Tackling the chemical diversity of microbial nonulosonic acids – a universal large-scale survey approach

Nonulosonic acids, commonly referred to as sialic acids, are a highly important group of nine-carbon sugars common to all domains of life. They all share biosynthetic and structural features, but otherwise display a remarkable chemical diversity. In humans, sialic acids cover all cells which makes them important for processes such as cellular protection, immunity and brain development. On the other hand, sialic acids and other nonulosonic acids have been associated with pathological processes including cancer and viral infections. In prokaryotes, nonulosonic acids are commonly associated with pathogens, which developed through molecular mimicry a strategy to circumvent the host''s immune response. However, the remarkably large chemical diversity of prokaryotic nonulosonic acids challenges their discovery, and research on molecular characteristics essential for medical applications are often not feasible. Here, we demonstrate a novel, universal large-scale discovery approach that tackles the unmapped diversity of prokaryotic nonulosonic acids. Thereby, we utilize selective chemical labelling combined with a newly established mass spectrometric all-ion-reaction scanning approach to identify nonulosonic acids and other ulosonic acid-like sugars. In doing so, we provide a first molecular-level comparative study on the frequency and diversity across different phyla. We not only illustrate their surprisingly wide-spread occurrence in non-pathogenic species, but also provide evidence of potential higher carbon variants. Many biomedical studies rely on synthetic routes for sialic acids, which are highly demanding and often of low product yields. Our approach enables large-scale exploration for alternative sources of these highly important compounds.

A novel large-scale survey approach for microbial nonulosonic acids (sialic acids) including a first molecular level comparative study is presented.     

Exploiting an inherent neighboring group effect of alpha-amino acids to synthesize extremely hindered dipeptides

The creation of highly hindered peptides that contain combinations of non-natural N-alkyl amino acids and N-alkyl-alpha,alpha-disubstituted amino acids presents a formidable challenge. Hindered, non-natural amino acids are of interest because they import resistance to proteolysis and unusual conformational properties to peptides that contain them. Toward a solution to this problem, we describe a new approach to creating extremely hindered dipeptides that is operationally simple and uses mild conditions and commercially available amino acids. The approach reduces the need for protecting groups and yields urethane-protected dipeptide acids that can be used as building blocks in the synthesis of larger peptides. We propose that the reaction proceeds through a previously unexploited intramolecular O,N-acyl transfer pathway.     

Simultaneous analysis of polar and non-polar components of cell membrane phospholipids by GC-MS

A rapid and selective GC-MS method was optimised for the simultaneous analysis of fatty acids, phosphoethanolamine, phosphoglycerol and phosphoserine, which comprise the polar headgroups of phospholipids. Enzymatic hydrolysis was used for sample preparation to selectively release fatty acids and prevent cleavage of the phosphoester bonds of the polar headgroups. A two-step consecutive derivatisation of the fatty acids and polar headgroups was applied to enable the simultaneous analysis of the selected analytes. The method was tested on samples of cell membrane phospholipids of Bacillus subtilis, a microbe with a broad spectrum of fatty acids. This approach can accelerate and simplify biotechnological research and quality control. The experimental conditions were optimised using a chemometric approach denoted as experimental design.     

Synthesis of Chiral beta 3-aminoxy peptides

A series of chiral beta(3)-aminoxy acids or amides with various side chains have been synthesized via two different approaches. One is the Arndt-Eistert homologation approach, using chiral alpha-aminoxy acids as starting materials. The other approach, utilizing the enantioselective reduction of beta-keto esters catalyzed by baker's yeast or chiral Ru(II) complexes, produces chiral beta(3)-aminoxy acids with nonproteinaceous side chains. The oligomers of beta(3)-aminoxy acids can be readily prepared using EDCI/HOAt as the coupling reagent.     

Spiegelbildliche Nukleinsäuren als pharmakologische Wirkstoffe

Within the last decades we witnessed the discovery of a number of mechanisms that enable the use of nucleic acids for therapeutic purposes. Small RNA and DNA molecules can be used to specifically suppress the expression of individual genes. Aptamers provide an alternative to monoclonal antibodies. A prerequisite for the pharmacological use of nucleic acids is an enhanced stability towards the body's degrading enzymes. This can be achieved for instance by employing non‐natural mirror‐image nucleic acids. The article describes the basic principles of stereochemistry underlying this approach and shows how these translate into the discovery of mirror‐image aptamers. Furthermore, it explains why the stereospecificity of Watson‐Crick base pairing has precluded mirror‐image nucleic acids from gene silencing methods and introduces a new approach that may help to overcome this.     

Imaging mass spectrometry with silver naeoparticles reveals the distribution of fatty acids in mouse retinal sections

A new approach to the visualization of fatty acids in mouse liver and retinal samples has been developed using silver nanoparticles (AgNPs) in nanoparticle-assisted laser desorption/ ionization imaging mass spectrometry (nano-PALDI-IMS) in negative ion mode. So far, IMS analysis has concentrated on main cell components, such as cell membrane phospholipids and cytoskeletal peptides. AgNPs modified with alkylcarboxylate and alkylamine were used for nano-PALDI-IMS to identify fatty acids, such as stearic, oleic, linoleic, arachidonic, and eicosapentaenoic acids, as well as palmitic acid, in mouse liver sections; these fatty acids are not detected using 2,5-dihydroxybenzoic acid (DHB) as a matrix. The limit of detection for the determination of palmitic acid was 50 pmol using nano-PALDI-IMS. The nano-PALDI-IMS method is successfully applied to the reconstruction of the ion images of fatty acids in mouse liver sections. We verified the detection of fatty acids in liver tissue sections of mice by analyzing standard lipid samples, which showed that fatty acids were from free fatty acids and dissociated fatty acids from lipids when irradiated with a laser. Additionally, we applied the proposed method to the identification of fatty acids in mouse retinal tissue sections, which enabled us to learn the six-zonal distribution of fatty acids in different layers of the retina. We believe that the current approach using AgNPs in nano-PALDI-IMS could lead to a new strategy to analyze basic biological mechanisms and several diseases through the distribution of fatty acids.     

Composition of the black crusts from the Saint Denis Basilica, France, as revealed by gas chromatography-mass spectrometry

The organic fraction of black crusts from Saint Denis Basilica, France, is composed of a complex mixture of aliphatic and aromatic compounds. These compounds were studied by two different analytical approaches: tetramethyl ammonium hydroxide (TMAH) thermochemolysis in combination with gas chromatography-mass spectrometry (GC-MS), and solvent extraction, fractionation by silica column, and identification of the fraction components by GC-MS. The first approach, feasible at the microscale level, is able to supply fairly general information on a wide range of compounds. Using the second approach, we were able to separate the complex mixture of compounds into four fractions, enabling a better identification of the extractable compounds. These compounds belong to different classes: aliphatic hydrocarbons (nalkanes, n-alkenes), aliphatic and aromatic carboxylic acids (n-fatty acids, alpha,omega-dicarboxylic acids, and benzenecarboxylic acids), polycyclic aromatic hydrocarbons (PAH), and molecular biomarkers (isoprenoid hydrocarbons, diterpenoids, and triterpenoids). With each approach, similar classes of compounds were identified, although TMAH thermochemolysis failed to identify compounds present at low concentrations in black crusts. The two proposed methodological approaches are complementary, particularly in the study of polar fractions.     

Protodecarboxylation of benzoic acids under radical conditions

A new approach to protodecarboxylation is described that enhances the substrate scope for benzoic acids. The reaction uses oxidative radical conditions to decarboxylate a variety of acids in acetonitrile.     

Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis

We have developed a metabolic flux analysis method that is based on (13)C-labeling patterns of the intracellular metabolites directly measured by capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The flux distribution of the central carbon metabolism in Escherichia coli was determined by this new approach and the results were compared with findings obtained by conventional GC-MS analysis based on isotopomer of the proteinogenic amino acids. There were some differences in estimation results between new approach using CE-TOFMS and conventional approach using GC-MS. These were thought to be attributable to variations in measured mass distributions between amino acids and the corresponding precursors and to differences in the sensitivity of the exchange coefficients to mass distributions. However, our CE-TOFMS method facilitates high-throughput flux analysis without requiring complicated sample preparation such as hydrolysis of proteins and derivatization of amino acids.     

Rapid analysis of amino acids using pre-column derivatization

A new approach to the pre-column derivatization and analysis of amino acids is described. The method is based upon formation of a phenylthiocarbamyl derivative of the amino acids. The derivatization method is rapid, efficient, sensitive, and specific for the analysis of primary and secondary amino acids in protein hydrolyzates. The liquid chromatographic system allows for the rapid, bonded-phase separation with ultraviolet detection of the common amino acids with 12-min analysis time and a 1-pmol sensitivity.     

Comparison of Two Approaches to Processing Titration Curves of a Dibasic Acid

Two approaches to processing titration curves of dibasic acids based on the use of sets of equations characteristic for dibasic acids and for a mixture of two monobasic acids were compared. With an example of processing of titration curves of glutamic, oxalic, and succinic acids using logarithmic relationships, it was demonstrated that the first approach provides a higher sensitivity to the influence of different factors. Recommendations were given for the use of the studied approaches for solving analytical problems.     

Syntheses of protected vinylic amino acids by intermolecular Lewis acid catalyzed ene reactions

Intermolecular ene reaction between ethylglyoxylate and allylic amino acid derivatives gave highly functionalized unsaturated pimelic acids in one step. This synthetic approach appears as a new efficient method for the synthesis of vinylic amino acids.     

Solid-phase synthesis of N-nosyl- and N-Fmoc-N-methyl-alpha-amino acids

We report here a convenient and simple solid-phase synthesis of N-nosyl-N-methyl-alpha-amino acids and N-Fmoc-N-methyl-alpha-amino acids, important building blocks for the synthesis of conformationally restricted and protease-resistant natural peptides and peptide analogues. The methodology involves the use of 2-chlorotrityl chloride resin to temporarily protect the carboxylic group of alpha-amino acids and of diazomethane as the reagent to methylate the sulfonamidic function. The approach developed is particularly efficient also with alpha-amino acids bearing appropriately protected functionalized side chains.     

Peptide-Chain Elongation Using Unprotected Amino Acids in a Micro-Flow Reactor

Conventional peptide synthesis requires a deprotection step after each amidation step, which decreases synthetic efficiency. Therefore, peptide synthesis using unprotected amino acids is considered an ideal approach. Here, we report peptide chain elongation using unprotected amino acids via a mixed carbonic anhydride. Micro-flow technology enabled rapid mixing of an organic layer containing a protected amino acid or dipeptide and an aqueous layer containing an unprotected amino acid or dipeptide to accelerate the desired amidation, and this approach successfully suppressed undesired racemization/epimerization (≤0.4 %). Various di-, tri-, and tetra-peptides were obtained in good to high yields. This is the first report on peptide chain elongation that proceeds without severe racemization from unprotected amino acids using inexpensive, nonexplosive, less wasteful, and less toxic reagents.     

Structural determination of modified fatty acids by collisional activation of cationized molecules

The nature and location of a variety of modifications of fatty acids are determined by collisional activation (CA) of [M + 2Li ? H]⁺ ions. The sample molecules are cationized in situ on the probe tip, desorbed by fast atom bombardment and, upon CA, undergo charge-remote decompositions. This approach is a direct, totally instrumental method for structure elucidation. Advantages of CA of [M + 2Li ? H]⁺ ions are that fatty acids with substituents in close proximity to the carboxylate terminus and modified short-chain acids are readily determined: decompositions of carboxylate anions of these fatty acids result in collision-activated dissociation (CAD) spectra that give incomplete structural information. However, the CAD spectra of some [M ? H]^? ions, such as those from epoxy acids, are simpler to interpret than those of the [M + 2Li ? H]⁺ ions. Thus, CA of fatty acid [M + 2Li ? H]⁺ ions is a complementary approach to CA of [M ? H]^? ions for determining the fatty acid structures investigated here. The use of this approach for analyzing complex mixtures of modified fatty acids is also evaluated.     

Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids

Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.     

A novel approach to the synthesis of amino acids based on cobalt bis(dicarbollide)

A novel approach to the synthesis of boron-containing amino acids based on ring opening of cyclic oxonium derivatives of polyhedral boron hydrides under the action of the terminal functional groups of natural amino acids was proposed. This approach was successfully implemented for the synthesis of cobalt bis(dicarbollide) — tyrosine conjugate.     

One-pot two-step conversion of aromatic carboxylic acids and esters to aromatic aldehydes via indium-catalyzed reductive thioacetalization and desulfurization

Described herein is that a new approach to a one-pot two-step conversion of aromatic carboxylic acids/esters to aromatic aldehydes, in which indium(III) iodide effectively catalyzes both the first reductive thioacetalization of carboxylic acids and a subsequent desulfurization of the in-situ formed thioacetal intermediates leading to aldehydes.     

CCR5 antagonists: 3-(pyrrolidin-1-yl)propionic acid analogues with potent anti-HIV activity

[reaction: see text] A novel approach to alpha,alpha-disubstituted-beta-amino acids (beta(2,2)-amino acids) was employed in the synthesis of a series of 3-(pyrrolidin-1-yl)propionic acids possessing high affinity for the CCR5 receptor and potent anti-HIV activity. The rat pharmacokinetics for these new analogues featured higher bioavailabilities and lower rates of clearance as compared to cyclopentane 1.     

Design of thiol-containing amino acids for native chemical ligation at non-Cys sites

<正>Protein chemical synthesis usually relies on the use of native chemical ligation that couples peptide thioester with a Cys-peptide.A limitation of this method is the difficulty of finding an appropriate Cys ligation site in many synthetic targets.To overcome this problem,the ligation-desulfurization approach has been developed.This approach involves the use of a thiol-containing amino acid as the ligation partner.After the sequence assembly is completed,the thiol group is removed through a desulfurization reaction to generate the standard amino acids.Currently this strategy has been applied to the ligations at a number of amino acids including Ala,Phe,Val,Lys,Thr,Leu,Pro and Gln.The present article reviews the design and synthesis of these thiol-containing amino acids for native chemical ligation at non-Cys sites.