Ribofuranose Ring Research Articles

Design and synthesis of novel carbohydrate-amino acid hybrids and their antioxidant and anti-β-amyloid aggregation activity

Herein we report the synthesis of new furanoid sugar amino acids and thioureas, prepared by coupling aromatic amino acids and dipeptides with isothiocyanato- functionalized ribofuranose ring. Since carbohydrate-derived structures possess many biological activities, synthesized compounds were evaluated as anti-amyloid and antioxidant agents. The anti-amyloid activity of the studied compounds was evaluated based on their potential to destroy amyloid fibrils of intrinsically disordered Aβ40 peptide and globular hen egg-white (HEW) lysozyme. The destructive efficiency of the compounds differed between the studied peptides. While the destruction activity of the compounds on the HEW lysozyme amyloid fibrils was negligible, the effect on Aβ40 amyloid fibrils was significantly higher. Furanoid sugar α-amino acid 1 and its dipeptide derivatives 8 (Trp-Trp) and 11 (Trp-Tyr) were the most potent anti-Aβ fibrils compounds. The antioxidant properties of synthesized compounds were estimated by three complementary in vitro assays (DPPH, ABTS, and FRAP). The ABTS assay was the most sensitive for assessing the radical scavenging activity of all tested compounds compared to the DPPH test. Significant antioxidant activity was detected for compounds in the group of aromatic amino acids depending on the present amino acid, with the highest activity in the case of dipeptides 11 and 12 containing the Tyr and Trp moiety. Regarding the FRAP assay, the best reducing antioxidant potential revealed Trp-containing compounds 5, 10, and 12.

Casimersen for the treatment of Duchenne muscular dystrophy

Casimersen is a single-stranded, antisense phosphorodiamidate morpholino oligonucleotide where six-membered morpholino rings substitute the ribofuranose rings of the natural DNA and RNA backbone. The morpholino is conjugated to the following monomer via a charge-neutral phosphorodiamidate instead of the phosphodiester linkage containing a negative charge. Phosphorodiamidate morpholino oligonucleotides are resistant to enzymatic degradation and their lack of charge facilitates cellular penetration.

Structure–Activity Relationship Exploration of 3′-Deoxy-7-deazapurine Nucleoside Analogues as Anti-Trypanosoma brucei Agents

Human African trypanosomiasis is a neglected tropical disease caused by Trypanosoma brucei parasites. These protists are unable to produce the purine ring, making them vulnerable to the effects of purine nucleoside analogues. Starting from 3'-deoxytubercidin (5), a lead compound with activity against central-nervous-stage human African trypanosomiasis, we investigate the structure-activity relationships of the purine and ribofuranose rings. The purine ring tolerated only modifications at C7, while from the many alterations of the 3'-deoxyribofuranosyl moiety only the arabino analogue 48 showed pronounced antitrypanosomal activity. Profiling of the most potent analogues against resistant T. brucei strains (resistant to pentamidine, diminazene, and isometamidium) showed reduced dependence on uptake mediated by the P2 aminopurine transporter relative to 5. The introduction of a 7-substituent confers up to 10-fold increased affinity for the P1 nucleoside transporter while generally retaining high affinity for P2. Four of the most promising analogues were found to be metabolically stable, earmarking them as suitable backup analogues for lead 5.

Identification of the C-Glycoside Synthases during Biosynthesis of the Pyrazole-C-Nucleosides Formycin and Pyrazofurin.

C-Nucleosides are characterized by a C-C rather than a C-N linkage between the heterocyclic base and the ribofuranose ring. While the biosynthesis of pseudouridine-C-nucleosides has been studied, less is known about the pyrazole-C-nucleosides such as the formycins and pyrazofurin. Herein, genome screening of Streptomyces candidus NRRL 3601 led to the discovery of the pyrazofurin biosynthetic gene cluster pyf. In vitro characterization of gene product PyfQ demonstrated that it is able to catalyze formation of the C-glycoside carboxyhydroxypyrazole ribonucleotide (CHPR) from 4-hydroxy-1H-pyrazole-3,5-dicarboxylic acid and phosphoribosyl pyrophosphate (PRPP). Similarly, ForT, the PyfQ homologue in the formycin pathway, can catalyze the coupling of 4-amino-1H-pyrazole-3,5-dicarboxylic acid and PRPP to form carboxyaminopyrazole ribonucleotide. Finally, PyfP and PyfT are shown to catalyze amidation of CHPR to pyrazofurin 5'-phosphate thereby establishing the latter stages of both pyrazofurin and formycin biosynthesis.

Identification of the C‐Glycoside Synthases during Biosynthesis of the Pyrazole‐C‐Nucleosides Formycin and Pyrazofurin

AbstractC‐Nucleosides are characterized by a C−C rather than a C−N linkage between the heterocyclic base and the ribofuranose ring. While the biosynthesis of pseudouridine‐C‐nucleosides has been studied, less is known about the pyrazole‐C‐nucleosides such as the formycins and pyrazofurin. Herein, genome screening of Streptomyces candidus NRRL 3601 led to the discovery of the pyrazofurin biosynthetic gene cluster pyf. In vitro characterization of gene product PyfQ demonstrated that it is able to catalyze formation of the C‐glycoside carboxyhydroxypyrazole ribonucleotide (CHPR) from 4‐hydroxy‐1H‐pyrazole‐3,5‐dicarboxylic acid and phosphoribosyl pyrophosphate (PRPP). Similarly, ForT, the PyfQ homologue in the formycin pathway, can catalyze the coupling of 4‐amino‐1H‐pyrazole‐3,5‐dicarboxylic acid and PRPP to form carboxyaminopyrazole ribonucleotide. Finally, PyfP and PyfT are shown to catalyze amidation of CHPR to pyrazofurin 5′‐phosphate thereby establishing the latter stages of both pyrazofurin and formycin biosynthesis.

Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.

Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p Ka, consistent with the expected electron-withdrawing effect. In HDV ribozyme reactions, we observed that the RNA substrates undergo transphosphorylation relatively efficiently, suggesting that the conformational constraints imposed by a ribofuranose ring are not strictly required for ribozyme catalysis. In contrast to the nonenzymatic reactions, however, substrate fluorination modestly increases the ribozyme reaction rate, consistent with a mechanism in which (1) the 2'-hydroxyl nucleophile exists predominantly in its neutral, protonated form in the ground state and (2) the 2'-hydroxyl bears some negative charge in the rate-determining step, consistent with a transition state in which the extent of 2'-OH deprotonation exceeds the extent of P-O bond formation.

Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling.

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH- anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.

Impact of modified ribose sugars on nucleic acid conformation and function

Abstract The modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.

The first structurally analysed nucleic acid building block containing the Reese protecting group: 2'-O-[1-(2-fluorophenyl)-4-methoxypiperidin-4-yl]-β-D-(1'R,2'R,3'R,4'R)-uridine.

The title compound, C21H26FN3O7, is assembled by N-H...O and O-H...O hydrogen bonds into well-separated two-dimensional layers of about 15 Å thickness. The crescent conformation of the molecules is stabilized by weak intramolecular C-H...O and C-H...F hydrogen bonds. The uridine moiety adopts an anti conformation. The ribofuranose ring exists in an envelope conformation. All the endocyclic uracil bonds are shorter than normal single C-N and C-C bonds, and five of them have comparable lengths, which implies a considerable degree of delocalization of the electron density within this ring.

Desulfurization of 2-thiouracil nucleosides: Conformational studies of 4-pyrimidinone nucleosides

4-Pyrimidinone ribofuranoside ( H 2o 4U ) and 4-pyrimidinone 2′-deoxyribofuranoside ( dH 2o 4U ) were synthesized by the oxidative desulfurization of parent 2–thiouracil nucleosides with m-chloroperbenzoic acid. The crystal structures of H 2o 4U and dH 2o 4U and their conformations in solution were determined and compared with corresponding 2-thiouracil and uracil nucleosides. The absence of a large 2-thiocarbonyl/2-carbonyl group in the nucleobase moiety results in C2′- endo puckering of the ribofuranose ring (S conformer) in the crystal structure of H 2o 4U , which is not typical of RNA nucleosides. Interestingly, the hydrogen bonding network in the crystals of dH 2o 4U stabilizes the sugar moiety conformation in the C3′- endo form (N conformer), rarely found in DNA nucleosides. In aqueous solution, dH 2o 4U reveals a similar population of the C2′- endo conformation (65%) to that of 2′-deoxy-2-thiouridine (62%), while the 62% population of the S conformer for H 2o 4U is significantly different from that of the parent 2-thiouridine, for which the N conformer is dominant (71%). Such a difference may be of biological importance, as the desulfurization process of natural tRNA 2-thiouridines may occur under conditions of oxidative stress in the cell and may influence the decoding process.

1-(2-Bromo-2-deoxy-β-D-xylofuranosyl)uracil

In the title compound, C9H11BrN2O5, the ribofuran­ose ring has a C2-exo, C3-endo twist configuration and is attached to the uracil unit via a β-N1-glycosidic bond. The crystal structure is stabilized by two inter­molecular O—H⋯O inter­actions and one inter­molecular N—H⋯O inter­action.

ChemInform Abstract: Facile Synthesis and Conformation of 3′-O,4′-C-Methyleneribonucleosides.

Bicyclic nucleoside analogues, 3′-O,4′-C-methyleneribonucleosides 1, including thymine, cytosine, adenine and guanine nucleobases, were conveniently synthesized from D-glucose, and the ribofuranose ring of 1 was found to exist predominantly in a S-conformation by means of 1H NMR and X-ray analysis.

Why is DNA polymorphic while RNA is not?

In DNA, the base-sugar hydrophobic interactions between the 2′-methylene group of the 2′-deoxyribose sugar and the base (H6 in pyrimidines and H8 in purines) on the 3′-side appear to act as a ball joint and facilitate the A-DNA B-DNA conformational interconversion by lowering the pseudorotational barrier. These and other sugar-base interactions coupled with the inherently more flexible 2′-deoxyribofuranose ring allow DNA to occur in a variety of polymorphic helical states. In contrast, the 2′-hydroxyl group in RNA not only sterically disfavors the B-type structure, but the inherently less flexible ribofuranose ring is further stabilized in the A-type structure by intramolecular hydrogen-bonded water bridge between the 2′-OH group and the base (O2 in pyrimidines and N3 in purines). This lack of flexibility of RNA dictates that DNA-RNA hybrid structures assume the A-type helix.

Methyl 1-deoxy-1-(N 1-thyminyl)-β-D-psicofuranoside

In the structure of the title compound, C12H18N2O7, the furanosyl ring adopts the S-type sugar pucker with the following pseudorotational parameters: PS = 159.6° (C2′-endo according to the designation of the ribofuranose ring of natural nucleosides; C3′-endo according to the numbering of the title compound) and νmax = 35.9°. The conformation around the C5′—C6′ bond is ap (gauche–trans; gt; −g), with a torsion angle γ of −170.3 (2)°. The structure of the thymine base is very similar to that of thymidine. There are intermolecular N—H...O and O—H...O hydrogen bonds.

Five- and Six-Membered Conformationally Locked 2‘,4‘-Carbocyclicribo-Thymidines: Synthesis, Structure, and Biochemical Studies

Two unusual reactions involving the 5-hexenyl or the 6-heptenyl radical cyclization of a distant double bond at C4' and the radical center at C2' of the ribofuranose ring of thymidine have been used as key steps to synthesize North-type conformationally constrained cis-fused bicyclic five-membered and six-membered carbocyclic analogues of LNA (carbocyclic-LNA-T) and ENA (carbocyclic-ENA-T) in high yields. Their structures have been confirmed unambiguously by long range 1H-13C NMR correlation (HMBC), TOCSY, COSY, and NOE experiments. The carbocyclic-LNA-T and carbocyclic-ENA-T were subsequently incorporated into the antisense oligonucleotides (AONs) to show that they enhance the Tm of the modified AON/RNA heteroduplexes by 3.5-5 degrees C and 1.5 degrees C/modification for carbocyclic-LNA-T and carbocyclic-ENA-T, respectively. Whereas the relative RNase H cleavage rates with carbocyclic-LNA-T, carbocyclic-ENA-T, aza-ENA-T, and LNA-T modified AON/RNA duplexes were found to be very similar to that of the native counterpart, irrespective of the type and the site modification in the AON strand, a single incorporation of carbocyclic-LNA and carbocyclic-ENA into AONs leads to very much more enhanced nuclease stability in the blood serum (stable >48 h) as compared to that of the native (fully degraded <3 h) and the LNA-modified AONs (fully degraded <9 h) and aza-ENA ( approximately 85% stable in 48 h). Clearly, remarkably enhanced lifetimes of these carbocyclic-modified AONs in the blood serum may produce the highly desired pharmacokinetic properties because of their unique stability and consequently a net reduction of the required dosage. This unique quality as well as their efficient use as the AON in the RNase H-promoted cleavage of the target RNA makes our carbocyclic-LNA and carbocyclic-ENA modifications excellent candidates as potential antisense therapeutic agents.

Synthesis of Purine Acyclonucleosides via Ribofuranose Ring Cleavage of Purine Nucleosides by Diisobutylaluminum Hydride

AbstractFor Abstract see ChemInform Abstract in Full Text.

Mycobacterium tuberculosis Thymidine Monophosphate Kinase Inhibitors: Biological Evaluation and Conformational Analysis of 2′‐ and 3′‐Modified Thymidine Analogues

AbstractMycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt) has recently been introduced as a potential target for the structure‐based design of anti‐tuberculosis drugs. Based on the TMPKmt X‐ray structure and previous S.A.R. studies, we synthesised the nucleoside analogues 3a−b, 6a−b, 7a−b, and 8a−b, modified in 2′‐ and 3′‐position of the ribofuranose ring moiety. To our surprise, these analogues showed only moderate binding affinity (i.e. Ki between 118 and 1260 μM). This prompted us to investigate the conformational features of these nucleosides. We concluded that compounds of this series, especially 8a−b, are strongly biased towards the “Northern” furanose ring conformation, whereas X‐ray crystallography reveals a preference of TMPKmt for the opposite “Southern” conformers. This paper covers the synthesis, biological evaluation and conformational features (i.e. preferred ring puckering) of the 2′‐ and 3′‐modified dT analogues. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)

CoC bond dissociation energy and reaction volume change of 2′,5′-dideoxyadenosylcobalamin studied by laser-induced time-resolved photoacoustic calorimetry

Time resolved photoacoustic calorimetry (PAC) was applied to a study of the photolysis of a coenzyme B 12 analog 2′,5′-dideoxyadenosylcobalamin, which lacks an OH group at the 2′ position of ribofuranose ring. In aqueous solution, we report for the first time the quantum yield Φ d (0.25±0.02), CoC bond dissociation energy (BDE; 31.8±2.5 kcal mol −1) and reaction volume change ΔV R (6.5±0.5 ml mol −1) due to conformation changes of the corrin ring and its side chains accompanying the cleavage of the CoC bond. These values for the analog are very similar to those for the natural cofactor. Based our results and previous studies, a possible explanation for the similarity in their structure and properties versus the large difference in their enzymatic activity is discussed.

Carbocyclic Nucleosides (Carbanucleosides) as New Therapeutic Leads

AbstractFor Abstract see ChemInform Abstract in Full Text.

Carbocyclic nucleosides (carbanucleosides) as new therapeutic leads.

Many structural modifications have been made on the naturally occurring nucleosides in the search for medicinal agents that will interfere with the utilization of the natural compounds. One such area of pursuit has been the replacement of the oxygen of the ribofuranose ring of common nucleosides with a methylene unit (resulting in a cyclopentyl ring) leading to biologically meaningful carbanucleosides (carbocyclic nucleosides). This review calls attention to new methods for preparing these compounds in enantiomeric forms with various heterocyclic bases and ring contracted and expanded cyclopentyl substituents.