Ulosonic Acids Research Articles

Structural dissection of the CMP-pseudaminic acid synthetase, PseF.

Pseudaminic acid is a non-mammalian sugar found in the surface glycoconjugates of many bacteria, including several human pathogens, and is a virulence factor thought to facilitate immune evasion. The final step in the biosynthesis of the nucleotide activated form of the sugar, CMP-Pse5Ac7Ac is performed by a CMP-Pse5Ac7Ac synthetase (PseF). Here we present the biochemical and structural characterization of PseF from Aeromonas caviae (AcPseF), with AcPseF displaying metal-dependent activity over a broad pH and temperature range. Upon binding to CMP-Pse5Ac7Ac, AcPseF undergoes dynamic movements akin to other CMP-ulosonic acid synthetases. The enzyme clearly discriminates Pse5Ac7Ac from other ulosonic acids, through active site interactions with side-chain functional groups and by positioning the molecule in a hydrophobic pocket. Finally, we show that AcPseF binds the CMP-Pse5Ac7Ac side chain in the lowest energy conformation, a trend that we observed in the structures of other enzymes of this class.

Biocatalytic Construction of Quaternary Centers by Aldol Addition of 3,3-Disubstituted 2-Oxoacid Derivatives to Aldehydes.

The congested nature of quaternary carbons hinders their preparation, most notably when stereocontrol is required. Here we report a biocatalytic method for the creation of quaternary carbon centers with broad substrate scope, leading to different compound classes bearing this structural feature. The key step comprises the aldol addition of 3,3-disubstituted 2-oxoacids to aldehydes catalyzed by metal dependent 3-methyl-2-oxobutanoate hydroxymethyltransferase from E. coli (KPHMT) and variants thereof. The 3,3,3-trisubstituted 2-oxoacids thus produced were converted into 2-oxolactones and 3-hydroxy acids and directly to ulosonic acid derivatives, all bearing gem-dialkyl, gem-cycloalkyl, and spirocyclic quaternary centers. In addition, some of these reactions use a single enantiomer from racemic nucleophiles to afford stereopure quaternary carbons. The notable substrate tolerance and stereocontrol of these enzymes are indicative of their potential for the synthesis of structurally intricate molecules.

Predictive Analysis of the Side Chain Conformation of the Higher Carbon Sugars: Application to the Preorganization of the Aminoglycoside Ring 1 Side Chain for Binding to the Bacterial Ribosomal Decoding A Site.

With a view to facilitating prediction of the exocyclic bond to the pyranoside ring in higher carbon sugars, a model is advanced that relates the relative configuration of the three stereogenic centers comprised of the branchpoint and of the two flanking centers (C4-C5-C6 in aldoheptoses and higher and C5-C6-C7 in sialic and ulosonic acids) to that of the simple ring-opened pentoses. Assignment of a given stereotriad as arabino, lxyo, ribo, or xylo by inspection of the Fischer projection formulas permits prediction of conformation of the exocyclic bond by comparison with the known solution (= crystal in all cases) conformations of the simple pentitols. More remote stereogenic centers in the side chain, as in the 8-position of N-acetylneuraminic acid, have little impact on the conformation of the exocyclic bond. On the basis of this model the conformation of the exocyclic bond in ring I of 6'-homologated 4,5-disubstituted 2-deoxystreptamine class aminoglycoside antibiotics was predicted and was borne out by NMR analysis of newly synthesized derivatives in D2O at pD5. The antiribosomal and antibacterial activity of these derivatives is briefly presented and discussed in terms of preorganization of the side chain for binding to the ribosomal decoding A site. It is anticipated that this predictive analysis will also find use in the prediction of the conformation of the exocyclic bonds in other 2-(1-hydroxyalkyl)-3-hydroxytetrahydropyrans and tetrahydrofurans.

Asymmetric hetero‐Diels‐Alder Reaction of trans‐1‐Methoxy‐3‐trimethylsilyloxy‐buta‐1,3‐diene Catalyzed by Zinc Complexes

Asymmetric hetero‐Diels‐Alder reactions of Danishefsky's diene and glyoxylate/pyruvate esters catalyzed by readily available zinc triflate complex with BOX ligand afforded the corresponding adduct which upon treatment with trifluoroacetic acid furnished the hetero‐Diels‐Alder product in 91 % enantiomeric excess and 87 % isolated yield. This reaction was applied to the concise synthesis of six‐membered ulosonic acid C‐glycoside.

The Structurally Unusual Retaining β‐Kdo Glycosyltransferase WbbB Uses a Double‐Displacement Mechanism with an Intermediate Adduct Rearrangement Step

WbbB is a modular, trifunctional glycosyltransferase (GT) which synthesizes lipopolysaccharide O‐antigen in Raoultella terrigena. The two C‐terminal WbbB GT domains build the polysaccharide repeat, while the N‐terminal GT domain acts as a terminator, adding a β‐Kdo (3‐deoxy‐d‐manno‐oct‐2‐ulosonic acid) residue to O3 to rhamnose as required for O‐antigen export. This N‐terminal GT domain is highly unusual in sequence and was not recognized as a GT by bioinformatics tools. The structure shows the dual Rossmann‐fold motifs characteristic of GT‐Bs, but with extensive deletions, insertions and rearrangements result in a unique architecture. The CMP‐binding site, however, retains motifs homologous to GT‐B sialyltransferases. WbbB is a retaining GT, transferring Kdo from the CMP‐®‐Kdo donor with net retention of anomeric configuration. All well‐characterized retaining GTs seem to employ a front‐side SNi substitution mechanism. This is somewhat surprising, as analogous retaining glycosyl hydrolases use a double‐displacement mechanism; here an essential catalytic acid residue attacks the donor saccharide to form a covalently bonded intermediate, with a second acidic residue acting as a general base to hydrolyse this adduct. We show, using mass spectrometry, that WbbB forms a Kdo adduct with Asp232 and its variants (D232N or D232C), while a D232A variant is both wholly inactive and forms no adduct. The x‐ray structure of D232N CMP‐®‐Kdo donor complex shows that the anomeric carbon of the donor is inaccessible to any potential acceptor but is instead positioned immediately in contact with, and in line with, the carboxylate of Asp232. Structures of D232N‐ and D232C‐Kdo adducts show that the Kdo adduct is rearranged into a second half‐site, interacting with a distinct set of catalytic residues. A ternary complex of D232C‐Kdo plus a synthetic acceptor shows that Glu158 forms direct hydrogen bonds with O3 of rhamnose, positioned adjacent to and in‐line with the anomeric carbon of Kdo, activating it for attack. Glu158 is also essential, with variants being wholly inactive. Together, this shows that WbbB uses a glycosyl hydrolase‐like double‐displacement mechanism. We propose that crowding around the anomeric carbon by the carboxylate group likely precludes retaining ulosonic acid transferases using the more straightforward SNi mechanism, while adduct rearrangement avoids having the acceptor compete with the leaving nucleotide for access to the anomeric carbon of the donor.Support or Funding InformationThis work was funded by an NSERC Discovery grant (04045‐2015) to MSK and support from the Canadian Glycomics Network (SD‐1) to TLL; TJBF is the recipient of a University of Guelph Graduate Excellence Entrance Scholarship and an Ontario Graduate Scholarship.

The K5 capsular polysaccharide of the bacterium Acinetobacter baumannii SDF with the same K unit containing Leg5Ac7Ac as the K7 capsular polysaccharide but a different linkage between the K units

The K5 capsular polysaccharide (CPS) was isolated from the bacterium Acinetobacter baumannii (A. baumannii) SDF and studied by 1D and 2D 1H and 13C NMR spectroscopy before and after O-deacetylation and partial acid hydrolysis. The CPS was found to be composed of branched tetrasaccharide repeats (K units) containing 5,7-diacetamido-3,5,7,9-tetradeoxy-d-glycero-d-galacto-non-2-ulosonic acid (Leg5Ac7Ac). The KL5 capsule biosynthesis gene cluster at the K locus is consistent with the composition and structure of the CPS. KL5 is almost identical to the KL7 gene ulosonic acid (Leg5Ac7Ac A. baumannii LUH5533 that has been characterized earlier, and differs only in the gene for Wzy polymerase that is responsible for the formation of the linkage between the K units. The K5 CPS from strain SDF and the K7 CPS from strain LUH5533 have the same K-unit structure but a different linkage between the K units, which is formed by distinct Wzy polymerases. As opposite to Leg5Ac7Ac in the K7 CPS, this monosaccharide is O-acetylated at position 4 in the K5 CPS. No acetyltransferase for this modification of the K5 CPS is present in the KL5 gene cluster, and hence it is encoded by a gene located elsewhere in the genome.

Sulfated O-polysaccharide with anticancer activity from the marine bacterium Poseidonocella sedimentorum KMM 9023T

The sulfated polysaccharides are of study interest due to their high structural diversity and broad spectrum of biological activity including antitumor properties. In this paper, we report on the structural analysis of sulfated O-specific polysaccharide (OPS) and in vitro anticancer activity of O-deacylated lipopolysaccharide (DPS) of the marine-derived bacterium Poseidonocella sedimentorum KMM 9023T achieved by a multidisciplinary approach (chemical analysis, NMR, MS, and bioassay). The OPS is shown to include two rare monosaccharide derivatives: 3-deoxy-9-O-methyl-d-glycero-d-galacto-non-2-ulosonic acid (Kdn9Me) and 3-O-acetyl-2-O-sulfate-d-glucuronic acid (D-GlcA2S3Ac). The structure of polysaccharide moiety of a previously unknown carbohydrate-containing biopolymer is established:→4)-α-Kdnp9Me-(2→4)-α-d-GlcpA2S3Ac-(1→.From a biological point of view, we demonstrate that DPS of the P. sedimentorum KMM 9023T has no cytotoxicity and inhibits colony formation of human HT-29, MCF-7 and SK-MEL-5 cells in a dose-dependent manner. The investigated polysaccharide is the second glycan isolated from the bacteria of the genus Poseidonocella: previously we studied the OPS of P. pacifica KMM 9010T (Kokoulin et al., 2017). Both polysaccharides are sulfated and contain rare residues of ulosonic acids. Thus, obtained findings provide a new knowledge about kinds and antitumor properties of sulfated polysaccharides and can be a starting point for further investigations of mechanisms of anticancer action of carbohydrate-containing biopolymers from marine Gram-negative bacteria.

A concise route to access C-glycosidic tetrazolyl analogues of Kdo as bioisosteres

Ulosonic acids are an important class of carbohydrates, including well-known representatives as 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo), 3-deoxy-d-glycero-d-galacto-non-2-ulosonic acid (Kdn) and N-Acetylneuraminic acid (Neu5Ac). As part of the lipopolysaccharides (LPS) and capsular polysaccharides (CPS, K-antigen), these carbohydrates can be found on the surfaces of, both, Gram-positive and Gram-negative bacteria. We developed a synthetic approach to access tetrazole-derivatives of these compounds. Tetrazoles have shown to be ideal analogues for the bioisosteric replacement of carboxylic acids in several drugs, improving biological activity and pharmacokinetic properties. The presented route features indium-mediated allylation with subsequent [2 + 3]-cycloaddition as key steps, leading to tetrazole-derivative of Kdo and its corresponding C-4 epimer. The route is flexible enough to be adapted to the preparation of further tetrazole ulosonic acids.

A Concise Organocatalytic Synthesis of 3‐Deoxy‐2‐ulosonic Acids through Cinchona‐Alkaloid‐Promoted Aldol Reactions of Pyruvate

Direct cross‐aldol reactions of a pyruvate ester with chiral aldehydes, mediated by purely organic catalysts, is described as a crucial step in the synthesis of ulosonic acids. Cinchona alkaloids containing a tertiary amine group efficiently promote direct aldol reactions of a sterically hindered pyruvate ester with various sugar aldehydes. The pyruvic acid ester can be directly used as chemical equivalent of PEP (phosphoenolpyruvate) in imitation of the synthetic principle used in nature. The appropriate combination of a chiral aldehyde with a chiral catalyst allows the flexible preparation of anti‐ or syn‐configured aldols, as desired. As a result, concise syntheses of diverse six‐, seven‐, eight‐, and nine‐carbon ulosonic acid esters are described, by using a biomimetic three‐carbon chain elongation of various sugar aldehydes. Consequently, short and practical syntheses of several ulosonic acids, including three important naturally occurring sugars – 3‐deoxy‐d‐erythro‐hex‐2‐ulosonic acid (KDG), 3‐deoxy‐d‐manno‐oct‐2‐ulosonic acid (KDO), and the rare 3‐deoxyglucosone (3DG), in good overall yields are presented.

Chemistry of Pyruvate Enolates: anti‐Selective Direct Aldol Reactions of Pyruvate Ester with Sugar Aldehydes Promoted by a Dinuclear Zinc Catalyst

AbstractA chiral dinuclear zinc complex can effectively catalyse the direct aldol reactions of pyruvic acid ester with various chiral sugar aldehydes, thus functionally mimicking the pyruvate‐dependent type II aldolases. Application of sterically hindered aryl esters allows for the elusive aldol reaction of the pyruvate donor with controlled anti‐selectivity en route to the short and efficient synthesis of 3‐deoxy‐2‐ulosonic acids. Pyruvic acid ester is here used as a chemical equivalent of phosphoenol pyruvate (PEP) in imitation of the synthetic principle used in nature. The presented biomimetic methodologies use enol formation for the highly efficient and flexible formation of various C6–C9 ulosonic acids. Particularly, efficient and concise syntheses of 3‐deoxy‐D‐erythro‐hex‐2‐ulosonic acid (KDG, overall 50% yield), 3‐deoxy‐D‐ribo‐hept‐2‐ulosonic acid (DRH, overall 53% yield) and 3‐deoxy‐D‐glycero‐D‐talo‐non‐2‐ulosonic acid (4‐epi‐KDN, overall 78% yield) are described. This direct efficient application of pyruvic esters does not require additional demasking steps and thus surpassess previously methodologies utilising masked pyruvic synthons such 2‐acetylthiazole and pyruvic aldehyde dimethyl acetal.magnified image

Direct Aldol Reaction of Pyruvic Derivatives: Catalytic Attempt To Synthesize Ulosonic Acids

AbstractThe catalytic asymmetric aldol reaction of pyruvic aldehyde dimethyl acetal and 2‐acetylthiazole with sugar aldehydes is demonstrated to be the key step in the synthesis of 3‐deoxy‐2‐ulosonic acids. Efficient and stereoselective pyruvate aldol reactions are catalyzed by metal‐based chiral Trost and Shibasaki catalysts. The presented synthetic methodology mimics aldolase‐catalyzed reactions by direct activation of C3 pyruvate equivalents with the use of metal‐based chiral catalysts en route to the synthesis of 2‐keto‐3‐deoxy‐D‐glucosonic acid and 3‐deoxy‐D‐manno‐2‐octulosonic acid derivatives.

A Straightforward Route to Novel α,α-Disubstituted Tetrahydrofuran β-Amino Acids and Spirodiketopiperazines from Sugar Lactones

Indium-mediated Reformatsky reactions of aldonolactones with ethyl α-bromoisobutyrate allowed the synthesis of ulosonic acid esters, which were readily transformed into the corresponding tetrahydrofuran β-azido esters in a stereoselective fashion. This approach provided monomeric components suitable for oligomerization to the carbopeptoid class of foldamers and prompted the total synthesis of the attractive novel spiro diketo-piperazine, which can be regarded as a spironucleoside.

ChemInform Abstract: Stereoselective Construction of Polyhydroxyalkyl 2-Thiazolyl Ketones ( Thiazole Ketoses) from D-Glyceraldehyde and D-Arabinose, Acetonides by Wittig-Michael Sequence. A Route to D-Gluco-KDO.

The carbonylolefination of the title alkoxy aldehydes by 2-thiazolecarbonylmethylenetriphenyl-phosphorane 3 affords the corresponding (E)-enones which undergo syn-diastereoselective (ds, 85–95%) 1,4-conjugate addition of henzyl oxide anion; acid catalyzed methanolysis of polyalkoxyalkyl ketones obtained in that way gives methyl 1-(2-thiazolyl)pyranoside precursors to ulosonic acids.

Studies on indium-mediated additions to lactones: synthesis of 2-deoxy-2-substituted-3-ulosonic acids

The indium-mediated Reformatsky reaction of a mannose-derived lactone with α,α-disubstituted-α-bromo esters yielded the corresponding ulosonic acid esters as mixtures of anomers. In contrast, the reaction with α-monosubstituted-α-bromo esters is highly stereoselective and afforded a single anomer of the corresponding (2 S)-ulosonic acid esters. A mechanistic proposal for the reaction and an explanation of its outcome is discussed. The indium-mediated Reformatsky reaction of the mannose-derived lactone with 2-bromo-lactones was also achieved and the products obtained were consistent with those of our proposed mechanism in all cases. Moreover, indium-mediated allylation of the model sugar lactone was also investigated.

ChemInform Abstract: An Efficient Approach to the 2-Nonulosonic Acid Skeleton Through a Hetero-Diels-Alder Reaction.

Abstract The hetero-Diels-Alder reaction of 1,3-diene-polyols with glyoxylates is an expeditious way to build up the skeleton of ulosonic acids. This paper reports an efficient means to improve the yields and the stereoselectivity associated with the hetero-cycloaddition of the activated 1,3-diene, 2S,3S-4E-1-O-Benzyl-2,3-O-isopropylidene-6-ter-butyldimethylsilyloxyhepta-4,6-diene-1,2,3-triol (3) with the dienophile ethyl glyoxylate. The effects of temperature, catalyst, and solvent on the outcome of the Diels-Alder reaction were investigated. The cycloaddition can proceed smoothly even at −78°C and the complex bis [3-(heptafluorobutyryl)camphorato]oxovanadium (8) was found to be a very efficient catalyst for the cycloaddition reaction. The satisfactory selectivity (endo/exo: 97:3 and re/si: 82:18) observed in this catalytic reaction shows that there is a match effect between the substrate and catalyst.

Against the rules: A marine bacterium, Loktanella rosea, possesses a unique lipopolysaccharide

Bacteria are an inimitable source of new glyco-structures potentially useful in medicinal and environmental chemistry. Lipopolysaccharides (LPS; endotoxins) are the major components of the outer membrane of Gram-negative bacteria; being exposed toward the external environment they can undergo structural changes and thus, they often possess peculiar chemical features that allow them to thrive in harsh chemical and physical environments. Marine bacteria have evolved and adapted over millions of years in order to succeed in different environments, finding a niche for their survival characterized by severe physical or chemical parameters. The present work focuses on the structural investigation of the LPS from Loktanella rosea, a marine Gram-negative bacterium. Through chemical analysis, 2D nuclear magnetic resonance and matrix-assisted laser desorption ionization mass spectrometry investigations, a unique LPS carbohydrate backbone has been defined. The lipid A skeleton consists of a trisaccharide backbone lacking the typical phosphate groups and is characterized by two beta-glucosamines and an alpha-galacturonic acid. The core region is built up of three ulosonic acids, with two 3-deoxy-d-manno-oct-2-ulopyranosonic acid residues, one of which is carrying a neuraminic acid. This carbohydrate structure is an exceptional variation from the typical architectural skeleton of endotoxins which consequently implies a very different biosynthesis.

Indium-mediated Reformatsky reaction on lactones: preparation of 2-deoxy-2,2′-dimethyl-3-ulosonic acids

Indium-mediated Reformatsky reactions of simple lactones and aldonolactones with ethyl α-bromoisobutyrate allow the synthesis of the corresponding ketals and ulosonic acid esters, respectively, in good yields.

Lessons from Nature: Biomimetic Organocatalytic Carbon−Carbon Bond Formations

Nature utilizes simple C2 and C3 building blocks, such as dihydroxyacetone phosphate (DHAP), phosphoenolpyruvate (PEP), and the "active aldehyde" in various enzyme-catalyzed carbon-carbon bond formations to efficiently build up complex organic molecules. In this Perspective, we describe the transition from using enantiopure chemical synthetic equivalents of these building blocks, employing our SAMP/RAMP hydrazone methodology and metalated chiral alpha-amino nitriles, to the asymmetric organocatalytic versions developed in our laboratory. Following this biomimetic strategy, the DHAP equivalent 2,2-dimethyl-1,3-dioxan-5-one (dioxanone) has been used in the proline-catalyzed synthesis of carbohydrates, aminosugars, carbasugars, polyoxamic acid, and various sphingosines. Proline-catalyzed aldol reactions involving a PEP-like equivalent have also allowed for the asymmetric synthesis of ulosonic acid precursors. By mimicking the "active aldehyde" nucleophilic acylations in Nature catalyzed by the thiamine-dependent enzyme, transketolase, enantioselective N-heterocyclic carbene-catalyzed benzoin and Stetter reactions have been developed. Finally, based on Nature's use of domino reactions to convert simple building blocks into complex and highly functionalized molecules, we report on our development of biomimetic asymmetric multicomponent domino reactions which couple enamine and iminium catalysis.

Proline Organocatalysis as a New Tool for the Asymmetric Synthesis of Ulosonic Acid Precursors.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Proline organocatalysis as a new tool for the asymmetric synthesis of ulosonic acid precursors

PEP and aldolase mimicry is the key for a direct organocatalytic entry to precursors of ulosonic acids, biomolecules of enormous importance in biology, chemistry and medicine; in the key aldol reaction the dimethylacetal of pyruvic aldehyde is used as phosphoenolpyruvate (PEP) equivalent and the amino acid proline functions as an organocatalyst, imitating the enzyme.