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

• affinity of CMA1-Nter to GalNAc in solution by isothermal calorimetry (ITC), obtaining a KD of 940 µM, confirming the low affinity (Figure S2c,d; Supporting Information File 2). Structural insights from the N-terminal domain of CMA1 Given the unusual binding specificity exhibited by CMA1, we were intrigued

• , Supporting Information File 2), supporting our ITC and SPR data where no multivalent binding effects were observed for the single-domain N-terminal construct. In the GalNAc-complexed structure (PDB ID 8R8C) [30], the N-acetyl group of GalNAc extended beyond C2 into the cavity noted in the LacNAc complex

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• . used 1H NMR titrations and isothermal titration calorimetry (ITC) to experimentally determine interactions energies for I-9 complexes (e.g., I-9-lig, −6.3 kcal/mol), they also discovered that simultaneous binding to both σ-holes was possible [90]. Given these observations, it is unsurprising that HVI

A fluorescent probe for detection of Hg²⁺ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene

• Xiaoqian Chen,
• Naqin Yang,
• Yue Ma,
• Xinan Yang and
• Peihua Ma

Beilstein J. Org. Chem. 2023, 19, 864–872, doi:10.3762/bjoc.19.63

• that a G and TMeQ[6] inclusion complex is formed with a 1:1 stoichiometry. Isothermal titration calorimetry (ITC) analysis The association constant and thermodynamic parameters of the host–guest interaction between G and TMeQ[6] can be obtained using ITC. At 25 °C, a neutral aqueous solution of TMeQ[6

• @TMeQ[6] aqueous solution at U = 520 V, slit = 5/5 and adding different equivalents of Hg2+ to G@TMeQ[6] aqueous solution at U = 500 V, slit = 5/5. Isothermal titration calorimetry (ITC) The neutral aqueous solution of TMeQ[6] (1.0 × 10–4 mol·L−1, 1.00 mL) was placed in a sample tank, and G solution

• (1.0 × 10–3 mol·L−1) was taken in a 250 μL syringe. The temperature was set at 25 °C, titrated 30 times (8 μL each time), and the titration time interval was 300 s. The thermodynamic parameters of each system were measured on a Nano ITC Isothermal Titration Calorimeter. After deleting the first

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• ) inactive enzyme mutant E451A was examined by fluorimetric titrations and ITC titrations and it was found that Phen-Py-1 binds to the protein with a high affinity (Table 3). This protein is a mono-zinc metalloexopeptidase and hydrolyses dipeptides from the N-termini of substrates that consist of at least

• increased upon addition of the enzyme (Figure 6), suggesting the important role of the hydrophobic pyrene subunit for protein binding [18]. Association constant and thermodynamical binding parameters were additionally determined by ITC titrations [17]. The resulting titration data were fitted to a single

• -site binding model (Figure 7, Table 3). ITC experiments confirmed the binding of the ligand with human DPP III mutant E451A. The experiment resulted in positive peaks as a result of an endothermic reaction, which took place with an increase in entropy (Figure 7C, Table 3). This means that the binding

Preparation of β-cyclodextrin-based dimers with selectively methylated rims and their use for solubilization of tetracene

• Konstantin Lebedinskiy,
• Volodymyr Lobaz and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2022, 18, 1596–1606, doi:10.3762/bjoc.18.170

• parameters is impossible. ITC (isothermal titration calorimetry) is a popular technique for evaluating supramolecular interaction with CDs [38], mainly in the aqueous medium. We performed the titrations of tetracene DMSO solution by the series of CDs used in the solubility experiments (Figure 7, Figure 8

• elsewhere, is always endothermic [39]. The DMSO with 0.02% of water (roughly 11 mM, given by the manufacturer) was used. The dilution experiments demonstrated that DMSO does not absorb additional water in the timescale of the ITC experiment, which may produce measurement artifacts. Additionally, the

• effective values for the sum of all interaction steps. Although from the sole ITC experiment, the formation of tetracene inclusion complex with CDs can't be affirmed, the observed stoichiometry favors this hypothesis. Additionally, the binding strength in terms of Ka (M−1) well matches the solubility

Study on the interactions between melamine-cored Schiff bases with cucurbit[n]urils of different sizes and its application in detecting silver ions

• Jun-Xian Gou,
• Yang Luo,
• Xi-Nan Yang,
• Wei Zhang,
• Ji-Hong Lu,
• Zhu Tao and
• Xin Xiao

Beilstein J. Org. Chem. 2021, 17, 2950–2958, doi:10.3762/bjoc.17.204

• inferred that Q[7] binds with the three “arms” of TBT at a molar ratio of 3:1 (NQ[7]/NTBT = 3:1) and forms a host–guest complex Q[7]-TBT. In addition, the ITC experiment also strongly supports the above results, which data can be fitted to a very suitable curve using the model of sequential three site

Host–guest interaction and properties of cucurbit[8]uril with chloramphenicol

• Lin Zhang,
• Jun Zheng,
• Guangyan Luo,
• Xiaoyue Li,
• Yunqian Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 2832–2839, doi:10.3762/bjoc.17.194

• (CPE) was investigated using single-crystal X-ray diffraction spectroscopy, isothermal titration calorimetry (ITC) and UV–vis, NMR and IR spectroscopy. The effects of Q[8] on the stability, in vitro release performance and antibacterial activity of CPE were also studied. The results showed that CPE and

• under neutral aqueous conditions. ITC study of the interaction between CPE and Q[8] ITC is a highly sensitive and automated microcalorimeter method, which can continuously and accurately monitor and record the calorimetric curve of each process to obtain the thermodynamic parameters and action ratio

• between the assemblies. Figure 4 and Table 1 show the exothermic isotherms and thermodynamic constants obtained for the titration of CPE with Q[8] interaction using ITC. From the data, it can be seen that the reaction was enthalpy driven and its binding constant was 8.057 × 105 L/mol. 1H NMR spectroscopy

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• , similar observations have been reported for DNA modified with methyl phosphotriester linkage (POMe) using isothermal titration calorimetry (ITC) measurements which provides ΔH values directly [37]. For the native DNA duplex (ON1/ON20), the more favourable ΔH at the low salt concentration (25 mM NaCl) was

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• particles, and information on the molecular structure was gained by UV–vis spectroscopy. Isothermal titration calorimetry (ITC) provided information on the thermodynamics and interaction forces in the supramolecular assembly formation. Keywords: electrostatic self-assembly; hydroxyflavylium

• . Thermodynamic analysis of the assembly process For understanding the differences of the assemblies, isothermal titration calorimetry (ITC) was performed to elucidate the thermodynamics and to gain insight into the building block interactions in the assembly process. Basically, ITC measures the association heat

• scenario can also be elucidated when comparing the ΔH1 value to the data from a poly(allylamine)–Flavy and a poly(allylamine)–photoacid ITC experiment that we have performed for comparison. In both binary cases ΔH1 exceeds the value in the ternary system, which again shows that poly(allylamine) competes

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

• 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

• Kd, can be calculated [36]. Another commonly used biophysical method is ITC. In ITC, the binding partner is mixed with the protein solution at various concentrations, and the heat released or absorbed as the proteins (or the protein and the ligand) interact is measured. Since the measurements are

• proportional to the concentration of the analytes, it is imperative that accurate measurements are used. ITC, in contrast to SPR, has the advantage of measuring the affinity in solution (and not in an immobilised form). Moreover, with the use of high-sensitivity equipment, ITC is used to determine an array of

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• redox-active units were investigated with respect to the impact of the functionalization on the thermodynamic binding properties towards secondary ammonium axles using isothermal titration calorimetry (ITC). The electrochemical switching properties of the redox-active crown ethers were examined using

• ion, which resulted in binding constants in the optimal range for ITC titrations [52][53]. The even more weakly coordinating tetrakis(3,5-bis(trifluoromethyl)phenyl)borate (BArF24−) anion exemplarily served for comparison to study the influence of the anion on the binding constant. Two different

• ). Moreover, ΔG0 follows the same trend as observed for crown-8 analogs with A1·PF6 (entries 9, 10, and 12 in Table 1) and discussed above: the binding energy decreases from BC7 over exTTFC7 to TTFC7. The azacrown-7 NDIC7 is an exception: The ITC titration with the ammonium axle A2·PF6 does not exhibit the

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• phosphonato-calix[n]arenes of different ring sizes (n = 4, 6 or 8) to Cyt c [20][23][24][26][27][28] and the antifungal protein PAF [25] as model proteins. These studies combined 15N-HSQC titrations with X-ray crystallography, isothermal titration calorimetry (ITC) and size exclusion with light scattering

• the lines and decreases the signal intensities even more. In addition, the stabilization of the 14-3-3 peptide interaction in the presence of the ligand was confirmed by biochemical assays such as isothermal titration calorimetry (ITC) and fluorescence anisotropy. On a quest for modulators of 14-3-3

• for measuring binding affinities, such as isothermal titration calorimetry (ITC) or fluorescence anisotropy/polarization, are only able to provide an averaged KD. Outlook In the last two decades, additional NMR methods have been developed to extend the size limits of NMR spectroscopy to very large

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• calorimetry experiments (ITC), which allowed us to determine all thermodynamic components simultaneously in a single experiment (the equilibrium binding constant (Ka), reaction Gibbs free energy of binding (ΔrG), reaction enthalpy (ΔrH), reaction entropy (ΔrS), and the stoichiometry (n) of the complex formed

• the free nucleic acid from Tm of the complex. Every ΔTm value reported herein was the average of at least two measurements. The error in ΔTm is ±0.5 °C. Isothermal titration calorimetry (ITC) experiments were performed on a MicroCal VP-ITC microcalorimeter (MicroCal, Inc., Northampton, MA, USA

• syringe (307 rpm) into the isothermal cell, equilibrated at 25.0 °C, containing 1.4406 mL of polynucleotide (c = 3.0–5.0 × 10−5 M). The spacing between each injection was 420 s. The initial delay before the first injection was 3000 s in all experiments. All solutions used for ITC experiments were degassed

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

• -induced emission quenching of acridine or 4,9-diazapyrene derivatives [43]. In order to confirm the fluorimetric data by an independent method, and also to characterise thermodynamic parameters of complex formation, ITC titrations were performed (Figure 6, Supporting Information File 1, Figures S28–S30

• ), and the results are summarised in Table 3. The values of logKs obtained from fluorimetric and ITC experiments were generally in good agreement and minor differences within the same order of magnitude. Also, our ITC titrations revealed for all dye–polynucleotide complexes similar sets of negative

• calculated by subtracting the Tm value of the free nucleic acid from the Tm value of the complex. Every ΔTm value here reported was the average of at least two measurements. The error in ΔTm is ±0.5 °C. In a similar manner as described in [62] ITC were carried out at 293 K on a MicroCal VP-iTC instrument. In

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• )2, respectively. The binding affinities and thermodynamic data were quantified by ITC measurements (Table 1, Figure 3 and Figures S5–S9, Supporting Information File 1). All investigated interactions show a negative enthalpy and are therefore exothermal. Though the magnitude of these values differs

• (Figure S10, Supporting Information File 1). This behavior does not contradict the ITC measurements and can be attributed to the kinetic isotope effect. Although, D-bonding is generally stronger than H-bonding, its contribution to the peptide–peptide binding can be weakened by even stronger competitive

• our initial assumption that dynamic peptides, due to their similarity towards enzymes, can bind a broad scope of biomolecules. ITC measurements suggest that the cyclic tripeptide dimers a(CFC)2 and p(CFC)2 are stronger binders for the aromatic dipeptides FF and YY (K ≈ 229–702 M−1), then for the non

One-pot synthesis of dicyclopenta-fused peropyrene via a fourfold alkyne annulation

• Ji Ma,
• Yubin Fu,
• Junzhi Liu and
• Xinliang Feng

Beilstein J. Org. Chem. 2020, 16, 791–797, doi:10.3762/bjoc.16.72

• European Social Fund and the Federal State of Saxony (ESFProject “GRAPHD”, TU Dresden) for financial support. J. Liu is grateful for the startup funding from The University of Hong Kong and the funding support from ITC to the SKL.

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• , titration of the host with the guest species did not cause appreciable spectral changes. Isotherm titration calorimetry (ITC) did not give satisfactory results either. Conclusion In summary, we have synthesized phthalimide-containing functionalized O6-corona[3]arene[3]tetrazines by means of a one-pot

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

• SdiA by greater than 30%. These compounds could be classified as follows: long chain AHLs (12–16 carbons); BHLs, PHLs and PPHLs with large substituents on the aryl ring; glycine ethyl ester replacements for the lactone head group; and compound 11 (ITC-12), originally reported by the Meijler lab [44

• ], which has an isothiocyanate (itc) at its acyl tail terminus installed for potential covalent capture in the AHL-binding site (vide infra). These 23 compounds were selected for further characterization to determine their relative inhibitory potencies in SdiA. Characterization of the efficacies and

• , C18, E6, E33, E34, and F13), and PHL-type derivatives with glycine ethyl ester head groups (F39, F40, F45, and F47). In addition, an AHL with an electrophilic warhead for covalent modification (11, ITC-12) and various non-AHL compounds (12, 13, 18, 19R, and 20) were found to be SdiA antagonists. Most

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

• thermodynamic profiles as measured via isothermal titration calorimetry (ITC) [55]. Despite its low molecular weight, 13 showed tight-binding kinetics and was able to reduce production of HHQ, as well as PQS. Furthermore, it was capable of attenuating biofilm production [54]. All the information gathered via

• . In order to block the thioesterase activity of the enzyme, a library of 500 fragments was screened via differential scanning fluorimetry (DSF) and the hit fragments 24–26 (Figure 11) were further validated using isothermal titration calorimetry (ITC) [66]. Binding to PqsE could be confirmed with KD

• observed for the nitro function it is crucial for the activity and thus believed to form an instable H-bond with T265. The Rahme group already demonstrated in a former ITC assay that M64 is directly bound in the PqsR LBD [77]. However, they were also suggesting inverse agonistic effect of M64 based on

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• −. NMR titrations and isothermal titration microcalorimetry (ITC) were then performed to obtain the association constants. For small guests such as 1+, 2+, 6+–9+, NMR titration experiments with ZB4 have been performed due to the fast equilibrium of the free and ZB4-complexed guests on the NMR time scale

• . All titration curves agreed well with a 1:1 stoichiometry (Figures S11–S14 in Supporting Information File 1). In case of guests 3+ and 10+, the binding heats were high enough to be measured. Thus the binding parameters were determined by ITC titrations (Figure S15 in Supporting Information File 1) and

• determined by ITC titrations (Figures S15–S26 in Supporting Information File 1), and the data are shown in Table 2. The logarithm of the corresponding association constants of 11+–21+ over 3+ were parabolic as the function of Hammett parameter (σp) [39] (Figure 2). For substituents C(Me)3, OMe, Me, SMe, F

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

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• pocket. Both of these terminal sugar residues show hydrogen bonding interactions with the protein and associated water molecules. The GM1 oligosaccharide (GM1os) binds very tightly to CTB with a dissociation constant (Kd) of around 40 nM (measured by isothermal titration calorimetry, ITC), while simple

• . Individually, the interactions are much weaker than the CTB-GM1os interaction (Kd ca. 1 mM measured by ITC), but even these weak binding interactions can still be functionally useful once the effect of multivalent binding enhancement has been taken into consideration. Indeed, ITC experiments have also shown

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

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• -(naphthalen-2-yl)allyl chloride as the alkylating reagent. Highly regioselective reaction conditions, which differ for each regioisomer in a used base, gave the monosubstituted isomers in yields between 12–19%. Supramolecular properties of these derivatives were studied by DLS, ITC, NMR, and Cryo-TEM

• were studied by a set of methods allowing characterization of supramolecular behavior at various levels – from binary complexation, over supramolecular oligomers to large assemblies; namely by isothermal titration calorimetry (ITC) [16], 1H nuclear magnetic resonance spectroscopy (1H NMR), dynamic

• preparation, we observed many sheet-like structures (Figure 6C), corresponding to the observations of Bonini et al [22]. Isothermal titration calorimetry (ITC) ITC experiments on NA-γ-CD cannot be carried out as classical titration experiments, i.e., by injecting the ligand solution into a solution of the

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• viscosity of the network as shown by ITC, 1H NMR and UV–vis spectroscopy, and rheological studies. Such networks potentially form a basis for the design of controlled drug release systems. Keywords: controlled release; cyclodextrin; network; poly(acrylate); self-assembly; Introduction The formation of

• designed into the structure of aqueous networks formed between a β-cyclodextrin-substituted poly(acrylate) and three adamantyl-substituted poly(acrylate)s. Accordingly, we report an ITC, 1H NMR and UV–vis spectroscopic and rheological study of three self-assembling networks formed between the 8.8% 6A-(2

• , chosen for this study (Figure 1). Results and Discussion Isothermal titration calorimetry (ITC) studies of substituted poly(acrylate) network formation In aqueous solution, the host β-CDen substituents of PAAβ-CDen complex the guest adamantyl substituents of PAAADen, PAAADhn and PAAADddn to form poly