Switchable Redox and Thermo-Responsive Supramolecular Polymers Based on Cyclodextrin-Polyoxometalate Tandem.

Supramolecular polymers built from stimuli-responsive host-guest interactions represent an attractive way of tailoring smart materials. Herein, we exploit the chaotropic effect of polyoxometalates and related host-guest properties to design unconventional polymer systems with reversible redox and thermo-responsive sol-gel transition. These supramolecular networks result from the association of cyclodextrin-based oligomers and Keggin-type POMs acting as electro-active crosslinking agents. The structure and the dynamics of such self-assembly systems have been investigated using a multiscale approach involving MALDI-TOF, viscosity measurements, cyclic voltammetry, 1H-NMR (1D and DOSY), and Small-Angle X-ray Scattering. Our results reveal that the chaotropic effect corresponds to a powerful and efficient force that can be used to induce responsiveness in hybrid supramolecular oligomeric systems.

In Situ Bioconjugation of a Maleimide-Functionalized Ruthenium-Based Photosensitizer to Albumin for Photodynamic Therapy.

Maleimide-containing prodrugs can quickly and selectively react with circulating serum albumin following their injection in the bloodstream. The drug-albumin complex then benefits from longer blood circulation times and better tumor accumulation. Herein, we have applied this strategy to a previously reported highly phototoxic Ru polypyridyl complex-based photosensitizer to increase its accumulation at the tumor, reduce off-target cytotoxicity, and therefore improve its pharmacological profile. Specifically, two complexes were synthesized bearing a maleimide group: one complex with the maleimide directly incorporated into the bipyridyl ligand, and the other has a hydrophilic linker between the ligand and the maleimide group. Their interaction with albumin was studied in-depth, revealing their ability to efficiently bind both covalently and noncovalently to the plasma protein. A crucial finding is that the maleimide-functionalized complexes exhibited significantly lower cytotoxicity in noncancerous cells under dark conditions compared to the nonfunctionalized complex, which is a highly desirable property for a photosensitizer. The binding to albumin also led to a decrease in the phototoxicity of the Ru bioconjugates in comparison to the nonfunctionalized complex, probably due to a decreased cellular uptake. Unfortunately, this decrease in phototoxicity was not compensated by a dramatic increase in tumor accumulation, as was demonstrated in a tumor-bearing mouse model using inductively coupled plasma mass spectrometry (ICP-MS) studies. Consequently, this study provides valuable insight into the future design of in situ albumin-binding complexes for photodynamic therapy in order to maximize their effectiveness and realize their full potential.

N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing.

Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases remain incompletely characterized. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last 'orphan' modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.

A new series of bioactive Mo(V)2O2S2-based thiosemicarbazone complexes: Solution and DFT studies, and antifungal and antioxidant activities.

This paper deals with the synthesis, characterization, and studies of biological properties of a series of 5 coordination compounds based on binuclear core [Mo(V)2O2S2]2+ with thiosemicarbazones ligands bearing different substituents on the R1 position of the ligand. The complexes are first studied using MALDI-TOF mass spectrometry and NMR spectroscopy to determine their structures in solution in relation to single-crystal X-Ray diffraction data. In a second part, the antifungal and antioxidative activities are explored and the high potential of these coordination compounds compared to the uncoordinated ligands is demonstrated for these properties. Finally, DFT calculation provides important support to the solution studies by identifying the most stable isomers in each [Mo2O2S2]2+/Ligand system, while the determination of HUMO and LUMO levels is performed to explain the antioxidative properties of these systems.

A Novel Near-IR Absorbing Ruthenium(II) Complex as Photosensitizer for Photodynamic Therapy and its Cetuximab Bioconjugates.

A novel Ru(II) cyclometalated photosensitizer (PS), Ru-NH2 , for photodynamic therapy (PDT) of formula [Ru(appy)(bphen)2 ]PF6 (where appy=4-amino-2-phenylpyridine and bphen=bathophenanthroline) and its cetuximab (CTX) bioconjugates, Ru-Mal-CTX and Ru-BAA-CTX (where Mal=maleimide and BAA=benzoylacrylic acid) were synthesised and characterised. The photophysical properties of Ru-NH2 revealed absorption maxima around 580 nm with an absorption up to 725 nm. The generation of singlet oxygen (1 O2 ) upon light irradiation was confirmed with a 1 O2 quantum yield of 0.19 in acetonitrile. Preliminary in vitro experiments revealed the Ru-NH2 was nontoxic in the dark in CT-26 and SQ20B cell lines but showed outstanding phototoxicity when irradiated, reaching interesting phototoxicity indexes (PI) >370 at 670 nm, and >150 at 740 nm for CT-26 cells and >50 with NIR light in SQ20B cells. The antibody CTX was successfully attached to the complexes in view of the selective delivery of the PS to cancer cells. Up to four ruthenium fragments were anchored to the antibody (Ab), as confirmed by MALDI-TOF mass spectrometry. Nonetheless, the bioconjugates were not as photoactive as the Ru-NH2 complex.

Tuning the nuclearity of [Mo2O2S2]2+-based assemblies by playing with the degree of flexibility of bis-thiosemicarbazone ligands.

[MoV2O2S2]2+-based thiosemicarbazone complexes appear as very promising molecules for biological applications due to the intrinsic properties of their components. This paper deals with the synthesis and characterization of six coordination complexes obtained by the reaction of [MoV2O2S2]2+ clusters with bis-thiosemicarbazone ligands that contain flexible or rigid spacers between the two thiosemicarbazone units. Interestingly, structural characterization by single-crystal X-ray diffraction, MALDI-TOF MS technique and NMR spectroscopy revealed that the nuclearity of the complex is controlled by the nature of the spacer between the thiosemicarbazone units. Binuclear complexes, namely [MoV2O2S2(L1-3)], are isolated with flexible spacers while tetranuclear complexes [(MoV2O2S2)2(L4-6)2] are formed when the bis-thiosemicarbazone ligands are built on rigid spacers.

Grafting of Anionic Decahydro-Closo-Decaborate Clusters on Keggin and Dawson-Type Polyoxometalates: Syntheses, Studies in Solution, DFT Calculations and Electrochemical Properties.

Herein we report the synthesis of a new class of compounds associating Keggin and Dawson-type Polyoxometalates (POMs) with a derivative of the anionic decahydro-closo-decaborate cluster [B10H10]2- through aminopropylsilyl ligand (APTES) acting as both a linker and a spacer between the two negatively charged species. Three new adducts were isolated and fully characterized by various NMR techniques and MALDI-TOF mass spectrometry, notably revealing the isolation of an unprecedented monofunctionalized SiW10 derivative stabilized through intramolecular H-H dihydrogen contacts. DFT as well as electrochemical studies allowed studying the electronic effect of grafting the decaborate cluster on the POM moiety and its consequences on the hydrogen evolution reaction (HER) properties.

Synthesis, Structures, and Solution Studies of a New Class of [Mo2O2S2]-Based Thiosemicarbazone Coordination Complexes.

This paper deals with the synthesis, structural studies, and behavior in solution of unprecedented coordination complexes built by the association of a panel of 14 representative thiosemicarbazone ligands with the cluster [Mo2O2S2]2+. These complexes have been thoroughly characterized both in the solid state and in solution by XRD and by NMR, respectively. In particular, HMBC 1H{15N} and 1H DOSY NMR experiments bring important elements for understanding the complexes' behavior in solution. These studies demonstrate that playing on the nature and the position of various substituents on the ligands strongly influences the coordination modes of the ligands as well as the numbers of isomers in solution, mainly 2 products for the majority of complexes and up to 5 for some of them.

Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis.

During the last two decades, MALDI-ToF mass spectrometry has become an efficient and widely-used tool for identifying clinical isolates. However, its use for classification and identification of environmental microorganisms remains limited by the lack of reference spectra in current databases. In addition, the interpretation of the classical dendrogram-based data representation is more difficult when the quantity of taxa or chemotaxa is larger, which implies problems of reproducibility between users. Here, we propose a workflow including a concurrent standardized protein and lipid extraction protocol as well as an analysis methodology using the reliable spectra comparison algorithm available in MetGem software. We first validated our method by comparing protein fingerprints of highly pathogenic bacteria from the Robert Koch Institute (RKI) open database and then implemented protein fingerprints of environmental isolates from French Guiana. We then applied our workflow for the classification of a set of protein and lipid fingerprints from environmental microorganisms and compared our results to classical genetic identifications using 16S and ITS region sequencing for bacteria and fungi, respectively. We demonstrated that our protocol allowed general classification at the order and genus level for bacteria whereas only the Botryosphaeriales order can be finely classified for fungi.

An enzymatic activation of formaldehyde for nucleotide methylation.

Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH2O-shunt may be relevant in several other important folate-dependent reactions.

Intermolecular dark resonance energy transfer (DRET): upgrading fluorogenic DNA sensing.

The sensitivity of FRET-based sensing is usually limited by the spectral overlaps of the FRET donor and acceptor, which generate a poor signal-to-noise ratio. To overcome this limitation, a quenched donor presenting a large Stokes shift can be combined with a bright acceptor to perform Dark Resonance Energy Transfer (DRET). The consequent fluorogenic response from the acceptor considerably improves the signal-to-noise ratio. To date, DRET has mainly relied on a donor that is covalently bound to the acceptor. In this context, our aim was to develop the first intermolecular DRET pair for specific sensing of nucleic acid sequences. To this end, we designed DFK, a push-pull probe based on a fluorenyl π-platform that is strongly quenched in water. DFK was incorporated into a series of oligonucleotides and used as a DRET donor with Cy5-labeled complementary sequences. In line with our expectations, excitation of the dark donor in the double-labeled duplex switched on the far-red Cy5 emission and remained free of cross-excitation. The DRET mechanism was supported by time-resolved fluorescence measurements. This concept was then applied with binary probes, which confirmed the distance dependence of DRET as well as its potency in detecting sequences of interest with low background noise.

Drimane Derivatives as the First Examples of Covalent BH3 Mimetics that Target MCL-1.

Drimane sesquiterpenoid dialdehydes are natural compounds with antiproliferative properties. Nevertheless, their mode of action has not yet been discovered. Herein, we demonstrate that various drimanes are potent inhibitors of MCL-1 and BCL-xL, two proteins of the BCL-2 family that are overexpressed in various cancers, including lymphoid malignancies. Subtle changes in their structure significantly modified their activity on the target proteins. The two most active compounds are MCL-1 selective and bind in the BH3 binding groove of the protein. Complementary studies by NMR spectroscopy and mass spectrometry analyses, but also synthesis, showed that they covalently inhibit MCL-1 though the formation of a pyrrole adduct. In addition, cytotoxic assays revealed that these two compounds show a cytotoxic selectivity for BL2, a MCL-1/BCL-xL-dependent cell line and induce apoptosis.

Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes.

Dihydrouridine (D) is a tRNA-modified base conserved throughout all kingdoms of life and assuming an important structural role. The conserved dihydrouridine synthases (Dus) carries out D-synthesis. DusA, DusB and DusC are bacterial members, and their substrate specificity has been determined in Escherichia coli. DusA synthesizes D20/D20a while DusB and DusC are responsible for the synthesis of D17 and D16, respectively. Here, we characterize the function of the unique dus gene encoding a DusB detected in Mollicutes, which are bacteria that evolved from a common Firmicute ancestor via massive genome reduction. Using in vitro activity tests as well as in vivo E. coli complementation assays with the enzyme from Mycoplasma capricolum (DusBMCap), a model organism for the study of these parasitic bacteria, we show that, as expected for a DusB homolog, DusBMCap modifies U17 to D17 but also synthetizes D20/D20a combining therefore both E. coli DusA and DusB activities. Hence, this is the first case of a Dus enzyme able to modify up to three different sites as well as the first example of a tRNA-modifying enzyme that can modify bases present on the two opposite sides of an RNA-loop structure. Comparative analysis of the distribution of DusB homologs in Firmicutes revealed the existence of three DusB subgroups namely DusB1, DusB2 and DusB3. The first two subgroups were likely present in the Firmicute ancestor, and Mollicutes have retained DusB1 and lost DusB2. Altogether, our results suggest that the multisite specificity of the M. capricolum DusB enzyme could be an ancestral property.

Metabolic control of DNA methylation in naive pluripotent cells.

Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.

Versatile one-pot synthesis of gold nanoclusters and nanoparticles using 3,6-(dipyridin-2-yl)-(1,2,4,5)-tetrazine.

A one-pot synthesis of gold nano-objects is described by simply mixing a gold salt (HAuCl4), dodecanethiol and 3,6-di-2-pyridyl-1,2,4,5-tetrazine. When a large excess of thiol is used, gold nanoclusters of 2 nm are obtained in a large amount and with a narrow size distribution. The reaction mechanism was investigated by absorption and emission spectroscopies and shows the in situ formation of dihydrotetrazine acting as the reductant of Au(iii) to make Au(0). Au nanoclusters were isolated from the molecular precursors by HPLC. The nature of the ligands stabilizing Au nanoclusters was investigated by various techniques such as mass spectrometry, SEM-EDS, XPS and NMR. Thiol and tetrazine are shown to play both the role of ligand stabilizing the clusters. Finally, when a much smaller amount of thiol is used, a mixture of Au nanoclusters and Au nanoparticles of 10-15 nm, sometimes aggregated into clusters of 50 nm is obtained. The formation of larger nanoobjects is explained by the lower amount of thiol available to block the growth at the early stage as shown by UV-vis absorption monitoring.

Identification and dereplication of endophytic Colletotrichum strains by MALDI TOF mass spectrometry and molecular networking.

The chemical diversity of biologically active fungal strains from 42 Colletotrichum, isolated from leaves of the tropical palm species Astrocaryum sciophilum collected in pristine forests of French Guiana, was investigated. The collection was first classified based on protein fingerprints acquired by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) correlated with cytotoxicity. Liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-HRMS/MS) data from ethyl acetate extracts were acquired and processed to generate a massive molecular network (MN) using the MetGem software. From five Colletotrichum strains producing cytotoxic specialized metabolites, we predicted the occurrence of peptide and cytochalasin analogues in four of them by MN, including a similar ion clusters in the MN algorithm provided by MetGem software. Chemoinformatics predictions were fully confirmed after isolation of three pentacyclopeptides (cyclo(Phe-Leu-Leu-Leu-Val), cyclo(Phe-Leu-Leu-Leu-Leu) and cyclo(Phe-Leu-Leu-Leu-Ile)) and two cytochalasins (cytochalasin C and cytochalasin D) exhibiting cytotoxicity at the micromolar concentration. Finally, the chemical study of the last active cytotoxic strain BSNB-0583 led to the isolation of four colletamides bearing an identical decadienamide chain.

Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator.

tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin.

Impact of the gut microbiota on the m6A epitranscriptome of mouse cecum and liver.

The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. Here we examine whether host epitranscriptomic marks are affected by the gut microbiota. We use methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to identify N6-methyladenosine (m6A) modifications in mRNA of mice carrying conventional, modified, or no microbiota. We find that variations in the gut microbiota correlate with m6A modifications in the cecum, and to a lesser extent in the liver, affecting pathways related to metabolism, inflammation and antimicrobial responses. We analyze expression levels of several known writer and eraser enzymes, and find that the methyltransferase Mettl16 is downregulated in absence of a microbiota, and one of its target mRNAs, encoding S-adenosylmethionine synthase Mat2a, is less methylated. We furthermore show that Akkermansia muciniphila and Lactobacillus plantarum affect specific m6A modifications in mono-associated mice. Our results highlight epitranscriptomic modifications as an additional level of interaction between commensal bacteria and their host.

tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila.

2'-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

Effect of the coordination of π-acceptor 4-cyanopyridine ligand on the structural and electronic properties of meso-tetra(para-methoxy) and meso-tetra(para-chlorophenyl) porphyrin cobalt(ii) coordination compounds. Application in the catalytic degradation of methylene blue dye.

To examine the influence of both the important π-acceptor character of the 4-cyanopyridine ligand and the nature of the para-substituted phenyls of meso-porphyrins on the electronic, electrochemical and structural properties of cobaltous metalloporphyrins, we prepared and fully characterized two coordination compounds: the (4-cyanopyridine)[meso-tetra(para-methoxyphenyl)porphyrinato]cobalt(ii) and the (4-cyanopyridine)[meso-tetra(para-chlorophenyl)porphyrinato]cobalt(ii) with the [CoII(TMPP)(4-CNpy)] and [CoII(TClPP)(4-CNpy)] formulas (complexes 1-2). The solution structures of compounds 1-2 were confirmed by 1H NMR spectroscopy and mass spectrometry methods. They were further characterized by cyclic voltammetry and photoluminescence studies. The X-ray molecular structure data show that the Co-TClPP-4-NCpy derivative (2) exhibits high ruffling deformation compared to that of the Co-TMPP-4-CNpy species (1). Notably, the crystal packing of complex 1 shows the formation of Co⋯Co supramolecular dimers with a distance of 5.663 Å. As an application of our two cobaltous compounds, an investigation involving complexes 1-2 in the degradation of the methylene blue dye in the presence and absence of H2O2 in aqueous solutions was carried out. These promising results show that 1-2 can be used as catalysts in the degradation processes of dyes.