1,2,3-Triazoles as leaving groups: S_NAr reactions of 2,6-bistriazolylpurines with O- and C-nucleophiles

• Dace Cīrule,
• Irina Novosjolova,
• Ērika Bizdēna and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 410–419, doi:10.3762/bjoc.17.37

• temperatures to be completed. Among the widely studied 1,2,3-triazolyl nucleoside conjugates [57][58], the synthesis of 2-triazolylpurine derivatives containing a designed substituent at C6 has been little discussed. 6-N-Substituted purines have been the most studied [11][59][60][61][62], but 6-S- [14][63] or

• ) were inert in SNAr reactions with 2,6-bistriazolylpurines and their attempted reactions resulted in an unidentifiable mixture of byproducts. The following experiments were performed on 2,6-bistriazolylpurine nucleoside 2b in MeOH, EtOH and PrOH used as solvents and nucleophiles in the presence of NaH

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

• 14 resulted in the formation of alcohol 22, which was then reacted with nucleoside analogs via a Mitsunobu reaction to generate the racemic difluorinated carbocyclic homonucleoside analogs 23 and 24 in good yields. (Triphenylphosphonio)difluoroacetate (PDFA, Ph3P+CF2CO2−) as a difluorocarbene source

1,2,3-Triazoles as leaving groups in S_NAr–Arbuzov reactions: synthesis of C6-phosphonated purine derivatives

• Kārlis-Ēriks Kriķis,
• Irina Novosjolova,
• Anatoly Mishnev and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 193–202, doi:10.3762/bjoc.17.19

• . Keywords: Arbuzov reaction; 2,6-bistriazolylpurines; nucleophilic aromatic substitution; purinylphosphonates; Introduction Acyclic nucleoside phosphonates (ANPs) are an important compound class due to their biological activity profile [1][2][3][4][5][6]. Compounds bearing a phosphonate moiety in their N9

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• biological applications. Review Nucleoside triphosphates detection Nucleoside triphosphates play crucial roles in several biological processes including energy transduction, cellular respiration, enzyme catalysis, and signaling [35][36][37][38]. They are the most targeted anionic species because of their

• ubiquitous presence in biological systems. Schmuck and co-workers reported a tweezer type peptide-based probe 1 for fluorescence detection of nucleoside triphosphates in aqueous media (Figure 2) [39]. The probe 1 consists of an environment-sensitive amino-naphthalimide fluorophore having two symmetric

• , UMP, TBAP, MMP or other anions (SO42−, NO3−, HCO3−, CH3COO−) does not show any enhancement of fluorescence enabling the probe as selective for nucleoside triphosphates. The probe 1 is not toxic and has been demonstrated by fluorescence imaging of ATP in HeLa cells (Figure 2A, inset). Nucleic acid

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• versatility. The metal-mediated base pair chosen for this study is based on the artificial imidazole 2’-deoxyribonucleoside (Im). This nucleoside is well known to form highly stabilizing Ag(I)-mediated Im–Ag(I)–Im base pairs (Figure 1) [30][31][32][33] and has already been proposed for a use in various

• phosphoramidite-protected imidazole nucleoside as required for automated DNA solid-phase synthesis was synthesized as previously reported [30]. The oligonucleotides were synthesized on a DNA/RNA synthesizer H-8 (K&A Laborgeräte) using standard protocols for automated solid-phase synthesis (coupling time: 1000 s

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• being preferentially formed. Optimization of the protection scheme lead to a new and economic route to the desired C8-alkynylated building block and its incorporation in RNA. Keywords: nucleoside chemistry; protecting groups; RNA synthesis; Sonogashira reaction; Introduction Oligoribonucleotides

• for 5’- or 3’-terminal attachment of a desired functionality, nucleoside derivatives that, upon site-specific incorporation at a pre-determined position of RNA, can be used for post-synthetic conjugation, are required. A number of chemistries are available to specifically attach a molecular entity to

• halide to iodine, taking into account that direct iodination of purines has been claimed being troublesome [26], although not impossible [27]. For C8-iodination of adenosine, first the hydroxy groups at the sugar moiety were protected with tert-butyldimethylsilyl (TBDMS) groups. The silylated nucleoside

Asymmetric Mannich reactions of (S)-N-tert-butylsulfinyl-3,3,3-trifluoroacetaldimines with yne nucleophiles

• Ziyi Li,
• Li Wang,
• Yunqi Huang,
• Haibo Mei,
• Hiroyuki Konno,
• Hiroki Moriwaki,
• Vadim A. Soloshonok and
• Jianlin Han

Beilstein J. Org. Chem. 2020, 16, 2671–2678, doi:10.3762/bjoc.16.217

• contains the trifluoromethylpropargylamine moiety and has been developed as the inhibitor against non-nucleoside reverse transcriptase for the treatment of human immunodeficiency virus [27] (Figure 1). Thus, the development of synthetic methods for the preparation of these compounds, featuring

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• ; purine nucleoside phosphorylases; recombinant E. coli uridine; thymidine; Introduction Diverse variants of enzymatic syntheses of nucleosides using nucleoside phosphorylases as biocatalysts have been repeatedly described in original studies and discussed in a number of recent reviews (see, e.g., [1][2

• ][3][4][5][6][7][8][9][10][11][12][13][14][15]). In the late forties and early fifties of the last century, α-ᴅ-pentofuranose-1-phosphates (PF-1Pis) were isolated from the phosphorolysis of natural nucleosides catalyzed by nucleoside phosphorylases and their structures and enzymatic reactions with

• heterocyclic bases were studied in detail [16][17][18][19][20]. The transglycosylation reaction, that is the transfer of a carbohydrate fragment from a nucleoside donor to another heterocyclic base acceptor, was discovered by Kalckar in 1945 [16] (for reviews of pioneering works, see [17][18]). In a brief

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• conditions. There are a few thorough studies on this reaction with pyrimidine and purine nucleoside bases and their derivatives which are most closely related to fluorine-containing substrates 1 [40][41][42]. However, considering the high sensitivity and capricious nature of CEL reaction, we wish to report

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• biological and physiological properties and can enhance the half-life of drugs in vivo [1][2][3][4]. During the last decade, fluorinated nucleoside analogues have received increasing interest, as is illustrated by the two pharmaceutical leads gemcitabine (I) and sofosbuvir (II), potent anticancer or

• antiviral agents, respectively (Figure 1) [5][6]. The field of acyclonucleotides (ACN) has been explored less, however, the introduction of fluorine atoms showed remarkable effects. The most representative examples are phosphate analogues such as the nucleoside phosphorylase inhibitor III and acyclic

• conformational changes [11][12][13]. For the latter, nucleoside analogues (Figure 2, VI) containing a trans-butenyl moiety where the endocyclic C–O bond was replaced by a C=C bond are recognized by kinases as dUMP surrogate (V) [11]. However, there is no existing data for the corresponding fluoroalkene (VII), as

Recent synthesis of thietanes

• Jiaxi Xu

Beilstein J. Org. Chem. 2020, 16, 1357–1410, doi:10.3762/bjoc.16.116

• of anal gland secretions of the stoat [1] and the ferret [2]. Some pharmaceutical and biological thietane-containing compounds include thiaanalogue thietanose nucleosides 1 and 2 [3][4], and the spiroannulated glyco-thietane nucleoside 3 [5] of the antiviral (anti-HIV and HSV) drug oxetanocin A, the

• into two different dimesylated nucleosides. After the deprotection with Hg(OAc)2 in the presence of TFA, the dimesylated thiols 127 and 130 generated companied with the thietane-fused nucleoside 128 in one case. Further the treatment of the dimesylated thiols 127 and 130 with DBU gave rise to the

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• -protected acid 120 in good yield. Finally, removal of the Boc group then generated the free amino acid (3R)-3-fluoro-ʟ-phenylalanine (121) [64] (Scheme 27). Okuda’s group used 121 in the synthesis of a nucleoside that could be used to assess the transition state of a ribosome-catalyzed peptide-bond

Synthesis of 4-amino-5-fluoropyrimidines and 5-amino-4-fluoropyrazoles from a β-fluoroenolate salt

• Tobias Lucas,
• Jule-Philipp Dietz and
• Till Opatz

Beilstein J. Org. Chem. 2020, 16, 445–450, doi:10.3762/bjoc.16.41

• nucleoside analogues which can either act as antimetabolites or as nucleoside reverse transcriptase inhibitors (NRTIs). Two of the most common 5-fluoropyrimidines are the cytostatic 5-fluorouracil (1) [27] and the antimycotic prodrug 5-fluorocytosine (2) [28][29], which is also part of the anti-HIV agents

Extension of the 5-alkynyluridine side chain via C–C-bond formation in modified organometallic nucleosides using the Nicholas reaction

• Renata Kaczmarek,
• Dariusz Korczyński,
• James R. Green and
• Roman Dembinski

Beilstein J. Org. Chem. 2020, 16, 1–8, doi:10.3762/bjoc.16.1

• , N9B 3P4, Canada, Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309-4479, USA 10.3762/bjoc.16.1 Abstract Dicobalt hexacarbonyl nucleoside complexes of propargyl ether or esters of 5-substituted uridines react with diverse C-nucleophiles. Synthetic outcomes

• confirmed that the Nicholas reaction can be carried out in a nucleoside presence, leading to a divergent synthesis of novel metallo-nucleosides enriched with alkene, arene, arylketo, and heterocyclic functions, in the deoxy and ribo series. Keywords: alkynes; 5-alkynyluridines; C–C-bond formation; dicobalt

• hexacarbonyl complexes; Nicholas reaction; nucleosides; propargyl cation; Introduction Nucleoside analogs are molecules of high pharmacological interest for the treatment of various conditions, especially cancer and viral diseases [1][2][3][4][5]. The substitution at C-5 of the uracil nucleobase provides a

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

• that are unstable under acidic, basic and strongly nucleophilic conditions, many formidable challenges remain [2]. The reason is that during ODN synthesis using traditional technologies, the 5'-hydroxy group of nucleoside monomers is protected with the 4,4'-dimethoxytrityl (DMTr) group, which has to be

• , which was phosphitylated to give 3b. The dG phosphoramidite monomer 3c had to be synthesized using a slightly different procedure (Scheme 2). The amide function in the nucleobase in the silyl protected nucleoside 19 [45] was temporarily protected with TBSCl to give 20 [49]. This intermediate was not

• -(ethylthio)-1H-tetrazole as activator instead of the typically used acetic anhydride. Oxidation was performed under standard conditions. The last nucleotide at the 5'-end of ODN was incorporated with a 5'-trityl nucleoside phosphoramidite instead of a 5'-DMTr counterpart. At the end of the synthesis, the 5

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

• relevant building blocks with mechanochemistry has further been shown by the recent mechanochemical protocols to transform nucleoside and nucleotide substrates (Figure 1) [18][19]. On the other hand, reports on mechanochemical protocols for the synthesis or derivatization of lipids are scarce [20][21

An improved synthesis of adefovir and related analogues

• David J. Jones,
• Eileen M. O’Leary and
• Timothy P. O’Sullivan

Beilstein J. Org. Chem. 2019, 15, 801–810, doi:10.3762/bjoc.15.77

• the versatility of our approach. Keywords: acyclic nucleoside phosphonate; adefovir; alkylation; antiviral; N-alkylation; purine; Introduction The acyclic nucleoside phosphonate adefovir (1) [1], administered as its dipivoxil prodrug form (2) [2], is used clinically for the treatment of infections

• the synthesis of acyclic nucleoside phosphonates including mesylates [42], tosylates [16][43][44] and alkyl chlorides [45][46][47][48][49][50][51]. Alkylation reactions conducted with these electrophiles generally require higher temperatures. Furthermore, these reagents typically afford products in

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

• . Some structural modifications have been introduced to overcome the chirality problem, e.g., the methoxytetrahydropyranyl group suggested in 1970’s for a substitute of THP in nucleoside chemistry [4][5]. For protection of highly sensitive compounds acetone-based acetals can be applied. However, of these

• group of a nucleoside [7]. The acid lability of MIP is comparable to that of the dimethoxytrityl group (DMTr) that is frequently used to protect this position. The DMTr group works more or less perfectly in solid-phase synthesis, however, in solution-phase processes there are several cases where

• cleaving of DMTr fails. This is due to the equilibrium formed between the protected and deprotected compounds. During our search for a highly acid-labile protection for the 5’-hydroxy group of a nucleoside we noticed that neither the DMTr nor the MIP are fully satisfactory. Whereas MIP is easily removable

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

• for this type of molecules. Traditionally, fluorescent purine nucleoside analogs were recognized as valuable fluorescent probes for DNA and RNA research [17]. This paved a way for development of various adenosine and guanosine analogs which in many cases contained an additional substituent at C(8

• →4) followed by a SNAr process (4→5) which showcases the use of 1,2,3-triazoles as leaving groups. It is well established during our previous research in the purine nucleoside series that such an approach provides 6-amino-2-(1,2,3-triazol-1-yl) derivatives [25]. On the other hand, it was also

• and 7-deaza-7-ethenyl-2'-deoxyadenosine or 5-(azidomethyl)-2'-deoxyuridine, we can assume that nucleoside analogs bearing fluorophores of our type would be susceptible to metabolic phosphorylation and incorporation into DNA in the living cells. Further studies are required to develop the newly

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

• step would proceed through the formation of an orthoester intermediate G (Figure 4) which Nam would subsequently attack. The removal of the benzoyl groups in 1 M methanolic ammonia was conducted at −15 °C for 4 days to afford the nucleoside NR+Cl− in the rather low yield of 34% with −37°. This optical

• also attempted to use the newly discovered reaction for the synthesis of N-alkyl-nicotinamide ribosides by reaction of 17 with alkylamines in methanol at 4 °C. However, these amines promoted the decomposition of the nucleoside and cleavage of the glycosidic bond, as the major products were the

• enzymatic synthesis of NR+ from α-D-ribose-1-phosphate and Nam by catalysis with purine nucleoside phosphorylase and sucrose phosphorylase is described in a US patent application by Velasquez et al. [46]. In the NMR experiments, the authors demonstrated the preparation of NR+ but did not isolate pure NR+. 3

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

• -DNA (6’-diF-bc4,3-DNA). The difluorinated thymidine phosphoramidite building block was synthesized starting from an already known gem-difluorinated tricyclic glycal. This tricyclic siloxydifluorocyclopropane was converted into the [4.3.0]bicyclic nucleoside via cyclopropane ring-opening through the

• addition of an electrophilic iodine during the nucleosidation step followed by reduction. The gem-difluorinated bicyclic nucleoside was then converted into the corresponding phosphoramidite building block which was incorporated into oligonucleotides. Thermal denaturation experiments of these

• oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was

New standards for collecting and fitting steady state kinetic data

• Kenneth A. Johnson

Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2

• the alternate substrates are well known. Moreover, it is easy to perform single turnover kinetic measurements to examine steps leading up to the chemical reaction by mixing an enzyme DNA complex with only one nucleoside triphosphate. Recent work on DNA polymerase fidelity has shown that the rate 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

• = −1.5 to −3.7 °C). Molecular dynamics simulation on the nucleoside and oligonucleotide level revealed the preference of the C1’-exo/C2’-endo alignment of the furanose ring. Moreover, the simulation of duplexes with complementary RNA disclosed a DNA/RNA-type duplex structure suggesting that this

• spectra (Supporting Information File 1). The plan for the pyrimidine nucleoside synthesis comprised the use of the meanwhile well-established β-selective N-iodosuccinimide (NIS)-mediated addition of a persilylated nucleobase to a tricyclic glycal [43][45][53][54]. Therefore, the gem-difluorinated

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

• Organische Chemie, Universität Münster, Corrensstrasse 40, 48149 Münster, Germany 10.3762/bjoc.14.217 Abstract Copper(I)-promoted "click" cyclization in the presence of TBTA afforded nucleoside macrocycles in very high yields (≈70%) without using protecting groups. To this end, dU and dC derivatives

• ’-azido-2’,5’-dideoxycytidine 2. Earlier, the nucleoside precursor 1 was used for DNA cross-linking and labelling [36]. The unprotected nucleoside 1 was treated with equimolar amounts of carbon tetrabromide and triphenylphosphine and a five-fold excess of sodium azide to obtain the azide derivative 2 (37

• reaction the use of the TBTA complex was essential for the cyclization of dC precursor 2 but not for dU precursor 7. Protection of precursor molecules is not required and only four steps are necessary to convert a nucleoside in a nucleoside macrocycle. The single crystal X-ray structure confirmed the click

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173