Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• , or the design of self-inclusion complexes, in which an outer cavity-attached rhodamine was intramolecularly bound in the CB7 cavity. As an alternative, it has been previously suggested that host-assisted protonation of a cavity-binding functional moiety (an “anchor group”) and a suitably attached

• the diffusion coefficient of the 2•CB7 complex in comparison to the free 2 dye. FCS autocorrelation curves (Figure 6) were analysed to obtain the diffusion times tdiff of 2 and the 2•CB7 complex and then converted into diffusion coefficients D using the reported standard rhodamine 6G (D = 2.80 × 10−6

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• targeting sequences alone (Figure 4). Rádis-Baptista et al. recently reported about the effective uptake of rhodamine B-labeled NrTP in different tumor cell lines [3][27]. Within their studies, the authors used higher concentrations, longer incubation times and other cell lines, what could probably explain

Development of a fluorogenic small substrate for dipeptidyl peptidase-4

• Futa Ogawa,
• Masanori Takeda,
• Kanae Miyanaga,
• Keita Tani,
• Ryuji Yamazawa,
• Kiyoshi Ito,
• Atsushi Tarui,
• Kazuyuki Sato and
• Masaaki Omote

Beilstein J. Org. Chem. 2017, 13, 2690–2697, doi:10.3762/bjoc.13.267

• proceed at a low concentration of DPP-4 (0.07 μg/mL). These results suggest that H-Gly-Pro-1 could be used as an OFF–ON-type fluorogenic substrate for enzymatic reactions of DPP-4, with release of 1 as a fluorophore. In comparison with existing fluorogenic substrates containing rhodamine fluorophore, non

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• ), trypsin-catalyzed conversion of a rhodamine substrate (S) to a fluorescent product (P) in the presence of a strong inhibitor (soybean trypsin inhibitor, STI), and trypsin-catalyzed fragmentation of a polycation (in purple) in the presence of a polyanion (in cyan). Adapted with permission from [94

Membrane properties of hydroxycholesterols related to the brain cholesterol metabolism

• Malte Hilsch,
• Ivan Haralampiev,
• Peter Müller,
• Daniel Huster and
• Holger A. Scheidt

Beilstein J. Org. Chem. 2017, 13, 720–727, doi:10.3762/bjoc.13.71

• known for the formation and coexistence of lateral disordered (ld) and ordered (lo) domains. The domain structure was visualized by labeling the membrane with the ld marker 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (ammonium salt) (N-Rh-DOPE) and recording z-stacks

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

• -yl)-4-methylmorpholinium chloride (DMTMMCl), a coupling reagent frequently used in peptide synthesis. Malanga et al. recently reported on the preparation of xanthene-dye-appended CDs with the most commonly used fluorescent probes rhodamine and fluorescein (Flu, 1). The conjugation of the 6-monoamino

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• protein reactive groups, which have been reported to exhibit selectivity for active site cysteines [19] (Supporting Information File 1, Figure S1). Each probe was equipped with a terminal alkyne handle for in-gel analysis by fluorescence tagging via click chemistry with a corresponding rhodamine azide

• Escherichia coli BL21 followed by affinity purification by an ÄKTA chromatography system equipped with a StrepTrap HP column. The individual probes were incubated with purified PqsD for 30 min and a rhodamine fluorescent reporter tag was appended by click chemistry. The remaining non-covalently bound probe

• probe CA2. Library of HHQ and PQS analogues. Competitive profiling platform. A) Schematic representation of the competitive labelling strategy with an alkyne probe (green) and potential inhibitors (blue). Rh = rhodamine. B) Initial screening of our small library of HHQ (1–9) and PQS (10–16) analogues

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

• increase P-gp inhibitory activity [18]. Based on the unaltered accumulation of rhodamine 123, a P-gp substrate fluorescent dye, in the P-gp transfected L5178MDR cells, we observed that none of the synthesized compounds inhibits this transporter. The antioxidant activity of dracocephins A and B was also

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

• , the use of fluorescent probes requires the covalent binding of large dye molecules (bodipy, cyanine, rhodamine etc, ...) to the drug conjugate, thus potentially modifying its physicochemical profile as well as the in vivo fate and the pharmacological activity. A simple encapsulation of an amphiphilic

New synthetic strategies for xanthene-dye-appended cyclodextrins

• Milo Malanga,
• Andras Darcsi,
• Mihaly Balint,
• Gabor Benkovics,
• Tamas Sohajda and
• Szabolcs Beni

Beilstein J. Org. Chem. 2016, 12, 537–548, doi:10.3762/bjoc.12.53

• inexpensive dyes, we prepared rhodamine- and fluorescein-appended cyclodextrins. The compounds were characterized by NMR and IR spectroscopy and MS spectrometry, their UV–vis spectra were recorded at various pH, and their purity was determined by capillary electrophoresis. Two potential models for the

• supramolecular assembly of the xanthene-dye-appended cyclodextrins were developed based on the set of data collected by the extensive NMR characterization. Keywords: DMT-MM; fluorescein; rhodamine; supramolecular assembly; Introduction Cyclodextrins (CDs) are cyclic oligosaccharides consisting of 6, 7 or 8

• representatives of this class are fluorescein and rhodamine (Figure 1), which have been applied as chemosensors [4] and have been widely exploited in various areas such as cell biology, microscopy, biotechnology, and ophthalmology due to their versatile photophysical properties. However, the chemical modification

Synthesis and spectroscopic properties of β-triazoloporphyrin–xanthone dyads

• Dileep Kumar Singh and
• Mahendra Nath

Beilstein J. Org. Chem. 2015, 11, 1434–1440, doi:10.3762/bjoc.11.155

• –tetrathiafulvalenes [14], porphyrin–cyanines [15], porphyrin–carotenes [16], porphyrin–arene diimide [17] and porphyrin–fluorocene or rhodamine [18] have also been synthesized in which the porphyrin unit acts as an electron acceptor. Recently, the 1,2,3-triazole scaffold has been successfully employed to connect

Potential of acylated peptides to target the influenza A virus

• Daniel Lauster,
• Damian Pawolski,
• Julian Storm,
• Kai Ludwig,
• Rudolf Volkmer,
• Henry Memczak,
• Andreas Herrmann and
• Sumati Bhatia

Beilstein J. Org. Chem. 2015, 11, 589–595, doi:10.3762/bjoc.11.65

• synthesized the s2s construct with a terminal rhodamine fluorophore. This compound was mixed with DOPC giant unilamellar vesicles (GUV) or human erythrocytes. In both cases clear membrane labeling could be detected (Figure 6). To assess how strong membrane incorporation of these peptides can perturb membranes

• for 24 h at 37 °C. Error bars indicate the standard deviation of three experiments. Fluorescence microscopy images of GUVs (left) and human erythrocytes (right) after incubation with C18-s2s-TAMRA. The overlap of DIC and rhodamine channels demonstrate the labeling of membranes by the fluorescent

Synthetic strategies for the fluorescent labeling of epichlorohydrin-branched cyclodextrin polymers

• Milo Malanga,
• Mihály Bálint,
• István Puskás,
• Kata Tuza,
• Tamás Sohajda,
• László Jicsinszky,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3007–3018, doi:10.3762/bjoc.10.319

• prepared either in well water-soluble form or as gels of high swelling. Two versatile synthetic strategies for introducing a fluorescent tag (rhodamine, fluorescein, nitrobenzofuran or coumarin) into the water-soluble epichlorohydrin branched cyclodextrin polymers were worked out and compared. The

• techniques and capillary electrophoresis. The applied synthetic routes were evaluated based on the molecular weight, cyclodextrin content of the products and the efficiency of labeling. Keywords: coumarin; fluorescein; functionalized monomers and polymers; nitrobenzofurazan; rhodamine; Introduction

• , we report the controlled, regioselective fluorescent labeling of neutral and cationic epichlorohydrin branched β-CD polymer with four different dyes (rhodamine, fluorescein, coumarin and nitrobenzofurazan). Our goal was the development of versatile synthetic strategies, yielding key intermediates of

Visible-light photoredox catalyzed synthesis of pyrroloisoquinolines via organocatalytic oxidation/[3 + 2] cycloaddition/oxidative aromatization reaction cascade with Rose Bengal

• Carlos Vila,
• Jonathan Lau and
• Magnus Rueping

Beilstein J. Org. Chem. 2014, 10, 1233–1238, doi:10.3762/bjoc.10.122

• Rhodamine B or Eosin Y were less efficient compared to Rose Bengal (Table 1, entries 2 and 3, respectively). Several solvents were tested without an improvement in the yield of the product (Table 1, entries 4–9). Finally, after tuning the relative amounts of the reagents, the product 3aa was isolated in 76

Metal and metal-free photocatalysts: mechanistic approach and application as photoinitiators of photopolymerization

• Jacques Lalevée,
• Sofia Telitel,
• Pu Xiao,
• Marc Lepeltier,
• Frédéric Dumur,
• Fabrice Morlet-Savary,
• Didier Gigmes and
• Jean-Pierre Fouassier

Beilstein J. Org. Chem. 2014, 10, 863–876, doi:10.3762/bjoc.10.83

• , potential toxicity and limited availability of these structures, metal-free organic dye compounds (e.g., Eosin-Y, Nile Red, Alizarine Red S, perylene derivative or Rhodamine B etc.) were recently proposed for cooperative asymmetric organophotoredox catalysis [13][14]. Photoredox catalysis was then

Synthesis and biological activities of the respiratory chain inhibitor aurachin D and new ring versus chain analogues

• Xu-Wen Li,
• Jennifer Herrmann,
• Yi Zang,
• Philippe Grellier,
• Soizic Prado,
• Rolf Müller and
• Bastien Nay

Beilstein J. Org. Chem. 2013, 9, 1551–1558, doi:10.3762/bjoc.9.176

• TMRM and imaged in the rhodamine channel at 200× magnification. Synthesis of aurachin D (4) and geranyl (9), prenyl (10) and methyl (11) analogues. Strategy toward the heterocyclic core of aurachin H. Synthesis of aurachin D analogues with aromatic variations. Cytotoxicity tests on HCT-116 human colon

Synthesis and spectroscopic properties of 4-amino-1,8-naphthalimide derivatives involving the carboxylic group: a new molecular probe for ZnO nanoparticles with unusual fluorescence features

• Laura Bekere,
• David Gachet,
• Vladimir Lokshin,
• Wladimir Marine and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2013, 9, 1311–1318, doi:10.3762/bjoc.9.147

• -photon absorption spectrum with that of rhodamine B (RhB) in methanol, and by normalizing by its quantum yield. The values for RhB found in the literature have been determined with the same typical pulse duration of about 150 fs [19]. Methyl 4-(6-chloro-1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)benzoate

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates

• Hao Xu,
• Hairat Sabit,
• Gordon L. Amidon and
• H. D. Hollis Showalter

Beilstein J. Org. Chem. 2013, 9, 89–96, doi:10.3762/bjoc.9.12

• hydrolase covalent inhibitor and from it have evolved analytical tools in which “handles“, such as biotin, rhodamine, and alkyne have been appended via a variety of linking chains [5][6][7][8]. These FP analogues have proven to be powerful tools in the profiling of complex proteome samples [9] and in the

• –biotin 1, a covalent serine hydrolases probe, to the study of enzyme substrates with high turnover. Discussion Fluorophosphonate probes with different analytical handles, such as rhodamine and alkyne, are being used to identify and characterize the in vivo proteome. Biotin-based probes that bind to

Peptoids and polyamines going sweet: Modular synthesis of glycosylated peptoids and polyamines using click chemistry

• Daniel Fürniss,
• Timo Mack,
• Frank Hahn,
• Sidonie B. L. Vollrath,
• Katarzyna Koroniak,
• Ute Schepers and
• Stefan Bräse

Beilstein J. Org. Chem. 2013, 9, 56–63, doi:10.3762/bjoc.9.7

• coupling sequence resulted in the peptoids, which were further modified with rhodamine B (Rho-CO2H) as an easily accessible and versatile fluorescent tag. Rhodamine B was coupled to the N-terminus in order to provide a label for future biological applications, such as the study of the cellular uptake. For

Chemical–biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target

• Jonathan W. Choy,
• Clifford Bryant,
• Claudia M. Calvet,
• Patricia S. Doyle,
• Shamila S. Gunatilleke,
• Siegfried S. F. Leung,
• Kenny K. H. Ang,
• Steven Chen,
• Jiri Gut,
• Juan A. Oses-Prieto,
• Jonathan B. Johnston,
• Michelle R. Arkin,
• Alma L. Burlingame,
• Jack Taunton,
• Matthew P. Jacobson,
• James M. McKerrow,
• Larissa M. Podust and
• Adam R. Renslo

Beilstein J. Org. Chem. 2013, 9, 15–25, doi:10.3762/bjoc.9.3

• conducted competition experiments in C2C12 cells. Hence, pre-incubation of cells with competitor compound at either 1 μM or 10 μM for one hour was followed by treatment for one hour with 9, followed by cell lysis, conjugation to 10, separation (SDS-PAGE), and detection by rhodamine fluorescence as before

• adducts of 9 were conjugated to rhodamide-based dye 10. The gel image at the top shows rhodamine fluorescence. The gel image at the bottom is of the coomassie stained gel. A successfully competed band is observed at ≈35 kDa, and this was subsequently identified as cathepsin B. MS/MS spectrum of the

Hydrophobic analogues of rhodamine B and rhodamine 101: potent fluorescent probes of mitochondria in living C. elegans

• Laurie F. Mottram,
• Safiyyah Forbes,
• Brian D. Ackley and
• Blake R. Peterson

Beilstein J. Org. Chem. 2012, 8, 2156–2165, doi:10.3762/bjoc.8.243

• . To provide new tools for imaging of mitochondria in vivo, we synthesized novel hydrophobic analogues of the red fluorescent dyes rhodamine B and rhodamine 101 that replace the carboxylate with a methyl group. Compared to the parent compounds, methyl analogues termed HRB and HR101 exhibit slightly red

• mitochondrial stains rhodamine 123, rhodamine 6G, and rhodamine B, as well as the structurally related fluorophores rhodamine 101, and basic violet 11, revealed that HRB and HR101 are the most potent mitochondrial probes, enabling imaging of mitochondrial motility, fusion, and fission in the germline and other

• ; fluorescence; fusion; imaging; in vivo; microscopy; mitochondria; model organisms; organelle; rhodamine; spectroscopy; Introduction Fluorescent molecular probes represent critical tools for studies of chemical biology [1]. These compounds allow the creation of sensitive enzyme substrates, sensors of a wide

Chemical modification allows phallotoxins and amatoxins to be used as tools in cell biology

• Jan Anderl,
• Hartmut Echner and
• Heinz Faulstich

Beilstein J. Org. Chem. 2012, 8, 2072–2084, doi:10.3762/bjoc.8.233

• cells Tetramethylrhodaminyl-phalloidin (Figure 6a) has been used to visualize actin fibers in fixed cells for 30 years. Here we show that the rhodamine residue also strongly enhanced cellular uptake, making this phalloidin derivative a tool for cell biology. With an IC50 value of 11 µM its toxicity is

• , albeit under toxic conditions. Using rhodamine-labeled phalloidin, we could also study how membrane-permeable peptides are incorporated into the cell. Immediately after exposure the toxin was located on the plasma membrane of the cells as shown by fluorescence microscopy (Figure 6c), while after 6 h

• increasing amounts of the toxin were found in endocytotic vesicles. After 24 h most of the rhodamine-labeled toxin was still in endosomes, while some of it had found its target, as concluded from the decoration of filaments. Phalloidin causes apoptosis of cells Under the microscope, cells treated with

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22