Stereoselective synthesis of 4-deoxy-4-nucleobase-2,5-anhydro-l-mannitol derivatives

Novel 1′-homo-N-2′-deoxy-α-nucleosides: synthesis, characterization and biological activity

For the first time, a series of novel 1′-homo-N-2′-deoxy-α-nucleosides containing natural nucleobases as well as 5-fluoro and 5-iodopyrimidine analogs have been synthesized in an efficient manner. Additionally, a high yield protocol for the assembly of a dimeric scaffold containing two sugar moieties linked to the N-1 and N-3 positions of a single pyrimidine base has been accomplished. The structures of the novel homonucleosides were established by a single crystal X-ray structure of 1′-homo-N-2′-deoxy-α-adenosine and NMR studies. The biological activity of these 1′-homo-N-2′-deoxy-α-nucleosides as antiviral (HIV-1 and HBV) and cytotoxic studies was measured in multiple cell systems. The unique structure and easy accessibility of these compounds may allow their use in the design of new nucleoside analogs with potential biological activity and as a scaffold for combinatorial chemistry.

Novel 1′-homo-N-2′-deoxy-α-nucleosides and dimers.

d-/l-Isothymidine incorporation in the core sequence of aptamer BC15 enhanced its binding affinity to the hnRNP A1 protein

The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was reported to participate in the development of a variety of tumors. BC15 is a DNA aptamer targeting hnRNP A1. Firstly, through sequence truncation, we identified 31-mer sequence BC15-31 as the core sequence of BC15 with a strong binding affinity and high selectivity to the hnRNP A1 protein. Isothymidine (isoT) modification was then applied for the structural optimization of BC15-31, systematic modification and biological evaluation were carried out. Incorporation of isoT in the 1,3 sites at the 5'-end of BC15-31 can significantly enhance the protein affinity. Chemical modifications close to the 3'-end can greatly improve the stability of the aptamer. Furthermore, BC15-31 modified with isoT at both the 5'-end and 3'-end displayed an additive effect with enhanced bioactivity and stability at the same time. Our study strategy on BC15 provides a useful guideline for chemical modification and optimization of the aptamer for further clinical application.

Chemical modification improves the stability of the DNA aptamer GBI-10 and its affinity towards tenascin-C

Aptamers are useful tools in molecular imaging due to their numerous attractive properties, such as excellent affinity and selectivity to diverse types of target molecules and biocompatibility. We carried out structure-activity relationship studies with the tenascin-C (TN-C) binding aptamer GBI-10, which is a promising candidate in tumor imaging. To increase the tumor targeting ability and nuclease resistance under physiological conditions, systematic modifications of GBI-10 with single and multiple 2'-deoxyinosine (2'-dI) or d-/l-isonucleoside (d-/l-isoNA) were performed. Results indicated that sector 3 of the proposed secondary structure is the most important region for specific binding with TN-C. By correlating the affinity of eighty-four GBI-10 derivatives with their predicted secondary structure by Zuker Mfold, we first validated the preferred secondary structure at 37 °C. We found that d-/l-isoNA modified GBI-10 derivatives exhibited improved affinity to the target as well as plasma stability. Affinity measurement and confocal imaging analysis highlighted one potent compound: 4A_L/26T_L/32T_L, which possessed a significantly increased targeting ability to tumor cells. These results revealed the types of modified nucleotides, and the position and number of substituents in GBI-10 that were critical to the TN-C binding ability. Stabilized TN-C-binding DNA aptamers were prepared and they could be further developed for tumor imaging. Our strategy to introduce 2'-dI and d-/l-isoNA modifications after the selection process is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding ability.

Ni-Pd Catalyzed Cyclization of Sulfanyl 1,6-Diynes: Synthesis of 1'-Homonucleoside Analogues

The Ni-Pd catalyzed addition-cyclization of sulfanyl 1,6-diynes 2-9 with nucleobases is described. The reactions of N-tethered 1,6-diynes with N³-benzoylthymine, N⁴,N⁴-bis(Boc)cytosine, N³-benzoyluracil and N⁶,N⁶-bis(Boc)adenine exclusively afforded the pyrrolylmethyl and furylmethyl nucleotides in good yields. Deprotection of nucleobases was completed by treatment with acids or bases. Furthermore, the reactions of pyrroles and furans with nucleophiles such as alkoxides and amines underwent detosylation and conversion to the alkoxymethyl- and arylaminomethyl-pyrroles and furans in good yields.

Spatial conservation studies of nucleobases in 10–23 DNAzyme by 2′-positioned isonucleotides and enantiomers for increased activity

d-/l-Isonucleotides were used to modify the catalytic core and recognition arms of 10–23 DNAzyme and prominently improved its bioactivity.

Stability and bioactivity of thrombin binding aptamers modified with D-/L-isothymidine in the loop regions

Thrombin binding aptamer (TBA) is a 15-mer single-strand DNA that was identified by SELEX screening technology. It adopts a chair-type antiparallel G-quadruplex and can specifically interact with thrombin, thus inhibiting blood coagulation. Isonucleoside (isoNA) is a type of nucleoside isomer in which the base is shifted to 2′-positions of the glycosyl group, endowed with the ability to modulate local conformation of nucleotides, and L-isoNA could alter the conformation more due to the inversion of glycosyl configuration. Incorporation of L-isothymidine (L-isoT) at T3, T9, T12 positions and D-isoT at the T7 position in TBA's loop regions promoted the formation of G-quadruplex, resulting in enhanced affinity with thrombin and an increased anticoagulant effect. Computer simulation indicated that TBA-12L showed the strongest binding with thrombin, which was consistent with experimental results. The bioactivity of double isoNA incorporated TBA with D-IsoT at T7 and L-IsoT at T12 was comparable to that of TBA-12L, suggesting that the T12 of TBA was very important in interaction with thrombin. Our study also suggested that TBA might interact with two thrombin molecules through the TT loops (T3T4, T12T13) and TGT loop, but the second bonding did not show additional biological effects.

Synthesis of 2'-deoxy-1'-homo-N-nucleosides with anti-influenza activity by catalytic methyltrioxorhenium (MTO)/H2O2 oxyfunctionalization

This paper describes a new route for the synthesis of 1'-homo-N-nucleoside derivatives by means of either methyltrioxorhenium (MTO) or supported MTO catalysts, with H(2)O(2) as the primary oxidant. Under these selective conditions, the oxyfunctionalization of the heterocyclic ring and the N heteroatom oxidation were operative processes, regardless of the type of substrate used, that is, purine or pyrimidine derivatives. In addition, the oxidation of 1'-homo-N-thionucleosides, showed the occurrence of site-specific oxidative nucleophilic substitutions of the heterocyclic ring. The MTO/H(2)O(2) system showed, in general, high reactivity under both homogeneous and heterogeneous conditions, affording the final products with high conversion values of substrates and from medium to high yields. Many of the novel 1'-homo-N-nucleoside analogues were active against the influenza A virus, without any cytotoxic effects, retaining their activity in both protected and unprotected forms.

Synthesis, physicochemical and biological properties of oligonucleotides incorporated with amino-isonucleosides

Antisense oligonucleotides (ASONs) and siRNAs have been applied extensively for the regulation of cellular and viral gene expression, and RNAi is currently one of the most promising new approaches for anti-tumor and anti-viral therapy. In order to improve bioactivity properties and physicochemical properties of siRNA, we synthesized a novel class of ASONs II–VII incorporated with amino-isonucleoside (isoA₁ and isoA₂) for investigation on basic physicochemical properties. Then we designed amino-isonucleoside (isoA₁, isoA₂ and isoT₁) incorporated siRNA 2–7. Some meaningful results have been obtained from the physicochemical property experiments in ASONs. In RNAi potency experiments, we investigated RNAi potency of each strand of the siRNA. These amino-isonucleosides incorporated siRNAs showed promising bioactivity properties and had position specificity. Reduced off target effect from sense strand loading in siRNA application was observed.

Synthesis and recognition of novel isonucleoside triphosphates by DNA polymerases

Isonucleosides have been attracting a lot of attention in recent years due to the chemical and enzymatic stability and potential anticancer and antiviral activities. We have reported some of the isonucleosides which exhibited significant anticancer activity and found that the oligonucleotide incorporated with isonucleoside could increase the enzymatic stability against the degradation by phosphodiesterase. In this paper, we investigated the recognition of the isonucleoside triphosphates 1-6 by Taq, Vent(exo(-)), DeepVent(exo(-)), 9 degrees Nm, and Therminator DNA polymerases by a non-radioactivity method. We found that most of the isonucleoside triphosphates can be recognized by various DNA polymerase and act as terminators. Isonucleoside triphosphates 2 and 6 can be incorporated as substrates into the primer at 3' terminus to lengthen the chain dependent on a DNA template by Vent(exo(-)) and DeepVent(exo(-)) DNA polymerases.

Nucleoside Analogues from Branched-Chain Pyranosides

Reaction of (pyranosid-3-yl)ethanal 2 with ethynylmagnesium bromide or lithium phenylacetylide in THF afforded (2R,S)-1-(methyl 2-O-benzyl-4,6-O-benzylidene-3-deoxy-α-d-altropyranosid-3-yl)but-3-yn-2-ols 3a and 3b, respectively. Oxidation of 3a and 3b yielded the 1-(methyl 2-O-benzyl-4,6-O-benzylidene-3-deoxy-α-d-altropyranosid-3-yl)but-3-yn-2-ones 4a and 4b, which upon treatment with hydrazine and hydrazine derivatives formed the 3-(methyl 2-O-benzyl-4,6-O-benzylidene-3-deoxy-α-d-altropyranosid-3-ylmethyl)pyrazoles 5a–5d. Compounds 4a and 4b also underwent reaction with amidinium and guanidinium salts under basic conditions to furnish the 4-(methyl 2-O-benzyl-4,6-O-benzylidene-3-deoxy-α-d-altropyranosid-3-ylmethyl)pyrimidines 8a–8f. Furthermore, treatment of 4a and 4b with 2-aminobenzimidazole yielded the 2-(methyl 2-O-benzyl-4,6-O-benzylidene-3-deoxy-α-d-altropyranosid-3-ylmethyl)benzo[4,5]imidazo[1,2-a]pyrimidines 11a and 11b. Deprotection of 5a and 8b in two steps afforded 3(5)-(methyl 3-deoxy-α-d-altropyranosid-3-ylmethyl)-1H(2H)-pyrazole 7 and 4-(methyl 3-deoxy-α-d-altropyranosid-3-ylmethyl)-2-phenylpyrimidine 10, respectively. Compound 11a was treated with AcOH/H2O to furnish 2-(methyl 2-O-benzyl-3-deoxy-α-d-altropyranosid-3-ylmethyl)benzo-[4,5]imidazo[1,2-a]pyrimidine 13.

Unexpected cycloreversion of a tosylated sugar oxetane under E2 conditions: The facile formation of 2-(2-furanyl)-1, 3-dioxolane from a novel 2, 5:4, 6-dianhydro-L-idose derivative (Preliminary commun

2,5:4,6-Dianhydro-3-O-p-toluenesulfonyl-L-idose ethylene acetal (4) was synthesized with the aim of studying its chemical behaviour in the presence of several basic agents (Bu4NF/MeCN, NaOMe/MeOH, KOBut/ButOH/THF, and NaH/DMSO). Treatment of 4 with sodium hydride in dimethyl sulphoxide at room temperature unexpectedly gave the 2-(2-furanyl)-1,3-dioxolane. The mechanism of the process presumably involved the initial conversion of 4 to the corresponding 2,3-unsaturated derivative 5, followed by a facile oxetane ring cycloreversion by the elimination of formaldehyde.

Synthesis of 3-C-(methyl beta-D-xylofuranosid-3-yl)-5-phenyl-1,2,4-oxadiazole

Nucleophilic addition of KCN to 5-O-benzoyl-1,2-O-isopropylidene-alpha-D-erythro-pentofuranos-3-++ +ulose gave the xylo cyanohydrin stereoselectively. Several xylos-3-yl-1,2,4-oxadiazole derivatives were synthesized from this cyanohydrin and were converted into 3-C-(methyl beta-D-xylofuranosid-3-yl)-5-phenyl-1,2,4-oxadiazole.