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International audience; Annonaceous acetogenins are natural products held responsible for atypical parkinsonism due to chronic consumption in traditional medicine or as food. Due to their long-term neurotoxic effects in humans, the complete chemical characterization of acetogenins in complex mixtures has become crucial. Characterization by tandem mass spectrometry (MS/MS) of acetogenins using collisioninduced dissociation (CID) from lithium adducts provides additional structural information compared to protonated or sodiated species such as ketone location on the acetogenins backbone. However, diagnostic ions are present at a very low intensity limiting this approach to abundant species in the extracts. Copper adducts led to diagnostic fragment ions that allow to identify the position of oxygen rings and hydroxyl substituents. Fragmentation rules were established based on acetogenin standards allowing the identification of 45 over the 77 analogues observed in an extract of Annona muricata by LC-MS/MS using post-column infusion of copper sulfate (CuSO4) solution. Molecular networks that were generated thanks to specific fragmentations obtained with copper, led to the distinction of THF ring position or to the identification of hydroxylated lactone for instance, while networks generated from lithium adducts mainly distinguish analogues with a hydroxyl group at C4 from the other structures.

International audience; An endolichenic strain of the Ascomycetaceous Xylaria hypoxylon, cultivated alone or in coculture with another endolichenic fungus Dendrothyrium variisporum, produced seven new bioactive eremophilane sesquiterpenes eremoxylarins D−J (1−7). The isolated compounds disclosed a high similarity with the eremophilane core of the bioactive integric acid, and structures were elucidated by 1D and 2D NMR spectra and electronic circular dichroism (ECD) analyses. Eremoxylarins D, F, G, and I showed a selective activity against Gram-positive bacteria such as methicillin-resistant Staphylococcus aureus with minimum inhibitory concentration (MIC) values between 0.39 and 12.5 μg/mL. Eremoxylarin I, the most antibacterial active sesquiterpene, was also active against HCoV-229E at a concentration nontoxic to the hepatoma Huh-7 cell line with an 50% inhibitory concentration (IC 50) of 18.1 μM and a 50% cytotoxic concentration (CC 50) of 46.6 μM.

Densities, viscosities, isothermal compressibilities, and thermal expansivities of carbonated hydroalcoholic solutions relevant for sparkling beverages are evaluated by molecular dynamics simulations as a function of temperature and alcoholic degree. They are compared with available experimental data, among which new measurements of densities and viscosities are performed in that respect. The OPC water model seems to yield the most accurate results, and the choice of CO

International audience; The first effective synthetic approach to naphthofuroquinones via a reaction involving lawsone, various aldehydes, and three isocyanides under microwave irradiation afforded derivatives in moderate to good yields. In addition, for less-reactive aldehydes, two naphtho-enaminodione quinones were obtained for the first time, as result of condensation between lawsone and isocyanides. X-ray structure determination for 9 and 2D-NMR spectra of 28 confirmed the obtained structures. All compounds were evaluated for their anti-infectious activities against Plasmodium falciparum, Leishmania donovani, and Mycobacterium tuberculosis. Among the naphthofuroquinone series, 17 exhibited comparatively the best activity against P. falciparum (IC50 = 2.5 μM) and M. tuberculosis (MIC = 9 μM) with better (P. falciparum) or equivalent (M. tuberculosis) values to already-known naphthofuroquinone compounds. Among the two naphtho-enaminodione quinones, 28 exhibited a moderate activity against P. falciparum with a good selectivity index (SI > 36) while also a very high potency against L. donovani (IC50 = 3.5 μM and SI > 28), rendering it very competitive to the reference drug miltefosine. All compounds were studied through molecular modeling on their potential targets for P. falciparum, Pfbc1, and PfDHODH, where 17 showed the most favorable interactions.

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International audience; Mimicking and extending the gating properties of biological pores is of paramount interest for the fabrication of membranes that could be used in filtration or drug processing. Here, we build a selective and switchable nanopore for macromolecular cargo transport. Our approach exploits polymer graftings within artificial nanopores to control the translocation of biomolecules. To measure transport at the scale of individual biomolecules, we use fluorescence microscopy with a zero-mode waveguide set up. We show that grafting polymers that exhibit a lower critical solution temperature creates a toggle switch between an open and closed state of the nanopore depending on the temperature. We demonstrate tight control over the transport of DNA and viral capsids with a sharp transition (∼1 °C) and present a simple physical model that predicts key features of this transition. Our approach provides the potential for controllable and responsive nanopores in a range of applications.

International audience; This paper reviews graph-theory-based methods that were recently developed in our group for post-processing molecular dynamics trajectories. We show that the use of algorithmic graph theory not only provides a direct and fast methodology to identify conformers sampled over time but also allows to follow the interconversions between the conformers through graphs of transitions in time. Examples of gas phase molecules and inhomogeneous aqueous solid interfaces are presented to demonstrate the power of topological 2D graphs and their versatility for post-processing molecular dynamics trajectories. An even more complex challenge is to predict 3D structures from topological 2D graphs. Our first attempts to tackle such a challenge are presented with the development of game theory and reinforcement learning methods for predicting the 3D structure of a gas-phase peptide.

The gas-phase reactivity towards cytosine (C) of alkylmercury cations CnH2n+1Hg+, and more particularly CH3Hg+, C2H5Hg+, n-C4H9Hg+ and t-C4H9Hg+, has been studied for the first time by combining tandem mass spectrometry, infrared multiple photon dissociation spectroscopy (IRMPD) and density functional theory (DFT) calculations. Under electrospray conditions, the interaction of C with the cations derived from alkylmercury chloride compounds gives rise to a single type of complex of general formula [RHg(C)]+, except for t-butylmercury which turned to be unreactive. Subsequent MS/MS experiments showed that [RHg]+ ions (R=Me, Et, n-Bu) exhibit a peculiar reactivity characterized by the transfer of the alkyl group, R, to the nucleobase leading to a [(C)R]+ ion, accompanied by the reduction of the metal and loss of 0 Hg. As the length of the alkyl chain increases (n 2), a new fragmentation path leading to protonated cytosine is opened, associated with the elimination of a Cn,H2n,Hg moiety. This latter process is clearly overwhelming with n-BuHg+. The mechanisms associated with both dissociation channels were examined through the use of IRMPD data in the fingerprint region, and by exploring the corresponding potential energy surfaces in the DFT framework, This work has been also supported by the “Fonds pour le Rayonnement de la Recherche (FRR, Université d’Evry Val d’Essonne) and by Project PID2021- 125207NB-C31 and PID2019-110091GB-I00 from the Ministerio de Ciencia e Innovación (MICINN) of Spain. M. M. Montero-Campillo thanks the Ministerio de Universidades for her ARPU (Ayudas para la Recualificación del Profesorado Universitario) fellowship at the Universidade de Vigo (Spain), supported by the Plan de Recuperación, Transformación y Resiliencia. Computational time at Centro de Computación Científica (CCC) of Universidad Autónoma de Madrid is also acknowledged

International audience; nhibiting receptor tyrosine kinases is commonly achieved by two main strategies targeting either the intracellular kinase domain by low molecular weight compounds or the extracellular ligand-binding domain by monoclonal antibodies. Identifying small molecules able to inhibit RTKs at the extracellular level would be highly desirable to gain exquisite selectivity but is believed to be challenging owing to the size of RTK endogenous ligands (cytokines, growth factors) and the topology of RTK extracellular domains. We here report the high-throughput screening of the French Chemical Library (48K compounds) for extracellular inhibitors of the Fms-like tyrosine kinase 3 (FLT3) receptor tyrosine kinase, by a homogeneous time-resolved fluorescence competition assay. A total of 679 small molecular weight ligands (1.4%) were confirmed to strongly inhibit (>75%) the binding of the fluorescent labeled FLT3 ligand (FL cytokine) to FLT3 overexpressed in HEK-293 cells, at two different concentrations (5 and 20 μM). Concentration-response curves, obtained for 111 lead-like molecules, confirmed the unexpected tolerance of the FLT3 extracellular domain for low molecular weight druggable inhibitors exhibiting submicromolar potencies, chemical diversity, and promising pharmacokinetic properties. Further investigation of one hit confirmed inhibitory properties in dorsal root ganglia neurons and in a mouse model of neuropathic pain.

The implementation of a reliable, rapid, inexpensive, and simple method for whole-proteome identification would greatly benefit cell biology research and clinical medicine. Proteins are currently identified by cleaving them with proteases, detecting the polypeptide fragments with mass spectrometry, and mapping the latter to sequences in genomic/proteomic databases. Here, we demonstrate that the polypeptide fragments can instead be detected and classified at the single-molecule limit using a nanometer-scale pore formed by the protein aerolysin. Specifically, three different water-soluble proteins treated with the same protease, trypsin, produce different polypeptide fragments defined by the degree by which the latter reduce the nanopore's ionic current. The fragments identified with the aerolysin nanopore are consistent with the predicted fragments that trypsin could produce.

A new vobasine–tryptamine-based monoterpene indole alkaloid pseudodimer was isolated from the stem bark of Voacanga africana. As a minor constituent occurring in a thoroughly investigated plant, this molecule was targeted based on a molecular networking strategy and a rational MS2-guided phytochemical investigation led to its isolation. Its structure was formally established based on HRMS, 1D/2D NMR data, and the application of the tool Small Molecule Accurate Recognition Technology (SMART 2.0). Its absolute configuration was assigned by the exciton chirality method and TD-DFT ECD calculations. Besides featuring an unprecedented intermonomeric linkage in the small group of vobasine/tryptamine hybrids, pyrrovobasine also represents the first pyrraline-containing representative in the whole monoterpene indole alkaloids group. Biosynthetic hypotheses possibly underpinning these structural oddities are proposed here.

The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.

Standardin vitrocell culture is one of the pillars of biomedical science. However, there is increasing evidence that 2D systems provide biological responses that are often in disagreement within vivoobservations, partially due to limitations in reproducing the native cellular microenvironment. 3D materials that are able to mimic the native cellular microenvironment to a greater extent tackle these limitations. Here, we report Porous yet Dense (PyD) type I collagen materials obtained by ice-templating followed by topotactic fibrillogenesis. These materials combine extensive macroporosity, favouring the cell migration and nutrients exchange, as well as dense collagen walls, which mimic locally the Extracellular Matrix. When seeded with Normal Human Dermal Fibroblasts (NHDFs), PyD matrices allow for a faster and more extensive colonisation when compared with equivalent Non-Porous matrices. The textural properties of the PyD materials also impact cytoskeletal and nuclear 3D morphometric parameters. Due to the effectiveness in creating a biomimetic 3D environment for NHDFs and the ability to promote cell culture for more than 28 days without subculture, we anticipate that PyD materials could configure an important step towardsin vitrosystems applicable to other cell types and with higher physiological relevance.

International audience; Several studies have reported that the tetracycline (TC) class antibiotic doxycycline (DOX) is effective against Parkinson’s disease (PD) pathomechanisms. The aim of the present work was three-fold: (i) Establish a model system to better characterize neuroprotection by DOX; (ii) Compare the rescue effect of DOX to that of other TC antibiotics; (iii) Discover novel neuroprotective TCs having reduced antibiotic activity. For that, we used cultures of mouse midbrain dopamine (DA) neurons and experimental conditions that model iron-mediated oxidative damage, a key mechanism in PD pathobiology. We found that DOX and the other TC antibiotic, demeclocycline (DMC), provided sustained protection to DA neurons enduring iron-mediated insults, whereas chlortetracycline and non-TC class antibiotics did not. Most interestingly, non-antibiotic derivatives of DOX and DMC, i.e., DDOX and DDMC, respectively, were also robustly protective for DA neurons. Interestingly, DOX, DDOX, DMC, and DDMC remained protective for DA neurons until advanced stages of neurodegeneration, and the rescue effects of TCs were observable regardless of the degree of maturity of midbrain cultures. Live imaging studies with the fluorogenic probes DHR-123 and TMRM revealed that protective TCs operated by preventing intracellular oxidative stress and mitochondrial membrane depolarization, i.e., cellular perturbations occurring in this model system as the ultimate consequence of ferroptosis-mediated lipid peroxidation. If oxidative/mitochondrial insults were generated acutely, DOX, DDOX, DMC, and DDMC were no longer neuroprotective, suggesting that these compounds are mostly effective when neuronal damage is chronic and of low-intensity. Overall, our data suggest that TC derivatives, particularly those lacking antibiotic activity, might be of potential therapeutic utility to combat low-level oxidative insults that develop chronically in the course of PD neurodegeneration.

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International audience; Hydrazone compounds represent an important area of research that includes, among others, synthetic approaches and biological studies. A series of 17 hydrazones have been synthesized by mechanochemical means. The fragments chosen were phenolic and furanyl aldehydes coupled with 12 heterocyclic hydrazines or hydrazinamides. All compounds can be obtained quantitatively when operating on a planetary ball mill and a maximum reaction time of 180 min (6 cycles of 30 min each). Complete spectroscopic analyses of hydrazones revealed eight compounds (3–5, 8–11, 16) present in one geometric form, six compounds (1, 2, 13–15) present in two isomeric forms, and three compounds (6, 7, 12) where one rotation is restricted giving rise to two different forms. The single crystal X-ray structure of one of the hydrazones bearing the isoniazid fragment (8) indicates a crystal lattice consisting of two symmetry-independent molecules with different geometries. All compounds obtained were tested for anti-infectious and antibacterial activities. Four compounds (1, 3, 5 and 8) showed good activity against Mycobacterium tuberculosis, and one (7) was very potent against Staphylococcus aureus. Most interesting, this series of compounds displayed very promising antileishmanial activity. Among all, compound 9 exhibited an IC50 value of 0.3 µM on the Leishmania donovani intramacrophage amastigote in vitro model and a good selectivity index, better than miltefosine, making it worth evaluating in vivo.

International audience; GLIC is a prokaryotic orthologue of brain pentameric neurotransmitter receptors. Using whole-cell patch-clamp electrophysiology in a host cell line, we show that short-chain di-carboxylate compounds are positive modulators of pHo 5-evoked GLIC activity, with a rank order of action fumarate > succinate > malonate > glutarate. Potentiation by fumarate depends on intracellular pH, mainly as a result of a strong decrease of the pHo 5-evoked current when intracellular pH decreases. The modulating effect of fumarate also depends on extracellular pH, as fumarate is a weak inhibitor at pHo 6 and shows no agonist action at neutral pHo. A mutational analysis of residue-dependency for succinate and fumarate effects, based on two carboxylate-binding pockets previously identified by crystallography (Fourati et al. 2020), shows that positive modulation involves both the inter-subunit pocket, homologous to the neurotransmitter-binding orthotopic site, and the intra-subunit (also called vestibular) pocket. An almost similar pattern of mutational impact is observed for the effect of caffeate, a known negative modulator. We propose, for both di- carboxylate compounds and caffeate, a model where the inter-subunit pocket is the actual binding site, and the region corresponding to the vestibular pocket is required either for inter-subunit binding itself, or for binding-to-gating coupling during the allosteric transitions involved in pore gating modulation.

Controlled dielectric breakdown (CDB) is gaining popularity for fabricating solid-state nanopores in situ with size control in a simple, low-cost, and scalable way. This technique could be used for a broad type of applications in the field of nucleic acid analysis and even for protein studies. In this work, we studied the entry and transport of double-stranded DNAs using a solid-state nanopore fabricated by CDB as a function of applied voltage for two different DNA lengths. We showed that the blockade rate increases exponentially with voltage up to 120 mV. The energy barrier depends on the chain length, and the dwell times decrease with applied voltage up to 120 mV. Moreover, no matter the chain length, it is possible to differentiate two families of blockade amplitudes, high and low ones, due to DNA folding.

International audience; A new and simple method for preparing confined copper and nickel nanoparticles by thermal treatment of their respective cations inside Mobil Composition of Matter 41 (MCM–41) hydrophobic nanopores is presented here. Surface modified MCM–41 hydrophobic materials were impregnated by using high-pressure treatment with copper II (Cu II) or nickel II (Ni II) aqueous solutions. After pressure release and washing, the remaining metal cations, confined exclusively within the nanopores, were heated, forming metallic nanoparticles. Reduction of the cations by a redox reaction between the hydrophobic organic surface and the confined metal cations is proposed. Transmission electronic microscopy (TEM), selected area electron diffraction (SAED), nitrogen (N2) adsorption at −196 °C (77 K), Fourier transform infrared (FTIR) and thermogravimetric (TGA) analyses evidenced the identification of copper and nickel nanoparticles (NPs).

International audience; Anion recognition represents an intense area of research in supramolecular chemistry. The last two decades have been marked by spectacular advances in the design of new anion receptors. Moreover, the development of approaches combining experimental and theoretical studies has proved to be particularly relevant, allowing a better understanding and rationalization of the phenomena involved in anion complexation processes. In this context, the combination of weak interactions within the same receptor and their synergistic effects, called cooperativity, has attracted increasing interest within the scientific community. This review focuses on the combination of anion-π and hydrogen bonds and the emerging concept of cooperativity. The most relevant anion-π donor families are presented. The concept of cooperativity is illustrated using the most recent examples present in current literature.

In the gut microbiota, resident bacteria prevent pathogens infection by producing specific metabolites. Among bacteria belonging to phylum Bacteroidota, we have previously shown that Bacteroides fragilis or its cell-free supernatant inhibited in vitro Salmonella Heidelberg translocation. In the present study, we have analyzed this supernatant to identify bioactive molecules after extraction and subsequent fractionation using a semi-preparative reversed-phase Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS). The results indicated that only two fractions (F3 and F4) strongly inhibited S. Heidelberg translocation in a model mimicking the intestinal epithelium. The efficiency of the bioactive fractions was evaluated in BALB/c mice, and the results showed a decrease of S. Heidelberg in Peyer’s patches and spleen, associated with a decrease in inflammatory cytokines and neutrophils infiltration. The reduction of the genus Alistipes in mice receiving the fractions could be related to the anti-inflammatory effects of bioactive fractions. Furthermore, these bioactive fractions did not alter the gut microbiota diversity in mice. To further characterize the compounds present in these bioactive fractions, Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) data were analyzed through molecular networking, highlighting cholic acid (CA) and deoxycholic acid. In vitro, CA had inhibitory activity against the translocation of S. Heidelberg by significantly decreasing the expression of Salmonella virulence genes such as sipA. The bioactive fractions also significantly downregulated the flagellar gene fliC, suggesting the involvement of other active molecules. This study showed the interest to characterize better the metabolites produced by B. fragilis to make them means of fighting pathogenic bacteria by targeting their virulence factor without modifying the gut microbiota.

The electrocatalytic epoxidation of alkenes at heterogeneous catalysts using water as the sole oxygen source is a promising safe route toward the sustainable synthesis of epoxides, which are essential building blocks in organic chemistry. However, the physico-chemical parameters governing the oxygen-atom transfer to the alkene and the impact of the electrolyte structure on the epoxidation reaction are yet to be understood. Here, we study the electrocatalytic epoxidation of cyclooctene at the surface of gold in hybrid organic/aqueous mixtures using acetonitrile (ACN) solvent. Gold was selected, as in ACN/water electrolytes gold oxide is formed by reactivity with water at potentials less anodic than the oxygen evolution reaction (OER). This unique property allows us to demonstrate that a sacrificial mechanism is responsible for cyclooctene epoxidation at metallic gold surfaces, proceeding through cyclooctene activation, while epoxidation at gold oxide shares similar reaction intermediates with the OER and proceeds via the activation of water. More importantly, we show that the hydrophilicity of the electrode/electrolyte interface can be tuned by changing the nature of the supporting salt cation, hence affecting the reaction selectivity. At low overpotential, hydrophilic interfaces formed by using strong Lewis acid cations are found to favor gold passivation. Instead, hydrophobic interfaces created by the use of large organic cations favor the oxidation of cyclooctene and the formation of epoxide. Our study directly demonstrates how tuning the hydrophilicity of electrochemical interfaces can improve both the yield and selectivity of anodic reactions at the surface of heterogeneous catalysts.

International audience; Modulation and fine-tuning of the strength of weak interactions to bind anions are described in a series of synthetic receptors. The general design of the receptors includes both a urea motif and a tetrazine motif. The synthetic sequence towards three receptors is detailed. Impacts of H-bond strength and linker length between urea and tetrazine on chloride complexation are studied. Binding properties of the chloride anion are examined in both the ground and excited states using a panel of analytical methods (NMR spectroscopy, mass spectrometry, UV/Visible spectroscopies, and fluorescence). A ranking of the receptors by complexation strength has been determined, allowing a better understanding of the structure-properties relationship on these compounds.

International audience; In this perspective article, we provide a bibliographic compilation of experimental and theoretical work on Cd, Hg, and Pb, and analyze in detail the bonding of M2+ and CH3M+ (M = Zn, Cd, Hg, Pb) with urea and thiourea as suitable models for larger biochemical bases.Through the use of DFT calculations, we have found that although in principle binding energies decrease according to ionic size (Zn2+ 4 Cd2+ 4 Pb2+), Hg2+ largely breaks the trend. Through the use of EDA (Energy Decomposition Analysis) it is possible to explain this behavior, which is essentially due to the strong contribution of polarization to the binding. This conclusion is ratified by the NEDA (Natural Energy Decomposition Analysis) formalism, showing that the charge transfer term is very large in all cases, but particularly in the case of the mercury–thiourea system. The general trends observed for the interactions with CH3M+ monocations show however CH3Hg+ binding energies systematically smaller than the CH3Zn+ ones, likely because the relativistic contraction of the Hg orbitals is very much attenuated by the attachment to the methyl group. Finally, we have investigated the gas-phase reactivity between EtHg+ and uracil to compare it with that exhibited by CH3Hg+ and n-ButHg+ previously described in the literature. This comparison gathers new information that highlights the importance of the length of the alkyl chain attached to the metal on the mechanisms of these reactions. For methyl mercury, only the alkyl transfer process is allowed; for butyl mercury, protonation is clearly favored, and for ethyl mercury, both paths are compe-titive experimentally.

International audience; Poly(ornithine-co-citrulline)s are ureido-based polymers which were shown to exhibit tunable upper critical solution temperature (UCST) behavior, a property that can be exploited to develop thermoresponsive nanoparticles for controlled drug delivery systems. To gain insight into the driving forces that govern the formation and dissolution processes of poly(ornithine-co-citrulline) nanoparticles, a molecular dynamics (MD) simulation study has been carried out using MARTINI-based protein coarse-grained models. Multi-microsecond simulations at temperatures ranging from 280 to 370 K show that the fully reparametrized version 3.0 of MARTINI force field is able to capture the dependence on temperature of poly(ornithine-co-citrulline) aggregation and 1 dissolution, while version 2.2 could not account for it. Furthermore, the phase separation observed in these simulations allowed to extrapolate a phase diagram based on the Flory-Huggins theory of polymer solution which could help in future rational design of drug delivery nanoparticles based on poly(amino acid)s.

The antibiotic tetracycline demeclocycline (DMC) was recently reported to rescue α-synuclein (α-Syn) fibril-induced pathology. However, the antimicrobial activity of DMC precludes its po-tential use in long-term neuroprotective treatments. Here, we synthesized a DMC derivative with residual antibiotic activity and improved neuroprotective effects. The molecule, called de-rivative demeclocycline (DDMC), was obtained by the removal of both dimethylamino substitu-ents at position 4 and the reduction of the hydroxyl group at position 12a on ring A of DMC. The modifications strongly diminished its antibiotic activity against Gram-positive and Gram-negative bacteria. Moreover, this compound preserved the low toxicity of DMC in dopaminergic cell lines while improving its ability to interfere with α-Syn amyloid-like aggregation, showing the highest effectiveness of all tetracyclines tested. Likewise, DDMC demonstrated the ability to reduce seeding induced by the exogenous addition of α-Syn preformed fibrils (α-SynPFF ) in ex vitro models and in SH-SY5Y-α-Syn-tRFP cells. In addition, in the presence of DDMC, α-SynPFF were less inflammogenic, as they dampened the release of tumor necrosis factor α (TNF-α) and glutamate by microglial cells compared to control fibrils. Our results suggest that DDMC may be a promising drug candidate for hit-to-lead development and preclinical studies in PD and other synucleinopathies.

Glycosaminoglycans are highly anionic functional polysaccharides with information content in their structure that plays a major role in the communication between the cell and the extracellular environment. The study presented here reports the label-free detection and analysis of glycosaminoglycan molecules at the single molecule level using sensing by biological nanopore, thus addressing the need to decipher structural information in oligo- and polysaccharide sequences, which remains a major challenge for glycoscience. We demonstrate that a wild-type aerolysin nanopore can detect and characterize glycosaminoglycan oligosaccharides with various sulfate patterns, osidic bonds and epimers of uronic acid residues. Size discrimination of tetra- to icosasaccharides from heparin, chondroitin sulfate and dermatan sulfate was investigated and we show that different contents and distributions of sulfate groups can be detected. Remarkably, differences in α/β anomerization and 1,4/1,3 osidic linkages can also be detected in heparosan and hyaluronic acid, as well as the subtle difference between the glucuronic/iduronic epimers in chondroitin and dermatan sulfate. Although, at this stage, discrimination of each of the constituent units of GAGs is not yet achieved at the single-molecule level, the resolution reached in this study is an essential step toward this ultimate goal.

Electromagnetic radiation-triggered therapeutic effect has attracted a great interest over the last 50 years. However, translation to clinical applications of photoactive molecular systems developed to date is dramatically limited, mainly because their activation requires excitation by low-energy photons from the ultraviolet to near infra-red range, preventing any activation deeper than few millimetres under the skin. Herein we conceive a strategy for photosensitive-system activation potentially adapted to biological tissues without any restriction in depth. High-energy stimuli, such as those employed for radiotherapy, are used to carry energy while molecular activation is provided by local energy conversion. This concept is applied to azobenzene, one of the most established photoswitches, to build a radioswitch. The radiation-responsive molecular system developed is used to trigger cytotoxic effect on cancer cells upon gamma-ray irradiation. This breakthrough activation concept is expected to expand the scope of applications of photosensitive systems and paves the way towards the development of original therapeutic approaches.

International audience; The clustering, collision, and relaxation dynamics of pristine and doped helium nanodroplets is theoretically investigated in cases of pickup and clustering of heliophilic argon, collision of heliophobic cesium atoms, and coalescence of two droplets brought into contact by their mutual long-range van der Waals interaction. Three approaches are used and compared with each other. The He time-dependent density functional theory method considers the droplet as a continuous medium and accounts for its superfluid character. The ring-polymer molecular dynamics method uses a path-integral description of nuclear motion and incorporates zero-point delocalization while bosonic exchange effects are ignored. Finally, the zero-point averaged dynamics approach is a mixed quantum–classical method in which quantum delocalization is described by attaching a frozen wavefunction to each He atom, equivalent to classical dynamics with effective interaction potentials. All three methods predict that the growth of argon clusters is significantly hindered by the helium host droplet due to the impeding shell structure around the dopants and kinematic effects freezing the growing cluster in metastable configurations. The effects of superfluidity are qualitatively manifested by different collision dynamics of the heliophilic atom at high velocities, as well as quadrupole oscillations that are not seen with particle-based methods, for droplets experiencing a collision with cesium atoms or merging with each other.

International audience; Cell shape changes that are fuelled by the dynamics of the actomyosin cytoskeleton control cellular processes such as motility and division. However, the mechanisms of interplay between cell membranes and actomyosin are complicated to decipher in the complex environment of the cytoplasm. Using biomimetic systems offers an alternative approach to studying cell shape changes in assays with controlled biochemical composition. Biomimetic systems allow quantitative experiments that can help to build physical models describing the processes of cell shape changes. This article reviews works in which actin networks are reconstructed inside or outside cell-sized Giant Unilamellar Vesicles (GUVs), which are models of cell membranes. We show how various actin networks affect the shape and mechanics of GUVs and how some cell shape changes can be reproduced in vitro using these minimal systems.

International audience; In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since they allow longer and faster simulations. We performed coarse-grained molecular dynamics of the ionic transport through the alpha-hemolysin protein nanopore, inserted into a lipid bilayer surrounded by solvent and ions. For this purpose, we used the MARTINI coarse-grained force field and its polarizable water solvent (PW). Moreover, the electric potential difference applied experimentally was mimicked by the application of an electric field to the system. We present, in this study, the results of 1.5 mu s long-molecular dynamics simulations of 12 different systems for which different charged amino acids were neutralized, each of them in the presence of nine different electric fields ranging between +/- 0.04 V/nm (a total of around 100 simulations). We were able to observe several specific features of this pore, current asymmetry and anion selectivity, in agreement with previous studies and experiments, and we identified the charged amino acids responsible for these current behaviors, therefore validating our coarse-grain approach to study ionic transport through nanopores. We also propose a microscopic explanation of these ionic current features using ionic density maps.

International audience; Erismadelphus exsul Mildbr bark is widely used in Gabonese folk medicine. However, little is known about the active compounds associated with its biological activities. In the present study, phytochemical profiling of the ethanolic extract of Erismadelphus exsul was performed using a de-replication strategy by coupling HPLC-ESI-Q/TOF with a molecular network approach. Eight families of natural compounds were putatively identified, including cyclopeptide alkaloids, esterified amino acids, isoflavonoid- and flavonoid-type polyphenols, glycerophospholipids, steroids and their derivatives, and quinoline alkaloids. All these compounds were identified for the first time in this plant. The use of molecular networking obtained a detailed phytochemical overview of this species. Furthermore, antioxidant (2,2-diphenyl-1-picryl-hydrazylhydrate (DPPH) and ferric reducing capacity (FRAP)) and in vitro antimicrobial activities were assessed. The crude extract, as well as fractions obtained from Erismadelphus exsul, showed a better reactivity to FRAP than DPPH. The fractions were two to four times more antioxidant than ascorbic acid while reacting to FRAP, and there was two to nine times less antioxidant than this reference while reacting to DPPH. In addition, several fractions and the crude extract exhibited a significant anti-oomycete activity towards the Solanaceae phytopathogen Phytophthora infestans in vitro, and, at a lower extent, the antifungal activity against the wheat pathogen Zymoseptoria tritici had growth inhibition rates ranging from 0 to 100%, depending on the tested concentration. This study provides new insights into the phytochemical characterization and the bioactivities of ethanolic extract from Erismadelphusexsul bark.

Hydrophobicity/hydrophilicity of aqueous interfaces at the molecular level results from a subtle balance in the water-water and water-surface interactions. This is characterized here via density functional theory-molecular dynamics (DFT-MD) coupled with vibrational sum frequency generation (SFG) and THz-IR absorption spectroscopies. We show that water at the interface with a series of weakly interacting materials is organized into a two-dimensional hydrogen-bonded network (2D-HB-network), which is also found above some macroscopically hydrophilic silica and alumina surfaces. These results are rationalized through a descriptor that measures the number of "vertical" and "horizontal" hydrogen bonds formed by interfacial water, quantifying the competition between water-surface and water-water interactions. The 2D-HB-network is directly revealed by THz-IR absorption spectroscopy, while the competition of water-water and water-surface interactions is quantified from SFG markers. The combination of SFG and THz-IR spectroscopies is thus found to be a compelling tool to characterize the finest details of molecular hydrophobicity at aqueous interfaces.

International audience; Towards the mavacurane and akuammilane monoterpene indole alkaloids, we developed divergent oxidative couplings between the indole nucleus (at N1 or C7) and the C16-malonate of a common tricyclic model related to strictosidine according to a biosynthetic hypothesis postulated by Hesse and Schmid. These oxidative cyclizations lead selectively to the formation of the N1-C16 bond of pleiocarpamine or to the C7-C16 bond of strictamine. We were then able to obtain the scaffold of talbotine.

Polyesters are omnipresent in our everyday lives and their synthesis via eco-friendly methods is becoming a major challenge today. The co-polymerization of cyclic anhydrides and epoxides was first reported by Fischer in 1960 involving a tertiary amine as an initiator. Since then, metal complexes have been used as catalysts in this process, Inoue being a major contributor in this area until Coates’ breakthrough using a zinc-based catalyst leading to high molecular weight polymers. Such a pathway to polyesters is the most promising method for accessing a large array of polyesters given the large pool of commercially available or easily synthesizable epoxides and cyclic anhydrides. To date, the use of metal-free organo-catalysts/initiators in this co-polymerization remains to be explored; this area is still in its infancy but interesting developments have been reported over the past five years. In this review, we provide a complete overview of such organo-catalyzed/initiated processes since 2015.

International audience; Phosphoramidates obtained according to the ProTide strategy are known for their ability to increase the biological activity of various nucleosides. A series of such prodrugs of SRO-91, a non-natural ribofuranosyl-1,2,3-triazole C-nucleoside obtained by a synthetic sequence involving an indium mediated alkynylation and a Huisgen cycloaddition, was prepared and the antitumor activity on 3 strains of tumor cells was investigated. Two compounds 9a and 9c exhibited interesting cell proliferative inhibitions (IC50 = 2.5–12.1 µM) on two cell lines (pancreas and lung). Moreover, concerning the antiviral activity, another phosphoramidate 14 bearing a different aryl masking group exhibited an IC50 of 5 µM on Crimean-Congo Hemorrhagic Fever orthonairovirus. In both cases, free SRO-91 presented no activity on these cell lines.

Nanopore-based single-molecule analysis technique is a promising approach in the field of proteomics. In this Technical Brief, the interaction between the biological nanopore of Aerolysin (AeL) and peptides is investigated, focusing on potential biases depending on the AeL activation protocol. Our results reveal that residual trypsin, which may be unintentionally introduced in analyte solution when using a classical AeL activation protocol, can induce a significant formation of shorter peptides by enzymatic degradation of longer ones, which may lead to unwanted effects and/or misinterpretations. AeL free-trypsin activation protocol eliminates this bias and appears more appropriate for peptide/proteins analysis, specifically in the perspective of nanopore-based molecular fingerprinting or of low-abundance species characterization.

International audience; Seven syntheses of (-)-spongidepsin, a natural product isolated from Spongia sp. with moderate antiproliferative activity, are described and the different analogs obtained during these syntheses are reported. A comparison between the different syntheses has been achieved.

International audience; We show that phase-sensitive vibrational sum frequency generation (SFG) spectra of solid/water and air/water interfaces, neutral and charged, can be successfully predicted using classical molecular dynamics (CMD) simulations in combination with simple nonpolarizable force fields (FFs). This can be achieved when employing velocity–velocity autocorrelation functions weighted by parameterized Raman and atomic polar tensors for the computation of the SFG. This procedure avoids computing polarizability tensors and dipole moments using either costly ab initio molecular dynamics (AIMD) simulations or CMD simulations with more complex and computationally demanding FFs. Such a methodology paves the way to a broad usage and computationally low-cost theoretical SFG spectroscopy, as even flexible nonpolarizable water models and common FFs for inorganic surfaces can provide good predictions of the SFG spectra, in rather good qualitative agreement with AIMD and/or experiments. The strongly reduced computational cost in our approach opens the possibility to study larger systems for long periods of time, for example, allowing a detailed characterization of the electric double-layer formation at interfaces with “environmentally relevant” ionic concentrations (mM), extracting fingerprints by theoretical CMD–SFG spectroscopy.

International audience; Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

With an increasing global population that is rapidly ageing, our society faces challenges that impact health, environment, and energy demand. With this ageing comes an accumulation of cellular changes that lead to the development of diseases and susceptibility to infections. This impacts not only the health system, but also the global economy. As the population increases, so does the demand for energy and the emission of pollutants, leading to a progressive degradation of our environment. This in turn impacts health through reduced access to arable land, clean water, and breathable air. New monitoring approaches to assist in environmental control and minimize the impact on health are urgently needed, leading to the development of new sensor technologies that are highly sensitive, rapid, and low-cost. Nanopore sensing is a new technology that helps to meet this purpose, with the potential to provide rapid point-of-care medical diagnosis, real-time on-site pollutant monitoring systems to manage environmental health, as well as integrated sensors to increase the efficiency and storage capacity of renewable energy sources. In this review we discuss how the powerful approach of nanopore based single-molecule, or particle, electrical promises to overcome existing and emerging societal challenges, providing new opportunities and tools for personalized medicine, localized environmental monitoring, and improved energy production and storage systems.

Membrane proteins are present in both cardiac T-tubule (TTM) and outer surface membrane (OSM), although at a different density. Classical pharmacology does not allow to explore the function of a membrane protein separately in OSM vs. TTM. Here, we developed a technology based on size exclusion to explore the function of β-adrenergic receptors (β-ARs) located in the OSM. We synthetized a PEG-Iso molecule by covalent linking between isoprenaline (Iso) and a 5000 Da PolyEthylene-Glycol (PEG). Using confocal microscopy, we show that PEGylation constrains molecules outside the T-tubule network. PEG-Iso produced similar effects as Iso on I ca,L , sarcomere shortening and Ca 2+ transients. However, PEG-Iso increased [cAMP] i with a lower efficacy than Iso, produced a much lower stimulation of nuclear PKA activity than Iso but a larger stimulation of cytosolic PKA at equivalent levels of [cAMP] i . Our results show that activation of OSM β-ARs is sufficient to activate cytosolic PKA and excitation-contraction coupling, but insufficient to activate nuclear PKA or nuclear protein phosphorylation for which additional activation of TTM β-ARs is needed.

The Human endosulfatase HSulf-2 catalyzes the 6-O-desulfation of heparan sulfate (HS) glycosaminoglycan present on proteoglycan at the surface of cells. The interaction properties of HS are thus finely regulated by its sulfation profile. HSulf-2 is synthesized as a pro-protein which matures after cleavage by furin. It has a molecular organization made up of two chains probably linked by disulfide bridges. A hydrophilic domain (HD) overflowing on the two chains and specific to these endosulfatases constitutes a recognition structure of the substrate HS. The organization of HSulf-2 resulting from a folding of the two chains remains to be determined. The objectives of this work aim both to characterize the structure, and to determine its influence on HSulf-2 catalytic activity. By biochemical and biophysical approaches such as mass spectrometry and NMR we have identified for the first time the positions and structures of post-translational modifications present on HSulf-2. Thus, 5 N-glycans have been characterized and 10 cysteines involved in disulfide bridges between the two chains have been identified. We further characterized a unique post-translational modification, which is a chondroitin sulfate-type glycosaminoglycan chain. We have also studied the role of this chain by spectroscopy that seems to act like an activity regulator for HSulf-2. The results obtained should increase the comprehension of this important mechanism for regulating HS interraction and activity. In addition, they should establish the structural bases for the development of new therapeutic approaches targeting HSulfs, that are biomarkers of tumoral progression, in particular by the design of specific inhibitors., L’endosulfatase humaine HSulf-2 catalyse la 6-O-désulfatation du glycosaminoglycane héparane sulfate (HS) présent à la surface cellulaire. Les propriétés d'interaction de HS sont ainsi finement régulée par son profil de sulfatation. HSulf-2 est synthétisée sous forme d'une protéine qui devient mature après clivage par la furine. Elle présente une organisation moléculaire constituée de deux chaînes reliées vraisemblablement par des ponts disulfures. Un domaine hydrophile (HD) débordant sur les deux chaînes et propre à ces endosulfatases constitue une structure de reconnaissance du substrat. L'organisation de HSulf-2 résultant d'un repliement des deux chaînes reste à déterminer. Les objectifs de ce travail visent à la fois à caractériser la structure, et à déterminer son influence sur l'activité catalytique de HSulf-2. Par des approches biochimiques et biophysiques telles que la spectrométrie de masse et la RMN, nous avons identifié pour la première fois les positions et structures des modifications post-traductionnelles présentes sur HSulf-2. Ainsi 5 N-glycanes ont été caractérisés et 10 cystéines impliquées dans des ponts disulfure ont été identifiées. Nous avons en outre caractérisé une modification post- traductionnelle unique qui est une chaîne de glycosaminoglycane de type chondroïtine sulfate. Nous avons également étudié le rôle de cette chaine qui semble réguler l’activité de HSulf-2. Les résultats obtenus ouvrent des voies de compréhension sur cet important mécanisme de régulation de l'activité de HS. Par ailleurs, ils devraient établir les bases structurales pour le développement de nouvelles approches thérapeutiques ciblant les HSulfs, notamment par la conception d'inhibiteurs spécifiques.

International audience; Complex battery degradation is an interplay of different processes correlated to the thermodynamic, chemical, and mechanical instability of materials. Their degradation kinetics and mechanisms are functions of several intrinsic and environmental conditions. The degradation of the battery cell can be minimized by using preventive steps, like artificial interphases, coatings, additives, or materials that operate within the thermodynamic stability voltage window. Like in most systems/applications degradation processes/aging cannot be avoided since battery cells operate in different environments. Self-healing functionalities have been proved in different areas of material science and they can significantly improve the performance of battery cells. Some of them have been demonstrated on the laboratory scale, while other degradation processes have been tackled only by the development of preventive approaches. Since self-healing functionalities add additional weight and cost to the battery cell, directions of development should be focused on modification of nonactive materials, preferably based on biosourced materials to lower environmental impact. Important issues include detection of degradation using sensors and the vectorization of self-healing components and their controlled release. In addition to this, a triggering process of extrinsic self-healing components together with manufacturability and recyclability should be considered from the early stages of the development phase.

International audience; This study aims to extend an innovative electrochemical process for a total elimination and/or separation of different soluble heavy metals. This objective is very important because today the water pollution, due to intense anthropogenic activities by toxic chemical substances and heavy metals in particular, becomes a serious problem for environment and human health. In this context, we have developed recently an efficient electrochemical process for removing soluble Pb(II) as adherent oxide(s) films on conductive substrate, leading to reach directly acceptable concentration levels for the environment and drinking water, and even in a complex medium. In the present study, this electrochemical process of depollution was extended to remove separately other heavy metals, and to recover them in the form of adherent films according to the same principle. The adequate parameters were researched and tested for each heavy metals present alone before to be applied on a synthetic aqueous solution containing a mixture of the studied heavy metals such as Pb(II), Cu(II), Ni(II), and Cd(II). In complement, some tests were performed with success on effluents, coming from wastewater plant (WWTP) containing different heavy metals, confirming the real interests of this innovative electrochemical treatment. These all results are very promising for future applications either for wastewater depollution either for very easy separation of different heavy metals, which generally requires complex and energy consuming chemical steps.

A biosensor device for the detection and characterization of protein-glycosaminoglycan interactions is being actively sought and constitutes the key to identifying specific carbohydrate ligands, an important issue in glycoscience. Mass spectrometry (MS) hyphenated methods are promising approaches for carbohydrate enrichment and subsequent structural characterization. In the study herein, we report the analysis of interactions between the glycosaminoglycans (GAGs) heparin (HP) and heparan sulfate (HS) and various cytokines by coupling surface plasmon resonance imaging (SPRi) for thermodynamic analysis method and MALDI-TOF MS for structural determination. To do so, we developed an SPR biochip in a microarray format and functionalized it with a self-assembled monolayer of short poly(ethylene oxide) chains for grafting the human cytokines stromal cell-derived factor-1 (SDF-1α), monocyte chemotactic protein-1 (MCP-1), and interferon-γ. The thermodynamic parameters of the interactions between these cytokines and unfractionated HP/HS and derived oligosaccharides were successively determined using SPRi monitoring, and the identification of the captured carbohydrates was carried out directly on the biochip surface using MALDI-TOF MS, revealing cytokine preferential affinity for GAGs. The MS identification was enhanced by on-chip digestion of the cytokine-bound GAGs with heparinase, leading to the detection of oligosaccharides likely involved in the binding sequence of GAG ligands. Although several carbohydrate array-based assays have been reported, this study is the first report of the successful analysis of protein-GAG interactions using SPRi-MS coupling.

Self-assembly of small molecules in water provides a powerful route to nanostructures with pristine molecular organization and small dimensions (, Molecular self-assembly in water is conventionally limited to amphiphilic molecules. This study harnesses sacrificial surface groups and a post-assembly chemical reaction to form nanostructures unachievable by spontaneous self-assembly alone.

Our increasing dependence on lithium-ion batteries for daily energy storage applications calls for the enhancement of their performances. Research efforts, which have so far relied on increasing energy densities, have recently been focused on durability and sustainability. In this context, the inspiration of life sciences has placed great hope on supramolecular chemistry to equip batteries with some added smart functionalities, in order to address their inherent failures such as electrodes swelling and partial dissolution, hence enhancing their lifespan. This work aims to evaluate how relevant this new worldwide research interest is, by focusing on cyclodextrins (CDs), which are bio-sourced cage molecules that can give reversible supramolecular host-guest interactions. We first successfully exploit the selective host-guest interaction of CDs towards polysulfides to discriminate these soluble lithium-sulfur batteries intermediates by nanopore, with a single sulfur atom resolution. Not only this approach lays the ground to the design of powerful sensors for electrolytes, but it also confers weight to a new sulfur confinement strategy based on CD. Next, we apply this host-guest interaction at the macromolecular scale by synthetizing mechanically interlocked architectures to be used as Si anode binders. Prepared from CDs-based polyrotaxanes (PRs) cross-linked with poly(acrylic acid), the PR-PAA prototypes disclose new routes of accommodating Si volume changes. Finally, we identify the crucial structural parameters involved in the better cyclability of Si anodes and provide an optimized design for PR-PAA binders., Pour satisfaire aux exigences du marché, les batteries lithium-ion, devenues aujourd’hui indispensables, font l’objet d’intenses études. Cette recherche, jusqu’alors concentrée sur l’augmentation de la densité énergétique des matériaux actifs, se tourne désormais vers les problématiques de durabilité ou plus généralement liées au développement durable. En s’inspirant de la nature, la chimie supramoléculaire suscite de nombreux espoirs pour résoudre certaines défaillances intrinsèques aux batteries, comme le gonflement ou la dissolution des électrodes, ce qui permettrait une augmentation de leur durée de vie. Dans ce contexte, cette thèse s’intéresse aux cyclodextrines (CDs), molécules biosourcées capables de former des complexes supramoléculaires d’inclusion de type hôte-invité. Tout d’abord, nous avons étudié la complexation de la CD avec les polysulfures, rendant ainsi possible la détection à l’atome de soufre près par nanopore de ces intermédiaires parasitant l’électrolyte des batteries lithium-soufre. Ces résultats prometteurs ouvrent la voie à l’utilisation de nanopores comme sondes ultra-sensibles des électrolytes, mais aussi au développement de nouvelles stratégies de confinement de la cathode de soufre impliquant la CD. Nous avons ensuite utilisé le pouvoir complexant de la CD à l’échelle macromoléculaire pour synthétiser des polyrotaxanes (PR), assemblages supra-moléculaires où les CDs ont l’aptitude de se mouvoir le long d’une chaîne polymère. Les architectures PR-PAA, qui résultent de la réticulation de l’acide poly(acrylique) sur les CDs portées par les PRs, constituent de nouveaux liants polymères pour anode de silicium, capables de remédier à leurs changements de volume conséquents. L’étude de la relation entre structure des PR-PAA et leurs performances ont permis de nettes améliorations en cyclage.