Institut de Chimie des Substances Naturelles

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.

This essential reference contains an authoritative and systematic description of the use of all reagents in organic chemistry. It includes approximately 3,500 alphabetically arranged articles, a comparison of reagents with others capable of similar chemistry, a pro and con assessment for each reagent, extensive cross-referencing, and substantial subject and molecular formula indexes.

Abstract Although the synthesis of β‐lactams by means of tethered Ugi reactions has been known since the early 1960s, the 1995 report from Ugi’s group could be regarded as a turning point in the development of novel multicomponent reactions (MCRs) for heterocycle syntheses. Indeed, the number of articles describing isocyanide‐based multicomponent syntheses of heterocycles has increased steadily since then. Although most of these novel MCRs still exploit the archetypal reactivity of isocyanide, its pronounced ability to undergo α‐addition with electrophiles (sp 2 ‐ and sp‐carbon atoms) and nucleophiles, new MCRs have also been discovered as a consequence of exploiting the different secondary reactions of this α‐adduct. Since most of these MCRs were devised on the basis of known bimolecular reactions, judicious combination of reactive functional groups within substrates is of fundamental importance. While the combinatorial principle can help in finding and exploring new MCRs, we would advocate a “substrate‐design approach” in searching for novel MCRs. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

Recent developments in catalytic C-H amination are discussed in this feature article. The careful design of reagents and catalysts now provides efficient conditions for exquisitely selective intramolecular as well as intermolecular nitrene C-H insertion. The parallel emergence of C-H activation/amination reactions opens new opportunities complementary to those offered by nitrenes.

Beta-Lactamase Database (BLDB) is a comprehensive, manually curated public resource providing up-to-date structural and functional information focused on this superfamily of enzymes with a great impact on antibiotic resistance. All the enzymes reported and characterised in the literature are presented according to the class (A, B, C and D), family and subfamily to which they belong. All three-dimensional structures of β-lactamases present in the Protein Data Bank are also shown. The characterisation of representative mutants and hydrolytic profiles (kinetics) completes the picture and altogether these four elements constitute the essential foundation for a better understanding of the structure-function relationship within this enzymes family. BLDB can be queried using different protein- and nucleotide-based BLAST searches, which represents a key feature of particular importance in the context of the surveillance of the evolution of the antibiotic resistance. BLDB is available online at http://bldb.eu without any registration and supports all modern browsers.

Catalytic C-H amination has recently emerged as a unique tool for the synthesis of amines. This tutorial review highlights the existing protocols catalyzed by metal complexes (rhodium, copper, ruthenium, manganese and palladium) allowing diastereo- and enantioselective C-H amination. Substrate-, catalyst- and reagent-controlled methodologies are detailed. They involve either catalytic nitrene C-H insertion or C-H activation.

Glycosylation is arguably the most important reaction in the field of glycochemistry, yet it involves one of the most empirically interpreted mechanisms in the science of organic chemistry. The beta-mannopyranosides, long considered one of the more difficult classes of glycosidic bond to prepare, were no exception to this rule. A number of logical but circuitous routes for their preparation were described in the literature, but they were accompanied by an even greater number of mostly ineffective recipes with which to access them directly. This situation changed in 1996 with the discovery of the 4,6-O-benzylidene acetal as a control element permitting direct entry into the beta-mannopyranosides, typically with high yield and selectivity. The unexpected nature of this phenomenon demanded study of the mechanism, leading first to the demonstration of the alpha-mannopyranosyl triflates as reaction intermediates and then to the development of alpha-deuterium kinetic isotope effect methods to probe their transformation into the product glycosides. In this Account, we assemble our observations into a comprehensive assessment consistent with a single mechanistic scheme. The realization that in the glucopyranose series the 4,6-O-benzylidene acetal is alpha- rather than beta-directing led to further investigations of substituent effects on the stereoselectivity of these glycosylation reactions, culminating in their explanation in terms of the covalent alpha-glycosyl triflates acting as a reservoir for a series of transient contact and solvent-separated ion pairs. The function of the benzylidene acetal, as explained by Bols and co-workers, is to lock the C6-O6 bond antiperiplanar to the C5-O5 bond, thereby maximizing its electron-withdrawing effect, destabilizing the glycosyl oxocarbenium ion, and shifting the equilibria as far as possible toward the covalent triflate. beta-Selective reactions result from attack of the nucleophile on the transient contact ion pair in which the alpha-face of the oxocarbenium ion is shielded by the triflate counterion. The alpha-products arise from attack either on the solvent-separated ion pair or on a free oxocarbenium ion, according to the dictates of the anomeric effect. Changes in selectivity from varying stereochemistry (glucose versus mannose) or from using different protecting groups can be explained by the shifting position of the key equilibria and, in particular, by the energy differences between the covalent triflate and the ion pairs. Of particular note is the importance of substitutents at the 3-position of the donor; an explanation is proposed that invokes their evolving torsional interaction with the substituent at C2 as the chair form of the covalent triflate moves toward the half-chair of the oxocarbenium ion.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMacrolactonizations in the Total Synthesis of Natural ProductsA. Parenty, X. Moreau, and J.-M. CampagneView Author Information Institut de Chimie des Substances Naturelles, Avenue de la Terrasse, F-91198 Gif sur Yvette, France, and Ecole Nationale Supérieure de Chimie, 8 rue de l'Ecole Normale, F-34296 Montpellier, France Cite this: Chem. Rev. 2006, 106, 3, 911–939Publication Date (Web):January 25, 2006Publication History Received19 January 2005Published online25 January 2006Published inissue 1 March 2006https://pubs.acs.org/doi/10.1021/cr0301402https://doi.org/10.1021/cr0301402research-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views13879Altmetric-Citations431LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Chemical synthesis,Lactones,Organic compounds,Organic synthesis,Reagents Get e-Alerts

The development of asymmetric Morita-Baylis-Hillman (MBH) reactions has evolved dramatically over the past few years, parallel to the emerging concept of bifunctional organocatalysis. Whereas organocatalysis is starting to compete with metal-based catalysis in several important organic transformations, the MBH reaction belongs to a group of prototypical reactions in which organocatalysts already display superiority over their metal-based counterparts. This Minireview summarizes recent mechanistic insights and advances in the design and synthesis of small organic molecules for enantioselective MBH and aza-MBH reactions.

The element nitrogen is essential to life. Considerable attention is thus paid to the development of synthetic methods for its introduction into molecules. Nitrenes, long regarded as highly reactive but poorly selective species, have recently emerged as useful tools for the formation of C-N bonds. Practical metal-catalyzed protocols are now available for the preparation of amines through either the aziridination of alkenes or the C-H amination of alkanes. Recent results highlighted in this Minireview suggest that synthetic nitrene chemistry is maturing with a wider scope not limited to these two reactions.

Abstract The use of free radical reactions in organic synthesis has witnessed an extraordinary development in recent years. When properly conceived, radical processes often exhibit many of the properties desired by synthetic organic chemists, such as flexibility, mildness, and selectivity. Unfortunately, the number of synthetically useful radical‐generating systems is still limited, and most applications have relied on tin hydride chemistry. Secondary O ‐alkyl‐ S ‐methyl xanthates, for example, eact with tributyltin hydride to give the corresponding alkane (the Barton‐McCombie reaction). It was, however, found that the isomeric O ‐methyl‐ S ‐alkyl xanthates undergo cleavage of the weaker carbon–sulfur bond and that a chain reaction can be sustained without tin or other heavy metals. A variety of synthetically interesting free radicals can thus be produced and captured, the last propagating step being a reversible transfer of the xanthate group. S ‐Propargyl xanthates represent a special class. Their radical chemistry can be easily overshadowed by hitherto unknown but equally interesting nonradical behavior. Upon heating, a thermal [3,3] sigmatropic rearrangement occurs to give the allenyl isomer, which is in equilibrium with a novel betaine structure. This species is at the heart of a number of new transformations, including formal [3+2] cycloadditions, formation of esters with inversion in the case of secondary alcohols, conversion into 1,3‐dithiol‐2‐ones, generation of cisoid dienes, carbon, carbon‐carbon bond formation through reaction with acid chlorides etc. This account provides a brief description of this original radical and nonradical chemistry of xanthates, an old family of compounds that still harbors many mysteries.

Down-regulation and mutations of the nuclear-architecture proteins lamin A and C cause misshapen nuclei and altered chromatin organization associated with cancer and laminopathies, including the premature-aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here, we identified the small molecule "Remodelin" that improved nuclear architecture, chromatin organization, and fitness of both human lamin A/C-depleted cells and HGPS-derived patient cells and decreased markers of DNA damage in these cells. Using a combination of chemical, cellular, and genetic approaches, we identified the acetyl-transferase protein NAT10 as the target of Remodelin that mediated nuclear shape rescue in laminopathic cells via microtubule reorganization. These findings provide insights into how NAT10 affects nuclear architecture and suggest alternative strategies for treating laminopathies and aging.

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It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s) may not be isolated during subsequent bioassay-guided purification. Herein, we present the concept of bioactive molecular networking to find candidate active molecules directly from fractionated bioactive extracts. By employing tandem mass spectrometry, it is possible to accelerate the dereplication of molecules using molecular networking prior to subsequent isolation of the compounds, and it is also possible to expose potentially bioactive molecules using bioactivity score prediction. Indeed, bioactivity score prediction can be calculated with the relative abundance of a molecule in fractions and the bioactivity level of each fraction. For that reason, we have developed a bioinformatic workflow able to map bioactivity score in molecular networks and applied it for discovery of antiviral compounds from a previously investigated extract of Euphorbia dendroides where the bioactive candidate molecules were not discovered following a classical bioassay-guided fractionation procedure. It can be expected that this approach will be implemented as a systematic strategy, not only in current and future bioactive lead discovery from natural extract collections but also for the reinvestigation of the untapped reservoir of bioactive analogues in previous bioassay-guided fractionation efforts.

Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition of crude extracts can be generated. An efficient exploitation of such data sets requires automated data treatment and access to dedicated fragmentation databases. Various novel bioinformatics approaches such as molecular networking (MN) and in-silico fragmentation tools have emerged recently and provide new perspective for early metabolite identification in natural products (NPs) research. Here we propose an innovative dereplication strategy based on the combination of MN with an extensive in-silico MS/MS fragmentation database of NPs. Using two case studies, we demonstrate that this combined approach offers a powerful tool to navigate through the chemistry of complex NPs extracts, dereplicate metabolites, and annotate analogues of database entries.

The three-component Povarov reaction of aldehydes (2), anilines (3), and benzyl N-vinylcarbamate 4 in the presence of 0.1 equiv of chiral phosphoric acid 5 afforded cis-2,4-disubstituted tetrahydroquinolines (1) in good yields and excellent enantiomeric excesses. The shortest synthesis of torcetrapib reported to date, which features this key three-component reaction, is documented.

Carboxylic acid esters derived from N-hydroxypyridine-2-thione undergo efficient radical chain decarboxylation to the corresponding nor-alkane on treatment with either tri-n-butylstannane or t-butylmercaptan; in the absence of these hydrogen atom donors a smooth decarboxylative rearrangement giving noralkyl 2-pyridyl sulphides is observed.

Abstract Elemental sulfur has been known since Antiquity and found widespread applications in the preparation of black gunpowder, the synthesis of sulfuric acid as well as other sulfur‐containing compounds, and the vulcanization of rubber. Over the last several years, we have come to better understand its properties and discover more applications of elemental sulfur in synthetic organic chemistry. This review summarizes the advances from 2000 in the construction of organic molecules using elemental sulfur via sulfuration, oxidation, reduction and redox condensation processes. magnified image

Microcins are gene-encoded antibacterial peptides, with molecular masses below 10 kDa, produced by enterobacteria. They are secreted under conditions of nutrient depletion and exert potent antibacterial activity against closely related species. Typical gene clusters encoding the microcin precursor, the self-immunity factor, the secretion proteins and frequently the post-translational modification enzymes are located either on plasmids or on the chromosome. In contrast to most of the antibiotics of microbial origin, which are non-ribosomally synthesized by multimodular enzymes termed peptide synthetases, microcins are ribosomally synthesized as precursors, which are further modified enzymatically. They form a restricted class of potent antibacterial peptides. Fourteen microcins have been reported so far, among which only seven have been isolated and characterized. Despite the low number of known representatives, microcins exhibit a diversity of structures and antibacterial mechanisms. This review provides an updated overview of microcin structures, antibacterial activities, genetic systems and biosyntheses, as well as of their mechanisms of action.

Reaction between a sulfur(VI) compound and an iodine(III) oxidant in the presence of a catalytic quantity (<=3 mol %) of a rhodium(II) catalyst leads to the formation of a chiral metallanitrene of unprecedented reactivity. The latter allows intermolecular C-H amination to proceed in very high yields up to 92% and excellent diastereoselectivities up to 99% with C-H bond containing starting materials as the limiting component. The scope of this C-H functionalization includes benzylic and allylic substrates as well as alkanes. Secondary positions react preferentially, but insertion into activated primary C-H bonds or sterically accessible tertiary sites is also possible. Cooperative effects between the nitrene precursor and the chiral catalyst at the origin of these good results have also been applied to kinetic resolution of racemic sulfonimidamide. This methodology paves the way to the use of Csp3-H bonds as synthetic precursors for the introduction of a nitrogen functionality into selected positions.