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

• nucleic acids (PNAs), a lipophilic triphenylphosphonium (TPP) cation was attached to the N-terminal extremity of a PNA through a biodegradable carbamate linker containing a disulfide bridge (Scheme 4B) [20]. It was shown that such PNA conjugates entered cells rapidly and efficiently. Furthermore, a 16-mer

• facilitate their uptake, a TAT-peptide delivery domain was conjugated to the siRNNs via A-SATE phosphotriester groups. Hence, a chimeric passenger strand containing four A-SATE phosphotriesters duplexed with an RNN guide strand was conjugated to the delivery domain TAT peptides. The resulting conjugates

• noncytotoxic fashion. Next, the authors prepared conjugates of the siRNNs via one A-SATE phosphotriester with a hepatocyte-specific tris-N-acetylgalactosamine targeting domain and demonstrated a stronger RNAi response in mouse liver (following subcutaneous or intravenous administration) than the same

Synthesis and biological evaluation of RGD and isoDGR peptidomimetic-α-amanitin conjugates for tumor-targeting

• Lizeth Bodero,
• Paula López Rivas,
• Barbara Korsak,
• Torsten Hechler,
• Andreas Pahl,
• Christoph Müller,
• Daniela Arosio,
• Luca Pignataro,
• Cesare Gennari and
• Umberto Piarulli

Beilstein J. Org. Chem. 2018, 14, 407–415, doi:10.3762/bjoc.14.29

• C. Golgi, 19, I-20133, Milan, Italy Heidelberg Pharma Research GmbH, Schriesheimer Strasse 101, 68526, Ladenburg, Germany CNR, Istituto di Scienze e Tecnologie Molecolare (ITSM), Via C. Golgi, 19, 20133, Milan, Italy 10.3762/bjoc.14.29 Abstract RGD-α-amanitin and isoDGR-α-amanitin conjugates were

• synthesized by joining integrin ligands to α-amanitin via various linkers and spacers. The conjugates were evaluated for their ability to inhibit biotinylated vitronectin binding to the purified αVβ3 receptor, retaining good binding affinity, in the same nanomolar range as the free ligands. The

• antiproliferative activity of the conjugates was evaluated in three cell lines possessing different levels of αVβ3 integrin expression: human glioblastoma U87 (αVβ3+), human lung carcinoma A549 (αVβ3−) and breast adenocarcinoma MDA-MB-468 (αVβ3−). In the U87, in the MDA-MB-468, and partly in the A549 cancer cell

5-Aminopyrazole as precursor in design and synthesis of fused pyrazoloazines

• Ranjana Aggarwal and
• Suresh Kumar

Beilstein J. Org. Chem. 2018, 14, 203–242, doi:10.3762/bjoc.14.15

• al. [94] reported the synthesis of aminobenzothiazole linked pyrazolo[1,5-a]pyrimidine conjugates (benzothiazolyl derivatives, 136). Methyl-2,7-diphenylpyrazolo[1,5-a]pyrimidine-5-carboxylates, obtained by the reactions of 5-aminopyrazole 16 with aryl-β-diketoesters 133 in ethanol, were hydrolyzed in

Synthesis and spectroscopic properties of β-meso directly linked porphyrin–corrole hybrid compounds

• Baris Temelli and
• Hilal Kalkan

Beilstein J. Org. Chem. 2018, 14, 187–193, doi:10.3762/bjoc.14.13

• obtaining multiporphyrin arrays [7][8][9] that could stabilize only metal ions in a bivalent state. To overcome this limitation, porphyrin conjugates with different chromophore groups such as fullerene [10][11][12], BODIPY [13][14][15], corrole [16][17][18][19][20][21][22][23], phthalocyanine [24][25][26

• characters, high fluorescence quantum yields and favorable electronic properties. Porphyrin–corrole conjugates have been successfully used as donor–acceptor systems in photoinduced charge separation processes. It was shown that derivatives of these conjugates could be potentially used in photovoltaic

• applications [21][22][23]. In order to achieve rapid energy and electron transfer between macrocycles, the short distance between subunits keeps an important place. Therefore, two important factors affect the physical and electronic properties of porphyrin–corrole conjugates: (i) type of linkers and (ii

Recent applications of click chemistry for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles

• Vivek Poonthiyil,
• Thisbe K. Lindhorst,
• Vladimir B. Golovko and
• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 11–24, doi:10.3762/bjoc.14.2

• surface modification of AuNPs. In 2006, Brennan et al. demonstrated that enzyme–AuNP conjugates could be synthesized by CuAAC [47]. Azide-functionalized AuNPs were first synthesized by treating standard 14 nm Cit-AuNPs [28] with an a queous solution of an azide-containing thiol ligand (Scheme 7). An

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• structure of Ecm1 which forms a substrate binding cleft rather than a pocket [94]. Vinylbenzyl-modified cap analogues (bearing the modification at either the N7 or N2-position) provided a platform for inverse electron-demand Diels–Alder reactions with tetrazine conjugates and for photo-click reactions using

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki and Wigury 101, 02-089 Warszawa, Poland 10.3762/bjoc.13.249 Abstract Fluorescent pyrene–linker–nucleobase (nucleobase = thymine, adenine) conjugates with carbonyl and hydroxy functionalities in the linker were synthesized and

• compounds. The conjugates bearing a carbonyl function represent weak emitters as compared to compounds with a hydroxy function in the linker. The self-assembly properties of pyrene nucleobases were investigated in respect to their binding to single and double strand oligonucleotides in water and in buffer

• detecting markers [14], as fluorescent DNA probes [15], non-covalent binders to canonical oligonucleotide templates [16], and antiviral agents [17][18]. Notably, pyrene excimer formation in DNA template assemblies is much less efficient than in normal pyrene conjugates due to the helical twist between

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• ][91] or a peptide [92]. For example, TFEO-Pcs conjugated with peptides (15) have been reported [93]. A3B type TFEO-Pc was successfully condensed with peptides by palladium-catalyzed cross-coupling reactions in good yield (Scheme 5). These TFEO-Pc-peptide conjugates, which show a sharp Q band in the UV

• under Sonogashira cross-coupling conditions (Scheme 6). UV–vis absorption measurements suggested that the deoxyribonucleoside-linked TFEO-Pcs had a non-aggregation property, as expected. Unfortunately, it was also found that these conjugates gradually decomposed under light irradiation, so their

• application as an anticancer agent was discontinued. After that TFEO-ZnPc/cyclodextrin conjugates 18 were reported under similar conditions (Scheme 7) [100]. That study revealed that cyclodextrin-linked TFEO-Pcs have a non-aggregation property and sufficient water solubility, similar to the

Superstructures with cyclodextrins: Chemistry and applications IV

• Gerhard Wenz

Beilstein J. Org. Chem. 2017, 13, 2157–2159, doi:10.3762/bjoc.13.215

• insulin and lysozyme were also conjugated to the guest adamantane. The complexation of these conjugates by pegylated β-CD gives rise to superstructures which provide slow release and maintain full biological activity [21]. Significant progress was also achieved in the field of CD rotaxanes. A [3]-rotaxane

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• phosphodiester linkage upon ammonolytical deprotection. In other words, the ODNs were used as PEG-conjugates in biological studies. In addition, a bifunctionalized PEG, bearing the acid labile DMTrO group at one end and a base labile Fmoc-NH functionality at the other end, has been used as a soluble support to

• obtain oligonucleotide–PEG–peptide conjugates [55][56]. The Fmoc protecting group was first removed and the peptide was assembled on the exposed amino function. Since the peptide moiety did not contain acid labile side chain protections, the oligonucleotide sequence could then be assembled by the

BODIPY-based fluorescent liposomes with sesquiterpene lactone trilobolide

• Ludmila Škorpilová,
• Silvie Rimpelová,
• Michal Jurášek,
• Miloš Buděšínský,
• Jana Lokajová,
• Roman Effenberg,
• Petr Slepička,
• Tomáš Ruml,
• Eva Kmoníčková,
• Pavel B. Drašar and
• Zdeněk Wimmer

Beilstein J. Org. Chem. 2017, 13, 1316–1324, doi:10.3762/bjoc.13.128

• theranostic applications. Keywords: BODIPY conjugates; cancer targeting; drug delivery; liposomes; natural compounds; sesquiterpene lactone trilobolide; Introduction Targeted (smart) drug delivery is a method for specific delivering of an active compound preferentially to some cells or tissues in the human

• class, which causes cell death via depleting intracellular Ca2+ ion stores by the irreversible inhibition of sarco-/endoplasmic reticulum Ca2+-ATPase (SERCA) already at nanomolar concentrations [27][28][29][30]. In our recent study, we reported the localization of fluorescent Tb-BODIPY conjugates in the

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• recognition with the elucidation of glycosyl hydrolases mechanism by X-ray crystallography, but the scope of applications in glycobiology is much broader: it encompasses the range of glycan containing (macro)-molecules and their conjugates. The present article reviews the application of synchrotron radiation

An eco-compatible strategy for the diversity-oriented synthesis of macrocycles exploiting carbohydrate-derived building blocks

• Sushil K. Maurya and
• Rohit Rana

Beilstein J. Org. Chem. 2017, 13, 1106–1118, doi:10.3762/bjoc.13.110

• carbohydrate conjugates in which the heterocyclic triazolyl ring serves as a shackle for joining the carbohydrate building blocks. Further, these carbohydrate conjugates decorated with appropriate coupling partner can be paired through ring closing metathesis (RCM) reaction. Carrying out the metathesis

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• -antibiotic conjugates, were prepared and resulted able to overcome antibiotic resistance of microbial biofilms, since CA NPs render streptomycin more accessible to biofilms, thereby more available to interact with biofilm bacteria [89]. Similarly, a novel recyclable E.coli-specific killing GAuNP

Cyclodextrins tethered with oligolactides – green synthesis and structural assessment

• Cristian Peptu,
• Mihaela Balan-Porcarasu,
• Alena Šišková,
• Ľudovít Škultéty and
• Jaroslav Mosnáček

Beilstein J. Org. Chem. 2017, 13, 779–792, doi:10.3762/bjoc.13.77

• not asses their products whether these were CD-VL, CD-LA or CD-VL/LA covalent conjugates [19][20]. The results presented by the Harada group generally evaluated the CD-oligoester samples by matrix-assisted laser desorption ionization mass spectrometry (MALDI–MS) and nuclear magnetic resonance (NMR

• The properties of cyclodextrin-oligoester covalent conjugates, situated at the border of low and high molecular weight compounds can be influenced by both the carbohydrate and the oligoester components. The properties of such materials like solubility, miscibility with other materials, inclusion

• spectroscopy. Liquid chromatography and tandem MS fragmentation studies [21][22][23] are also important additions in deeper structural characterization of CD-oligoester conjugates. The L-LA was reacted with α-, β- and γ-CD (Scheme 1) in bulk at 110 °C in order to ensure a good dispersion of reactants. The

Pd- and Cu-catalyzed approaches in the syntheses of new cholane aminoanthraquinone pincer-like ligands

• Nikolay V. Lukashev,
• Gennadii A. Grabovyi,
• Dmitry A. Erzunov,
• Alexey V. Kazantsev,
• Gennadij V. Latyshev,
• Alexei D. Averin and
• Irina P. Beletskaya.

Beilstein J. Org. Chem. 2017, 13, 564–570, doi:10.3762/bjoc.13.55

• transport of anions through lipid membranes [19][20][21][22]. Some of similar pincer compounds can be used as receptors for organic molecules; e.g., polyamino derivatives based on cholane skeleton can form complexes with amino acids [23] and pincer-like conjugates of deoxycholic acid and aminopyrene can

Novel β-cyclodextrin–eosin conjugates

• Gábor Benkovics,
• Damien Afonso,
• András Darcsi,
• Szabolcs Béni,
• Sabrina Conoci,
• Éva Fenyvesi,
• Lajos Szente,
• Milo Malanga and
• Salvatore Sortino

Beilstein J. Org. Chem. 2017, 13, 543–551, doi:10.3762/bjoc.13.52

• using the coupling agent 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride. The molecular conjugates, well soluble in aqueous medium, were extensively characterized by 1D and 2D NMR spectroscopy and mass spectrometry. Preliminary spectroscopic investigations showed that the β

• available hydroxy groups of the CD and the carboxylic acid group of the dye [21]. These conjugates, however, cannot be used in biomedical applications because of the lability of the ester bond towards enzymatic degradation. Any cleavage of the conjugate would result in an increased free dye concentration in

• from the literature [27][28], to the best of our knowledge Eo–CD conjugates have not been prepared up to date. Results and Discussion Synthesis of eosin Y (EoY, 2) and eosin B (EoB, 4) The purity of the commercially available dyes eosin Y and eosin B, purchased from different providers (two different

Synthesis and evaluation of anti-oxidant and cytotoxic activities of novel 10-undecenoic acid methyl ester based lipoconjugates of phenolic acids

• Naganna Narra,
• Shiva Shanker Kaki,
• Rachapudi Badari Narayana Prasad,
• Sunil Misra,
• Koude Dhevendar,
• Venkateshwarlu Kontham and
• Padmaja V. Korlipara

Beilstein J. Org. Chem. 2017, 13, 26–32, doi:10.3762/bjoc.13.4

• acids have been derivatized with other functionalities apart from esters. The reported compounds other than esters were amides where bioconjugates of fatty acids and amino acids were prepared and evaluated for their anti-oxidant activity by a DPPH radical assay [9]. In view of developing new conjugates

Biomimetic synthesis and HPLC–ECD analysis of the isomers of dracocephins A and B

• Viktor Ilkei,
• András Spaits,
• Anita Prechl,
• Áron Szigetvári,
• Zoltán Béni,
• Miklós Dékány,
• Csaba Szántay Jr,
• Judit Müller,
• Árpád Könczöl,
• Ádám Szappanos,
• Attila Mándi,
• Sándor Antus,
• Ana Martins,
• Attila Hunyadi,
• György Tibor Balogh,
• György Kalaus (†),
• Hedvig Bölcskei,
• László Hazai and
• Tibor Kurtán

Beilstein J. Org. Chem. 2016, 12, 2523–2534, doi:10.3762/bjoc.12.247

• conjugates of racemic naringenin ((±)-1) with pyrrolidine-2-one with C-6–C-5” and C-8–C-5” linkage, respectively. Due to the two chirality centers, four possible stereoisomers exist for each regioisomer, and accordingly, the isolated substances were verified to be 1:1 mixtures of two diastereoisomeric

• –pyrrolidone conjugates is proposed by Leete [3] and Tanaka et al. [4] to proceed via an acylaminocarbinol intermediate, which presumably arises through the Strecker-degradation of the corresponding amino acids, which is L-glutamine (4) in the case of dracocephins A and B as shown in Scheme 1. The spontaneous

Thiophene-forming one-pot synthesis of three thienyl-bridged oligophenothiazines and their electronic properties

• Dominik Urselmann,
• Konstantin Deilhof,
• Bernhard Mayer and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2016, 12, 2055–2064, doi:10.3762/bjoc.12.194

• [53][54][55] substituted (oligo)phenothiazines. Their pronounced reversible oxidation potentials, their electro- and photochromicity [56], and their luminescence [57][58] have rendered (oligo)phenothiazines interesting candidates as donors in donor–acceptor conjugates with photo-induced electron

• magnitude of the oscillator strengths f, corresponding with significant decadic molar extinction coefficients of the associated bands (Figure 5). In principle these phenothiazine conjugates can be considered as donor–acceptor–donor systems, a topology that can be favorably developed further in molecular

Synthesis and NMR studies of malonyl-linked glycoconjugates of N-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries

• Markus Nörrlinger,
• Sven Hafner and
• Thomas Ziegler

Beilstein J. Org. Chem. 2016, 12, 1939–1948, doi:10.3762/bjoc.12.183

• 2:1 which was in accordance with similar rotamers described in literature [22]. Hereupon, we report on our investigations concerning the structures of the fully protected conjugates 1 and 4 for the rotamers of which around the C–N bond we calculated the respective ΔG‡r-values. Results and Discussion

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

• conditions [4][5][6]. The CuAAC reaction has found broad application in the preparation of peptide-conjugates [7][8], multicomponent syntheses [9], preparation of hydrogels, microgels and nanogels [10], (anion) supramolecular chemistry [11][12], in medicinal chemistry [13], therapeutics, biomaterials and

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• synthesis of conjugates of pyrrole–imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple

• helices by TFO-MGB conjugates was evaluated by gel-shift experiments. The presence of MGB in these conjugates did not affect the binding parameters (affinity and triplex stability) of the parent TFOs. Keywords: binding affinity; click chemistry; Cu(I)-catalyzed azide–alkyne cycloaddition; pyrrole

• (>10–12 base pairs) that results in promiscuous binding events. To resolve the mentioned problems, a chemical conjugation of several DNA-binding ligands (TFOs, MGBs) was used in order to profit from useful properties of both components in the resulting TFO-MGB conjugates [10][11] and MGB tandems [12

Artificial Diels–Alderase based on the transmembrane protein FhuA

• Hassan Osseili,
• Daniel F. Sauer,
• Klaus Beckerle,
• Marcus Arlt,
• Tomoki Himiyama,
• Tino Polen,
• Akira Onoda,
• Ulrich Schwaneberg,
• Takashi Hayashi and
• Jun Okuda

Beilstein J. Org. Chem. 2016, 12, 1314–1321, doi:10.3762/bjoc.12.124

• proteins [15]. Conclusion Herein, we report the synthesis of Cu(I) NHC and Cu(II) terpyridyl complexes equipped with a maleimide moiety which underwent covalent conjugation at the cysteine residue 545 of the transmembrane protein FhuAΔCVFtev. These biohybrid conjugates were analyzed by CD spectroscopy

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

• developed covering all aspects of medicine. Among them, lipid drug conjugates (LDC) were especially developed for the delivery of hydrophilic drugs by covalent coupling with lipid components [3][4]. In this context we recently found that the chemical conjugation of squalene, a natural and biocompatible