Synthesis of Disaccharide Nucleosides by the O‐Glycosylation of Natural Nucleosides with Thioglycoside Donors

Disaccharide nucleosides constitute an important group of naturally‐occurring sugar derivatives. In this study, we report on the synthesis of disaccharide nucleosides by the direct O‐glycosylation of nucleoside acceptors, such as adenosine, guanosine, thymidine, and cytidine, with glycosyl donors. Among the glycosyl donors tested, thioglycosides were found to give the corresponding disaccharide nucleosides in moderate to high chemical yields with the above nucleoside acceptors using p‐toluenesulfenyl chloride (TolSCl) and silver triflate (AgOTf) as promoters. The interaction of these promoters with nucleoside acceptors was examined by ¹H NMR spectroscopic experiments.     

7‐Iodo‐5‐aza‐7‐deazaguanine ribonucleoside: crystal structure,physical properties,base‐pair stability and functionalization

The positional change of nitrogen‐7 of the RNA constituent guanosine to the bridgehead position‐5 leads to the base‐modified nucleoside 5‐aza‐7‐deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton‐acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all‐purine' DNA and DNA with silver‐mediated base pairs. The present work reports the single‐crystal X‐ray structure of 7‐iodo‐5‐aza‐7‐deazaguanosine, C<sub>10</sub>H<sub>12</sub>IN<sub>5</sub>O<sub>5</sub> ( 1 ). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′‐endo) for the ribose moiety, with an antiperiplanar orientation of the 5′‐hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7‐iodo substituent forms a contact to oxygen‐2′ of the ribose moiety. Self‐pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H…O and N—H…O). The concept of pK‐value differences to evaluate base‐pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all‐purine' RNA. Furthermore, the 7‐iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.     

Synthesis and Antimicrobial Activity of New 2,5‐Disubstituted 1,3,4‐Oxadiazoles and 1,2,4‐Triazoles and Their Sugar Derivatives

A series of new 2,5‐disubstituted‐1,3,4‐oxadiazole and 1,2,4‐triazole derivatives were synthesized by heterocyclization of acid hydrazide 1 and thiosemicarbazide derivative 2 . Furthermore, the acyclic C‐nucleoside analogs were prepared by cyclization of their corresponding sugar hydrazones by reaction with acetic anhydride. The antimicrobial activity of the prepared compounds was evaluated and some of the synthesized compounds revealed good activities against fungi.     

A combination chemical and enzymatic approach for the preparation of azole carboxamide nucleoside triphosphate

Alternative substrates for DNA and RNA polymerases offer an important set of biochemical tools. Many of the standard methods for nucleoside triphosphate synthesis fail in the cases of nonpurine and nonpyrimidine nucleosides. An efficient preparation of the 5'-O-tosylates for both the deoxy- and ribonucleosides enabled preparation of the diphosphate esters by displacement with tris(tetra-n-butylammonium) pyrophosphate. Enzymatic synthesis of the azole carboxamide deoxyribonucleoside triphosphate was based on ATP as the phosphate donor, nucleoside diphosphate kinase as the catalyst, coupled with phosphoenol pyruvate (PEP) and pyruvate kinase as an ATP regeneration system. Ribonucleoside triphosphate synthesis required PEP as the phosphate donor and pyruvate kinase as the catalyst. An optimized purification procedure based upon boronate affinity gel was developed to yield highly purified nucleoside triphosphates. The strategy outlined here provides a new and efficient method for preparation of nucleoside 5'-triphosphate and is likely applicable to a broad variety of base and sugar modified nucleoside analogues.     

Synthesis of Phospholipid?Ribavirin Conjugates

New conjugates of antiviral nucleoside Ribavirin (=1‐(β‐D ‐ribofuranosyl)‐1H‐1,2,4‐triazole‐3‐carboxamide; 1 ) with 1,2‐ and 1,3‐diacyl glycerophosphates have been synthesized by the phosphoramidite method. A combination of 2′,3′‐phenylboronate protecting group for the sugar moiety of the ribonucleoside 1 and 2‐cyanoethyl protection for the phosphate fragment ensured the preparation of the desired compounds with reasonable yields via a small number of synthetic steps.     

Synthesis of nucleoside analogues bearing the five naturally occurring nucleic acid bases built on a 2-oxabicylo[3.1.0]hexane scaffold

Hitherto unknown nucleoside analogues incorporating the five naturally occurring nucleic acid bases built on a 2-oxabicyclo[3.1.0]hexane template were synthesized. The synthesis of these new conformationally restricted nucleoside analogues involved the preparation of a suitable sugar precursor bearing the 2-oxabicyclo[3.1.0]hexane scaffold. This sugar was readily obtained from [(3aS,6aS)-2,2-dimethyl-3a,6a-dihydrofuro[2,3-d][1,3]dioxol-5-yl]methyl benzyl ether (4) following a Simons-Smith-type cyclopropanation reaction. Finally, glycosylation reactions and deprotection provided the nucleoside analogues. Using nucleoside 14 bearing thymine base as a model, we found that the conformation of such nucleoside analogue was restricted toward a (0)T(1) conformation.     

Synthesis and Anti‐HIV Activity of Triazolo‐Fused 3′,5′‐Cyclic Nucleoside Analogues Derived from an Intramolecular Huisgen 1,3‐Dipolar Cycloaddition

Triazolo‐fused 3′,5′‐cyclic nucleoside analogues were synthesized by an intramolecular 1,3‐dipolar cycloaddition of nucleoside‐derived azido‐alkynes in a regio‐ and stereospecific manner. The thymine nucleoside base in these target compounds was transformed successfully into the corresponding 5‐methylcytosine component. The synthesized compounds were examined in a MAGI assay for exploring the anti‐HIV activity and in a H9 T lymphocytes assay for measuring the cell toxicity.     

Synthesis and Crystal Structures of O‐2′,3′‐Cyclic Cyclopentanone and Cyclohexanone Ketals of the Cytostatic 5‐Fluorouridine

The synthesis of two O‐2′,3′‐cyclic ketals, i.e., 5 and 6 , of the cytostatic 5‐fluorouridine ( 2 ), carrying a cyclopentane and/or a cyclohexane ring, respectively, is described. The novel compounds were characterized by ¹H‐, ¹⁹F‐, and ¹³C‐NMR, and UV spectroscopy, as well as by elemental analyses. Their crystal structures were determined by X‐ray analysis. Both compounds 5 and 6 show an anti‐conformation at the N‐glycosidic bond which is biased from +ac to +ap compared to the parent nucleoside 2 . The sugar puckering is changed from ^2′E to _3′E going along with a reduction of the puckering amplitude τ_m by ca. 10–13° due to the ketalization. The conformation about the sugar exocyclic bond C(4′)? C(5′) of 5 and 6 remains unchanged, i.e., g⁺, compared with compound 2 .     

Synthesis of 1,3,4‐Oxadiazole Acyclo C‐Nucleosides Bearing 5‐Methylthio{7‐substituted‐1,2,4‐triazolo[1,5‐d]tetrazol‐6‐yl}moieties

Oxidative cyclization of the sugar hydrazones ( 3_a‐f ) derived from {7H‐1,2,4‐triazolo[1,5‐d]tetrazol‐6‐ylsulfanyl}acetic acid hydrazide ( 1 ) and aldopentoses 2_a‐c or aldohexoses 2_d‐f with bromine in acetic acid in the presence of anhydrous sodium acetate, followed by acetylation with acetic anhydride gave the corresponding 2‐(per‐O‐acetyl‐alditol‐l‐yl)‐5‐methylthio{7H‐1,2,4‐triazolo[1,5‐d]tetrazol‐6‐yl}‐1,3,4‐oxadiazoles ( 5_a‐f ). Condensative cyclization of the sugar hydrazones ( 3_a‐f ) by heating with acetic anhydride gave the corresponding 3‐acetyl‐2‐(per‐O‐acetyl‐alditol‐1‐yl)‐2,3‐dihydro‐5‐methylthio{7‐acetyl‐1,2,4‐triazolo[1,5‐d]tetrazol‐6‐yl}‐1,3,4‐oxadiazoles ( 11_a‐f ). De‐O‐acetylation of the acyclo C‐nucleoside peracetates ( 5 and 11 ) with methanolic ammonia afforded the hydrazono lactones ( 7 ) and the acyclo C‐nucleosides ( 12 ), respectively. The structures of new oxadiazole derivatives were confirmed by analytical and spectral data.     

Synthesis and Anti‐HIV Activity of Triazolo‐Fused 2′,3′‐Cyclic Nucleoside Analogs Prepared by an Intramolecular Huisgen 1,3‐Dipolar Cycloaddition

Triazolo‐fused 2′,3′‐cyclic nucleoside analogs were synthesized by an intramolecular 1,3‐dipolar cycloaddition of nucleoside‐derived azido alkynes in a regio‐ and stereospecific manner. The uracil base in these target compounds was successfully transformed to the corresponding cytosine. The synthesized compounds were examined in a MAGI assay for their anti‐HIV activities, and in a H9 T lymphocytes assay for their cell toxicities.     

1,3‐Dicyclohexylcarbodiimide,an Effective Activating Agent for H‐Phosphonate Chemistry

1,3‐Dicyclohexylcarbodiimide (DCC) has been exploited as an activating agent for nucleoside‐H‐phosphonates in the solution as well as solid phase synthesis of oligonucleotide and is effective in terms of speed and coupling efficiency.     

Synthesis of Galactosyl‐Queuosine and Distribution of Hypermodified Q‐Nucleosides in Mouse Tissues

Queuosine (Q) is a hypermodified RNA nucleoside that is found in tRNA^His, tRNA^Asn, tRNA^Tyr, and tRNA^Asp. It is located at the wobble position of the tRNA anticodon loop, where it can interact with U as well as C bases located at the respective position of the corresponding mRNA codons. In tRNA^Tyr and tRNA^Asp of higher eukaryotes, including humans, the Q base is for yet unknown reasons further modified by the addition of a galactose and a mannose sugar, respectively. The reason for this additional modification, and how the sugar modification is orchestrated with Q formation and insertion, is unknown. Here, we report a total synthesis of the hypermodified nucleoside galactosyl‐queuosine (galQ). The availability of the compound enabled us to study the absolute levels of the Q‐family nucleosides in six different organs of newborn and adult mice, and also in human cytosolic tRNA. Our synthesis now paves the way to a more detailed analysis of the biological function of the Q‐nucleoside family.     

Convenient Synthesis of Nucleoside‐5′‐Diphosphates from the Corresponding Ribonucleoside‐5′‐phosphoroimidazole

The reaction of ribonucleoside‐5′‐phosphoroimidazolide with a tributylammonium orthophosphate in anhydrous dimethylformamide at room temperature provides a general method for the synthesis of nucleoside‐5′‐diphosphates. The novelty of the approach is to use the triethylammonium salt of 5′‐monophosphate nucleoside derivative prior to the imidazolate reaction with imidazole, triphenylphosphine, and 2,2′‐dithiodipyridine. Deprotection, followed by displacement of the imidazole moiety using tributylammonium orthophosphate and a catalytic amount of zinc chloride in dimethylformamide gave the desired 5′‐diphosphate products. The triethyl ammonium salt of 5′‐diphosphate nucleosides was purified by flash chromatography using DEAE (diethylaminoethyl weak anion exchange resin) Sepharosa fast flow packed in an XK 50/60 column on an Akta FPLC (Fast Protein Liquid Chromatography). Synthesis procedures are reported for adenosine‐5′‐diphosphate, uridine‐5′‐diphosphate, cytidine‐5′‐diphosphate, and guanosine‐5′‐diphosphate. Yields for the displacement reactions ranged from 95 to 97%. Thus, this method offers the advantages of shorter reaction time, greater product yield, and a more cost‐effective synthetic route.     

Amipurimycin: Total Synthesis of the Proposed Structures and Diastereoisomers

The proposed diastereoisomers ( 1 a – d ) together with their C8′‐epimers ( 1 e – h ) of amipurimycin, a unique antifungal peptidyl nucleoside antibiotic, have been synthesized for the first time. The synthetic approach is efficient and stereodivergent, and features a stereoselective aldol condensation to build the branched C9 sugar amino acid skeleton and a regio‐ and stereocontrolled gold(I)‐catalyzed N‐glycosylation to furnish the purine nucleoside. Analysis of the NMR data suggests that the previously assigned configuration of the tertiary C3′ in amipurimycin should be of opposite configuration.     

Cyclometalated Iridium(III) Complexes with Deoxyribose Substituents

Fundamental study of enzymatic nucleoside transport suffers for lack of optical probes that can be tracked noninvasively. Nucleoside transporters are integral membrane glycoproteins that mediate the salvage of nucleosides and their passage across cell membranes. The substrate recognition site is the deoxyribose sugar, often with little distinction among nucleobases. Reported here are nucleoside analogues in which emissive, cyclometalated iridium(III) complexes are “clicked” to C‐1 of deoxyribose in place of canonical nucleobases. The resulting complexes show visible luminescence at room temperature and 77 K with microsecond‐length triplet lifetimes. A representative complex is crystallographically characterized. Transport and luminescence are demonstrated in cultured human carcinoma (KB3‐1) cells.     

Total Synthesis of Antitumor Antibiotic Derhodinosylurdamycin A

The first total synthesis of derhodinosylurdamycin A, an angucycline antitumor antibiotic, has been described. The synthesis features a Hauser annulation followed by pinacol coupling to construct the tetracyclic angular aglycon, a Stille coupling of glycal stannane and tetracyclic aryliodide followed by stereoselective reduction to afford the 2‐deoxy β‐C‐arylglycoside, and a late‐stage stereoselective glycosylation for the preparation of derhodinosylurdamycin A. This synthetic strategy should be amenable to the chemical synthesis of analogs of derhodinosylurdamycin A bearing diverse 2‐deoxy sugar subunits for structure and activity relationship studies.     

Covalent Labeling of Nucleosides with VIII‐ and VI‐Valent Osmium Complexes

Osmium tetroxide complexes with nitrogen ligands [Os(VIII)L] have been widely applied as probes of the DNA structure and as electroactive labels of DNA. Here we describe the electrochemical behavior of Os(VIII)2,2‐bipyridine (Os, bipy)‐base‐labeled nucleosides. We show that electroactive label can be introduced also in the nucleoside ribose residues using six‐valent osmium complex. Cyclic voltammograms of sugar‐Os(VI)‐modified ribosides are similar but not identical to those of the base‐modified ribosides. Our results showing the electroactivity of sugar modified ribosides pave the way to facile end‐labeling of RNA.     

Non‐covalent Versus Covalent Control of Self‐Assembly and Chirality of Nile Red‐modified Nucleoside and DNA

A DNA‐based covalent versus a non‐covalent approach is demonstrated to control the optical, chirooptical and higher order structures of Nile red ( Nr ) aggregation. Dynamic light scattering and TEM studies revealed that in aqueous media Nr ‐modified 2′‐deoxyuridine aggregates through the co‐operative effect of various non‐covalent interactions including the hydrogen bonding ability of the nucleoside and sugar moieties and the π‐stacking tendency of the highly hydrophobic dye. This results in the formation of optically active nanovesicles. A left‐handed helically twisted H‐type packing of the dye is observed in the bilayer of the vesicle as evidenced from the optical and chirooptical studies. On the other hand, a left‐handed helically twisted J‐type packing in vesicles was obtained from a non‐polar solvent (toluene). Even though the primary stacking interaction of the dye aggregates transformed from H→J while going from aqueous to non‐polar media, the induced supramolecular chirality of the aggregates remained the same (left‐handed). Circular dichroism studies of DNA that contained several synthetically incorporated and covalently attached Nr ‐modified nucleosides revealed the formation of helically stacked H‐aggregates of Nr but—in comparison to the noncovalent aggregates—an inversed chirality (right‐handed). This self‐assembly propensity difference can, in principle, be applied to other hydrophobic dyes and chromophores and thus open a DNA‐based approach to modulate the primary stacking interactions and supramolecular chirality of dye aggregates.     

Ultra‐small sugar‐substituted N‐heterocyclic carbene‐protected palladium nanoparticles and catalytic activity

Ultra‐small Pd nanoparticles (UNPs) represent a distinctive type of nanomaterial making them very attractive for a range of applications. Herein, chiral sugar‐substituted N‐heterocyclic carbenes (NHCs) with various lengths of alkyl chain (sugar‐NHCs‐ⁿC_nH_2n+1) were first used to prepare water‐soluble Pd@NHCs‐sugar UNPs via an efficient ligand‐exchange strategy, which can be handled under air and are stable over 10 months. The Pd@NHCs‐sugar UNPs were highly monodisperse, with tunable core diameters from 1.7 to 2.1 nm, and an effect of the particle size on the N‐substituted aliphatic chains was observed. To investigate the accessibility of the surface, the Pd@NHCs‐sugar UNPs were studied as catalysts for C–C coupling reaction in eco‐friendly ethanol aqueous solution without any precipitation of metallic Pd. The presence of the longest aliphatic group in the Pd@NHCs‐sugar UNPs imparts to them the highest catalyst activity (turnover number and turnover frequency up to 196 000 and 3 920 000 h^?1).     

The Miharamycins and Amipurimycin: their Structural Revision and the Total Synthesis of the Latter

The structural puzzle of amipurimycin, a peptidyl nucleoside antibiotic, is solved by total synthesis and X‐ray diffraction analysis, with the originally proposed configurations at C3′ and C8′ inverted and those at C6′, C2′′, and C3′′ corrected. A similar structural revision of the relevant miharamycins is proposed via chemical transformations and then validated by X‐ray diffraction analysis. The miharamycins bear an unusual trans‐fused dioxabicyclo[4.3.0]nonane sugar scaffold, which was previously assigned as being in the cis configuration.