Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• overlay of streptavidin-Alexa Fluor 647 (Molecular Probes) at 1 µg/mL. The microarray slides were scanned with GenePix 4300A scanner instrument (50% laser power at PMT 350), and the image analysis (quantitation) was performed with GenePix® Pro 7 software. The results can be found in Supporting Information

A novel spirocyclic scaffold accessed via tandem Claisen rearrangement/intramolecular oxa-Michael addition

• Anastasia Vepreva,
• Alexander Yanovich,
• Dmitry Dar’in,
• Grigory Kantin,
• Alexander Bunev and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1649–1655, doi:10.3762/bjoc.18.177

• adenocarcinoma) and NCI-H460 (lung cancer) cell lines and proved completely non-cytotoxic. This validates these new compounds as suitable molecular probes for interrogating various biological targets via screening in cell-based assays. Conclusion We have developed a straightforward access to novel spiro

Microelectrode arrays, electrosynthesis, and the optimization of signaling on an inert, stable surface

• Kendra Drayton-White,
• Siyue Liu,
• Yu-Chia Chang,
• Sakashi Uppal and
• Kevin D. Moeller

Beilstein J. Org. Chem. 2022, 18, 1488–1498, doi:10.3762/bjoc.18.156

• solution and recording the corresponding change in current, a binding curve for the interaction can be generated. While this approach can be very effective, it has limitations. We are interested in using microelectrode arrays to guide synthetic efforts to build molecular probes for protein active sites

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• electrostatic potential grid into energy grids suitable for the Hamiltonian, chemically relevant polymer fragments were used as molecular probes in Epitopsy [26]. Epitopsy is a tool designed to calculate the electrostatic energy of a protein–ligand system from the protein potential grid and ligand charge

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• Academy of Higher Education, Manipal-576104, Karnataka, India 10.3762/bjoc.17.182 Abstract Sugar-modified nucleosides have gained considerable attention in the scientific community, either for use as molecular probes or as therapeutic agents. When the methylene group of the ribose ring is replaced with a

The fluorescence of a mercury probe based on osthol

• Guangyan Luo,
• Zhishu Zeng,
• Lin Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 22–27, doi:10.3762/bjoc.17.3

• , and high sensitivity [10][11][12]. In recent years, many fluorescent molecular probes have been reported. Because Hg2+ has a very strong quenching effect on fluorescence, most of the fluorescent molecular Hg2+ probes are of the fluorescence-quenching type and are easily interfered with by other

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• essential for obtaining FRET between the dyes and the resulting emission fingerprints. Message encryption In a recent report [5], we showed how pattern-generating fluorescent molecular probes can serve as ‘enigma-like’ cipher machines for encrypting secret messages. In the following experiment (Figure 5) we

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• stronger quenching for GC-DNA and the weaker for AT(U)-polynucleotides (Figure 5a and b). Because guanine is the most electron-rich nucleobase, this behaviour points at a fluorescence quenching mechanism by charge transfer from the electron-rich purine bases to the electron-poor NDI molecular probes

• compounds 3a and 3b a clear preference toward GC-DNA in respect to AT(U) sequences. We assume that this is due to the fact that the more electron-rich guanines quench the fluorescence most efficiently via charge transfer interactions with the NDI molecular probes, similar as noted for specific guanine

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• Bern, Switzerland Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, 10065 New York, United States of America 10.3762/bjoc.16.145 Abstract The chemical synthesis of molecular probes to identify and study membrane proteins involved in the biological pathway of protein

• individual building blocks (e.g., the phosphoramidites) will enable the creation of a series of molecular probes with different functional groups and varying linker lengths with relatively little effort. The crucial step in the synthetic pathway consists of the conversion of the carbohydrate intermediates

• yield of about 45% was achieved when no further purification was carried out (for details see Supporting Information File 1). The major goal of this work was the synthesis of molecular probes with a configurationally defined mannosyl headgroup, i.e., a pure β-anomer. In order to verify the preferred

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

• related to this component responsible for the boundaries of the cells [2][3][4]. Various details have emerged due to the development of new sensitive molecular probes capable of staining organelles and cell components selectively, however, many open questions remain. Plasma membranes are the natural

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years. Keywords: DNA; fluorescence; molecular beacons; molecular probes; oligonucelotides; RNA; Review Introduction The development of molecular probes that

• areas, including clinical diagnostics and drug discovery amongst others. Molecular probes generally consist of a recognition element that can bind to the specific target, and a reporter group that, in combination with an appropriate signal transduction mechanism, translates the molecular interaction

Total syntheses of the archazolids: an emerging class of novel anticancer drugs

• Stephan Scheeff and
• Dirk Menche

Beilstein J. Org. Chem. 2017, 13, 1085–1098, doi:10.3762/bjoc.13.108

• ][9]. In many cases, total synthesis is of critical importance to enhance the supply of these often scarce metabolites and even complex polyketides have been prepared on an industrial scale [10][11]. These natural products are also valuable molecular probes for the discovery and evaluation of novel

Synthesis, fluorescence properties and the promising cytotoxicity of pyrene–derived aminophosphonates

• Jarosław Lewkowski,
• Maria Rodriguez Moya,
• Anna Wrona-Piotrowicz,
• Janusz Zakrzewski,
• Renata Kontek and
• Gabriela Gajek

Beilstein J. Org. Chem. 2016, 12, 1229–1235, doi:10.3762/bjoc.12.117

• corresponding aminophosphonate was earlier reported [29]. The aforementioned data suggest possible application of compound 3Aj (and other exhibiting similar emission quantum yield) as molecular probes monitoring micropolarity of the fluorophore environment. On the other hand, water-soluble 4a might be used for

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• Molecular Probes. The directions that Vincent Rotello is taking the field of differential sensing, toward that of biological applications, is one clear future. We are similarly moving to biological applications with kinase and lipid analysis, and cellular classification. But, even beverage analysis, complex

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• it is hard” [11]. We realized that most of the targeted fluorescent molecular probes for phospholipids were derivatives of large protein systems and we felt that we could devise small synthetic mimics of the binding pockets. Our primary phospholipid target was phosphatidylserine, which gets exposed

• conjugated with targeting ligands, and bioimaging studies have shown that they enable fluorescence microscopy and mesoscale imaging of diverse biomedical targets such as tumors, infection, bone, cell death, and brown adipose tissue [37][38] (Figure 3). Several of these molecular probes are commercially

• significant contribution to academic research is to publish high impact papers, and there is tremendous gratification when other investigators employ ideas or techniques that were first developed in your own lab. A tangible outcome of our lab is production of new fluorescent molecular probes and I am proud

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• which has attracted much attention due to the applications in various molecular probes and luminescent materials because of the remarkable photophysical properties of the ESIPT (excited state intramolecular proton transfer) chromophores [33][34]. UV-irradiation of solutions of these compounds in

Glycodendrimers: tools to explore multivalent galectin-1 interactions

• Jonathan M. Cousin and
• Mary J. Cloninger

Beilstein J. Org. Chem. 2015, 11, 739–747, doi:10.3762/bjoc.11.84

• concentration of the dendrimer (220:1, 9:1, or 3:1 ratio of galectin-1 to dendrimer, respectively). Fluorescent microsphere standards (FluoSpheres Fluorescent Microspheres, Molecular Probes) and image analysis software (Pixcavator 6.0) were used for size quantifications. The results from the fluorescence

• characterized according to the reported procedure [32]. Fluorescence microscopy Reagents for fluorescence microscopy were purchased from Molecular Probes. To measure galectin-1 nanoparticles formed using glycodendrimers with fluorescence microscopy, both species were fluorescently labeled. Galectin-1 was

• labeled with Alexa Fluor A555 NHS Ester (succinimidyl ester) (Molecular Probes) [42]. Fluorescent images were captured on an Olympus BX-61 motorized microscope with MicroSuite software with a 100× oil immersion objective at an exposure time of 2 ms. Size quantification was achieved using fluorescent

Design, synthesis and photochemical properties of the first examples of iminosugar clusters based on fluorescent cores

• Mathieu L. Lepage,
• Antoine Mirloup,
• Manon Ripoll,
• Fabien Stauffert,
• Anne Bodlenner,
• Raymond Ziessel and
• Philippe Compain

Beilstein J. Org. Chem. 2015, 11, 659–667, doi:10.3762/bjoc.11.74

• molecular probes and synthesized by way of Cu(I)-catalysed azide–alkyne cycloadditions are fluorescent analogues of potent pharmacological chaperones/correctors recently reported in the field of Gaucher disease and cystic fibrosis, two rare genetic diseases caused by protein misfolding. Keywords: BODIPY

Efficient deprotection of F-BODIPY derivatives: removal of BF₂ using Brønsted acids

• Mingfeng Yu,
• Joseph K.-H. Wong,
• Cyril Tang,
• Peter Turner,
• Matthew H. Todd and
• Peter J. Rutledge

Beilstein J. Org. Chem. 2015, 11, 37–41, doi:10.3762/bjoc.11.6

• ; Findings Compounds incorporating the 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (F-BODIPY) motif 1 have found widespread use in fluorescent molecular probes [1][2], photovoltaic devices [3][4] and photodynamic therapy agents [5][6][7][8]. Accordingly, there is considerable interest in extending and

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• Macromolecular Chemistry, Friedrich Schiller University, Humboldtstr. 10, 07743 Jena, Germany Institute for Physical Chemistry, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany 10.3762/bjoc.10.258 Abstract Molecular probes are widely used tools in chemical biology that allow tracing of

• -Hydroxythiazoles are now becoming commercially available but are also easily accessible by synthesis with a broad range of substitution patterns. Substantial manipulations of the UV–vis excitation and emission wavelengths of these compounds are thus possible [6]. The design of molecular probes based on

Multicomponent reactions in nucleoside chemistry

• Mariola Koszytkowska-Stawińska and
• Włodzimierz Buchowicz

Beilstein J. Org. Chem. 2014, 10, 1706–1732, doi:10.3762/bjoc.10.179

• ][9], anti-infective agents [10][11][12], or molecular probes [13][14]. Taking into account the importance of nucleoside analogs in medicine and biotechnology, there is a considerable interest in the development of simple and efficient synthesis of these compounds. Multicomponent reactions (MCRs

Human dendritic cell activation induced by a permannosylated dendron containing an antigenic GM₃-lactone mimetic

• Renato Ribeiro-Viana,
• Elena Bonechi,
• Javier Rojo,
• Clara Ballerini,
• Giuseppina Comito,
• Barbara Richichi and
• Cristina Nativi

Beilstein J. Org. Chem. 2014, 10, 1317–1324, doi:10.3762/bjoc.10.133

• (Immunotech) directed against the following antigens (the tags are given in parentheses): CD80 (FITC), CD86 (PE), HLA-DR (ECD), CD83 (PC5). Cell vitality was tested with propidium iodide (PI, molecular probes). The cells were labelled in PBS with 1% FCS for 15 min at room temperature (rt), washed twice and

An organocatalytic route to 2-heteroarylmethylene decorated N-arylpyrroles

• Alexandre Jean,
• Jérôme Blanchet,
• Jacques Rouden,
• Jacques Maddaluno and
• Michaël De Paolis

Beilstein J. Org. Chem. 2013, 9, 1480–1486, doi:10.3762/bjoc.9.168

• presents an ideal push–pull configuration tunable with the pH by protonation of the pyridine ring. This is likely to lead to applications of 10a such as for new water-soluble molecular probes. Conclusion A new catalytic and regioselective preparation of substituted N-arylpyrroles decorated with various 2

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

• to be efficient fluorescent molecular probes [7][8]. Recently, the potential of amino-1,8-naphthalimides as fluorescent sensors in living cells has been reviewed [9]. Dendrimers involving the amino-1,8-naphthalimide moieties were showed to be promising active nondoping emitters [10]. 4-Amino

Amyloid-β probes: Review of structure–activity and brain-kinetics relationships

• Todd J. Eckroat,
• Abdelrahman S. Mayhoub and
• Sylvie Garneau-Tsodikova

Beilstein J. Org. Chem. 2013, 9, 1012–1044, doi:10.3762/bjoc.9.116

• resulted in a variety of radiolabeled molecular probes for in vivo PET/SPECT imaging. The scaffolds from which these newer radiolabeled probes are derived include chalcone (5) and its conformationally restricted analogues flavone (6) and aurone (7); stilbene (8) and its analogues diphenyl-1,2,4-oxadiazole

• (NIRF) imaging. Review Radiolabels used in PET/SPECT molecular probes Even though they decay rapidly, [11C] (t1/2 = 20 min) and [18F] (t1/2 = 110 min) are the most commonly used radiolabels in PET/SPECT molecular probes for in vivo imaging of Aβ plaques [4]. With a half-life (t1/2) of 6.01 h compatible