Sugar Scaffold Research Articles

Nonreducing Sugar Scaffold Enables the Development of Immunomodulatory TLR4-specific LPS Mimetics with Picomolar Potency.

Innate immune defense mechanisms against infection and cancer encompass the modulation of pattern recognition receptor (PRR)-mediated inflammation, including upregulation of various transcription factors and the activation of pro-inflammatory pathways important for immune surveillance. Dysfunction of PRRs-mediated signaling has been implicated in cancer and autoimmune diseases, while the overactivation of PRRs-driven responses during infection can lead to devastating consequences such as acute lung injury or sepsis. We used crystal structure-based design to develop immunomodulatory lipopolysaccharide (LPS) mimetics targeting one of the ubiquitous PRRs, Toll-like Receptor 4 (TLR4). Taking advantage of an exo-anomeric conformation and specific molecular shape of synthetic nonreducing β,β-diglucosamine, which was investigated by NMR, we developed two sets of lipid A mimicking glycolipids capable of either potently activating innate immune responses or inhibiting pro-inflammatory signaling. Stereoselective 1,1'-glycosylation towards fully orthogonally protected nonreducing GlcNβ(1↔1')βGlcN followed by stepwise assembly of differently functionalised phosphorylated glycolipids provided biologically active molecules that were evaluated for their ability to trigger or to inhibit cellular innate immune responses. Two LPS mimetics, identified as potent TLR4-specific inducers of the intracellular signaling pathways, serve as vaccine adjuvant- and immunotherapy candidates, while anionic glycolipids with TLR4-inhibitory potential hold therapeutic promise for the management of acute or chronic inflammation.

Nonreducing Sugar Scaffold Enables the Development of Immunomodulatory TLR4‐specific LPS Mimetics with Picomolar Potency

AbstractInnate immune defense mechanisms against infection and cancer encompass the modulation of pattern recognition receptor (PRR)‐mediated inflammation, including upregulation of various transcription factors and the activation of pro‐inflammatory pathways important for immune surveillance. Dysfunction of PRRs‐mediated signaling has been implicated in cancer and autoimmune diseases, while the overactivation of PRRs‐driven responses during infection can lead to devastating consequences such as acute lung injury or sepsis. We used crystal structure‐based design to develop immunomodulatory lipopolysaccharide (LPS) mimetics targeting one of the ubiquitous PRRs, Toll‐like Receptor 4 (TLR4). Taking advantage of an exo‐anomeric conformation and specific molecular shape of synthetic nonreducing β,β‐diglucosamine, which was investigated by NMR, we developed two sets of lipid A mimicking glycolipids capable of either potently activating innate immune responses or inhibiting pro‐inflammatory signaling. Stereoselective 1,1′‐glycosylation towards fully orthogonally protected nonreducing GlcNβ(1↔1′)βGlcN followed by stepwise assembly of differently functionalised phosphorylated glycolipids provided biologically active molecules that were evaluated for their ability to trigger or to inhibit cellular innate immune responses. Two LPS mimetics, identified as potent TLR4‐specific inducers of the intracellular signaling pathways, serve as vaccine adjuvant‐ and immunotherapy candidates, while anionic glycolipids with TLR4‐inhibitory potential hold therapeutic promise for the management of acute or chronic inflammation.

Synthesis of 4-Deoxy-4-Fluoro-d-Sedoheptulose: A Promising New Sugar to Apply the Principle of Metabolic Trapping.

Fluorinated carbohydrates are important tools for understanding the deregulation of metabolic fluxes and pathways. Fluorinating specific positions within the sugar scaffold can lead to enhanced metabolic stability and subsequent metabolic trapping in cells. This principle has, however, never been applied to study the metabolism of the rare sugars of the pentose phosphate pathway (PPP). In this study, two fluorinated derivatives of d-sedoheptulose were designed and synthesized: 4-deoxy-4-fluoro-d-sedoheptulose (4DFS) and 3-deoxy-3-fluoro-d-sedoheptulose (3DFS). Both sugars are taken up by human fibroblasts but only 4DFS is phosphorylated. Fluorination of d-sedoheptulose at C-4 effectively halts the enzymatic degradation by transaldolase and transketolase. 4DFS thus has a high potential as a new PPP imaging probe based on the principle of metabolic trapping. Therefore, the synthesis of potential radiolabeling precursors for 4DFS for future radiofluorinations with fluorine-18 is presented.

Selective Reduction Leading to 3,5-cis-3-Aminosugars: Synthesis and Stereoselective Glycosylation.

Synthesis of 3,5-cis-3-amino glycals with a cis-fused cyclic sulfamidate group has been achieved by selective reduction of sulfamidate ketimine groups. The efficient access to the structurally unique glycals allowed the subsequent divergent synthesis of various naturally occurring 3-amino-2,3,6-trideoxysugars. In addition, Lewis acid-promoted glycosylation of the glycals provided a simple solution for the stereoselective installation of O- and C-linked aglycons on the amino sugar scaffolds.

Small Carbohydrate Derivatives as Potent Antibiofilm Agents.

Biofilm formation by most pathogenic bacteria is considered as one of the key mechanisms associated with virulence and antibiotic resistance. Biofilm-forming bacteria adhere to the surfaces of biological or implant medical devices and create communities within their self-produced extracellular matrix that are difficult to treat by existing antibiotics. There is an urgent need to synthesize and screen structurally diverse molecules for their antibiofilm activity that can remove or minimize the bacterial biofilm. The development of carbohydrate-based small molecules as antibiofilm agents holds a great promise in addressing the problem of the eradication of biofilm-related infections. Owing to their structural diversity and specificity, the sugar scaffolds are valuable entities for developing antibiofilm agents. In this perspective, we discuss the literature pertaining to carbohydrate-based natural antibiofilm agents and provide an overview of the design, activity, and mode of action of potent synthetic carbohydrate-based molecules.

Synthesis, biochemical, and biological evaluation of C2 linkage derivatives of amino sugars, inhibitors of glucokinase from Trypanosoma cruzi

Eighteen amino sugar analogues were screened against Trypanosoma cruzi glucokinase (TcGlcK), a potential drug-target of the protozoan parasite in order to assess for viable enzyme inhibition. The analogues were divided into three amino sugar scaffolds that included d-glucosamine (d-GlcN), d-mannosamine (d-ManN), and d-galactosamine (d-GalN); moreover, all but one of these compounds were novel. TcGlcK is an important metabolic enzyme that has a role in producing G6P for glycolysis and the pentose phosphate pathway (PPP). The inhibition of these pathways via glucose kinases (i.e., glucokinase and hexokinase) appears to be a strategic approach for drug discovery. Glucose kinases phosphorylate d-glucose with co-substrate ATP to yield G6P and the formed G6P enters both pathways for catabolism. The compound screen revealed five on-target confirmed inhibitors that were all from the d-GlcN series, such as compounds 1, 2, 4, 5, and 6. Four of these compounds were strong TcGlcK inhibitors (1, 2, 4, and 6) since they were found to have micromolar inhibitory constant (Ki) values around 20 μM. Three of the on-target confirmed inhibitors (1, 5, and 6) revealed notable in vitro anti-T. cruzi activity with IC50 values being less than 50 μM. Compound 1 was benzoyl glucosamine (BENZ-GlcN), a known TcGlcK inhibitor that was the starting point for the design of the compounds in this study; in addition, TcGlcK – compound 1 inhibition properties were previously determined [D’Antonio, E. L. et al. (2015) Mol. Biochem. Parasitol. 204, 64–76]. As such, compounds 5 and 6 were further evaluated biochemically, where formal Ki values were determined as well as their mode of TcGlcK inhibition. The Ki values determined for compounds 5 and 6 were 107 ± 4 μM and 15.2 ± 3.3 μM, respectively, and both of these compounds exhibited the competitive inhibition mode.

Tailored Modulation of Cellular Pro-inflammatory Responses With Disaccharide Lipid A Mimetics.

Pro-inflammatory signaling mediated by Toll-like receptor 4 (TLR4)/myeloid differentiation-2 (MD-2) complex plays a crucial role in the instantaneous protection against infectious challenge and largely contributes to recovery from Gram-negative infection. Activation of TLR4 also boosts the adaptive immunity which is implemented in the development of vaccine adjuvants by application of minimally toxic TLR4 activating ligands. The modulation of pro-inflammatory responses via the TLR4 signaling pathway was found beneficial for management of acute and chronic inflammatory disorders including asthma, allergy, arthritis, Alzheimer disease pathology, sepsis, and cancer. The TLR4/MD-2 complex can recognize the terminal motif of Gram-negative bacterial lipopolysaccharide (LPS)—a glycophospholipid lipid A. Although immense progress in understanding the molecular basis of LPS-induced TLR4-mediated signaling has been achieved, gradual, and predictable TLR4 activation by structurally defined ligands has not yet been attained. We report on controllable modulation of cellular pro-inflammatory responses by application of novel synthetic glycolipids—disaccharide-based lipid A mimetics (DLAMs) having picomolar affinity for TLR4/MD-2. Using crystal structure inspired design we have developed endotoxin mimetics where the inherently flexible β(1 → 6)-linked diglucosamine backbone of lipid A is replaced by a conformationally restricted α,α-(1↔1)-linked disaccharide scaffold. The tertiary structure of the disaccharide skeleton of DLAMs mirrors the 3-dimensional shape of TLR4/MD-2 bound E. coli lipid A. Due to exceptional conformational rigidity of the sugar scaffold, the specific 3D organization of DLAM must be preserved upon interaction with proteins. These structural factors along with specific acylation and phosphorylation pattern can ensure picomolar affinity for TLR4 and permit efficient dimerization of TLR4/MD-2/DLAM complexes. Since the binding pose of lipid A in the binding pocket of MD-2 (±180°) is crucial for the expression of biological activity, the chemical structure of DLAMs was designed to permit a predefined binding orientation in the binding groove of MD-2, which ensured tailored and species-independent (human and mice) TLR4 activation. Manipulating phosphorylation and acylation pattern at the sugar moiety facing the secondary dimerization interface allowed for adjustable modulation of the TLR4-mediated signaling. Tailored modulation of cellular pro-inflammatory responses by distinct modifications of the molecular structure of DLAMs was attained in primary human and mouse immune cells, lung epithelial cells and TLR4 transfected HEK293 cells.

Profiling protein expression in Klebsiella pneumoniae with a carbohydrate-based covalent probe

We report the application of a covalent probe based on a d-glucosamine scaffold for the profiling of the bacterial pathogen Klebsiella pneumoniae. Incubation of K. pneumoniae lysates with the probe followed by electrophoretic separation and in-gel fluorescence detection allowed the generation of strain-specific signatures and the differentiation of a carbapenem-resistant strain. The labelling profile of the probe was independent of its anomeric configuration and included several low-abundance proteins not readily detectable by conventional protein staining. Initial target identification experiments by mass spectrometry suggest that target proteins include several carbohydrate-recognising proteins, which indicates that the sugar scaffold may have a role for target recognition.

Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars.

The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, “naked” conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5′ and OH-3′ are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3′ is “born free” in the “naked” lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for “life’s code” and suggest a mechanism by which the resulting freedom of OH-3′ (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5′-to-3′.

3D‐Printed Sugar Scaffold for High‐Precision and Highly Sensitive Active and Passive Wearable Sensors

In this study, a pairing of a previously unidentified 3D printing technique and soft materials is introduced in order to achieve not only high‐resolution printed features and flexibility of the 3D‐printed materials, but also its light‐weight and electrical conductivity. Using the developed technique and materials, high‐precision and highly sensitive patient‐specific wearable active or passive devices are fabricated for personalized health monitoring. The fabricated biosensors show low density and substantial flexibility because of 3D microcellular network‐type interconnected conductive materials that are readily printed using an inkjet head. Using high‐resolution 3D scanned body‐shape data, on‐demand personalized wearable sensors made of the 3D‐printed soft and conductive materials are fabricated. These sensors successfully detect both actively changing body strain signals and passively changing signals such as electromyography (EMG), electrodermal activity (EDA), and electroencephalogram EEG. The accurately tailored subject‐specific shape of the developed sensors exhibits higher sensitivity and faster real‐time sensing performances in the monitoring of rapidly changing human body signals. The newly developed 3D printing technique and materials can be widely applied to various types of wearable, flexible, and light‐weight biosensors for use in a variety of inexpensive on‐demand and personalized point‐of‐care diagnostics.

The Miharamycins and Amipurimycin: their Structural Revision and the Total Synthesis of the Latter

AbstractThe structural puzzle of amipurimycin, a peptidyl nucleoside antibiotic, is solved by total synthesis and X‐ray diffraction analysis, with the originally proposed configurations at C3′ and C8′ inverted and those at C6′, C2′′, and C3′′ corrected. A similar structural revision of the relevant miharamycins is proposed via chemical transformations and then validated by X‐ray diffraction analysis. The miharamycins bear an unusual trans‐fused dioxabicyclo[4.3.0]nonane sugar scaffold, which was previously assigned as being in the cis configuration.

The Miharamycins and Amipurimycin: their Structural Revision and the Total Synthesis of the Latter.

The structural puzzle of amipurimycin, a peptidyl nucleoside antibiotic, is solved by total synthesis and X-ray diffraction analysis, with the originally proposed configurations at C3' and C8' inverted and those at C6', C2'', and C3'' corrected. A similar structural revision of the relevant miharamycins is proposed via chemical transformations and then validated by X-ray diffraction analysis. The miharamycins bear an unusual trans-fused dioxabicyclo[4.3.0]nonane sugar scaffold, which was previously assigned as being in the cis configuration.

Synthesis of a 3′-C-ethynyl-β-d-ribofuranose purine nucleoside library: Discovery of C7-deazapurine analogs as potent antiproliferative nucleosides

A focused nucleoside library was constructed around a 3′-C-ethynyl-d-ribofuranose sugar scaffold, which was coupled to variously modified purine nucleobases. The resulting nucleosides were probed for their ability to inhibit tumor cell proliferation, as well as for their activity against a panel of relevant human viruses. While C6-aryl substituted purine nucleosides were found to be weakly active, several C7-substituted 7-deazapurine nucleosides elicited potent antiproliferative activity. Their activity spectrum was evaluated in the NCI-60 tumor cell line panel indicating activity against several solid tumor derived cell lines. Analog 32, equipped with a 7-deaza 7-chloro-6-amino-purin-9-yl base was evaluated in a metastatic breast tumor (MDA-MB-231-LM2) xenograft model. It inhibited both tumor growth and reduced the formation of lung metastases as revealed by BLI analysis. The dideazanucleoside analog 66 showed interesting activity against hCMV. These results highlight the potential advantages of recombining known sugar and nucleobase motifs as a library design strategy to discover novel antiviral or antitumor agents.

Synthesis of Novel Bis-Triazolyl Glycoconjugates via Dual Click Reaction for the Selective Recognition of Cu(II) Ions

Glycosyl-β-azidoester, obtained from corresponding olefinic ester via one-pot tandem Michael-diazotransfer reaction, on click coupling with di-O-propargylated ethers afforded high yields of novel bis-triazolyl glycoconjugates. The resulting two distinct class of bis-triazolyl glycoconjugates includes the bidentate 3-O-protected-α-D-glucofuranose bearing two triazolyl glycosylated-β-triazoloester groups at 5,6-positions of sugar scaffold and 1,4:3,6-dianhydro-D-mannitol-based bidentate glycoconjugate with two triazole groups at 2,5 position of sugar scaffold (S1), and all the triazolyl glycoconjugates been characterization using standard spectral analysis. One of the developed bis-triazolyl glycoconjugate 7 a has sucessfully been explored as a promissing sensor for the selective recognition of Cu2+ ions. The probe S1 displayed moderate selective detection of Cu2+ ions by means of ultraviolet spectroscopy. The Job plot experiment suggested 1:1 complexation of probe S1 (compound 7 a) with Cu2+ ions having a detection limit of 8.00 μM.

ChemInform Abstract: Biosynthetic and Synthetic Access to Amino Sugars

AbstractReview: 265 refs.

ChemInform Abstract: 1′‐Homonucleosides and Their Structural Analogues: A Review

AbstractReview: 132 refs.

ChemInform Abstract: From Glycals to Aminosugars: A Challenging Test for New Stereoselective Aminohydroxylation and Related Methodologies

AbstractReview: [89 refs.

Chemoenzymatic Synthesis of a Novel Sugar Scaffold for Targeting Ligand Development

The capsular polysaccharides (CPSs) that encapsulate bacteria aids in overall virulence of the microbe. The bacterial capsules differ across species of bacteria from benign, pathogenic, or symbiotic bacteria. Specific targeting of the surface of the differing organisms would be advantageous in order to select certain types of bacteria over others, for either targeting or detection purposes.In our lab, we have developed a new strategy to specifically target surfaces of certain types of bacteria. The developed targeting strategy is based on the surface coating of Vibrio vulnificus, and specifically the rare N‐acetyl‐quinovosamine (QuiNAc) sugar contained in the sugar polymer, as well as other sugars from the V. vulnificus polysaccharide biosynthesis pathway. The targeting strategy involves naturally occurring enzyme sugar products, as well as an isoprenoid anchor analogue that was developed for use with elucidation of polysaccharide biosynthesis pathways in our lab.Determination of the sugar linkage to the isoprenoid anchor has been analyzed by RP‐HPLC with the use of a modified fluorescent isoprenoid analogue. A further developed analogue has been synthesized in our lab, which contains a different reactive group. This reactive group is used in the development of the targeting ligand for the rare QuiNAc sugar. Following the development of the targeting ligand associated with the rare sugars on specific types of bacteria, the use of the targeting agent is useful in applications of bacterial detection or in antibacterial schemes.Support or Funding InformationNational Institutes of Health AREA Grants R15GM100402 (J.M.T.), R15GM114773 (J.M.T.) and National Science Foundation Instrumentation Grant 1337873 (UNC‐Charlotte Chemistry)

Design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity.

A series of doubly flexible nucleoside analogues were designed based on the acyclic sugar scaffold of acyclovir and the flex-base moiety found in the fleximers. The target compounds were evaluated for their antiviral potential and found to inhibit several coronaviruses. Significantly, compound 2 displayed selective antiviral activity (CC50 >3× EC50) towards human coronavirus (HCoV)-NL63 and Middle East respiratory syndrome-coronavirus, but not severe acute respiratory syndrome-coronavirus. In the case of HCoV-NL63 the activity was highly promising with an EC50 <10 μM and a CC50 >100 μM. As such, these doubly flexible nucleoside analogues are viewed as a novel new class of drug candidates with potential for potent inhibition of coronaviruses.

Entasis through hook-and-loop fastening in a glycoligand with cumulative weak forces stabilizing Cu(I).

The idea of a possible control of metal ion properties by constraining the coordination sphere geometry was introduced by Vallee and Williams with the concept of entasis, which is frequently postulated to be at stake in metallobiomolecules. However, the interactions controlling the geometry at metal centers remain often elusive. In this study, the coordination properties toward copper ions—Cu(II) or Cu(I)—of a geometrically constrained glycoligand centered on a sugar scaffold were compared with those of an analogous ligand built on an unconstrained alkyl chain. The sugar-centered ligand was shown to be more preorganized for Cu(II) coordination than its open-chain analogue, with an unusual additional stabilization of the Cu(I) redox state. This preference for Cu(I) was suggested to arise from geometric constraints favoring an optimized folding of the glycoligand minimizing steric repulsions. In other words, the Cu(I) d(10) species is stabilized by valence shell electron pair repulsion (VSEPR). This idea was rationalized by a theoretical noncovalent interactions (NCI) analysis. The cumulative effects of weak forces were shown to create an efficient buckle as in a hook-and-loop fastener, and fine structural features within the glycoligand reduce repulsive interactions for the Cu(I) state. This study emphasizes that monosaccharide platforms are appropriate ligand backbones for a delicate geometric control at the metal center, with a network of weak interactions within the ligand. This structuration availing in glycoligands makes them attractive for metallic entasis.