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

• cyclopentenyl bridge, which may also be perfluorinated. Substituents on the aryl rings tune the photophysical and chemical properties, such as absorption and isomerization wavelengths, thermal stability, and fatigue resistance. In 2010 our group reported the first diarylethene-based photoswitchable nucleosides

• -based photoswitchable nucleosides. The design of these molecules challenged two of the established design rules for diarylethene-based photoswitches (Figure 1C) [45]: (1) They incorporated a six-membered pyrimidine ring, and (2) – more importantly – only one methyl group, rather than two, was present at

• diarylethenes by direct comparison, and ii) we wanted to test whether our prior successful violation of this “rule” with photochromic pyrimidine nucleosides could be expanded to purine nucleosides. Our analysis reveals that – depending on the substituents – the one-methyl 7-deaza-2’-deoxyadenosine compounds can

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; nucleosides; peptides; structure–activity relationship; Introduction The treatment of infectious diseases caused by bacteria is a severe issue. With multiresistant bacterial strains rendering well-established therapeutic procedures ineffective, the exploration of novel antimicrobial

Nucleic acids through condensation of nucleosides and phosphorous acid in the presence of sulfur

• Tuomas Lönnberg

Beilstein J. Org. Chem. 2016, 12, 670–673, doi:10.3762/bjoc.12.67

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

• bands of such nucleosides (black lines in Figure 5): at 1690 and 1625 cm−1 (C2=O and C5=C6 bonds stretching of the S4TdR ring), at 1500–1600 cm−1 (C=N stretching), at 1465 cm−1 (bending of CH2 groups), at 1270 cm−1 (twisting modes of C4′C5′H2OH) and bands at ca. 3350 cm−1 (OH groups), at 2900–3000 cm−1

Synthesis of cyclic N¹-pentylinosine phosphate, a new structurally reduced cADPR analogue with calcium-mobilizing activity on PC12 cells

• Ahmed Mahal,
• Stefano D’Errico,
• Nicola Borbone,
• Brunella Pinto,
• Agnese Secondo,
• Valeria Costantino,
• Valentina Tedeschi,
• Giorgia Oliviero,
• Vincenzo Piccialli and
• Gennaro Piccialli

Beilstein J. Org. Chem. 2015, 11, 2689–2695, doi:10.3762/bjoc.11.289

• neuronal cells. Keywords: calcium mobilization; cIDPR analogues; cyclic ADP-ribose (cADPR); cyclization; Introduction Nucleosides and nucleotides (NNs) are widely used as key intermediates and important core structures in the field of synthetic medicinal chemistry [1][2]. They represent versatile

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

• ’-fluororibofuranose intermediate. Employing Suzuki and Stille cross-coupling reactions, fifteen 3’-fluororibose purine nucleosides 1–15 and eight 3’-fluororibose 2-chloro/2-aminopurine nucleosides 16–23 with various substituents at position 6 of the purine ring were efficiently synthesized. Furthermore, 3’-fluorine

• 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

• largest classes of drugs. Most antimetabolite drugs are nucleoside derivatives that substitute for endogenous nucleosides and prevent DNA and protein replication [1]. Many of the drugs described by the World Health Organization as "essential medicines" are nucleoside derivatives [2] and nearly 20% of all

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

• ) 2-(pyridine-2-yldisulfanyl)ethanol, MeCN/DCM/MeOH, 0.5 h. Activation of nucleosides. Reagents and conditions: (i) pyridine, dry dioxane, room temperature, 3 h. Synthesis of oligonucleotides. Reagents and conditions: (i) 4–6, 1-methylimidazole, dioxane, under N2; (ii) precipitation with MeOH; (iii) 1

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

• , India 10.3762/bjoc.11.119 Abstract A novel and convenient method utilizing the Aubé reaction to access a new class of compounds that are similar to carbocyclic nucleosides is reported. The azido alcohol derived from Vince lactam undergoes the Aubé reaction with various cyclic ketones to give

• 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

• : Aubé reaction; biological activity; carbocyclic nucleosides; cyclopentenylated lactams; cyclopentylated lactams; Introduction One popular method for the synthesis of N-substituted lactams is the Aubé reaction [1][2][3][4]. Over the last few decades, this reaction has gained popularity and resulted in

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

• -, sesqui-, and diterpenes as well as single and double-chained alkyl groups (completed by an alicyclic alkyl group), have been introduced for the lipophilization of the pyrimidine nucleosides. The resulting nucleolipids were converted into their corresponding 2-cyanoethyl phosphoramidites 4b–9b. Figure 3

• of 66%). Thus they prove significantly smaller than the value of the corresponding lipo-oligonucleotides. The log P data gives insight into the augmentation of the lipophilicity of the nucleosides 4a–9a. Calculations and experimental measurements of hydrodynamic properties of lipo-oligonucleotides

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

• quantities of NTP than NDP [15][16]. Nuceloside-5’-diphosphates can, however, be accessed via SN2 displacement at 5’-activated nucleosides using pyrophosphate as the nucleophile. This approach, developed by Poulter and co-workers [17], forms a cornerstone in the armoury towards the synthesis of nucleoside-5

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

• of 5.0–40 μM. The synthesized compounds do not show any antiviral activity. Keywords: antitumor activity; click chemistry; 1,3-dipolar cycloaddition; nucleic acids; 2’-oxa-3’-aza-4’a-carbanucleoside analogs; Introduction Synthetic modified nucleosides are of great interest as potential new lead

• structures in particular as antiviral or anticancer agents [1][2][3][4][5][6][7][8]. As analogues these compounds can interfere in nucleic acid synthesis or block nucleosides- and/or nucleotide-dependent biological processes by mimicking natural nucleosides and serving as inhibitors or building units [9][10

• ][11][12]. Many structural variations of the natural nucleosides have been exploited. In general, the performed modifications included the replacement of the furanose moiety by other carbon or heterocyclic systems [13][14] or even acyclic fragments [15][16], the substitution of pyrimidine or purine

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

• deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) connected to the exocyclic amino group; TA directly and UA as well as UC through a urea linkage. TA and UC showed a minor destabilization of a DNA duplex, as registered by a small decrease

• ][41][42], non-native base-pairing properties of nucleobases [43][44][45][46] and their dynamics [42][47][48]. Fluorescence spectroscopy, using environmentally sensitive fluorescent nucleosides has been used for detection of local structural perturbations [49][50][51][52][53][54][55][56][57], including

• UC-containing oligonucleotides The phosphoramidites of TA (5), UA (10) and UC (14) were used to incorporate the spin-labeled nucleosides into DNA oligonucleotides using solid-phase synthesis [77]. The low stability of the nitroxide functional group in the TEMPO moiety towards acids lead to almost ca

The Shono-type electroorganic oxidation of unfunctionalised amides. Carbon–carbon bond formation via electrogenerated N-acyliminium ions

• Alan M. Jones and
• Craig E. Banks

Beilstein J. Org. Chem. 2014, 10, 3056–3072, doi:10.3762/bjoc.10.323

• synthetically challenging aza-nucleosides employing an electrochemical step [88]. Synthesis of a bridged tricyclic diproline analogue 93 that induces α-helix conformation into linear peptides [90]. Synthesis of (i) a peptidomimetic and (ii) a functionalised peptide from silyl electroauxiliary precursors [91

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

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

• -intermediates in DNA- and RNAzymes via an efficient and straightforward domino carboxamidation reaction. Keywords: amino acids; bioorganic chemistry; carboxamidation reaction; chemically modified; DNA nucleosides; nucleic acids; Introduction For decades DNA has been known as the carrier of the genetic

• . This was illustrated in previous research in our laboratory where introduction of modified nucleosides on the 2’-position in a DNA double helix resulted in a destabilization of the duplex of 5 °C per modified unit [32]. Although this destabilization depends on many different aspects, such as the type

• functionalities on the nucleoside. As proof of principle and with the catalytic serine–histidine–aspartate catalytic triad of serine proteases in mind, we illustrate the preparation of three different nucleosides equipped with three functional amino acids containing hydroxy, imidazole, amine and carboxylate

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

• : diaminocyclopentanols; epoxides; regioselectivity; ring opening; stereoselectivity; Introduction In recent years mimicry of aminoglycosides [1][2][3][4][5][6][7] and nucleosides [8][9][10] has become an important field in pharmaceutical research. Regio- and stereochemical diversities within a sugar-like moiety in

• aminoglycosides [7], and nucleosides containing 9H-purin-6-amine as a nucleobase portion. High levels of stereoselectivity have been observed in substrate-controlled diastereoselective epoxidation of cyclic alkenes with O- and N-allylic directing groups [20][21]. Several 3-substituted diastereomeric epoxides have

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

• -linking reaction itself is straight-forward, the vinyl-substituted nucleosides need to be chemically synthesized and subsequently converted into their phosphoamidites for chemical DNA synthesis. The same holds true for cross-links based on aldehyde [8][35][36][37] or click chemistry [38]. In addition

• protocol. ODN with convertible nucleosides IOPh and UTri were deprotected and converted to their thionucleoside containing counterparts as described in [51]. Duplexes were annealed before use at a concentration of 100 µM in the respective experiment buffer by heating to 95 °C for 2 min followed by slow

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

• -catalyzed acetalization with 2-methoxypropene in THF. The subsequent 3'-O desilylation of the fully protected nucleosides (3a–d) then required careful adjustment of conditions. Desilylation with NH4F in MeOH turned out to be successful in the sense that the 2'-O and 5'-O protecting groups remained intact

Second generation silver(I)-mediated imidazole base pairs

• Susanne Hensel,
• Nicole Megger,
• Kristina Schweizer and
• Jens Müller

Beilstein J. Org. Chem. 2014, 10, 2139–2144, doi:10.3762/bjoc.10.221

• to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair. Keywords: bioinorganic chemistry; DNA; imidazole

• ; metal-mediated base pairs; nucleic acids; nucleosides; Introduction Nucleic acids with their evolutionary optimized self-assembling properties represent an ideal basis for the generation of artificial, site-specifically functionalized supramolecular aggregates [1][2][3][4]. In this context, numerous

• linearly coordinated silver(I) ion inserted in-between two complementary artificial imidazole nucleosides (Scheme 1, top). The NMR-based solution structure of a DNA duplex with three contiguous imidazole–Ag(I)–imidazole represented the first experimental proof that a B-DNA conformation is compatible with

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

• the backbone and base-pairing properties [9]. We are continuing our investigation of isoGNA oligonucleotides within the context of chimeric sequences and collaborative intercalation studies and thus have a continuing need for the synthesis of isoGNA building blocks. While iso-glycerol nucleosides are

• known [10][11][12][13][14][15], the published synthetic routes and efficiencies of these vary widely and primarily depend on the nature of the nucleobase. Herein, we detail our synthetic efforts and the current improvements for the synthesis of all four isoGNA nucleosides and their phosphoramidites

• . Initial routes towards the synthesis of iso-glycerol nucleosides. Preparation of thymine and adenine containing phosphoramidites of isoGNA. Preparation of guanine- and cytosine-containing phosphoramidites of isoGNA. Preparation of adenine containing phosphoramidite of isoGNA. Mitsunobu reaction with the

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• , nucleosides and nucleobases play an important role in all biological systems. Therefore, it is not surprising that many of their analogs possess interesting biological properties. Potent antiviral drugs based on phosphonate nucleotides 1a–c [1][2], 2a–d and 3a–d (Figure 1) have been reported. Prodrugs of

• thereof to an active site of a particular enzyme. The knowledge of the conformation of nucleosides, nucleotides and their analogs is therefore essential for the understanding or even prediction of their biological properties. There are several approaches providing information on the conformation of a five

• minima by plotting the calculated energy against phase angle P (Figure 13). The curves in Figure 13 proved a two-state equilibrium used as a prerequisite in PSEUROT-based programs and known for furanose conformation in natural nucleosides and nucleotides. The two energy minima were then fully optimized

Facile synthesis of 1-alkoxy-1H-benzo- and 7-azabenzotriazoles from peptide coupling agents, mechanistic studies, and synthetic applications

• Mahesh K. Lakshman,
• Manish K. Singh,
• Mukesh Kumar,
• Raghu Ram Chamala,
• Vijayender R. Yedulla,
• Domenick Wagner,
• Evan Leung,
• Lijia Yang,
• Asha Matin and
• Sadia Ahmad

Beilstein J. Org. Chem. 2014, 10, 1919–1932, doi:10.3762/bjoc.10.200

• appeared implausible on the basis of prior observations, where no reaction of BOP with the free hydroxy groups of nucleosides was observed [23][25]. Our recent work on a two-step one-pot etherification of purine nucleosides, quinazoline, and pyrimidines, had led some interesting preliminary observations

• ]. Compounds 3a,b and 5a,b shown in Scheme 5 are both N-substituted benzotriazoles and, upon appropriate folding of the aliphatic chain, they resemble acyclic nucleosides (3a,b) and ribonucleosides (5a,b). Reaction of Bt-OTs and At-OTs with 1,3-propanediol gave products 3a and 3b, arising from reaction at one

Syntheses of ¹⁵N-labeled pre-queuosine nucleobase derivatives

• Jasmin Levic and
• Ronald Micura

Beilstein J. Org. Chem. 2014, 10, 1914–1918, doi:10.3762/bjoc.10.199

• . Keywords: heterocycles; ligands; nucleic acids; nucleobases; nucleosides; pyrrolopyrimidinones; Introduction The small pyrrolo[2,3-d]pyrimidine 7-(aminomethyl)-7-deazaguanine is a natural product, also termed prequeuosine base (preQ1 base) [1][2]. This guanine derivative is involved in the complex

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

• Nico Rublack and
• Sabine Müller

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• the introduced terminal thiophosphate [18][19], or by chemical conversion of the 5'-terminal primary OH group into an amine or azide to be used for further conjugation with NHS-esters [20] or with alkynes [21]. Alternatively, natural and modified nucleosides can be attached to the 3'-terminus by the

• ], the 5'-OH group of tris-silylated nucleosides can be selectively removed by treatment with a THF/TFA/H2O mix (4:1:1, v/v/v) at 0 °C. Since cleavage of Boc-groups requires strong Brønsted acids [37][38][39], we varied the protocol of Zhu et al. with respect to the acid concentration and to reaction

Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc^en-T and iso-tricyclo-T nucleosides

• Branislav Dugovic,
• Michael Wagner and
• Christian J. Leumann

Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

• Branislav Dugovic Michael Wagner Christian J. Leumann Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland 10.3762/bjoc.10.194 Abstract We present the synthesis of the two novel nucleosides iso-tc-T and bcen-T, belonging to the bicyclo-/tricyclo

• -DNA molecular platform. In both modifications the torsion around C6’–C7’ within the carbocyclic ring is planarized by either the presence of a C6’–C7’ double bond or a cyclopropane ring. Structural analysis of these two nucleosides by X-ray analysis reveals a clear preference of torsion angle γ for

• of single modifications with nucleosides of the bicyclo-/tricyclo-DNA platform within deoxyoligonucleotides are not predictive for the stability of fully modified oligonucleotides. Keywords: DNA/RNA affinity; nucleic acids; nucleosides; oligonucleotides; oligonucleotide therapy; X-ray structures