Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• removed with an acid in each synthetic cycle. The exo-amino groups of nucleosides dA, dC and dG are protected with acyl groups, the nascent ODN is anchored to a solid support via a base- or nucleophile-cleavable linker, and in the most widely used phosphoramidite technology the phosphate groups are

Synthesis of acylglycerol derivatives by mechanochemistry

• Karen J. Ardila-Fierro,
• Andrij Pich,
• Marc Spehr,
• José G. Hernández and
• Carsten Bolm

Beilstein J. Org. Chem. 2019, 15, 811–817, doi:10.3762/bjoc.15.78

• Chemosensation, Institute for Biology II, RWTH Aachen University, D-52074 Aachen, Germany 10.3762/bjoc.15.78 Abstract In recent times, many biologically relevant building blocks such as amino acids, peptides, saccharides, nucleotides and nucleosides, etc. have been prepared by mechanochemical synthesis. However

• transformations. Additionally, synthesizing lipid structures mechanochemically would complement the preparation of biologically relevant building blocks (amino acids, peptides, saccharides, nucleosides, etc.) by mechanochemistry, thereby highlighting the importance of mechanical forces in the chemistry of life

Tuning the stability of alkoxyisopropyl protection groups

• Zehong Liang,
• Henna Koivikko,
• Mikko Oivanen and
• Petri Heinonen

Beilstein J. Org. Chem. 2019, 15, 746–751, doi:10.3762/bjoc.15.70

• place practically instantaneous at room temperature with reagents 1a–d. In order to avoid formation of the vinyl ether analog as a side product, the reaction time should not exceed 5 minutes. The isolated yields of the protected nucleosides are typically between 70–90%. However, reagent 1e forms an

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• reported that 2,6-diazidopurine nucleosides exhibit opposite regioselectivity with aliphatic thiols, which do SNAr reactions at C(2) position of purines [50][51]. Taking this information into account, we performed an SNAr reaction between 2,6-diazidopurine 2a and piperidine and obtained the C(2

Syntheses and chemical properties of β-nicotinamide riboside and its analogues and derivatives

• Mikhail V. Makarov and
• Marie E. Migaud

Beilstein J. Org. Chem. 2019, 15, 401–430, doi:10.3762/bjoc.15.36

• efficient synthesis of NAD+ in humans. Unlike other nucleosides, ribosylated nicotinamide displays a relatively labile glycosidic bond, which renders its synthesis and its manipulation challenging. Yet, modifications of NR+ through the introduction of appendages and synthesis of structural analogues open

• + chemistry. Finally, Lee et al. [27] studied in detail the regiochemical outcomes of the synthesis of the bromosugars 7a and 7b of the glycosylation of Nam (1a) with these bromosugars as well as the deprotection of the acylated nucleosides 8a,b. It was observed that the bromination of 2a with HBr gas in

• appropriate work-up procedures for NR+/NRH derivatives, as this class of nucleoside greatly differs from the canonical purine and pyrimidine nucleosides. For instance, the glycosyl bond of NR+ was shown to be very susceptible to cleavage in methanolic solutions of ammonia [39]. As such, to get the

Synthesis of nonracemic hydroxyglutamic acids

• Dorota G. Piotrowska,
• Iwona E. Głowacka,
• Andrzej E. Wróblewski and
• Liwia Lubowiecka

Beilstein J. Org. Chem. 2019, 15, 236–255, doi:10.3762/bjoc.15.22

• into 2'-deoxy-L-thymidine and other nucleosides [119]. Syntheses of all four enantiomers of tricholomic acid of interest as a flycidal compound as well as in receptor studies [120] were accomplished starting from enantiomeric 3-hydroxyglutamic acid, e.g., (2S,3R)-3-hydroxyglutamic acid was converted in

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• conducted. This experiment revealed that the oligonucleotide containing five modified units was able to elicit the RNase H-mediated cleavage of the complementary RNA strand. Keywords: DNA/RNA affinity; fluorinated cyclopropanes; fluorinated nucleic acids; RNase H activity; sugar modified nucleosides

• the presence of persilylated thymine to produce the iodine intermediates 2α/β (Scheme 1, Table 1, entry 1). These instable intermediates were then directly reduced with tributyltin hydride (Bu3SnH) to yield the tricyclic nucleosides 5α/β as main compounds. However, we observed the occurrence of the

• formation of the nucleoside 6 took place, they had to be analyzed separately. Therefore, a sample of the iodinated nucleosides 2α/β was purified and subjected to the reduction reaction, where nucleosides 5α/β were formed as single products (Table 1, entry 2). Also, the conversion of the nucleosides 5α/β

Thermophilic phosphoribosyltransferases Thermus thermophilus HB27 in nucleotide synthesis

• Ilja V. Fateev,
• Ekaterina V. Sinitsina,
• Aiguzel U. Bikanasova,
• Maria A. Kostromina,
• Elena S. Tuzova,
• Larisa V. Esipova,
• Tatiana I. Muravyova,
• Alexei L. Kayushin,
• Irina D. Konstantinova and
• Roman S. Esipov

Beilstein J. Org. Chem. 2018, 14, 3098–3105, doi:10.3762/bjoc.14.289

• the preparation of nucleosides and nucleotides due to the regio- and stereospecificity of enzymes [4][10][11], performing metabolic transformations of substrates. Phosphoribosyltransferases are increasingly being widely used as key enzymes in multi-enzymatic systems [2]. The substrate specificity of

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• either by a NIS-mediated or Vorbrüggen nucleosidation yielded in both cases the β-tricyclic nucleoside as major anomer. Subsequent desilylation and cyclopropane ring opening of these tricyclic intermediates afforded the unsaturated 6’F-bc4,3 nucleosides. The successful incorporation of the corresponding

• modification might be a substrate for RNase H. Keywords: DNA/RNA affinity; fluorinated cyclopropanes; fluorinated nucleic acids; molecular dynamics simulations; sugar modified nucleosides; Introduction A powerful strategy for the treatment of various disorders like cancer, viral and inherited diseases is the

• were then used to calculate the atomic charges of the corresponding nucleosides using the R.E.D. III.5 tools package [66]. The obtained parameters were added to the Amber94 force field [67] which besides the GROMACS 5.0.6 simulation package [68] was utilized for the molecular dynamics simulations. The

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• and 1H,1H-NMR coupling constants. The sugar conformation (N vs S) was different in solution as compared to the solid state. Keywords: click cyclization; conformation; macrocycles; nucleosides; X-ray; Introduction The field of macrocycles was initiated by the work of Ruzicka and his structure

• . Monomeric purine and pyrimidine nucleosides form smaller ring systems known as cyclonucleosides incorporating O, N or S-bridges within the sugar moiety or between the nucleobase and the sugar residue [6]. Macrocycles can be obtained by a variety of chemical reactions [7][8][9][10]. Often, several protection

• macrocyclic systems [18][19][20][21][22][23][24][25]. DNA mimics with triazole linkages were constructed [26][27]. The click reaction was used to generate a cyclic ADP-ribose second messenger mimic [28]. Modelling studies using MM+ energy minimization showed that pyrimidine nucleosides are useful synthons for

Practical tetrafluoroethylene fragment installation through a coupling reaction of (1,1,2,2-tetrafluorobut-3-en-1-yl)zinc bromide with various electrophiles

• Ken Tamamoto,
• Shigeyuki Yamada and
• Tsutomu Konno

Beilstein J. Org. Chem. 2018, 14, 2375–2383, doi:10.3762/bjoc.14.213

• intriguing biological activities of CF2CF2-containing pyranose and furanose derivatives (Figure 1a) [7][8][9]. Subsequently, Gouverneur et al. also developed novel CF2CF2-containing C-nucleosides (Figure 1b) [10]. Meanwhile, in the field of materials sciences, Kirsch et al. revealed that the incorporation of

Artificial bioconjugates with naturally occurring linkages: the use of phosphodiester

• Takao Shoji,
• Hiroki Fukutomi,
• Yohei Okada and
• Kazuhiro Chiba

Beilstein J. Org. Chem. 2018, 14, 1946–1955, doi:10.3762/bjoc.14.169

• , chemical syntheses can technically be divided into two parts; deprotection and coupling reactions, enabling simple repeated procedures for their production, and bioactivities can potentially be tuned by alteration of their sequences. Nowadays, not only canonical amino acids and/or nucleosides but also

• solvents, and washing the precipitates with polar solvents simultaneously rinses away excess amino acids or nucleosides and coupling reagents. We have demonstrated multistep syntheses of up to 28-mers for peptides and 21-mers for oligonucleotides without column purification. In all cases, the C-terminal

• -activated amino acids or 3’-terminal-activated nucleosides are coupled to the N- or 5’-terminus of the supported reactants via amide or phosphodiester linkages (Figure 1). Such couplings could also be possible in the opposite activating manner. Namely, the activation of the N- or 5’-terminus of the

Anomeric modification of carbohydrates using the Mitsunobu reaction

• Julia Hain,
• Patrick Rollin,
• Werner Klaffke and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1619–1636, doi:10.3762/bjoc.14.138

• 6-chloropurine with various reducing sugars using methyldiphenylphosphine as activator. Extension to the D-ribo series with 6-chloro- and 2,6-dichloropurines was later reported by Hertel and co-workers [103]. In the course of an exploration of modified L-nucleosides, 6-chloropurin-9-yl derivatives

• were obtained in moderate yields [104]. Aiming at an improved procedure to synthesize nucleosides with glycosylation of the nucleobase, De Napoli et al. used the Bu3P-ADDP system to connect inosine and uridine derivatives with D-ribofurano and D-glucopyrano moieties [105]. Hocek’s group in 2015

• published a direct one-pot synthesis of exclusively β-configured nucleosides from unprotected or 5-O-monoprotected D-ribose using optimized Mitsunobu conditions with various purine- and pyrimidine-based heterocycles. Here, DBU was applied first, followed by DIAD and P(n-Bu)3 [106]. Two years later Seio and

Glycosylation reactions mediated by hypervalent iodine: application to the synthesis of nucleosides and carbohydrates

• Yuichi Yoshimura,
• Hideaki Wakamatsu,
• Yoshihiro Natori,
• Yukako Saito and
• Noriaki Minakawa

Beilstein J. Org. Chem. 2018, 14, 1595–1618, doi:10.3762/bjoc.14.137

• well. The extension of hypervalent iodine-mediated glycosylation allowed us to couple a nucleobase with cyclic allylsilanes and glycal derivatives to yield carbocyclic nucleosides and 2’,3’-unsaturated nucleosides, respectively. In addition, the combination of hypervalent iodine and Lewis acid could be

• used for the glycosylation of glycals and thioglycosides to produce disaccharides. In this paper, we review the use of hypervalent iodine-mediated glycosylation reactions for the synthesis of nucleosides and oligosaccharide derivatives. Keywords: glycosylation; hypervalent iodine; Lewis acid

• reaction coupled with oxidation. The concept of the oxidative glycosylation reaction was successfully applied to the synthesis of other nucleoside derivatives, including 4’-selenonucleosides and carbocyclic nucleosides. The hypervalent iodine-mediated glycosylation has also been used for oligosaccharide

Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• , Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany 10.3762/bjoc.14.133 Abstract TEMPO spin labels protected with 2-nitrobenzyloxymethyl groups were attached to the amino residues of three different nucleosides: deoxycytidine, deoxyadenosine, and adenosine. The corresponding phosphoramidites

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• ' (Figure 5) [72][73][74]. In principle, the NAA-modification is inspired by 'high-carbon' nucleoside structures (i.e., nucleosides having more than five carbon atoms in the sugar unit) found in naturally occurring nucleoside antibiotics [75][76][77]. In muraymycin- and caprazamycin-type nucleoside

• antibiotics, among others, such 'high-carbon' nucleosides are uridine-derived amino acid structures ('glycyluridine', GlyU) [78][79][80], which are aminoribosylated at the 5'-hydroxy group. As part of our ongoing research program on muraymycin nucleoside antibiotics (e.g., muraymycin A1 (44)) and their

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• commercially-available equipment which, for reactions of nucleosides and related materials has most commonly been the mixer ball mill (MBM – e.g., Figure 1a). Using a MBM, high energy collisions between reactants and one or more balls within a closed vessel (jar) are induced by vibrating the jar through a

• levels of involatile solvent usage typically employed in the solution-based synthesis of such compounds can be gauged by the ability of Roche to eliminate 1.12 million kilograms of solvent per annum [38]. Review Mechanochemical transformations of nucleosides and related materials involving covalent bonds

• observed within one to three hours and only in the case of adenosine was any (minor) side-product formation found. In all cases, facile purification using a scrubber column enabled pure 2′,3′,5′-tri-O-TBDMS-protected nucleosides to be isolated in 87–99% yields. In situ benzoylation of the persilylated

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• , Baltimore, MD 21250, United States 10.3762/bjoc.14.65 Abstract C-nucleosides have intrigued biologists and medicinal chemists since their discovery in 1950's. In that regard, C-nucleosides and their synthetic analogues have resulted in promising leads in drug design. Concurrently, advances in chemical

• maneuver stereochemistry as well as to incorporate structural modifications. In this review, we describe recent reports on the modular synthesis of C-nucleosides with a focus on D-ribonolactone and sugar modifications that have resulted in potent lead molecules. Keywords: C-nucleosides; convergent

• modified nucleosides arise from changes in hydrogen bonding motifs, electronic effects, hydrophobic interactions, acid-base properties and chemical reactivity [25][26][27][28][29][30][31][32][33][34][35][36][37]. One such modification is the change in the nature of the glycosidic bond [29][37]. Although

AuBr₃-catalyzed azidation of per-O-acetylated and per-O-benzoylated sugars

• Jayashree Rajput,
• Srinivas Hotha and
• Madhuri Vangala

Beilstein J. Org. Chem. 2018, 14, 682–687, doi:10.3762/bjoc.14.56

• purine and pyrimidine nucleoside synthesis using per-O-acyl/per-O-benzoyl furanosyl and pyranosyl o-hexynylbenzoates [23]. Subsequently, Hotha and co-workers utilized propargyl 1,2-orthoesters and alkynyl glycosyl carbonate donors for the synthesis of pyrimidine nucleosides [24][25]. In addition, N

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• the applied conditions, can be efficiently cleaved, at the same time leaving all other protecting groups intact. Thus, a full set of all 20 trimers was synthesized by phosphotriester chemistry starting with the condensation of N-acyl-3'-O-(o-chlorophenylphosphate)nucleosides to 3'-O-(2

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• sodium-salt method [42]. The deoxyribosylation was then achieved using the same Hoffer’s α-chloro sugar, but in presence of a Lewis acid yielding the protected nucleosides 19a–c [48]. The cleavage of the protection groups was achieved with sodium methoxide to furnish compounds 20a–c. The improved

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• derivatives are optically active. The π→π* transitions of the bases (Scheme 1) contribute to the electronic circular dichroism mostly as a result of the chiral perturbation exerted by the sugar moiety. The ECD signals of single nucleosides/nucleotides are, accordingly, quite small. Coupling into

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols

• Katrina Tait,
• Alysia Horvath,
• Nicolas Blanchard and
• William Tam

Beilstein J. Org. Chem. 2017, 13, 2888–2894, doi:10.3762/bjoc.13.281

• the synthesis of 2’,3’-methano carbocyclic nucleosides via compound 24 (Scheme 5) [17]. Carbocyclic nucleosides are important synthetic targets because of their use as antiviral and antitumor agents [17]. Replacing the oxygen unit in the parent furanose ring with a methylene unit helps to stabilize