Nathalie Berthet

High affinity glycodendrimers for the lectin LecB from Pseudomonas aeruginosa.

Following an iterative oxime ligation procedure, cyclopeptide (R) and lysine-based dendron (D) were combined in all possible arrangements and successively functionalized with α-fucose and β-fucose to provide a new series of hexadecavalent glycosylated scaffolds (i.e., scaffolds RD16, RR16, DR16, and DD16). These compounds and smaller analogs (tetra- and hexavalent scaffolds R4 and R6) were used to evaluate the influence of the ligand valency and architecture, and of the anomer configuration in the binding to the αFuc-specific lectin LecB from Pseudomonas aeruginosa . Competitive enzyme-linked lectin assays (ELLA) revealed that only the RD16 architecture displaying αFuc (9A) reaches strong binding improvement (IC50 of 0.6 nM) over αMeFuc, and increases the α-selectivity of LecB. Dissociation constant of 28 nM was measured by isothermal titration micorcalorimetry (ITC) for 9A, which represents the highest affinity ligand ever reported for LecB. ITC and molecular modeling suggested that the high affinity observed might be due to an aggregative chelate binding involving four sugar head groups and two lectins. Interestingly, unprecedented binding effects were observed with β-fucosylated conjugates, albeit being less active than the corresponding ligands of the αFuc series. In particular, the more flexible lysine-based dendritic structures (15B and 18B) showed a slight inhibitory enhancement in comparison with those having cyclopeptide core.

Tetravalent glycocyclopeptide with nanomolar affinity to wheat germ agglutinin

A series of tetravalent glycocyclopeptides functionalized with GlcNAc was synthesized using copper(i)-catalysed alkyne-azide cycloaddition, oxime ligation and thiol-ene coupling. The binding ability of these compounds towards wheat germ agglutinin was studied by a competitive ELLA test and ITC experiments. While all compounds were able to inhibit WGA binding to GlcNAc-polymer coated surfaces at low concentrations, derivative 17 having an aliphatic spacer and thioether linkage was 4.9 × 10(6) times more potent on a per sugar basis than GlcNAc. This remarkably strong effect was confirmed by ITC experiments as these revealed an association constant of 9 nM for this compound, therefore presenting a gain of 200,000 times over GlcNAc. These results for compound 17 represent the highest binding properties reported for WGA.

Synthesis of Glycocyclopeptides by Click Chemistry and Inhibition Assays with Lectins

A new series of tetravalent glycocyclopeptides has been prepared using the copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC). When compared with our oximation procedure previously described, we found that the CuAAC strategy led to glycoclusters with similar yield and purity. In addition, the binding properties of these two series of glycoclusters (i.e., with oxime or triazole linkage) were studied with several lectins. Interestingly, while no difference of binding was observed with the mannose-specific lectin from Canavalia ensiformis (ConA), the compound displaying αFuc through oxime linkage has revealed a significant binding improvement with the fucose-specific lectin from Ulex europaeus (UEA-I).

Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog

Universal DNA base analogs having photocleavable properties would be of great interest for development of new nucleic acid fragmentation tools. The photocleavable 7-nitroindole 2′-deoxyribonucleoside d(7-Ni) was previously shown to furnish a highly efficient approach to photochemically trigger DNA backbone cleavage at preselected position when inserted in a DNA fragment. In the present report, we examine its potential use as universal DNA nucleoside, by analogy with the 5-nitroindole analog that is generally considered as universal base. The d(7-Ni) phosphoramidite was incorporated into oligonucleotides. Hybridization properties of resulting 11mer duplexes indicated a behavior close to that of the 5-nitroindole analog. Enzymatic recognition by Klenow fragment exonuclease-free using 40mers containing the unnatural bases as templates indicated notably a decrease of the polymerase activity with preferential incorporation of dAMP opposite both the 7-Ni and 5-Ni bases. Incorporation of the d(7-Ni) triphosphate was also studied indicating absence of significant differences between the incorporation kinetics opposite each natural base in the template. All the hybridization and enzymatic data indicate that 7-nitroindole can be considered as a cleavable base analog, although not strictly fulfilling, like the 5-nitro isomer, all properties required for a universal base.

DNA repair inhibitors

DNA repair is essential for cell survival by preventing the formation of mutations which can be lethal and in some cases at the origin of tumours. The DNA repair may occur directly by enzymatic removal of damage from the nucleobase or indirectly, step by step (recognition of the damage, excision, DNA resynthesis). During chemotherapeutic treatment of cancer, the action of DNA repair proteins may lead to tumour cell resistance. This resistance might be overcome by the use of DNA repair inhibitors. The better characterised repair proteins are O6-alkylguanine alkyltransferases (AGT) and poly(ADP-ribose) polymerase (PARP). AGT removes alkylgroups from guanine O6 position via a one step suicide mechanism. The inhibition of AGT activity results from alkylation of the enzyme with a reactive O6modified guanine analogue. Encouraging results were obtained in combination with mono-alkylating agents on cell cultures. O6-benzylguanine (O6-BG) has been used in clinical trials. PARP is implicated in single strand break ...

Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2′-deoxyadenosine mimic

The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2′-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (λ > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue.

New glycopolymers as multivalent systems for lectin recognition

New types of glycopolymers have been designed and evaluated as multivalent systems for lectin recognition. They were prepared by living Anionic Ring-Opening Polymerization (AROP) of disubstituted cyclopropane-1,1-dicarboxylates and thiol–ene post-modification. Fully modified oligomers with single or geminal sugar substituents located on every third carbon alongside the macromolecular scaffold were obtained under mild conditions. The resulting glycopolymers have shown efficient binding potency towards concanavalin A.

Specific Recognition and Stabilization of an Abasic Site-Containing DNA Duplex by a Macrocyclic Bisacridine

Abstract A strong and specific stabilization of a DNA undecamer containing an analog of the abasic site has been induced by the macrocyclic Bisacridine 1 . 1H NMR analysis and molecular modeling of the structure of the complex showed that the drug was specifically docked into the apurinic pocket.

The abasic site as a target for generation of locally multiply damaged sites.

Abasic sites in DNA have been specifically targeted by synthetic compounds able to cleave DNA at abasic sites and to induce photodamages in the vicinity of the lesion. The synthesis and the photoactivity of the drugs on abasic sites containing DNA and oligonucleotides are reported.