Efficient removal of persistent and emerging organic pollutants by biosorption using abundant biomass wastes

Persistent and emerging organic pollutants represent a serious and global threat to human health and ecosystems. We describe here a simple, efficient and affordable technology for removing such organic pollutants from aquatic systems. Biosorption process was chosen, meeting these three criteria, and so that biosorbents should be biomass wastes combining the following characteristics: natural, cheap and abundant. Powdered dead roots from invasive alien species (Eichhornia crassipes, Pistia stratiotes and Fallopia japonica), and wastes rich in tannins such as coffee grounds and green tea grounds were tested as biosorbents for removing extensively used organic pollutants: organic UV-filters, insecticides and herbicides. The elemental composition and morphology of the biosorbents were fully determined. The biosorption kinetics for each pair of biosorbent/pollutant was described by a pseudo-second order model. Excellent biosorption efficiency was obtained for 10 μM solution of oxybenzone (89 ± 1%), octocrylene (90 ± 2%), lindane (88 ± 0%) and diuron (90 ± 1%) in only 2 h. And total removal of 10 μM of chlordecone (100 ± 0%) could be achieved, which could be of high concern for the population living in chlordecone-contaminated areas. As such pollutants can be found in aquatic ecosystems, an interference study with salts showed that biosorption efficiency remained as efficient in reconstituted seawater. A principal component analysis was performed as an attempt to rationalise the biosorption results. The solubility of the organic pollutants in water and the concentration of tanins in the biosorbents were key parameters.

Structural insights into recognition of chemokine receptors by Staphylococcus aureus leukotoxins

Staphylococcus aureus (SA) leukocidin ED (LukED) belongs to a family of bicomponent pore forming toxins that play important roles in SA immune evasion and nutrient acquisition. LukED targets specific G protein-coupled chemokine receptors to lyse human erythrocytes (red blood cells) and leukocytes (white blood cells). The first recognition step of receptors is critical for specific cell targeting and lysis. The structural and molecular bases for this mechanism are not well understood but could constitute essential information to guide antibiotic development. Here, we characterized the interaction of LukE with chemokine receptors ACKR1, CCR2, and CCR5 using a combination of structural, pharmacological, and computational approaches. First, crystal structures of LukE in complex with a small molecule mimicking sulfotyrosine side chain (p-cresyl sulfate) and with peptides containing sulfotyrosines issued from receptor sequences revealed the location of receptor sulfotyrosine binding sites in the toxins. Then, by combining previous and novel experimental data with protein docking, classical and accelerated weight histogram (AWH) molecular dynamics we propose models of the ACKR1-LukE and CCR5-LukE complexes. This work provides novel insights into chemokine receptor recognition by leukotoxins and suggests that the conserved sulfotyrosine binding pocket could be a target of choice for future drug development.

Control of conformation in α-helix mimicking aromatic oligoamide foldamers through interactions between adjacent side-chains

The design, synthesis and structural characterization of non-natural oligomers that adopt well-defined conformations, so called foldamers, is a key objective in developing biomimetic 3D functional architectures. For the aromatic oligoamide foldamer family, use of interactions between side-chains to control conformation is underexplored. The current manuscript addresses this objective through the design, synthesis and conformational analyses of model dimers derived from 3-O-alkylated para-aminobenzoic acid monomers. The O-alkyl groups on these foldamers are capable of adopting syn- or anti-conformers through rotation around the Ar-CO/NH axes. In the syn-conformation this allows the foldamer to act as a topographical mimic of the α-helix whereby the O-alkyl groups mimic the spatial orientation of the i and i + 4 side-chains from the α-helix. Using molecular modelling and 2D NMR analyses, this work illustrates that covalent links and hydrogen-bonding interactions between side-chains can bias the conformation in favour of the α-helix mimicking syn-conformer, offering insight that may be more widely applied to control secondary structure in foldamers.

A catalytic protein-proteomimetic complex: using aromatic oligoamide foldamers as activators of RNase S

Foldamers are abiotic molecules that mimic the ability of bio-macromolecules to adopt well-defined and organised secondary, tertiary or quaternary structure. Such templates have enabled the generation of defined architectures which present structurally defined surfaces that can achieve molecular recognition of diverse and complex targets. Far less explored is whether this mimicry of nature can extend to more advanced functions of biological macromolecules such as the generation and activation of catalytic function. In this work, we adopt a novel replacement strategy whereby a segment of protein structure (the S-peptide from RNase S) is replaced by a foldamer that mimics an α-helix. The resultant prosthetic replacement forms a non-covalent complex with the S-protein leading to restoration of catalytic function, despite the absence of a key catalytic residue. Thus this functional protein-proteomimetic complex provides proof that significant segments of protein can be replaced with non-natural building blocks that may, in turn, confer advantageous properties.

Double quick, double click reversible peptide "stapling"

A versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation and bearing a functional handle for inhibition of protein–protein interactions is described.

The development of constrained peptides for inhibition of protein–protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein–protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne–azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions

A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction.

13-Helix folding of a β/γ-peptide manifold designed from a “minimal-constraint” blueprint

A bottom-up design rationale was used to select an alternating β/γ-peptide motif which folds into a well-defined 13-helix in solution.

Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052T (98.4 %), Rhizobium tibeticum CCBAU 85039T (98.1 %), Rhizobium grahamii CCGE 502T (98.0 %) and Rhizobium mesoamericanum CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with R. endophyticum CCGE 2052T, R. tibeticum CCBAU 85039T, R. mesoamericanum CCGE 52T, Rhizobium grahamii CCGE 502T, Rhizobium etli CCBAU 85039T and Rhizobium radiobacter KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus Rhizobium with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).

The leguminous species Anthyllis vulneraria as a Zn-hyperaccumulator and eco-Zn catalyst resources

Anthyllis vulneraria was highlighted here as a Zn-hyperaccumulator for the development of a pilot phytoextraction process in the mine site of Les Avinières in the district of Saint-Laurent-Le-Minier. A. vulneraria appeared to hyperaccumulate the highest concentration of Zn in shoots with a better metal selectivity relative to Cd and Pb than the reference Zn-hyperaccumulator Noccea caerulescens. A bigger biomass production associated to a higher Zn concentration conducted A. vulneraria to the highest total zinc gain per hectare per year. As a legume, A. vulneraria was infected by rhizobia symbionts. Inoculation of A. vulneraria seeds showed a positive impact on Zn hyperaccumulation. A large-scale culture process of symbiotic rhizobia of A. vulneraria was investigated and optimized to allow large-scale inoculation process. Contaminated shoots of A. vulneraria were not considered as wastes and were recovered as Eco-Zn catalyst in particular, examples of organic synthesis, electrophilic aromatic substitution. Eco-Zn catalyst was much more efficient than conventional catalysts and allowed greener chemical processes.

Metallophytes for organic synthesis: towards new bio-based selective protection/deprotection procedures

We propose for the first time using metal hyperaccumulating plants for the construction of a repertoire of protection and deprotection conditions in a concept of orthogonal sets. Protection of alcohol, carbonyl, carboxyl, and amino groups are considered. The ecocatalysts derived from metal-rich plants allow selective, mild, eco-friendly, and efficient protection or deprotection reactions. The selectivity is controlled by the choice of the metal, which is hyperaccumulated by the metallophyte.

Pushing the limits of signal resolution to make coupling measurement easier

Novel band selective decoupled pure shift selective refocusing experiments allowed simplification of the measurement of all δ¹H, and J_HH couplings with an ultrahigh spectral resolution in peptides.

Conformational preferences in the β-peptide oligomers of cis-2-amino-1-fluorocyclobutane-1-carboxylic acid

These oligomers adopt a regular zig-zag strand-like secondary structure which does not rely on intra-residue 6-ring hydrogen bonds for stability.

The discovery of 9/8-ribbons, β/γ-peptides with curved shapes governed by a combined configuration-conformation code

The design of a β/γ-peptide reveals an unprecedented 9/8-ribbon whose curvature depends on the β-residue configuration and the γ-residue conformation.

A simple synthesis of 2-keto-3-deoxy-D-erythro-hexonic acid isopropyl ester, a key sugar for the bacterial population living under metallic stress

2-Keto-3-deoxy-D-erythro-hexonic acid (KDG) is the key intermediate metabolite of the Entner Doudoroff (ED) pathway. A simple, efficient and stereoselective synthesis of KDG isopropyl ester is described in five steps from 2,3-O-isopropylidene-D-threitol with an overall yield of 47%. KDG isopropyl ester is studied as an attractive marker of a functional Entner Doudoroff pathway. KDG isopropyl ester is used to promote growth of ammonium producing bacterial strains, showing interesting features in the remediation of heavy-metal polluted soils.