIVE: To demonstrate the capabilities of using the LipidXplorer data results along with molecular networking to identify nodes and aid sequential structure elucidation of unknown compounds. MATERIAL AND METHODS: Molecular fragmentation query language (MFQL) files were written to identify glycoalkaloids based on known structures described for Solanum species. A dataset generated from liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis of Solanum pseudoquina sample were submitted to dereplication on both LipidXplorer software and Global Natural Products Social Molecular Network (GNPS) online system. The resulting attribute table from GNPS calculations was merged with the LipidXplorer results and this merged file was used for network visualisation in Cytoscape. Nodes in the molecular network were labelled using the LipidXplorer identifiers, thus assisting the structure elucidation of unidentified compounds. RESULTS: The combination of the LipidXplorer glycoalkaloids list and GNPS analysis was used in Cytoscape to label nodes in the molecular network. The analysis of the network using these labelled starting points triggered the structure elucidation of closely related nodes leading to the identification of 30 compounds using the LipidXplorer output and four purified and structure elucidated compounds, including a new glycoalkaloids identified as 3-O-(ß-d-xylopyranosyl)-(20R,25S)-22,26-epimino-16-acetyl-cholesta-5,22(N)-diene. CONCLUSION: A significant compound identification completely based on molecular formula and fragmentation queries was achieved. This new and effective approach could help researches to expand the identification rate of compounds in dereplication studies using molecular networks.
Assuntos
Alcaloides/química , Bases de Dados Factuais , Lipídeos/química , Solanum/química , Espectroscopia de Ressonância Magnética Nuclear de Carbono-13 , Cromatografia Líquida/métodos , Estrutura Molecular , Estudo de Prova de Conceito , Espectroscopia de Prótons por Ressonância Magnética , Espectrometria de Massas em Tandem/métodosRESUMO
Athenaea (Solanaceae) is an endemic genus belonging to the Brazilian Atlantic Rainforest. Recently, botanical investigations suggested the re-evaluation of the generic status of the genus Athenaea as a synonym of Aureliana. In this study, the first investigation of the Athenaea genus performed on Athenaea martiana by means of HPLC-HR-MS-SPE-NMR combined with high-resolution radical scavenging profile led to identification of several phenolic acids as radical scavengers: protocatechuic acid (1), 4-hydroxybenzoic acid (2), caffeic acid (3), vanillic acid (4), and ferulic acid (6). Additional analysis revealed a new steroidal lactone, named athenolide A (9). Their structures were elucidated by extensive use of NMR spectroscopy as well as HR-MS. Chemotaxonomic considerations based on these results supported the chemical relationships between the Athenaea and Aureliana genera, in agreement with the recent botanical findings.
Assuntos
Lactonas/química , Extratos Vegetais/química , Folhas de Planta/química , Solanaceae/química , Extração em Fase Sólida , Esteroides/química , Cromatografia Líquida de Alta Pressão , Lactonas/isolamento & purificação , Espectroscopia de Ressonância Magnética , Espectrometria de Massas , Estrutura Molecular , Extratos Vegetais/isolamento & purificação , Esteroides/isolamento & purificaçãoRESUMO
Solanum americanum is one of the most prominent species used to treat type 2 diabetes in Guatemala. In our ongoing efforts to find antidiabetic and antioxidative compounds from natural sources, an ethyl acetate extract of this medicinal herb was investigated using dual high-resolution α-glucosidase/radical scavenging inhibition profiling. The high-resolution biochromatograms obtained by this technique were used to target subsequent structural elucidation by HPLC-HRMS-SPE-NMR analysis towards the bioactive constituents. This led to identification of 4-hydroxybenzoic acid (1) and 3-indolecarboxylic acid (6) associated with radical scavenging activity, and the amide alkaloids N-trans-p-coumaroyloctopamine (3), N-trans-p-feruloyloctopamine (4), N-trans-p-coumaroyltyramine (8) and N-trans-p-feruloyltyramine (9) correlated with α-glucosidase inhibitory activity as well as radical scavenging activity. Further analysis revealed a new lactone, methyl 5-ethyl-4-hydroxy-5-methyl-2-oxotetrahydro-2H-pyran-4-carboxylate (7) and a new steroid with a rare F ring (11). Corchorifatty acid B (12) was reported for the first time in the Solanaceae family. Their structures were elucidated by extensive use of 1D and 2D NMR spectroscopy as well as HRMS analysis.
Assuntos
Sequestradores de Radicais Livres/química , Inibidores de Glicosídeo Hidrolases/química , Solanum/química , Cromatografia Líquida de Alta Pressão , Sequestradores de Radicais Livres/isolamento & purificação , Inibidores de Glicosídeo Hidrolases/isolamento & purificação , Espectroscopia de Ressonância Magnética , Estrutura Molecular , Componentes Aéreos da Planta/química , Extratos Vegetais/química , Plantas Medicinais/química , alfa-Glucosidases/metabolismoRESUMO
(-)-Centratherin is a bioactive sesquiterpenoid lactone, whose absolute configuration (AC) was not established, but has been proposed based on those of germacrane precursors. To verify this proposal, the experimental electronic circular dichroism (ECD), electronic dissymmetry factor (EDF), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and vibrational dissymmetry factor (VDF) spectra of (-)-centratherin have been analyzed with the corresponding density functional theoretical predictions. These analyses suggest the AC of naturally occurring (-)-centratherin to be (6R,7R,8S,10R,2'Z).
Assuntos
Lactonas/química , Sesquiterpenos/química , Dicroísmo Circular , Lactonas/farmacologia , Modelos Químicos , Estrutura Molecular , Ressonância Magnética Nuclear Biomolecular , Dispersão Óptica Rotatória , Sesquiterpenos/farmacologia , EstereoisomerismoRESUMO
3-Ishwarone, (1), a sesquiterpene with a rare ishwarane skeleton, was isolated from Peperomia scandens Ruiz & Pavon (Piperaceae). Its structure was unambiguously determined by 1D- and 2D-NMR and infrared analyses, as well as by comparative theoretical studies which involved calculations of 13C-NMR chemical shifts, using the Density Functional Theory (DFT) with the mPW1PW91 hybrid functional and Pople's 6-31G(d) basis set, and of vibrational frequencies, using the B3LYP hybrid functional and triple ζ Dunning's correlation consistent basis set (cc-pVTZ), of (1) and three of its possible diastereomers, compounds 2-4.