On the interaction of different types of ligands binding to the same molecule Part II: systems with n to 2 and n to 3 binding sites

In the first part of this work we formulated the decoupled sites representation for two different types of ligands and highlighted special properties of the case of n binding sites for ligand L ₁ and one binding site for ligand L ₂. Moreover, for this case, we identified the microstate constants as unique components all decoupled molecules share. In the second part on hand, we investigate the cases with (n, 2) and (n, 3) binding sites. As it is difficult to solve the system of equations occurring when a molecule with more than one binding site for both ligands shall be decoupled, we present applicable calculation methods which exploit the special structure of the system of equations. Moreover, we investigate which unique properties all decoupled molecules share and show that for two different decoupled molecules with the same binding polynomial, not all microstate constants of a certain macrostate are permutations of the microstate constants of the other molecule.     

Microcalorimetry, energetics and binding studies of DNA-dimethyltin dichloride complexes

The interaction of dimethyltin dichloride (Me₂SnCl₂) with calf thymus DNA was studied at 27 °C, pH 7.6 using various techniques including isothermal titration calorimetry (ITC) and UV-Vis, fluorescence and IR spectrophotometries. The binding isotherm and enthalpy curve for Me₂SnCl₂-DNA interaction was a biphasic transition process. This was determined by the analysis of the binding data with the Hill equation. The first phase of the enthalpy curve (exothermic process) was consistent with the first set of binding site, the second phase (endothermic process, less exothermicity) was consistent with second set of binding site from the cited interactions. Our results showed that the first set of binding sites is occupied by one mole of ligand bound per near 1 base pair of DNA. The DNA-ethidium bromide (EB) complex, in the presence of Me₂SnCl₂, caused the quenching of the fluorescence emission. The Scatchard plots illustrated a non-intercalating manner for such quenching. The DNA-EB complex results indicated that the binding of Me₂SnCl₂ is with the phosphate groups of DNA at low ligand concentrations (<9 mM). This was confirmed with the IR spectrophotometric spectra. However, the binding at higher ligand concentrations (>9 mM) was with the base groups of DNA. Therefore, these results suggest that the Me₂SnCl₂ binding to DNA at low concentrations occurs through an outside interaction by an exothermic process. However, the partial unfolding of the DNA caused at higher concentrations of Me₂SnCl₂ is through an endothermic process involving interactions with the base groups.     

Calculation of equilibrium constants of ligand binding by a metal ion in solution using a chemometric procedure

The method of calculating equilibrium constants has been considered in the work using a chemometric procedure based on the factor analysis of systems, in which a ligand added to a central ion forms in solution a number of complexes [MX _n ], n = 1?4. Spectrophotometric titration curves were simulated by means of a matrix model of complex formation. The analysis of the simulated multivariable dependences has shown an opportunity to apply the evolutiing factor analysis to the adequate estimation of complex-formation parameters in the absence of spectral selectivity of separate spectral forms, and also in the absence of concentration regions of full domination of separate components and products of their interaction. The algorithm was developed, which allows true values of matrix model parameters determining the shape of spectrophotometric titration curves to be found without preliminary postulation of a chemical model of the system.     

Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1

The 41 amino acid neuropeptide, corticotropin-releasing factor (CRF) and its associated receptors CRF₁-R and CRF₂-R have been targeted for treating stress related disorders. Both CRF₁-R and CRF₂-R belong to the class B G-protein coupled receptors for which little information is known regarding the small molecule antagonist binding characteristics. However, it has been shown recently that different non-peptide allosteric ligands stabilize different receptor conformations for CRF₁-R and hence an understanding of the ligand induced receptor conformational changes is important in the pharmacology of ligand binding. In this study, we modeled the receptor and identified the binding sites of representative small molecule allosteric antagonists for CRF₁-R. The predicted binding sites of the investigated compounds are located within the transmembrane (TM) domain encompassing TM helices 3, 5 and 6. The docked compounds show strong interactions with H228 on TM3 and M305 on TM5 that have also been implicated in the binding by site directed mutation studies. H228 forms a hydrogen bond of varied strengths with all the antagonists in this study and this is in agreement with the decreased binding affinity of several compounds with H228F mutation. Also mutating M305 to Ile showed a sharp decrease in the calculated binding energy whereas the binding energy loss on M305 to Leu was less significant. These results are in qualitative agreement with the decrease in binding affinities observed experimentally. We further predicted the conformational changes in CRF₁-R induced by the allosteric antagonist NBI-27914. Movement of TM helices 3 and 5 are dominant and generates three degenerate conformational states two of which are separated by an energy barrier from the third, when bound to NBI-27914. Binding of NBI-27914 was predicted to improve the interaction of the ligand with M305 and also enhanced the aromatic stacking between the ligand and F232 on TM3. A virtual ligand screening of ~13,000 compounds seeded with ~350 CRF₁-R specific active antagonists performed on the NBI-27914 stabilized conformation of CRF₁-R yielded a 44% increase in enrichment compared to the initially modeled receptor conformation at a 10% cutoff. The NBI-27914 stabilized conformation also shows a high enrichment for high affinity antagonists compared to the weaker ones. Thus, the conformational changes induced by NBI-27914 improved the ligand screening efficiency of the CRF₁-R model and demonstrate a generalized application of the method in drug discovery.     

Modeling data from titration,amide H/D exchange,and mass spectrometry to obtain protein-ligand binding constants

We recently reported a new method for quantification of protein-ligand interaction by mass spectrometry, titration and H/D exchange (PLIMSTEX) for determining the binding stoichiometry and affinity of a wide range of protein-ligand interactions. Here we describe the method for analyzing the PLIMSTEX titration curves and evaluate the effect of various models on the precision and accuracy for determining binding constants using H/D exchange and a titration. The titration data were fitted using a 1:n protein:ligand sequential binding model, where n is the number of binding sites for the same ligand. An ordinary differential equation was used for the first time in calculating the free ligand concentration from the total ligand concentration. A nonlinear least squares regression method was applied to minimize the error between the calculated and the experimentally measured deuterium shift by varying the unknown parameters. A resampling method and second-order statistics were used to evaluate the uncertainties of the fitting parameters. The interaction of intestinal fatty-acid-binding protein (IFABP) with a fatty-acid carboxylate and that of calmodulin with Ca(2+) are used as two tests. The modeling process described here not only is a new tool for analyzing H/D exchange data acquired by ESI-MS, but also possesses novel aspects in modeling experimental titration data to determine the affinity of ligand binding.     

A review on the ligand binding studies by isothermal titration calorimetry

Thermodynamics of biomacromolecule ligand interaction is very important to understand the structure function relationship in proteins. One of the most powerful techniques useful to obtain additional information about the structure of proteins in biophysical chemistry field is isothermal titration calorimetry (ITC). An ITC experiment is a titration of a biomacromolecule solution by a solution containing a reactant (ligand) at constant temperature to obtain the exchanged heat of the reaction. The total concentration of ligand is the independent variable under experimental control. There are many reports on data analysis for ITC to find the number of binding sites (g), the equilibrium constant (K), the Gibbs free energy of binding process (ΔG), the enthalpy of binding (ΔH) and the entropy of binding (ΔS). Moreover, ITC gives information about the type of reaction, electrostatic and hydrophobic interactions, including determination of cooperativity characterization in binding process by calculating the Hill coefficient (n). A double reciprocal plot and a graphical fitting method are two simple methods used in the enzyme inhibition and metal binding to a protein. Determination of a binding isotherm needs more ITC experiments and more complex data analysis. Protein denaturation by ligand includes two processes of binding and denaturation so that ITC data analysis are more complex. However, the enthalpy of denaturation process obtained by ITC help to understand the fine structure of a protein.     

Calculations of the intrinsic constants of the complexation between Cu(II) and halide ions in solution

Experimental curves of spectrophotometric titration for systems containing mononuclear homoleptic complexes were interpreted in an alternative way involving calculation of the intrinsic constants of binding of the ligand by a central ion with fixed coordination sites. This matrix approach allows one to reduce the number of variables in least-squares optimization of titration curves, describing the formation of complexes [MX _n ] (n = 1–4) via three independent variables (\(\bar K\), ω _cis and ω _trans ) for a square planar geometry and via two variables (\(\bar K\) and ω) for a tetrahedral geometry. Differences in the mutual cis-and trans-influences of coordinated ligands were quantitatively estimated for labile complexes in solution. The method proposed was used to calculate the intrinsic constants of complexation between Cu²⁺ and the chloride ion in methanol from spectrophotometric titration data.     

Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures

Hydration is a critical factor in the ligand binding process. Herein, to examine the hydration states of ligand binding sites, the three-dimensional distribution function for the water oxygen site, g_O( r ) , is computed for 3,706 ligand-free protein structures based on the corresponding small molecule–protein complexes using the 3D-RISM theory. For crystallographic waters (CWs) close to the ligand, g_O( r ) reveals that several CWs are stabilized by interaction networks formed between the ligand, CW, and protein. Based on the g_O( r ) for the crystallographic binding pose of the ligand, hydrogen bond interactions are dominant in the highly hydrated regions while weak interactions such as CH-O are dominant in the moderately hydrated regions. The polar heteroatoms of the ligand occupy the highly hydrated and moderately hydrated regions in the crystallographic (correct) and wrongly docked (incorrect) poses, respectively. Thus, the g_O( r ) of polar heteroatoms may be used to distinguish the correct binding poses.     

Synthesis, luminescence properties of a novel aromatic carboxylic acid (L) and corresponding Eu(III) and Tb(III) compounds as well as the binding characteristics of L with bovine serum albumin (BSA)

A novel polyamino polycarboxylic pyridine derivative ligand, N,N,N¹,N¹-(2,6-bis((3-(aminoethyl)-5-methyl-1H-pyrazol-1-yl)methyl)pyridine)hexakis(acetic acid) (L), was designed and synthesized with the motive that it is able to sensitize the emission of lanthanides. Its corresponding Eu(III) and Tb(III) complexes Na₄EuLCl₃·3H₂O and Na₄TbLCl₃·5H₂O were successfully prepared. The ligand and the complexes were characterized by elemental analysis, IR, MS, NMR and TG-DTA. The luminescence properties of the compounds in solid state were investigated; each complex had very narrow emission bands and strong luminescence intensity up to about 10,000. The TG-DTA studies showed that the initial decomposition temperature of both complexes was over 250 °C, elucidating the complexes had a high thermal stability. Meanwhile, the comparison with similar complexes suggested that the ligand with more coordination sites possessed more efficient antenna effect. To explore the potential medicinal value of L, the binding interaction of L and bovine serum albumin (BSA) was carried out by fluorescence spectrum. The studies indicated that the reaction between L and BSA was a static quenching procedure. The binding site number n and binding constant Ka were calculated according to the double logarithm regression equation. The thermodynamic parameters showed the Van der Waals and hydrogen bond interactions were the mainly impulse to the reaction.     

DNA binding and cleavage behaviors of copper(II) complexes with amidino-O-methylurea and N-methylphenyl-amidino-O-methylurea,and their antibacterial activities

The two designed copper(II) complexes, [Cu(L^1m)₂]Cl₂ (1) (L^1m = amidino-O-methylurea) and [Cu(L^2m)₂]Cl₂ (2) (L^2m = N-methylphenyl-amidino-O-methylurea), have been investigated for their interaction with calf thymus DNA by utilizing the absorption titration method, viscometric studies and thermal denaturation. The cleavage reaction on pBR322 DNA has been monitored by agarose gel electrophoresis. The results suggest that the two complexes can bind to DNA by non-intercalative modes and exhibit nuclease activities in which supercoiled plasmid DNA is converted to the linear form. Complex 2, with an intrinsic binding constant (K_b) of 1.16 × 10⁵ M⁻¹, shows a higher binding efficiency and a better nuclease activity than complex 1, with a K_b value of 5.67 × 10⁴ M⁻¹. Their DNA cleavage potential can be significantly enhanced by hydrogen peroxide, indicating an oxidative cleavage process. Further examination of the antibacterial activities against Campylobacter has revealed inhibition zones of 9.0 (for 1) and 14.5 mm (for 2), which are in agreement with their minimum inhibitory concentration (MIC) values of 1.56 and 0.78 mg mL⁻¹, respectively. The substantially better reactivity of 2 results from the aromatic moieties on the side chain of the L^2m ligand which act as an additional binding site.     

Review of binding methods and detection of Al(III) binding events in trypsin and DL-DPPC liposomes by a general thermodynamic model

In this paper are reviewed some of the most useful binding formalisms which have been developed in order to investigate the diversity of the commonly encountered receptor-ligand systems. Particularly, our attention is focused on the presentation and application of a general and rigorous thermodynamic treatment which explains in a simple and coherent way the non-linear profiles observed in the experimental binding, Scatchard, Hill and Adair plots. By applying this model, both qualitative and detailed quantitative investigations were carried out on the binding process of Al(III) to trypsin and dl-dipalmitoylphosphatidylcholine (DPPC) liposomes. Particularly, it has been demonstrated that: Al(III) interacts with liposomes in two binding sites with very different dissociation constants. The first one has been calculated to be 0.0168 μmol l⁻¹ and the second 2.833 μmol l⁻¹. The first is referred to the preferential interaction of Al³⁺ with the polar head of the phospholipid, while the second most likely regards the interaction of Al³⁺ with other peripheral sites. On the other hand, Al³⁺ interacts with trypsin in two types of binding sites. The first binding site with K_1,1=0.2531 μmol l⁻¹ and the second with K_2,1=1.424 μmol l⁻¹.     

Synthesis, crystal structure, electrochemistry and studies on protein binding, antioxidant and biocidal activities of Ni(II) and Co(II) hydrazone complexes

Bivalent transition metal hydrazone complexes of the composition [Ni(L₁)₂] (1), [Co(L₁)₂] (2), [Ni(L₂)₂] (3) and [Co(L₂)₂] (4) have been synthesised from the reactions of [MCl₂(PPh₃)₂] (where M = Ni or Co) with hydrazones derived from 2-acetyl pyridine and carboxylic acid hydrazides of benzhydrazide (HL₁) or thiophene-2-carboxylic acid hydrazide (HL₂), respectively. Structure of the ligands HL₁ and HL₂ and their corresponding complexes with Ni(II) and Co(II) ions were proposed based on the elemental analysis, infrared and ¹H NMR spectral methods. Single crystal X-ray diffraction study of complex 1 revealed a distorted octahedral geometry around the metal ion provided by two units of the ligand. To explore the potential medicinal value of the new complexes, binding interaction of all the complexes with bovine serum albumin (BSA) was studied at normal physiological conditions using fluorescence and UV-Vis spectral techniques. The number of binding sites (n) and binding constant (K_a) were calculated according to the double logarithm regression equation. The results of synchronous fluorescence spectrum showed that binding of metal hydrazones with BSA induced conformational changes in BSA. The in vitro antioxidant and antimicrobial potentials of the new chelates were also carried out.     

Application of an extended solvation theory to study on the binding of magnesium ion with myelin basic protein

Binding properties of myelin basic protein (MBP) from bovine central nervous system due to the interaction by divalent magnesium ion (Mg²⁺) was investigated at 27°C in aqueous solution using isothermal titration calorimetry (ITC) technique. An extended solvation model was used to reproduce the enthalpies of Mg²⁺-MBP interaction over the whole Mg²⁺ concentrations. It was found that there is a set of two identical and noninteracting binding sites for Mg²⁺ ions. The dissociation equilibrium constant is K _d=45.5 μM. The molar enthalpy of binding site is identical for both sites; ΔH=−15.24 kJ mol⁻¹. The solvation parameters recovered from the solvation model were attributed to the structural change of MBP due to the metal ion interaction.     

Distance geometry analysis of ligand binding to drug receptor sites

Summary The method known as distance geometry approach for receptor mapping procedures is discussed. In this method a ligand binding to a certain receptor is considered as a collection of ligand points. Binding sites of the receptor are either empty or filled site points; a ligand point might bind to an empty site point; filled site points indicate that at that point no binding is possible. A binding mode of a ligand is a list of which ligand points coincide with which empty binding sites. The applicability of the method for QSAR studies is discussed; as examples are mentioned the dihydrofolate reductase, ₁- and ₂-receptors. Finally, some ideas on future developments in receptor mapping are discussed.DEDICATION This article is dedicated to the late Dr. Teake Bultsma who introduced the distance geometry approach into our department.     

A New Approach for Titration Calorimetric Data Analysis on the Binding of Magnesium Ion with Myelin Basic Protein

The interaction of the myelin basic protein (MBP) from the bovine central nervous system with divalent magnesium ion was studied by isothermal titration calorimetry at 27 °C in aqueous solution. A simple rapid method for determination of the dissociation binding constants for Mg²⁺-MBP interaction was introduced using the isothermal titration calometric data. The binding isotherm for Mg²⁺-MBP interaction is easily obtained by carrying out a titration calorimetric experiment using only one set of concentrations of MBP. There are two identical independent intrinsic association constants equal to 0.021 μmol⋅L⁻¹ in the first- and second-binding sites, respectively.     

Synthesis,spectral characterization,theoretical, antimicrobial,DNA interaction and in vitro anticancer studies of Cu(II) and Zn(II) complexes with pyrimidine-morpholine based Schiff base ligand

Novel Cu(II) (1) and Zn(II) (2) complexes with 4-(1-(4-morpholinophenyl)ethylideneamino)pyrimidine-5-carbonitrile) (L) have been synthesized and characterized by various spectroscopic and analytical techniques. DFT (density functional theory) studies result confirms that, LMCT mechanism have been done between L and M(II) ions. The antimicrobial studies indicate that the ligand L and complexes 1 & 2 exhibit higher activity against the E. coli bacteria and C. albicans fungi. The groove binding mode of ligand L and complexes 1 & 2 with CT-DNA have been confirmed by electronic absorption, competitive binding, viscometric and cyclic voltammetric studies. The electronic absorption titration of ligand L and complexes 1 & 2 with DNA have been carried out in different buffer solutions (pH 4.0, 7.0 & 10.0). The K_b values of ligand L and complexes 1 & 2 are higher in acidic buffer at pH 4.0 (K_b = 2.42 × 10⁵, L; 2.8 × 10⁵, 1; 2.65 × 10⁵, 2) and the results revealed that, the interaction of synthesized compounds with DNA were higher in the acidic medium than basic and neutral medium. Furthermore, CT-DNA cleavage studies of ligand L and complexes 1 & 2 have been studied. The in vitro anticancer activities results show that complexes 1 & 2 have moderate cytotoxicity against cancer cell lines and low toxicity on normal cell line than ligand L.     

Statistical mechanical approach to competitive binding of metal ions to multi-center receptors

A microscopic site binding model to treat binding of several metal ions to multi-center receptors is proposed. The model introduces the appropriate parameterization in terms of microscopic complexation constants and metal-metal pair interaction energies. The model is solved with statistical mechanical techniques, including direct enumeration or transfer matrices. We obtain microscopic and macroscopic complexation constants, microstate probabilities, and binding isotherms for chain-like receptors, including the long-chain limit. Various examples to illustrate the usefulness of the model are given.     

Cooperativity and anti-cooperativity between ligand binding and the dimerization of ristocetin A: asymmetry of a homodimer complex and implications for signal transduction

Background: Recent work has indicated that dimerization is important in the mode of action of the vancomycin group of glycopeptide antibiotics. NMR studies have shown that one member of this group, ristocetin A₁ forms an asymmetric dimer with two physically different binding sites for cell wall peptides. Ligand binding by ristocetin A and dimerization are slightly anti-cooperative. In contrast, for the other glycopeptide antibiotics of the vancomycin group that have been examined so far, binding of cell wall peptides and dimerization are cooperative.Results: Here we show that the two halves of the asymmetric homodimer formed by ristocetin A have different affinities for ligand binding. One of these sites is preferentially filled before the other, and binding to this site is cooperative with dimerization. Ligand binding to the other, less favored half of the dimer, is anti-cooperative with dimerization.Conclusions: In dinner complexes, anti-cooperativity of dimerization upon ligand binding can be a result of asymmetry, in which two binding sites have different affinities for ligands. Such a system, in which one binding site is filled preferentially, may be a mechanism by which the cooperativity between ligand binding and dimerization is fine tuned and may thus have relevance to the control of signal transduction in biological systems.