Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

高效毛细管电泳前沿分析法研究酸性药物那格列奈与人血浆白蛋白的结合

用高效毛细管电泳前沿分析法研究了酸性药物那格列奈与人血浆白蛋白的结合常数、结合位点和结合率。使用未涂层的毛细管柱 (4 0cm× 5 0 μmi.d .;有效柱长 32cm) ,磷酸盐缓冲溶液 (pH 7.4 ,离子强度0 .17)为背景溶液 ,在紫外检测波长 2 14nm、运行电压 18kV和重力进样 10 0s的条件下 ,利用那格列奈谱峰的平台高度和游离药物浓度的良好线性关系 (r>0 .999,n =6 ) ,测定了那格列奈的游离药物浓度。固定药物浓度 (2 0 0 μmol L ,2 5 0 μmol L) ,考察不同的蛋白质浓度对结合的影响 ;固定蛋白质浓度 (10 0 μmol L) ,考察不同的药物浓度对结合的影响。实验数据采用非线性拟和程序进行处理 ,得到了那格列奈的蛋白质结合参数。高效毛细管电泳前沿分析法测定的数据重现性良好 (RSD <2 .5 % ,n =3) ,在药代动力学和药效学研究方面具有简便、准确的优点。     

Cross-linking chemistry and biology: development of multifunctional photoaffinity probes

An efficient method of photoaffinity labeling has been developed based on rationally designed multifunctional photoprobes. Photoaffinity techniques have been used to elucidate the protein structure at the interface of biomolecules by the photochemical labeling of interacting sites. However, the identification of labeled sites within target proteins is often difficult. Novel biotinyl bioprobes bearing a diazirine photophore have contributed significantly to the rapid elucidation of ligand binding sites within proteins, thereby extending conventional photoaffinity methods. This article discusses the synthesis and applications of various photoprobes bearing a biotin, including strategies using cleavable linkages between photophores. The combination of photoaffinity methods with chip technology is also described as a novel entry to rapid affinity-based screening of inhibitors. This review focuses on a rapid and reliable photoaffinity method utilizing diazirine-based multifunctional photoprobes with numerous potential applications in functional proteomics of biomolecular interactions.     

NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

A study of carboxylic-modified mesoporous silica in controlled delivery for drug famotidine

A series of pure silica MSU and carboxylic-modified MSU materials were prepared. The formation of mesoporous silica materials with terminal carboxylic groups on pore surface was performed by the acid-catalyzed hydrolysis of cyano to carboxylic. Then their potential applications in controlled drug delivery carriers were investigated. Drug famotidine was selected as a model molecule out of the consideration of the terminal amino groups in its molecule. The adsorption experiments show significant adsorption of famotidine on the carboxylic-modified MSU materials. And, the functionalization level of carboxylic groups has been found to be the key factor affecting the adsorption capacities of the modified MSU materials for famotidine. Subsequently, three kinds of release fluids, including simulated gastric medium, simulated intestinal medium, and simulated body fluid, were used to test the famotidine release rate from the carboxylic-modified MSU material. Obvious delayed effect has been observed for the famotidine release from the carboxylic-modified mesoporous silica material under the in vitro assays.     

Determination of binding constants and stoichiometries for platinum anticancer drugs and serum transport proteins by capillary electrophoresis using the Hummel-Dreyer method

A CE method has been developed to evidence and quantitatively characterize the interaction between platinum-based antitumor drugs and human serum proteins. This method is a variant of affinity CE modified regarding both experimental setup and data treatment so as to measure the peaks (or vacancies) that correspond to the bound drug when it slowly binds to the protein. Using the formalism of the Hummel-Dreyer method and cisplatin and oxaliplatin as test compounds, a protocol for determining albumin and transferrin binding constants and stoichiometries, including (and distinguished by) 48 hours of incubation of the reaction mixture, was elaborated. Relative affinities of drugs toward different proteins in aqueous solution at physiological pH, chloride concentration, and temperature were compared in terms of overall binding constants and numbers of drug molecules attached to the protein. The results indicate that both platinum drugs bind to albumin more strongly than to transferrin, supporting the concept that the albumin fraction is a major drug supply route for chemotherapeutical needs. From a comparison with the binding parameters measured previously for cisplatin by other methods, conclusions were drawn about the validity of CE as a simple and convenient method for assaying protein-drug reactions with slow kinetics.     

药品物流多中心选址优化研究

为降低药品物流配送成本、提高药品配送效率。本文针对国家带量集中采购药品配送问题,构建了药品物流多中心选址-路径优化双目标模型。并结合模糊C-均值聚类算法(FCMA)、模拟退火算法和禁忌搜索算法各自优点,设计出了FCM-TS-SA混合算法,最后通过真实案例进行了验证、对比和分析。     

基于前景理论的药品质量安全监管演化博弈分析

现有药品质量安全监管的相关研究多从理性假设出发探讨政府与企业的互动机理,鲜有考虑企业质量安全意识的有限理性,导致模型对现实的解释能力不足。运用前景理论,通过价值函数和权重函数构建演化博弈的收益前景矩阵,研究了政府和药品生产企业的博弈过程,得到了影响企业质量安全意识的约束条件及因素。同时,研究了上市许可持有人质量激励、惩罚机制对药品生产企业质量安全意识的影响。研究结果表明:过度自信、风险偏好等是影响企业质量安全意识的重要因素;上市许可持有人的质量激励与惩罚能否发挥作用取决于企业的风险态度;在质量激励、惩罚条件下,上市许可持有人需加大监督或惩罚力度来改善企业的质量安全意识。     

A genetic algorithm for the automated generation of molecules within constraints

Summary A genetic algorithm has been designed which generates molecular structures within constraints. The constraints may be any useful function, for example an enzyme active site, a pharmacophore or molecular properties from pattern recognition or rule-induction analyses. The starting point may be random or may utilise known molecules. These are modified to grow into families of structures which, using the evolutionary operators of selection, crossover and mutation evolve to better fit the constraints. The basis of the algorithm is described together with some applications in lead generation, 3D database construction and drug design. Genetic algorithms of this type may have wider applications in chemistry, for example in the design and optimisation of new polymers, materials (e.g. superconducting materials) or synthetic enzymes.     

Direct analysis of thin-layer chromatographic spots of narcotics by means of diffuse reflectance Fourier transform infrared spectroscopy

The technique of diffuse reflectance Fourier transform infrared spectrometry (DRIFT) as an in situ detection method was used for the qualitative and quantitative analysis of drugs (heroin, cocaine and codeine) separated by thin layer chromatography.It was found that at a given interferometer throughput and detector sensitivity the quality of the spectrum depends strongly in the type of the chromatographic thin layer used. A detection limit of approx. 2 g was attained on a microcrystalline cellulose thin layer with a dynamically aligned Bio-Rad Digilab FTS 60A/896 type interferometer and room temperature DTGS detector. A reliable qualitative analysis can be made with as little as 10 to 15 g drug per spot.