Exploring the binding mechanism of dihydropyrimidinones to human serum albumin: spectroscopic and molecular modeling techniques

The binding mechanism of molecular interaction between 5-(ethoxycarbonyl)-6-methyl-4-phenyl-3,4-dihydropyrimidin-2(1H)-one (a dihydropyrimidinones derivative, EMPD) and human serum albumin (HSA) was studied using spectroscopic methods and modeling technique. The quenching mechanism was investigated in terms of the binding constants and the basic thermodynamic parameters. The results of spectroscopic measurements suggested that EMPD have a strong ability to quench the intrinsic fluorescence of HSA through static quenching procedure. The drug-protein complex was stabilized by hydrophobic forces and hydrogen bonding as indicated from the thermodynamic parameters and synchronous fluorescence spectra, which was consistent with the results of molecular docking and accessible surface area calculation. Competitive experiments indicated that a displacement of warfarin by EMPD, which revealed that the binding site of EMPD to HSA was located at the subdomains IIA. The distance between the donor and the acceptor was 4.85nm as estimated according to F?rster's theory of non-radiation energy transfer. The effect of metal ions on the binding constants was also investigated. The results indicated that the binding constants between EMPD and HSA increased in the presence of common metal ions.     

Polarographic Detection of Arenediazonium Ions. Optimization of the Method and Application for Investigating Dediazoniation Mechanisms

The use of differential pulse polarography (DPP) at the dropping mercury electrode (DME) to detect and to investigate the mechanisms for decomposition of arenediazonium ions, ArN₂⁺, under different experimental conditions is discussed. The effect of a number of experimental and instrumental parameters on the polarographic peaks of a model arenediazonium ion was explored and representative applications to investigate their reaction mechanisms are given. The composite data shows that DPP provides an alternative, relatively cheap, technique to monitor ArN₂⁺ decomposition in, for example, opaque systems where, for obvious reasons, spectroscopic detection does not work; meanwhile in homogeneous systems, DPP complements the results obtained by employing spectroscopic or chromatographic techniques. In addition, a variety of valuable mechanistic information such as detection of transient intermediates or estimation of the binding constants of aryl radicals with macromolecular systems, that otherwise cannot be easily obtained, is readily available by using DPP.     

Anthracene coupled trans-pyridylcinnamide: a new fluororeceptor for selective sensing of dicarboxylates

trans-Pyridylcinnamide has been established as an alternative hydrogen bonding synthon, in place of urea for carboxylate binding. This alternative motif has been used in the design and synthesis of new fluorescent ‘On-Off’ signalling chemical sensor 1, which is found to bind aliphatic dicarboxylates with moderate binding constants. The recognition ability has been established by fluorescence, UV-vis and ¹H NMR spectroscopic methods. The receptor is found to be selective for long chain pimelate.     

Synthesis, optical properties, and LFER analysis of solvent-dependent binding constants of Hamilton-receptor-connected merocyanine chromophores

A merocyanine dye equipped with a Hamilton-receptor unit has been synthesized that enables strong noncovalent binding of other merocyanine dyes bearing barbituric acid acceptor groups by six hydrogen bonds. NMR and UV/vis titration experiments in toluene, chloroform, dichloromethane, dioxane, and THF provide evidence for the formation of 1:1 complexes even in the dipolar solvents. An enhanced binding strength is observed for the more dipolar merocyanine dyes in the head-to-tail assembly structure with binding constants up to >10 (8) M (-1) in toluene. In the present bimolecular complexes two merocyanine chromophores are assembled in a head-to-tail fashion that affords increased dipole moments as demanded for efficient electric field induced poling processes in nonlinear optical and photorefractive polymeric hosts. The solvent dependency of the binding constants for various barbituric acid dye-Hamilton receptor complexes as well as a perylene imide-melamine complex reveals linear free energy relationships (LFER) that allow for an estimation of binding constants larger than 10 (12) M (-1) for Hamilton receptor organized head-to-tail merocyanine bimolecular complexes in aliphatic solvents. It is suggested that such LFER are valuable tools for the estimation of binding constants in solvents where experimental binding constants cannot be determined because of solubility or spectroscopic problems.     

Side chain-dependent binding of antitumor indoloquinoxaline derivatives to DNA: comparative spectroscopic and viscometric measurements

NCA0424 (1) and its side chain positional isomer, NCA0465 (2), are indoloquinoxaline derivatives with potent antitumor activity. To investigate the effect of side chain position for binding with DNA, the interactions of 2 with various B-form DNAs were studied by spectroscopic (circular dichroism (CD), fluorescence and UV) and viscosity measurements and were compared with those of 1. The binding preference for the base sequence was different in each case. The CD spectra showed that 2 formed an asymmetric binding of indoloquinoxaline ring with adenine in DNA, whereas such a base selectivity was not found with 1. The binding features are discussed based on association constants and thermodynamic parameters, indicating the importance of the side chain position for binding specificity for DNA.     

四种黄酮类化合物与牛血清白蛋白相互作用的光谱分析

在人体生理pH条件下,利用紫外吸收光谱和荧光光谱研究了槲皮素(QUE)、大豆甙元(DAI)、4′,7-二甲氧基-3′-异黄酮磺酸钠(DISS)和3′-大豆甙元磺酸钠(DSS)四种黄酮类化合物与牛血清白蛋白(BSA)的相互作用,结合反应机理对其进行了初步探讨;并计算了结合位点数和结合常数.紫外吸收光谱分析结果表明,在pH=7.4条件下,黄酮类化合物中疏水性的苯环与BSA疏水腔中的氨基酸残基发生作用,从而导致药物分子的吸收峰红移,用Scatchard拟合法可求得DAI及DSS与BSA的结合常数.荧光光谱分析结果表明,BSA对DAI、DISS和DSS均有明显的敏化增强效应,计算得到的增强速率常数分别为1.39×1011,7.72×1011和1.93×1012L·s-1·mol-1,并可求得结合位点数和结合常数.     

Affinity Capillary Electrophoresis: From Binding Measurement to Combinatorial Library Screening

Affinity capillary electrophoresis is a new procedure for receptor-ligand binding studies. Since its introduction in the early 1990s, this method has proved valuable in chiral separation of racemates, the measurement of binding constants, the estimation of kinetic rate constants, the determination of stoichiometries, the investigation of electrostatic interactions, the estimation of effective charges and molecular weights of biomolecules, the characterization of enzymatic catalysis, and, most recently, combinatorial library screening in solutions. This technique demands small amounts of samples, involves no radiolabeled materials or chemically immobilized ligands, and does not require changes in spectroscopic characteristics upon binding. This paper reviews the most recent applications of affinity capillary electrophoresis in binding measurement and combinatorial library screening.     

Development of a fluorescence model for the determination of constants associated with binding,quenching, and Förster resonance energy transfer efficiency

Determining accurate dissociation constants for equilibrium processes involving a fluorescent mechanism can prove to be quite challenging. Typically, titration curves and nonlinear least squares fitting of the data using computer programs are employed to obtain such constants. However, these approaches only consider the total fluorescence signal and often ignore other energy transfer processes within the system. The current model considers the impact on fluorescence from equilibrium binding (viz., metal-ligand, ligand-substrate, etc.), quenching, and resonance energy transfer. This model should provide more accurate binding constant as well as insights into other photonic processes. The equations developed for this model are discussed and are applied to experimental data from titrimetric experiments. Since the experimental data are generally in excess of the number of parameters that are needed to define the system, fitting is operated in an overdetermined mode and employs error minimization (either absolute or relative) to define goodness of fit. Examples of how changes in certain parameters affect the shape of the titrimetric curve are also presented. The current model does not consider chelation-enhanced fluorescence.     

Spectroscopic studies on the interaction between riboflavin and albumins

The interactions between riboflavin (RF) and human and bovine serum albumin (HSA and BSA) were studied by using absorption and fluorescence spectroscopic methods. Intrinsic fluorescence emission spectra of serum albumin in the presence of RF show that the endogenous photosensitizer acts as a quencher. The decrease of fluorescence intensity at about 350 nm is attributed to changes in the environment of the protein fluorophores caused by the ligand. The quenching mechanisms of albumins by RF were discussed. The binding constants and binding site number were obtained at various temperatures. The distance between albumins and RF in the complexes suggests that the primary binding site for RF is close to tryptophan residue (Trp214) of HSA and Trp212 of BSA. The hydration process of albumins has also been discussed.     

Binding of methyl orange and the hydrophobic fluorescent probe, 2-p-toluidinylnaphthalene-6-sulfonate,by 2-dialkylaminoethyl methacrylate-N-vinyl-2-pyrrolidone and related copolymers

The copolymers of N-vinyl-2-pyrrolidone and 2-dimethylaminoethyl methacrylate, 2-diethylaminoethyl methacrylate, 2-dimethylaminoethyl acrylate, or 2-dimethylaminopropyl acrylamide have been prepared. Studies were made of the binding of a “binding probe,” methyl orange, by the copolymers in aqueous solution. The first binding constants accompanying the binding were evaluated. Furthermore, the intensity of fluorescence of a hydrophobic fluorescent probe, 2-p-toluidinylnaphthalene-6-sulfonate, in the presence of these polymers was investigated. The nature and phenomena of dye binding and hydrophobic fluorescent probe binding with the polymers are discussed.     

Porphyrin dyads linked by a rotatable 3,3'-biphenyl scaffold: a new binding motif for small ditopic molecules

Synthetic access to a set of metallo- and free base bis-porphyrins has been provided by a stepwise approach involving sequential peptide and Suzuki couplings. Linking these porphyrins through a 3,3'-biphenyl bridge enables cooperative binding to ditopic ligands such as the bipyridyls. Association constants and binding stoichiometry has been determined by spectroscopic/spectrophotometric means and the differences in the binding affinities of a small series of diaza ligands is discussed in the context of structural fit and microscopic association constants.     

Application of cyclodextrin-mediated capillary electrophoresis to simultaneously determine the apparent binding constants and thermodynamic parameters of naphthalenesulfonate derivatives

Application of capillary electrophoresis (CE) to simultaneously determine the apparent binding constants and thermodynamic parameters for six positional and structural naphthalenesulfonate derivatives with β-cyclodextrin (β-CD) is presented. The change in electrophoresis mobilities was used to assess the binding constants by non-linear regression and three different linear plots methods (named double reciprocal, x-reciprocal and y-reciprocal). The substituent group(s) attached to the naphthalene ring considerably affected the inclusion behaviors of these naphthalenesulfonate derivatives. The binding constant varies over almost one order of magnitude and a highly selective sequence is obtained between these guest model compounds. Naphthalenesulfonates with the substituent(s) at the 2-position(s) displayed stronger interaction with β-CD, and gave well compatible results by these four plot methods. While at least one substituent was substituted into the 1-position of naphthalene showed the weak interaction or no interaction with β-CD. Comparison to three linear regression methods, the non-linear regression method proves to be the most suitable for these determinations. Additionally, apparent binding constants for each structural isomer with β-CD at several temperature, and thermodynamic parameters for binding were also calculated and discussed.     

Amphiphilic copolymers with increased affinity for substrates

The copolymers of methyl quaternized 2-dimethylaminoethyl acrylate and styrene, 2-vinyl naphthalene, acrylic acid iso-octyl ester, or acrylic acid n-butyl ester have been prepared. Studies were made of the binding of a “binding probe,” methyl orange, by the copolymers in aqueous solution. The first binding constants and the thermodynamic parameters in the course of the binding were evaluated. Furthermore, the intensity of fluorescence of a hydrophobic fluorescent probe, 2-p-toluidinylnaphthalene-6-sulfonate, in the presence of these polymers was investigated. In addition, the fluorescence spectra of monomer and excimer emissions of the polymers with aromatic residues were measured. The excimer/monomer fluorescence intensity ratio was studied in the presence of various additives such as methyl orange, urea, methanol, and NaCl to gain an insight into the nature of microdomains in the polymer. The nature and phenomena of dye binding and hydrophobic fluorescent probe binding with the polymers are discussed. © 1993 John Wiley & Sons, Inc.     

Selective binding behaviors of p-sulfonatocalixarenes in aqueous solution

The complex structures, binding abilities, molecular selectivities, and thermodynamic origin of p-sulfonatocalixarenes upon complexation with kinds of guests are outlined in this review article, including inorganic cations, organic ammonium cations, pyridiniums and viologens, neutral organic molecules, dye molecules, and others. Calorimetric and spectroscopic investigations afford the complex stability constants, thermodynamic parameters and binding manners of the inclusion complexation of p-sulfonatocalixarenes with guest molecules. The π-stacking, hydrophobic and charge interactions are the main driving-forces during the course of the host–guest inclusion complexation. The molecular binding abilities and selectivities are influenced by not only the frameworks of calixarene cavities, structures of guest molecules, and their binding manners but also the conditions of solutions (mainly pH), which are discussed from the correlation between the structural features and molecular-recognition abilities. Moreover, the further applications and potentials of p-sulfonatocalixarenes are briefly described.     

Independent linear combinations of spectroscopic constants for axially symmetric molecules

The problems of indeterminacy and correlation of spectroscopic constants of axially symmetric molecules are discussed in the dependence on the selection rules of the data set used in analysis of high resolution infrared spectra. Derivation of independent linear combinations of the correlated spectroscopic parameters, for several cases of the allowed and forbidden bands, is carried out for the most important molecular point groups, up to the third order theory. The significance of the forbidden, overtone and hot band transitions in the separate determination of individual constants is also evaluated.     

苯胺蓝黑与人血清白蛋白的相互作用及对其构象的影响

利用荧光光谱和同步荧光光谱研究了不同温度下苯胺蓝黑与人血清白蛋白相互作用时的荧光猝灭及构象的变化情况。实验结果表明,苯胺蓝黑与人血清白蛋白之间可以发生相互作用,而且有较强的结合。同步荧光光谱研究了人血清白蛋白与苯胺蓝黑的相互作用中人血清白蛋白构象的变化,结果显示二者结合改变了蛋白质的微环境。热力学参数说明小分子与蛋白质的作用以疏水作用为主。     

Resolution and uniqueness of estimated parameters of a model of thin filament regulation in solution

The estimation of chemical kinetic rate constants for any non-trivial model is complex due to the nonlinear effects of second order chemical reactions. We developed an algorithm to accomplish this goal based on the Damped Least Squares (DLS) inversion method and then tested the effectiveness of this method on the McKillop–Geeves (MG) model of thin filament regulation. The kinetics of MG model is defined by a set of nonlinear ordinary differential equations (ODEs) that predict the evolution of troponin–tropomyosin–actin and actin–myosin states. The values of the rate constants are estimated by integrating these ODEs numerically and fitting them to a series of stopped-flow pyrene fluorescence transients of myosin-S1 fragment binding to regulated actin in solution. The accuracy and robustness of the estimated rate constants are evaluated for DLS and two other methods, namely quasi-Newton (QN) and simulated annealing (SA). The comparison of these methods revealed that SA provides the best estimates of the model parameters because of its global optimization scheme. However it converges slowly and does quantify the uniqueness of the estimated parameters. On the other hand the QN method converges rapidly but only if the initial guess of the parameters is close to the optimum values, otherwise it diverges. Overall, the DLS method proves to be the most convenient method. It converges fast and was able to provide excellent estimates of kinetic parameters. Furthermore, DLS provides the model resolution matrix, which quantifies the interdependence of model parameters thereby evaluating the uniqueness of their estimated values. This property is essential for estimating of the dependence of the model parameters on experimental conditions (e.g. Ca²⁺ concentration) when it is assessed from noisy experimental data such as pyrene fluorescence from stopped-flow transients. The advantages of the DLS method observed in this study should be further examined in other physicochemical systems to firmly establish the observed effectiveness of DSL vs. the other parameter estimation methods.     

用光谱法研究奥硝唑与人血清白蛋白的相互作用

采用荧光光谱法和紫外可见吸收光谱法研究了奥硝唑与人血清白蛋白之间的相互作用;求得了二者在不同温度下的结合常数KA和结合位点数n,以及对应温度下结合反应的热力学参数,同时采用同步荧光分析技术探讨了蛋白质与药物结合时构象的变化.结果表明,在生理条件下奥硝唑对人血清白蛋白的荧光猝灭主要为静态猝灭;奥硝唑与人血清白蛋白主要靠静电作用力结合.     

The weakly bound He-HCCCN complex: high-resolution microwave spectra and intermolecular potential-energy surface

Rotational spectra of the weakly bound He-HCCCN and He-DCCCN van der Waals complexes were observed using a pulsed-nozzle Fourier-transform microwave spectrometer in the 7-26-GHz frequency region. Nuclear quadrupole hyperfine structures due to the 14N and D nuclei (both with nuclear-spin quantum number I = 1) were resolved and assigned. Both strong a and weaker b-type transitions were observed and the assigned transitions were used to fit the parameters of a distortable asymmetric rotor model. The dimers are floppy, near T-shaped complexes. Three intermolecular potential-energy surfaces were calculated using the coupled-cluster method with single and double excitations and noniterative inclusion of triple excitations. Bound-state rotational energy levels supported by these surfaces were determined. The quality of the potential-energy surfaces was assessed by comparing the experimental and calculated transition frequencies and also the corresponding spectroscopic parameters. Simple scaling of the surfaces improved both the transition frequencies and spectroscopic constants. Five other recently reported surfaces [O. Akin-Ojo, R. Bukowski, and K. Szalewicz, J. Chem. Phys. 119, 8379 (2003)], calculated using a variety of methods, and their agreement with spectroscopic properties of He-HCCCN are discussed.     

Synthesis and Basicity of 4-Amino-2-phenylquinazolines

 A new group of 6- and 7-substituted compounds of 4-amino-2-phenylquinazoline were synthesized by reaction of N-arylbenzimidoyl chlorides with cyanamide in the presence of TiCl₄. The products were identified by spectroscopic methods, their dissociation constants were determined and are discussed.