Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

• Elisabeth Mairhofer,
• Elisabeth Fuchs and
• Ronald Micura

Beilstein J. Org. Chem. 2016, 12, 2556–2562, doi:10.3762/bjoc.12.250

• -amino-3-deazapurine and benzoyl-protected 1-O-acetylribose. The novel path is superior to previously described syntheses in terms of efficacy and ease of laboratory handling. Keywords: deazapurine nucleoside; nucleosidation; protection groups; ribozymes; Introduction The synthesis of 3-deazaadenosine

• mechanisms. Therefore, 1-deazaadenosine (c1A), 1-deaza-2’-deoxyadenosine (c1dA), 3-deazaadenosine (c3A), and 3-deaza-2’-deoxyadenosine (c3dA), and the corresponding phosphoramidites to prepare oligoribonucleotides are highly requested nucleoside modifications. Unfortunately, synthetic approaches to achieve

• them are troublesome and time consuming, in particular for c3A. To the best of our knowledge, only two papers have reported the synthesis of c3A phosphoramidites so far [16][17]. Thereby, the major bottleneck is access to the naked nucleoside. Although the c3A nucleoside is commercially available

Synthesis of medronic acid monoesters and their purification by high-performance countercurrent chromatography or by hydroxyapatite

• Elina Puljula,
• Jouko Vepsäläinen and
• Petri A. Turhanen

Beilstein J. Org. Chem. 2016, 12, 2145–2149, doi:10.3762/bjoc.12.204

• could prove the achieved degree of purity. Some other methods have also been used for the synthesis of nucleoside methylene-BPs which could structurally be considered as medronic acid monoesters [21][22]. Interestingly, there are only a few publications describing the synthesis of medronic acid

Synthesis of the C8’-epimeric thymine pyranosyl amino acid core of amipurimycin

• Pramod R. Markad,
• Navanath Kumbhar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2016, 12, 1765–1771, doi:10.3762/bjoc.12.165

• the formation of the pyranose ring skeleton to give 2,7-dioxabicyclo[3.2.1]octane 12. Functional group manipulation in 12 gave 21 that on stereoselective β-glycosylation afforded the pyranosyl thymine nucleoside 2 – a core of amipurimycin. Keywords: amipurimycin; 1,3-anhydrosugar; anti-fungal agent

• ; carbohydrate; peptidyl nucleosides; Introduction Peptidyl nucleoside antibiotics are a class of complex molecules that encompass an extensive array of natural products [1]. The notable structural features of peptidyl nucleosides are responsible for their miscellaneous biological activities such as antitumor

• -dioxabicyclo[3.2.1]octane A could be glycosylated stereoselectively with the requisite nucleobase to give β-nucleoside pyranosyl skeleton 2. The bridged bicyclic system A was visualized from the azido diol B. Thus, hydrolysis of the 1,2-acetonide functionality in B will lead to in situ generation of

Dinuclear thiazolylidene copper complex as highly active catalyst for azid–alkyne cycloadditions

• Anne L. Schöffler,
• Ata Makarem,
• Frank Rominger and
• Bernd F. Straub

Beilstein J. Org. Chem. 2016, 12, 1566–1572, doi:10.3762/bjoc.12.151

• ][22][23][24][25][26], nucleoside, nucleotide, and oligonucleotide chemistry [27][28][29], in fluorogenic reactions [30], and in the syntheses of dendrimers [25][31]. The detailed mechanism of this reaction and the exact role of copper(I) and the species involved in the catalytic cycle had remained

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• “click-fleximer” as expanded nucleobase mimicking the purine [14]. “Click-fleximer” nucleoside analogues are easily accessible derivatives using copper-catalysed alkyne–azide cycloaddition (CuAAC) and this synthetic methodology allows generating a small library of derivatives depending on the nature of

• acids. Thus, nucleoside phosphonate analogues 1a–q (Scheme 2) were isolated as their sodium salts with yields ranging from 21 to 77% over three steps. Structures of all final compounds were unambiguously confirmed on the basis of NMR (1H, 13C and 31P) and MS (MS and HRMS) data analysis (see Supporting

Synthesis of a deuterated probe for the confocal Raman microscopy imaging of squalenoyl nanomedicines

• Eric Buchy,
• Branko Vukosavljevic,
• Maike Windbergs,
• Dunja Sobot,
• Camille Dejean,
• Simona Mura,
• Patrick Couvreur and
• Didier Desmaële

Beilstein J. Org. Chem. 2016, 12, 1127–1135, doi:10.3762/bjoc.12.109

• was extended to other nucleoside analogues such as antiretroviral agents, ddC, ddI and AZT [14] and to siRNA oligonucleotides [15]. More notably, squalenoylation of adenosine and the subsequent formation of NAs, allowed prolonged circulation of this nucleoside, providing neuroprotection in mice with

• when dealing with low drug concentrations or biological-like structures such as peptide drugs or nucleoside analogues. To overcome this issue, deuterium can be introduced to a sample molecule, as it exhibits a significant Raman signal at around 2200 cm−1, which is in a so called “silent region” (1800

The role of alkyl substituents in deazaadenine-based diarylethene photoswitches

• Christopher Sarter,
• Michael Heimes and
• Andres Jäschke

Beilstein J. Org. Chem. 2016, 12, 1103–1110, doi:10.3762/bjoc.12.106

• DNA photoswitches for the application in bionanotechnology and synthetic biology. Keywords: diarylethene; nucleoside; electrocyclic rearrangement; photochromism; photoswitch; Introduction Most biomacromolecules are per se not responsive to light. Their conversion into photoresponsive molecules opens

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

• natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY), a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic

• replication and folate metabolism [21]. Promising candidates meeting the requirements for new drugs are nucleoside antibiotics, i.e., uridine-derived compounds that address the enzyme translocase I (MraY) as a novel target, thereby interfering with a membrane-associated intracellular step of peptidoglycan

• biosynthesis. This review will focus on muraymycins as a subclass of nucleoside antibiotics, covering their mode of action, synthetic approaches as well as SAR studies on several derivatives. Furthermore, first insights into the biosynthesis of these Streptomyces-produced secondary metabolites will be

Interactions between 4-thiothymidine and water-soluble cyclodextrins: Evidence for supramolecular structures in aqueous solutions

• Vito Rizzi,
• Sergio Matera,
• Paola Semeraro,
• Paola Fini and
• Pinalysa Cosma

Beilstein J. Org. Chem. 2016, 12, 549–563, doi:10.3762/bjoc.12.54

• described in [18], the preparation of simple physical mixtures with CDs was already shown to be effective in terms of protective activity. Starting from these considerations, the main goal of this work is to study the ability of the modified nucleoside S4TdR to form inclusion complexes with five CDs: 2-HP-α

• carefully investigated by some authors of this paper elucidating the behavior of such a nucleoside in aqueous solution. The main form of the nucleoside, absorbing at 337 nm, is the protonated structure reported in Figure 1. The deprotonation, on the nitrogen atom in position 3, started only at pH values

• nucleoside (indicated by an asterisk in Figure 5, in the wavenumber region of 1700–1600 cm−1) changed distinctly. The dip between the two signals is reduced with important variations of the C=O vibration mode. The effect is even stronger with TRIMEB and DIMEB CDs (Figure 5D,E). Moreover, when inclusion

Versatile synthesis and biological evaluation of novel 3’-fluorinated purine nucleosides

• Hang Ren,
• Haoyun An,
• Paul J. Hatala,
• William C. Stevens Jr,
• Jingchao Tao and
• Baicheng He

Beilstein J. Org. Chem. 2015, 11, 2509–2520, doi:10.3762/bjoc.11.272

• University of Chicago Medical Center, Chicago, Illinois 60637, USA 10.3762/bjoc.11.272 Abstract A unified synthetic strategy accessing novel 3'-fluorinated purine nucleoside derivatives and their biological evaluation were achieved. Novel 3’-fluorinated analogues were constructed from a common 3’-deoxy-3

• analogs of natural products nebularine and 6-methylpurine riboside were constructed via our convergent synthetic strategy. Synthesized nucleosides were tested against HT116 (colon cancer) and 143B (osteosarcoma cancer) tumor cell lines. We have demonstrated 3’-fluorine purine nucleoside analogues display

• potent tumor cell growth inhibition activity at sub- or low micromolar concentration. Keywords: anticancer; 3’-fluororibonucleoside; purine nucleoside; 6-substituted purine; synthesis; Introduction Antimetabolites are extremely useful for the treatment of cancers and viral infections and are one of the

Dicarboxylic esters: Useful tools for the biocatalyzed synthesis of hybrid compounds and polymers

• Ivan Bassanini,
• Karl Hult and
• Sergio Riva

Beilstein J. Org. Chem. 2015, 11, 1583–1595, doi:10.3762/bjoc.11.174

• parent compound 12. A similar approach was followed later on by Lin and coworkers, who described the enzymatic esterification of the nucleoside 5-fluorouridine (13) and of other polyhydroxylated bioactive molecules with divinyl esters of dicarboxylic acids [31][32][33][34][35]. The monovinyl esters

Preparation of a disulfide-linked precipitative soluble support for solution-phase synthesis of trimeric oligodeoxyribonucleotide 3´-(2-chlorophenylphosphate) building blocks

• Amit M. Jabgunde,
• Alejandro Gimenez Molina,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2015, 11, 1553–1560, doi:10.3762/bjoc.11.171

• previously shown [26] that the disulfide linkage may be cleaved by reduction with dithiotreitol or TCEP at pH buffered to 7.6 without detritylation taking place. Elongated treatment with TCEP appeared, however, to be too harsh. Evidently, the 5´-terminal nucleoside should be inserted as a more acid tolerant

• support enabled efficient purification of the support-bound intermediates and product by virtually quantitative precipitation from MeOH after each coupling and 5´-O-deprotection. However, on assembling the trimeric 3´-(2-chlorophenyl phosphate) building blocks, the 5´-terminal nucleoside should be

• 2 h to obtain the tetravalent nucleoside cluster 7a, transferred to a stoppered 50 mL plastic tube, and MeOH (46 mL) was added. The precipitate formed was kept at −20 °C overnight, isolated by centrifugation, and dried to give 7a (0.20 g, 70%) as a white solid. The precipitate and supernatant were

Synthesis of novel N-cyclopentenyl-lactams using the Aubé reaction

• Madhuri V. Shinde,
• Rohini S. Ople,
• Ekta Sangtani,
• Rajesh Gonnade and
• D. Srinivasa Reddy

Beilstein J. Org. Chem. 2015, 11, 1060–1067, doi:10.3762/bjoc.11.119

• cyclopentenyl-substituted lactams. Upon dihydroxylation, this affords the N-cyclopentenyl-lactam compounds in racemic form. Given the numerous uses of nucleosides and related compounds, we were interested in the synthesis of carbocylic nucleoside mimics. The attempts and results are described herein. Keywords

• –1.83 (series of multiplets, 5H), 1.74–1.61 (series of multiplets, 3H); 13C NMR (100 MHz, CD3OD) δ 178.6, 73.7, 70.5, 62.6, 61.8, 47.3, 37.5, 37.0, 32.9 29.3, 28.0, 23.0; HRMS calculated for C12H21NO4, [M + Na]+: 266.1363, found 266.1358. Selective carbocyclic nucleoside analogues from the literature

Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2015, 11, 913–929, doi:10.3762/bjoc.11.103

• shows the energy-minimized 3D structures of the lipophilic nucleoside headgroups 4a–9a. The reactive building blocks 4b–9b were subsequently used to synthesize the following lipo-oligonucleotides (LONs), which have an identical nucleotide sequence in common as well as a cyanine-5 (Cy5) fluorophore at

• the three-dimensional structure of the latter, (ii) from the length of the lipophilic moiety and (iii) from the position of the lipid residue at the nucleoside. For the LONs 10 and 11 we observed that the elongation of the C-atom chain length from 5 to 17 does not necessarily lead to an enhancement of

• pyrimidine β-D-ribonucleoside head groups 1–3 [18]. Chemical formulae 1–9 and lipo-oligonucleotide sequences 10–15. Energy-minimized 3D structures of the lipophilic nucleoside headgroups 4a–9a. All 3D structures were calculated using the program ChemBio3D Ultra v. 12.0 (number of iterations, 387 ± 147

A procedure for the preparation and isolation of nucleoside-5’-diphosphates

• Heidi J. Korhonen,
• Hannah L. Bolt and
• David R. W. Hodgson

Beilstein J. Org. Chem. 2015, 11, 469–472, doi:10.3762/bjoc.11.52

• (triphenylphosphoranylidene)ammonium] pyrophosphate (PPN pyrophosphate) was used in the SN2 displacements of the tosylate ion from 5’-tosylnucleosides to afford nucleoside-5’-diphosphates. Selective precipitation permitted the direct isolation of nucleoside-5’-diphosphates from crude reaction mixtures. Keywords: NDP

• synthesis; nucleic acids; nucleoside-5’-diphosphate; phosphorylation; Introduction Nucleoside-5'-phosphates are key to many mechanistic studies and chemical biology applications [1][2][3]. Synthetic approaches towards nucleoside-5'-phosphates are well-established [4], however, the methods tend to be

• cumbersome. Newer approaches have started to become available over the last decade, where a key driver in these approaches is limiting the effects of moisture on the reaction outcome [5][6][7][8][9][10][11]. Nucleoside-5'-triphosphates (NTPs) are frequently accessed via the Ludwig modification [12] of the

C-5’-Triazolyl-2’-oxa-3’-aza-4’a-carbanucleosides: Synthesis and biological evaluation

• Roberto Romeo,
• Caterina Carnovale,
• Salvatore V. Giofrè,
• Maria A. Chiacchio,
• Adriana Garozzo,
• Emanuele Amata,
• Giovanni Romeo and
• Ugo Chiacchio

Beilstein J. Org. Chem. 2015, 11, 328–334, doi:10.3762/bjoc.11.38

• natural nucleobases with unnaturally-substituted heteroaromatics or homoaromatic systems, or the modification of the phosphate P(O)–O–C bond with the non–hydrolyzable phosphonate P(O)–C linkage [17][18]. In this context, nucleoside analogues, where different carbon or heterocyclic systems replace the

• can interact with intracellular targets to induce cytotoxicity [28][29][30][31][32]. Several functionalities have been inserted as linkers on the 2’-oxa-3’-aza-4’a-carbanucleoside skeleton in order to confer novel mechanisms of action for nucleoside mimics: in this context, the 1,2,3-triazole unit

• lead to interesting biological properties, we report in this paper the preparation of a small library of nucleoside analogues 7 (Figure 2), where the furanose ring is substituted by an isoxazolidine system and a triazole unit replaces the phosphodiester linker at 5’ position of the 2’-oxa-3’-aza-4’a

TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

• Dnyaneshwar B. Gophane and
• Snorri Th. Sigurdsson

Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

• nucleoside TA and its corresponding phosphoramidite were prepared by a previously reported procedure [74] with minor modifications. The synthesis started with the reaction between 3′,5′-diacetyl-2′-deoxyinosine (1) and 2,4,6-triisopropylbenzenesulfonyl chloride to obtain compound 2 (Scheme 1). Coupling of 2

• gave compound 8 in low yields (Scheme 2). Cleavage of the TBDMS groups using TBAF gave spin-labeled nucleoside UA, which was tritylated to give compound 9 and phosphitylated to give phosphoramidite 10. The synthesis of UC, the urea-cytidine analogue, started by reaction of 3′,5′-TBDMS-protected 2

• ′-deoxycytidine (11) with 4-isocyanato-TEMPO (7) [64][76] to give 12 in good yields (Scheme 3). Removal of the TBDMS groups using TBAF gave spin-labeled nucleoside UC, which was tritylated to give compound 13 and subsequent phosphitylation yielded phosphoramidite 14. Synthesis and characterization of TA-, UA- and

Synthesis of dinucleoside acylphosphonites by phosphonodiamidite chemistry and investigation of phosphorus epimerization

• William H. Hersh

Beilstein J. Org. Chem. 2015, 11, 184–191, doi:10.3762/bjoc.11.19

• acylphosphonite would require different nucleoside moieties. One example can be found in the literature of a non-Arbuzov route leading to the dinucleoside analog of 3 where as reported by Hata et al., 3a [41] gives 3b via sequential coupling [42][43] (Scheme 1). While the deoxygenation of phosphine oxides is

• , the reaction of H-phosphonodiamidite 4 with chloroformate 5 gave acyl diamidite 6, which by following standard nucleoside coupling protocols gave the formate phosphonite 1a. The initial P–C bond formation yielding 6 was odd, since although the addition of sodium was intended to give the phosphorus

• lone pair orbitals. However, as noted above, this does not result in an amide-like 13C chemical shift. Nucleoside coupling. The initial attempts at coupling 7 and 9 with 5′-O-DMTr-thymidine were carried out using the Caruthers procedure with 4,5-dicyanoimidazole (DCI) as the activator. While formation

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• temperature (110 °C). This protocol furnished 3'-azido derivative 25 in a moderate, but reliably obtained yield of 42% over 3 steps from 23. Azido nucleoside 25 was finally reduced to the 3'-amino analogue 8 by standard hydrogenation in 92% yield (Scheme 3). With all building blocks 8, (S)-9 and (R)-9 in hand

Nucleic acid chemistry

• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2014, 10, 2928–2929, doi:10.3762/bjoc.10.311

• phosphordiesters or -triesters. Finally, this approach using phosphoramidites as nucleoside building blocks was significantly further developed in 1981 by Beaucage and Caruthers [4]. Since then, oligonucleotides of up to 50-mers in length have become available by an extremely efficient solid-phase methodology that

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

• Vicky Gheerardijn,
• Jos Van den Begin and
• Annemieke Madder

Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

• group, we present here a straightforward method for direct linking of functionalized amino acids to the nucleoside base, thus equipping the nucleoside with two extra functionalities at once. As a proof of principle, we have introduced three amino acids with functional groups frequently used as key

• modification is the most common as it causes only minor disturbance in the helical structure [31]. Depending on the position of the incorporation on the nucleoside structure, the introduced functionalities can be pointed towards the major or the minor groove of the duplex. Modification of position 1’ and 2

• per nucleoside, mainly for synthetic reasons, and preferably making use of commercially available building blocks. We therefore considered the incorporation of moieties containing multiple functionalities on a nucleoside residue and present a straightforward method for the introduction of side chain

Regio- and stereoselective synthesis of new diaminocyclopentanols

• Evgeni A. Larin,
• Valeri S. Kochubei and
• Yuri M. Atroshchenko

Beilstein J. Org. Chem. 2014, 10, 2513–2520, doi:10.3762/bjoc.10.262

• those mimics may subtly influence their biological activity [11][12][13][14]. The functionalization of synthetic, unnatural aminocyclitols represents an attractive strategy towards the preparation of aminoglycoside and nucleoside mimics, and the development of common synthesis routes to various regio

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• Figure 17), as well as of lipid derivatives of nucleoside antimetabolites [23][24]. Moreover, studies of a transdermal application of lipo-oligonucleotides through the human Stratum corneum by iontophoresis techniques are underway. Experimental Materials 1-Palmitoyl-2-oleyl-sn-glycero-3

Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

• Christine Beuck and
• Elmar Weinhold

Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

• strand will need to be filled in with orthogonal 5' to 3' chemistry. A dT nucleoside analog with an exocyclic aziridine moiety has been chemically incorporated into poly-T ODN. Upon hybridization with a complementary poly-A strand, the aziridine group is attacked by the exocyclic amino group of the

• opposing adenine, resulting in ring opening and formation of an ethylene cross-linked base pair [29][30]. Other aziridine-substituted nucleobases have been incorporated enzymatically by a DNA polymerase, but elongation past the modified nucleoside has not been reported [31]. Another approach uses

• , long linkers that might interfere with protein binding are typically employed. The Verdine group has developed a cross-linking approach based on the easy postsynthetic introduction of cystamine or longer amino-alkylthiol linkers into ODN using a convertible nucleoside approach [39][40][41][42][43][44

Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

• Alejandro Gimenez Molina,
• Amit M. Jabgunde,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• '-UUGCA-5', has been prepared on a precipitative tetrapodal tetrakis(4-azidomethylphenyl)pentaerythritol support. The 3'-terminal nucleoside was coupled to the support as a 3'-O-(4-pentynoyl) derivative by Cu(I) promoted 1,3-dipolar cycloaddition. Couplings were carried out with 1.5 equiv of the building

• them has so far been applied to the synthesis of RNA. Tetrakis(4-azidomethylphenyl)pentaerythritol has recently been introduced as a practical soluble support for the synthesis of short oligodeoxyribonucleotides [16]. The 3'-terminal nucleoside is attached as a 3'-O-(4-pentynoyl) derivative to the

• immobilization of the 3'-terminal nucleoside to the azido functionalized support, 3-benzoyl-2-O-cyanoethyl-5-(1-methoxy-1-methylethyl)uridine (4a) was transformed to its 3'-O-(4-pentynoyl) derivative 6a. To accomplish this, 4-pentynoic acid was first converted to its anhydride by DCC activation in dioxane and