Ligand Dissociation Constants Research Articles

Molecular docking, theoretical calculations and potentiometric studies of some azo phenols

The ligands 5-amino-2-(phenyldiazenyl)phenol and its derivatives (HLn) were synthesized from the coupling of 3-aminophenol with aniline and its p-derivatives and characterized by different spectroscopic techniques. The molecular and electronic structures of the investigated compounds (HLn) were also studied using quantum chemical calculations. Molecular docking was used to predict the binding between azo compounds with the receptor of prostate cancer 2q7k-Hormone and 3hb5-oxidoreductase receptor of breast cancer. The proton–ligand dissociation constant of the azo compounds (HLn) and metal–ligand stability constants of their complexes with metal ions (Mn2+, Co2+, Ni2+ and Cu2+) have been determined by potentiometric technique in 0.1M KCl and 40% (by volume) DMF–water mixture. For the same ligand at constant temperature, the stability constants of the formed complexes increase in the order Mn2+, Co2+, Ni2+ and Cu2+. The effect of temperature was studied at 303, 313 and 323K and the corresponding thermodynamic parameters (∆G, ∆H and ∆S) were derived and discussed. The dissociation process is non-spontaneous, endothermic and entropic ally unfavorable. The formation of the metal complexes has been found to be spontaneous, endothermic and entropic ally favorable.

Geometrical structure, molecular docking, potentiometric and thermodynamic studies of 3-aminophenol azodye and its metal complexes

The proton–ligand dissociation constants of 4-(2,3-dimethyl-1-phenylpyrazol-5-one azo)-3-aminophenol (HL) and its metal stability constants with Mn(II), Co(II), Ni(II) and Cu(II) ions have been determined using potentiometric studies. The molecular structure of the ligand is optimized theoretically and the quantum chemical parameters are calculated. The proton–ligand dissociation constants of HL and its metal stability constants with Mn(II), Co(II), Ni(II) and Cu(II) have been determined potentiometrically. The potentiometric studies were carried out in 0.1M KCl and 20% (by volume) DMF–water mixture. At constant temperature the stability constants of the formed complexes decrease in the order of Cu(II)>Ni(II)>Co(II)>Mn(II). The effect of temperature was studied at 298, 308 and 318K and the corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were derived and discussed. The dissociation process is non-spontaneous, endothermic and entropically unfavorable. The formation of the metal complexes has been found to be spontaneous, endothermic and entropically favorable. Molecular docking was used to predict the binding between azodye ligand and the receptor of prostate cancer mutant 2q2k-Hormon and receptor of breast cancer mutant 3hb5-Oxidoreductase.

Potentiometry and geometrical structure of some azodye compounds and their metal complexes

A series of ligands of quinoline azodye derivatives (HLI–HLVI) have been prepared and characterized by elemental analysis, X-ray diffraction analysis, 1H NMR and IR spectra. The proton–ligand dissociation constant of the ligands (HLI–HLVI) and the metal stability constant of their Mn2+, Co2+, Ni2+, Cu2+, La3+, UO22+ and Th4+ complexes have been determined potentiometrically in 1M KC1 and 40% (V:V) EtOH–water mixture. The molecular structure of each ligand was optimized theoretically and the quantum chemical parameters were calculated. The influence of derivatives on the dissociation and stability constants was examined on the basis of the electron repelling property of the derivatives. Order of the stability constant of the formed complexes was found to be Mn2+Co2+Ni2+Cu2+La3+UO22+Th4+. The effect of temperature was studied and the corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were derived and discussed. The dissociation process was found to be non-spontaneous, endothermic and entropically unfavorable. On the other hand the formation of the metal complexes was found to be spontaneous, endothermic and entropically favorable.

Supramolecular structure of azodye rhodanine compounds and their complexes: a review

The optical absorption properties of 5-(4′-derivatives phenylazo)-2-thioxothiazolidin-4-one (HLn) (where X = H) thin films have been studied. It was found that the values of the energy band gap, Eg, for derivatives were in the range of 1.77–2.29 eV depending on the nature of the substituent. The optical values of the energy band gap (Eg) for all derivatives near the absorption edge were found to be direct allowed transition. The synthesized ligands (HLn) (where X = H) were screened as antibacterial and antifungal agents. The proton–ligand dissociation constant of the rhodanine azo derivatives (HLn) (where X = H and X = P-OCH3Ph) and metal–ligand stability constants of their complexes with metal ions (Mn2+, Co2+, Ni2+, Cu2+ and Zn2+) have been determined potentiometrically in 0.1 M KCl. The stoichiometries of copper(II) and cadmium(II) complexes of HLn (where X = Ph) were determined conductometrically and indicated the formation of 1:1 and 1:2 (metal:ligand) complexes. The molar ratio of ligand (HLn) (where X = H) and Ru(III) complexes is (1:2)/(1:3)(M:Ln), respectively. The study revealed octahedral geometry around Ru(III) complexes. A series of heterocyclic mixed ligands of oxovanadium(IV) complexes have been synthesized by the reaction of vanadium(IV) sulfate with rhodanine azo (HLn) (where X = H) in the presence of β-diketone (LH). Palladium(II) complexes of the general formula [Pd(Ln)L] (where LH = diketone = acetylacetone, HLn = azorhodanine) have been synthesized. In these complexes, the azo ligand acts as a monobasic bidentate ligand and is coordinated to the metal ion through the azo-nitrogen, enolic oxygen atoms forming stable six-membered heterocyclic rings. The D.C. electrical conductivity of HLn (where X = Ph) and their complexes were measured. The bond lengths and the force constants have been calculated for uranyl complexes (26–30) of HLn (where X = Ph). The plotting of r1, r2 and r3 (bond distance, rU–O) versus ν3 give a straight line with increasing the value of ν3 and decreasing rU–O.

Geometrical structure and potentiometric studies of 5-chloro-2,3-dihydroxy pyridine azo derivatives and their metal complexes

5-Chloro-3-hydroxy-4-(phenylediazenyl)pyridine-2(1H)-one and its derivatives (HLn) were synthesized and characterized using different spectroscopic techniques. The geometrical structures of the ligands are carried out by HF method with 3-21G basis set. The proton–ligand dissociation constant of the ligands (HLn) and their metal–ligand stability constants with (Mn2+, Co2+, Ni2+ and Cd2+) have been determined potentiometrically. The potentiometric studies were carried out in 0.1M (KCl) and 10% (by volume) DMF–water mixture. The effect of temperature was studied at (298, 308 and 318K) and the corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were derived and discussed. The dissociation process is non-spontaneous, endothermic and entropically unfavorable. The formation of the metal complexes has been found to be spontaneous, endothermic and entropically favorable.

Geometrical structure, potentiometric and thermodynamic studies of rhodanine azodye and its metal complexes

5-(2,3-Dimethyl-1-phenylpyrazol-5-one azo)-2-thioxo-4-thiazolidinone (HL) was synthesized and characterized using different spectroscopic techniques. The molecular structures of the ligand are optimized theoretically and the quantum chemical parameters are calculated. The proton–ligand dissociation constants of HL and its metal stability constants with Mn2+, Co2+, Ni2+ and Cu2+ have been determined potentiometrically. The potentiometric studies were carried out in 0.1M KCl and 10% (by volume) DMF–water mixture. At constant temperature the stability constants of the formed complexes decreases in the order Cu2+, Ni2+, Co2+ and Mn2+. The effect of temperature was studied at (298, 308 and 318K) and the corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were derived and discussed. The dissociation process is non-spontaneous, endothermic and entropically unfavorable. The formation of the metal complexes has been found to be spontaneous, endothermic and entropically favorable

Spectroscopic, potentiometric and thermodynamic studies of azo rhodanines and their metal complexes

The proton–ligand dissociation constant of 5-(4′-arylazo)-2-thioxothiazolidin-4-one (HLn) and metal–ligand stability constants of their complexes with metal ions (Mn2+, Co2+, Ni2+, Cu2+ and Zn2+) have been determined potentiometrically in 0.1M KCl and 50% (by volume) methanol–water mixture. The molecular and electronic structures of the investigated compounds (HLn) were also studied using quantum chemical calculations. For the same ligand at constant temperature, the stability constants of the formed complexes increase in the order Cu2+>Zn2+>Ni2+>Co2+>Mn2+. The effect of temperature was studied at (303, 313 and 323) K and the corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were derived and discussed. The dissociation process is non-spontaneous, endothermic and entropically unfavorable. The formation of the metal complexes has been found to be spontaneous, endothermic and entropically favorable. The pKH value of the ligands increases in the order HL1>HL2>HL3.

Colloidal potentials mediated by specific biomolecular interactions.

We present a systematic study of receptor-ligand interactions with increasing complexity from interactions in bulk solution, on planar and colloid surfaces, and as part of mediating colloidal pair interactions. We report analytical models that relate receptor-ligand dissociation constants (KD), interactions potentials (U(r)), and adsorbed amounts (θ) for different ligand sizes, concentrations and immobilized receptor coverages. Analytical results are validated for hard core + harmonic well receptor-ligand interactions in bulk and interfacial systems using Monte Carlo (MC) simulations, although any biomolecular interaction can be incorporated into the reported analysis via a "B2 device". Results from analytical models are used to understand potentials of mean force (W(L)) for ligand mediated interactions between receptor decorated colloids. W(L) are generated using MC-umbrella sampling (MC-US) simulations with cluster moves, which provide self-consistent comparisons of net colloid scale interactions with receptor-ligand scale information. Our findings capture how receptor-ligand interactions mediate colloid scale interactions relevant to self-assembly, drug delivery, and biosensing.

Oxo-Bridged Dinuclear Chromium(III) Complexes: Correlation between the Optical and Magnetic Properties and the Basicity of the Oxo Bridge

The synthesis and X-ray structure of a new member of the series of oxo-bridged, dinuclear chromium(III) complexes, the methyl isocyanide complex [(CH3NC)5CrOCr(CNCH3)5](PF6)4·2CH3CN, is reported. This constitutes only the third oxo-bridged, dinuclear chromium(III) complex with a homoleptic auxillay ligand sphere. Experimentally, the system shows unshifted narrow nuclear magnetic resonance (NMR) spectra that are consistent with calculations using broken symmetry density functional theory (DFT), which suggests it to be the strongest coupled, dinuclear chromium(III) complex known. Furthermore, we report the crystal structure and computed magnetic properties for [(bpy)2(SCN)CrOCr(NCS)(bpy)2](ClO4)2·2H2O (bpy = 2,2'-bipyridine), which differs from other reported oxo-bridged species by featuring a bent CrOCr(4+) core. We also interpret the spectacular 10-orders-of-magnitude variation in acid dissociation constant of the bridging hydroxo ligand in mono hydroxo-bridged dinuclear chromium(III) complexes, in terms of a valence bond model parametrized by metal-to-metal charge transfer (MMCT) and ligand-to-metal charge transfer (LMCT) energies.

The Role of Conformational Flexibility in Inhibitor Binding and Substrate Recognition for Cyp119

Conformational flexibility of several cytochromes P450 has been observed in response to substrate and ligand binding, and thus may play an important role in catalysis. CYP119, a bacterial thermophilic protein from cytochrome P450 superfamily has been observed in three different conformations with different inhibitors bound using X-ray crystallography, but the significance of these states in solution and in the function of the enzyme is not well known. According to the crystal structures, much of the diversity in conformational states arises in F and G helices, which fold around the substrate binding site at the distal heme face. Double electron electron resonance (DEER) was used to measure the average distances and the distance distributions between spin-labels for populated conformational states in solution. Pairs of spin-labels were introduced by coupling to engineered cysteines on the protein surface, and the effects of labeling on ligand dissociation constants (Kd) and enzyme function were characterized. DEER results from three different mutants of CYP119 indicated that 4-Phenylimidazole binding results in a conformational state that is distinct substrate-free and Imidazole-bound forms. The DEER distance changes between the two conformational states were determined as 10A for two of the mutants and 12A for the other one. Data will also be presented for the complex between CYP119 its proposed substrate, lauric acid. These results will be discussed in terms of models for substrate recognition and gated functional behavior in these enzymes.

19F NMR spectroscopy monitors ligand binding to recombinantly fluorine-labelled b′x from human protein disulphide isomerase (hPDI)

We report a protein-observe (19)F NMR-based ligand titration binding study of human PDI b'x with Δ-somatostatin that also emphasises the need to optimise recombinant protein fluorination when using 5- or 6-fluoroindole. This study highlights a recombinant preference for 5-fluoroindole over 6-fluoroindole; most likely due to the influence of fluorine atomic packing within the folded protein structure. Fluorination affords a single (19)F resonance probe to follow displacement of the protein x-linker as ligand is titrated and provides a dissociation constant of 23 ± 4 μM.

The N-terminal fragment of Acanthamoeba polyphaga mimivirus tyrosyl-tRNA synthetase (TyrRSapm) is a monomer in solution

Acanthamoeba polyphaga mimivirus tyrosyl-tRNA synthetase (TyrRSapm) was the first reported aminoacyl-tRNA synthetase of viral origin. The previous crystal structure of TyrRSapm showed a non-canonical orientation of the dimer conformation and the CP1 domain, responsible for dimer formation, displays a major modification of a motif structurally conserved in other TyrRS structures. An earlier study reported that Bacillus stearothermophilus N-terminal TyrRS exists as a dimer under native conditions. N-terminal TyrRSapm (ΔTyrRSapm, 1–234 aa) was constructed to remove the C-terminal anticodon-binding domain. Here we show by Ferguson plot analysis and analytical ultracentrifugation that ΔTyrRSapm exists as a monomer and contains a disulfide-bridge. The ΔTyrRSapm loses the ability to bind tRNATyr, however it remains active in pyrophosphate exchange with similar ligand dissociation constants as the full-length enzyme. Structured summary of protein interactionsTyrRSapm and TyrRSapmbind by cosedimentation in solution (View interaction) TyrRSapmandTyrRSapmbindbyblue native page(View interaction)TyrRSapmandTyrRSapmbindbyfluorescence technology(View interaction)TyrRSapmandTyrRSapmbindbyfluorescence technology(View interaction)

Quantitative analysis of pheromone‐binding protein specificity

Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins, using β-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila odorant-binding protein that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in Escherichia coli was assessed by measuring N-phenyl-1-naphthylamine (NPN) binding and Förster resonance energy transfer between LUSH tryptophan 123 (W123) and NPN. Binding of cVA was measured from quenching of W123 fluorescence as a function of cVA concentration. The equilibrium constant for transfer of cVA between β-cyclodextrin and LUSH was determined from a linked equilibria model. This constant, multiplied by the β-cyclodextrin-cVA dissociation constant, gives the LUSH-cVA dissociation constant: ∼100 nM. It was also found that other ligands quench W123 fluorescence. The LUSH-ligand dissociation constants were determined to be ∼200 nM for the silk moth pheromone bombykol and ∼90 nM for methyl oleate. The results indicate that the ligand-binding cavity of LUSH can accommodate a variety ligands with strong binding interactions. Implications of this for the Laughlin, Ha, Jones and Smith model of pheromone reception are discussed.

Increased precision for analysis of protein–ligand dissociation constants determined from chemical shift titrations

NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K ( D )) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K ( D ), and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K ( D ) and the maximum chemical shift change (Δδ(max)). During a typical NMR titration, the initial protein concentration, [P (0)], is held nearly constant. For this condition, to determine the most accurate parameters for K ( D ) and Δδ(max) from nonlinear least squares analyses requires initial protein concentrations that are ~0.5 × K ( D ), and a maximum concentration for the ligand, or titrant, of ~10 × [P (0)]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K ( D ) and Δδ(max) values when [P (0)] > K ( D ). Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K ( D ) and Δδ(max)) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

Weak affinity ligands selection using quartz crystal microbalance biosensor: Multi-hydroxyl amine ligands for protein separation

Multi-hydroxyl amines including tris(hydroxymethyl)aminomethane (Tris), serinol and ethanolamine were selected as weak affinity ligands using a rapid screening by quartz crystal microbalance (QCM) biosensor. Based on the specific recognition between the ligands and two proteins, lysozyme (LZM) and cytochrome c (Cyt c), a weak affinity chromatography method was developed for specific separation of the two proteins. The frontal analysis results showed that the apparent dissociation constants ( K D) of ligand–protein complexes were all in the order of weak affinity (10 −4 M). By weak affinity columns modified with the three multi-hydroxyl amines individually, LZM and Cyt c were baseline separated as retarded peaks from non-specific protein and each other in a single cycle of loading and eluting. Moreover, the Tris-modified column typically showed the satisfactory repeatability and stability as a new type of weak affinity columns. The present strategy composed of QCM selecting and affinity chromatography separating was promising to extend the variety of weak affinity ligands and develop inexpensive specific affinity methods for separation and purification of multiple proteins on one single column.

The L76V Drug Resistance Mutation Decreases the Dimer Stability and Rate of Autoprocessing of HIV-1 Protease by Reducing Internal Hydrophobic Contacts

The mature HIV-1 protease (PR) bearing the L76V drug resistance mutation (PR(L76V)) is significantly less stable, with a >7-fold higher dimer dissociation constant (K(d)) of 71 ± 24 nM and twice the sensitivity to urea denaturation (UC(50) = 0.85 M) relative to those of PR. Differential scanning calorimetry showed decreases in T(m) of 12 °C for PR(L76V) in the absence of inhibitors and 5-7 °C in the presence of inhibitors darunavir (DRV), saquinavir (SQV), and lopinavir (LPV), relative to that of PR. Isothermal titration calorimetry gave a ligand dissociation constant of 0.8 nM for DRV, ∼160-fold higher than that of PR, consistent with DRV resistance. Crystal structures of PR(L76V) in complexes with DRV and SQV were determined at resolutions of 1.45-1.46 Å. Compared to the corresponding PR complexes, the mutated Val76 lacks hydrophobic interactions with Asp30, Lys45, Ile47, and Thr74 and exhibits closer interactions with Val32 and Val56. The bound DRV lacks one hydrogen bond with the main chain of Asp30 in PR(L76V) relative to PR, possibly accounting for the resistance to DRV. SQV shows slightly improved polar interactions with PR(L76V) compared to those with PR. Although the L76V mutation significantly slows the N-terminal autoprocessing of the precursor TFR-PR(L76V) to give rise to the mature PR(L76V), the coselected M46I mutation counteracts the effect by enhancing this rate but renders the TFR-PR(M46I/L76V) precursor less responsive to inhibition by 6 μM LPV while preserving inhibition by SQV and DRV. The correlation of lowered stability, higher K(d), and impaired autoprocessing with reduced internal hydrophobic contacts suggests a novel molecular mechanism for drug resistance.

Effect of ionic strength on the stabilities of ciprofloxacin – Metal complexes

Proton–ligand dissociation constant of 1-cyclopropyl-1,4-dihydro-4-oxo-7-(1-piperazinyl) quinolone-3-carboxylic acid is ciprofloxacin and metal–ligand stability constants of its complexes with some metal ions have been determined potentiometrically in the presence of (0.01, 0.02 and 0.03 mol/dm3) NaClO4. The order of the stability constants of the formed complexes increases in the sequence Cu2+, Fe3+, Ni2+ and Zn2+ and decreases with increase in the concentration of ionic strength.

Potentiometric and Thermodynamic Studies of 4-(1H-Indol-3-yl)butanoic Acid and Its Metal Complexes

The proton−ligand dissociation constants of 4-(1H-indol-3-yl)butanoic acid and the stability constants of its metal−ligand complexes with (Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+, and UO22+) have ...

Nickel(II) and Cobalt(II) 3‐Hydroxy‐4‐pyridinone Complexes: Synthesis, Characterization and Speciation Studies in Aqueous Solution

AbstractThe interaction of nickel(II) and cobalt(II) with a set of 3‐hydroxy‐4‐pyridinone ligands (Hmpp, Hmepp, Hetpp, Hempp, Hdepp and Hdmpp) was investigated in aqueous solution. The family of chelators under study is pharmaceutically relevant in the treatment of iron‐overloaded patients and it is foreseen to be of use in occupational health situations associated with accumulation of nickel and cobalt such as nasal/pulmonary and skin hazards and allergies. Ligand dissociation constants and stability constants for the cobalt(II) and nickel(II) complexes have been determined by potentiometric methods allowing the establishment of the corresponding speciation plots as a function of pH. The values of the stability constants are consistent with the Irving–Williams series and indicate the formation of stable ML2 complexes which were isolated and characterized. Following the trend observed for 3‐hydroxy‐4‐pyridinone ligands the solids were obtained as hydrates whose composition was characterized as [ML2(H2O)2]·xH2O complexes. DFT calculations allowed geometry optimization and provided information about bond lengths and angles.

Potentiometric and Thermodynamic Studies of Vanillin and Its Metal Complexes

The proton−ligand dissociation constant of vanillin (4-hydroxy-3-methoxy benzaldehyde) and metal−ligand stability constants of its complexes with metal ions (Mn2+, Co2+, Ni2+, Cu2+, and Zn2+) have been determined potentiometrically in 0.1 mol·dm−3 KCl and 10 % (by volume) ethanol−water mixture and at (298, 308, and 318) K. The stability constants of the formed complexes increase in the order Mn2+, Co2+, Ni2+, Zn2+, and Cu2+. The effect of temperature was studied, and the corresponding thermodynamic parameters (ΔG, ΔH, and ΔS) were derived and discussed. The dissociation process is nonspontaneous, endothermic, and entropically unfavorable. The formation of the metal complexes has been found to be spontaneous, endothermic, and entropically favorable.