Prediction of human serum albumin-drug binding affinity without albumin

A new liquid chromatographic system was developed to measure protein-drug binding affinity indirectly without albumin and was evaluated using log nK values of drugs measured by a modified Hummel-Dreyer method using purified human serum albumin. The retention factors of acidic and basic drugs were measured by reversed-phase and ion-exchange liquid chromatography in sodium phosphate buffer, pH 7.40, containing 50 vol.% methanol at 37 °C. The bonded phases were pentyl, guanidino and carboxyl phases. The combined retention factors were correlated with the log nK values measured by a modified Hummel-Dreyer method because glycosylation of human serum albumin did not significantly affect log nK value. The correlation coefficients were 0.949 (n=7) for acidic drugs and 0.978 (n=5) for basic drugs. The log nK values of 26 acidic and 18 basic drugs were predicted from their retention factors measured by reversed-phase and ion-exchange liquid chromatography.     

Protein ligand docking based on empirical method for binding affinity estimation

An empirical protein-ligand binding affinity estimation method, SCORE, was incorporated into a popular docking program, DOCK4. The combined program, ScoreDock, was used to reconstruct the 200 protein-ligand complex structures and found to give good results for the complexes with high binding affinities. A quality assessment method for docking results from ScoreDock was developed based on the whole test set and tested by additionally selected complexes. The method significantly improves the docking accuracy and was shown to be reliable in docking quality assessment. As a docking tool in structural based drug design, ScoreDock can screen out final hits directly based on the predicted negative logarithms of dissociation equilibrium constants of protein-ligand complexes, and can explicitly deal with structure water molecules, as well as metal atoms.     

Hydrogen-bonded assembly and binding affinity of the multi-point acceptor and isophthalic acid

Supermolecular complexes formed by oligophenyleneethynylene derivatives and isophthalic acid were studied using AM1 method to obtain binding energy. Electronic spectra and IR spectra of the complexes were calculated by INDO/CIS and AM1 methods based on AM1 geometries. Results indicated that the dimer could be formed by the monomers via hydrogen bonding because of the negative binding energy. Binding energy of the complexes was affected by electronegativity and steric effects of the substituents. The first UV absorptions and IR frequencies of N-H bonds of the complexes were both red-shifted compared with those of the monomers. The complexes could bind small molecules via hydrogen bonds, resulting in the change in UV absorptions and an increase in IR frequencies of N-H bonds.     

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have been implemented to calculate the hydrophobic effect term, which results in three parallel scoring functions. All three scoring functions are calibrated through multivariate regression analysis of a set of 200 protein-ligand complexes and they reproduce the binding free energies of the entire training set with standard deviations of 2.2 kcal/mol, 2.1 kcal/mol, and 2.0 kcal/mol, respectively. These three scoring functions are further combined into a consensus scoring function, X-CSCORE. When tested on an independent set of 30 protein-ligand complexes, X-CSCORE is able to predict their binding free energies with a standard deviation of 2.2 kcal/mol. The potential application of X-CSCORE to molecular docking is also investigated. Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking.     

QSAR studies on estrogen receptor binding affinity of 2-phenylindoles using first-order valence molecular connectivity

The estrogen receptor binding affinity of 2-phenylindoles is found to be significantly correlated with Kier’s first-order valence molecular connectivity index. The correlation equations obtained provide a much simple rationale to design more potent compounds and help in predicting the potency of new compounds.     

Screening of inhibitors for influenza A virus using high-performance affinity chromatography and combinatorial peptide libraries

The affinity inhibitor of fusion peptide of influenza A virus has been studied using a combination of high-performance affinity chromatography (HPAC) and combinatorial peptide libraries. Fusion peptide (FP) (1-11) of influenza A virus was used as the affinity ligand and immobilized onto the poly(glycidyl methacrylate) (PGMA) beads. Positional scanning peptide libraries based on antisense peptide strategy and extended peptide libraries were designed and synthesized. The screening was carried out at acidic pH (5.5) in order to imitate the environment of virus fusion. A hendecapeptide FHRKKGRGKHK was identified to have a strong affinity to the FP (1-11). The dissociation constant of the complex of the hendecapeptide and the FP (1-11) is 3.10 x 10(-6) mol l(-1) in a physiological buffer condition. The polypeptide has a fairly inhibitory effect on three different strains of influenza A virus H1N1 subtype.     

AC electrokinetic immobilization of influenza virus

The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.     

Absolute and relative binding affinity of cucurbit[7]uril towards a series of cationic guests

We determined the relative binding constants (K_rel) for guests 1–19 towards cucurbit[7]uril by ¹H NMR competition experiments in 100 mM Na₃PO₄-buffered D₂O. In these experiments, we use guest 11 as the reference guest because of its strong binding towards CB[7] and its advantageous spectroscopic properties (e.g. slow exchange on NMR timescale and distinct resonances for key protons). To convert the determined K_rel values to absolute binding constants, we performed a direct UV–vis titration of 1 with CB[7] to determine K_a for CB[7]√1. The trends in the determined values of K_rel and K_a are discussed with respect to the importance of the concentration of metal ions in the buffer, the influence of hydroxyl groups located at the portals or inside the CB[7] cavity, geometry of the guest (e.g. regioisomers), the number of guest C atoms and secondary electrostatic interactions.     

Prediction of the binding mode of N2-phenylguanine derivative inhibitors to herpes simplex virus type 1 thymidine kinase

The probable binding mode of the herpes simplex virus thymidine kinase (HSV1 TK) N²-[substituted]-phenylguanine inhibitors is proposed. A computational experiment was designed to check some qualitative binding parameters and to calculate the interaction binding energies of alternative binding modes of N²-phenylguanines. The known binding modes of the HSV1 TK natural substrate deoxythymidine and one of its competitive inhibitors ganciclovir were used as templates. Both the qualitative and quantitative parts of the computational experiment indicated that the N²-phenylguanine derivatives bind to the HSV1 TK active site in the deoxythymidine-like binding mode. An experimental observation that N²-phenylguanosine derivatives are not phosphorylated during the interaction with the HSV1 TK gives support to the proposed binding mode.     

Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities

Binding mode calculations for complexes between an artificial paracyclophane receptor and digoxins, cholic acids as well as cortisone steroids show encapsulation of different ring combinations. Docking experiments were performed between the 26-10 antibody and digoxins. Coordination affinity arises from hydrophobic desolvation and van der Waals interactions rather than from hydrogen bonds. The specificity and affinity arises mainly from shape complementarity. Computed binding free energies and Kohonen neural network computations both point to physicochemical and structural similarities of natural antibodies and artificial receptors.     

Studies of the binding mechanism between aptamers and thrombin by circular dichroism, surface plasmon resonance and isothermal titration calorimetry

Thrombin, a multifunctional serine protease, has both procoagulant and anticoagulant functions in human blood. Thrombin has two electropositive exosites. One is the fibrinogen-binding site and the other is the heparin-binding site. Over the past decade, two thrombin-binding aptamers (15-mer and 29-mer) were reported by SELEX technique. Recently, many studies examined the interactions between the 15-mer aptamer and thrombin extensively, but the data on the difference of these two aptamers binding to thrombin are still lacking and worth investigating for fundamental understanding. In the present study, we combined conformational data from circular dichroism (CD), kinetics and thermodynamics information from surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to compare the binding mechanism between the two aptamers with thrombin. Special attentions were paid to the formation of G-quadruplex and the effects of ions on the aptamer conformation on the binding and the kinetics discrimination between specific and nonspecific interactions of the binding. The results indicated reasonably that the 15-mer aptamer bound to fibrinogen-binding site of thrombin using a G-quadruplex structure and was dominated by electrostatic interactions, while the 29-mer aptamer bound to heparin-binding site thrombin using a duplex structure and was driven mainly by hydrophobic effects.     

流感病毒糖蛋白糖链的作用和功能研究

流感病毒是近几年的研究热点之一.糖链在流感病毒生活周期中发挥重要作用,例如宿主细胞表面的唾液酸化糖链是病毒侵染细胞时的特异性受体,宿主决定的病毒糖蛋白糖链结构影响病毒的宿主范围和毒力.本文从糖组学角度综述糖链在甲型流感病毒生活周期中的重要作用,着重阐述病毒血凝素糖基化的影响因素及其对病毒宿主范围、毒力的影响和在病毒演化...     

喷射式流动注射电化学发光免疫检测禽流感H9亚型

利用磁分离和生物素亲和素技术,形成亲和素化磁微球-生物素化抗体-抗原-钌标抗体的免疫夹心复合物,初步建立了体外免疫诊断试剂的制备方法,并利用喷射式流动注射电化学发光体系对制备出的禽流感病毒H9免疫复合物进行检测。实验选择最适的包被抗体,检测抗体和封闭剂,优化Ru标抗体的最佳稀释度。在生物素化的兔抗H9多抗作为亲和素化的磁微球的结合抗体,鼠抗H9单抗作为Ru(bpy)32+标记抗体,2%BSA作为封闭剂,1:50倍稀释的Ru-鼠抗H9单抗条件下,非特异性吸附最低。测定不同浓度的H9抗原,发现抗原浓度在3.125～100μg/mL范围内与电化学发光强度呈较好的线性关系。实验还测定了不同亚型的禽流感病毒、不同来源的毒株和鸡的棉拭子样品。     

人工神经网络法预测炸药组分的色谱保留值参数

 以分子拓扑指数作为炸药组分的结构描述符 ,利用反向传播算法 (BP)人工神经网络 ,以Sigmoid函数为传递函数 ,分子连接性指数0 χ ,1χ ,2 χ与边邻接指数 (ε)为输入向量 ,反相高效液相色谱保留值参数logkw 和S为输出向量 ,将输入向量归一化至 - 3～ 3区间 ,输出向量归一化至 0～ 1区间 ,网络精度取 0 5 ,学习步长 η的初始值取0 2 ,动量因子α取 0 5 ,通过对 2 0种炸药的网络模型进行训练 ,建立了炸药分子结构与logkw 和S之间的定量模型。结果表明 ,该模型较好地反映了炸药分子结构与保留值之间的关系。     

Origins of the reassortant 2009 pandemic influenza virus through proteotyping with mass spectrometry

The application of a proteotyping approach employing high resolution mass spectrometry based is shown to be able to determine the gene origin of all major viral proteins in a triple reassortant pandemic 2009 influenza strain. Key to this approach is the identification of unique swine‐host‐specific signature and indicator peptides that are characteristic of influenza viruses circulating in North American and Eurasian swine herds in the years prior to the 2009 influenza pandemic. These swine‐and human pandemic‐specific signatures enable the origins of viral proteins in a clinical virus specimen to be determined and such strains to be rapidly and directly differentiated from other co‐circulating seasonal influenza viruses from the same period. The proteotyping strategy offers advantages over traditional RT‐PCR‐based approaches that are currently the mainstay of influenza surveillance at the molecular level. Copyright © 2014 John Wiley & Sons, Ltd.