Understanding the DNA binding of novel non-symmetrical guanidinium/2-aminoimidazolinium derivatives

Biophysical studies have been carried out on a family of asymmetric guanidinium-based diaromatic derivatives to assess their potential as DNA minor groove binding agents. To experimentally assess the binding of these compounds to DNA, solution phase biophysical studies have been performed. Thus, surface plasmon resonance, UV-visible spectroscopy and circular and linear dichroism have been utilized to evaluate binding constants, stoichiometry and mode of binding. In addition, the thermodynamics of the binding process have been determined by using isothermal titration calorimetry. These results show significant DNA binding affinity that correlates with the expected 1?:?1 binding ratio usually observed for minor groove binders. Moreover, a simple computational approach has been devised to assess the potential as DNA binders of this family of compounds.     

Heterotropic binding of alclofenac and dansylsarcosine to bovine serum albumin

The binding data for the interaction of alclofenac (AF) and dansylsarcosine (DS) to bovine serum albumin (BSA) have respectively yielded nonlinear Scatchard plots. The plots have been subjected to Rosenthal’s method of analysis and thus the ligands have been found to possess two different kinds of sites in BSA. The binding capacities of these sites have been evaluated. The fluorescence competition studies have revealed that the binding of DS to BSA is noncompetitively inhibited by AF. Therefore, the presence of distinct binding sites for AF and DS in BSA could be inferred. The fluorescence quenching studies have also been able to demonstrate this aforesaid fact. The analysis of the quenching data by the modified Stern-Volmer plot has indicated that both the tryptophan (Trp) residues of BSA are accessible to DS for the quenching in absence of AF, but only one of them is accessible in presence of AF. This has led to suggest that the binding site of DS has been in the vicinity of loop 3–4, involving Trp-134 and Trp-212. The binding of AF at a distinct site from that of DS has exerted heterotropic interactions at the DS binding site and thereby inhibited the binding of DS to BSA.     

丝裂霉素C与牛血清蛋白结合作用的研究

结合光谱法与微量热法研究了水溶液中丝裂霉素C与牛血清白蛋白分子间的结合反应,测定了反应的结合常数K~A,结合位点数n及热力学函数△~rG~m,△~rH~m和△~rS~m,并确定了分子间作用力性质;依据Forster非辐射能量转移机制,确定了授体-受体间的结合距离和能量转移效率;采用同步荧光技术考察了丝裂霉素C对牛血清白蛋白构象的影响。     

Binding of cetylpyridinum chloride to glucose oxidase

The binding of cetylpyridinum chloride (CPC) with glucose oxidase (GOD) has been extensively studied at various experimental conditions such as ionic strength, urea concentration and pH at 25 °C, using ion-selective membrane electrodes, UV–vis absorption spectroscopy and enzyme activity assay method. The accurate binding isotherms have been obtained and analyzed in terms of Scatchard plot and binding capacity concept. The results represent two binding set system for most of studied conditions. The values of Hill equation parameters have been estimated and used for calculation of intrinsic Gibbs free energy of binding. The results have been interpreted in terms of structural viewpoint of GOD and nature of interactions in the solution. The interpretations are in good agreement with denaturation experiment. Activity measurements represent the significant activation of enzyme due to binding of first CPC molecules. However, the binding of subsequent CPC diminished the activity of enzyme which may be due to the binding of second CPC to enzyme active site. The complete deactivation of enzyme is reached due to binding of about five CPC ions.     

毛细管电泳测定物质三元相互作用体系的结合系数

毛细管电泳一般只能对二元结合体系的结合常数进行测定。研究了三元相互竞争体系的毛细管电泳测定方法,测定了金属锌离子与酒石酸和半胱氨酸以及锌离子与乳酸和半胱氨酸两个三元结合体系的结合常数,并以此比较了两种锌形态与半胱氨酸结合能力的大小。本法可用于测定两配体相互竞争结合体系的结合常数。     

SYNTHESIS OF NEW ESTRONE DERIVATIVES OF AMINO ACIDS AND PEPTIDES

A series of estrone derivatives of amino acids and peptides haze beensynthesized by different coupling reagents and the binding affinity of deblocked derivativesto the estrogen receptor of rats uteri have been measured by a comptetive radiometric bind-ing assay.     

On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues

The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar complexes have been obtained. The thermodynamic analysis of the interactions that occur upon complex formation have also been carried out. Regarding binding affinity, the obtained data have permitted the deduction that the larger the aromatic group, the higher the association constant and the binding enthalpy. In all cases, entropy opposes binding. In contrast, deactivation of the aromatic rings by attaching fluorine atoms decreases the binding affinity, with a concomitant decrease in enthalpy. The role of the chemical nature of the aromatic ring for establishing sugar contacts has been thus evaluated.     

Towards a rational spacer design for bivalent inhibition of estrogen receptor

Estrogen receptors are known drug targets that have been linked to several kinds of cancer. The structure of the estrogen receptor ligand binding domain is available and reveals a homodimeric layout. In order to improve the binding affinity of known estrogen receptor inhibitors, bivalent compounds have been developed that consist of two individual ligands linked by flexible tethers serving as spacers. So far, binding affinities of the bivalent compounds do not surpass their monovalent counterparts. In this article, we focus our attention on the molecular spacers that are used to connect the individual ligands to form bivalent compounds, and describe their thermodynamic contribution during the ligand binding process. We use computational methods to predict structural and entropic parameters of different spacer structures. We find that flexible spacers introduce a number of effects that may interfere with ligand binding and possibly can be connected to the low binding affinities that have been reported in binding assays. Based on these findings, we try to provide guidelines for the design of novel molecular spacers.     

Novel enantioselective receptors for N-protected glutamate and aspartate

A series of chiral bisthiourea macrocycles 1-4 have been prepared and their binding properties with various dicarboxylate salts have been examined by using NMR titration and isothermal calorimetry experiments. Macrocycle 1, in particular, favours the 1:1 binding of N-protected L-glutamate and aspartate, but favours 1:2 binding of the corresponding D-amino acids in polar solvents (dimethyl sulfoxide and acetonitrile). The macrocycles, however, do not bind carboxylates at all in the less competitive solvent chloroform. The binding properties of these macrocyles are sensitive to small structural changes as demonstrated by the altered binding properties of macrocycles 2-4 compared with 1.     

银团簇结构与特性的分子动力学研究

用分子动力学方法模拟了银团簇的结构与力能学.计算模拟中使用了一种基于第一性原理的原子间互作用多体势函数.通过分子动力学模拟确定了银微团簇(原子个数3～13)的稳态结构;模拟了原子个数为13～141的银FCC晶体结构理想球形团簇的力能学,发现球形银团簇形成三雏紧密结构;计算了平均结合能,给出了结合能随团簇原子数N的变化图,发现随N增大团簇结合能逐渐接近块材的数值.     

电动势法研究蛋白质与季铵盐Gemini表面活性剂的相互作用

利用自制的季铵盐Gemini表面活性剂二溴化-N,N′-二（二甲基十二烷基）丙二铵（C12-3-C12·2Br）离子选择电极,通过电动势(EMF)法研究了C12-3-C12·2Br与牛血清白蛋白(BSA)之间的相互作用,得到了C12-3-C12·2Br在BSA大分子上结合过程的结合等温线和对应的Scatchard曲线,并通过结合能力的概念得到了结合过程的结合位点数、Hill系数及Hill结合常数。通过研究发现,C12-3-C12·2Br与BSA大分子的结合具有正的协同作用,相互结合的位点可以分为两类,第一类为主要通过静电作用结合的强结合位点,第二类为主要通过疏水作用结合的弱结合位点。     

PHOTOCHEMICALLY INDUCED BINDING OF Rh(phen)2Cl2+ TO DNA†

The photoinduced covalent binding of the title compound to native and heat denatured DNA is described. The level of binding has been measured by UV (for DNA) and atomic absorption (for Rh) analysis. Quantum efficiencies of 6.4 x 10(-4) mol Rh per mol photons and 1.6 x 10(-3) mol Rh per mol photons have been determined for binding to native and denatured calf thymus DNA, respectively. Levels of bound rhodium as high as 1 molecule per five bases have been achieved. There is no binding of the complex in the absence of light, and there is evidence that at least a portion of the binding may be due to the photolytic conversion of the complex into one or more stable intermediates. Studies with polyribonucleotides indicate a strong preference for binding to the purine bases.     

Interaction of azide ion with hemin and cytochrome c immobilized on Au and Ag nanoparticles

This paper presents a set of investigations on the binding of a metabolic inhibitor, azide with prosthetic heme group of biomolecules, hemin chloride (Hem) and cytochrome c (Cyt c) immobilized on Au and Ag nanoparticles. A variety of spectroscopic tools have been used to understand the chemistry occurring on the nanoparticle surface. While the nature of binding of the model system, hemin has been investigated by UV-visible, fluorescence, FTIR, and Raman spectroscopies, the azide binding has been studied in detail by MALDI-TOF MS. Hemin binding on the nanoparticle surface occurs through the carboxylic acid groups. The hemin-N(3) adduct on the nanoparticle surface has been detected by mass spectrometry and its fragments have been studied by post source decay analysis. The chemistry of hemin on the nanoparticle surface has been compared with that of the protein, Cyt c. Azide binding of Cyt c requires thermal activation due to reduced accessibility of the heme center, unlike in the case of hemin. The binding chemistry is similar for free Cyt c and Cyt c bound to the nanoparticles.     

Reversible binding of multivalent ions by surfactant self-assembly

High molecular weight nonionic surfactants have been chemically modified to bind multivalent ions reversibly by using a moderate temperature stimulus as an on/off mechanism. Only above the critical micellization temperature (CMT) does binding of multivalent ions take place, whereas below the CMT, no binding occurs to the free surfactant molecules. Different calorimetric techniques have been used to prove the reversible binding of multivalent ions. This tunable binding of multivalent metal ions allows for the improvement of many ion-exchange processes and offers attractive opportunities in the biomedical field.     

疏水相互作用对阳离子聚电解质与染料键合的影响

用平衡渗析法研究了阳离子聚电解质PAm·MG 和P(St-Am·MG)与甲基橙(MO)及P(St-Am·MG)与MO的同系物乙基橙(EO)、橙武Ⅳ(O-Ⅳ)在25、35、45和55 ℃下相互作用的热力学. 由K1otz方程, 求得键合常数K_1和热力学参数ΔG、ΔH及ΔS. 含疏水基的P(St-Am·MG)与MO的键合能力比不含疏水基的PAm·MG 强. P(St-Am·MG)与不同染料作用时, 键合程度为O-Ⅳ>EO>MO, 即染料的疏水性越强, 与高聚物的作用程度越大.键合体系加入脲或甲醇, 疏水相互作用受到破坏, 导致高聚物与染料之间的键合受到削弱.     

Interaction of Zn(II) with quinolone drugs: structure and biological evaluation

Zinc complexes with the third-generation quinolone antibacterial drugs levofloxacin and sparfloxacin have been synthesized and characterized. The deprotonated quinolones act as bidentate ligands coordinated to zinc ion through the pyridone and a carboxylato oxygen atom. The crystal structures of [bis(aqua)bis(levofloxacinato)zinc(II)], 1, and [bis(sparfloxacinato)(1,10-phenanthroline)zinc(II)], 3, have been determined by X-ray crystallography. The biological activity of the complexes has been evaluated by examining their ability to bind to calf-thymus DNA (CT DNA) by UV spectroscopy and viscosity measurements. UV studies of the interaction of the complexes with DNA have revealed that they can bind to CT DNA probably by the intercalative binding mode which has also been verified by DNA solution viscosity measurements. The DNA binding constants have been also calculated. A competitive study with ethidium bromide (EB) showed that the complexes exhibit the ability to displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB for the intercalative binding site. The interaction of the complexes with human and bovine serum albumin proteins has been studied by fluorescence spectroscopy showing that the complexes exhibit good binding propensity to these proteins having relatively high binding constant values. The biological properties of the complexes have been evaluated in comparison to the previously reported Zn(II) complexes with the first- and second-generation quinolones oxolinic acid and enrofloxacin.     

硝酸甲酯分子间相互作用的DFT和ab initio比较

用密度泛函理论(DFT)和从头算(ab initio)方法,分别在B3LYP/6 31G和HF/6 31G水平上求得硝酸甲酯三种二聚体的全优化几何构型和电子结构,并用6 311G和6 311＋＋G基组进行总能量计算.对HF/6 31G计算结果进行MP4SDTQ电子相关校正.在各基组下均进行基组叠加误差(BSSE)和零点能(ZPE)校正求得结合能.对6 31G优化构型作振动分析并基于统计热力学求得200～600 K温度下单体和二聚体的热力学性质.详细比较两种方法的相应计算结果,发现DFT求得的分子间距离较短,分子内键长较长,所得结合能均小于相应ab initio计算值.     

Rational in silico design of aptamers for organophosphates based on the example of paraoxon

Poisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its three-dimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed.     

Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

Since the discovery of the intercalative binding mode, almost half a century ago, intense efforts have been devoted to design, synthesize and test new small molecules that can bind nucleic acids with improved recognition and affinity. Among them, metal bearing compounds play a principal role. Despite the plethora of different metal complexes which have been designed to react with DNA and which have been tested, the binding mechanisms have often not been analysed. This is unfortunate, considering the importance of understanding of the binding features in depth in order to optimise their biological effects. This review covers articles where an analysis of the kinetic aspects of the interaction between the target metal compound and nucleic acids has been carried out and details of the reaction mechanism are provided. Flat metal complexes (porphyrins), spherical complexes with protruding intercalating residues, azamacrocycle metallo-intercalators and intercalators with metal bearing pendant arms are the classes of molecules that have been taken into account. The limits of the SDS method, employed to measure the rates of drug dissociation from polynucleotides, are also discussed.     

Binding of 8-anilinonaphthalene sulfonate to dimeric and tetrameric concanavalin A: energetics and its implications on saccharide binding studied by isothermal titration calorimetry and spectroscopy

The binding of 8-anilinonaphthalene sulfonate to concanavalin A has been investigated. Isothermal titration calorimetry (ITC) and circular dichroism studies have been performed under different experimental conditions to understand the binding quantitatively and evaluate contributions of different forces responsible for it. Isothermal titration calorimetric results of concanavalin A with ANS at pH 5.2 and 2.5, where it exists as a dimer, indicated binding heterogeneity and two classes of noninteracting sites. Enhancement of the binding constants from native to pH 2.5 suggests that the ANS binding is strongly influenced by the protein charge and the favorable alteration in the structure of concanavalin A as suggested by near-UV CD results. No binding was observed with the tetrameric form of concanavalin A, indicating shielding of sites due to dimerization of canonical dimers. The results have also demonstrated existence of a hydrophobic binding site that is distinct from the saccharide binding site.