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.

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.

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...

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.

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.

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.

Characterization of β-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, β-sheet and random coil secondary structures, previous studies showed important discrepancies for β-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized β-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 β-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 β-turns based on circular dichroism spectroscopy.

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

Alkyllitium mixed aggregates: dynamics-free value of the ²J_Li–Li as a simple access to various structural factors, including the dynamics, solvation and the steric hindrance of alkyl chains.

Binding mode of Pyridoclax to myeloid cell leukemia-1 (Mcl-1) revealed by nuclear magnetic resonance spectroscopy, docking and molecular dynamics approaches

Myeloid cell leukemia-1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family proteins. Its amplification is one of the most frequent genetic aberrations found in human cancers. Pyridoclax, a promising BH3 mimetic inhibitor, interacts directly with Mcl-1 and induces massive apoptosis at a concentration of 15 µM in combination with anti-Bcl-x_L strategies in chemo-resistant ovarian cancer cell lines. In this study, a combined experimental and theoretical approach was used to investigate the binding mode of Pyridoclax to Mcl-1. The representative poses generated from dynamics simulations compared with NMR data revealed: (i) Pyridoclax bound to P1 and P2 pockets of Mcl-1 BH3 binding groove through its styryl and methyl groups establishing mainly hydrophobic contacts, (ii) one of the ending pyridines interacts through electrostatic interaction with K234 side chain, a negatively charged residue present only in this position in Mcl-1. Communicated by Ramaswamy H. Sarma.

Recent Advances in NMR: Aggregation, Solvation, and Dynamics of Selected Organolithium Compounds

Nuclear magnetic resonance (NMR) spectroscopy is the most widely used analytical technique to study the structure and dynamics of organolithium compounds, which are the most popular reagents in organic synthesis due to their great diversity and high reactivity. The main strength of this method is that it allows direct analysis in solution of the aggregation, dynamic, and solvation state of reactive intermediates. In this review, we present the NMR tools (nD) involving the 6Li isotope and DOSY experiments with internal references and illustrate their contribution in the structural and dynamic characterization of organolithium compounds in solution through some selected example.

1 Introduction

2 Advantages of the 6Li isotope

3 NMR Experiments Involving the 6Li Isotope

4 Diffusion Ordered NMR Experiments

5 Application of NMR to the Structural Characterization of Organolithium Species

6 Conclusion

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.

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.

2D 7Li Ultrafast CT-COSY: a new tool for the rapid measurement of tiny homonuclear lithium scalar couplings

We report on the first examples of ⁷Li Ultrafast (UF) CT-COSY spectra from lithiated samples and on the usefulness of these experiments for the quantitative estimation of the ²J_7Li–7Li in a much shorter time.

Radical Cyclisation of α-Halo Aluminium Acetals: A Mechanistic Study

α-Bromo aluminium acetals are suitable substrates for Ueno-Stork-like radical cyclisations affording γ-lactols and acid-sensitive methylene-γ-lactols in high yields. The mechanistic study herein sets the scope and limitation of this reaction. The influence of the halide (or chalcogenide) atom X (X=Cl, Br, I, SPh, SePh) in the precursors α-haloesters, as well as influence of the solvent and temperature was studied. The structure of the aluminium acetal intermediates resulting from the reduction of the corresponding α-haloesters has been investigated by low-temperature (13) C-INEPT diffusion-ordered NMR spectroscopy (DOSY) experiments and quantum calculations, providing new insights into the structures of these thermally labile intermediates. Oxygen-bridged dimeric structures with a planar Al2 O2 ring are proposed for the least hindered aluminium acetals, while monomeric structures seem to prevail for the most hindered species. A comparison against the radical cyclisation of aluminium acetals derived from allyl and propargyl alcohols with the parent Ueno-Stork has been made at the BHandHLYP/6-311++G(d,p) level of theory, highlighting mechanistic similarities and differences.

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

A glucosyltransferase is able to catalyze the formation of the thioglycosidic bond and lead to desulfoglycosinolates.

Probing solvent effects on mixed aggregates associating a chiral lithium amide and n-BuLi by NMR: from structure to reactivity

An NMR study of a 1 : 1 mixture of a chiral lithium amide (4a) and n-BuLi shows that depending on the solvent employed (Et2O or THF) a mixed aggregate can form in proportions that are directly related to the ees measured during the enantioselective alkylation of o-tolualdehyde by these same species.

1H Pure Shift DOSY: a handy tool to evaluate the aggregation and solvation of organolithium derivatives

The first successful application of ¹H PS-DOSY for a quantitative estimation of the degree of solvation and aggregation state of organolithium derivatives.

First substoichiometric version of the catalytic enantioselective addition of an alkyllithium to an aldehyde

A substoichiometric enantioselective version of the extremely fast nucleophilic addition of Alk-Li to RCHO is made possible thanks to a thorough analysis of the aggregation phenomena involved in the reaction: calculated quantities of LiCl must be added to the medium at the right time to keep the catalytic cycle running.

The conformation of tetrafluorinated methyl galactoside anomers: crystallographic and NMR studies

The first single-crystal X-ray diffraction study of tetrafluorinated monosaccharide derivatives is presented. Both α- and β-methyl 2,3-dideoxy-2,2,3,3-tetrafluoro-d-galactopyranoside anomers adopt the (4)C(1) conformation. The values for the C1-O1 and C1-O5 bond lengths and the O5-C1-O1-CH(3) dihedral angles are in line with what can be expected from the anomeric and exo-anomeric effects. The chair conformations are slightly distorted, presumably due to repulsion between 1,3-diaxial C-O and C-F bonds. The asymmetric unit of both compounds contains up to three independent molecules, which differ in the conformation of the hydroxymethyl group (including in one case a 'forbidden'gg rotamer). The molecular packing of the β-anomer shows a clear segregation between fluorinated and hydrophilic domains, while for the α-anomer the regions of fluorine segregation are broken by interleafing of OMe groups. There is one close OH⋯F contact, which is likely to arise from the crystal packing. NMR studies show that the two anomers also adopt a (4)C(1) conformation in solution (D(2)O, CDCl(3)).