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

Regioselectively α- and β-alkynylated BODIPY dyes via gold(I)-catalyzed direct C–H functionalization and their photophysical properties

• Takahide Shimada,
• Shigeki Mori,
• Masatoshi Ishida and
• Hiroyuki Furuta

Beilstein J. Org. Chem. 2020, 16, 587–595, doi:10.3762/bjoc.16.53

• -EBX reagents. This atom-economical method for the late-stage alkynylation of BODIPY dyes could be an alternate approach for functionalized fluorescent dyes without the need of preparing unstable halogenated pyrrole precursors. The resulting α- and β-ethynyl-substituted BODIPYs displayed distinct

• novel functional fluorescent materials. (a) Chemical structures of BODIPY (1) and dipyrromethane (2). (b) C–C bond forming alkynylations of pyrrole and its derivatives by Sonogashira coupling and electrophilic alkynylation. (c) Peripheral alkynylated BODIPY derivatives (3–6) prepared in this work. TIPS

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• less as aforementioned molecular ovens. Recently development of light sources in the NIR based on LEDs brought new hope in this field [65]. Furthermore, the fact that still some fluorescence occurs makes them interesting as fluorescent probes for imaging applications. NIR radiation possesses a

Recent developments in photoredox-catalyzed remote ortho and para C–H bond functionalizations

• Rafia Siddiqui and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 248–280, doi:10.3762/bjoc.16.26

• catalysts, such as low toxicity, their functioning at room temperature, and smooth irradiation requirements with low-energy lights (e.g., LEDs, fluorescent bulbs, etc.) made this area of research very interesting. Within a very short time, photoredox catalysis has emerged as an important future direction

Potent hemithioindigo-based antimitotics photocontrol the microtubule cytoskeleton in cellulo

• Alexander Sailer,
• Franziska Ermer,
• Yvonne Kraus,
• Rebekkah Bingham,
• Ferdinand H. Lutter,
• Julia Ahlfeld and
• Oliver Thorn-Seshold

Beilstein J. Org. Chem. 2020, 16, 125–134, doi:10.3762/bjoc.16.14

• heterostilbenes that deliver green fluorescent protein (GFP)-orthogonal MT photocontrol [17]. However, in both azobenzene and heterostilbene scaffolds, the steric properties of the E- and Z-isomer are so different that the protein binding site shape determines that the Z-isomer (the lit-form) is the more

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• the ligands E-P1–E-P3 did not bind significantly to the oligonucleotide sequences D1–D3. However, considering their polyamide structure, they should at least exhibt a weak affinity toward double-stranded DNA. The fluorescent indicator displacement (FID) assay was performed with E-P1 as representative

• ligand to examine the propensity of these derivatives to bind to DNA. The known intercalator thiazole orange (TO) was chosen as indicator because it exhibits an intense fluorescence band at 526 nm when bound to DNA, whereas it is only weakly fluorescent in solution. The displacement of TO from its DNA

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

• ; chromium(III) ion; tetraperimidine; Introduction Fluorescent chemosensors are an attractive and efficient tool for the detection of metal ions in environmental and biological science because of their high sensitivity, selectivity, and simple usage [1][2][3][4][5][6][7][8]. Among metal ions, the detection

• monitoring. In recent years, some fluorescent chemosensors for the detection of chromium(III) have been developed [15][16][17][18][19][20][21][22][23]. Generally, chemosensors with fluorescence enhancement are more efficient than fluorescence turn-off chemosensors [24][25][26][27][28][29] because the

• ethylenediaminetetraacetic acid (EDTA) were added to a solution of Cr3+ (c = 1.5⋅10−4 M) and 3 (c = 5.0⋅10−6 M), which led to a reduction of the fluorescence intensity at 388–500 nm. This reduced fluorescent intensity was analogous to that of free 3, displaying that 3 was regenerated in its uncomplexed form. When Cr3+ was

Design, synthesis and investigation of water-soluble hemi-indigo photoswitches for bioapplications

• Daria V. Berdnikova

Beilstein J. Org. Chem. 2019, 15, 2822–2829, doi:10.3762/bjoc.15.275

• that allowed to obtain an RNA-binding hemi-indigo derivative with photoswitchable fluorescent properties. Keywords: hemi-indigo; molecular switches; photochromism; photoswitching; visible light; water solubility; Introduction The application of organic photochromes in biological systems is fraught

• methoxy group to the 3-position of the phenyl ring in Z-1c did not shift the absorption maximum and just slightly affected the extinction (Table 1). Hemi-indigo derivatives Z-1a–c are not fluorescent in aqueous solution. To assess the potential applicability of hemi-indigo derivatives Z-1a–c in biological

• -1b and E-1c are not fluorescent in aqueous medium. The analysis of the isomeric compositions of the photostationary states was performed by the Fischer method [21] because NMR-spectroscopic analysis was precluded by insufficient solubility or/and possible aggregation at higher concentrations. Thus

Chemical tuning of photoswitchable azobenzenes: a photopharmacological case study using nicotinic transmission

• Lorenzo Sansalone,
• Jun Zhao,
• Matthew T. Richers and
• Graham C. R. Ellis-Davies

Beilstein J. Org. Chem. 2019, 15, 2812–2821, doi:10.3762/bjoc.15.274

• an internal solution containing (in mM): 135 potassium gluconate, 4 MgCl2, 10 HEPES, 4 Na2-ATP, 0.4 Na2-GTP, 10 Na2-phosphocreatine, pH 7.35. The red fluorescent dye Alexa 594 (0.05 mM, ThermoFisher Scientific, Waltham, MA, USA) was added to visualize the morphology of the neurons. Normal ACSF was

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

• μM, respectively). Reversible photoliberation/uptake leading to a variation of free calcium concentration in solution was detected using a fluorescent Ca2+ chemosensor. Keywords: azobenzene; BAPTA; calcium binding; photorelease; photoswitch; Introduction In terms of synthetic calcium binding

• , as elucidated by the crystallographic structure of a 1:1 host–guest BAPTA system [2]. This moiety has been exploited in the development of various fluorescent supramolecular chemosensor systems and even molecular logic systems [3][4][5][6][7][8][9][10][11]. Equally, the incorporation of

• liberation of Ca2+ upon photexcitation in solution, azobenzene macrocyle 1 was used as a reversible Ca2+ photoejector in the presence of a Ca2+-selective “turn-on” fluorescent probe (3, Figure 7) [41]. The fluorescence of BODIPY dye 3 in the absence of calcium, is quenched by an intramolecular photoinduced

Dyes in modern organic chemistry

• Heiko Ihmels

Beilstein J. Org. Chem. 2019, 15, 2798–2800, doi:10.3762/bjoc.15.272

• properties. Traditionally, organic dyes are the basis of well-established color indicators for qualitative and quantitative analysis. Nowadays, we cannot imagine research in the life sciences or in medical diagnostics without the sophisticated applications of organic dyes as fluorescent probes, dye labels

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

• prerequisites for the application of fluorescent substances in chemistry, medicine and materials science [1]. With this respect emissive small molecules [2], fluorescent proteins [3], and quantum dots have received considerable attention and remarkable progress in their synthesis and photophysics has been

• increasingly used in OLEDs [6][7][8][9][10] and LCDs [11][12][13] of mobile phones [14]. Fluorescent compounds often intensively emit in solution but only weakly or not in the solid state [15]. Dyes which fluoresce both in the solid state and in solution are still relatively rare, due to the fact that often

• considerably depending on the substituent pattern. The absorption and emission maxima are shifted bathochromically with increasing donor strength. α-Pyrones are only weakly fluorescent in solution. However, with distinct p-N,N-dimethylaminophenyl substitution in 6-position, an extraordinarily high fluorescence

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

• , Brazil Laboratory of Molecular Catalysis, Institute of Chemistry, Graduate Program (PPGQ), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil 10.3762/bjoc.15.257 Abstract This work describes a novel fluorescent 2,1,3-benzothiadiazole derivative designed to act as a water

• agreement with the experimental data and helped to understand the stabilizing intramolecular charge-transfer process from the first excited state. The new fluorescent derivative could be applied as selective bioprobe in several cell lines and displayed plasma-membrane affinity during the imaging experiments

• and by poor performances related to most of them. Therefore, many studies are still based on the use of WGA [16] (wheat germ agglutinin) or membrane proteins bearing fluorescent protein tags [11]. Water solubility is another issue that has to be considered. For the development of new fluorogenic dyes

Arylisoquinoline-derived organoboron dyes with a triaryl skeleton show dual fluorescence

• Vânia F. Pais,
• Tristan Neumann,
• Ignacio Vayá,
• M. Consuelo Jiménez,
• Abel Ros and
• Uwe Pischel

Beilstein J. Org. Chem. 2019, 15, 2612–2622, doi:10.3762/bjoc.15.254

• quenching effects, as the result of the formation of fluoroboronate complexes. In the case of the pyrenyl- and anthryl-substituted dyes a clear ratiometric behavior was noted. No quenching was seen for the addition of cyanide ions or bromide and chloride. This makes the new dyes selective fluorescent

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

• functionalized with free acid moieties are directly accessible in contrast to previously described methods. Keywords: cross coupling; fluorescent dyes; near-infrared (NIR) dyes; silicon rhodamines; Suzuki–Miyaura coupling; Introduction Silicon rhodamines are versatile fluorescent dyes that found extensive use

α,ß-Didehydrosuberoylanilide hydroxamic acid (DDSAHA) as precursor and possible analogue of the anticancer drug SAHA

• Shital K. Chattopadhyay,
• Subhankar Ghosh,
• Sarita Sarkar and
• Kakali Bhadra

Beilstein J. Org. Chem. 2019, 15, 2524–2533, doi:10.3762/bjoc.15.245

• presence of ROS sensitive probe DCFH-DA (dichlorodihydrofluorescein hydrate diacetate) by using FACS (Figure 4). Cellular ROS levels were found to be increased with dose. The mean fluorescent intensities for four compounds were presented in Table 4 and maximum changed intensity for 11b was observed from

• with DAPI staining revealed a significant increase in nucleosomal fragmentation and nuclear condensation in 11b treated cells with increasing doses (Figure 6 upper panel) [39]. Furthermore, a cellular functional assay by JC-1 probe, a voltage sensitive fluorescent cationic dye, exhibits membrane

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• (TM) obtained by the first derivative of the data in A. Outline of the displacement assay principle, in which a photoswitchable PNA probe (blue) hybridizes to a complementary quencher-labelled single-stranded (ss) DNA (black) and replaces a fluorescent-labelled ssDNA (grey); F = fluorescein; Q = black

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• show that this can be a successful alternative to evaluate two-photon properties, particularly useful in case of non-fluorescent molecules. Results and Discussion Spectroscopic properties The UV–vis absorption spectrum of hydrazone 1 shows an intense absorption band peaked at 395 nm in toluene, as

• signal intensity slightly decreases on the 7.5 ps timescale, as the result of vibrational relaxation, and mostly recovers on a ca. 140 ps timescale. Transient absorption measurements upon 400 nm excitation were also performed in acetonitrile and methanol. While the Z-form is fluorescent in acetonitrile

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

• obvious morphology of nanosheets which presented a large 2D and ultrathin plane with a diameter of ca. 200 nm (Figure 2B) [33][34]. By virtue of the expansive surface, 2D MnO2 nanosheets possess the ability to load dozens of fluorophores. An array of fluorescent reporters thus formed, which facilitate

• fluorescence spectroscopy. As shown in Figure S3A (Supporting Information File 1), GSH showed a distinct selectivity over other analytes, suggesting a specific GSH detection performance of Glyco-DTE@MnO2. A linear response of the normalized fluorescent intensity I/Imax at 535 nm within 0–0.4 mM GSH

• fluorescent sensors for detecting intracellular GSH or discriminative sensing of GSH with other common biothiols (e.g., Cys and Hcy) [45][46]. In this work, the highly accessible 2D MnO2 nanosheet is used as the GSH responsive site instead of traditional functional groups that require elaborate design for

Excited state dynamics for visible-light sensitization of a photochromic benzil-subsituted phenoxyl-imidazolyl radical complex

• Yoichi Kobayashi,
• Yukie Mamiya,
• Katsuya Mutoh,
• Hikaru Sotome,
• Masafumi Koga,
• Hiroshi Miyasaka and
• Jiro Abe

Beilstein J. Org. Chem. 2019, 15, 2369–2379, doi:10.3762/bjoc.15.229

• molecular design [25]. The wide ranges of thermal back reactions of photoswitches expand the potential applications of photochromic materials such as to dynamic holographic display [26][27][28], switchable fluorescent markers [29][30][31], and anticounterfeit inks. However, PIC is photosensitive only in the

Mono- and bithiophene-substituted diarylethene photoswitches with emissive open or closed forms

• A. Lennart Schleper,
• Mariano L. Bossi,
• Vladimir N. Belov and
• Stefan W. Hell

Beilstein J. Org. Chem. 2019, 15, 2344–2354, doi:10.3762/bjoc.15.227

• with mono- (Th1) and bithiophene (Th2) units attached to positions 6 and 6′ (Sy = symmetric) or only to position 6 (As = asymmetric). “Oxidized” compounds have highly fluorescent closed forms emitting in the visible region (yellow to red). The dyes with nonoxidized benzothiophenes possess fluorescent

• highly fluorescent “closed” forms combine photochromic and fluorescent entities in one molecule [1] and contain a perfluorocyclopentene bridge linking two 2-alkyl-1-benzothiophene-1,1-oxide residues with a C=C bond via C-3 and C-3′ atoms [2][3]. The “open” form of the DAE core (see graphical abstract and

• Table 1) is only weakly fluorescent (φFl ≈ 0.01) [4]. In general, diarylethenes with fluorescent open forms are rare, while photoswitchable compounds with highly fluorescent “open” and “closed” forms represent a yet unknown and unique class of ratiometric fluorophores. Recently, we demonstrated that

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

• branches of the dendrimer structures, respectively. Also the functionalization in two compartments (core and surface, or branches and surface) was achieved. The consequences of the location of the fluorophores on the fluorescence and TPA properties have been studied. Several of these TPA fluorescent

• dendrimers have water-solubilizing functions as terminal groups, and fluorophores at the core or in the branches. They have been used as fluorescent tools in biology for different purposes, such as tracers for imaging blood vessels of living animals, for determining the phenotype of cells, for deciphering

• instance, fluorescein, which is a widely used fluorescent tracer for many applications, was synthesized for the first time in 1871 [1]. Besides this classical type of one-photon-induced fluorescence, a theoretical work by M. Göppert-Mayer in 1931 [2] predicted the possibility of the simultaneous absorption

Recent advances in transition-metal-catalyzed incorporation of fluorine-containing groups

• Xiaowei Li,
• Xiaolin Shi,
• Xiangqian Li and
• Dayong Shi

Beilstein J. Org. Chem. 2019, 15, 2213–2270, doi:10.3762/bjoc.15.218

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene

• Luna Kono,
• Yuma Nakagawa,
• Ayako Fujimoto,
• Ryo Nishimura,
• Yohei Hattori,
• Toshiki Mutai,
• Nobuhiro Yasuda,
• Kenichi Koizumi,
• Satoshi Yokojima,
• Shinichiro Nakamura and
• Kingo Uchida

Beilstein J. Org. Chem. 2019, 15, 2204–2212, doi:10.3762/bjoc.15.217

• , diarylethene derivatives with photoswitchable fluorescent properties were prepared. They are applicable for fluorescence imaging including bio-imaging. On the other hand, a new system called “excited state intramolecular proton transfer (ESIPT)” is reported. In the system, absorption and emission bands are

• largely separated due to the proton transfer, hence it showed strong fluorescence even in the crystalline state. We aimed to construct the photochromic system incorporating the ESIPT mechanism. Results: A diarylethene incorporating a fluorescent moiety that exhibit ESIPT behavior was prepared. The ESIPT

• fluorescent turn-off behavior during photochromism in aprotic solvents as well as in crystalline state upon UV light irradiation. Furthermore, it showed AIE in THF/water mixtures with blue-shift of the emission. Keywords: AIE; diarylethene; ESIPT fluorescent switching; turn-off fluorescence; Introduction

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• enzyme assay. The long irradiation periods that were necessary to obtain significant amounts of the (Z)-isomers did not permit switching of the inhibitors in the enzyme assay mixture, as the fluorescent substrate and the enzyme would be harmed by long-term UV radiation. We envisioned to replace the

• a fluorescent readout. Inhibition was determined by comparing percentage substrate conversion to a DMSO control after subtraction of the blank fluorescence signal. All compounds were tested at 100 µM, 50 µM and 10 µM, respectively. For compounds that showed more than 50% inhibition at 10 µM an IC50