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1.
Environ Sci Technol ; 57(15): 6238-6247, 2023 04 18.
Artículo en Inglés | MEDLINE | ID: mdl-37018345

RESUMEN

Direct comparison of high-resolution mass spectrometry (HRMS) data acquired with different instrumentation or parameters remains problematic as the derived lists of molecular species via HRMS, even for the same sample, appear distinct. This inconsistency is caused by inherent inaccuracies associated with instrumental limitations and sample conditions. Hence, experimental data may not reflect a corresponding sample. We propose a method that classifies HRMS data based on the differences in the number of elements between each pair of molecular formulae within the formulae list to preserve the essence of the given sample. The novel metric, formulae difference chains expected length (FDCEL), allowed for comparing and classifying samples measured by different instruments. We also demonstrate a web application and a prototype for a uniform database for HRMS data serving as a benchmark for future biogeochemical and environmental applications. FDCEL metric was successfully employed for both spectrum quality control and examination of samples of various nature.


Asunto(s)
Espectrometría de Masas , Espectrometría de Masas/métodos
2.
Plants (Basel) ; 12(3)2023 Jan 26.
Artículo en Inglés | MEDLINE | ID: mdl-36771648

RESUMEN

Prostate cancer (PCa) is one of the most common male malignancies worldwide. In the current study, we evaluated the effects of a natural deep eutectic solvent (NADES) extract of Pueraria lobata roots rich in isoflavones (ISF) and Phaffia rhodozyma extract rich in astaxanthin (ASX) on an N-methyl-N-nitrosourea plus testosterone PCa model in rats. ISF consisted of puerarin, daidzein, genistein, formononetin and other polyphenols, while ASX contained lipids and unsaturated species in addition to astaxanthin. Extracts were administered through a whole promotion period in daily doses shown by our group to successfully inhibit benign prostate hyperplasia (BPH) development - 200 mg/kg for ISF and 25 mg/kg for ASX. Though a similar effect was found for BPH processes accompanying PCa induction, the incidence of PCa in animals treated with placebo, ISF and ASX was 37%, 37% and 41%, respectively, showing no chemopreventive activity of ISF and ASX. PCa development was associated with a decrease in the Ca/Mg ratio in serum and an increase in prostate tissue. Treatment with both extracts produced a normalization effect on Ca balance in serum, which, combined with a decrease in the prostatic index, suggests some positive health effects of ISF and ASX.

3.
Int J Mol Sci ; 23(24)2022 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-36555683

RESUMEN

Chronic liver diseases affect more than 1 billion people worldwide and represent one of the main public health issues. Nonalcoholic fatty liver disease (NAFLD) accounts for the majority of mortal cases, while there is no currently approved therapeutics for its treatment. One of the prospective approaches to NAFLD therapy is to use a mixture of natural compounds. They showed effectiveness in alleviating NAFLD-related conditions including steatosis, fibrosis, etc. However, understanding the mechanism of action of such mixtures is important for their rational application. In this work, we propose a new dereplication workflow for deciphering the mechanism of action of the lignin-derived natural compound mixture. The workflow combines the analysis of molecular components with high-resolution mass spectrometry, selective chemical tagging and deuterium labeling, liver tissue penetration examination, assessment of biological activity in vitro, and computational chemistry tools used to generate putative structural candidates. Molecular docking was used to propose the potential mechanism of action of these structures, which was assessed by a proteomic experiment.


Asunto(s)
Aprendizaje Profundo , Enfermedad del Hígado Graso no Alcohólico , Humanos , Enfermedad del Hígado Graso no Alcohólico/tratamiento farmacológico , Lignina/farmacología , Polifenoles/farmacología , Polifenoles/uso terapéutico , Polifenoles/análisis , Proteómica , Simulación del Acoplamiento Molecular , Espectrometría de Masas
4.
J Agric Food Chem ; 70(23): 7122-7129, 2022 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-35649262

RESUMEN

Due to the ever-increasing demand for healthy and safe food, much attention has been gained by natural food colorants. This study showed the culture fluid extract of the fungus Aspergillus cavernicola VKM F-906 to contain red pigment and monasnicotinic acid (MNA) in predominant amounts. The structure of the pigment corresponded to cis-cavernamine (red pigment, RP). Two tautomers, NH and OH forms, in rapid equilibrium were present in a solution of RP. The critical factors for RP to form were the presence of NH4+ salt and pH 6.3-6.5. In vitro experiments showed that MNA was synthesized from RP as a result of chemical transformations without the participation of enzymes. In this case, the main influence on the reaction rate is exerted by the pH of the medium, which is associated with the keto-enol tautomerism of RP in solution. The culture broth extract and MNA exhibited antifungal activity against Fusarium fungi.


Asunto(s)
Hongos , Pigmentos Biológicos , Aspergillus , Benzopiranos , Pigmentos Biológicos/química , Pigmentos Biológicos/farmacología , Extractos Vegetales
5.
Sci Total Environ ; 843: 157009, 2022 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-35772561

RESUMEN

In land-based recirculating aquaculture systems (RAS), the accumulation of dissolved organic matter (DOM) can have detrimental effects on water quality impacting the system performance, microbial community, and consequently fish health and welfare. Ozone is used in the RAS water treatment process to improve water quality and remove DOM. However, little is known about the molecular composition of DOM in RAS and its transformation when exposed to ozone. In this study, we performed a detailed molecular characterization of DOM in RAS and explored its transformation induced by ozonation of RAS waters. Ultra-high resolution (UHR) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) was used to characterize the DOM matrix of RAS waters (pump-sump and tanks) and to evaluate its transformation by ozonation. The analysis of DOM extracted from makeup water and feed samples allowed for the determination of DOM sources in RAS prior to ozonation. The CHO and unsaturated group of compounds were the most abundant class found in water samples. On the contrary, the DOM from feed samples was unique and consisted mainly of CHO, CHON and unsaturated group of compounds. After the ozonation of RAS waters, humic-like and unsaturated compounds [positive oxygen subtracted double bond equivalent per carbon (DBE-O)/C)] were decomposed, particularly the CHO-DOM that contained fewer -CH2- features. Fulvic-like compounds and several hundred saturated compounds [negative (DBE-O)/C)] were formed post ozonation, particularly the CHON and CHONS group of compounds that were associated with fish diets, makeup waters and transformation products from the ozonation of the RAS waters. This study showed that the high accuracy of the ultra-high resolution FTICR MS can be applied to characterize and monitor the changes of DOM at a molecular level in RAS waters. To our knowledge, this is the first study where FTICR MS was incorporated for the characterization of DOM and its sources in RAS.


Asunto(s)
Ozono , Animales , Acuicultura , Ciclotrones , Materia Orgánica Disuelta , Análisis de Fourier , Espectrometría de Masas
6.
ACS Omega ; 7(11): 9710-9719, 2022 Mar 22.
Artículo en Inglés | MEDLINE | ID: mdl-35350354

RESUMEN

Dissociation induced by the accumulation of internal energy via collisions of ions with neutral molecules is one of the most important fragmentation techniques in mass spectrometry (MS), and the identification of small singly charged molecules is based mainly on the consideration of the fragmentation spectrum. Many research studies have been dedicated to the creation of databases of experimentally measured tandem mass spectrometry (MS/MS) spectra (such as MzCloud, Metlin, etc.) and developing software for predicting MS/MS fragments in silico from the molecular structure (such as MetFrag, CFM-ID, CSI:FingerID, etc.). However, the fragmentation mechanisms and pathways are still not fully understood. One of the limiting obstacles is that protomers (positive ions protonated at different sites) produce different fragmentation spectra, and these spectra overlap in the case of the presence of different protomers. Here, we are proposing to use a combination of two powerful approaches: computing fragmentation trees that carry information of all consecutive fragmentations and consideration of the MS/MS data of isotopically labeled compounds. We have created PyFragMS-a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and/or 16O/18O exchange) and a collection of instruments for computing fragmentation trees for an arbitrary molecule. Using PyFragMS, we investigated how the site of protonation influences the fragmentation pathway for small molecules. Also, PyFragMS offers capabilities for performing database search when MS/MS data of the isotopically labeled compounds are taken into account.

7.
Environ Sci Technol ; 56(4): 2729-2737, 2022 02 15.
Artículo en Inglés | MEDLINE | ID: mdl-35084826

RESUMEN

Natural organic matter (NOM) components measured with ultrahigh-resolution mass spectrometry (UHRMS) are often assessed by molecular formula-based indices, particularly related to their aromaticity, which are further used as proxies to explain biogeochemical reactivity. An aromaticity index (AI) is calculated mostly with respect to carboxylic groups abundant in NOM. Here, we propose a new constrained AIcon based on the measured distribution of carboxylic groups among individual NOM components obtained by deuteromethylation and UHRMS. Applied to samples from diverse sources (coal, marine, peat, permafrost, blackwater river, and soil), the method revealed that the most probable number of carboxylic groups was two, which enabled to set a reference point n = 2 for carboxyl-accounted AIcon calculation. The examination of the proposed AIcon showed the smallest deviation to the experimentally determined index for all NOM samples under study as well as for individual natural compounds obtained from the Coconut database. In particular, AIcon performed better than AImod for all compound classes in which aromatic moieties are expected: aromatics, condensed aromatics, and unsaturated compounds. Therefore, AIcon referenced with two carboxyl groups is preferred over conventional AI and AImod for biogeochemical studies where the aromaticity of compounds is important to understand the transformations and fate of NOM compounds.


Asunto(s)
Compuestos Orgánicos , Suelo , Carbón Mineral , Sustancias Húmicas , Espectrometría de Masas , Ríos
8.
J Am Soc Mass Spectrom ; 33(2): 390-398, 2022 Feb 02.
Artículo en Inglés | MEDLINE | ID: mdl-35077167

RESUMEN

LC-MS is a key technique for the identification of small molecules in complex samples. Accurate mass, retention time, and fragmentation spectra from LC-MS experiments are compared to reference values for pure chemical standards. However, this information is often unavailable or insufficient, leading to an assignment to a list of candidates instead of a single hit; therefore, additional features are desired to filter candidates. One such promising feature is the number of specific functional groups of a molecule that can be counted via derivatization or isotope-exchange techniques. Hydrogen/deuterium exchange (HDX) is the most widespread implementation of isotope exchange for mass spectrometry, while oxygen 16O/18O exchange is not applied as frequently as HDX. Nevertheless, it is known that some functional groups may be selectively exchanged in 18O enriched media. Here, we propose an implementation of 16O/18O isotope exchange to highlight various functional groups. We evaluated the possibility of using the number of exchanged oxygen atoms as a descriptor to filter database candidates in untargeted LC-MS-based workflows. It was shown that 16O/18O exchange provides 62% (median, n = 45) search space reduction for a panel of drug molecules. Additionally, it was demonstrated that studying the fragmentation spectra after 16O/18O can aid in eliminating false positives and, in some cases, help to annotate fragments formed with water traces in the collisional cell.

9.
ACS Omega ; 6(37): 23873-23883, 2021 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-34568667

RESUMEN

Antimicrobial resistance is a global threat. The use of biologically active natural products alone or in combination with the clinically proven antimicrobial agents might be a useful strategy to fight the resistance. The scientific hypotheses of this study were twofold: (1) the natural humic substances rich in dicarboxyl, phenolic, heteroaryl, and other fragments might possess inhibitory activity against ß-lactamases, and (2) this inhibitory activity might be linked to the molecular composition of the humic ensemble. To test these hypotheses, we used humic substances (HS) from different sources (coal, peat, and soil) and of different fractional compositions (humic acids, hymatomelanic acids, and narrow fractions from solid-phase extraction) for inhibiting serine ß-lactamase TEM-1. Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) was used to characterize the molecular composition of all humic materials used in this study. The kinetic assay with chromogenic substrate CENTA was used for assessment of inhibitory activity. The inhibition data have shown that among all humic materials tested, a distinct activity was observed within apolar fractions of hymatomelanic acid isolated from lignite. The decrease in the hydrolysis rate in the presence of most active fractions was 42% (with sulbactam-87%). Of particular importance is that these very fractions caused a synergistic effect (2-fold) for the combinations with sulbactam. Linking the observed inhibition effects to molecular composition revealed the preferential contribution of low-oxidized aromatic and acyclic components such as flavonoid-, lignin, and terpenoid-like molecules. The binding of single low-molecular-weight components to the cryptic allosteric site along with supramolecular interactions of humic aggregates with the protein surface could be considered as a major contributor to the observed inhibition. We believe that fine fractionation of hydrophobic humic materials along with molecular modeling studies on the interaction between humic molecules and ß-lactamases might contribute to the development of novel ß-lactamase inhibitors of humic nature.

10.
Environ Sci Technol ; 55(15): 10365-10377, 2021 08 03.
Artículo en Inglés | MEDLINE | ID: mdl-34260209

RESUMEN

Humification is a ubiquitous natural process of biomass degradation that creates multicomponent systems of nonliving organic matter, including dissolved organic matter (DOM) and humic substances (HS) in water environments, soils, and organic rocks. Despite significant differences in molecular composition, the optical properties of DOM and HS are remarkably similar, and the reason for this remains largely unknown. Here, we employed fluorescence spectroscopy with (sub)picosecond resolution to elucidate the role of electronic interactions within DOM and HS. We revealed an ultrafast decay component with a characteristic decay lifetime of 0.5-1.5 ps and spectral diffusion originating from excitation energy transfer (EET) in the system. The rate of EET was positively correlated to the fraction of aromatic species and tightness of aromatic species packing. Diminishing the number of EET donor-acceptor pairs by reduction with NaBH4 (decrease of the acceptor number), decrease of pH (decrease of the electron-donating ability), or decrease of the average particle size by filtration (less donor-acceptor pairs within a particle) resulted in a lower impact of the ultrafast component on fluorescence decay. Our results uncover the role of electronic coupling among fluorophores in the formation of DOM and HS optical properties and provide a framework for studying photophysical processes in heterogeneous systems of natural fluorophores.


Asunto(s)
Sustancias Húmicas , Suelo , Biomasa , Transferencia de Energía , Sustancias Húmicas/análisis , Espectrometría de Fluorescencia
11.
Angew Chem Int Ed Engl ; 60(34): 18694-18703, 2021 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-34009717

RESUMEN

We report a novel family of natural lipoglycopeptides produced by Streptomyces sp. INA-Ac-5812. Two major components of the mixture, named gausemycins A and B, were isolated, and their structures were elucidated. The compounds are cyclic peptides with a unique peptide core and several remarkable structural features, including unusual positions of d-amino acids, lack of the Ca2+ -binding Asp-X-Asp-Gly (DXDG) motif, tyrosine glycosylation with arabinose, presence of 2-amino-4-hydroxy-4-phenylbutyric acid (Ahpb) and chlorinated kynurenine (ClKyn), and N-acylation of the ornithine side chain. Gausemycins have pronounced activity against Gram-positive bacteria. Mechanistic studies highlight significant differences compared to known glyco- and lipopeptides. Gausemycins exhibit only slight Ca2+ -dependence of activity and induce no pore formation at low concentrations. Moreover, there is no detectable accumulation of cell wall biosynthesis precursors under treatment with gausemycins.


Asunto(s)
Lipoglucopéptidos/aislamiento & purificación , Streptomyces/química , Lipoglucopéptidos/química , Conformación Molecular
12.
Bioresour Technol ; 335: 125229, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-34010738

RESUMEN

The process of kraft lignin modification by the white-rot fungus Trametes hirsuta was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS), and groups of systematically changing compounds were delineated. In the course of cultivation, fungus tended to degrade progressively more reduced compounds and produced more oxidized ones. However, this process was not gradual - the substantial discontinuity was observed between 6th and 10th days of cultivation. Simultaneously, the secretion of ligninolytic peroxidases by the fungus was changing in a cascade manner - new isoenzymes were added to the mixture of the already secreted ones, and once new isoenzyme appeared both its relative quantity and number of isoforms increased as cultivation proceeded. It was proposed, that the later secreted peroxidases (MnP7 and MnP1) possess higher substrate affinity for some phenolic compounds and act in more specialized manner than the early secreted ones (MnP5 and VP2).


Asunto(s)
Lignina , Trametes , Peroxidasas , Polyporaceae , Proteoma
13.
Sci Rep ; 11(1): 7410, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33795703

RESUMEN

Despite broad application of different analytical techniques for studies on organic matter of chondrite meteorites, information about composition and structure of individual compounds is still very limited due to extreme molecular diversity of extraterrestrial organic matter. Here we present the first application of isotopic exchange assisted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for analysis of alkali extractable fraction of insoluble organic matter (IOM) of the Murchison and Allende meteorites. This allowed us to determine the individual S-containing ions with different types of sulfur atoms in IOM. Thiols, thiophenes, sulfoxides, sulfonyls and sulfonates were identified in both samples but with different proportions, which contribution corroborated with the hydrothermal and thermal history of the meteorites. The results were supported by XPS and thermogravimetric analysis coupled to FTICR MS. The latter was applied for the first time for analysis of chondritic IOM. To emphasize the peculiar extraterrestrial origin of IOM we have compared it with coal kerogen, which is characterized by the comparable complexity of molecular composition but its aromatic nature and low oxygen content can be ascribed almost exclusively to degradation of biomacromolecules.

14.
Environ Res ; 193: 110312, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33065073

RESUMEN

Natural products, such as humic substances (HS) and shilajit, are known to possess antiviral activity. Humic-like components are often called as carriers of biological activity of shilajit. The goal of this study was to evaluate anti-HIV activity of well characterized HS isolated from coal, peat, and peloids, and compare it to that of water-soluble organic matter (OM) isolated from different samples of Shilajit. The set of humic materials included 16 samples of different fractional composition: humic acid (HA), hymatomelanic acid (HMA), fulvic acid (FA). The set of shilajit OM included 19 samples of different geographic origin and level of alteration. The HIV-1 p24 antigen assay and cell viability test were used for assessment of antiviral activity. The HIV-1 Bru strain was used to infect CEM-SS cells. The obtained EC50 values varied from 0.37 to 1.4 mg L-1 for the humic materials, and from 14 to 142 mg L-1 for the shilajit OM. Hence, all humic materials used in this study outcompeted largely the shilajit materials with respect to anti-HIV activity: For the humic materials, the structure-activity relationships revealed strong correlation between the EC50 values and the content of aromatic carbon indicating the most important role of aromatic structures. For shilajit OM, the reverse relationship was obtained indicating the different mechanism of shilajit activity. The FTICRMS molecular assignments were used for ChEMBL data mining in search of the active humic molecules. As potential carriers of antiviral activity were identified aromatic structures with alkyl substituents, terpenoids, N-containing analogs of typical flavonoids, and aza-podophyllotoxins. The conclusion was made that the typical humic materials and Shilajit differ greatly in molecular composition, and the humic materials have substantial preferences as a natural source of antiviral agents as compared to shilajit.


Asunto(s)
VIH-1 , Sustancias Húmicas , Antivirales/farmacología , Benzopiranos/farmacología , Sustancias Húmicas/análisis , Minerales , Resinas de Plantas , Suelo
15.
Anal Chem ; 92(13): 9032-9038, 2020 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-32484343

RESUMEN

Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides a unique opportunity for molecular analysis of natural complex mixtures. In many geochemical and environmental studies structure-propertry relations are based solely on the elemental compositional information. Several calculated parameters were proposed to increase reliability of structural attribution, among which aromaticity indices (AI and AImod) are widely used. Herein, we applied a combination of selective labeling reactions in order to obtain direct structural information on the individual components of lignin-derived polyphenolic material. Carboxylic (COOH), carbonyl (C═O), and hydroxyl (OH) groups were enumerated by esterification, reducing, and acetylation reactions, respectively, followed by FTICR MS analyses. Obtained information was enabled to constrain aromaticity accounting for the carbon skeleton only. We found that actual aromaticity of components may be both higher or lower than approximated values depending on the abundance of COOH, C═O, and OH groups. The results are of importance for the geochemical community studying terrestrial NOM with structural gradients.

16.
Rapid Commun Mass Spectrom ; 34(18): e8850, 2020 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-32492216

RESUMEN

Complex plant-derived polyphenols are promising for biomedical application. Their high complexity prevents the use of conventional pharmacopoeia techniques to perform quality control. The goal of this study was to apply ultra-high-resolution mass spectrometry to evaluate the batch-to-batch consistency of the molecular composition of a polyphenolic ligand using appropriate statistical metrics. METHODS: Polyphenols were obtained by hydrolyzed-lignin oxidation. Manufacturing was performed under a range of reaction conditions: heating cycles, oxygen flows, purification. Direct-injection Fourier transform ion cyclotron resonance mass spectrometry (DI FTICR-MS) was applied to analyze reaction products. For pairwise comparison Jaccard and Tanimoto similarities calculations were proposed. In addition, principal component analysis (PCA) was applied for sample grouping based on the molecular class contributions. RESULTS: FTICR-MS analysis revealed moderate Jaccard similarity of products synthesized under the same conditions, which shared about 50% of the formulae calculated in each sample. The intensity-based Tanimoto index indicated high similarity of major components distribution of samples synthesized under standard conditions, while products obtained with variations in synthetic conditions were significantly different. PCA of molecular class contributions showed similar grouping with a high cumulative score. CONCLUSIONS: FTICR-MS provides robust metrics for the examination of batch-to-batch consistency of synthetic polyphenol materials. This approach can be proposed for the analysis of reference samples and for development of complementary methods for quality control of medicinal agents based on various biologically active matrices.


Asunto(s)
Espectrometría de Masas/métodos , Plantas/química , Polifenoles/análisis , Espectroscopía Infrarroja por Transformada de Fourier/métodos , Fitoquímicos/análisis
17.
Eur J Mass Spectrom (Chichester) ; 26(4): 292-300, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32264711

RESUMEN

The goal of this study was to establish reactivity of lignin-derived synthetic polyphenolic material under irradiation by ultraviolet (254 nm) and visible (460 and 525 nm) light in order to deeper examine relationships between the optical properties of this complex mixture and its individual constituents. In all photoirradiation experiments, blue shift of the fluorescence spectrum was observed. We aimed at understanding whether these changes could be explained on the basis of the chromophore interactions hypothesis, which implies destruction of electron-acceptor pairs via free radical transformations to be responsible for the alteration of optical properties. For this, changes in molecular composition were explored by Fourier transform ion cyclotron resonance mass spectrometry. Irradiation with UV resulted in a pronounced oxidation of polyphenols, which was manifested in the van Krevelen diagram by the formation of components with higher O/C ratio. At the same time, irradiation by visible light had led to the appearance of more condensed molecules depleted of oxygen. Consideration of changes in relative contribution of 500 most abundant components in polyphenol materials revealed higher transformation yields under UV light as compared to the visible light. Further studies using deuteromethylation followed by Fourier transform ion cyclotron resonance mass spectrometry enabled to enumerate the number of carboxylic groups in individual components of the parent polyphenol material. It was shown that at all wavelengths irradiation mainly impacted carboxylic-rich unsaturated and aromatic compounds, which can be considered as strong electron-acceptors. We suggest that their transformation is responsible for the blue shift of fluorescence spectrum, thus emphasizing the role of chromophore interaction mechanism of the optical properties formation.

18.
Anal Chem ; 92(10): 6877-6885, 2020 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-32167749

RESUMEN

Accurate and reliable identification of chemical compounds is the ultimate goal of mass spectrometry analyses. Currently, identification of compounds is usually based on the measurement of the accurate mass and fragmentation spectrum, chromatographic elution time, and collisional cross section. Unfortunately, despite the growth of databases of experimentally measured MS/MS spectra (such as MzCloud and Metlin) and developing software for predicting MS/MS fragments in silico from SMILES patterns (such as MetFrag, CFM-ID, and Ms-Finder), the problem of identification is still unsolved. The major issue is that the elution time and fragmentation spectra depend considerably on the equipment used and are not the same for different LC-MS systems. It means that any additional descriptors depending only on the structure of the chemical compound will be of big help for LC-MS/MS-based omics. Our approach is based on the characterization of compounds by the number of labile hydrogen and oxygen atoms in the molecule, which can be measured using hydrogen/deuterium and 16O/18O-exchange approaches. The number of labile atoms (those from -OH, -NH, ═O, and -COOH groups) can be predicted from SMILES patterns and serves as an additional structural descriptor when performing a database search. In addition, distribution of isotope labels among MS/MS fragments can be roughly predicted by software such as MetFrag or CFM-ID. Here, we present an approach utilizing the selection of structural candidates from a database on the basis of the number of functional groups and analysis of isotope labels distribution among fragments. It was found that our approach allows reduction of the search space by a factor of 10 and considerably increases the reliability of the compound identification.

19.
Environ Sci Technol ; 54(5): 2667-2677, 2020 03 03.
Artículo en Inglés | MEDLINE | ID: mdl-32045519

RESUMEN

The goal of this study was to establish a relationship between the optical properties of soil dissolved organic matter (DOM) and acidic functions carried out by its individual constituents. We obtained 12 fractions of DOM samples using sequential solid phase extraction on nonionic sorbent at steadily lowered pH values: 7, 5, 3, 2, which correspond to low bounds of pKa values of phenols, aliphatic, and aromatic carboxylic acids, and ketoacids. The structural studies were conducted with the use of NMR and selective deuteromethylation of isolated fractions coupled to ultrahigh resolution mass spectrometry. First, a gradual shift of molecular compositions was observed from reduced components to aromatic oxidized compounds isolated at pH 7 and 2, respectively. Changes in molecular compositions were accompanied by a red shift of fluorescence spectra. Further application of deuteromethylation enabled us to distinguish DOM constituents with different amounts of carboxylic groups. Moreover, identification of structural isomers in a single DOM sample was achieved. Statistical analysis revealed that red shift of fluorescence is facilitated by the increase of a contribution of aromatic poly(carboxylic acid)s with high conjugation lengths. Additionally, analysis of the labeled fractionated permafrost thaw DOM directly showed carboxyl-rich alicyclic molecules, while the same components from lower-latitude DOM were assigned to lignin-like species.


Asunto(s)
Compuestos Orgánicos , Suelo , Ácidos , Espectrometría de Masas , Extracción en Fase Sólida
20.
Bioorg Med Chem Lett ; 29(22): 126708, 2019 11 15.
Artículo en Inglés | MEDLINE | ID: mdl-31607610

RESUMEN

Two new austalide meroterpenoids, named austalides V and W (1 and 2), were isolated from the fungus Aspergillus ustus VKM F-4692. Their structures were elucidated by extensive spectroscopic analysis and by comparison with related known compounds. The main structural feature of both compounds is a tetrahydrofuranyl ring (G), a structural fragment, first found in austalides. Austalides V (1) and W (2) were able to inhibit the propagation of prostate and bladder cancer cells; this biologic activity is possibly related to the inhibition of a number of key pathways regulating cell growth and migration.


Asunto(s)
Antineoplásicos/farmacología , Aspergillus/química , Terpenos/farmacología , Antineoplásicos/química , Antineoplásicos/aislamiento & purificación , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Ensayos de Selección de Medicamentos Antitumorales , Humanos , Estructura Molecular , Relación Estructura-Actividad , Terpenos/química , Terpenos/aislamiento & purificación
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