Unusual deoxygenation and reactivity studies related to O6-(benzotriazol-1-yl)inosine derivatives

New and unusual developments related to the chemistry of O6-(benzotriazol-1-yl)inosine derivatives are reported. First, a simple, scalable method for their syntheses via the use of PPh3/I2/HOBt has been developed and has been mechanistically investigated by 31P(1H) NMR. Studies were then conducted into a unique oxygen transfer reaction between O6-(benzotriazol-1-yl)inosine nucleosides and bis(pinacolato)diboron (pinB-Bpin) leading to the formation of C-6 (benzotriazol-1-yl)purine nucleoside derivatives and pinB-O-Bpin. This reaction has been investigated by 11B(1H) NMR and compared to pinB-O-Bpin obtained by oxidation of pinB-Bpin. The structures of the C-6 (benzotriazol-1-yl)purine nucleosides have been unequivocally established via Pd-mediated C-N bond formation between bromo purine nucleosides and 1H-benzotriazole. Finally, short and extremely simple synthesis of 1,N6-ethano- and 1,N6-propano-2'-deoxyadenosine are reported in order to demonstrate the synthetic versatility of the O6-(benzotriazol-1-yl)inosine nucleoside derivatives for the assembly of relatively complex compounds.     

O6-(benzotriazol-1-yl)inosine derivatives: easily synthesized, reactive nucleosides

A novel class of O6-(benzotriazol-1-yl)inosine as well as the corresponding 2'-deoxy derivatives can be conveniently prepared by a reaction between sugar-protected or -unprotected inosine or 2'-deoxyinosine nucleosides and 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP). The reaction appears to proceed via a nucleoside phosphonium salt, and in the absence of any additional nucleophile, the released 1-hydroxybenzotriazole undergoes reaction with the formed phosphonium salt leading to the requisite O6-(benzotriazol-1-yl)inosine or 2'-deoxyinosine derivatives. Isolation and characterization of the phosphonium salt as well as analysis by 31P{1H} NMR appear to be consistent with this reaction pathway. The resulting O6-(benzotriazol-1-yl)inosine derivatives are effective as electrophilic nucleosides, undergoing facile reactions with a variety of nucleophiles such as alcohols, phenols, amines, and a thiol. Unusual and challenging nucleoside derivatives such as an aryl-bridged dimer, a nucleoside-amino acid conjugate, and a nucleoside-nucleoside dimer have also been synthesized from the O6-(benzotriazol-1-yl)-2'-deoxyinosine derivative. Finally, a fully protected DNA building block, the O6-(benzotriazol-1-yl)-2'-deoxyinosine 5'-O-DMT 3'-O-phosphoramidite, has been prepared and a preliminary evaluation of its use for DNA modification has been performed. Results from these studies indicate several important facts: A single, simple methodological approach provides a class of stable, isolable ribo and 2'-deoxyribonucleoside derivatives that possess excellent reactivity for SNAr chemistry with a wide range of nucleophiles. Also, a benzotriazolyl nucleoside phosphoramidite appears to be a suitable reagent for incorporation into DNA for purposes of site-specific DNA modification.     

Photochemistry on soluble polymer supports: synthesis of nucleosides

[reaction: see text] A new soluble polymer support synthesis of nucleosides is described. The photochemical ring expansion of cyclobutanones in the presence of poly(ethylene glycol) (PEG) results in polymer-supported ribosides. These photoadducts can be cleaved from the polymer under Vorbrüggen coupling conditions with TMS-protected purines and pyrimidines to give ribonucleosides. The method has been extended to include modified PEGs with dendritic end-groups in order to improve the loading levels for these coupling reactions.     

Cyclic polymers: past,present and future

Methods for characterising cyclic polymers are illustrated by reference first to dilute solution methods for cyclic poly(dimethylsiloxane) (PDMS) and then to the entrapment of cyclic polymers in networks. Preparative routes to cyclic polymers are then reviewed, including ring-chain equilibration reactions, coupling and condensation reactions and new methods using polymer-supported reagents. Some of the properties of cyclic PDMS are discussed, including differences between ring and chain polymer properties such as their melt viscosities and glass transition temperatures. Methods for preparing the first polymeric catenanes are described, using polymer-supported reagents. Future directions for cyclic polymer chemistry are indicated, including topological polymer chemistry.     

Chemoselective Acylation of Nucleosides

Acylated nucleoside analogues play an important role in medicinal chemistry and are extremely useful precursors to various other nucleoside analogues. However, chemoselective acylation of nucleosides usually requires several protection and deprotection steps due to the competing nucleophilicity of hydroxy and amino groups. In contrast, direct protecting-group-free chemoselective acylation of nucleosides is a preferred strategy due to lower cost and fewer overall synthetic steps. Herein, a simple and efficient chemoselective acylation of nucleosides and nucleotides under mild reaction conditions, giving either O- or N-acylated products respectively with excellent chemoselectivity is reported.     

钯催化合成嘧啶核苷衍生物的研究进展

嘧啶核苷衍生物在药物化学、生物探针和核酸化学的研究中具有重要的作用, 金属催化碳碳的形成广泛应用于嘧啶核苷衍生物的合成. 综述了钯催化的Sonogashira反应、Stille反应、Heck反应以及Hiyama反应在嘧啶类核苷衍生物合成中的应用.     

Nucleosides. CXXXV. Synthesis of some 9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-9H-purines and their biological activities

Seven purine nucleosides containing the 2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl moiety were synthesized and tested for their antitumor activity. Direct condensation of 3-O-acetyl-5-O-benzoyl-2-deoxy-2-fluoro-D-arabinofuranosyl bromide (1) with N6-benzoyladenine in CH2Cl2 followed by saponification of the product afforded the adenine nucleoside (I, 2'-F-ara-A). Deamination of I with NaNO2 in HOAc gave the hypoxanthine analogue (II, 2'-F-ara-H). The 6-thiopurine nucleoside (III, 2'-F-ara-6MP) was prepared by condensation of 1 with 6-chloropurine by the mercury procedure followed by thiourea treatment and saponification of the product. Methylation of III gave the 6-SCH3 analogue (IV). Raney Ni desulfurization of III afforded the unsubstituted purine nucleoside (V, 2'-F-ara-P). Condensation of 1 with 2-acetamido-6-chloropurine by the silyl procedure afforded the protected 2-acetamido-6-chloropurine nucleoside which served as the precursor for both the guanine and 6-thioguanine nucleosides (VI, 2'-F-ara-G and VII, 2'-F-ara-TG, respectively). Thus, alkaline hydrolysis of the precursor gave VI. Thiourea treatment prior to alkaline hydrolysis gave VII. The new nucleoside, 2'-F-ara-G (VI) is found to be selectively toxic to human T-cell leukemia CCRF-CEM.     

The "resin-capture-release" hybrid technique: a merger between solid- and solution-phase synthesis

A polymer-assisted organic synthesis that combines the concept of solid-phase synthesis with the idea of polymer-supported scavenging reagents has recently appeared on the chemistry scene. This technique has frequently been termed the "resin-capture-release" methodology and is initiated by the immobilization of a small molecule on a polymeric support. This intermediate is subjected to a second transformation by adding a new reaction partner in solution. This reactant plays two roles: a) the chemical alteration of the polymer-bound intermediate and b) the simultaneous release of this reaction product from the resin back into solution. This new concept is presented and future prospects are discussed.     

Toward amide-modified RNA: synthesis of 3'-aminomethyl-5'-carboxy-3',5'-dideoxy nucleosides

Recent discovery of RNA interference has reinvigorated the interest in chemically modified RNA. Chemical approaches may be used to optimize properties of small interfering RNAs, such as thermal stability, cellular delivery, in vivo half-life, and pharmacokinetics. From this perspective, amides as neutral and hydrophobic internucleoside linkages in RNA are highly interesting modifications that so far have not been tested in RNA interference. Amides are remarkably good mimics of the phosphodiester backbone of RNA and can be prepared using a relatively straightforward peptide coupling chemistry. The synthetic challenge that has hampered the progress in this field has been preparation of monomeric building blocks for such couplings, the nucleoside amino acid equivalents. Herein, we report two synthetic routes to enantiomerically pure 3'-aminomethyl-5'-carboxy-3',5'-dideoxy nucleosides, monomers for preparation of amide-modified RNA. Modification of uridine, a representative of natural nucleosides, using nitroaldol chemistry gives the target amino acid in 16 steps and 9% overall yield. The alternative synthesis starting from glucose is somewhat less efficient (17 steps and 6% yield of 3'-azidomethyl-5'-carboxy-3',5'-dideoxy uridine), but provides easier access to modified nucleosides having other heterocyclic bases. The syntheses developed herein will allow preparation of amide-modified RNA analogues and exploration of their potential as tools and probes for RNA interference, fundamental biochemistry, and bio- and nanotechnology.     

INTRAMOLECULAR ENERGY TRANSFER IN NATIVE tRNA AT ROOM TEMPERATURE

Abstract— The odd nucleoside 4-thiouridine, which is present in position 8 of 70% of E. coli tRNAs, possesses unusual spectroscopic properties which make it suitable for intramolecular energy transfer studies. Both its luminescence excitation spectrum and the action spectrum (230–380 nm) for the 8–13 link formation have been established in native E. coli tRNA at room temperature. The spectra are identical and present a new unexpected peak around 260 nm. At this wavelength, they are amplified by a factor of nine as compared with the absorption and excitation spectra of the free nucleoside in aqueous solution.
The origin of this new peak is discussed and it is concluded that energy transfer does occur from the common nucleosides to the 4-thiouridine residue. Using the values of the nucleosides to 4-thiouridine distances inferred from the sets of atomic coordinates obtained on yeast tRNA^phe crystals, a satisfactory account of our finding can be obtained assuming singlet-singlet energy transfer. The efficiency of the mechanism is probably favoured by a good overlap between the emission spectra of the common nucleosides and the absorption spectrum of 4-thiouridine.     

Modified Nucleosides,Nucleotides and Nucleic Acids via Click Azide-Alkyne Cycloaddition for Pharmacological Applications

The click azide = alkyne 1,3-dipolar cycloaddition (click chemistry) has become the approach of choice for bioconjugations in medicinal chemistry, providing facile reaction conditions amenable to both small and biological molecules. Many nucleoside analogs are known for their marked impact in cancer therapy and for the treatment of virus diseases and new targeted oligonucleotides have been developed for different purposes. The click chemistry allowing the tolerated union between units with a wide diversity of functional groups represents a robust means of designing new hybrid compounds with an extraordinary diversity of applications. This review provides an overview of the most recent works related to the use of click chemistry methodology in the field of nucleosides, nucleotides and nucleic acids for pharmacological applications.     

Vertical excitation energies for ribose and deoxyribose nucleosides

Vertical excitation energies for DNA and RNA nucleosides are determined with electron structure calculations using the time-dependent density functional theory (TDDFT) method at the B3LYP/6-311++G(d,p) level for nucleoside structures optimized at the same level of theory. The excitation energies and state assignments are verified using B3LYP/aug-cc-pVDZ level calculations. The nature of the first four excited states of the nucleosides are studied and compared with those of isolated bases. The lowest npi* and pipi* transitions in the nucleoside remain localized on the aromatic rings of the base moiety. New low-energy npi* and pisigma* transitions are introduced in the nucleosides as a result of bonding to the ribose and deoxyribose molecules. The effect on the low-lying excited state transitions of the binding to phosphate groups at the 5'- and 3',5'-hydroxyl sites of the uracil ribose nucleoside are also studied. Some implications of these calculations on the de-excitation dynamics of nucleic acids are discussed.     

Some developments in the phosphitetriester method for synthesis of oligonucleotides

1,l-Dimethyl-2,2,2-trichloroethyl has merit as a protecting group for P-O in the phosphite-triester synthesis of oligonucleotides. Use of this group enables one to simplify procedures for preparing active nucleoside phosphorochloridite reagents, to remove oligonucleotide phosphotriester intermediates intact from a solid support, and to conduct block syntheses in solution or on a silica support viaphosphite chemistry. Deprotection can be achieved by warming the trihaloethyl phosphotriesters with tributylphosphine. The high efficiency of the coupling and deprotection reactions for oligomers bound to an insoluble support make this chemistry especially attractive.     

Iterative Synthesis of Nucleoside Oligophosphates with Phosphoramidites

P‐Amidites can be used in iterative couplings to selectively give mixed P^III–P^V anhydrides. These intermediates can be oxidized followed by a rapid removal of the two terminal fluorenylmethyl groups. An iterative synthesis (coupling, oxidation, deprotection) of nucleoside oligophosphates can be carried out in solution and on a solid support. The coupling rates and yields are high, the procedures convenient (non‐dry reagents and solvents, ambient conditions, unprotected nucleotides), and the purification is very simple. The method works with all canonical nucleosides and holds promise for significant simplification of the usually cumbersome process of P‐anhydride bond construction.     

Nucleoside-boron cluster conjugates - Beyond pyrimidine nucleosides and carboranes

General methods for the synthesis of new purine and pyrimidine nucleosides modified with borane clusters and metallacarborane complexes are presented. They include: (1) attachment of carborane modification at 2′ position of nucleoside via formacetal linkage formation, (2) tethering of the metallacarborane group at nucleobase part of the nucleoside via dioxane ring opening in oxonium metallacarborane, carborane or dodecaborate derivatives, and (3) ‘‘click” chemistry approach based on Huisgen 1,3-dipolar cycloaddition. Proposed methodologies extend the range of nucleoside-boron cluster conjugates available and open new areas for their applications.     

Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications**

Biocatalytic nucleoside (trans-)glycosylations catalyzed by nucleoside phosphorylases have evolved into a practical and convenient approach to the preparation of modified nucleosides, which are important pharmaceuticals for the treatment of various cancers and viral infections. However, the obtained yields in these reactions are generally determined exclusively by the innate thermodynamic properties of the nucleosides involved, hampering the biocatalytic access to many sought-after target nucleosides. We herein report an additional means for reaction engineering of these systems. We show how apparent equilibrium shifts in phosphorolysis and glycosylation reactions can be effected through entropically driven, biased esterification of nucleosides and ribosyl phosphates with inorganic borate. Our multifaceted analysis further describes the kinetic implications of this in situ reactant esterification for a model phosphorylase.     

Complexes of palladium (II) with L-proline. Mixed L-prolinato nucleoside complexes of Palladium (II)

The reaction of Palladium (II) chloride and L-proline (ProH) in aqueous solution gave the dimeric complex, Pd(Pro)Cl₂, which was characterized by elemental analysis, molecular weight, conductivity measurements and IR and NMR spectra. The complex, reacted further with the purine nucleosides inosine or guanosine (Nucl) and the complexes Pd(Pro)(Nucl-H⁺) were isolated from aqueous solution. The insolubility of these complexes suggested a rather polymeric structure in which the nucleoside bridges two adjacent palladium atoms through its N(7) and the exocyclic O(6) atoms. Reaction in dmso gave the complex Pd(Pro)(Nucl)Cl in which the nucleoside act as monodentate ligands with their N(7) atom as ligation site. In aqueous solutions these complexes are quantitatively transformed to the polymeric analogues with the liberation of HCl. The nucleoside adenosine (Ado) reacted in a different way giving only the dimeric complex [Cl(Pro)PdAdoPd(Pro)Cl] in which adenosine bridges two palladium atoms through its N(1) and N(7) atoms. Finally with the pyrimidine nucleoside cytidine (Cyd) the monomer Pd(Pro)(Cyd)Cl was isolated.     

Synthesis and NMR studies of some imidazo[4,5-d]pyridazine nucleosides

Unlike imidazo[4,5-d]pyridazin-4(5H)-one ( 1a ), which undergoes ribosylation at N-6 in the Vorbruggen procedure for nucleoside synthesis, the 5-benzyloxymethyl derivative 12 undergoes ribosylation at N-1 and N-3 to give a separable mixture of 14 and 15 . Removal of the N-5 blocking groups from 14 and 15 by treatment with boron trichloride at −78° affords the intermediates 16 and 17 , which were debenzoylated to give the 4-oxo nucleosides 5 and 6 . Thiation of 16 and 17 , followed by S-methylation and ammonolysis leads to the 4-amino nucleosides 2 and 3 . The glycosylation sites of these nucleosides were assigned by using a combination of ¹H and ¹³C nmr data, especially measurements of the spin-lattice relaxation times (T₁) of the base protons. Using these techniques, it is shown that a nucleoside previously reported to be 3 is in fact the N-6 isomer.     

Synthesis and biophysical characterization of tRNA(Lys,3) anticodon stem-loop RNAs containing the mcm(5)s(2)U nucleoside

[reaction: see text] Phosphoramidite reagents of the naturally occurring modified nucleosides mcm(5)s(2)U and mcm(5)U were synthesized and along with pseudouridine were incorporated into 17-nucleotide lysine tRNA anticodon stem-loop domains. Standard RNA phosphoramidite coupling chemistry allowed us to systematically investigate the thermodynamic effects of nucleoside modification and to correlate thermodynamic trends with qualitative structure effects seen by NMR spectroscopy.