A stereospecific synthesis of l-deoxyribose, l-ribose and l-ribosides

Purine nucleosides as selective inhibitors of butyrylcholinesterase - a multidisciplinary study

The computational study of the most relevant interactions of the nanomolar purine nucleoside BuChE selective inhibitor has shown that the benzyl group at position 2 and the purine acetamido group are required for activity. In addition, the synthesis of a 6-iodinated radiolabelled analogue and the study of in vivo bioavailability have shown a low percentage of uptake by the brain after 1 hour. These results encouraged the synthesis of a small library of new compounds, focussing on deoxygenation at other positions aiming to access active and more bioavailable structures. Deoxygenation at positions 4 and 3,4 afforded new nucleosides that displayed low inhibition of both cholinesterases, while deoxygenation at position 6 and the lyxopyranosyl group afforded the two most active compounds (IC50 ranging from 3.7 to 7.8 μM); one of them was not cytotoxic at the bioactive concentration, while the other one showed a slight cytotoxicity. Interestingly, these structures exhibited the same anomeric stereochemistry and were purine N7-linked, similar to the lead compound 3 (IC50 = 50 nM), thus confirming the importance of the αDN7 purine nucleoside structure. Thus, optimization of the purine nucleoside synthetic procedure was carried out by changing the reaction temperature, the anomeric leaving group or the Lewis acid. The most satisfactory reaction yields and regioselectivity were obtained by using the original N-glycosylation conditions at 25 °C, which afforded the highest yield of 25% when compared to the 8% of the αDN7 purine nucleoside, and an increase in N7 regioselectivity, with the total N7 nucleoside yield increasing from 36% to 52%.

Easy Access to Sauropunols A-D: Synthesis and Spectroscopy Correlation of Their Natural Methyl and Ethyl Glycosides

3,6-Anhydro-2-deoxy-hexofuranoside, the natural product core, is present in natural sauropunols (A-D) and in their natural methyl and ethyl glycosides, now, namely, sauropunol H and sauropunol F. The easily synthesized d-glucose-derived 3,6-anhydro-1,2-O-isopropylidene-5-O-benzoyl-α-d-glucofuranose was elaborated to final targets employing the TsOH·H2O-catalyzed glycosylation reaction with seven different alcohols, subsequent radical deoxygenation, and appropriate deprotection reactions involving mild conditions with excellent functional group tolerance. A short total synthesis of sauropunols (A-D), sauropunol H, and the first total synthesis of sauropunol F are reported herein. The correlation of spectroscopy data of sauropunol H and sauropunol F has been derived through these syntheses.

From a Carbohydrate Raw Material to an Important Building Block: Cost-Efficient Conversion of d-Fructose into 2-Deoxy-l-ribose

A straightforward method for the conversion of a low-cost carbohydrate (d-fructose) into an important carbohydrate building block (2-deoxy-l-ribose) is reported. This methodology involves a novel radical cyclization followed by a fragmentation reaction, selective enzymatic hydrolysis using a lipase, and oxidative cleavage of the vicinal diol. This method uses the cheapest starting material and employs the shortest synthetic route (7 steps) for converting a d-sugar into 2-deoxy-l-ribose.

Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal

DNA amplification circuits that rely on thermodynamically-driven hybridization events triggered by a target nucleic acid are becoming increasingly utilized due to their relative simplicity. A drawback of these circuits is that non-specific amplification, or circuit leakage, must be estimated using a separate "no-target" control reaction to eliminate false positives. Aside from requiring an additional reaction, the problem with this approach is the difficulty of creating a no-target control for biological specimens. To overcome this limitation, we propose a strategy that combines both reactions into the same tube using naturally-occurring right-handed D-DNA circuit elements for the target detection reaction and identical synthetic mirror-image left-handed L-DNA circuit elements for the no-target control reaction. We illustrate this approach using catalyzed hairpin assembly (CHA), one of the most studied DNA amplification circuits. In a dual-chirality CHA design, the right-handed circuit signal is produced by target-specific amplification and circuit leakage, whereas the left-handed circuit signal is produced only by circuit leakage. The target-specific amplification is calculated as the difference between the two signals. The limit of detection of this dual-chirality CHA reaction was found to be similar to that of traditional CHA (81 vs 92 pM, respectively). Furthermore, the left-handed no-target signal matched the right-handed leakage across a wide range of sample conditions including background DNA, increased salt concentration, increased temperature, and urine. These results demonstrate the robustness of a dual-chirality design and the potential utility of left-handed DNA in the development of new DNA amplification circuits better-suited for target detection applications in biological samples.

Mirror-Image Oligonucleotides: History and Emerging Applications

As chiral molecules, naturally occurring d-oligonucleotides have enantiomers, l-DNA and l-RNA, which are comprised of l-(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d-counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l-oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d-oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d- and l-oligonucleotides to form contiguous Watson-Crick base pairs with each other has ultimately led to the perception that l-oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l-oligonucleotides, while overcoming (and even exploiting) their inability to Watson-Crick base pair with the natural polymer. Herein, a brief history of l-oligonucleotide research is presented and emerging l-oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.

Design, Synthesis and Biological Evaluation of Nitrate Derivatives of Sauropunol A and B as Potent Vasodilatory Agents

A group of nitrate derivatives of naturally occurring sauropunol A and B were designed and synthesized. Nitric oxide (NO) releasing capacity and vasodilatory capacity studies were performed to explore the structure-activity relationship of resulted nitrates. Biological evaluation of these compounds revealed that most of the synthesized mononitrate derivatives demonstrated superior releasing capacity than isosorbide mononitrate (ISMN), and 2MNS-6 even demonstrated stronger NO releasing capacity than isosorbide dinitrate (ISDN). Two dinitrates, DNS-1 and DNS-2, showed higher NO releasing capacity than ISDN. Evaluation of inhibitory activities to the contractions in mesenteric artery rings revealed that 2MNS-8 and DNS-2 showed stronger vasorelaxation activities than ISDN. High level of NO and soluble guanylyl cyclase (sGC) may be essential for the potent vasodilatory effect of DNS-2. The vasodilatory effects of DNS-2 may result from cellular signal transduction of NO-sGC-cGMP. DNS-2 was found to be the most potent sauropunol-derived nitrate vasodilatory agent for further pharmaceutical investigation against cardiovascular diseases.

Synthesis of l-Deoxyribonucleosides from d-Ribose

The preparation of 2-deoxy-l-ribose derivatives or mirror image deoxyribonucleosides (l-deoxyribonucleosides) from d-ribose is reported. Starting from inexpensive d-ribose, an acyclic d-form carbohydrate precursor was synthesized to study a unique carbonyl translocation process. In this novel radical reaction, not only was the configuration of the sugar transformed from the d-form to the l-form, but also deoxygenation at the C(2) position of the sugar was successfully achieved. This is one of the most practical methods for converting a d-sugar to a 2-deoxy-l-sugar in a one-step reaction. To further identify the reaction product, radical reactions followed by treatment with 1,3-propanedithiol and then benzoylation were performed to afford a dithioacetal derivative. The stereochemistry and configuration of the 2-deoxy-l-ribose dithioacetal derivative were confirmed by its X-ray crystal structure. To further apply this methodology, a diethyl thioacetal derivative was formed, followed by selective benzoyl protection, and an NIS-initiated cyclization reaction to give the desired ethyl S-l-2-deoxyriboside, which can be used as a 2-deoxy-l-ribosyl synthon in the formal total synthesis of various l-deoxyribonucleosides, such as l-dT.

Total synthesis, structural elucidation and anti-inflammatory activity evaluation of 2-deoxy-3,6-anhydro hexofuranoside derivatives isolated from Sauropus rostratus

The first total synthesis of four 2-deoxy-3,6-anhydro hexofuranoside derivatives isolated from Genus Sauropus rostratus was accomplished.

Characterization of a mannose-6-phosphate isomerase from Thermus thermophilus and increased L-ribose production by its R142N mutant

An uncharacterized gene from Thermus thermophilus, thought to encode a mannose-6-phosphate isomerase, was cloned and expressed in Escherichia coli. The maximal activity of the recombinant enzyme for L-ribulose isomerization was observed at pH 7.0 and 75°C in the presence of 0.5 mM Cu(2+). Among all of the pentoses and hexoses evaluated, the enzyme exhibited the highest activity for the conversion of L-ribulose to L-ribose, a potential starting material for many L-nucleoside-based pharmaceutical compounds. The active-site residues, predicted according to a homology-based model, were separately replaced with Ala. The residue at position 142 was correlated with an increase in L-ribulose isomerization activity. The R142N mutant showed the highest activity among mutants modified with Ala, Glu, Tyr, Lys, Asn, or Gln. The specific activity and catalytic efficiency (k(cat)/K(m)) for L-ribulose using the R142N mutant were 1.4- and 1.6-fold higher than those of the wild-type enzyme, respectively. The k(cat)/K(m) of the R142N mutant was 3.8-fold higher than that of Geobacillus thermodenitrificans mannose-6-phosphate isomerase, which exhibited the highest activity to date for the previously reported k(cat)/K(m). The R142N mutant enzyme produced 213 g/liter L-ribose from 300 g/liter L-ribulose for 2 h, with a volumetric productivity of 107 g liter(-1) h(-1), which was 1.5-fold higher than that of the wild-type enzyme.

Synthesis of L-2'-deoxypentofuranonucleoside derivatives of thymine from D-glucose

Convergent synthesis of L-2'-deoxypentofuranonucleoside derivatives of thymine was carried out from D-glucose via 6-O-toluoyl-3-deoxy-1,2-O-isopropylidene-beta-L-lyxo-hexofuranose as a key intermediate.

Cohnella laeviribosi sp. nov., isolated from a volcanic pond

A novel thermophilic and endospore-forming Gram-positive bacterium capable of assimilating and isomerizingl-ribose was isolated from a volcanic area in Likupang, Indonesia. The isolate, RI-39T, was able to grow at high temperatures (37–60 °C); optimum growth was observed at pH 6.5 and 45 °C. The strain contained MK-7 (87 %) as the main respiratory quinone and had a DNA G+C content of 51 mol%. The major cellular fatty acids of the isolate were iso-C16 : 0and anteiso-C15 : 0and the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents an evolutionary lineage that is distinct from those of otherCohnellaspecies. Based on morphological, physiological and chemotaxonomic characteristics and 16S rRNA gene sequence comparisons, it is proposed that strain RI-39Trepresents a novel species,Cohnella laeviribosisp. nov. The type strain is RI-39T(=KCTC 3987T=KCCM 10653PT=CCUG 52217T).

Characterization of a novel D-lyxose isomerase from Cohnella laevoribosii RI-39 sp. nov

A newly isolated bacterium, Cohnella laevoribosii RI-39, could grow in a defined medium with L-ribose as the sole carbon source. A 21-kDa protein isomerizing L-ribose to L-ribulose, as well as D-lyxose to D-xylulose, was purified to homogeneity from this bacterium. Based on the N-terminal and internal amino acid sequences of the purified enzyme obtained by N-terminal sequencing and quantitative time of flight mass spectrometry-mass spectrometry analyses, a 549-bp gene (lyxA) encoding D-lyxose (L-ribose) isomerase was cloned and expressed in Escherichia coli. The purified endogenous enzyme and the recombinant enzyme formed homodimers that were activated by Mn(2+). C. laevoribosii D-lyxose (L-ribose) isomerase (CLLI) exhibits maximal activity at pH 6.5 and 70 degrees C in the presence of Mn(2+) for D-lyxose and L-ribose, and its isoelectric point (pI) is 4.2 (calculated pI, 4.9). The enzyme is specific for D-lyxose, L-ribose, and D-mannose, with apparent K(m) values of 22.4 +/- 1.5 mM, 121.7 +/- 10.8 mM, and 34.0 +/- 1.1 mM, respectively. The catalytic efficiencies (k(cat)/K(m)) of CLLI were 84.9 +/- 5.8 mM(-1) s(-1) for D-lyxose (V(max), 5,434.8 U mg(-1)), 0.2 mM(-1) s(-1) for L-ribose (V(max), 75.5 +/- 6.0 U mg(-1)), and 1.4 +/- 0.1 mM(-1) s(-1) for D-mannose (V(max), 131.8 +/- 7.4 U mg(-1)). The ability of lyxA to permit E. coli cells to grow on D-lyxose and L-ribose and homology searches of other sugar-related enzymes, as well as previously described sugar isomerases, suggest that CLLI is a novel type of rare sugar isomerase.