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Natural Products Chemistry Breaking News
A recompilation of news and links about natural products, organic chemistry and science more generally ...
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The Polymorphs of L-Phenylalanine - Ihlefeldt - 2014 - Angewandte Chemie International Edition - Wiley Online Library

The Polymorphs of L-Phenylalanine - Ihlefeldt - 2014 - Angewandte Chemie International Edition - Wiley Online Library | Natural Products Chemistry Breaking News | Scoop.it

The solid-state structure of the amino acid phenylalanine (Phe) offers a potential key to understanding the behavior of a large class of important aromatic compounds. Obtaining good single crystals is, however, notoriously difficult. The structure of the common polymorph of Phe, form I, was first reported by Weissbuch et al. (as D-Phe) in 1990, but the correctness of the published C2 unit cell with two disordered molecules in the asymmetric unit was later questioned and other space groups suggested. The identity of form I of L-Phe is here established to be P21 with Z′=4, based on data from a well-diffracting single crystal grown from an acetic acid solution of the amino acid. A second new polymorph, form IV, together with the two recently described forms II and III provide unprecedented information on the structural complexity of this essential amino acid. It is furthermore documented that the racemate, dl-Phe, does not grow proper single crystals.


Franziska Stefanie Ihlefeldt, Fredrik Bjarte Pettersen, Aidan von Bonin, Malgorzata Zawadzka and Prof. Carl Henrik Görbitz

Angewandte Chemie International Edition

Article first published online: 21 OCT 2014

DOI: 10.1002/anie.201406886

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Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects - Natural Product Reports (RSC Publishing)

Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects - Natural Product Reports (RSC Publishing) | Natural Products Chemistry Breaking News | Scoop.it


Covering: 2000 to 2014

Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways. This review covers the approximate period of 2000 to 2014, and highlights specific examples of the discovery and characterization of novel genes and enzymes associated with the biosynthesis of natural products such as flavonoids, glucosinolates, terpenoids, and alkaloids. Additional examples of the integration of metabolomics with genome-based functional characterizations of plant natural products that are important to modern pharmaceutical technology are also reviewed. This article also provides a substantial review of recent technical advances in mass spectrometry imaging, nuclear magnetic resonance imaging, integrated LC-MS-SPE-NMR for metabolite identifications, and X-ray crystallography of microgram quantities for structural determinations. The review closes with a discussion on the future prospects of metabolomics related to crop species and herbal medicine.



Nat. Prod. Rep., 2015, Advance Article

DOI: 10.1039/C4NP00072B
Received 30 May 2014, First published online 24 Oct 2014


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A new family of iron-dependent halogenases acts on freestanding substrates : Nature Chemical Biology

A new family of iron-dependent halogenases acts on freestanding substrates : Nature Chemical Biology | Natural Products Chemistry Breaking News | Scoop.it
Nonheme iron halogenases, or enzymes that perform oxidative halogenations, exist in a variety of biosynthetic pathways and modify substrates attached to carrier proteins. Biochemical evidence defines a chlorinase that breaks this rule, acting on soluble substrates.


Nature Chemical Biology
10,
921–923
(2014)
doi:10.1038/nchembio.1625
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Pegaharmalines A and B, two novel β-carboline alkaloids with unprecedented carbon skeletons from Peganum harmala

Pegaharmalines A and B, two novel β-carboline alkaloids with unprecedented carbon skeletons from Peganum harmala | Natural Products Chemistry Breaking News | Scoop.it

Pegaharmaline A (1) and B (2), two novel β-carboline alkaloids with unprecedented carbon skeletons, were isolated from the seeds of Peganum harmala. Their structures were determined by spectroscopic methods and the absolute configuration of 1 was elucidated by CD analysis. 1 and 2 exhibited significant cytotoxicities on HL-60 cells with IC50 values of 9.4 and 13.6 µM, respectively.


RSC Adv., 2014, Accepted Manuscript


DOI: 10.1039/C4RA07985J
Received 01 Aug 2014, Accepted 15 Oct 2014



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Hot off the press - Natural Product Reports

Hot off the press - Natural Product Reports | Natural Products Chemistry Breaking News | Scoop.it
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as sinulariaoid A from a Sinularia species.
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Not The Sort Of Thing You'd Work With, Given a Choice.

Not The Sort Of Thing You'd Work With, Given a Choice. | Natural Products Chemistry Breaking News | Scoop.it

« When you search for them, actually, you find compounds like the ones in this paper. Most medicinal chemists will look at these, say the word "quinone", perhaps take a moment spit on the floor or add a rude adjective, and move on to see if there's anything better to look at. Quinones are that unpopular, and with good reason. They're redox-active, can pick up nucleophiles as Michael acceptors, react with amines - they have a whole suite of unattractive behaviors. And that explains their profile in cells and whole animals, with a range of toxic, carcinogenic, and immunologic liabilities. A lot of very active natural products have a quinone in them - it's a real warhead. No medicinal chemist with any experience would feel good about trying to advance one as a lead compound, and (for the same reasons) they tend to make poor tool compounds as well. You just don't know what else they're hitting, and the chance of them hitting something else are too high. »


NatProdChem's insight:

There's a link in the article about getting rid of PAINS (pan assay interference compounds):

http://cen.acs.org/articles/92/i35/Getting-Rid-Painful-Compounds.html

There's some hope in this article… Sometimes you may still be able to optimize them.


J.

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Antitrypanosomal Quinoline Alkaloids from the Roots of Waltheria indica

Antitrypanosomal Quinoline Alkaloids from the Roots of Waltheria indica | Natural Products Chemistry Breaking News | Scoop.it

Chemical investigation of the dichloromethane root extract of Waltheria indica led to the isolation and characterization of 10 quinoline alkaloids, namely, 8-deoxoantidesmone (1), waltheriones E–L (29), and antidesmone (10). Among these, compounds 29 have not yet been described in the literature. Their chemical structures were established by means of spectroscopic data interpretation including 1H and 13C NMR, HSQC, HMBC, COSY, and NOESY experiments and UV, IR, and HRESIMS. The absolute configurations of the compounds were established by comparison of experimental and TDDFT-calculated ECD spectra. In addition, the isolated constituents were evaluated for their in vitro antitrypanosomal activity. Compounds 4, 5, and 8 showed potent and selective growth inhibition toward Trypanosoma cruzi with IC50 values between 0.02 and 0.04 μM. Cytotoxicity for mouse skeletal L-6 cells was also determined for these compounds.

J. Nat. Prod., Article ASAP
DOI: 10.1021/np5006554
Publication Date (Web): October 14, 2014
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A perspective on targeting non-structural proteins to combat neglected tropical diseases: Dengue, West Nile and Chikungunya viruses

A perspective on targeting non-structural proteins to combat neglected tropical diseases: Dengue, West Nile and Chikungunya viruses | Natural Products Chemistry Breaking News | Scoop.it
Highlights

The potential risk of arboviruses; DENV, WNV & CHIKV is emphasised.

Non-structural proteins have emerged as key targets in combating arboviruses.

Inhibitors targeting non-structural proteins from a medicinal chemistry view.

Crowd computing approach against arboviruses is highlighted.

Futuristic scope of drug development against arboviruses is presented.



Volume 87, 24 November 2014, Pages 677–702

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Uncovering the structures of modular polyketide synthases

Uncovering the structures of modular polyketide synthases | Natural Products Chemistry Breaking News | Scoop.it

The modular polyketide synthases (PKSs) are multienzyme proteins responsible for the assembly of diverse secondary metabolites of high economic and therapeutic importance. These molecular ‘assembly lines’ consist of repeated functional units called ‘modules’ organized into gigantic polypeptides. For several decades, concerted efforts have been made to understand in detail the structure and function of PKSs in order to facilitate genetic engineering of the systems towards the production of polyketide analogues for evaluation as drug leads. Despite this intense activity, it has not yet been possible to solve the crystal structure of a single module, let alone a multimodular subunit. Nonetheless, on the basis of analysis of the structures of modular fragments and the study of the related multienzyme of animal fatty acid synthase (FAS), several models of modular PKS architecture have been proposed. This year, however, the situation has changed – three modular structures have been characterized, not by X-ray crystallography, but by the complementary methods of single-particle cryo-electron microscopy and small-angle X-ray scattering. This review aims to compare the cryo-EM structures and SAXS-derived structural models, and to interpret them in the context of previously obtained data and existing architectural proposals. The consequences for genetic engineering of the systems will also be discussed, as well as unresolved questions and future directions.


Show Affiliations
Nat. Prod. Rep., 2015, Advance Article


DOI: 10.1039/C4NP00098F

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Swedish Scientists Square Off Over Who Can Sneak In Most Dylan Lyrics

Swedish Scientists Square Off Over Who Can Sneak In Most Dylan Lyrics | Natural Products Chemistry Breaking News | Scoop.it
It all started in 1997, when two professors from the Karolinska Institute in Stockholm published an article on flatulence titled "Nitric Oxide and inflammation: The answer is blowing in the wind."
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De la plante au médicament

De la plante au médicament | Natural Products Chemistry Breaking News | Scoop.it
Comment le protocole de Nagoya prétend changer le rapport de force entre les pays du Sud, riches en biodiversité, et les pays du Nord, dont l'industrie pharmaceutique tire profit.
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Importance of Purity Evaluation and the Potential of Quantitative 1H NMR as a Purity Assay

Importance of Purity Evaluation and the Potential of Quantitative 1H NMR as a Purity Assay | Natural Products Chemistry Breaking News | Scoop.it

In any biomedical and chemical context, a truthful description of chemical constitution requires coverage of both structure and purity. This qualification affects all drug molecules, regardless of development stage (early discovery to approved drug) and source (natural product or synthetic). Purity assessment is particularly critical in discovery programs and whenever chemistry is linked with biological and/or therapeutic outcome. Compared with chromatography and elemental analysis, quantitative NMR (qNMR) uses nearly universal detection and provides a versatile and orthogonal means of purity evaluation. Absolute qNMR with flexible calibration captures analytes that frequently escape detection (water, sorbents). Widely accepted structural NMR workflows require minimal or no adjustments to become practical 1H qNMR (qHNMR) procedures with simultaneous qualitative and (absolute) quantitative capability. This study reviews underlying concepts, provides a framework for standard qHNMR purity assays, and shows how adequate accuracy and precision are achieved for the intended use of the material.


J. Med. Chem., Article ASAP
DOI: 10.1021/jm500734a
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Curvulamine, a New Antibacterial Alkaloid Incorporating Two Undescribed Units from a Curvularia Species

Curvulamine, a New Antibacterial Alkaloid Incorporating Two Undescribed Units from a Curvularia Species | Natural Products Chemistry Breaking News | Scoop.it

The white croaker (Argyrosomus argentatus) derived Curvularia sp. IFB-Z10 produces curvulamine as a skeletally unprecedented alkaloid incorporating two undescribed extender units. Curvulamine is more selectively antibacterial than tinidazole and biosynthetically unique in the new extenders formed through a decarboxylative condensation between an oligoketide motif and alanine.


Org. Lett., Article ASAP
DOI: 10.1021/ol502572g


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Chlorinated Polyketide Obtained from a Daldinia sp. Treated with the Epigenetic Modifier Suberoylanilide Hydroxamic Acid - Journal of Natural Products (ACS Publications and Am. Soc. of Pharmacognosy)

Chlorinated Polyketide Obtained from a Daldinia sp. Treated with the Epigenetic Modifier Suberoylanilide Hydroxamic Acid - Journal of Natural Products (ACS Publications and Am. Soc. of Pharmacognosy) | Natural Products Chemistry Breaking News | Scoop.it

A new chlorinated pentacyclic polyketide, daldinone E (1), was purified from a Daldinia sp. fungal isolate treated with the epigenetic modifier suberoylanilide hydroxamic acid (SAHA). A biosynthetically related epoxide-containing daldinone analogue, 2, was also purified from the same fungus. The structures of both compounds were established by spectroscopic methods, and the absolute configurations were assigned by analysis of their NMR data (coupling constants and ROESY correlations) and DFT calculations of specific rotations and ECD spectra. During the course of these studies it was determined that metabolite 2 and the previously reported daldinone B shared the same spectroscopic data, leading to a revision of the reported structure. Both compounds 1 and 2 also exhibited DPPH radical scavenging activities with potency comparable to the positive control ascorbic acid.



J. Nat. Prod., Article ASAP

DOI: 10.1021/np500522z
Publication Date (Web): October 22, 2014
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Triterpenoids - Review (NPR)

Triterpenoids - Review (NPR) | Natural Products Chemistry Breaking News | Scoop.it
Covering: 2012. Previous review: Nat. Prod. Rep., 2013, 29, 1028–1065

This review covers the isolation and structure determination of triterpenoids reported during 2012 including squalene derivatives, lanostanes, holostanes, cycloartanes, cucurbitanes, dammaranes, euphanes, tirucallanes, tetranortriterpenoids, quassinoids, lupanes, oleananes, friedelanes, ursanes, hopanes, serratanes, isomalabaricanes and saponins; 348 references are cited.



Nat. Prod. Rep., 2015, Advance Article

DOI: 10.1039/C4NP00101J
Received 30 Jul 2014, First published online 24 Oct 2014
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A roadmap for natural product discovery based on large-scale genomics and metabolomics : Nature Chemical Biology

A roadmap for natural product discovery based on large-scale genomics and metabolomics : Nature Chemical Biology | Natural Products Chemistry Breaking News | Scoop.it
A global bioinformatic classification of >11,000 biosynthetic gene clusters from >800 bacterial genomes and cross-correlation with metabolomics data from nearly 200 strains sets the stage for targeted natural product discovery.


Nature Chemical Biology
10,
963–968
(2014)
doi:10.1038/nchembio.1659
Received
11 March 2014
Accepted
04 September 2014
Published online
28 September 2014
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Computing: Keep files small to curb energy use : Nature

Electronic publishing circumvents environmental issues caused by paper use and the shipment of heavy journals. But more thrift is needed to reduce the energy consumed by Internet servers, which already accounts for 2% of global energy production (see, for instance, go.nature.com/dmqn9a).

Large video and PDF files are downloaded and distributed by e-mail, often thousands of times. Minimizing the size of such files would reduce server energy usage and allow easier access by people in developing countries and rural areas that have slow Internet connections.

Server energy is also wasted in distributing figures at unnecessarily high resolution. Governments and public organizations are particularly guilty (see, for example, an 11-megabyte PDF from the European Research Council: go.nature.com/lwcuyx).

More scientific journals should ask authors to submit their manuscripts with low-resolution illustrations, which can then be upgraded for publication. Publishers of open-access journals might even consider offering a discount on publication charges for manuscript files that are smaller than, say, one megabyte.


  1. Tel-Aviv University, Israel.
    • David Gurwitz
NatProdChem's insight:

Nice proposition !

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Antiviral drug discovery: broad-spectrum drugs from nature - Natural Product Reports (RSC Publishing)

Antiviral drug discovery: broad-spectrum drugs from nature - Natural Product Reports (RSC Publishing) | Natural Products Chemistry Breaking News | Scoop.it

« The development of drugs with broad-spectrum antiviral activities is a long pursued goal in drug discovery. It has been shown that blocking co-opted host-factors abrogates the replication of many viruses, yet the development of such host-targeting drugs has been met with scepticism mainly due to toxicity issues and poor translation to in vivo models. With the advent of new and more powerful screening assays and prediction tools, the idea of a drug that can efficiently treat a wide range of viral infections by blocking specific host functions has re-bloomed. Here we critically review the state-of-the-art in broad-spectrum antiviral drug discovery. We discuss putative targets and treatment strategies, with particular focus on natural products as promising starting points for antiviral lead development. »


Nat. Prod. Rep., 2015, Advance Article
DOI: 10.1039/C4NP00085D
Received 18 Jun 2014, First published online 15 Oct 2014
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MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra | Natural Products Chemistry Breaking News | Scoop.it

Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae.


Yan Ma Tobias Kind Dawei Yang Carlos Leon§, and Oliver Fiehn *

Anal. Chem., Article ASAP
DOI: 10.1021/ac502818e
Publication Date (Web): September 28, 2014


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Proposed quantitative and alphanumeric metabolite identification metrics - Online First - Springer

Proposed quantitative and alphanumeric metabolite identification metrics - Online First - Springer | Natural Products Chemistry Breaking News | Scoop.it

To the Editor,

In June, 2014 the Metabolomics Identification Task Group published an article entitled “Metabolite identification: are you sure? And how do your peers gauge your confidence?”(Creek et al. 2014). This article invited additional feedback and we would like to respond publically with a few more details regarding accurate reporting of metabolite identifications.

The community consensus is that the leading challenge of metabolomics is the chemically accurate identification of large numbers of metabolites observed in various nontargeted profiling techniques. Metabolite identification is critically important because it provides the fundamental biological and biochemical context to the metabolomics data. However, accurate structure identification requires significant effort which increases dramatically with the increased scale of nontargeted metabolomics and typically involves hundreds or thousands of metabolites per analysis.

The metabolomics community has been discussing the chall ...

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Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study

Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study | Natural Products Chemistry Breaking News | Scoop.it
Abstract

The metabo-ring initiative brought together five nuclear magnetic resonance instruments (NMR) and 11 different mass spectrometers with the objective of assessing the reliability of untargeted metabolomics approaches in obtaining comparable metabolomics profiles. This was estimated by measuring the proportion of common spectral information extracted from the different LCMS and NMR platforms. Biological samples obtained from 2 different conditions were analysed by the partners using their own in-house protocols. Test #1 examined urine samples from adult volunteers either spiked or not spiked with 32 metabolite standards. Test #2 involved a low biological contrast situation comparing the plasma of rats fed a diet either supplemented or not with vitamin D. The spectral information from each instrument was assembled into separate statistical blocks. Correlations between blocks (e.g., instruments) were examined (RV coefficients) along with the structure of the common spectral information (common components and specific weights analysis). In addition, in Test #1, an outlier individual was blindly introduced, and its identification by the various platforms was evaluated. Despite large differences in the number of spectral features produced after post-processing and the heterogeneity of the analytical conditions and the data treatment, the spectral information both within (NMR and LCMS) and across methods (NMR vs. LCMS) was highly convergent (from 64 to 91 % on average). No effect of the LCMS instrumentation (TOF, QTOF, LTQ-Orbitrap) was noted. The outlier individual was best detected and characterised by LCMS instruments. In conclusion, untargeted metabolomics analyses report consistent information within and across instruments of various technologies, even without prior standardisation.

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Merremins A–G, Resin Glycosides from Merremia hederacea with Multidrug Resistance Reversal Activity

Merremins A–G, Resin Glycosides from Merremia hederacea with Multidrug Resistance Reversal Activity | Natural Products Chemistry Breaking News | Scoop.it

Five new pentasaccharide resin glycosides, named merremins A–E (15), two new pentasaccharide resin glycoside methyl esters, named merremins F and G (6, 7), and four known resin glycosides, murucoidin IV, murucoidin V, stoloniferin IV, and murucoidin XVII, were obtained from the aerial parts of Merremia hederacea. This is the first report of resin glycosides obtained from M. hederacea. In addition, the new compounds can be divided into three types: those possessing an 18-membered ring (14), compound 5 with a 20-membered ring, and those with an acyclic core (6, 7). Furthermore, the different types of resin glycosides were evaluated for their multidrug resistance reversal activities. Compounds 1, 5, 6, and murucoidin V were noncytotoxic and enhanced the cytotoxicity of vinblastine by 2.3–142.5-fold at 25 μM. Compound 5 and murucoidin V, with 20-membered rings, were more active than compound 1, with an 18-membered ring.


J. Nat. Prod., Article ASAP
DOI: 10.1021/np500483d


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Tramadol—A True Natural Product? - Kusari - 2014 - Angewandte Chemie International Edition - Wiley Online Library

Tramadol—A True Natural Product? - Kusari - 2014 - Angewandte Chemie International Edition - Wiley Online Library | Natural Products Chemistry Breaking News | Scoop.it

We have independently investigated the source of tramadol, a synthetic analgesic largely used for treating moderate to severe pain in humans, recently found in the roots of the Cameroonian medicinal plant, Nauclea latifolia. We found tramadol and its three major mammalian metabolites (O-desmethyltramadol, N-desmethyltramadol, and 4-hydroxycyclohexyltramadol) in the roots of N. latifolia and five other plant species, and also in soil and local water bodies only in the Far North region of Cameroon. The off-label administration of tramadol to cattle in this region leads to cross-contamination of the soil and water through feces and urine containing parent tramadol as well as tramadol metabolites produced in the animals. These compounds can then be absorbed by the plant roots and also leached into the local water supplies. The presence of tramadol in roots is, thus, due to an anthropogenic contamination with the synthetic compound.

NatProdChem's insight:

Arf pour le Prof BOUMENDJEL.

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Recent Studies on the Chemical Constituents of Trigonostemon Plants - Organic Chemistry Frontiers

Recent Studies on the Chemical Constituents of Trigonostemon Plants - Organic Chemistry Frontiers | Natural Products Chemistry Breaking News | Scoop.it

The plants of Trigonostemon genus (Euphorbiaceae family) possessing about 50 species are mainly distributed in the tropical and subtropical Asia. Chemical studies on this plant genus have led to the discovery of about 200 structurally diverse compounds in the past two decades, and some of which showed promising biological activities. Diterpenoids and alkaloids are the major and most important components of Trigonostemon plants, and are also the hot topics of synthetic chemistry. This review attempted to provide the timely and comprehensive coverage of the chemical and biological studies on Trigonostemon plants, and especially to focus on the recent research progress.


Jianmin Yue and   Jin-Biao Xu  
Org. Chem. Front., 2014, Accepted Manuscript


DOI: 10.1039/C4QO00161C
Received 30 May 2014, Accepted 05 Oct 2014



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Scientific writing: the online cooperative

Scientific writing: the online cooperative | Natural Products Chemistry Breaking News | Scoop.it
Collaborative browser-based tools aim to change the way researchers write and publish their papers.


NATURE | TOOLBOX

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Ms. Moon's curator insight, October 9, 10:30 PM

EVERYONE LEARNS TO WORK TOGETHER EVENTUALLY. :)