Providing insight into the mechanism of action of cationic lipidated oligomers using metabolomics.

The increasing resistance of clinically relevant microbes against current commercially available antimicrobials underpins the urgent need for alternative and novel treatment strategies. Cationic lipidated oligomers (CLOs) are innovative alternatives to antimicrobial peptides and have reported antimicrobial potential. An understanding of their antimicrobial mechanism of action is required to rationally design future treatment strategies for CLOs, either in monotherapy or synergistic combinations. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of one CLO, C12-o-(BG-D)-10, which we have previously shown to be effective against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. The metabolomes of MRSA ATCC 43300 at 1, 3, and 6 h following treatment with C12-o-(BG-D)-10 (48 µg/mL, i.e., 3× MIC) were compared to those of the untreated controls. Our findings reveal that the studied CLO, C12-o-(BG-D)-10, disorganized the bacterial membrane as the first step toward its antimicrobial effect, as evidenced by marked perturbations in the bacterial membrane lipids and peptidoglycan biosynthesis observed at early time points, i.e., 1 and 3 h. Central carbon metabolism and the biosynthesis of DNA, RNA, and arginine were also vigorously perturbed, mainly at early time points. Moreover, bacterial cells were under osmotic and oxidative stress across all time points, as evident by perturbations of trehalose biosynthesis and pentose phosphate shunt. Overall, this metabolomics study has, for the first time, revealed that the antimicrobial action of C12-o-(BG-D)-10 may potentially stem from the dysregulation of multiple metabolic pathways.IMPORTANCEAntimicrobial resistance poses a significant challenge to healthcare systems worldwide. Novel anti-infective therapeutics are urgently needed to combat drug-resistant microorganisms. Cationic lipidated oligomers (CLOs) show promise as new antibacterial agents against Gram-positive pathogens like methicillin-resistant Staphylococcus aureus (MRSA). Understanding their molecular mechanism(s) of antimicrobial action may help design synergistic CLO treatments along with monotherapy. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of CLOs against MRSA. The results of our study indicate that the CLO, C12-o-(BG-D)-10, had a notable impact on the biosynthesis and organization of the bacterial cell envelope. C12-o-(BG-D)-10 also inhibits arginine, histidine, central carbon metabolism, and trehalose production, adding to its antibacterial characteristics. This work illuminates the unique mechanism of action of C12-o-(BG-D)-10 and opens an avenue to design innovative antibacterial oligomers/polymers for future clinical applications.

Bacterial bioindicators enable biological status classification along the continental Danube river.

Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium, and Rhodoluna, and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2-3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems.

ROMP-based Glycopolymers with High Affinity for Mannose-Binding Lectins.

Well-defined, highly reactive poly(norbornenyl azlactone)s of controlled length (number-average degree of polymerization DPn¯ = 10 to 1,000) were made by ring-opening metathesis polymerization (ROMP) of pure exo-norbornenyl azlactone. These were converted into glycopolymers using a facile postpolymerization modification (PPM) strategy based on click aminolysis of azlactone side groups by amino-functionalized glycosides. Pegylated mannoside, heptyl-mannoside, and pegylated glucoside were used in the PPM. Binding inhibition of the resulting glycopolymers was evaluated against a lectin panel (Bc2L-A, FimH, langerin, DC-SIGN, ConA). Inhibition profiles depended on the sugars and the degrees of polymerization. Glycopolymers from pegylated-mannoside-functionalized polynorbornene, with DPn¯ = 100, showed strong binding inhibition, with subnanomolar range inhibitory concentrations (IC50s). Polymers surpassed the inhibitory potential of their monovalent analogues by four to five orders of magnitude thanks to a multivalent (synergistic) effect. Sugar-functionalized poly(norbornenyl azlactone)s are therefore promising tools to study multivalent carbohydrate-lectin interactions and for applications against lectin-promoted bacterial/viral binding to host cells.

Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat.

Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.

Multiple thresholds and trajectories of microbial biodiversity predicted across browning gradients by neural networks and decision tree learning.

Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that nonmonotonic relations dominate in nature. Here, we apply machine-learning algorithms to reveal the nonmonotonic association between microbial diversity and an anthropogenic-induced large-scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha-diversity) showed nonmonotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta-diversity) when applying standard methods assuming monotonic relations and up to 45% with machine-learning methods taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of nonmonotonic responses of individual bacterial sequence variants to browning. Furthermore, the nonmonotonic models provide the position of thresholds and predict alternative bacterial diversity trajectories in boreal freshwater as a result of ongoing climate and land-use changes, which in turn will affect entire ecosystem metabolism and likely greenhouse gas production.

Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases*.

Bacterial sialidases (SA) are validated drug targets expressed by common human pathogens such as Streptococcus pneumoniae, Vibrio cholerae, or Clostridium perfringens. Noncovalent inhibitors of bacterial SA capable of reaching the submicromolar level are rarely reported. In this work, multi- and polyvalent compounds are developed, based on the transition-state analogue 2-deoxy-2,3-didehydro-N-acetylneuraminic (DANA). Poly-DANA inhibits the catalytic activity of SA from S. pneumoniae (NanA) and the symbiotic microorganism B. thetaiotaomicron (BtSA) at the picomolar and low nanomolar levels (expressed in moles of molecules and of DANA, respectively). Each DANA grafted to the polymer surpasses the inhibitory potential of the monovalent analogue by more than four orders of magnitude, which represents the highest multivalent effect reported so far for an enzyme inhibition. The synergistic interaction is shown to operate exclusively in the catalytic domain, and not in the flanked carbohydrate-binding module (CBM). These results offer interesting perspectives for the multivalent inhibition of other SA families lacking a CBM, such as viral, parasitic, or human SA.

Hydrogen-Bonding UCST-Thermosensitive Nanogels by Direct Photo-RAFT Polymerization-Induced Self-Assembly in Aqueous Dispersion.

Hydrogen-bonding upper critical solution temperature (UCST) thermosensitive nanogels based on poly(N-acryloyl glycinamide) (PNAGA) are synthesized by photo-reversible addition-fragmentation chain transfer mediated polymerization-induced self-assembly (photo-RAFT PISA) in aqueous dispersion using N,N'-methylenebis(acrylamide) as crosslinker and poly(oligo(ethylene glycol) methyl ether acrylate) as both stabilizer and macromolecular chain transfer agent (macro-CTA). Highly stable, spherical nanogels with narrow polydispersity are efficiently produced up to complete monomer conversion within 1 h under UV irradiation at low temperature (3 °C). The thermosensitive behavior of PNAGA-based nanogels, as assessed by dynamic light scattering and UV-vis spectrophotometry, exhibits reversible heating-induced swelling and cooling-induced shrinking corresponding to the expected UCST behavior. The hydrodynamic diameter, swelling ratio, and phase transition temperature of nanogels can be tuned by modifying the initial molar ratio of monomer-to-macro-CTA and the amount of crosslinker in the photo-RAFT PISA of NAGA.

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.

An optimised Cu(0)-RDRP approach for the synthesis of lipidated oligomeric vinyl azlactone: toward a versatile antimicrobial materials screening platform.

This report details the synthesis of lipidated 2-vinyl-4,4-dimethyl-5-oxazolone (VDM) oligomers via an optimised Cu(0)-mediated reversible-deactivation radical polymerisation approach, and the use of these oligomers as a versatile functional platform for the rapid generation of antimicrobial materials. The relative amounts of CuBr2 and Me6TREN were optimised to allow the fast and controlled polymerisation of VDM. These conditions were then used with the initiators ethyl 2-bromoisobutyrate, dodecyl 2-bromoisobutyrate, and (R)-3-((2-bromo-2-methylpropanoyl)oxy)propane-1,2-diyl didodecanoate to synthesise a library of oligo(VDM) (degree of polymerisation = 10) with ethyl, dodecyl or diglyceride end-groups. Subsequently, ring-opening of the pendant oxazolone group with various amines (i.e., 2-(2-aminoethyl)-1,3-di-Boc-guanidine, 1-(3-aminopropyl)imidazole, N-Boc-ethylenediamine, or N,N-dimethylethylenediamine) expanded the library to give 12 functional oligomers incorporating different cationic and lipid elements. The antimicrobial activities of these oligomers were assessed against a palette of bacteria and fungi: i.e. Staphylococcus aureus, Escherichia coli, Candida albicans, and Cryptococcus neoformans. The oligomers generally exhibited the greatest activity against the fungus, C. neoformans, with a minimum inhibitory concentration of 1 µg mL-1 (comparable to the clinically approved antifungal fluconazole). To assess haemocompatibility, the oligomers were assayed against erythrocytes, with the primary amine or guanidine containing C12 and 2C12 oligomers exhibiting greater lysis against the red blood cells (HC10 values between 7.1 and 43 µg mL-1) than their imidazole and tertiary amine counterparts (HC10 of >217 µg mL-1). Oligomers showed the greatest selectivity for C. neoformans, with the C12- and 2C12-tertiary amine and C12-imidazole oligomers possessing the greatest selectivity of >54-109. These results demonstrate the utility of reactive oligomers for rapidly assessing structure-property relationships for antibacterial and antifungal materials.

Azlactone-based heterobifunctional linkers with orthogonal clickable groups: efficient tools for bioconjugation with complete atom economy.

We report the efficient synthesis of a series of new azlactone-based heterofunctional linkers bearing two orthogonal clickable groups that proceed with full atom economy. These new linkers comprise an azlactone (oxazolone) group that quickly reacts with amino groups in biologically relevant medium without byproduct elimination and a (bio)orthogonal handle which further undergoes facile and selective click reactions such as thiol-ene coupling, Diels-Alder or azide-alkyne cycloadditions. As an example, the application of this methodology to lysozyme PEGylation in aqueous medium is described.

Tuning the Molar Composition of "Charge-Shifting" Cationic Copolymers Based on 2-(N,N-Dimethylamino)Ethyl Acrylate and 2-(tert-Boc-Amino)Ethyl Acrylate.

Copolymers of 2-(N,N-dimethylamino)ethyl acrylate (DMAEA) and 2-(tert-Boc-amino)ethyl acrylate (tBocAEA) are synthesized by reversible addition-fragmentation chain transfer polymerization in a controlled manner with defined molar masses and narrow molar masses distributions (Ð ≤ 1.17). Molar compositions of the P(DMAEA-co-tBocAEA) copolymers are assessed by means of 1 H NMR. A complete screening in molar composition is studied from 0% of DMAEA to 100% of DMAEA. Reactivity ratios of both comonomers are determined by the extended Kelen-Tüdos method (r DMAEA = 0.81 and rtBocAEA = 0.99).

Recyclable magnetic nanocluster crosslinked with poly(ethylene oxide)-block-poly(2-vinyl-4,4-dimethylazlactone) copolymer for adsorption with antibody.

Surface modification of magnetic nanoparticle (MNP) with poly(ethylene oxide)-block-poly(2-vinyl-4,4-dimethylazlactone) (PEO-b-PVDM) diblock copolymers and its application as recyclable magnetic nano-support for adsorption with antibody were reported herein. PEO-b-PVDM copolymers were first synthesized via a reversible addition-fragmentation chain-transfer (RAFT) polymerization using poly(ethylene oxide) chain-transfer agent as a macromolecular chain transfer agent to mediate the RAFT polymerization of VDM. They were then grafted on amino-functionalized MNP by coupling with some azlactone rings of the PVDM block to form magnetic nanoclusters with tunable cluster size. The nanocluster size could be tuned by adjusting the chain length of the PVDM block. The nanoclusters were successfully used as efficient and recyclable nano-supports for adsorption with anti-rabbit IgG antibody. They retained higher than 95% adsorption of the antibody during eight adsorption-separation-desorption cycles, indicating the potential feasibility in using this novel hybrid nanocluster as recyclable support in cell separation applications.

Amine-reactive polymers synthesized by RAFT polymerization using an azlactone functional trithiocarbonate RAFT agent.

A new azlactone-derived trithiocarbonate is prepared and used as a chain-transfer agent to mediate the reversible addition-fragmentation chain transfer (RAFT) polymerization of styrene, ethyl acrylate, and N-isopropyl acrylamide. Well-defined polymers with controlled molecular weights (M(n) = 1000-7000 g mol(-1) ) and narrow molecular weight distributions (PDI = 1.05-1.10) are thus obtained that retain the azlactone functionality at the chain end. The ability of the resulting end-functionalized polymers to react quantitatively at room temperature with a stoichiometric amount of amino groups with retention of the thiocarbonylthio moiety is ascertained by using 4-fluorobenzylamine and allylamine.

Preparation of a new electro-optic polymer cross-linkable via copper-free thermal Huisgen cyclo-addition and fabrication of optical waveguides by Reactive Ion Etching.

High-quality trails of ridge waveguides were successfully fabricated using a new cross-linkable polymer (PCC01) by UV photolithography followed by Reactive-Ion Etching (RIE) process. The cross-linking reaction of PCC01 is based on the copper-free Huisgen cyclo-addition between an azide and an acetylene group. The new cross-linkable polymer (PCC01) consists of a structural modification of the previously described materials (Scarpaci et al. Polym. Chem.2011, 2, 157), because the ethynyl group is functionalized by a methyl group instead of the TMS protecting group. This feature prevents the formation of silica (SiO(2)) generated by trimethylsilyl groups and which was stopping the engraving process before completion. Herein, we describe the synthesis, the NLO characterizations, and the fabrication of a high-quality ridge waveguide with PCC01. The new cross-linkable polymer PCC01 not only solves the problems encountered with our previously described polymers, but also presents an enhancement of the electro-optic stability, because d(33) coefficients up to 30 pm/V stable at 150 °C were recorded.

Solid-phase de novo synthesis of a (+/-)-2-deoxy-glycoside.

The solid-phase synthesis of methyl 2-deoxy-3-O-benzyl-D,L-arabino-hexopyranoside was achieved in a six-step sequence via a de novo strategy based on the hetero-Diels-Alder reaction of a vinyl ether supported on an azalactone-functionalized polystyrene resin, followed by the functional modification of the heteroadduct and the final release of the methyl glycoside by acidic solvolysis.

Synthesis and characterization of functionalized poly(gamma-benzyl-L-glutamate) derivates and corresponding nanoparticles preparation and characterization.

For being fully efficient a targeted delivery system should associate simultaneously multiple functionalities. In this context, the association of several polymeric materials to form composite multifunctional particles can be foreseen. The present work describes the synthesis of different derivates of poly(gamma-benzyl-L-glutamate) and their use for the preparation of nanoparticles exhibiting different properties, including surface hydrophilization by PEG, fluorescence imaging by FITC and target recognition through easy attachment of desired ligands by using the avidin-biotin interaction, after the nanoparticles preparation. Four PBLG derivates were successfully obtained by ring-opening polymerization (ROP) of NCA, using various initiators corresponding to the molecules to be introduced into the copolymers. Further, nanoparticles smaller than 100 nm could be prepared using a nanoprecipitation technique and the presence of the active moieties introduced within the particles as well as their functionality has been checked. Very interestingly, it has been shown that biotin molecules could be efficiently introduced at the surface of the nanoparticles, which (for 75% of the theoretical amount) could be engaged in a complexation with avidin. It is suggested that this strategy offers the possibility to easily decorate these nanoparticles with various recognition ligands for specific targeting applications by using the well known biotin-avidin sandwich technique.

A new crosslinkable system based on thermal Huisgen reaction to enhance the stability of electro-optic polymers.

The thermal Huisgen cycloaddition reaction is a new and efficient process to crosslink electro-optic polymers, since it leads to an effective increase of the thermal alignment stability of the NLO chromophores.

Synthesis and nonlinear optical properties of a peripherally functionalized hyperbranched polymer by DR1 chromophores.

The first peripheral postfunctionalization of a hyperbranched polyimide by nonlinear optic chromophores (DR1 derivative) was achieved using two different routes. The first one consists in the esterification of the terminal carboxylic acid groups, whereas the second is based on copper-catalyzed Huisgen reaction of the terminal propargylic ester groups. The resulting polymers display good solubility in classical organic solvents and good filmability because thick films can be prepared (up to 2.7 mum). The second-order nonlinear optical properties were measured by SHG at 1064 nm and we show that these hyperbranched polymers exhibit good poling efficiency and good thermal stability since the electro-optic activity remains stable up to 130 degrees C. These results illustrate the potential of hyperbranched polymers to host second-order nonlinear optical chromophores to replace dendrimers or classical linear polymers generally used in this area.

Synthesis and ITC characterization of novel nanoparticles constituted by poly(gamma-benzyl L-glutamate)-beta-cyclodextrin.

Imparting desired technological characteristics to polymeric nanoparticles requires the development of original polymers. In the present work, the synthesis and characterization of a novel PBLG-derivative, the poly(gamma-benzyl L-glutamate)-beta-cyclodextrin (PBLG-beta-CD-50), have been carried out. Nanoparticles from either PBLG-beta-CD-50 polymer or from mixtures with PBLG have been prepared using a modified nanoprecipitation method. Spherically shaped nanoparticles with diameter in the range of 50-70 nm were obtained, as determined by dynamic laser light scattering and transmission electron microscopy. The presence of a surfactant in the suspension medium had almost no influence on these parameters and was not necessary to the shelf-stability of the suspension. Further, isothermal titration microcalorimetry (ITC) experiments have been used to show unambiguously that about 20% of the cyclodextrins remain functional within the particles. Consequently, this system may be of interest when association of large amounts of hydrophobic drugs to nanoparticles is required.