Micelle‐Triggered β‐Hairpin to α‐Helix Transition in a 14‐Residue Peptide from a Choline‐Binding Repeat of the Pneumococcal Autolysin LytA

Choline‐binding modules (CBMs) have a ββ‐solenoid structure composed of choline‐binding repeats (CBR), which consist of a β‐hairpin followed by a short linker. To find minimal peptides that are able to maintain the CBR native structure and to evaluate their remaining choline‐binding ability, we have analysed the third β‐hairpin of the CBM from the pneumococcal LytA autolysin. Circular dichroism and NMR data reveal that this peptide forms a highly stable native‐like β‐hairpin both in aqueous solution and in the presence of trifluoroethanol, but, strikingly, the peptide structure is a stable amphipathic α‐helix in both zwitterionic (dodecylphosphocholine) and anionic (sodium dodecylsulfate) detergent micelles, as well as in small unilamellar vesicles. This β‐hairpin to α‐helix conversion is reversible. Given that the β‐hairpin and α‐helix differ greatly in the distribution of hydrophobic and hydrophilic side chains, we propose that the amphipathicity is a requirement for a peptide structure to interact and to be stable in micelles or lipid vesicles. To our knowledge, this “chameleonic” behaviour is the only described case of a micelle‐induced structural transition between two ordered peptide structures.     

Efficient Iterative Synthesis of O‐Acetylated Tri‐ to Pentadecasaccharides Related to the Lipopolysaccharide of Shigella flexneri Type 3 a through Di‐ and Trisaccharide Glycosyl Donors

Protection against bacterial infections, including shigellosis, can be achieved by antibodies against the bacterial surface polysaccharide. In line with our efforts to develop vaccine candidates for shigellosis, we report herein the synthesis of penta‐, deca‐, and pentadecasaccharides as well as tri‐, octa‐, and tridecasaccharides as the endchain and intrachain fragments, respectively, of the surface polysaccharide of Shigella flexneri 3 a, a prevalent serotype. The syntheses relied on the efficiency of the trichloroacetimidate glycosylation chemistry, whereby iteration with di‐ and trisaccharide building blocks provided fragments made of up to three mono‐O‐acetylated polysaccharide repeating units. Pd(OH)₂‐mediated hydrogenation/hydrogenolysis enabled the concomitant removal or conversion of up to 31 protecting groups of 4 different origins to provide the targets as propyl glycosides. Oligosaccharides comprising the octasaccharide segment were shown to display high conformational similarities in solution.     

Structural and Kinetic Dissection of the endo‐α‐1,2‐Mannanase Activity of Bacterial GH99 Glycoside Hydrolases from Bacteroides spp.

Glycoside hydrolase family 99 (GH99) was created to categorize sequence‐related glycosidases possessing endo‐α‐mannosidase activity: the cleavage of mannosidic linkages within eukaryotic N‐glycan precursors (Glc_1–3Man₉GlcNAc₂), releasing mono‐, di‐ and triglucosylated‐mannose (Glc_1–3‐1,3‐Man). GH99 family members have recently been implicated in the ability of Bacteroides spp., present within the gut microbiota, to metabolize fungal cell wall α‐mannans, releasing α‐1,3‐mannobiose by hydrolysing αMan‐1,3‐αMan→1,2‐αMan‐1,2‐αMan sequences within branches off the main α‐1,6‐mannan backbone. We report the development of a series of substrates and inhibitors, which we use to kinetically and structurally characterise this novel endo‐α‐1,2‐mannanase activity of bacterial GH99 enzymes from Bacteroides thetaiotaomicron and xylanisolvens. These data reveal an approximate 5 kJ mol^?1 preference for mannose‐configured substrates in the ?2 subsite (relative to glucose), which inspired the development of a new inhibitor, α‐mannopyranosyl‐1,3‐isofagomine (ManIFG), the most potent (bacterial) GH99 inhibitor reported to date. X‐ray structures of ManIFG or a substrate in complex with wild‐type or inactive mutants, respectively, of B. xylanisolvens GH99 reveal the structural basis for binding to D ‐mannose‐ rather than D ‐glucose‐configured substrates.     

sp2‐Iminosugar O‐, S‐, and N‐Glycosides as Conformational Mimics of α‐Linked Disaccharides; Implications for Glycosidase Inhibition

The synthesis of mimics of the α(1→6)‐ and α(1→4)‐linked disaccharides isomaltose and maltose featuring a bicyclic sp²‐iminosugar nonreducing moiety O‐, S‐, or N‐linked to a glucopyranoside residue is reported. The strong generalized anomeric effect operating in sp²‐iminosugars determines the α‐stereochemical outcome of the glycosylation reactions, independent of the presence or not of participating protecting groups and of the nature of the heteroatom. It also imparts chemical stability to the resulting aminoacetal, aminothioacetal, or gem‐diamine functionalities. All the three isomaltose mimics behave as potent and very selective inhibitors of isomaltase and maltase, two α‐glucosidases that bind the parent disaccharides either as substrate or inhibitor. In contrast, large differences in the inhibitory properties were observed among the maltose mimics, with the O‐linked derivative being a more potent inhibitor than the N‐linked analogue; the S‐linked pseudodisaccharide did not inhibit either of the two target enzymes. A comparative conformational analysis based on NMR and molecular modelling revealed remarkable differences in the flexibility about the glycosidic linkage as a function of the nature of the linking atom in this series. Thus, the N‐pseudodisaccharide is more rigid than the O‐linked derivative, which exhibits conformational properties very similar to those of the natural maltose. The analogous pseudothiomaltoside is much more flexible than the N‐ or O‐linked derivatives, and can access a broader area of the conformational space, which probably implies a strong entropic penalty upon binding to the enzymes. Together, the present results illustrate the importance of taking conformational aspects into consideration in the design of functional oligosaccharide mimetics.     

[Zn2(thf)2(EtZn)6Zn4(μ4‐O)(tBuPO3)8]: A Dodecanuclear Zincophosphonate Aggregate with a Zn4(μ4‐O) Core

The largest multinuclear zinc framework synthesized is in the title compound (see picture), which contains structural features closely related to the motifs found in layered and three‐dimensional zincophosphates and zincophosphonates. The reactive centers make this zincophosphonate a viable precursor for the synthesis of porous zincophosphonate materials.     

Pac13 is a Small,Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.     

A novel dinuclear bismuth(III) coordination compound: bis(μ‐pyridine‐2,6‐dicarboxylato)‐κ4O2,N,O6:O6′;κ4O2:O2′,N,O6‐bis[(azido‐κN)(1,10‐phenanthroline‐κ2N,N′)bismuth(III)] tetrahydrate

A novel dinuclear bismuth(III) coordination compound, [Bi₂(C₇H₃NO₄)₂(N₃)₂(C₁₂H₈N₂)₂]·4H₂O, has been synthesized by an ionothermal method and characterized by elemental analysis, energy‐dispersive X‐ray spectroscopy, IR, X‐ray photoelectron spectroscopy and single‐crystal X‐ray diffraction. The molecular structure consists of one centrosymmetric dinuclear neutral fragment and four water molecules. Within the dinuclear fragment, each Bi^III centre is seven‐coordinated by three O atoms and four N atoms. The coordination geometry of each Bi^III atom is distorted pentagonal–bipyramidal (BiO₃N₄), with one azide N atom and one bridging carboxylate O atom located in axial positions. The carboxylate O atoms and water molecules are assembled via O—H...O hydrogen bonds, resulting in the formation of a three‐dimensional supramolecular structure. Two types of π–π stacking interactions are found, with centroid‐to‐centroid distances of 3.461 (4) and 3.641 (4) Å.     

Identification and X‐ray Co‐crystal Structure of a Small‐Molecule Activator of LFA‐1‐ICAM‐1 Binding

Stabilization of protein–protein interactions by small molecules is a concept with few examples reported to date. Herein we describe the identification and X‐ray co‐crystal structure determination of IBE‐667, an ICAM‐1 binding enhancer for LFA‐1. IBE‐667 was designed based on the SAR information obtained from an on‐bead screen of tagged one‐bead one‐compound combinatorial libraries by confocal nanoscanning and bead picking (CONA). Cellular assays demonstrate the activity of IBE‐667 in promoting the binding of LFA‐1 on activated immune cells to ICAM‐1.     

Biopolymer Skeleton Produced by Rhizobium radiobacter: Stoichiometric Alternation of Glycosidic and Amidic Bonds in the Lipopolysaccharide O‐Antigen

The lipopolysaccharide (LPS) O‐antigen structure of the plant pathogen Rhizobium radiobacter strain TT9 and its possible role in a plant‐microbe interaction was investigated. The analyses disclosed the presence of two O‐antigens, named Poly1 and Poly2. The repetitive unit of Poly2 constitutes a 4‐α‐l ‐rhamnose linked to a 3‐α‐d ‐fucose residue. Surprisingly, Poly1 turned out to be a novel type of biopolymer in which the repeating unit is formed by a monosaccharide and an amino‐acid derivative, so that the polymer has alternating glycosidic and amidic bonds joining the two units: 4‐amino‐4‐deoxy‐3‐O‐methyl‐d ‐fucose and (2′R,3′R,4′S)‐N‐methyl‐3′,4′‐dihydroxy‐3′‐methyl‐5′‐oxoproline). Differently from the O‐antigens of LPSs from other pathogenic Gram‐negative bacteria, these two O‐antigens do not activate the oxidative burst, an early innate immune response in the model plant Arabidopsis thaliana, explaining at least in part the ability of this R. radiobacter strain to avoid host defenses during a plant infection process.     

C3′‐Deoxygenation of Paromamine Catalyzed by a Radical S‐Adenosylmethionine Enzyme: Characterization of the Enzyme AprD4 and Its Reductase Partner AprD3

C3′‐deoxygenation of aminoglycosides results in their decreased susceptibility to phosphorylation thereby increasing their efficacy as antibiotics. However, the biosynthetic mechanism of C3′‐deoxygenation is unknown. To address this issue, aprD4 and aprD3 genes from the apramycin gene cluster in Streptomyces tenebrarius were expressed in E. coli and the resulting gene products were characterized in vitro. AprD4 is shown to be a radical S‐adenosylmethionine (SAM) enzyme, catalyzing homolysis of SAM to 5′‐deoxyadenosine (5′‐dAdo) in the presence of paromamine. [4′‐²H]‐Paromamine was prepared and used to show that its C4′‐H is transferred to 5′‐dAdo by AprD4, during which the substrate is dehydrated to a product consistent with 4′‐oxolividamine. In contrast, paromamine is reduced to a deoxy product when incubated with AprD4/AprD3/NADPH. These results show that AprD4 is the first radical SAM diol‐dehydratase and, along with AprD3, is responsible for 3′‐deoxygenation in aminoglycoside biosynthesis.     

Solid‐state NMR Study of the YadA Membrane‐Anchor Domain in the Bacterial Outer Membrane

MAS‐NMR was used to study the structure and dynamics at ambient temperatures of the membrane‐anchor domain of YadA (YadA‐M) in a pellet of the outer membrane of E. coli in which it was expressed. YadA is an adhesin from the pathogen Yersinia enterocolitica that is involved in interactions with the host cell, and it is a model protein for studying the autotransport process. Existing assignments were sucessfully transferred to a large part of the YadA‐M protein in the E. coli lipid environment by using ¹³C‐¹³C DARR and PDSD spectra at different mixing times. The chemical shifts in most regions of YadA‐M are unchanged relative to those in microcrystalline YadA‐M preparations from which a structure has previously been solved, including the ASSA region that is proposed to be involved in transition‐state hairpin formation for transport of the soluble domain. Comparisons of the dynamics between the microcrystalline and membrane‐embedded samples indicate greater flexibility of the ASSA region in the outer‐membrane preparation at physiological temperatures. This study will pave the way towards MAS‐NMR structure determination of membrane proteins, and a better understanding of functionally important dynamic residues in native membrane environments.     

Synthetic Studies on Actinorhodin and γ‐Actinorhodin: Synthesis of Deoxyactinorhodin and Deoxy‐γ‐actinorhodin/Crisamicin A Isomer

A strategy based on bidirectional Dötz benzannulation and the oxa‐Pictet–Spengler reaction toward the synthesis of actinorhodin and γ‐actinorhodin has been explored. This work has resulted in the synthesis of deoxyactinorhodin and deoxy‐γ‐actinorhodin. The latter is a regioisomer of crisamicin A (which has 10,10′‐dihydroxy groups).     

Syntheses of 2‐Keto‐3‐deoxy‐D‐xylonate and 2‐Keto‐3‐deoxy‐L‐arabinonate as Stereochemical Probes for Demonstrating the Metabolic Promiscuity of Sulfolobus solfataricus Towards D‐Xylose and L‐Arabinose

Practical syntheses of 2‐keto‐3‐deoxy‐D ‐xylonate (D ‐KDX) and 2‐keto‐3‐deoxy‐L ‐arabinonate (L ‐KDA) that rely on reaction of the anion of ethyl 2‐[(tert‐butyldimethylsilyl)oxy]‐2‐(dimethoxy phosphoryl) acetate with enantiopure glyceraldehyde acetonide, followed by global deprotection of the resultant O‐silyl‐enol esters, have been developed. This has enabled us to confirm that a 2‐keto‐3‐deoxy‐D ‐gluconate aldolase from the archaeon Sulfolobus solfataricus demonstrates good activity for catalysis of the retro‐aldol cleavage of both these enantiomers to afford pyruvate and glycolaldehyde. The stereochemical promiscuity of this aldolase towards these enantiomeric aldol substrates confirms that this organism employs a metabolically promiscuous pathway to catabolise the C5‐sugars D ‐xylose and L ‐arabinose.     

Assembly of a New Cyano‐bridged 4f‐3d Dimer Sm(DMSO)4‐ (H2O)3Cr(CN)6 and Crystal Structure of [K3(18‐crown‐6)3‐(H2O)4]Cr(CN)6·3H2O

A new cyano‐bridged binuclear 4f‐3d complex Sm(DMSO)₄‐(H₂O)₃Cr(CN)₆ was synthesized and characterized by single crystal structure analysis. It crystallizes in monoclinic, space group P2₁ with a=0.9367(2) nm, b = 1.3917(3) nm, c = 1.1212(2) run, β = 99.88(3)° and Z = 2. In this binuclear complex, Sm atom is eight coordinated and linked to the Cr atom by a cyano bridge. The molecules packs to form 3D structure due to the hydrogen bonds among them. [K₃(18‐C‐6)₃(H₂O)₄]Cr(CN)₆·3H₂O (18‐C‐6 represents 18‐crown‐6‐ether) that was synthesized as a byproduct in the preparation of a Gd—Cr complex is also structurally characterized. Crystal data: triclinic, space group P‐l with a = 1.0496(7) nm, b= 1.1567(14) nm, c = 1.3530(13) nm, a = 94.15(9)°, β = 96.04(8)°, γ = 95.25(9)° and Z = l. [K₃(18‐C‐6)₃(H₂O)₄]‐Cr(CN)₆·3H₂O consists of ionic [K₃(18‐C‐6)₃(H₂O)₄]³⁺ and [Cr(CN)₆]^3‐ pairs, of which the [K₃(18‐C‐6)₃(H₂O)₄]³⁺ ion is a trinuclear duster connected by water, and K atoms are eight coordinated by eight oxygen atoms of one 18‐C‐6 and two water molecules.     

6‐TIPS‐β‐Cyclodextrin‐Modified Fe3O4 for Facile Enantioseparation of 1‐(1‐Naphthyl)ethylamine

A new type of chiral magnetic nanoparticle was prepared from covalently linked magnetic nanoparticles (Fe₃O₄) and heptakis‐(6‐O‐triisopropylsilyl)‐β‐cyclodextrin (6‐TIPS‐β‐CD). The resulting selectors (TIPS‐β‐CD‐MNPs) combined the good magnetic properties Fe₃O₄ and efficient chiral recognition ability of 6‐TIPS‐β‐CD. The enantioselectivity of TIPS‐β‐CD‐MNPs towards 1‐(1‐naphthyl)ethylamine was six times higher than that of the parent β‐CD modified Fe₃O₄ particles.