Probing replacement of pyrophosphate via click chemistry; synthesis of UDP-sugar analogues as potential glycosyl transferase inhibitors

Synthetic Route to Glycosyl β-1C-(phosphino)-phosphonates as Unprecedented Stable Glycosyl Diphosphate Analogs and Their Preliminary Biological Evaluation

The synthesis of glycosyl-β-1C-(phosphino)-phosphonates is a challenge since it has not yet been described. In this paper, we report an innovative synthetic method for their preparation from Glc-, Man-, and GlcNAc- lactone derivatives. The proposed original strategy involves the addition of the corresponding δ-hexonolactones onto the dianion of (methylphosphino) phosphonate as a key step, followed by dehydration and stereoselective addition of dihydrogen on the resulting double bond. Final deprotection provides the new glycosyl diphosphate analogs in 35%, 36%, and 10% yield over 6 steps from the corresponding δ-hexonolactones. The synthetized compounds were evaluated as inhibitors of phosphatase and diphosphatase activities and found to have complex concentration-dependent activatory and inhibitory properties on alkaline phosphatase. The synthetized tools should be useful to study other enzymes such as transferases.

Design and Synthesis of Various 5'-Deoxy-5'-(4-Substituted-1,2,3-Triazol-1-yl)-Uridine Analogues as Inhibitors of Mycobacterium tuberculosis Mur Ligases

The synthesis of hitherto unknown 5′-deoxy-5′-(4-substituted-1,2,3-triazol-1-yl)-uridine and its evaluation, through an one-pot screening assay, against MurA-F enzymes involved in Mycobacterium tuberculosis (Mtb), are described. Starting from UDP-N-acetylmuramic acid (UDP-MurNAc), the natural substrate involved in the peptidoglycan biosynthesis, our strategy was to substitute the diphosphate group of UDP-MurNAc by a 1,2,3-triazolo spacer under copper-catalyzed azide-alkyne cycloaddition conditions. The structure-activity relationship was discussed and among the 23 novel compounds developed, N-acetylglucosamine analogues 11c and 11e emerged as the best inhibitors against the Mtb MurA-F enzymes reconstruction pathway with an inhibitory effect of 56% and 50%, respectively, at 100 μM. Both compounds are selective inhibitors of Mtb MurE, the molecular docking and molecular dynamic simulation suggesting that 11c and 11e are occupying the active site of Mtb MurE ligase.

Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3

We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.

The uncommon strong inhibition of α-glucosidase by multivalent glycoclusters based on cyclodextrin scaffolds

New inhibitors of α-glucosidase based on perglycosylated cyclodextrins were synthesized via click-chemistry and compared to acarbose.

UDP-GlcNAc Analogues as Inhibitors of O-GlcNAc Transferase (OGT): Spectroscopic, Computational, and Biological Studies

A series of glycomimetics of UDP-GlcNAc, in which the β-phosphate has been replaced by either an alkyl chain or a triazolyl ring and the sugar moiety has been replaced by a pyrrolidine ring, has been synthesized by the application of different click-chemistry procedures. Their affinities for human O-GlcNAc transferase (hOGT) have been evaluated and studied both spectroscopically and computationally. The binding epitopes of the best ligands have been determined in solution by means of saturation transfer difference (STD) NMR spectroscopy. Experimental, spectroscopic, and computational results are in agreement, pointing out the essential role of the binding of β-phosphate. We have found that the loss of interactions from the β-phosphate can be counterbalanced by the presence of hydrophobic groups at a pyrroline ring acting as a surrogate of the carbohydrate unit. Two of the prepared glycomimetics show inhibition at a micromolar level.

A double-click approach to the protecting group free synthesis of glycoconjugates

The use of a bi-functional linker, containing an alkyne and an alkene, allows the protecting group free conjugation of reducing sugars to thiols via a double click process.

Divergent and convergent synthesis of GalNAc-conjugated dendrimers using dual orthogonal ligations

The synthesis of glycodendrimers remains a challenging task. In this paper we propose a protocol based on both oxime ligation (OL) to combine cyclopeptide repeating units as the dendritic core and the copper(i)-catalyzed azide-alkyne cycloaddition (CuAAC) to conjugate peripheral α and β propargylated GalNAc. By contrast with the oxime-based iterative protocol reported in our group, our current strategy can be used in both divergent and convergent routes with similar efficiency and the resulting hexadecavalent glycodendrimers can be easily characterized compared to oxime-linked analogues. A series of glycoconjugates displaying four or sixteen copies of both α and β GalNAc have been prepared and their ability to inhibit the adhesion of the soybean agglutinin (SBA) lectin to polymeric-GalNAc immobilized on microtiter plates has been evaluated. As was anticipated, the higher inhibitory effect (IC50 = 0.46 μM) was measured with the structure displaying αGalNAc with the higher valency (compound 13), which demonstrates that the binding properties of these glycoconjugates are strongly dependent on the orientation and distribution of the GalNAc units.

1,2-cis Alkyl glycosides: straightforward glycosylation from unprotected 1-thioglycosyl donors

A 1,2-cis-alkyl glycosidation protocol that makes use of unprotected phenyl 1-thioglycosyl donors is reported. Glycosylation of various functionalized alcohols was accomplished in moderate to high yield and selectivity to give the 1,2-cis-glycosides. In order to quickly develop optimum glycosylation conditions, an FIA (flow injection analysis)-ESI-TOF-MS method was developed that enabled rapid and quantitative evaluation of yield on small scale. This methodology, coupled with NMR spectroscopy, allowed for rapid evaluation of the overall reactions.

'Click cyclic ADP-ribose': a neutral second messenger mimic

Analogues of the potent Ca(2+) releasing second messenger cyclic ADP-ribose (cADPR) with a 1,2,3-triazole pyrophosphate bioisostere were synthesised by click-mediated macrocyclisation. The ability to activate Ca(2+) release was surprisingly retained, and hydrolysis of cADPR by CD38 could also be inhibited, illustrating the potential of this approach to design drug-like signalling pathway modulators.

Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate

A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination of glycosylation, the Staudinger-Vilarrasa amide-bond formation, and azide-alkyne click chemistry. The compounds were evaluated as inhibitors of five metal-dependent galactosyltransferases. Crystallographic analyses of three inhibitors complexed in the active site of one of the enzymes confirmed that the pyridine moiety chelates the Mn(2+) ion causing a slight displacement (2 Å) from its original position. The carbohydrate head group occupies a different position than in the natural uridine diphosphate (UDP)-Gal substrate with little interaction with the enzyme.

Iron oxide magnetic nanoparticles with versatile surface functions based on dopamine anchors

The synthesis of multifunctional magnetic nanoparticles (MF-MPs) is one of the most active research areas in advanced materials as their multifunctional surfaces allow conjugation of biological and chemical molecules, thus making it possible to achieve target-specific diagnostic in parallel to therapeutics. We report here a simple strategy to integrate in a one-step reaction several reactive sites onto the particles. The preparation of MF-MPs is based on their simultaneous modification with differently functionalized dopamine derivatives using simple solution chemistry. The formed MF-MPs show comparable magnetic properties to those of naked nanoparticles with almost unaltered particle size of around 25 nm. The different termini, amine, azide and maleimide functions, enable further functionalization of MF-MPs by the grafting-on approach. Michael addition, Cu(i) catalyzed « click » chemistry and amidation reactions are performed on the MF-MPs integrating subsequently 6-(ferrocenyl)-hexanethiol, horseradish peroxidase (HRP) and mannose.

Preparation of a responsive carbohydrate-coated biointerface based on graphene/azido-terminated tetrathiafulvalene nanohybrid material

A one-step method for the reduction of graphene oxide (GO) to reduced graphene oxide (rGO) is reported taking advantage of the electron-donor properties of an azido-terminated tetrathiafulvalene (TTF-N(3)). The resulting graphene/TTF-N(3) nanohybrid material is characterized by X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FT-IR) spectroscopy, and by electrical and electrochemical means. The accessibility of the azide function to chemoselective modification by any alkyne-terminated partner molecule via Cu(I)-catalyzed "click" chemistry is demonstrated. In a proof of principle and motivated by the importance of glycan-modified materials, many alkynyl-terminated mannose units were grated onto graphene/TTF-N(3). The TTF-mannose units could be released efficiently from the graphene matrix by chemical oxidation of TTF-mannose surface units to TTF(2+)-mannose, using Fe(ClO(4))(3) or the electron-deficient tetracationic cyclophane cyclobis(paraquat-p-phenylene) (CBPQT(4+)).

Synthesis of bivalent glycoclusters containing GlcNAc as hexasaccharide mimetics. Bactericidal activity against Helicobacter pylori

The Cu(I) catalysed cycloaddition reaction of azides and alkynes has been used to generate a series of divalent GlcNAc clusters with both α and β configurations. These glycoclusters can be considered as potential mimetics of an anti Helicobacter pylori hexasaccharide as they present two GlcNAc residues grafted onto a core scaffold. Two bivalent compounds based on α-O-GlcNAc were identified that selectively reduced the viability of H. pylori. These compounds showed activity towards different strains of H. pylori (Pu4 vs P12). The activity of the oligosaccharide mimetics is speculated to be due to the GlcNAc residues being able to adopt spatial arrangements accessible to the anti H. pylori hexasaccharide which may be important for activity.

Synthesis and biological evaluation of potential new inhibitors of the bacterial transferase MraY with a β-ketophosphonate structure

Stable analogs of bacterial transferase MraY substrate or product with a pyrophosphate surrogate in their structure are described. β-ketophosphonates were designed as pyrophosphate bioisosteres and were investigated as UDP-GlcNAc mimics. The developed strategy allows introduction of structural diversity at a late stage of the synthesis. The biological activity of the synthesized compounds was evaluated on the MraY enzyme.

The first C-glycosidic analogue of a novel galactosyltransferase inhibitor

Structural analogues and mimics of the natural sugar-nucleotide UDP-galactose (UDP-Gal) are sought after as chemical tools for glycobiology and drug discovery. We have recently developed a novel class of galactosyltransferase (GalT) inhibitors derived from UDP-Gal, bearing an additional substituent at the 5-position of the uracil base. Herein we report the first C-glycosidic derivative of this new class of GalT inhibitors. We describe a practical convergent synthesis of the new UDP-C-Gal derivative, including a systematic study into the use of radical chemistry for the preparation of galactosyl ethylphosphonate, a key synthetic intermediate. The new inhibitor showed activity against a bacterial UDP-Gal 4'-epimerase at micromolar concentrations. This is the first example of a base-modified UDP-sugar as an inhibitor of a UDP-sugar-dependent enzyme which is not a glycosyltransferase, and these results may therefore have implications for the design of inhibitors of these enzymes in the future.

Ultrasonic assisted Fischer glycosylation: generating diversity for glycochemistry

In this study ultrasound has been utilised for the Fischer glycosylation using free sugars and sulphuric acid immobilized on silica as catalyst. N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, D-glucose, D-galactose, D-mannose, L-fucose, and lactose were glycosylated with propargyl alcohol or 2-azidoethanol affording the corresponding glycosides, with the production of the α-glycopyranoside as the dominant product. Remarkable acceleration of the glycosylation reactions (15 min-2 h compared to several hours) over reported procedures together with good yields were always observed.

Nucleoside triphosphate mimicry: a sugar triazolyl nucleoside as an ATP-competitive inhibitor of B. anthracis pantothenate kinase

The synthesis of a library of nucleoside triphosphate mimetics is described where the Mg(2+) chelated triphosphate sidechain is replaced by an uncharged methylene-triazole linked monosaccharide sidechain. The compounds have been evaluated as inhibitors of Bacillus anthracis pantothenate kinase and a competitive inhibitor has been identified with a K(i) that is 3-fold lower than the K(m) value of ATP.