基于酪氨酸磷酸酶(PTP1B)的Ⅱ型糖尿病药物设计、合成和体外活性及毒性的初步评价

酪氨酸磷酸酶PTP1B已被公认为治疗Ⅱ型糖尿病药物的理想靶标蛋白.通过重组表达制备PTP1B蛋白及其蛋白质晶体,并尝试将其与768种小分子片段进行以结构为基础的筛选,得到了数个与PTP1B结合的小分子片段及其化学结构.在此基础上利用计算机辅助药物设计方法设计与优化出一种新型PTP1B抑制剂,并经13步反应合成了该目标分子.体外药理活性和毒性的初步评价的结果表明,其对体外重组人源PTP1B的酪氨酸磷酸酶活性半数抑制浓度IC50值达到(3.4±1.2) μmol/L,优于阳性对照;在HepG2细胞胰岛素抵抗模型中,该化合物能有效改善胰岛素抵抗细胞对葡萄糖的利用能力,其改善效果与阳性药匹格列酮相当.初步的斑马鱼毒性检测表明,目标该化合物在浓度为500μmol/L时未对幼鱼产生明显毒性.新化合物的发现为新型PTP1B抑制剂的后续开发开辟了新基础.     

靶向葡萄糖转运蛋白(GLUTs)抗癌药物的开发

基于肿瘤细胞与正常细胞葡萄糖代谢差异的肿瘤沃伯格效应,是目前新型靶向抗肿瘤药物开发的研究热点之一。本文以沃伯格效应的代谢特征和特异性生物标识物为出发点,从靶向葡萄糖转运蛋白(GLUTs)生物靶点和利用肿瘤葡萄糖代谢亢进的生物特征这两个层面,综述了具有代表性的GLUTs抑制剂以及GLUTs靶向型糖偶联抗肿瘤药物的研发现状,讨论并解析通过靶向沃伯格效应开发抗肿瘤药物的设计思路、实施策略与推广前景。     

牛视紫红质蛋白质中视黄醛的活性位点

视紫红质蛋白是一个跨膜蛋白, 视黄醛(RET)在该蛋白中的活性结合位点涉及到视觉过程机理, 与一些眼科疾病病理有关. 基于牛视紫红质蛋白1U19的蛋白质晶体结构数据, 采用密度泛函理论的B3LYP方法计算RET-Lys296残基与视黄醛分子周围半径为0.6 nm的空间范围30个氨基酸残基相互作用和结合能. 数值显示1U19蛋白中的残基Glu113、Glu181和Glu122是质子化的RET-Lys296残基的活性结合位点, 结合能分别为-333.38、-205.67和-194.56 kJ·mol-1. 这些氨基酸残基带有一个负电荷, 与质子化的RET-Lys296残基发生强烈的离子静电相互作用. 另外几个残基Ala292、Cys187、Phe293、Pro291以及Trp265等与质子化RET-Lys296残基也有相互吸引作用. 当RET-Lys296残基非质子化, 上述相互作用消失, 促使视黄醛分子与视蛋白分离. 研究发现残基Glu113和Glu181周围各自有一个结晶水分子通过双氢键形式起着稳定作用.     

人类谷胱甘肽硫转移酶家族等位基因蛋白B与抑制剂作用模型的理论研究

采用分子动力学模拟方法系统地研究了谷胱甘肽硫转移酶家族(Glutathione S-transferases,GSTs)的等位基因蛋白B(GSTP1*B)与抑制剂利尿酸(EA)以及EA的谷胱甘肽(GSH)共轭物EAG(I),EAG(O)的具体结合方式.抑制剂及其谷胱甘肽共轭物与蛋白的相互作用能计算结果及分子动力学轨迹的统计分析结果表明,GSTP1*B与EA的谷胱甘肽共轭物的结合能力优于其与EA的结合能力,Phe8,Arg13,Trp38和Tyr108是作用过程中的关键残基,对稳定抑制剂及其谷胱甘肽共轭物在GSTP1*B的G和H位点的构象具有重要的作用.通过对构象的统计分析发现,残基Phe8和Tyr108与GSTP1*B酶对抑制剂的选择性密切相关.     

大鼠小肠壁细胞葡萄糖转运蛋白一级结构及功能的研究

应用序列同源性cDNA作探针,从大鼠小肠壁细胞cDNA文库中筛选出了葡萄糖转运蛋白cDNA克隆。经双脱氧法测定该克隆的cDNA全序列为2466bp,翻译区1566bp,编码522个氨基酸。从氨基酸全序列分析得到12个疏水区段,每区段为21个氨基酸。此葡萄糖转运蛋白可能在细胞膜上跨膜12次,构成葡萄糖通道。     

具有生物活性的芳基咪唑并邻菲啰啉衍生物的合成及用作pH荧光传感探针

以1,10-邻菲啰啉为基本骨架设计合成了6种咪唑[4,5-f][1,10]邻菲啰啉的衍生物(3a~3f);研究了目标化合物对蛋白酪氨酸磷酸酶1B(PTP1B)的抑制作用,其最高抑制率可达(84.56±1.78)%,是潜在的PTP1B的抑制剂药物;基于1,10-邻菲啰啉优良的光学性能,通过荧光测试研究了不同pH对化合物3a~3f的影响,探讨了化合物在Britton-Robison(B-R)缓冲溶液中的质子化和去质子化现象;以硫酸奎宁为参比,计算了相应的荧光量子产率.结果表明,目标化合物均有较高的荧光量子产率,最高可达0.53.     

α2A肾上腺素受体的同源模建及与Yohimbine的对接研究

通过对比多个与α2A-肾上腺素受体同属G-蛋白偶联受体的视紫红质蛋白序列,选择以相似性最大的牛视紫红质蛋白为模板,同源模建了α2A-肾上腺素受体的跨膜结构,并在结构中找到了体积为0.090 nm3,已被报导的活性残基包围的活性位点.运用分子力学与动力学方法研究了此结构突变前后与抑制剂Yohimbine的对接情况,得到了与文献报道相吻合的结果.同时对接研究结果发现,在α2A-肾上腺素受体的结合位点周围的一个由色氨酸和两个苯丙氨酸组成的局部疏水区对抑制剂有稳定作用,并且天冬氨酸113作为氢键受体也对稳定抑制剂有重要作用.     

分子梭协助离子跨膜运输的机理研究

采用增强采样分子动力学模拟研究了一轮烷型分子梭协助K⁺跨膜转运的机制, 该轮烷由两亲性的轴和套在轴上的大冠醚环及连接在大冠醚环上的小冠醚环构成, 轴上有3个带正电的结合位点. 通过计算穿梭过程的自由能变化, 探索了溶剂(氯仿、 乙腈、 水、 氯仿-乙腈)以及中间结合位点对该轮烷穿梭运动的影响, 并分析了中间位点在其携带K⁺穿越细胞膜(采用水-氯仿-水模拟)过程中的重要作用. 结果表明, 改变溶剂不会改变轮烷(不携带K⁺)的运动模式, 但随着溶剂极性的增加穿梭所需克服的自由能能垒显著降低; 在氯仿-乙腈混合溶剂中, 中间结合位点的质子化状态, 不影响轮烷(不携带K⁺)的穿梭能垒; 然而在模拟细胞膜的环境中, 该结合位点的质子化与去质子化相比大幅降低了穿梭的能垒, 促进了K⁺的跨膜转运, 表明中间位点的质子化对于离子转运至关重要, 进一步分析表明轮烷中大环穿梭和小环摆动的协同作用, 也是加速离子跨膜转运的另一关键因素.     

辅酶NADH与色氨酸共振能量转移的荧光动力学研究

采用时间相关单光子计数技术, 结合紫外-可见吸收光谱和稳态荧光光谱, 对不同环境下的色氨酸和辅酶还原型烟酰胺腺嘌呤二核苷酸(NADH)之间的共振能量转移荧光动力学进行了研究. 单体色氨酸、 牛血清白蛋白以及乳酸脱氢酶蛋白与NADH之间相互作用的光谱数据表明, 只有存在NADH结合位点的乳酸脱氢酶和NADH之间发生了荧光共振能量转移. 进一步通过加入丙酮酸来阻断乳酸脱氢酶和NADH之间的荧光共振能量转移通道, 时间分辨荧光光谱和衰减相关光谱(DAS)证实, 蛋白结合位点的存在是NADH和色氨酸之间发生荧光共振能量转移的前提条件. DAS揭示了乳酸脱氢酶平均荧光寿命的减小主要是源于色氨酸中7.35 ns的荧光寿命成分与NADH之间的荧光共振能量转移, 同时给出了NADH和色氨酸之间的能量转移效率, 为研究NADH和蛋白之间的相互作用提供了新思路.     

作用于秋水仙碱位点的微管蛋白抑制剂的结合模式 研究与结构模型的构建

采用对接的方法建立了秋水仙碱位点抑制剂与微管蛋白的结合模式, 并构建了其结构模型. 结果表明: 抑制剂主要借助于与口袋I和II的疏水作用, 以及同α-Thr178, α-Val181和β-Cys241之间的氢键来实现与微管蛋白的结合. 根据抑制剂的结合构象, 将抑制剂的结构分为A, B以及AB间的桥连三个部分, 从而建立了由A部分中的疏水中心H1、氢键受体A1, B部分中的疏水中心H2、疏水基团H3和极性原子P以及桥连结构中的氢键受体A2组成的结构模型. 并指出H1与H2对活性的影响因素分别为疏水基团的体积和平面特征, 而桥连部分则应以刚性的形式保证AB处于桥连的同侧(即顺式构象). 还提出在A2与loop区之间存在一个的潜在氢键受体A3. 研究结果为设计新型小分子微管蛋白抑制剂提供指导.     

Biomembrane-affinity centrifugal analyses of solute interactions with membrane proteins.

We have developed a rapid centrifugal method for analyzing solute interactions with membrane proteins in cytoskeleton-depleted membrane vesicles or proteoliposomes sterically immobilized in Superdex 200 gel beads. The size and density of the gel beads allow fast sedimentation in a bench-top centrifuge. Biospecific interactions of cytochalasin B and D-glucose with the human red cell glucose transporter, Glut1, were analyzed. The binding constants and the molar ratio of inhibitor sites per protein monomer agreed well with recent results obtained by frontal affinity chromatography.     

Ethanol weakens cytochalasin B binding to the GLUT1 glucose transporter and drug partitioning into lipid bilayers

Ethanol weakens the specific interaction between the human red blood cell (RBC) glucose transporter GLUT1 and the inhibitor cytochalasin B (CB). The chromatographic retention volume of cytochalasin B on stationary phases consisting of GLUT1-containing membranes decreased with increasing ethanol concentration in the eluent. The apparent Kd values for the ethanol-GLUT1 interaction were 0.37, 0.45 and 0.64 M for red blood cells, red blood cell membrane vesicles and proteoliposomes, respectively, all much higher than the Kd values for D-glucose or cytochalasin B interaction with GLUT1. Ethanol also decreased the partitioning of cytochalasin B and drugs into phospholipid bilayers.     

Computational Insights into Allosteric Conformational Modulation of P-Glycoprotein by Substrate and Inhibitor Binding

The ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) is a physiologically essential membrane protein that protects many tissues against xenobiotic molecules, but limits the access of chemotherapeutics into tumor cells, thus contributing to multidrug resistance. The atomic-level mechanism of how substrates and inhibitors differentially affect the ATP hydrolysis by P-gp remains to be elucidated. In this work, atomistic molecular dynamics simulations in an explicit membrane/water environment were performed to explore the effects of substrate and inhibitor binding on the conformational dynamics of P-gp. Distinct differences in conformational changes that mainly occurred in the nucleotide-binding domains (NBDs) were observed from the substrate- and inhibitor-bound simulations. The binding of rhodamine-123 can increase the probability of the formation of an intermediate conformation, in which the NBDs were closer and better aligned, suggesting that substrate binding may prime the transporter for ATP hydrolysis. By contrast, the inhibitor QZ-Leu stabilized NBDs in a much more separated and misaligned conformation, which may result in the deficiency of ATP hydrolysis. The significant differences in conformational modulation of P-gp by substrate and inhibitor binding provided a molecular explanation of how these small molecules exert opposite effects on the ATPase activity. A further structural analysis suggested that the allosteric communication between transmembrane domains (TMDs) and NBDs was primarily mediated by two intracellular coupling helices. Our computational simulations provide not only valuable insights into the transport mechanism of P-gp substrates, but also for the molecular design of P-gp inhibitors.     

Interaction of bis(1-anilino-8-naphthalenesulfonate) with yeast hexokinase: a steady-state fluorescence study

Bis(1-analino-8-naphthalenesulfonate) (bis-ANS) is a useful probe for hydrophobic areas on protein molecules and it has been proposed that it has a general affinity for the nucleotide binding site(s). There appear to be two different classes of binding sites for bis-ANS on hexokinase and these can be tentatively assigned as primary and secondary binding sites. The rate of binding of bis-ANS at the primary binding site is fast, whereas binding at secondary site(s) is slow. The slow increase in the fluorescence intensity on binding with bis-ANS is not due to conformational change in the enzyme, which may lead to the increase in the quantum yield of the bound dye. Circular dichroism measurements indicate that there is no significant change in the secondary structure on binding with this probe. In the presence of saturating amounts of glucose, the increase in fluorescence intensity due to binding at the secondary binding site(s) is significantly lowered. This indicates that glucose-induced conformational change has been sensed by this probe. From kinetic studies, it has been observed that bis-ANS is an effective competitive inhibitor of yeast hexokinase with respect to ATP. The stoichiometry of binding of this fluorescent probe is about one per subunit at the primary site both in the presence and absence of glucose, and the dissociation constant of bis-ANS is unaffected by glucose. It is possible to decrease significantly the amount of fluorescence intensity at the primary site by nucleotides. These results indicate that bis-ANS interacts at the site where nucleotide interacts. Energy transfer experiments indicate the proximity of some tryptophan(s) and bound bis-ANS molecule(s).     

Solid-state NMR spectroscopy detects interactions between tryptophan residues of the E. coli sugar transporter GalP and the alpha-anomer of the D-glucose substrate

An experimental approach is described in which high resolution 13C solid-state NMR (SSNMR) spectroscopy has been used to detect interactions between specific residues of membrane-embedded transport proteins and weakly binding noncovalent ligands. This procedure has provided insight into the binding site for the substrate D-glucose in the Escherichia coli sugar transport protein GalP. Cross-polarization magic-angle spinning (CP-MAS) SSNMR spectra of GalP in its natural membrane at 4 degrees C indicated that the alpha- and beta-anomers of D-[1-(13)C]glucose were bound by GalP with equal affinity and underwent fast exchange between the free and bound environments. Further experiments confirmed that by lowering the measurement temperature to -10 degrees C, peaks could be detected selectively from the substrate when restrained within the binding site. Dipolar-assisted rotational resonance (DARR) SSNMR experiments at -10 degrees C showed a selective interaction between the alpha-anomer of D-[1-(13)C]glucose and 13C-labels within [13C]tryptophan-labeled GalP, which places the carbon atom at C-1 in the alpha-anomer of D-glucose to within 6 A of the carbonyl carbon of one or more tryptophan residues in the protein. No interaction was detected for the beta-isomer. The role of tryptophan residues in substrate binding was investigated further in CP-MAS experiments to detect D-[1-(13)C]glucose binding to the GalP mutants W371F and W395F before and after the addition of the inhibitor forskolin. The results suggest that both mutants bind D-glucose with similar affinities, but have different affinities for forskolin. This work highlights a useful general experimental strategy for probing the binding sites of membrane proteins, using methodology which overcomes the problems associated with the unfavorable dynamics of weak ligands.     

新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算

通过分子对接建立了一系列含二氟甲基磷酸基团(DFMP)或二氟甲基硫酸基团(DFMS)的抑制剂与酪氨酸蛋白磷酸酯酶1B(PTP1B)的相互作用模式, 并通过1 ns的分子动力学模拟和molecular mechanics/generalized Born surface area (MM/GBSA)方法计算了其结合自由能. 计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致; 通过基于主方程的自由能计算方法, 获得了抑制剂与靶酶残基间相互作用的信息, 这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性, 进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

Immobilization of active facilitated glucose transporters (GLUT-1) in supported biological membranes

Membrane fragments or membrane proteins within a lipid mixture were immobilized over metal electrodes. This procedure has been developed to study biological membranes without interferences from cell machinery. To obtain a smooth hydrophilic biomembrane support and a mode of binding of the membrane, either a crosslinked gel or an aromatic polyamine-polymer doped with avidin was deposited at the metal electrode by electropolymerization. This layer (less than 10 nm thick) also served as a submembrane compartment. The facilitated glucose transporter (GLUT-1) purified from human erythrocytes was integrated into a lipid membrane containing artificial biotinylated lipids and reacted with the activated surface of the glucose sensitive electrode. It was demonstrated that the lipid layer was attached to the polymer-containing avidin and could only be removed by detergent extraction. The presence of an active membrane transporter was demonstrated by electrochemical detection of glucose in the submembrane compartment, and by inhibition of glucose transport with the specific inhibitor Cytochalasin-B.     

反相液相色谱-串联质谱法鉴定油菜蜂花粉中的蛋白质及活性肽

基于鸟枪法蛋白质组学分析方法,使用反相液相色谱-串联质谱（RPLC-MS/MS）系统分析油菜蜂花粉蛋白质的胰蛋白酶酶解产物,结合数据库检索,共鉴定到353条肽段。鉴定到的肽段所归属的蛋白质中有239个蛋白质可检索到其分子生物学功能,主要功能为结合活性、酶活性、运输活性、抑制活性等。根据血管紧张素转化酶（ACE）抑制肽活性与多肽构效之间的关系,从鉴定到的肽段中筛选并适当修饰后得到5条可能具有ACE抑制活性的肽段,化学合成肽段后进行了活性验证。结果表明5条肽段均具有良好的活性,其中肽段AELDIVLALF和LAVNLIPFP表现出较高的ACE抑制活性,半数抑制浓度（IC₅₀）分别为（10.65±0.50）μmol/L和（23.66±1.08）μmol/L。该方法速度快,成本低,大大缩短了鉴定周期,达到了高通量筛选生物活性肽的目的。     

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.