A new efficient and practical synthesis of 2-deoxy-l-ribose

Enantioselective Total Synthesis of (+)-Penostatins A and C

A stereoselective and column-economic approach to (+)-penostatins A and C has been developed. The multisubstituted A ring and B/C rings in their unique tricyclic framework are constructed through a Diels-Alder reaction/ozonolysis sequence and an exo intramolecular hetero-Diels-Alder reaction with high chemo-, regio-, and stereoselectivity. Using this route, (+)-penostatins A and C can be synthesized in 19 and 20 steps, respectively, with a good overall yield involving only five or six column chromatographic purifications.

Immobilization of L-ribose isomerase on the surface of activated mesoporous MCM41 and SBA15 for the synthesis of L-ribose

A hexagonal mesoporous molecular sieve-like structure of MCM41 and SBA15 with a large surface area was used to immobilize protein L-ribose isomerase (L-RI) through covalent linkages. The amino group of APTES functionalized nanosilica support MCM41 and SBA15 interacted with glutaraldehyde to promote bidentate linkage and on other side with amino group of enzyme. The use of mesoporous silica matrix for immobilization was observed to conserve the distinctive properties of the protein. The various operational conditions optimized for covalent conjugation of protein with the silica support were found to be dependent on enzyme support ratio, immobilization temperature and time. The immobilization yield of L-RI on MCM41 and SBA15 was achieved to be 60 % (600 mg enzyme /g matrix) and 45 % (450 mg enzyme/g matrix), respectively under the optimized conditions. The immobilized biocatalyst was characterized by various analytical techniques like HR-TEM, EDS, FTIR, TGA and BET. Effects of different experimental conditions were optimized to study enzyme kinetics, pH, temperature, bioconversion, reusability, metal ion effect and storage stability. The biocatalytic efficiency (k_cat/K_m) was increased by 1.2 fold on immobilization with the catalytic activity of 39.64 IU. Increase in the catalytic efficiency after immobilization could be due to the suitable orientation of enzyme active site and improved accessibility for substrate binding. The immobilization of L-RI on mesoporous silica support could improve the biocatalytic activity, storage stability and reusability. The immobilized biocatalyst was found to be reusable for more than 4 cycles retaining more than 50 % of catalytic activity and promoting the synthesis of a rare sugar L-ribose from L-ribulose with a conversion yield of 22 % in 2 h time.

A review on l-ribose isomerases for the biocatalytic production of l-ribose and l-ribulose

Presently, because of the extraordinary roles and potential applications, rare sugars turn into a focus point for countless researchers in the field of carbohydrates. l-ribose and l-ribulose are rare sugars and isomers of each other. This aldo and ketopentose are expensive but can be utilized as an antecedent for the manufacturing of various rare sugars and l-nucleoside analogue. The bioconversion approach turns into an excellent alternative method to l-ribulose and l-ribose production, as compared to the complex and lengthy chemical methods. The basic purpose of this research was to describe the importance of rare sugars in various fields and their easy production by using enzymatic methods. l-Ribose isomerase (L-RI) is an enzyme discovered by Tsuyoshi Shimonishi and Ken Izumori in 1996 from Acinetobacter sp. strain DL-28. L-RI structure was cupin-type-β-barrel shaped with a catalytic site between two β-sheets surrounded by metal ions. The crystal structures of the L-RI showed that it contains a homotetramer structure. Current review have concentrated on the sources, characteristics, applications, conclusions and future prospects including the potentials of l-ribose isomerase for the commercial production of l-ribose and l-ribulose. The MmL-RIse and CrL-RIse have the potential to produce the l-ribulose up to 32% and 31%, respectively. The CrL-RIse is highly stable as compared to other L-RIs. The results explained that the L-RIs have great potential in the production of rare sugars especially, l-ribose and l-ribulose, while the immobilization technique can enhance its functionality and properties. The present study precises the applications of L-RIs acquired from various sources for l-ribose and l-ribulose production.

Characterization of an L-Arabinose Isomerase from Bacillus velezensis and Its Application for L-Ribulose and L-Ribose Biosynthesis

L-Ribulose and L-ribose are two high-value unnatural sugars that can be biosynthesized by sugar isomerases. In this paper, an L-arabinose isomerase (BvAI) from Bacillus velezensis CICC 24777 was cloned and overexpressed in Escherichia coli BL21 (DE3) strain. The maximum activity of recombinant BvAI was observed at 45 °C and pH 8.0, in the presence of 1.0 mM Mn²⁺. Approximately 207.2 g/L L-ribulose was obtained from 300 g/L L-arabinose in 1.5 h by E. coli harboring BvAI. In addition, approximately 74.25 g/L L-ribose was produced from 300 g/L L-arabinose in 7 h by E. coli co-expressing BvAI and L-RI from Actinotalea fermentans ATCC 43279 (AfRI). This study provides a feasible approach for producing L-ribose from L-arabinose using a co-expression system harboring L-Al and L-RI.

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.

Production of L-ribose from L-ribulose by a triple-site variant of mannose-6-phosphate isomerase from Geobacillus thermodenitrificans

A triple-site variant (W17Q N90A L129F) of mannose-6-phosphate isomerase from Geobacillus thermodenitrificans was obtained by combining variants with residue substitutions at different positions after random and site-directed mutagenesis. The specific activity and catalytic efficiency (k(cat)/K(m)) for L-ribulose isomerization of this variant were 3.1- and 7.1-fold higher, respectively, than those of the wild-type enzyme at pH 7.0 and 70°C in the presence of 1 mM Co(2+). The triple-site variant produced 213 g/liter l-ribose from 300 g/liter L-ribulose for 60 min, with a volumetric productivity of 213 g liter(-1) h(-1), which was 4.5-fold higher than that of the wild-type enzyme. The k(cat)/K(m) and productivity of the triple-site variant were approximately 2-fold higher than those of the Thermus thermophilus R142N variant of mannose-6-phosphate isomerase, which exhibited the highest values previously reported.

What are the differences between ascorbic acid and NADH as hydride and electron sources in vivo on thermodynamics, kinetics, and mechanism?

Ascorbic acid (AscH(2)) and dihydronicotinamide adenine dinucleotide (NADH) are two very important natural redox cofactors, which can be used as hydride, electron, and hydrogen atom sources to take part in many important bioreduction processes in vivo. The differences of the two natural reducing agents as hydride, hydrogen atom, and electron donors in thermodynamics, kinetics, and mechanisms were examined by using 5,6-isopropylidene ascorbate (iAscH(-)) and β-D-glucopyranosyl-1,4-dihydronicotinamide acetate (GluNAH) as their models, respectively. The results show that the hydride-donating ability of iAscH(-) is smaller than that of GluNAH by 6.0 kcal/mol, but the electron-donating ability and hydrogen-donating ability of iAscH(-) are larger than those of GluNAH by 20.8 and 8.4 kcal/mol, respectively, which indicates that iAscH(-) is a good electron donor and a good hydrogen atom donor, but GluNAH is a good hydride donor. The kinetic intrinsic barrier energy of iAscH(-) to release hydride anion in acetonitrile is larger than that of GluNAH to release hydride anion in acetonitrile by 6.9 kcal/mol. The mechanisms of hydride transfer from iAscH(-) and GluNAH to phenylxanthium perchlorate (PhXn(+)), a well-known hydride acceptor, were examined, and the results show that hydride transfer from GluNAH adopted a one-step mechanism, but the hydride transfer from iAscH(-) adopted a two-step mechanism (e-H(•)). The thermodynamic relation charts (TRC) of the iAscH(-) family (including iAscH(-), iAscH(•), iAsc(•-), and iAsc) and of the GluNAH family (including GluNAH, GluNAH(•+), GluNA(•), and GluNA(+)) in acetonitrile were constructed as Molecule ID Cards of iAscH(-) and of GluNAH in acetonitrile. By using the Molecule ID Cards of iAscH(-) and GluNAH, the character chemical properties not only of iAscH(-) and GluNAH but also of the various reaction intermediates of iAscH(-) and GluNAH all have been quantitatively diagnosed and compared. It is clear that these comparisons of the thermodynamics, kinetics, and mechanisms between iAscH(-) and GluNAH as hydride and electron donors in acetonitrile should be quite important and valuable to diagnose and understand the different roles and functions of ascorbic acid and NADH as hydride, hydrogen atom, and electron sources in vivo.

Characterization of an L-arabinose isomerase from Bacillus subtilis

An isolated gene from Bacillus subtilis str. 168 encoding a putative isomerase was proposed as an L-arabinose isomerase (L-AI), cloned into Escherichia coli, and its nucleotide sequence was determined. DNA sequence analysis revealed an open reading frame of 1,491 bp, capable of encoding a polypeptide of 496 amino acid residues. The gene was overexpressed in E. coli and the protein was purified using nickel-nitrilotriacetic acid chromatography. The purified enzyme showed the highest catalytic efficiency ever reported, with a k(cat) of 14,504 min(-1) and a k(cat)/K(m) of 121 min(-1) mM(-1) for L-arabinose. A homology model of B. subtilis L-AI was constructed based on the X-ray crystal structure of E. coli L-AI. Molecular dynamics simulation studies of the enzyme with the natural substrate, L-arabinose, and an analogue, D-galactose, shed light on the unique substrate specificity displayed by B. subtilis L-AI only towards L-arabinose. Although L-AIs have been characterized from several other sources, B. subtilis L-AI is distinguished from other L-AIs by its high substrate specificity and catalytic efficiency for L-arabinose.

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.

Dehydrogenation of ribitol with Gluconobacter oxydans: production and stability of L-ribulose

l-Ribulose is an important chiral lead molecule used for the synthesis of, among others, l-ribose, a high-value rare sugar used in the preparation of antiviral drugs. These drugs--nucleoside-analogues--gain importance in the treatment of severe viral diseases, like those caused by the HIV or hepatitis virus. In this study, factors that may have an impact on l-ribulose production with Gluconobacter oxydans and on the stability of l-ribulose were investigated. A bioconversion-type process, using washed resting cells, was chosen to produce l-ribulose from ribitol. In this process, the cell production and bioconversion phase were separated. The former was first optimized and a maximum cell mass of 1.5 g CDWL(-1) could be produced. For the bioconversion phase, the aeration level of the system proved to be one of the most critical factors; a maximal production rate of 15.7 g L(-1)h(-1) or 5.9 g(g CDW)(-1)h(-1) of l-ribulose could be reached. Furthermore, resting cells were found capable of completely converting ribitol solutions of up to 300 g L(-1) within 30 h, although the kinetics indicated a rather low affinity of the dehydrogenase enzymes for the substrate.