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

• ), which we contrasted with the established R-type lectin Ricinus communis agglutinin 1 (RCA1). We also report binding of specific glycosaminoglycan subtypes and a general enhancement of binding by sulfation. Further validation using agglutination, thermal shift assays, and surface plasmon resonance

• affinity of CMA1 to its ligands. Lectins often only exhibit weak to moderate binding affinities, which is somewhat ameliorated by an increased avidity on the side of the lectin but also a dense presentation of the bound glycan epitope on the cell surface. We therefore used surface plasmon resonance (SPR

• raised by 1 °C/min from 25 to 100 °C, and fluorescence readings were taken at each step. Surface plasmon resonance spectroscopy Experiments were performed using a Biacore X100 instrument (Cytiva) at 25 °C in HBS-T running buffer (10 mM HEPES pH 7.4, 150 mM NaCl and 0.05% Tween 20). Biotinylated PAA

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• towards L-selectin has been evaluated using surface plasmon resonance (SPR) experiments. Results and Discussion Dendritic peptide amphiphile design and synthesis Two different peptide amphiphiles were synthesized, i.e., a non-sulfated, neutral amphiphile I as well as a dPGS-coupled, sulfated amphiphile II

• competitive surface plasmon resonance (SPR) binding assay, whereby neutral supramolecular polymers of I were used as control experiment. L-Selectin-coated gold nanoparticles were incubated with analyte solutions of different concentrations and subsequently probed on an SPR-chip modified with immobilized

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• methods are used to characterise the protein complex and to confirm the presence of certain interactions. Biophysical approaches are important to determine binding affinities, enthalpy changes, entropy changes, and the on- and off-rates of binding, amongst others. Examples include surface plasmon

• resonance (SPR) spectroscopy [27][28], gel filtration [29], isothermal titration calorimetry (ITC) [30][31], fluorescence resonance energy transfer [32], and microscale thermophoresis [33]. In SPR spectroscopy, one of the protein molecules that make up the complex is first immobilised on a metal surface

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• surface plasmon resonance of the individual AuNPs starts to couple when they approach each other [7][8][9]. Early examples of optical probes working in this way are the nanoparticles introduced by Mirkin et al., containing immobilized oligonucleotides that aggregated in the presence of single-stranded DNA

• bis(carbazolyl)urea-derived receptor allowed the sensitive detection of diphosphate in water by surface plasmon resonance (SPR) [29]. Silica nanoparticles containing a dye coordinated to a bis(zinc(II)–DPA) receptor released the dye upon diphosphate binding [30], and thus producing an optical signal

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• absorptions. This is due to the oscillating electron density within metallic NPs, which can couple with the electric field of photons with wavelengths similar to the dimensions of the NPs [181]. This is called the localised surface plasmon resonance (LSPR), and is responsible for the brilliant colours

Reversible end-to-end assembly of selectively functionalized gold nanorods by light-responsive arylazopyrazole–cyclodextrin interaction

• Maximilian Niehues,
• Patricia Tegeder and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2019, 15, 1407–1415, doi:10.3762/bjoc.15.140

• sensing properties [4][5]. In particular, noble metal nanoparticles of sizes smaller than the wavelength of the incident light show interesting optical behavior as a result of collective oscillations of the valence electrons. This leads to surface plasmon resonance (SPR), which is highly dependent on size

A chemically contiguous hapten approach for a heroin–fentanyl vaccine

• Yoshihiro Natori,
• Candy S. Hwang,
• Lucy Lin,
• Lauren C. Smith,
• Bin Zhou and
• Kim D. Janda

Beilstein J. Org. Chem. 2019, 15, 1020–1031, doi:10.3762/bjoc.15.100

• the synthesis of nine unique chemically contiguous heroin–fentanyl haptens and their evaluation as conjugate vaccines to induce a polyclonal antibody response, as measured by ELISA, surface plasmon resonance (SPR), and in a behavioral assay (Figure 1). Results As a starting point for our exploration

• µL whole blood. All sera were tested against both Her-BSA and Fent-BSA antigens, and sera from each chemically contiguous vaccine group were tested against their own antigen. For heroin analysis, 6-acetylmorphine (6-AM) was used as the primary analyte in surface plasmon resonance (SPR) analysis as it

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• , Figure 5) with enhanced affinity for the β-clamp (IC50 = 1.12 μM, measured by surface plasmon resonance). This acetylated peptide was used as a lead and further modified at the second position, where the leucine residue was replaced by a cyclohexyl-L-alanyl group (Cha), and also on the terminal

• protein of griselimycins, surface plasmon resonance (SPR) was used, analysis that demonstrated that they bound with high affinity to the sliding clamps of M. tuberculosis (Kd ranging from 1.0 × 10−10 M to 2.0 × 10−10 M). Encouragingly, no binding was detected between griselimycins and the human sliding

• a challenge. Thus far, extensive in silico and high throughput screening campaigns of libraries of compounds, combinatorial synthesis and structure-based design approaches, biophysical screening techniques (i.e., fluorescence polarization, surface plasmon resonance and differential scanning

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

• site-directed mutagenesis combined with thermodynamic profiling, as well as surface plasmon resonance (SPR) experiments with and without covalent active site blockade, corroborated that the nitrophenylmethanol class directly binds to the active site near the reactive cysteine of PqsD [55]. This is in

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

• surface plasmon resonance, X-ray crystallography and molecular modeling [130]. These experiments revealed that these novel conjugates form 1:1 complexes

Recent applications of click chemistry for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles

• Vivek Poonthiyil,
• Thisbe K. Lindhorst,
• Vladimir B. Golovko and
• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 11–24, doi:10.3762/bjoc.14.2

• -containing ligands and the other with alkyne-containing ligands. When these two were mixed in the presence of the required reagents and the corresponding analyte, a click reaction occurred causing aggregation of the AuNPs. The colour change and the surface plasmon resonance band shift induced by the particle

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• of hepatocellular carcinoma growth in a rat model [82]. Recently, an artificially capped RNA was prepared bearing an orthosteric eIF4E inhibitor at its 5′-end [83][84]. RNA with this cap surrogate retained binding to eIF4E as measured by surface plasmon resonance (SPR). This work provides the basis

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• the gold Fermi wavelength, the nanoparticles acquire photoluminescence properties [31]. These small clusters typically present a diameter between 0.5 and 2 nm. When clusters are bigger, they do not present fluorescent emission but they show a localized surface plasmon resonance (LSPR) around 520 nm

• . This phenomenon consists in a collective oscillation of the free electrons of the metal, induced by the light impinging on the AuNPs [31][39]. The AuNP surface plasmon resonance is dependent upon a vast number of parameters like size, shape, morphology and environment surrounding AuNPs [40]. By

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• spectroscopy, quartz crystal microbalance (QCM), surface plasmon resonance (SPR) and atomic force microscopy (AFM) have been employed to quantify the strength of the multivalent interactions [8]. Because binding affinities can be very high for multivalent supramolecular systems, the constituents are commonly

Influence of length and flexibility of spacers on the binding affinity of divalent ligands

• Susanne Liese and
• Roland R. Netz

Beilstein J. Org. Chem. 2015, 11, 804–816, doi:10.3762/bjoc.11.90

• inhibition for divalent receptors. We first adopt a heuristic definition where half of all receptor binding pockets are occupied by a ligand unit. This definition is most relevant for competitive binding assays, for instance surface plasmon resonance measurements [27], since the measured signal in a

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• electronic properties [1]. In particular, the distinct colour of gold nanoparticles is a result of the localised surface plasmon resonance (LSPR) band caused by collective electron oscillations. The LSPR induces a certain excitation band at visible wavelengths in the absorption spectrum, the position and

Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds

• Michaela Mühlberg,
• Michael G. Hoesl,
• Christian Kuehne,
• Jens Dernedde,
• Nediljko Budisa and
• Christian P. R. Hackenberger

Beilstein J. Org. Chem. 2015, 11, 784–791, doi:10.3762/bjoc.11.88

• conjugated with biotin using oxime ligation, by which the protein scaffold was immobilized on a streptavidin gold chip to monitor carbohydrate–protein binding studies by surface plasmon resonance (SPR). This immobilization strategy allowed easy handling and reproducible orientation, which are notable

• (see Supporting Information File 1). Finally, we also conducted surface plasmon resonance (SPR) studies to show the general applicability of our dual modified protein scaffold for measuring lectin binding constants (Figure 2 and Supporting Information File 1). We first probed the qualitative binding of

• the same volume of 50 mM Tris·HCl pH 8.0 instead of enzyme (background measurement). The samples were shaken at 50 °C for 1 h. Absorbance of released p-nitrophenol was measured at λ = 410 nm (Figure S10, Supporting Information File 1). Surface-plasmon-resonance (SPR). SPR measurements were performed

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

• surface plasmon resonance, quartz crystal microbalance or impedance spectroscopy where the affinity of ligands is measured against only one surface, the biochip surface [4][5][6][7]. In addition, other typical affinity assays like micro-calorimetry or the agglutination do not take the effect of

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• helical structure and thermal stability. Surface plasmon resonance (SPR) affinity measurements with murine C-type lectin receptor (mMGL) showed specific binding only for duplexes containing two or four Lewis-X units. Alternatively, Ebara and co-workers have shown that glycan–DNA conjugates can be accessed

Synthesis of multivalent carbohydrate mimetics with aminopolyol end groups and their evaluation as L-selectin inhibitors

• Joana Salta,
• Jens Dernedde and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2015, 11, 638–646, doi:10.3762/bjoc.11.72

• evaluation of the synthesized carbohydrate mimetics as potential selectin inhibitors, surface plasmon resonance (SPR) spectroscopy [37] was applied. Following the same competitive binding assay previously established for the test of such compounds [38][39], only a few of the presented unsulfated or sulfated

Clicked and long spaced galactosyl- and lactosylcalix[4]arenes: new multivalent galectin-3 ligands

• Silvia Bernardi,
• Paola Fezzardi,
• Gabriele Rispoli,
• Stefania E. Sestito,
• Francesco Peri,
• Francesco Sansone and
• Alessandro Casnati

Beilstein J. Org. Chem. 2014, 10, 1672–1680, doi:10.3762/bjoc.10.175

• other one in the 1,3-alternate structure. Preliminary studies of the interactions of these novel glycocalixarenes with galectin-3 were carried out by using a lectin-functionalized chip and surface plasmon resonance. These studies indicate a higher affinity of lactosyl- over galactosylcalixarenes

• hydrophilic spacers between the glycosyl units and the multivalent calixarene scaffold. We also report on preliminary studies of the interaction of the novel subfamily of galactosyl- and lactosylcalix[4]arenes with Gal-3 by surface plasmon resonance (SPR). Results and Discussion Synthesis of the

• plasmon resonance; Introduction Lectins are carbohydrate-binding proteins (CBP) [1][2][3] without any catalytic or immunogenic activity. In the latest decades, they attracted an increasing interest due to their involvement in a series of fundamental biological processes such as cell adhesion, cell

Photoswitchable precision glycooligomers and their lectin binding

• Daniela Ponader,
• Sinaida Igde,
• Marko Wehle,
• Katharina Märker,
• Mark Santer,
• David Bléger and
• Laura Hartmann

Beilstein J. Org. Chem. 2014, 10, 1603–1612, doi:10.3762/bjoc.10.166

• –receptor binding and thus the resulting binding affinity. In order to determine the binding affinity of the precision glycooligomers to PA-IL, surface plasmon resonance (SPR) experiments were performed. At first, an inhibition/competition assay was carried out. The SPR chip was modified with a β-D

Synthesis and solvodynamic diameter measurements of closely related mannodendrimers for the study of multivalent carbohydrate–protein interactions

• Yoann M. Chabre,
• Alex Papadopoulos,
• Alexandre A. Arnold and
• René Roy

Beilstein J. Org. Chem. 2014, 10, 1524–1535, doi:10.3762/bjoc.10.157

• precipitation of the complexes [30][31]. Alternatively, the application of surface plasmon resonance (SPR) also creates artificial situations not sufficiently related to the natural cellular events, thus requiring complex mathematical algorithms [32]. Most solid-phase immunoassays (ELLA, ELISA) also fall under