Development of a root exudate collection protocol for metabolomics analysis using Nuclear Magnetic Resonance.

Large amounts of root exudates are released by plant roots into the soil. Due to their importance in regulating the rhizosphere properties, it is necessary to unravel the precise composition and function of exudates at the root-soil interface. However, obtaining root exudates without inducing artefacts is a difficult task. To analyse the low molecular weight molecules secreted by pea roots, a protocol of root exudate collection was developed to perform a metabolomics analysis using Nuclear Magnetic Resonance (NMR). To date a few NMR studies are dedicated to root exudates. Plant culture, exudates collection and sample preparation methods had thus to be adapted to the NMR approach. Here, pea seedlings were hydroponically grown. The obtained NMR fingerprints show that osmotic stress increases the quantity of the exudates but not their diversity. We therefore selected a protocol reducing the harvest time and using an ionic solvent and applied it to the analysis of faba bean exudates. NMR analysis of the metabolic profiles allowed to discriminate between pea and faba bean according to their exudate composition. This protocol is therefore very promising for studying the composition of root exudates from different plant species as well as their evolution in response to different environmental conditions or pathophysiological events.

NMR and DFT Studies with a Doubly Labelled 15 N/6 Li S-Trifluoromethyl Sulfoximine Reveal Why a Directed ortho-Lithiation Requires an Excess of n-BuLi.

This work shows why it is imperious to use an excess of butyllithium for a directed ortho-lithiation of a trifluoromethyl sulfoximine. The analysis of mixtures of n-BuLi and sulfoximine 1 in THF-d8 using {1 H, 6 Li, 13 C, 15 N, 19 F} NMR experiments at low temperatures reveal that a first deprotonation occurs that leads to dimeric and tetrameric N-lithiated sulfoximine (93 : 7). Using an excess n-BuLi (5 equivalents), the second deprotonation on the ortho-position of the aromatic occurs. Six species were observed and characterized on the way. It includes three aggregates involving a sulfoximine: i) a [dilithiated sulfoximine/(n-BuLi)] dimer solvated by four molecules of THF (Agg2, 39 %); ii) a [dilithiated sulfoximine/(n-BuLi)3 ] tetramer solvated by six molecules of THF (Agg3, 39 %); iii) a [dilithiated sulfoximine/(n-BuOLi)3 ] tetramer solvated by four molecules of THF (Agg1, 22 %). A DFT study afforded optimized solvated structures for all these aggregates, fully consistent with the NMR data.

High pressure promoted dearomatization of nitroarenes by [4+2] cycloadditions with silyloxydienes.

Simple nitroarenes such as nitronaphthalenes and nitroquinolines smoothly undergo dearomatizing [4+2] cycloadditions with silyloxydienes under 16 kbar. Highly functionalized 3-dimensional polycyclic adducts bearing a tetrasubstituted carbon centre at the ring junction are obtained in one step from simple raw materials. This unprecedented dearomative Diels-Alder process is performed at room temperature without any chemical promoter, illustrating the exceptional role of high pressure as a physical promoter.

Fluorocyclopropane-Containing Proline Analogue: Synthesis and Conformation of an Item in the Peptide Chemist's Toolbox.

Over the years, numerous modifications to the structure of proline have been made in order to tune its effects on bioactive compounds. Notably, the introduction of a cyclopropane ring or a fluorine atom has produced interesting results. Herein, we describe the synthesis of a proline containing fluorocyclopropane. This modified amino acid was inserted into a tripeptide, whose conformation was studied by nuclear magnetic resonance and density functional theory calculations.

Drug Repurposing: Deferasirox Inhibits the Anti-Apoptotic Activity of Mcl-1.

INTRODUCTION: With the aim of repositioning commercially available drugs for the inhibition of the anti-apoptotic myeloid cell leukemia protein, Mcl-1, implied in various cancers, five molecules, highlighted from a published theoretical screening, were selected to experimentally validate their affinity toward Mcl-1. RESULTS: A detailed NMR study revealed that only two of the five tested drugs, Torsemide and Deferasirox, interacted with Mcl-1. NMR data analysis allowed the complete characterization of the binding mode of both drugs to Mcl-1, including the estimation of their affinity for Mcl-1. Biological assays evidenced that the biological activity of Torsemide was lower as compared to the Deferasirox, which was able to efficiently and selectively inhibit the anti-apoptotic activity of Mcl-1. Finally, docking and molecular dynamics led to a 3D model for the Deferasirox:Mcl-1 complex and revealed the positioning of the drug in the Mcl-1 P2/P3 pockets as well as almost all synthetic Mcl-1 inhibitors. Interestingly, contrary to known synthetic Mcl-1 inhibitors which interact through Arg263, Deferasirox, establishes a salt bridge with Lys234. CONCLUSION: Deferasirox could be a potential candidate for drug repositioning as Mcl-1 inhibitor.

Bonding analysis in ytterbium(II) distannyl and related tetryls.

The syntheses of the ytterbium(II) distannyl [Yb{Sn(SiMe3)3}2·(thf)4] (Yb-Sn) and of its digermyl analogue [Yb{Ge(SiMe3)3}2·(thf)3] (Yb-Ge) are presented. The compounds were characterised by multinuclear high-resolution solution NMR spectroscopy, including 171Yb NMR, and by X-ray diffraction crystallography. The bonding and electronic properties of the two complexes, along with those of the known ytterbium(II) disilyl derivative [Yb{Si(SiMe3)3}2·(thf)3] (Yb-Si) and those of the congeneric calcium distannyl [Ca{Sn(SiMe3)3}2·(thf)4] (Ca-Sn), were investigated in detail by DFT calculations. This analysis points at a primarily ionic Yb-tetrel bonding, with a small covalent contribution, attributed principally to the 5d(Yb) participation. This weak covalent character is found to be larger for the distannyl Yb-Sn than for its lighter Si- and Ge-derivatives. The covalent component is also found to be greater in Yb-Sn than in Ca-Sn, due to the availability of the 5d(Yb) orbitals for bonding.

Metabolic and Anti-Inflammatory Protective Properties of Human Enriched Serum Following Artichoke Leaf Extract Absorption: Results from an Innovative Ex Vivo Clinical Trial.

The aging of our population is accompanied by an increased prevalence of chronic diseases. Among those, liver, joint and adipose tissue-related pathologies have a major socio-economic impact. They share common origins as they result from a dysregulation of the inflammatory and metabolic status. Plant-derived nutrients and especially polyphenols, exert a large range of beneficial effects in the prevention of chronic diseases but require clinically validated approaches for optimized care management. In this study, we designed an innovative clinical approach considering the metabolites produced by the digestive tract following the ingestion of an artichoke leaf extract. Human serum, enriched with metabolites deriving from the extract, was collected and incubated with human hepatocytes, human primary chondrocytes and adipocytes to determine the biological activity of the extract. Changes in cellular behavior demonstrated that the artichoke leaf extract protects hepatocytes from lipotoxic stress, prevents adipocytes differentiation and hyperplasia, and exerts chondroprotective properties in an inflammatory context. These data validate the beneficial health properties of an artichoke leaf extract at the clinical level and provide both insights and further evidence that plant-derived nutrients and especially polyphenols from artichoke may represent a relevant alternative for nutritional strategies addressing chronic disease issues.

Metal-metal bonded alkaline-earth distannyls.

The first families of alkaline-earth stannylides [Ae(SnPh3)2·(thf) x ] (Ae = Ca, x = 3, 1; Sr, x = 3, 2; Ba, x = 4, 3) and [Ae{Sn(SiMe3)3}2·(thf) x ] (Ae = Ca, x = 4, 4; Sr, x = 4, 5; Ba, x = 4, 6), where Ae is a large alkaline earth with direct Ae-Sn bonds, are presented. All complexes have been characterised by high-resolution solution NMR spectroscopy, including 119Sn NMR, and by X-ray diffraction crystallography. The molecular structures of [Ca(SnPh3)2·(thf)4] (1'), [Sr(SnPh3)2·(thf)4] (2'), [Ba(SnPh3)2·(thf)5] (3'), 4, 5 and [Ba{Sn(SiMe3)3}2·(thf)5] (6'), most of which crystallised as higher thf solvates than their parents 1-6, were established by XRD analysis; the experimentally determined Sn-Ae-Sn' angles lie in the range 158.10(3)-179.33(4)°. In a given series, the 119Sn NMR chemical shifts are slightly deshielded upon descending group 2 from Ca to Ba, while the silyl-substituted stannyls are much more shielded than the phenyl ones (δ 119Sn/ppm: 1', -133.4; 2', -123.6; 3', -95.5; 4, -856.8; 5, -848.2; 6', -792.7). The bonding and electronic properties of these complexes were also analysed by DFT calculations. The combined spectroscopic, crystallographic and computational analysis of these complexes provide some insight into the main features of these unique families of homoleptic complexes. A comprehensive DFT study (Wiberg bond index, QTAIM and energy decomposition analysis) points at a primarily ionic Ae-Sn bonding, with a small covalent contribution, in these series of complexes; the Sn-Ae-Sn' angle is associated with a flat energy potential surface around its minimum, consistent with the broad range of values determined by experimental and computational methods.

Bis(imino)carbazolate lead(II) fluoride and related halides.

The versatility of a bulky bis(imino)carbazolate ligand in lead(ii) chemistry is illustrated by the synthesis of a soluble, heteroleptic lead(ii) fluoride and several halide (Cl, Br and I), amide and hydrocarbyl congeners. All complexes have been structurally authenticated, and a full set of 207Pb NMR data is discussed.

Intertwined Analytical, Experimental and Theoretical Studies on the Formation and Structure of a Copper Dienolate.

The reaction of a silyl dienolate, a Cu(II) salt and TBAT yielding the corresponding copper dienolate is addressed. A combined NMR and cyclic voltammetry analysis first highlight the role of TBAT in the Cu(II) to Cu(I) reduction and the structure of the precatalytic species. From these first results a second set of NMR and theoretical studies enable the determination of the structure and the mechanism of formation of the copper dienolate catalytic species. Finally, we showed that that the copper catalyst promote the E/Z s-cis/s-trans equilibration of the silyl dienolate precursor through a copper dienolate intermediate. All of these results unveil some peculiarities of the catalytic and asymmetric vinylogous Mukaiyama reaction.

Accurate measurement of effective Li-Li scalar coupling constants: the NMR missing link for alkyllithium aggregates.

Scalar coupling in organolithium systems can provide access to useful structural and dynamic informations. In this work, we propose a robust method for the accurate measurement of the effective 2JLi-Li coupling constant in tetramerics alkyllithium aggregates. This crucial information, unavalaible to date, gives a simple access to various structural factors, including the dynamics, solvation and the operative steric hindrance of alkyl chains.

Corrigendum: Characterization of Milkisin, a Novel Lipopeptide With Antimicrobial Properties Produced By Pseudomonas sp. UCMA 17988 Isolated From Bovine Raw Milk.

[This corrects the article DOI: 10.3389/fmicb.2018.01030.].

Characterization of ß-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.

Electronic circular dichroism is one of the most used spectroscopic techniques for peptide and protein structural characterization. However, while valuable experimental spectra exist for α-helix, ß-sheet and random coil secondary structures, previous studies showed important discrepancies for ß-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized ß-turns in peptides, namely types I, II, I' and II'. In particular, by combining classical molecular dynamics simulations and state-of-the-art quantum time-dependent density functional theory (with the polarizable embedding multiscale model) computations, two common electronic circular dichroism patterns were found for couples of ß-turn types (namely, type I/type II' and type II/type I'), at first for a minimal di-peptide model (Ace-Ala-Ala-NHMe), but also for all sequences tested with non-aromatic residues in the central positions. On the other hand, as expected, aromatic substitution causes important perturbations to the previously found ECD patterns. Finally, by applying suitable approximations, these patterns were subsequently rationalized based on the exciton chirality rule. All these results provide useful predictions and pave the way for a possible experimental characterization of ß-turns based on circular dichroism spectroscopy.

Dearomatization of 3-Nitroindoles with Highly γ-Functionalized Allenoates in Formal (3+2) Cycloadditions.

3-Nitroindoles are easily reacted with highly substituted γ-allenoates in the presence of a commercially available phosphine catalyst. For instance, allenoates derived from biomolecules such as amino and deoxycholic acids are combined for the first time with 3-nitroindole. The corresponding dearomatized (3+2) tricyclic cycloadducts are obtained as α-regioisomers exclusively. DFT computations shed light on this multi-step reaction mechanism and on the selectivities observed in the sequence.

Characterization of Milkisin, a Novel Lipopeptide With Antimicrobial Properties Produced By Pseudomonas sp. UCMA 17988 Isolated From Bovine Raw Milk.

Biosurfactants such as lipopeptides are amphiphilic compounds produced by microorganisms such as bacteria of the genera of Pseudomonas and Bacillus. Some of these molecules proved to have interesting antimicrobial, antiviral, insecticide, and/or tensioactive properties that are potentially useful for the agricultural, chemical, food, and pharmaceutical industries. Raw milk provides a physicochemical environment that is favorable to the multiplication of a broad spectrum of microorganisms. Among them, psychrotrophic bacterial species, especially members of the genus Pseudomonas, are predominant and colonize milk during cold storage and/or processing. We isolated the strain Pseudomonas sp. UCMA 17988 from raw cow milk, with antagonistic activity against Listeria monocytogenes, Staphylococcus aureus, and Salmonella enterica Newport. Antimicrobial molecules involved in the antagonistic activity of this strain were characterized. A mass spectrometry analysis highlighted the presence of four lipopeptides isoforms. The major isoform (1409 m/z), composed of 10 carbons in the lipidic chain, was named milkisin C. The three other isoforms detected at 1381, 1395, and 1423 m/z, that are concomitantly produced, were named milkisin A, B, and D, respectively. The structure of milkisin, as confirmed by nuclear magnetic resonance analyses, is closely related to amphisin family. Indeed, the peptidic chain was composed of 11 amino acids, 6 of which are conserved among the family. In conclusion, Pseudomonas sp. UCMA 17988 produces new members of the amphisin family which are responsible for the antagonistic activity of this strain.

Rational design of carbamate-based dual binding site and central AChE inhibitors by a "biooxidisable" prodrug approach: Synthesis, in vitro evaluation and docking studies.

Herein, we report a new class of dual binding site AChE inhibitor 4 designed to exert a central cholinergic activation thanks to a redox-activation step of a prodrug precursor 3. Starting from potent pseudo-irreversible quinolinium salts AChE inhibitors 2 previously reported, a new set of diversely substituted quinolinium salts 2a-p was prepared and assayed for their inhibitory activity against AChE. Structure-activity relationship (SAR) analysis of 2a-p coupled with molecular docking studies allowed us to determine which position of the quinolinium scaffold may be considered to anchor the phtalimide fragment presumed to interact with the peripheral anionic site (PAS). In addition, molecular docking provided insight on the linker length required to connect both quinolinium and phatlimide moieties without disrupting the crucial role of quinolinium salt moiety within the catalytic active site (CAS); namely placing the carbamate in the correct position to trigger carbamylation of the active-site serine hydroxyl. Based on this rational design, the putative dual binding site inhibitor 4 and its prodrug 3 were synthesized and subsequently evaluated in vitro against AChE. Pleasingly, whereas compound 4 showed to be a highly potent inhibitor of AChE (IC50 = 6 nM) and binds to AChE-PAS to the same extent as donepezil, its prodrug 3 revealed to be inactive (IC50 > 10 µM). These preliminary results constitute one of the few examples of carbamate-based dual binding site AChE inhibitors.

Synthesis and Identification of Aryl and Alkyl Gem-Dilithium Phosphido-Boranes: A Boost to the Chemistry of Phosphandiides.

The synthesis and identification of unprecedented gem-dianionic phosphorus compounds, that is, gem-dilithium phosphido-boranes Li2 [RP⋅BH3 ], with R=Ph or Cy, are reported in THF solution. These were obtained by double deprotonation of the corresponding primary phosphine-borane precursors RPH2 ⋅BH3 . Their in-depth structural study, based on multinuclear (1 H, 6 Li, 7 Li, 11 B, 13 C, 31 P) mono- and bi-dimensional NMR analyses, indicates a strong influence of the phosphorus substituent on the structure of the gem-dianionic phosphorus structure; a monomeric arrangement was obtained when R=phenyl, whereas a cyclic oligomer was observed for R=cyclohexyl. These compounds represent a new type of useful reagent, and their access paves the way for the concept of "RP synthons" (i.e., RP2- phosphandiides), likely to be the most flexible precursors of a variety of phosphorus targets.

Revisiting absorption and electronic circular dichroism spectra of cholesterol in solution: a joint experimental and theoretical study.

Cholesterol is doubtless one of the most studied bio-molecules, which unfortunately features low emitting properties, precluding its in vivo study by fluorescence experiments. The design of fluorescent analogues of cholesterol is thus an appealing challenge in biochemistry, which simultaneously requires minor changes in its chemical structure (to retain main biological properties) and considerable enhancement of light emission. To this aim, the photochemical behaviour of the native molecule has to be deeply understood. In this work, we focused our attention on the electronic absorption of cholesterol in several common organic solutions, combining experimental (through ultraviolet-visible and electronic circular dichroism spectroscopy) and theoretical approaches (at the time-dependent density functional theory level) in order to solve the important discrepancies previously reported in the literature on the maximum absorption wavelengths and on the nature (Rydberg and/or π → π*) of the associated electronic transition.

A Combined 1 H/6 Li†NMR DOSY Strategy Finally Uncovers the Structure of Isopropyllithium in THF.

Despite its common use in synthesis, the structure of isopropylliyhium in THF has never been determined, a dimer being generally proposed but not supported. This paper fills this data gap through a sophisticated NMR study that shows that, in THF at low-temperature, isopropyllithium is in the form of a 1:2 mixture of a trisolvated monomer and a disolvated dimer in equilibrium. The presence of the monomer, never evoked before, together with a hypo-solvation of the dimer hinted by DFT calculations, provides a rational explanation to the remarkable reactivity of this organolithium reagent in ethereal solvents.

UGT74B1 from Arabidopsis thaliana as a versatile biocatalyst for the synthesis of desulfoglycosinolates.

Thioglycosides, even if rare in Nature, have gained increased interest for their biological properties. Chemical syntheses of this class of compounds have been largely studied but little has been reported on their biosynthesis. Herein, combining experiments from the different fields of enzymology, bioorganic chemistry and molecular modeling, we wish to demonstrate the versatility of the glucosyltransferase UGT74B1 and its synthetic potency for the preparation of a variety of natural and unnatural desulfoglycosinolates.