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What is life? How chemistry becomes biology | Chemistry World

What is life? How chemistry becomes biology | Chemistry World | Natural Products Chemistry Breaking News | Scoop.it
The ultimate question

 

The question of how life on Earth (or indeed anywhere else) began is one that has been pondered and debated by scientists, philosophers and the common man throughout history. The title of this book repeats that of an essay written by Erwin Schrödinger in the 1940s. While it is not necessary to have read Schrödinger’s essay to understand this book, anyone interested in the knotty problem of life’s origins should probably take a look.

 

Addy ProssOxford University Press2012 | 200pp | £16.99 (HB)ISBN 9780199641017Reviewed by Phillip Broadwithhttp://rsc.li/CW_130601

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Fascinating fi shure !

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you know a software of animation,the better?
Natural Products Chemistry Breaking News
A recompilation of news and links about natural products, organic chemistry and science more generally ...
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Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles | Natural Products Chemistry Breaking News | Scoop.it

The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.

 

Alice E. Williamson, Paul M. Ylioja, Murray N. Robertson, Yevgeniya Antonova-Koch§, Vicky Avery, Jonathan B. Baell, Harikrishna Batchu#, Sanjay Batra#, Jeremy N. Burrows, Soumya Bhattacharyya#, Felix Calderonα, Susan A. Charman, Julie Clarkβ, Benigno Crespoα, Matin Dean, Stefan L. Debbertγ, Michael Delvesδ, Adelaide S. M. Dennisϵ, Frederik Derooseζ, Sandra Duffy, Sabine Fletcher, Guri Giaeverη, Irene Hallyburtonθ, Francisco-Javier Gamoα, Marinella Gebbiaη, R. Kiplin Guyβ, Zoe Hungerford, Kiaran Kirkϵ, Maria J. Lafuente-Monasterioα, Anna Leeη, Stephan Meister§, Corey Nislowη, John P. Overingtonι, George Papadatosι, Luc Patinyκ, James Phamλ, Stuart A. Ralphλ, Andrea Rueckerδ, Eileen Ryan, Christopher Southanμ, Kumkum Srivastava#, Chris Swainν, Matthew J. Tarnowski, Patrick Thomsonξ, Peter Turner, Iain M. Wallaceι, Timothy N. C. Wells, Karen White, Laura White, Paul Willis, Elizabeth A. Winzeler§, Sergio Wittlinπ, and Matthew H. Todd*
ACS Cent. Sci., Article ASAP
DOI: 10.1021/acscentsci.6b00086
Publication Date (Web): September 14, 2016
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Open Source Power !

The way to go ....

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How DNA could store all the world’s data

How DNA could store all the world’s data | Natural Products Chemistry Breaking News | Scoop.it
Modern archiving technology cannot keep up with the growing tsunami of bits. But nature may hold an answer to that problem already.
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Future of data storage !

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Targeted Isolation of Indolopyridoquinazoline Alkaloids from Conchocarpus fontanesianus Based on Molecular Networks

Targeted Isolation of Indolopyridoquinazoline Alkaloids from Conchocarpus fontanesianus Based on Molecular Networks | Natural Products Chemistry Breaking News | Scoop.it

A dichloromethane-soluble fraction of the stem bark of Conchocarpus fontanesianus showed antifungal activity against Candida albicans in a bioautography assay. Off-line high-pressure liquid chromatography activity-based profiling of this extract enabled a precise localization of the compounds responsible for the antifungal activity that were isolated and identified as the known compounds flindersine (17) and 8-methoxyflindersine (18). As well as the identification of the bioactive principles, the ultra-high-pressure liquid chromatography–high-resolution mass spectrometry metabolite profiling of the dichloromethane stem bark fraction allowed the detection of more than 1000 components. Some of these could be assigned putatively to secondary metabolites previously isolated from the family Rutaceae. Generation of a molecular network based on MS2 spectra indicated the presence of indolopyridoquinazoline alkaloids and related scaffolds. Efficient targeted isolation of these compounds was performed by geometric transfer of the analytical high-pressure liquid chromatography profiling conditions to preparative medium-pressure liquid chromatography. This yielded six new indolopyridoquinazoline alkaloids (5, 16, 1922) that were assigned structurally. The medium-pressure liquid chromatography separations afforded additionally 16 other compounds. This work has demonstrated the usefulness of molecular networks to target the isolation of new natural products and the value of this approach for dereplication. A detailed analysis of the constituents of the stem bark of C. fontanesianus was conducted.

 

 
J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00379
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Molecular networking application to target isolation of specific scaffolds and analogues.

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Nanoscale Strategies for Light Harvesting

Nanoscale Strategies for Light Harvesting | Natural Products Chemistry Breaking News | Scoop.it

Recent advances and the current status of challenging light-harvesting nanomaterials, such as semiconducting quantum dots (QDs), metal nanoparticles, semiconductor–metal heterostructures, π-conjugated semiconductor nanoparticles, organic–inorganic heterostructures, and porphyrin-based nanostructures, have been highlighted in this review. The significance of size-, shape-, and composition-dependent exciton decay dynamics and photoinduced energy transfer of QDs is addressed. A fundamental knowledge of these photophysical processes is crucial for the development of efficient light-harvesting systems, like photocatalytic and photovoltaic ones. Again, we have pointed out the impact of the metal-nanoparticle-based surface energy transfer process for developing light-harvesting systems. On the other hand, metal–semiconductor hybrid nanostructures are found to be very promising for photonic applications due to their exciton–plasmon interactions. Potential light-harvesting systems based on dye-doped π-conjugated semiconductor polymer nanoparticles and self-assembled structures of π-conjugated polymer are highlighted. We also discuss the significance of porphyrin-based nanostructures for potential light-harvesting systems. Finally, the future perspective of this research field is given.

 

Department of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
Chem. Rev., Article ASAP
DOI: 10.1021/acs.chemrev.6b00036
Publication Date (Web): August 5, 2016
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Go green !

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Rhizovarins A–F, Indole-Diterpenes from the Mangrove-Derived Endophytic Fungus Mucor irregularis QEN-189

Rhizovarins A–F, Indole-Diterpenes from the Mangrove-Derived Endophytic Fungus Mucor irregularis QEN-189 | Natural Products Chemistry Breaking News | Scoop.it
Genome mining of the fungus Mucor irregularis (formerly known as Rhizomucor variabilis) revealed the presence of various gene clusters for secondary metabolite biosynthesis, including several terpene-based clusters. Investigation into the chemical diversity of M. irregularis QEN-189, an endophytic fungus isolated from the fresh inner tissue of the marine mangrove plant Rhizophora stylosa, resulted in the discovery of 20 structurally diverse indole-diterpenes including six new compounds, namely, rhizovarins A–F (1–6). Among them, compounds 1–3 represent the most complex members of the reported indole-diterpenes. The presence of an unusual acetal linked to a hemiketal (1) or a ketal (2 and 3) in an unprecedented 4,6,6,8,5,6,6,6,6-fused indole-diterpene ring system makes them chemically unique. Their structures and absolute configurations were elucidated by spectroscopic analysis, modified Mosher’s method, and chemical calculations. Each of the isolated compounds was evaluated for antitumor activity against HL-60 and A-549 cell lines.

 

 
J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00403
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WoW ! That's a nice one !

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Cytotoxic Guanidine Alkaloids from a French Polynesian Monanchora n. sp. Sponge

Cytotoxic Guanidine Alkaloids from a French Polynesian Monanchora n. sp. Sponge | Natural Products Chemistry Breaking News | Scoop.it
Four bicyclic and three pentacyclic guanidine alkaloids (1–7) were isolated from a French Polynesian Monanchora n. sp. sponge, along with the known alkaloids monalidine A (8), enantiomers 9–11 of known natural product crambescins, and the known crambescidins 12–15. Structures were assigned by spectroscopic data interpretation. The relative and absolute configurations of the alkaloids were established by analysis of 1H NMR and NOESY spectra and by circular dichroism analysis. The new norcrambescidic acid (7) corresponds to interesting biosynthetic variation within the pentacyclic core. All compounds exhibited antiproliferative and cytotoxic efficacy against KB, HCT116, HL60, MRC5, and B16F10 cancer cells, with IC50 values ranging from 4 nM to 10 μM.

 

J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00168
Publication Date (Web): July 15, 2016
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Yayyyy guanidines !!!

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Extending the Dynamic Range in Metabolomics Experiments by Automatic Correction of Peaks Exceeding the Detection Limit

Extending the Dynamic Range in Metabolomics Experiments by Automatic Correction of Peaks Exceeding the Detection Limit | Natural Products Chemistry Breaking News | Scoop.it
Metabolomics, the analysis of potentially all small molecules within a biological system, has become a valuable tool for biomarker identification and the elucidation of biological processes. While metabolites are often present in complex mixtures at extremely different concentrations, the dynamic range of available analytical methods to capture this variance is generally limited. Here, we show that gas chromatography coupled to atmospheric pressure chemical ionization mass spectrometry (GC-APCI-MS), a state of the art analytical technology applied in metabolomics analyses, shows an average linear range (LR) of 2.39 orders of magnitude for a set of 62 metabolites from a representative compound mixture. We further developed a computational tool to extend this dynamic range on average by more than 1 order of magnitude, demonstrated with a dilution series of the compound mixture, using robust and automatic reconstruction of intensity values exceeding the detection limit. The tool is freely available as an R package (CorrectOverloadedPeaks) from CRAN (https://cran.r-project.org/) and can be incorporated in a metabolomics data processing pipeline facilitating large screening assays.

 

Anal. Chem., Article ASAP
DOI: 10.1021/acs.analchem.6b02515
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Extending the Dynamic Range in Metabolomics Experiments by Automatic Correction of Peaks Exceeding the Detection Limit

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Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics

Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics | Natural Products Chemistry Breaking News | Scoop.it

Bottromycin A2 is a structurally unique ribosomally synthesized and post-translationally modified peptide (RiPP) that possesses potent antibacterial activity towards multidrug-resistant bacteria. The structural novelty of bottromycin stems from its unprecedented macrocyclic amidine and rare β-methylated amino acid residues. The N-terminus of a precursor peptide (BtmD) is converted into bottromycin A2 by tailoring enzymes encoded in the btm gene cluster. However, little was known about key transformations in this pathway, including the unprecedented macrocyclization. To understand the pathway in detail, an untargeted metabolomic approach that harnesses mass spectral networking was used to assess the metabolomes of a series of pathway mutants. This analysis has yielded key information on the function of a variety of previously uncharacterized biosynthetic enzymes, including a YcaO domain protein and a partner protein that together catalyze the macrocyclization.

 

William J. K. Crone, Natalia M. Vior, Javier Santos-Aberturas, Lukas G. Schmitz,
Finian J. Leeper, and Andrew W. Truman*

Angewandte Chemistry International Edition: DOI: 10.1002/anie.201604304

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Application of molecular networks for biosynthetics pathways elucidation

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The Metabolic Plant Feedback Hypothesis: How Plant Secondary Metabolites Nonspecifically Impact Human Health - Planta Medica

The Metabolic Plant Feedback Hypothesis: How Plant Secondary Metabolites Nonspecifically Impact Human Health - Planta Medica | Natural Products Chemistry Breaking News | Scoop.it

« Humans can ingest gram amounts of plant secondary metabolites daily through diet. Many of these phytochemicals are bioactive beyond our current understanding because they act through weak negative biological feedback mechanisms, undetectable in vitro. Homeostatic-type assessments shed light on the evolutionary implications of the human diet from plants, giving rise to the metabolic plant feedback hypothesis. The hypothesis states that ancient diets rich in carbohydrates coincide with bulk dietary phytochemicals that act as nonspecific inhibitors of metabolic and inflammatory processes. Consequently, food-derived phytochemicals are likely to be equally effective as herbal medicines for these indications. In addition to the ubiquitous flavonoids, terpenoids, and fatty acids in the diet, the likely impact of chronic chlorophyll ingestion on human health is discussed, and data on its modulation of blood glucose levels are presented. A major deduction of this hypothesis is that starchy diets lacking plant secondary metabolites are associated with multimorbidity (lifestyle diseases) including obesity, type 2 diabetes, and cardiovascular disease. It is proposed that the intake of leafy vegetables, spices, and herbal remedies rich in phytochemicals matches the transition and genetic adaptation to early agriculture, playing a compensatory role in the mismatch of old genes and new diets. »

 

Jürg Gertsch

Planta Med
DOI: 10.1055/s-0042-108340

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« A must-read on how we shaped our diet, how our diet shaped us and how our current diet may shape us way more than we think. And how we should cure what can be cured by our diet with our diet before digging for hypothetical magic bullets. »

J.

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Hard Cap Espresso Machines in Analytical Chemistry: What Else? - Analytical Chemistry (ACS Publications)

Hard Cap Espresso Machines in Analytical Chemistry: What Else? - Analytical Chemistry (ACS Publications) | Natural Products Chemistry Breaking News | Scoop.it

« A hard cap espresso machine has been used in combination with liquid chromatography with molecular fluorescence detection for the determination of polycyclic aromatic hydrocarbons (PAHs) from contaminated soils and sediments providing appropriate extraction efficiencies and quantitative results. Naphthalene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, chrysene, benz[b]fluoranthene, benz[k]fluoranthene, benz[a]pyrene, dibenz[a,h]anthracene, benz[ghi]perylene, and indeno[1,2,3-cd]pyrene were used as target compounds. It should be mentioned that the pairs benz[a]anthracene–chrysene and dibenz[a,h]anthracene–benz[ghi]perylene peaks coelute under the employed chromatographic conditions; thus, those compounds were determined together. PAHs were extracted from 5.0 g of soil, previously homogenized, freeze-dried, and sieved to 250 μm, with 50 mL of 40% (v/v) acetonitrile in water at a temperature of 72 ± 3 °C. The proposed procedure is really fast, with an extraction time of 11 s, and it reduces the required amount of organic solvent to do the sample preparation. The obtained limit of detection for the evaluated PAHs was from 1 to 38 μg kg–1. Recoveries were calculated using clean soils spiked with 100, 500, 1000, and 2000 μg kg–1 PAHs with values ranging from 81 to 121% and good precision with relative standard deviation values lower than 30%. The method was validated using soil and sediment certified reference materials and also using real samples by comparison with ultrasound-assisted extraction, as reference methodology, obtaining statistically comparable results. Thus, the use of hard cap espresso machines in the analytical laboratories offers tremendous possibilities as low cost extraction units for the extraction of solid samples. »

 

Hard Cap Espresso Machines in Analytical Chemistry: What Else?
Department of Analytical Chemistry, University of Valencia, 50th Dr. Moliner Street, 46100 Burjassot, Spain
Anal. Chem., Article ASAP
DOI: 10.1021/acs.analchem.6b01400
Publication Date (Web): May 25, 2016
Copyright © 2016 American Chemical Society
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Selecting the Most Appropriate NMR Experiment to Access Weak and/or Very Long-Range Heteronuclear Correlations

Selecting the Most Appropriate NMR Experiment to Access Weak and/or Very Long-Range Heteronuclear Correlations | Natural Products Chemistry Breaking News | Scoop.it

Heteronuclear long-range NMR experiments are well established as essential NMR techniques for the structure elucidation of unknown natural products and small molecules. It is generally accepted that the absence of a given nJXH correlation in an HMBC or HSQMBC spectrum would automatically place the proton at least four bonds away from the carbon in question. This assumption can, however, be misleading in the case of a mismatch between the actual coupling constant and the delay used to optimize the experiment, which can lead to structural misassignments. Another scenario arises when an investigator, for whatever reason, needs to have access to very long-range correlations to confirm or refute a structure. In such cases, a conventional HMBC experiment will most likely fail to provide the requisite correlation, regardless of the delay optimization. Two recent methods for visualizing extremely weak or very long-range connectivities are the LR-HSQMBC and the HSQMBC-TOCSY experiments. Although they are intended to provide similar structural information, they utilize different transfer mechanisms, which differentiates the experiments, making each better suited for specific classes of compounds. In this report we have sought to examine the considerations implicit in choosing the best experiment to access weak or very long-range correlations for different types of molecules.

 

 
J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00139
Publication Date (Web): May 3, 2016
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Selecting the Most Appropriate NMR Experiment to Access Weak and/or Very Long-Range Heteronuclear Correlations

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The Chemical Ecology of Predatory Soil Bacteria

The Chemical Ecology of Predatory Soil Bacteria | Natural Products Chemistry Breaking News | Scoop.it

ClickThe study of natural products is entering a renaissance, driven by the discovery that the majority of bacterial secondary metabolites are not produced under standard laboratory conditions. Understanding the ecological role of natural products is key to efficiently directing our screening efforts, and to ensuring that each screen efficiently captures the full biosynthetic repertoire of the producing organisms. Myxobacteria represent one of the most common and diverse groups of bacteria, with roughly 2500 strains publically available. Fed largely through predation, the myxobacteria have developed a large repertoire of natural products that target other microorganisms, including bacteria and fungi. Many of these interactions can be observed in predation assays, providing direct evidence for environmental interactions. With a focus on Myxococcus xanthus, this review will highlight how recent advances in myxobacteria are revealing the chemical ecology of bacterial natural products.

 

Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, Montreal, Quebec, Canada H4B 1R6
ACS Chem. Biol., Article ASAP
DOI: 10.1021/acschembio.6b00176
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War, peace & chemistry ... just under our feets.

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Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites | Natural Products Chemistry Breaking News | Scoop.it
Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches for the optimal production of various prokaryotic secondary metabolites: native versus heterologous hosts (e.g., Escherichia coli) and rational versus random approaches. This comparative analysis is followed by discussions on systems biology tools deployed in optimizing the production of secondary metabolites. The potential contributions of additional systems biology tools are also discussed in the context of current challenges encountered during optimization of secondary metabolite production.

 

 

Nat. Prod. Rep., 2016, Advance Article


DOI: 10.1039/C6NP00019C

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Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

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NMR Tube Degradation Method for Sugar Analysis of Glycosides - Journal of Natural Products

NMR Tube Degradation Method for Sugar Analysis of Glycosides - Journal of Natural Products | Natural Products Chemistry Breaking News | Scoop.it

The sugar subunits of natural glycosides can be conveniently determined by acid hydrolysis and 1H NMR spectroscopy without isolation or derivatization. The chemical shifts, coupling constants, and integral ratios of the anomeric signals allow each monosaccharide to be identified and its molar ratio to other monosaccharides to be quantified. The NMR data for the anomeric signals of 28 monosaccharides and three disaccharides are reported. Application of the method is demonstrated with the flavonoid glycoside naringin (1), the aminoglycoside antibiotics kanamycin (2) and tobramycin (3), and the saponin digitonin (4).

 

J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00180
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Sweet !

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Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.unity Algorithm

Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.unity Algorithm | Natural Products Chemistry Breaking News | Scoop.it
Analysis of a single analyte by mass spectrometry can result in the detection of more than 100 degenerate peaks. These degenerate peaks complicate spectral interpretation and are challenging to annotate. In mass spectrometry-based metabolomics, this degeneracy leads to inflated false discovery rates, data sets containing an order of magnitude more features than analytes, and an inefficient use of resources during data analysis. Although software has been introduced to annotate spectral degeneracy, current approaches are unable to represent several important classes of peak relationships. These include heterodimers and higher complex adducts, distal fragments, relationships between peaks in different polarities, and complex adducts between features and background peaks. Here we outline sources of peak degeneracy in mass spectra that are not annotated by current approaches and introduce a software package called mz.unity to detect these relationships in accurate mass data. Using mz.unity, we find that data sets contain many more complex relationships than we anticipated. Examples include the adduct of glutamate and nicotinamide adenine dinucleotide (NAD), fragments of NAD detected in the same or opposite polarities, and the adduct of glutamate and a background peak. Further, the complex relationships we identify show that several assumptions commonly made when interpreting mass spectral degeneracy do not hold in general. These contributions provide new tools and insight to aid in the annotation of complex spectral relationships and provide a foundation for improved data set identification. Mz.unity is an R package and is freely available at https://github.com/nathaniel-mahieu/mz.unity as well as our laboratory Web site http://pattilab.wustl.edu/software/.

 

Anal. Chem., Article ASAP
DOI: 10.1021/acs.analchem.6b01702
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After CAMERA comes Mz.unity !

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Research Ideas and Outcomes

Research Ideas and Outcomes | Natural Products Chemistry Breaking News | Scoop.it

The Research Ideas and Outcomes (RIO) journal publishes all outputs of the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform, with the most transparent, open and public peer-review process. Our scope encompasses all areas of academic research, including science, technology, humanities and the social sciences.

 

 

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Your next journal ?!

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Natural Product Isolation (2) – Purification of Crude Mixtures Overview — Master Organic Chemistry

Natural Product Isolation (2) – Purification of Crude Mixtures Overview — Master Organic Chemistry | Natural Products Chemistry Breaking News | Scoop.it
  Previously,  we showed a few examples of preparing crude extracts from plants and other organisms. While sometimes (rarely) we get lucky and obtain an extract that is predominantly one compound, a more representative situation is that a mixture of compounds is obtained.
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Excellent website MOC (Master Organic Chemistry) sums up some of Natural Products isolations techniques ... perfect for students ! Check out the crystal glamour shots !

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking | Natural Products Chemistry Breaking News | Scoop.it

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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After several years of development, and of outstanding applications by the community, the GNPS paper is finally out. A milestone, for Mass Spec in Natural Products Chemistry and Metabolomics. More than 13,000 users worldwide.

 

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Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification - Analytical Chemistry (ACS Publications)

Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification - Analytical Chemistry (ACS Publications) | Natural Products Chemistry Breaking News | Scoop.it
We describe a tool, competitive fragmentation modeling for electron ionization (CFM-EI) that, given a chemical structure (e.g., in SMILES or InChI format), computationally predicts an electron ionization mass spectrum (EI-MS) (i.e., the type of mass spectrum commonly generated by gas chromatography mass spectrometry). The predicted spectra produced by this tool can be used for putative compound identification, complementing measured spectra in reference databases by expanding the range of compounds able to be considered when availability of measured spectra is limited. The tool extends CFM-ESI, a recently developed method for computational prediction of electrospray tandem mass spectra (ESI-MS/MS), but unlike CFM-ESI, CFM-EI can handle odd-electron ions and isotopes and incorporates an artificial neural network. Tests on EI-MS data from the NIST database demonstrate that CFM-EI is able to model fragmentation likelihoods in low-resolution EI-MS data, producing predicted spectra whose dot product scores are significantly better than full enumeration “bar-code” spectra. CFM-EI also outperformed previously reported results for MetFrag, MOLGEN-MS, and Mass Frontier on one compound identification task. It also outperformed MetFrag in a range of other compound identification tasks involving a much larger data set, containing both derivatized and nonderivatized compounds. While replicate EI-MS measurements of chemical standards are still a more accurate point of comparison, CFM-EI’s predictions provide a much-needed alternative when no reference standard is available for measurement. CFM-EI is available at https://sourceforge.net/projects/cfm-id/ for download and http://cfmid.wishartlab.com as a web service.

 

Department of Computing Science, University of Alberta, Edmonton T6G 2E8, Canada
Anal. Chem., Article ASAP
DOI: 10.1021/acs.analchem.6b01622
Publication Date (Web): July 06, 2016
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CFM is now for EI too ! Great news :)

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Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns

Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns | Natural Products Chemistry Breaking News | Scoop.it
The determination of the molecular formula is one of the earliest and most important steps when investigating the chemical nature of an unknown compound. Common approaches use the isotopic pattern of a compound measured using mass spectrometry. Computational methods to determine the molecular formula from this isotopic pattern require a fixed set of elements. Considering all possible elements severely increases running times and more importantly the chance for false positive identifications as the number of candidate formulas for a given target mass rises significantly if the constituting elements are not prefiltered. This negative effect grows stronger for compounds of higher molecular mass as the effect of a single atom on the overall isotopic pattern grows smaller. On the other hand, hand-selected restrictions on this set of elements may prevent the identification of the correct molecular formula. Thus, it is a crucial step to determine the set of elements most likely comprising the compound prior to the assignment of an elemental formula to an exact mass. In this paper, we present a method to determine the presence of certain elements (sulfur, chlorine, bromine, boron, and selenium) in the compound from its (high mass accuracy) isotopic pattern. We limit ourselves to biomolecules, in the sense of products from nature or synthetic products with potential bioactivity. The classifiers developed here predict the presence of an element with a very high sensitivity and high specificity. We evaluate classifiers on three real-world data sets with 663 isotope patterns in total: 184 isotope patterns containing sulfur, 187 containing chlorine, 14 containing bromine, one containing boron, one containing selenium. In no case do we make a false negative prediction; for chlorine, bromine, boron, and selenium, we make ten false positive predictions in total. We also demonstrate the impact of our method on the identification of molecular formulas, in particular on the number of considered candidates and running time. The element prediction will be part of the next SIRIUS release, available from https://bio.informatik.uni-jena.de/software/sirius/.

 

Anal. Chem., Article ASAP
DOI: 10.1021/acs.analchem.6b01015
Publication Date (Web): July 11, 2016
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New stuff in Sirius !!!

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New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans

New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans | Natural Products Chemistry Breaking News | Scoop.it

Unlocking the biochemical stores of fungi is key for developing future pharmaceuticals. Through reduced expression of a critical histone deacetylase in Aspergillus nidulans, increases of up to 100-fold were observed in the levels of 15 new aspercryptins, recently described lipopeptides with two noncanonical amino acids derived from octanoic and dodecanoic acids. In addition to two NMR-verified structures, MS/MS networking helped uncover an additional 13 aspercryptins. The aspercryptins break the conventional structural orientation of lipopeptides and appear “backward” when compared to known compounds of this class. We have also confirmed the 14-gene aspercryptin biosynthetic gene cluster, which encodes two fatty acid synthases and several enzymes to convert saturated octanoic and dodecanoic acid to α-amino acids.

 

ACS Chem. Biol., Article ASAP
DOI: 10.1021/acschembio.6b00398
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New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans
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Drug discovery returns to the wild

Drug discovery returns to the wild | Natural Products Chemistry Breaking News | Scoop.it

Researchers now have the tools to unlock the potential of previously uncultivated microbes, prompting a return to drug discovery from natural products.

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Researchers now have the tools to unlock the potential of previously uncultivated microbes, prompting a return to drug discovery from natural products.

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Emergence of diversity and stereochemical outcomes in the biosynthetic pathways of cyclobutane-centered marine alkaloid dimers

Emergence of diversity and stereochemical outcomes in the biosynthetic pathways of cyclobutane-centered marine alkaloid dimers | Natural Products Chemistry Breaking News | Scoop.it

Covering: up to 2016" 

Dictazoles and sceptrins are singular metabolites of marine origin. The present dichotomic case study provides a comprehensive perspective on these cyclobutane-centered alkaloids and their respective families. Indeed, their upstream and downstream chemistry are both treated herein. Relevant isolation reports and bio-inspired total syntheses are used to decipher the currently admitted biosynthetic hypotheses as well as the emergence of diversity in the two series. This review proposes a transversal vision of the topic, where most aspects of natural product chemistry have a critical importance.

Mehdi A. Beniddir,a   Laurent Evanno,a   Delphine Joseph,a  Adam Skiredj*a and   Erwan Poupon*a  

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A deep-sea dive into the ecology and chemistry of surprising cyclobutanes from marine invertebrates.

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Nitric Oxide Inhibitory Meroterpenoids from the Fungus Penicillium purpurogenum MHZ 111

Nitric Oxide Inhibitory Meroterpenoids from the Fungus Penicillium purpurogenum MHZ 111 | Natural Products Chemistry Breaking News | Scoop.it

Five new meroterpenoids, purpurogenolides A–E (15), and four known metabolites (69) were isolated from the solid substrate fermentation cultures of the fungus Penicillium purpurogenum MHz 111. The structures of the new meroterpenoids were elucidated by analysis of spectroscopic and spectrometric data (1D and 2D NMR, IR, and HRESIMS). The absolute configurations of 1 and 5 were determined by single-crystal X-ray crystallographic analysis, and those of 24 were elucidated on the basis of experimental and calculated electronic circular dichroism spectra. Compounds 24 and 6 showed inhibition of nitric oxide production in lipopolysaccharide-activated BV-2 microglial cells with IC50 values of 0.8–30.0 μM.

 

J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00160
Publication Date (Web): April 27, 2016
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Nitric Oxide Inhibitory Meroterpenoids from the Fungus Penicillium purpurogenum MHZ 111

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Ibogan, Aspidosperman, Vincamine, and Bisindole Alkaloids from a Malayan Tabernaemontana corymbosa: Iboga Alkaloids with C-20α Substitution

Ibogan, Aspidosperman, Vincamine, and Bisindole Alkaloids from a Malayan Tabernaemontana corymbosa: Iboga Alkaloids with C-20α Substitution | Natural Products Chemistry Breaking News | Scoop.it

Click here to Ten new indole alkaloids (110) comprising five ibogan, two aspidosperman, one vincamine, and two bisindole alkaloids, in addition to 32 known alkaloids, were isolated from the stem-bark extract of a Malayan Tabernaemontana corymbosa. The structures of these alkaloids were determined based on analysis of the NMR and MS data and, in five instances (1, 3, 5, 6, 8), confirmed by X-ray diffraction analysis. Two of the iboga alkaloids, conodusines B (2) and C (3), and the iboga-containing bisindole tabernamidine B (10) are notable for the presence of an α-substituted acetyl group at C-20 of the iboga carbon skeleton. The iboga alkaloid (+)-conodusine E (5) had MS and NMR data that were identical to those of (−)-ervatamine I, recently isolated from Ervatamia hainanensis. Establishment of the absolute configuration of (+)-conodusine E (5) was based on analysis of the ECD data, correlation with (−)-heyneanine, and X-ray analysis, which showed that (+)-5 belongs to the same enantiomeric series as exemplified by (−)-coronaridine. The configuration at C-20′ of the previously reported Tabernaemontana bisindole alkaloid 19′-oxotabernamine (renamed tabernamidine B) required revision based on the present results. Several of the bisindoles showed pronounced in vitro growth inhibitory activity against drug-sensitive and vincristine-resistant KB cells.

 

Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.6b00129
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