Fluorometric and liquid chromatographic study of the binding of two coumarins to β-cyclodextrin

The fluorescences of warfarin and phenprocoumon are enhanced following complexation with β-cyclodextrin; (+)-(R)- and (?)-(S)-phenprocoumons have different affinities for this cyclodextrin, whereas the corresponding enantiomers of warfarin have similar binding constants. Apparently, hemiketal formation in the case of warfarin minimizes chiral discrimination. This is confirmed using a β-cyclodextrin bonded chromatography column on which the phenprocoumon enantiomers are separated, whereas those of warfarin are not.     

Theoretical and Molecular Docking Study of Ketoconazole on Heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin as Chiral Selector

A molecular docking study, using molecular mechanics calculations with AutoDock and semi‐empirical PM3 calculations, was used to predict the enantiodiscrimination of heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin (TMβCD) and ketoconazole (KTZ) enantiomers. A Density Functional Theory (DFT) single‐point calculation at the level of B3LYP/6‐311G (d,p) was performed for the PM3‐optimized complexes to obtain more accurate binding energy and the electronic structures of the complexes. The difference in energies of the inclusion complexes between the KTZ enantiomers and TMβCD is probably a measure of chiral discrimination, which results in the separation of the enantiomers as observed in the experimental studies. Chirality 28:209–214, 2016. © 2015 Wiley Periodicals, Inc.     

Spectral study on inclusion interaction and enantiorecognition of 2-aryl carboxylic acids with hydroxypropyl-β-cyclodextrin

The inclusion interaction between hydroxypropyl-β-cyclodextrin (HP-β-CD) and 21 2-aryl carboxylic acids was investigated by UV (ultraviolet) spectrophotometer. The inclusion constant of each 2-aryl carboxylic acids with HP-β-CD was determined by Benesi–Hildebrand's equation. According to our previous work, it was found that a high inclusion constant for inclusion complex formed by a racemate and cyclodextrin was always observed with the fact that a high enantioseparation factor was achieved for the racemate in enantioseparation by liquid–liquid chromatography, which suggested that high binding combination between racemate and cyclodextrin is very important for a successful enantioseparation in enantioselective liquid–liquid extraction. Among all the studied subjects, mandelic acid enantiomer, 2,3-diphenylpropionic acid enantiomer, and naproxen enantiomer were selected for the further study. The inclusion constants of enantiomers of these three subjects were determined by UV spectra, which indicated that a necessary difference in inclusion constants between enantiomer and cyclodextrin was also essential. It was found in UV spectra that the absorbance of the analytes with the addition of cyclodextrin would increase or decrease, which was determined by the type of electron excitation. The conformation changes of small molecules can lead to the changes of chromophore valence electron clouds distribution, causing the HOMO-LUMO energy difference decreased. Thus, a red shift of the wavelength of the maximum absorption was produced indicating that the possibility of the molecular interaction of enantiomers with HP-β-CD exists.     

Size makes a difference: Chiral recognition in complexes of fenchone with cyclodextrins studied by means of NMR titration

Gibbs energies of complex formation between enantiomers of bicyclic terpenoid, fenchone, and naturally occurring cyclodextrins, βCD and γCD, were determined by means of ¹³C and ¹H nuclear magnetic resonance (NMR) titration data. These results were compared with the corresponding data obtained previously for the diastereomeric fenchone/αCD complexes. The size of the inner cavity of host molecules significantly influences stoichiometry, association constants, and enantiomeric differentiation of the studied complexes. These complementary data allow us to discuss qualitatively the influence of the host size on the guest–host interactions. A method of the simultaneous use of titration data collected for several resonances of different isotopes in the determination of association constants was worked out and thoroughly analyzed. Comparison of the results of global data analyses with weighted means of individual ones revealed that both these approaches are equally trustworthy.     

The determination of binding constants with a differential thermal and potentiometric titration apparatus. II. EDTA, EGTA and calcium

A differential pH and thermal titrimeter has been used to determine the ionization constants of EDTA and EGTA as well as their calcium complexes. The intrinsic heat of binding is a constant for the pH range 2-11.5 for both substances and is found to be -5.4 kcal mol for EDTA and -7.9 kcal mol-1 for EGTA. The binding constants evaluated by fitting to the potentiometric curves and expressed as the log are 10.25 and 11.0, respectively. These values compare reasonably well to those reported in the literature. We have proposed that the binding of calcium occurs even at acid pH based on the pH drop observed at pH 2 when calcium is added, the reversibility of the thermal and the potentiometric curves, the lack of hysteresis upon rapid titration, the constancy of the intrinsic heat of binding and fitting of the entire potentiometric curves using the appropriate binding constants.     

Determination of thermodynamic parameters of cadmium(II) association to glutathione using the fluorescent reagent FluoZin-1

A method was developed to determine the conditional association constants of cadmium(II) [Cd(II)] complexes based on the reagent FluoZin-1, which forms a fluorescent complex with Cd(II). A solution containing Cd(II) and FluoZin-1 was titrated with glutathione while determining fluorescence intensity of FluoZin-1 to estimate levels of free Cd(II). The results were analyzed with a nonlinear least-squares method using the Solver algorithm of Microsoft Excel to yield conditional association constants for 1:1 and 1:2 Cd(II)-glutathione complexes. The values obtained were consistent with those reported previously using isothermal titration calorimetry.     

Chiral discrimination of the analgesic cizolirtine by using cyclodextrins: A (1)H NMR study on the solution structures of their host-guest complexes.

The use of four cyclodextrins (three native and one beta-CD derivative) as NMR chiral solvating agents to resolve the enantiomers of (+/-)-cizolirtine, 1, and its chemical precursor (the carbinol, (+/-)-2), was investigated. The best enantiodiscrimination occurred when beta-cyclodextrin was used. ROESY experiments were performed to qualitatively ascertain the most probable host-guest structures in D(2)O solution, and the binding features found were explained in terms of spatial fitting of the guest molecules into the macrocyclic cavities. No geometrical differences were noted between the two diastereomeric complexes formed by a cyclodextrin and a racemic substrate, so the magnetic nonequivalence induced on guest protons by the enantioselective binding had to be explained as a result of subtle disparities in the orientation and/or the conformational state of the complexed enantiomers.     

Ligand binding affinity determined by temperature-dependent circular dichroism: cyclin-dependent kinase 2 inhibitors

To support drug discovery efforts for cyclin-dependent kinase 2 (CDK2), a moderate-throughput binding assay that can rank order or estimate the affinity of lead inhibitors has been developed. The method referred to as temperature-dependent circular dichroism (TdCD) uses the classical temperature-dependent unfolding of proteins by circular dichroism (CD) to measure the degree of protein unfolding in the absence and presence of potential inhibitors. The midpoint of unfolding is the Tm value. Rank ordering the affinity and predictions of the dissociation constant of compounds is obtained by measuring the increase in Tm for different protein-inhibitor complexes. This is the first time an extensive characterization of the TdCD method has been described for characterizing lead inhibitors in a drug discovery mode. The method has several favorable properties. Using the new six-cell Peltier temperature controller for the Jasco 810 spectropolarimeter, one can determine the affinity of 12-18 compounds per day. The method also requires only 20-40 microg protein per sample and can be used to estimate the affinity of compounds with dissociation constants of picomolar to micromolar. An important property of the method for lead discovery is that dissociation constants of approximately 5 microM can be estimated from a single experiment using a low concentration of compound such as 20 microM, which is generally low enough for most small molecules to be soluble for testing. In addition, the method does not require labeling the compound or protein. Although other methods such as isothermal titration calorimetry (ITC) can provide a full thermodynamic characterization of binding, ITC requires 1-2 mg protein per sample, cannot readily determine binding constants below nanomolar values, is most versatile with soluble compounds, and has a throughput of two to three experiments per day. The ITC method is not usually used in a high-throughput drug discovery mode; however, using the thermodynamic information from several ITC experiments can make the TdCD method very robust in determining reliable binding constants. Using the kinase inhibitors BMS-250595, purvalanol B, AG-12275, flavopiridol, and several other compounds, it is demonstrated that one can obtain excellent comparisons between the Kd values of binding to CDK2 obtained by TdCD and ITC.     

Chiral recognition of verapamil by cyclodextrins studied with capillary electrophoresis,NMR spectroscopy,and electrospray ionization mass spectrometry

Capillary electrophoresis (CE) allows the observation of the opposite affinities of the enantiomers of (±)‐verapamil [2‐isopropyl‐2,8‐bis(3,4‐dimethoxyphenyl)‐6‐methyl‐6‐azaoctannitrile, VP] toward β‐cyclodextrin (β‐CD) and heptakis(2,3,6‐tri‐O‐methyl)‐β‐CD (TM‐β‐CD). In addition, in the presence of β‐CD in the background electrolyte, longer migration times and lower separation factors were observed compared to TM‐β‐CD. The binding constants of (+)‐ and (−)‐VP with β‐CD and TM‐β‐CD determined using ¹³C NMR spectroscopy explain the results observed in CE. Electrospray ionization mass spectrometry (ESI‐MS) was used as an alternative technique for the characterization of VP‐CD complexes. Chirality 11:635–644, 1999. © 1999 Wiley‐Liss, Inc.     

A Phase Solubility Study on the Chiral Discrimination of Ibuprofen by ??-Cyclodextrin Complexes

The effects of chiral discrimination in inclusion complexes formed by native β-cyclodextrin and its substituted form (namely methyl-β-cyclodextrin) with racemate or pure enantiomers of the non-steroidal anti-inflammatory drug ibuprofen have been investigated in water. Stability constants and complexation efficiency have been determined for these host–guest systems with a 1:1 molar ratio from phase solubility profiles, showing that in aqueous solution, methylated cyclodextrin is a better complex agent than native cyclodextrin, with more enhanced effects for the (R)-enantiomer. These results have been validated using NMR technique. In particular, ¹H NMR spectra in D₂O show a splitting of the signals for the methyl group and the aromatic protons close to the asymmetric centre of the racemate ibuprofen included in cyclodextrin cavity.     

Metal binding by melanins: studies of colloidal dihydroxyindole-melanin, and its complexation by Cu(II) and Zn(II) ions

Melanins are colloidal pigments known to have a high affinity for metal ions. In this work, the nature of the metal-binding sites are determined and the binding affinities are quantified. Initial potentiometric titrations have been performed on synthetic dihydroxyindole (DHI) melanin solutions to determine the chemical speciation of quinole/quinone subunits. Two types of acidic functionalities are assignable: catechol groups, with pK(a) between 9 and 13, and quinone imines (QI), with pK(a) of 6.3. The presence of the quinone-imine tautomer has, to our knowledge, never been assessed in polymeric melanins. Melanin solutions obtained from N-methylated DHI lack the pK(a) 6.3 buffer, consistent with its inability to form the quinone-imine tautomer. EPR spectroscopy of the DHI-melanin samples demonstrates that the semiquinone radical is in too low a concentration to contribute to the bulk binding of metals. Changes in the titration curves after addition of Cu(II) and Zn(II) ions were analyzed to obtain the binding constants and stoichiometry of the metal-melanin complexes, using the BEST7 program. UV-Vis spectra at neutral and high pH are used to identify absorbances due to Cu-bound quinone imine and catechol groups. The derived binding constants were used to determine speciation of the Cu(II) and Zn(II) ions coordinated to the quinone imine and catechol groups at various pH. The mixed complexes, Zn(QI)(Cat)(-) and Cu(QI)(Cat)(-) are shown to dominate at physiological pH.     

Combination of isothermal titration calorimetry and time-resolved luminescence for high affinity antibody-ligand interaction thermodynamics and kinetics

For experiments using synthetic ligands as probes for biological experiments, it is useful to determine the specificity and affinity of the ligands for their receptors. As ligands with higher affinities are developed (K(A)>10(8)M(-1); K(D)<10(-8)M), a new challenge arises: to measure these values accurately. Isothermal titration calorimetry measures heat produced or consumed during ligand binding, and also provides the equilibrium binding constant. However, as normally practiced, its range is limited. Displacement titration, where a competing weaker ligand is used to lower the apparent affinity of the stronger ligand, can be used to determine the binding affinity as well as the complete thermodynamic data for ligand-antibody complexes with very high affinity. These equilibrium data have been combined with kinetic measurements to yield the rate constants as well. We describe this methodology, using as an example antibody 2D12.5, which captures yttrium S-2-(4-aminobenzyl)-1, 4, 7, 10-tetraazacyclododecanetetraacetate.     

The development of a continuous isothermal titration calorimetric method for equilibrium studies

A continuous isothermal titration calorimetry (cITC) method for microcalorimeters has been developed. The method is based on continuous slow injection of a titrant into the calorimetric vessel. The experimental time for a cITC binding experiment is 12-20 min and the number of data points obtained is on the order of 1000. This gives an advantage over classical isothermal titration calorimetry (ITC) binding experiments that need 60-180 min to generate 20-30 data points. The method was validated using two types of calorimeters, which differ in calorimetric principle, geometry, stirring, and way of delivering the titrant into the calorimetric vessel. Two different experimental systems were used to validate the method: the binding of Ba(2+) to 18-crown-6 and the binding of cytidine 2'-monophosphate to RNAse A. Both systems are used as standard test systems for titration calorimetry. Computer simulations show that the dynamic range for determination of equilibrium constants can be increased by three orders of magnitude compared to that of classical ITC, making it possible to determine high affinities. Simulations also show an improved possibility to elucidate the actual binding model from cITC data. The simulated data demonstrate that cITC makes it easier to discriminate between different thermodynamic binding models due to the higher density of data points obtained from one experiment.     

Applications of isothermal titration calorimetry – the research and technical developments from 2011 to 2015

Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5 years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level. This review highlights work carried out using binding sites characterized using x‐ray crystallography techniques that allow speculation about individual bond formation and the displacement of individual water molecules during ligand binding and link these events to the thermodynamic constants for binding. The review also considers research conducted with synthetic binding partners where specific binding events like anion‐π and π‐π interactions were studied. The revival of assays that enable both thermodynamic and kinetic information to be collected from ITC data is highlighted. Lastly, published criticism of ITC research from a physical chemistry perspective is appraised and practical advice provided for researchers unfamiliar with thermodynamics and its interpretation. Copyright © 2016 John Wiley & Sons, Ltd.     

Potentiometric measurement of stability constants of complexes between fulvic acid carboxylate and Fe3+

The stability constants of complexes formed between iron (III) and fulvic acid extracted from organic manures and wastes such as urban domestic sewage sludge, farmyard manure, poultry manure and sulfitation pressmud were investigated by the potentiometric titration method in an ionic medium of 0.1 M KNO₃ at 25±1 °C. A modification of the Katchalsky's model was employed for the estimation of stability constants. The displacement of the titration curves due to presence of Fe³⁺ in FA solutions formed the basis of calculations. The weak acidic property of fulvic acids due to carboxyl groups resulted in buffering over a wide range of pH; fulvic acids were completely neutralized in the pH range of 7.00–8.85. Apparent dissociation constants (pK_APP) of weakly acidic carboxyl groups were a direct function of degree of dissociation (α_L) in the mid-range of titration curves but were non-linear at high and low α_L values. The stability constants for formation of Fe–FA complexes (log β_Fe) calculated from the titration data were in the range of 5.64–7.55, depending upon α_L and electrostatic properties of fulvic acids. The relatively high stability constants of Fe–FA complexes in comparison to those with other competing cations suggest that the Fe–FA complexes are relatively stable in a soil environment. This revised version was published online in June 2006 with corrections to the Cover Date.     

Calorimetric determination of cooperative interactions in high affinity binding processes

It is demonstrated that isothermal titration calorimetry can be used to determine cooperative interaction energetics even for extremely tight binding processes in which the binding affinity constants are beyond the limits of experimental determination. The approach is based on the capability of calorimetry to measure the apparent binding enthalpy at any degree of ligand saturation. When calorimetric measurements are performed under conditions of total association at partial saturation, the dependence of the apparent binding enthalpy on the degree of saturation is a function only of the cooperative binding interactions. The method developed in this paper allows an independent estimation of cooperative energetic parameters without the need to simultaneously estimate or precisely know the value of the association constants. Since total ligand association at partial saturation is achieved only at macromolecular concentrations much larger than the dissociation constants, the method is especially suited for high and very high affinity processes. Biological associations in this category include fundamental cellular processes like cell surface receptor binding or protein-DNA interactions.     

Chiral discrimination by NMR spectroscopy of ephedrine and N-methylephedrine induced by β-cyclodextrin,heptakis(2,3-di-O-acetyl)β-cyclodextrin,and heptakis (6-O-acetyl)β-cyclodextrin

NMR spectroxcopy has been used to compare the interaction of ephedrine and N-methylephedrine with β-cyclodextrin, heptakis(2,3-di-O-acetyl)β-cyclodextrin, heptakis(6-O-acetyl)β-cyclodextrin. The stoichiometry of the complexes formed between all three cyclodextrins and N-methylephedrine was found to be 1:1 by UV spectroscopy by means of the Job technique. NMR spectra of the single enantiomers of ephedrine and N-methylephedrine in the presence of all three cyclodextrins gave information about the parts of the ligands which interact differently with the host molecules and may be responsible for the chiral discrimination. To quantify the complex stabilities, binding constants were calculated from the changes in the chemical shifts of the ligand signals upon complexation. Analyses of the coupling constants of both species showed that no significant conformational change occurs upon complexation. ROESY spectra of these optical isomers with all three cyclodextrins provided detailed information about the geometry of the complexes. Different intermolecular cross-peaks between the individual isomers of ephedrine and N-Methylephedrine were found for native β-cyclodextrin and its 2,3-diacetylated derivative but not for 6-acetyl cyclodextrin. Analyses of the intramolecular cross-signals of the ligands confirmed that no significant conformational change occurs upon complexation. Chirality 9:211–219, 1997. © 1997 Wiley-Liss, Inc.     

Metal binding to ligands: cadmium complexes with glutathione revisited

We studied the interaction of gamma-L-glutamyl-L-cysteinyl-glycine (glutathione, GSH) with cadmium ions (Cd(2+)) by first performing classical potentiometric pH titration measurements and then turning to additional spectroscopic methods. To estimate the residual concentrations of free cadmium, we studied the competition of glutathione with a Cd(2+)-sensitive dye, either an absorbing dye (murexide) or a fluorescent one (FluoZin-1), and consistent results were obtained with the two dyes. In KCl-containing Tes, Mops, or Tris buffer at pH 7.0 to 7.1 and 37 degrees C (and at a total Cd(2+) concentration of 0.01 mM), results suggest that free cadmium concentration is halved when the concentration of glutathione is approximately 0.05 mM; this mainly reflects the combined apparent dissociation constant for the Cd(glutathione) 1:1 complex under these conditions. To identify the other complexes formed, we used far-UV spectroscopy of the ligand-to-metal charge transfer absorption bands. The Cd(glutathione)(2) 1:2 complex predominated over the 1:1 complex only at high millimolar concentrations of total glutathione and not at low submillimolar concentrations of total glutathione. The apparent conditional constants derived from these spectroscopy results made it possible to discriminate between sets of absolute constants that would otherwise have simulated the pH titration data similarly well in this complicated system. Related experiments showed that although the Cl(-) ions in our media competed (modestly) with glutathione for binding to Cd(2+), the buffers we had chosen did not bind Cd(2+) significantly under our conditions. Our experiments also revealed that Cd(2+) may be adsorbed onto quartz or glass vessel walls, reducing the accuracy of theoretical predictions of the concentrations of species in solution. Lastly, the experiments confirmed the rapid kinetics of formation and dissociation of the UV-absorbing Cd(glutathione)(2) 1:2 complexes. The methods described here may be useful for biochemists needing to determine conditional binding constants for charge transfer metal-ligand complexes under their own conditions.     

Interactions of nucleotide cofactors with the Escherichia coli replication factor DnaC protein

Quantitative analyses of the interactions of nucleotide cofactors with the Escherichia coli replicative factor DnaC protein have been performed using thermodynamically rigorous fluorescence titration techniques. This approach allowed us to obtain stoichiometries of the formed complexes and interaction parameters, without any assumptions about the relationship between the observed signal and the degree of binding. The stoichiometry of the DnaC-nucleotide complex has been determined in direct binding experiments with fluorescent nucleotide analogues, MANT-ATP and MANT-ADP. The stoichiometry of the DnaC complexes with unmodified ATP and ADP has been determined using the macromolecular competition titration method (MCT). The obtained results established that at saturation the DnaC protein binds a single nucleotide molecule per protein monomer. Analyses of the binding of fluorescent analogues and unmodified nucleotides to the DnaC protein show that ATP and ADP have the same affinities for the nucleotide-binding site, albeit the corresponding complexes have different structures, specifically affected by the presence of magnesium cations in solution. Although the presence of the gamma-phosphate does not affect the affinity, the structure of the triphosphate group is critical. While the affinity of ATP-gamma-S is the same as the affinity of ATP, the affinities of AMP-PNP and AMP-PCP are approximately 2 and approximately 4 orders lower than that of ATP, respectively. Moreover, the ribose plays a significant role in forming a stable complex. The binding constants of dATP and dADP are approximately 2 orders of magnitude lower than those for ribose nucleotides. The nucleotide-binding site of the DnaC protein is highly base specific. The intrinsic affinity of adenosine triphosphates and diphosphates is at least 3-4 orders of magnitude higher than for any of the other examined nucleotides. The obtained data indicate that the recognition mechanism of the nucleotide by the structural elements of the binding site is complex with the base providing the specificity and the ribose, as well as the second phosphate group contributing to the affinity. The significance of the results for the functioning of the DnaC protein is discussed.     

CymA of Klebsiella oxytoca outer membrane: binding of cyclodextrins and study of the current noise of the open channel

CymA, the outer membrane component of the cyclodextrin (CD) uptake and metabolism system of Klebsiella oxytoca, was reconstituted into lipid bilayer membranes. The channel properties of this unusual porin were studied in detail. The binding of CDs to the channel resulted in its complete block for ion transport. This result allowed the detailed investigation of carbohydrate binding, and the stability constants for the binding of cyclic and linear carbohydrates to the binding site inside the channel were calculated from titration experiments of the membrane conductance with the carbohydrates. Highest stability constant was observed for alpha-cyclodextrin (alpha-CD; K = 32,000 1/M) followed by beta-cyclodextrin (beta-CD; K = 1970 1/M) and gamma-cyclodextrin (gamma-CD; K = 310 1/M). Linear maltooligosaccharides bound also to CymA but with much smaller stability constants as compared to cyclic ones. The noise of the current through CymA in multi- and single-channel experiments was investigated using fast Fourier transformation. The current through the open channels had a rather high spectral density, which was a Lorentzian function of the frequency up to 2000 Hz. Upon addition of cyclic dextrins to the aqueous phase the spectral density decreased in a dose-dependent manner, which made it impossible to evaluate the binding kinetics. Experiments with single CymA-channels demonstrated the channel is highly asymmetric concerning channel flickers and current noise.