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

Probing multivalency in ligand–receptor-mediated adhesion of soft, biomimetic interfaces

• Stephan Schmidt,
• Hanqing Wang,
• Daniel Pussak,
• Simone Mosca and
• Laura Hartmann

Beilstein J. Org. Chem. 2015, 11, 720–729, doi:10.3762/bjoc.11.82

• a concanavalin A (ConA) layer via poly(ethylene glycol)-(PEG)-based soft colloidal probes (SCPs). Special emphasis is on the dependence of multivalent presentation and density of carbohydrate units on specific adhesion. Consequently, we first present a synthetic strategy that allows for controlled

• of surface anchored carbohydrate ligands with a receptor surface, we developed a new method using carbohydrate coated hydrogel particles, also called soft colloidal probes (SCPs) that undergo mechanical deformation when coming into contact a with receptor surface [8][9][10][11]. The mechanical

• Recently, we introduced micrometer-sized SCPs composed of crosslinked PEG-diacrylamide hydrogels as probes [15]. Here, we used the ability of PEG-diacrylamide to phase separate from an aqueous solution to form microscopic droplets by means of precipitation using sodium sulfate as a kosmotrope. At

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

• ; fluorescent probes; iminosugars; 4-methylumbelliferone; multivalency; pyrene; Introduction Since the isolation in the 1970’s of 1-deoxynojirimycin (DNJ) from natural sources and the finding of its biological activity as an α-glucosidase inhibitor, thousands of sugar mimetics with a nitrogen atom replacing

• Discussion Synthetic design The fluorescent probes were designed as analogues of the best multivalent pharmacological chaperones/correctors reported so far that typically display three to four copies of a DNJ ligand linked to a central core via an alkyl chain spacer (Figure 1) [24][25][26]. The choice of the

Fluoride-driven ‘turn on’ ESPT in the binding with a novel benzimidazole-based sensor

• Kai Liu,
• Xiaojun Zhao,
• Qingxiang Liu,
• Jianzhong Huo,
• Bolin Zhu and
• Shihua Diao

Beilstein J. Org. Chem. 2015, 11, 563–567, doi:10.3762/bjoc.11.61

• ]. However, to OH-based anion sensors it has been paid less attention [25][26]. In fact, we have succeeded in designing and synthesizing the anion fluorescent probes, based on ESPT [15][16], containing phenolic OH as H-bond donor. In these systems, the probe displayed a narrower linear range for fluoride

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• to develop oligonucleotide-based drug candidates or biomedical chemical probes [5][6]. Native nucleic acids are connected by phosphate diesters as linking units, thus leading to a polyanionic backbone structure. Implications of this characteristic feature of nucleic acid architecture have been

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 comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences. Keywords: DNA ligands; fluorescent probes; ILPR; nucleic acids; quadruplex DNA; Introduction The “insulin-linked polymorphic region” (ILPR) is a physiologically relevant G-rich DNA sequence

• show high selectivity towards quadruplex as compared to double stranded DNA [20]. Therefore, these ligands may be used as probes for the detection of quadruplex DNA. Although the CD-spectroscopic analysis only provides qualitative information about the binding between the ligand and the DNA, they may

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• - and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of

Nucleic acid chemistry

• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2014, 10, 2928–2929, doi:10.3762/bjoc.10.311

• runs automatically on machines, so-called DNA synthesizers. With special care during each synthesis step, even longer oligonucleotides can be prepared in a similar, almost routine fashion. The field of nucleic acid chemistry has exploded: natural and artificial functionalities, as well as probes

• cases, postsynthetic strategies can allow for the desired oligonucleotides modification. This becomes an even more important issue for functionalities, probes or biologically relevant molecules that are incompatible with routine phosphoramidite chemistry. Although nucleic acid chemistry appears to be a

• mature part of organic and bioorganic chemistry, the many questions that are still being raised by research in biology and chemical biology give sufficient motivation to continue to synthesize new nucleic acid probes and thereby further develop nucleic acid chemistry. Moreover, in addition to their

Synthesis and biological evaluation of novel N-α-haloacylated homoserine lactones as quorum sensing modulators

• Michail Syrpas,
• Ewout Ruysbergh,
• Christian V. Stevens,
• Norbert De Kimpe and
• Sven Mangelinckx

Beilstein J. Org. Chem. 2014, 10, 2539–2549, doi:10.3762/bjoc.10.265

• . Most of the α-haloacylated analogues did not exhibit a significant reduction when tested in the QS inhibition test. Therefore, these novel analogues could be utilized as chemical probes for QS structure–activity studies. Keywords: halogenated fatty acids; halogenation; N-acylated homoserine lactones

• , inhibition of bacterial QS was recently demonstrated by a set of electrophilic probes (which included halogenated analogues of AHLs) that could covalently bind in the LasR binding pocket of Pseudomonas aeruginosa [15]. Therefore, designing analogues with small reactive moieties, such as halogenated carbon

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

• bioactive metabolites and selective labeling of proteins and other biomacromolecules. A common structural motif for such probes consists of a reporter that can be attached by copper(I)-catalyzed 1,2,3-triazole formation between terminal alkynes and azides to a reactive headgroup. Here we introduce the

• -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

Multivalent glycosystems for nanoscience

• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2014, 10, 2345–2347, doi:10.3762/bjoc.10.244

• nanoscience”. Bruce Turnbull (United Kingdom) has amassed contributions dedicated to “Synthetic methods to make multivalent glycosystems”, Alessandro Casnati (Italy) has delivered manuscripts regarding “Glycoconjugates for the delivery of drugs and diagnostic probes” for review, Roland Pieters (The

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• shows several unique properties [26][27][28]. Its potential applications as a probe for DNA sensing are well-established. For example, we have developed singly labeled acpcPNA probes that can give a fluorescence change in response to hybridization to DNA [29][30][31]. Due to its solvatochromic

Expeditive synthesis of trithiotriazine-cored glycoclusters and inhibition of Pseudomonas aeruginosa biofilm formation

• Meriem Smadhi,
• Sophie de Bentzmann,
• Anne Imberty,
• Marc Gingras,
• Raoudha Abderrahim and
• Peter G. Goekjian

Beilstein J. Org. Chem. 2014, 10, 1981–1990, doi:10.3762/bjoc.10.206

• good affinity for Pseudomonas aeruginosa lectin lecA. They are convenient biological probes for investigating the roles of lecA and lecB in biofilm formation. Keywords: antibiotic; biofilm; glycocluster; lectin; multivalency effect; multivalent glycosystems; Introduction Pseudomonas aeruginosa (PA

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

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• 7, 14183, Huddinge, Sweden 10.3762/bjoc.10.154 Abstract Pyrene derivatives can be incorporated into nucleic acid analogs in order to obtain switchable probes or supramolecular architectures. In this paper, peptide nucleic acids (PNAs) containing 1 to 3 1-pyreneacetic acid units (PNA1–6) with a

• recognition; triplex stabilization; Introduction Peptide nucleic acid (PNA) probes are very selective in the recognition of DNA and have been used in a large variety of diagnostic methods, easily allowing the detection of point mutations at very low concentrations [1][2][3]. Poly-pyrimidine PNA can form very

• the fluorescence properties can be observed upon interaction with DNA, thus enabling to study the occurring interactions and to produce switching PNA probes. Fluorescent switching probes for DNA detection are very useful tools in diagnostics applications such as real-time PCR and in situ hybridisation

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

Synthesis of fluorescent (benzyloxycarbonylamino)(aryl)methylphosphonates

• Michał Górny vel Górniak,
• Anna Czernicka,
• Piotr Młynarz,
• Waldemar Balcerzak and
• Paweł Kafarski

Beilstein J. Org. Chem. 2014, 10, 741–745, doi:10.3762/bjoc.10.68

• Screening of the activity of large libraries of fluorogenic substrates of chosen enzymes is an emerging approach to determine their substrate preferences and thus to provide a set of data useful for the preparation of their selective inhibitors [1][2][3][4][5]. Such fluorogenic probes have been also used

• for profiling the proteolytic secretomes with the obtained profiles being useful as diagnostic tools [6][7][8]. Also conjugates of drugs with fluorescent probes have been used as so called theranostics (combination of therapeutics and diagnostics) [9][10]. Diaryl esters of α-aminoalkanephosphonic

• carrying fluorescent probes in their side chains or in the ester phosphonate moieties might find an application in constructing fluorescent probes for studying structural requirements of enzymes having serine in their active sites (proteinases and phosphatases) or to study their elevated level in various

Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics

• Gijs Koopmanschap,
• Eelco Ruijter and
• Romano V.A. Orru

Beilstein J. Org. Chem. 2014, 10, 544–598, doi:10.3762/bjoc.10.50

Synthesis of the B-seco limonoid core scaffold

• Hanna Bruss,
• Hannah Schuster,
• Rémi Martinez,
• Markus Kaiser,
• Andrey P. Antonchick and
• Herbert Waldmann

Beilstein J. Org. Chem. 2014, 10, 194–208, doi:10.3762/bjoc.10.15

• natural product classes to inspire the synthesis of probes and reagents for chemical biology and medicinal chemistry research, we aimed at the development of a synthetic strategy to get access to the B-seco limonoid scaffold by means of a [3,3]-sigmatropic rearrangement as key step enabling the formation

Physalin H from Solanum nigrum as an Hh signaling inhibitor blocks GLI1–DNA-complex formation

• Midori A. Arai,
• Kyoko Uchida,
• Samir K. Sadhu,
• Firoj Ahmed and
• Masami Ishibashi

Beilstein J. Org. Chem. 2014, 10, 134–140, doi:10.3762/bjoc.10.10

• Education and Research (Development of SPECT Probes for Pharmaceutical Innovation) from MEXT and the Iodine Research Project in the Chiba University, the Asian Core Program (JSPS), Takeda Science Foundation, Hayashi Memorial Foundation for Female Natural Scientists, the Naito Foundation and the Tokyo

Flow microreactor synthesis in organo-fluorine chemistry

• Hideki Amii,
• Aiichiro Nagaki and
• Jun-ichi Yoshida

Beilstein J. Org. Chem. 2013, 9, 2793–2802, doi:10.3762/bjoc.9.314

• production of PET agents with automation and ease of in-line purification is suitable for hospital use. To date, continuous flow microreactor technology has shown potential for synthesis of [18F]-radiolabeled molecular imaging probes such as [18F]FDG, [18F]fallypride, [18F]annexin, and so on, which were made

• [18F]-radiolabeled molecular imaging probes. Flow microreactor synthesis of dipeptides. Flow synthesis involving SNAr reactions. Flow synthesis of fluoroquinolone antibiotics. Highly controlled formation of PFPMgBr. Selective flow synthesis of photochromic diarylethenes. Flow microreactor system for

A one-pot synthesis of 3-trifluoromethyl-2-isoxazolines from trifluoromethyl aldoxime

• Raoni S. B. Gonçalves,
• Michael Dos Santos,
• Guillaume Bernadat,
• Danièle Bonnet-Delpon and
• Benoit Crousse

Beilstein J. Org. Chem. 2013, 9, 2387–2394, doi:10.3762/bjoc.9.275

• inhibitors [17][18][19][20][21]. Another powerful area, yet a somewhat less utilised role for fluorine is as a tag for 19F NMR that offers several analytical advantages including speed, sensitivity and selectivity [22][23]. Fluorinated molecules have served as valuable 19F NMR probes in high-throughput

Synthesis of enantiomerically pure N-(2,3-dihydroxypropyl)arylamides via oxidative esterification

• Akula Raghunadh,
• Satish S More,
• T. Krishna Chaitanya,
• Yadla Sateesh Kumar,
• Suresh Babu Meruva,
• L. Vaikunta Rao and
• U. K. Syam Kumar

Beilstein J. Org. Chem. 2013, 9, 2129–2136, doi:10.3762/bjoc.9.250

• research probes. The development of synthetic routes to these structures is often challenging. Chiral building blocks with three carbon atoms such as glycidol, 1-bromo-2,3-dihydroxypropane and 3-amino-1,2-dihydroxypropane (1) are considered powerful tools by synthetic chemists in organic synthesis [1][2][3

Temperature measurements with two different IR sensors in a continuous-flow microwave heated system

• Jonas Rydfjord,
• Fredrik Svensson,
• Magnus Fagrell,
• Jonas Sävmarker,
• Måns Thulin and
• Mats Larhed

Beilstein J. Org. Chem. 2013, 9, 2079–2087, doi:10.3762/bjoc.9.244

• ][15][16]. In contrast, microwave transparent fiber optic probes can be used for correct temperature measurements. In a recent tutorial review Kappe highlighted the difficulties of temperature monitoring under microwave heating [16]. We recently described the concept of a nonresonant microwave

• quite sensitive to rough handling and may break, and, according to our experience, fiber optic probes are generally susceptible towards higher temperatures at elevated pressures in organic solvents. Considering the above points the option of using the fiber optic probe as the standard tool for