Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• fluorescent dye that is tethered to an acetyllysine-containing peptide. If the acetyl moiety of the fluorophore is enzymatically hydrolyzed by HDAC8, it will produce a strongly fluorescent signal at 360 nm. Table 1 shows the percentage of HDAC8 inhibition at 100, 10, and 1 µM concentration of the designed

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3’,2’-e]pyridines (BBZFPys)

• Ryo Takishima,
• Yuji Nishii,
• Tomoaki Hinoue,
• Yoshitane Imai and
• Masahiro Miura

Beilstein J. Org. Chem. 2020, 16, 325–336, doi:10.3762/bjoc.16.32

• fluorophore unit in certain light-emitting functional materials (Scheme 1) [14]. Meanwhile, organic optoelectronic materials with circularly polarized luminescence (CPL) characteristics have attracted significant research interests in recent years [18][19][20][21] for their potential applications in three

Preparation of anthracene-based tetraperimidine hexafluorophosphate and selective recognition of chromium(III) ions

• Qing-Xiang Liu,
• Feng Yang,
• Zhi-Xiang Zhao,
• Shao-Cong Yu and
• Yue Ding

Beilstein J. Org. Chem. 2019, 15, 2847–2855, doi:10.3762/bjoc.15.278

• paramagnetic nature of chromium(III) can cause fluorescence quenching of the fluorophore via the enhancement of spin–orbit coupling [30][31][32][33][34][35]. So far, only a few successful examples of fluorescence enhancement sensors for Cr3+ have been reported [36][37][38][39][40]. Thus, developing new and

• effective fluorescence turn-on chemosensors for Cr3+ is necessary. In the process of our research, a tetradentate compound bearing a fluorophore aroused our interest. In this paper, we report the synthesis of a novel anthracene-based tetraperimidine hexafluorophosphate 3, and its structure was determined by

Photoreversible stretching of a BAPTA chelator marshalling Ca²⁺-binding in aqueous media

• Aurélien Ducrot,
• Arnaud Tron,
• Robin Bofinger,
• Ingrid Sanz Beguer,
• Jean-Luc Pozzo and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2019, 15, 2801–2811, doi:10.3762/bjoc.15.273

• +, giving rise to a highly fluorescent species upon excitation at 485 nm. The fluorescence is greatly diminished after the addition of 10 equivalents of 1E, as the azobenzene macrocycle abstracts the Ca2+ ion from fluorophore 3. Upon irradiation of the ensemble at 365 nm at these low concentrations, a small

Emission solvatochromic, solid-state and aggregation-induced emissive α-pyrones and emission-tuneable 1H-pyridines by Michael addition–cyclocondensation sequences

• Natascha Breuer,
• Irina Gruber,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 2684–2703, doi:10.3762/bjoc.15.262

• alkynylation–Michael addition–cyclocondensation (AMAC) multicomponent syntheses of α-pyrones [23]. While most α-pyrones neither fluoresce in solution nor in the solid state specific substitution patterns have been identified for fluorophore design for this heterocyclic family. Tominaga and co-workers

Plasma membrane imaging with a fluorescent benzothiadiazole derivative

• Pedro H. P. R. Carvalho,
• Jose R. Correa,
• Karen L. R. Paiva,
• Daniel F. S. Machado,
• Jackson D. Scholten and
• Brenno A. D. Neto

Beilstein J. Org. Chem. 2019, 15, 2644–2654, doi:10.3762/bjoc.15.257

• design and synthesis of small organic fluorescence imaging probes capable of selectively stain plasma membranes has been proven, however, often as a challenging task. The development of small organic probes, in general, has been hindered by the requirement of multistep syntheses to obtain the fluorophore

• effects and the concentrations to use the probe without causing any harm to the cells (Figure 5). Only at concentrations up to 100 μM cytotoxic effects were noted and at 10 μM no effect was observed for the designed BTD-4APTEG. For the subsequent bioimaging experiments, the fluorophore was tested at 1 μM

• signal has then contributed to the image formation. Finally, the developed fluorophore was tested in additional cell lines to show its efficiency. A2780 (human ovarian carcinoma) cells, T47D (human breast tumor) cells and HUVEC (human umbilical vein endothelial) cells were tested and the results are

A new approach to silicon rhodamines by Suzuki–Miyaura coupling – scope and limitations

• Thines Kanagasundaram,
• Antje Timmermann,
• Carsten S. Kramer and
• Klaus Kopka

Beilstein J. Org. Chem. 2019, 15, 2569–2576, doi:10.3762/bjoc.15.250

• triflate, resulting in the corresponding xanthone [29]. Applying standard conditions on xanthone 12 by treatment with triflic anhydride in dry acetonitrile and subsequent addition of base, catalyst and boroxine 18b yielded the desired fluorophore 22 in 41% yield together with unreacted xanthone 12 (Table 1

• optimizations of the reaction conditions could lead to the silicon rhodamine 22 in moderate yields, an inseparable impurity of the cationic fluorophore was detected. After identifying this impurity as the tetraphenylphosphonium cation, we exchanged the triphenylphosphine ligand of the catalyst with dppf (1,1

• 24c only in traces (Table 2, entry 3). Usage of the tert-butyl-protected boronobenzoic acid 25a, or its boroxine counterpart 25b, respectively, gave fluorophore 25c suitable for later coupling reactions in reasonable yields of 43% and 53%, depending on the catalyst used (Table 2, entries 4 and 5

Probing of local polarity in poly(methyl methacrylate) with the charge transfer transition in Nile red

• Aydan Yadigarli,
• Qimeng Song,
• Sergey I. Druzhinin and
• Holger Schönherr

Beilstein J. Org. Chem. 2019, 15, 2552–2562, doi:10.3762/bjoc.15.248

• dipole moment can be determined from a plot of the fluorescence maxima of the studied fluorophore versus the fluorescence maxima of a standard fluorophore with known ground and excited dipole moments μgs and μes [38][39]. Application of Equation 1 to the spectra of the standard fluorophore and

• rearrangement in order to express solvent polarity function yields Then substitution of the solvent polarity function again into Equation 1 for the studied fluorophore gives a linear correlation (Equation 8) of νf and νfs The subscript s indicates values related to the above mentioned standard. In Equation 8

• , 2 and 4), see Table 2. Substitution of the polarity function (Equation 7), calculated with the reference fluorophore in Equation 2, gives the following relations between absorption maxima of NR and emission maxima of the dipole moment standard: With the slope of the linear function (10) The excited

Targeted photoswitchable imaging of intracellular glutathione by a photochromic glycosheet sensor

• Xianzhi Chai,
• Hai-Hao Han,
• Yi Zang,
• Jia Li,
• Xiao-Peng He,
• Junji Zhang and
• He Tian

Beilstein J. Org. Chem. 2019, 15, 2380–2389, doi:10.3762/bjoc.15.230

• precise outputs can be obtained for targeted analytes even at low concentrations. Though promising, common “photochromophore–fluorophore”-type sensors require elaborate designs to integrate multifunctionality (e.g., photoswitching, fluorescence sensing, targetability, water solubility, etc.) into one

• synthesis of dithienylethene fluorescence reporter Glyco-DTE is shown in Scheme 2. The dithienylethene derivative 3 was prepared by Suzuki coupling of dithienylethene 1 with methyl 4-bromobenzoate followed by hydrolysis with lithium hydroxide. The naphthalimide fluorophore 6 was synthesized through bromide

• 4 according to reported methods [27]. Then, the photochromic fluorophore intermediate 7 was synthesized by coupling compounds 3 and 6 through amidation. The Glyco-DTE reporter was prepared by click reaction between compound 7 and acetylated β-ᴅ-galactoside, followed by deacetylation. Similarly, a

Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement

• Jessica Matthias,
• Thines Kanagasundaram,
• Klaus Kopka and
• Carsten S. Kramer

Beilstein J. Org. Chem. 2019, 15, 2333–2343, doi:10.3762/bjoc.15.226

• restricted rotation of the xanthene pyridine bond. The 2-chloropyridinyl moiety in 15 is not only attractive because of its option for convenient fluorination, but also since its intrinsic targeting ability to acidic cellular compartments (such as the lysosomal-selective fluorophore 13). We assumed that our

• proposed bimodal fluorophore would show a better selectivity for mitochondria because of its more lipophilic nature (clogP for 15 3.712, for 16 3.142) compared to 13 (clogP 2.136). Medical imaging of mitochondrial activity is highly interesting for various indications, ranging from neurodegenerative and

Fluorescent phosphorus dendrimers excited by two photons: synthesis, two-photon absorption properties and biological uses

• Anne-Marie Caminade,
• Artem Zibarov,
• Eduardo Cueto Diaz,
• Aurélien Hameau,
• Maxime Klausen,
• Kathleen Moineau-Chane Ching,
• Jean-Pierre Majoral,
• Jean-Baptiste Verlhac,
• Olivier Mongin and
• Mireille Blanchard-Desce

Beilstein J. Org. Chem. 2019, 15, 2287–2303, doi:10.3762/bjoc.15.221

• exceptions [10] for specifically engineered fluorophores [11]. The main reason is that a single organic fluorophore having TPA properties cannot be as brilliant as a quantum dot, mostly based on its smaller size (or number of delocalized electrons). In view of this problem of brilliance, came the idea to

• generation from the N3P3Cl6 core [34], and up to the twelfth generation from the (S)PCl3 core [35]. Thus, to incorporate the TPA fluorophores on the surface, it should have one function being able to react with P–Cl (or aldehyde) functions. For the incorporation of a TPA fluorophore at the core, it should

• dendrimers functionalized with TPA fluorophores used a blue-emitting quadrupolar fluorophore based on a fluorene core [37][38][39][40][41] and functionalized by a phenol on one side. The synthesis was carried out from generation 1 (12 fluorophores) to generation 4 (96 fluorophores) (Scheme 2). The

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• highest affinity of this receptor was for acetate (Ka = 1.5 × 105 M−1) and dihydrogen phosphate (Ka = 4.5 × 104 M−1). Because of the excellent properties of perylene diimide (PDI) as a chromophore, fluorophore, or redox center, this unit has become increasingly popular in the construction of

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• cells, we synthesized a blue-emitting derivative employing a dansyl label. This fluorophore is convenient not only for its small size but also for its membrane permeability. Moreover, it was successfully used in other studies of visualizing other natural compounds [15][16][17]. The synthesis (Scheme 1

• partial co-localization also in mitochondria, in which SERCA is not present. Localization of a control (dansyl fluorophore) was not organelle-specific and the fluorescence intensity was very weak even at 2 µM concentration (Supporting Information File 1, Figure S18). Impact of compound 1 on cell viability

• study U-2 OS and MRC-5 cells (1·105 cells per well) were seeded on 35 mm glass bottom dishes for live-cell imaging (MatTek Corporation, USA) and left to adhere for 24 h. Then, the cells were washed with phosphate-buffered saline (PBS) and incubated with compound 5 or dansyl amide fluorophore (0.1–2.0 µM

Host–guest interactions in nor-seco-cucurbit[10]uril: novel guest-dependent molecular recognition and stereoisomerism

• Xiaodong Zhang,
• Wei Wu,
• Zhu Tao and
• Xin-Long Ni

Beilstein J. Org. Chem. 2019, 15, 1705–1711, doi:10.3762/bjoc.15.166

• , the top–center isomer of G2 within both host-1 and host-2 could be characterized because of the novel monomer and excimer photophysical property of pyrene as fluorophore. As a result, we demonstrated here a novel guest-controlled molecular recognition and stereoisomerism for the first time. Results

• the fluorescence emission spectra of G2 in the presence of host-1. As can be seen, free G2 produced typical monomer emissions at around 378 and 396 nm in aqueous solution (pH 2) upon excitation of the pyrene fluorophore at 340 nm. When we added host-1 at increasing concentrations to the G2 solution

Synthesis, enantioseparation and photophysical properties of planar-chiral pillar[5]arene derivatives bearing fluorophore fragments

• Guojuan Li,
• Chunying Fan,
• Guo Cheng,
• Wanhua Wu and
• Cheng Yang

Beilstein J. Org. Chem. 2019, 15, 1601–1611, doi:10.3762/bjoc.15.164

• assigned to the excimer emission of Py (Figure S23, Supporting Information File 1) [54]. Conclusion Two new planar chiral macrocyclic hosts P5A-DPA and P5A-Py were synthesized by grafting two fluorophore pigments (DPA or Py) on pillar[5]arene through CuAAC “click” reaction. The new macrocyclic compounds

Photochemical generation of the 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radical from caged nitroxides by near-infrared two-photon irradiation and its cytocidal effect on lung cancer cells

• Ayato Yamada,
• Manabu Abe,
• Yoshinobu Nishimura,
• Shoji Ishizaka,
• Masashi Namba,
• Taku Nakashima,
• Kiyofumi Shimoji and
• Noboru Hattori

Beilstein J. Org. Chem. 2019, 15, 863–873, doi:10.3762/bjoc.15.84

• sciences. These applications include spin-labels [5][6][7], fluorophore-nitroxide probes [8], contrast agents in magnetic resonance imaging (MRI) [9], polarization transfer agents for nuclear magnetic resonance (NMR) [10][11][12][13], and radical batteries [14][15]. Furthermore, the efficient synthesis of

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• designed, with a tethered fluorophore. Further attachment of the glycodendrimer to a biocompatible, surface eroding microparticle allows for targeted uptake and internalization of the pathogen-associated oligosaccharide by phagocytic immune cells. The α-1,2-trimannose-linked bioerodible microparticles were

• pathogen (1 μm in diameter) and provide a multivalent display of the synthetic α-1,2-trimannose similar to the Leishmania promastigote cell-wall glycans. Furthermore, a tethered fluorophore would allow for immunofluorescence assays, intracellular trafficking, and validation of T cell-mediated antigen

• recognition. To allow for both surface functionalization of this glycan to the bioerodible microparticles and conjugation of the fluorophore, two amine handles would be necessary (Figure 3). The design would also benefit from the development of a more efficient synthesis of the mannose oligomer sidechain

Cyclopropene derivatives of aminosugars for metabolic glycoengineering

• Jessica Hassenrück and
• Valentin Wittmann

Beilstein J. Org. Chem. 2019, 15, 584–601, doi:10.3762/bjoc.15.54

• ) [29][30][31]. As described earlier [20], DMB selectively reacts with α-keto acids such as N-acetylneuraminic acid (Neu5Ac), the most abundant natural sialic acid in human cells [1], forming a fluorophore. Analysis by RP-HPLC equipped with a fluorescence detector allows the detection of natural and

Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer

• Sagnik Sengupta,
• Mena Asha Krishnan,
• Premansh Dudhe,
• Ramesh B. Reddy,
• Bishnubasu Giri,
• Sudeshna Chattopadhyay and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244

• during the bioconjugate synthesis. The synthesis is carried out from a relatively non-expensive and commercially available H-Cys(trt)-(2-Cltrt) resin. The mode of linking the fluorophore to the growing peptide chain using a lysine derivative such as Fmoc-Lys(Tfa)-OH containing differentially protected

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

• fluorophore. After centrifugation and washing of the polymer particles, surface-bound 5 could be clearly visualized by fluorescence microscopy on CB7-functionalized polymer particles, whereas polymer particles lacking CB7 on the surface did not show any fluorescence (Figure 7). This result is consistent with

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

• structures as a result of peptide/lipid aggregation [34]. However, since only the fluorescence of the fluorophore can be detected, it can of course not be ruled out that degradation of the peptides has been already started. Quantifying the amount of the novel peptides after 120 min demonstrated further that

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• by reducing aggregation and also helps to conduct a detailed thermodynamic study for the 8-ring HP polyamides for the very first time. Recently, Hartley et al. designed and synthesized a hybrid fluorescent HP polyamide conjugate 22 (Figure 6) by attaching the A·T recognizing fluorophore, p

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

• Eirinaios I. Vrettos,
• Gábor Mező and
• Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80

• in sufficient levels to pump inside the cell efficacious doses of the drug. The peptide-carrier should be constructed in such way that the conjugation with a drug or/and a fluorophore is feasible. Conjugation usually occurs on lysine, cysteine and glutamic acid [34] via orthogonal coupling or on the

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of

• . Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum. Keywords: ATP sensing; base-pairing; fluorescent probes; 3-hydroxyflavone

• way to enhance the selectivity. Since ATP has one adenine nucleobase, a simple uracil/thymine unit appended to a neutral chemosensor operating mainly through π-interaction could be a good model for investigation. We selected DMHF as the fluorophore and core scaffold because of its easy synthesis and

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• incorporation of reactive 3'-amino-2',3'-dideoxynucleotide building blocks, activated as OAt esters [47]. This methodology can, in principle, be automated, and was established with a view towards sequencing, using fluorophore-labeled nucleotides [48][49]. To avoid cyclization or oligomerization of the monomer