N8-Glycosylated 8-Azapurine and Methylated Purine Nucleobases: Synthesis and Study of Base Pairing Properties.

In this report, we present the synthesis of N8-glycosylated 8-aza-2-methylhypoxanthine and 8-aza-6-thiohypoxanthine 2'-deoxynucleosides as well as methylated 2'-deoxynebularine derivatives. In vitro base pairing properties between each modified and canonical nucleobase were studied. As demonstrated by Tm, incorporation of the modified bases in DNA resulted, with few exceptions, in low stability of duplexes. Modified bases studied in this report are preferentially recognized by T (for N8-glycosylated 8-aza-2-methylhypoxanthine and methylated purines) and G (N8-glycosylated 8-aza-2-methylhypoxanthine). The base pair formed between N8-glycosylated 8-aza-6-thiohypoxanthine and N9-glycosylated 2-methyl-6-thiohypoxanthine (X2:X6) showed, to some extent, an orthogonal interaction. Based on Tm studies, the only potential self-pairing system is formed by the N8-glycosylated 8-aza-6-thiohypoxanthine nucleoside (X2) but only in the absence of canonical G and T. This study indicated that the canonical thymine base is the preferential base partner of methylated purine bases.

Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In†Vitro and In†Vivo.

The synthesis, base pairing properties and in vitro (polymerase) and in vivo (E. coli) recognition of 2'-deoxynucleotides with a 2-amino-6-methyl-8-oxo-7,8-dihydro-purine (X), a 2-methyl-6-thiopurine (Y) and a 6-methyl-4-pyrimidone (Z) base moiety are described. As demonstrated by Tm measurements, the X and Y bases fail to form a self-complementary base pair. Despite this failure, enzymatic incorporation experiments show that selected DNA polymerases recognize the X nucleotide and incorporate this modified nucleotide versus X in the template. In vivo, X is mainly recognized as a A/G or C base; Y is recognized as a G or C base and Z is mostly recognized as T or C. Replacing functional groups in nucleobases normally involved in W-C recognition (6-carbonyl and 2-amino group of purine; 6-carbonyl of pyrimidine) readily leads to orthogonality (absence of base pairing with natural bases).

Enzymatic Incorporation of Modified Purine Nucleotides in DNA.

A series of nucleotide analogues, with a hypoxanthine base moiety (8-aminohypoxanthine, 1-methyl-8-aminohypoxanthine, and 8-oxohypoxanthine), together with 5-methylisocytosine were tested as potential pairing partners of N8 -glycosylated nucleotides with an 8-azaguanine or 8-aza-9-deazaguanine base moiety by using DNA polymerases (incorporation studies). The best results were obtained with the 5-methylisocytosine nucleotide followed by the 1-methyl-8-aminohypoxanthine nucleotide. The experiments demonstrated that small differences in the structure (8-azaguanine versus 8-aza-9-deazaguanine) might lead to significant differences in recognition efficiency and selectivity, base pairing by Hoogsteen recognition at the polymerase level is possible, 8-aza-9-deazaguanine represents a self-complementary base pair, and a correlation exists between in vitro incorporation studies and in vivo recognition by natural bases in Escherichia coli, but this recognition is not absolute (exceptions were observed).

Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo.

The synthesis, base-pairing properties and in vitro and in vivo characteristics of 5-methyl-isocytosine (isoC(Me) ) and isoguanine (isoG) nucleosides, incorporated in an HNA(h) (hexitol nucleic acid)-DNA(d) mosaic backbone, are described. The required h-isoG phosphoramidite was prepared by a selective deamination as a key step. As demonstrated by Tm measurements the hexitol sugar showed slightly better mismatch discrimination against dT. The d-isoG base mispairing follows the order T>G>C while the h-isoG base mispairing follows the order G>C>T. The h- and d-isoC(Me) bases mainly mispair with G. Enzymatic incorporation experiments show that the hexitol backbone has a variable effect on selectivity. In the enzymatic assays, isoG misincorporates mainly with T, and isoC(Me) misincorporates mainly with A. Further analysis in vivo confirmed the patterns of base-pair interpretation for the deoxyribose and hexitol isoC(Me) /isoG bases in a cellular context, through incorporation of the bases into plasmidic DNA. Results in vivo demonstrated that mispairing and misincorporation was dependent on the backbone scaffold of the base, which indicates rational advances towards orthogonality.

Toward multifunctional "clickable" diamond nanoparticles.

Nanodiamonds (NDs) are among the most promising new carbon based materials for biomedical applications, and the simultaneous integration of various functions onto NDs is an urgent necessity. A multifunctional nanodiamond based formulation is proposed here. Our strategy relies on orthogonal surface modification using different dopamine anchors. NDs simultaneously functionalized with triethylene glycol (EG) and azide (-N3) functions were fabricated through a stoichiometrically controlled integration of the dopamine ligands onto the surface of hydroxylated NDs. The presence of EG functionalities rendered NDs soluble in water and biological media, while the -N3 group allowed postsynthetic modification of the NDs using "click" chemistry. As a proof of principle, alkynyl terminated di(amido amine) ligands were linked to these ND particles.

Synthesis of 1,5-dideoxy-1,5-iminoribitol C-glycosides through a nitrone-olefin cycloaddition domino strategy: identification of pharmacological chaperones of mutant human lysosomal ß-galactosidase.

We report herein a newly developed domino reaction that facilitates the synthesis of new 1,5-dideoxy-1,5-iminoribitol iminosugar C-glycosides 7a-e and 8. The key intermediate in this approach is a six-membered cyclic sugar nitrone that is generated in situ and trapped by an alkene dipolarophile via a [2 + 3] cycloaddition reaction to give the corresponding isooxazolidines 10a-e in a "one-pot" protocol. The iminoribitol C-glycosides 7a-e and 8 were found to be modest ß-galactosidase (bGal) inhibitors. However, compounds 7c and 7e showed "pharmacological chaperone" activity for mutant lysosomal bGal activity and facilitated its recovery in GM1 gangliosidosis patient fibroblasts by 2-6-fold.

Organophosphorus-catalyzed diaza-Wittig reaction: application to the synthesis of pyridazines.

The elaboration of the first organophosphorus-catalyzed diaza-Wittig reaction is reported. This catalytic reaction is applied to the synthesis of substituted pyridazine and phthalazine derivatives bearing electron-withdrawing groups with good to excellent yields from substrates containing a diazo functionality as the starting material and a phospholene oxide as the catalyst.

Strategy for the synthesis of pyridazine heterocycles and their derivatives.

The first synthesis of novel fused pyridazines has been realized starting from 1,3-diketones involving a Diaza-Wittig reaction as a key step. A convenient strategy was elaborated to access versatile pyridazine derivatives allowing the variation of substituents at position 6 of the heterocyclic ring. In a first part, pyridazines bearing an ester group were synthesized as a model to evaluate the methodology. In a second part, an improved procedure has been used for the synthesis of pyridazines bearing a ketone group and different methods of cyclization were carried out, leading to several hitherto unknown biheterocyclic compounds. This reaction scheme represents an attractive methodology for the synthesis of novel fused pyridazine derivatives.

The reaction coordinate of a bacterial GH47 α-mannosidase: a combined quantum mechanical and structural approach.

Mannosides in the southern hemisphere: Conformational analysis of enzymatic mannoside hydrolysis informs strategies for enzyme inhibition and inspires solutions to mannoside synthesis. Atomic resolution structures along the reaction coordinate of an inverting α-mannosidase show how the enzyme distorts the substrate and transition state. QM/MM calculations reveal how the free energy landscape of isolated α-D-mannose is molded on enzyme to only allow one conformationally accessible reaction coordinate.

Vitamin-guanosine monophosphate conjugates for in vitro transcription priming.

Expanding the catalytic repertoire of ribozymes to include vitamin synthesis requires efficient labelling of RNA with the substrate of interest, prior to in vitro selection. For this purpose, we rationally designed and synthesized six GMP-conjugates carrying a synthetic pre-thiamine or biotin precursor and investigated their transcription incorporation properties by T7 RNA polymerase.

Synthesis and conformational study of chiral oxepines: the Baylis-Hillman reaction and RCM approach with sugar aldehyde.

The Baylis-Hillman reaction of 3-O-allyl-alpha-d-xylo-pentodialdo-1,4-furanose 3 afforded a diastereomeric mixture of d-gluco- and l-ido-configured alpha-methylene-beta-hydroxy esters 4a and 4b, respectively, in a ratio of 2:3. Reduction of the ester functionality in 4a/4b gave alcohols 5a/5b. The diene thus formed in 5a/5b was subjected to ring-closing metathesis (Grubbs' second-generation catalyst) to afford oxa-bicyclic ring system 6a/6b in high yield. Further manipulation of the acetonide functionality in 6a and 6b afforded new polyhydroxylated oxepines 1a/2a and 1b/2b, respectively. The (1)H NMR of oxepines 1a and 1b in D(2)O showed doubling of signals indicating their existence in two different rotamers/conformers. This fact was substantiated by calculating energetics of 1 and 2 conformers using the density functional theory and correlating the calculated (1)H NMR chemical shift pattern with that of the experimental spectra.

Correction: Base pairing involving artificial bases in vitro and in vivo.

[This corrects the article DOI: 10.1039/C5SC03474D.].

Base pairing involving artificial bases in vitro and in vivo.

Herein we report the synthesis of N8-glycosylated 8-aza-deoxyguanosine (N8-8-aza-dG) and 8-aza-9-deaza-deoxyguanosine (N8-8-aza-9-deaza-dG) nucleotides and their base pairing properties with 5-methyl-isocytosine (d-isoCMe), 8-amino-deoxyinosine (8-NH2-dI), 1-N-methyl-8-amino-deoxyinosine (1-Me-8-NH2-dI), 7,8-dihydro-8-oxo-deoxyinosine (8-Oxo-dI), 7,8-dihydro-8-oxo-deoxyadenosine (8-Oxo-dA), and 7,8-dihydro-8-oxo-deoxyguanosine (8-Oxo-dG), in comparison with the d-isoCMe:d-isoG artificial genetic system. As demonstrated by Tm measurements, the N8-8-aza-dG:d-isoCMe base pair formed less stable duplexes as the C:G and d-isoCMe:d-isoG pairs. Incorporation of 8-NH2-dI versus the N8-8-aza-dG nucleoside resulted in a greater reduction in Tm stability, compared to d-isoCMe:d-isoG. Insertion of the methyl group at the N1 position of 8-NH2-dI did not affect duplex stability with N8-8-aza-dG, thus suggesting that the base paring takes place through Hoogsteen base pairing. The cellular interpretation of the nucleosides was studied, whereby a lack of recognition or mispairing of the incorporated nucleotides with the canonical DNA bases indicated the extent of orthogonality in vivo. The most biologically orthogonal nucleosides identified included the 8-amino-deoxyinosines (1-Me-8-NH2-dI and 8-NH2-dI) and N8-8-aza-9-deaza-dG. The 8-oxo modifications mimic oxidative damage ahead of cancer development, and the impact of the MutM mediated recognition of these 8-oxo-deoxynucleosides was studied, finding no significant impact in their in vivo assay.

Glycan-functionalized diamond nanoparticles as potent E. coli anti-adhesives.

Bacterial attachment and subsequent biofilm formation on biotic surfaces or medical devices is an increasing source of infections in clinical settings. A large proportion of these biofilm-related infections are caused by Escherichia coli, a major nosocomial pathogen, in which the major adhesion factor is the FimH adhesin located at the tip of type 1 fimbriae. Inhibition of FimH-mediated adhesion has been identified as an efficient antibiotic-alternative strategy to potentially reduce E. coli-related infections. In this article we demonstrate that nanodiamond particles, covently modified with mannose moieties by a "click" chemistry approach, are able to efficiently inhibit E. coli type 1 fimbriae-mediated adhesion to eukaryotic cells with relative inhibitory potency (RIP) of as high as 9259 (bladder cell adhesion assay), which is unprecedented when compared with RIP values previously reported for alternate multivalent mannose-functionalized nanostructures designed to inhibit E. coli adhesion. Also remarkable is that these novel mannose-modified NDs reduce E. coli biofilm formation, a property previously not observed for multivalent glyco-nanoparticles and rarely demonstrated for other multivalent or monovalent mannose glycans. This work sets the stage for the further evaluation of these novel NDs as an anti-adhesive therapeutic strategy against E. coli-derived infections.

Phenylboronic-acid-modified nanoparticles: potential antiviral therapeutics.

Phenylboronic-acid-modified nanoparticles (NPs) are attracting considerable attention for biological and biomedical applications. We describe here a convenient and general protocol for attaching multiple copies of para-substituted phenylboronic acid moieties onto either iron-oxide-, silica- or diamond-derived NPs. The boronic acid functionalized NPs are all fabricated by first modifying the surface of each particle type with 4-azidobenzoic ester functions. These azide-terminated nanostructures were then reacted with 4-[1-oxo-4-pentyn-1-yl) amino]phenylboronic acid units via a Cu(I) catalyzed Huisgen cycloaddition to furnish, conveniently, the corresponding boronic-acid modified NPs (or "borono-lectins") targeted in this work. The potential of these novel "borono-lectins" as antiviral inhibitors was investigated against the Hepatitis C virus (HCV) exploiting a bioassay that measures the potential of drugs to interfere with the ability of cell-culture-derived JFH1 virus particles to infect healthy hepatocytes. As far as we are aware, this is the first report that describes NP-derived viral entry inhibitors and thus serves as a "proof-of-concept" study. The novel viral entry activity demonstrated, and the fact that the described boronic-acid-functionalized NPs all display much reduced cellular toxicities compared with alternate NPs, sets the stage for their further investigation. The data supports that NP-derived borono-lectins should be pursued as a potential therapeutic strategy for blocking viral entry of HCV.

Catechuic acid and ethyl 2,4,5-trihydroxybenzoate from D-glucose.

Synthesis of catechuic acid (1) and ethyl 2,4,5-trihydroxybenzoate (2) from D-glucose-derived beta-ketoester is described. The polyhydroxylated beta-ketoester obtained from the hydrolysis of sugar beta-ketoester 3 was subjected to an aldol-type condensation to get 4 that on enolization, dehydration, and hydrogenation afforded ethyl 2,4,5-trihydroxybenzoate (2). On the other hand, hydrogenation of aldol product 4 afforded polyhydroxylated keto-carbasugar 6, which on mild acid treatment and ester hydrolysis in basic media led to catechuic acid 1. Intermediate 4 is co-related to 3-dehydroshikimic acid, a biochemical intermediate from D-glucose in the synthesis of pro-catechuic acid.