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

• complex molecular processes in a cell are discerned by tagging fluorescent probes or radioactive tracers to a targeting ligand that will undergo internalization after binding to cell surface proteins overexpressed in diseased conditions. The internalized tracers along with the targeting ligand act as a

• imaging (MRI) are exploited and each modality has its own strengths and weaknesses [3]. However, imaging studies using fluorescent probes [4] or radioactive isotopes [5][6] offers real-time, non-invasive, high-resolution images, during the examination of pathological diseased state. Prostate specific

• folate receptors. The in vitro uptake study has been performed using laser scanning confocal microscopy and the bioconjugates are found to be delivered specifically to cells expressing corresponding cell surface proteins. The small molecule targeted imaging probes prepared in this study are designed for

Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium

• Matthew J. Styles and
• Helen E. Blackwell

Beilstein J. Org. Chem. 2018, 14, 2651–2664, doi:10.3762/bjoc.14.243

• chemical probes for exploring the mechanisms by which SdiA functions during infection and its role in interspecies interactions. Moreover, as SdiA is highly stable when produced in vitro, these compounds could advance fundamental studies of LuxR-type receptor:ligand interactions that engender both agonism

• ][48][49][50]. The majority of these compounds have been based on the AHL scaffold. The development of small molecule probes for SdiA has lagged relative to these prior studies. Indeed, to our knowledge, there have only been two reports of experimental studies of AHL-type ligand activity in SdiA in any

• utility as chemical probes due to their longer half-lives in biological media. These results suggest that this structural motif could be installed to potentially improve the potencies of other lactone-based SdiA agonists and antagonists. Characterization of the efficacies and potencies of SdiA antagonists

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• , a novel competition assay employing ‘clickable’ active-site-labelling probes was developed. These compounds contain terminal alkyne moieties, which can be exploited for straightforward decoration via copper(I)-catalyzed alkyne–azide cycloaddition (CuAAC), the prototypic click reaction. This

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• pyrene and eosin Y as dye probes. The CAC values of tetraalkyl-substituted macrocycles 12a,b (5 µM for both) are significantly lower than those for dialkyl-substituted macrocycles 10a,b (790 and 160 µM, respectively). Premicellar aggregates of macrocycles 10a,b and 12a,b with the dye eosin Y were used

• performed by the dye micellization method using pyrene and eosin Y (EY) as fluorescent and spectrophotometric probes, respectively (Table 1). The nonpolar pyrene can be incorporated into hydrophobic domains of the aggregates due to hydrophobic interactions. Pyrene insertion is measured by analyzing the

• with average hydrodynamic diameters of 150–200 nm and electrokinetic potentials about +40 to +60 mV. CAC values measured by the dye micellization method with pyrene and eosin Y (EY) as dye probes were used to identify optimal concentration conditions for the design of supramolecular architectures for

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

• stability under various conditions, particularly under physiological conditions. Although most BODIPYs are insensitive to pH changes, pH-activatable optical probes for cancer imaging have been reported, in which an aniline substituent in the meso-position of the BODIPY core led to efficient fluorescence

Recent advances in phosphorescent platinum complexes for organic light-emitting diodes

• Cristina Cebrián and
• Matteo Mauro

Beilstein J. Org. Chem. 2018, 14, 1459–1481, doi:10.3762/bjoc.14.124

• found numerous applications as emitting materials in areas such as emitters in PhOLEDs [55][56] and luminescent probes in bio-imaging [57][58][59]. Noteworthy, NIR-emitting OLED were fabricated by using complexes 23g and 23h, which presented a π-delocalized substituent at the 5-position of the central

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• chemically modify ON structures in order to make them suitable drug candidates or chemical probes, e.g., for diagnostic purposes [6][7]. The relevance of the polyanionic phosphate diester-linked backbone to the overall function of nucleic acids has been discussed by Westheimer [8], Benner [9][10], and others

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

• fluorescein dyes to target mouse major satellite DNA using thermal denaturation, gel-shift electrophoresis, circular dichroism and fluorescence spectroscopy [89][90]. Some of these fluorescent probes were found to detect target sequences in mouse living cell lines and the nuclear substructures formed by

• pairs at micromolar to high nanomolar concentration range [91]. Richert et al. designed a novel set of three-pronged probes (TPPs) comprising of cap, β-alanines and oligopyrrolamides in order to bind A·T-rich target strands from three sides (Watson–Crick face, terminus, and minor groove) resulting in

Polysubstituted ferrocenes as tunable redox mediators

• Sven D. Waniek,
• Jan Klett,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2018, 14, 1004–1015, doi:10.3762/bjoc.14.86

• potential application of 1–4 and their ferrocenium ions as selective redox mediators or SET reagents. Apart from the redox potentials of the redox mediators FcH and 1–4, the stability of the 18 and 17 valence electron species as well as their solubility and the availability of spectroscopic probes to

• and 1+–4+ are stable under conditions of electrolysis (CH2Cl2, [n-Bu4N][B(C6F5)4]) as demonstrated by IR and UV–vis spectroelectrochemical experiments and 1H NMR spectroscopy. The C=O stretching vibrations of the ester substituents as characteristic probes in the IR spectra are consistently shifted to

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• introductory part, phosphorothiolate oligonucleotides containing a bridging 3´- or 5´-thiosubstitution, are used as mechanistic probes of enzyme catalysis. Non-bridging thiosubstitution, in turn, creates RP and SP diastereomeric phosphorothioate linkages which have extensively been used for elucidation of 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

• . 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

• electric fields generated by ions and molecules in solution. This property along the ESIPT process (excited state intramolecular proton transfer) [35] makes them ideal for ratiometric environment-sensitive probes and sensors [36][37][38][39][40][41][42][43]. Among them the 4’-dimethylamino derivative (DMHF

• -based probes exploit the ESIPT nature of these fluorophores to generate multiple emission bands [39][41][42][43]. In this case, however, a new fluorescence band appears in the excitation spectra due to an intermolecular proton transfer from the flavone to the phosphate chain of the nucleotide. Therefore

Fluorogenic PNA probes

• Tirayut Vilaivan

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

• Tirayut Vilaivan Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand 10.3762/bjoc.14.17 Abstract Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding

• . The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little

• attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• FRET probes (Figure 5) [14][25]. In the fit we used the associated phase angle (angle between the transition dipole moments of the donor and the acceptor) and the spectral overlap (JDA) as the fitting parameters. The phase angles for the tCO–tCnitro and the qAN1–qAnitro FRET pairs were 67° and 33

• measurements [62][63]. In conclusion, the FRETmatrix (base–base FRET) and Seidel’s methodology are in a way two extremes, firmly vs randomly oriented probes, both giving high control of the κ2 value which in turn facilitates high detail structure information determination. Studying nucleic acid conformation

• external probes as developed by Seidel et al. [4] comprise a highly interesting opportunity to investigate structure and dynamics of nucleic acid containing systems. Recent progress in the field of fluorescent base analogues also starts to close the gap in brightness to external fluorophores like Cy

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• paramount interest because many biological processes, drugs and biochemical tools/probes rely on them [7][8]. Due to the possibly multifaceted nature of the complex formed between a small-molecule ligand and a large receptor (DNA/RNA), several complementary methods are needed for the accurate

• turbulent flow and 5000 rpm is an indicative figure. A necessary prerequisite for a macromolecule such as DNA is a minimum length of at least 1000 base pairs to be successfully oriented [10]. LD probes the orientation of base transition moments relative to the DNA helical axis. Thus, standard B-DNA whose

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

• synthetic lipid A derivative had a bias towards MyD88- or TRIF-dependent immune responses [78]. 1.3. Synthesis of fluorescent-labeled lipid A analogues For studying the structural basis and the dynamics of TLR4-lipid A interplay, the application of labeled synthetic lipid A derivatives as versatile probes

Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• [12][13], DNA fragment sizing [14][15], as reporter groups in hybridization probes [16][17][18][19][20][21][22][23], single DNA molecule fluorescence microscopy [24][25], gel staining [26], in real-time PCR analysis [27][28]) because of their excellent staining properties. Unsymmetrical cyanines have

• ]. Hybridization-sensitive fluorescent probes in which TO is tethered to a nucleic acid: DNA [22][23][33][34][35][36], RNA [20][36] or PNA [18][19][21][31]) strands have been constructed by several research groups (the Krull, Kubista, Seitz and Wagenknecht groups). The continued scientific and commercial interest

• in the preparation and application of cyanine dyes as bio-probes [37][38] and our research in this area [39][40][41] has led us to search for novel representatives of this interesting family of compounds. The main goal of the study described here was to investigate the influence of different halogen

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• activity [3][4]. Fluorinated amino acids can also be used as powerful 19F NMR probes for the study of protein–ligand interactions and enzymatic activities [5][6][7][8]. However, the development of fluorinated peptides as drug candidates seems to be largely under-exploited. Investigation on the influence of

Vinylphosphonium and 2-aminovinylphosphonium salts – preparation and applications in organic synthesis

• Anna Kuźnik,
• Roman Mazurkiewicz and
• Beata Fryczkowska

Beilstein J. Org. Chem. 2017, 13, 2710–2738, doi:10.3762/bjoc.13.269

• anticancer drugs, antioxidants, or functional probes into the mitochondria [5][6][7][8]. Review 1. Synthesis of vinylphosphonium salts 1.1. Alkylation of phosphines with alkyl halides One of the most common methods for the preparation of vinylphosphonium salts 1 is the quaternization of vinylphosphines with

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

• the reaction medium. The results suggest that 1 could be used as fluorophore in OFF–ON-type fluorogenic probes. Keywords: dipeptidyl peptidase-4; fluorogenic substrate; fluorometry; small fluorescent molecule; Introduction Fluorescent organic probes have become indispensable for bio-imaging or

• molecular imaging to visualize the presence of species such as particular enzymes and biologically important inorganic ions. In biomedicine, these probes are used for the detection of a wide range of significant biomarkers and are essential for the diagnosis of critical diseases [1][2][3]. Selective and

• accurate determinations of specific enzymes, including β-galactosidase [4][5][6], exoglycosidases [7], cyclooxygenases [8], and others [9][10][11][12][13], have been achieved using the OFF–ON-type fluorogenic probes with fluorescence that can be turned on by enzymatic transformations. These fluorescent

Regioselective decarboxylative addition of malonic acid and its mono(thio)esters to 4-trifluoromethylpyrimidin-2(1H)-ones

• Sergii V. Melnykov,
• Andrii S. Pataman,
• Yurii V. Dmytriv,
• Svitlana V. Shishkina,
• Mykhailo V. Vovk and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2017, 13, 2617–2625, doi:10.3762/bjoc.13.259

• Organofluorine compounds now play an essential role in the development of new materials for solar cells [1][2][3], radiotracers for PET imaging [4], agrochemicals [5][6], sensitive chemical probes for 19F nuclear magnetic resonance investigation of biological experiments [7][8], and are most widely used in the

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

• synthesis [3]. Pyrenyl derivatives have also attracted considerable attention as fluorescent probes in nucleic acid chemistry and closely related research areas. In particular the pyrene scaffold has been utilized for the construction of abiotic oligopyrenotides with nucleic acid-like structural properties

• 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

• better to single-stranded T10 and double-stranded (dA)10-T10. Confocal microscopy Over the past years, there has been an increased interest in the development of luminescent probes for bioimaging. In that respect, both metal-containing [35] as well as organic [36] luminophores were examined. We found

Structure–property relationships and third-order nonlinearities in diketopyrrolopyrrole based D–π–A–π–D molecules

• Jan Podlesný,
• Lenka Dokládalová,
• Oldřich Pytela,
• Adam Urbanec,
• Milan Klikar,
• Numan Almonasy,
• Tomáš Mikysek,
• Jaroslav Jedryka,
• Iwan V. Kityk and
• Filip Bureš

Beilstein J. Org. Chem. 2017, 13, 2374–2384, doi:10.3762/bjoc.13.235

• -emitting diodes (OLED), fluorophores, probes for ion sensing, functional polymers, and more recently also chromophores with nonlinear optical (NLO) activity. The latter property is mostly dictated by their conjugated character, electron-accepting behavior of the DPP scaffold, strong emissive character, and

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

• of trifluoroethoxy-substituted phthalocyanines to biology Phthalocyanines are expected to be applied to medical fields [85][86] such as biological image probes and as agents for photodynamic therapy because of their excellent spectroscopic properties, allowing phthalocyanine to be a useful medical

• –vis spectrum, do not aggregate in solution. These dyes are expected to be developed into medical imaging probes. Phthalocyanine is expected to be used not only as a biological imaging agent but also in cancer treatment. Photodynamic therapy (PDT) is a laser cancer therapy that introduces organic dyes

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• ) [120] rescued L929 fibroblasts from mycolactone-promoted apoptosis while silencing FoxO3 by RNA interference was only partially protective. The latter finding might be explained by the compensating effects of other FoxO proteins. Two synthetic mycolactone-derived probes bearing a biotin tag as a

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• biological probes synthesized by automated synthesis by iterative coupling of different building blocks (colors). TBDPSE, tert-butyldiphenylsilylethyl; TMSE, trimethylsilylethyl. Adapted with permission from [37]; copyright 2015 American Association for the Advancement of Science. An example of a composition