紫杉醚与αβ微管蛋白的分子对接

采用Insight II/Affinity对紫杉醚与αβ微管蛋白进行分子对接, 共得到10个对接构象. 应用密度泛函B3LYP/6-31G 方法计算对接口袋构象的结合能, 筛选出结合能达-190.53 kJ·mol-1的最优对接构象5. 通过构象分析建立紫杉醚与受体结合的作用模型, 结果表明, 在活性口袋的底部紫杉醚与受体间的作用主要是疏水作用, 而在活性口袋的顶部两者间主要是氢键作用. 氢键作用位置可分为A和B两个作用区, 其中A区有3个氢键, 由C13侧链分别与受体的ASP26和ARG369作用形成; B区也有3个氢键, 是由紫杉醚母环上的极性基团分别与受体的THR276、ARG278和GLN282作用产生的. 紫杉醚与αβ微管蛋白间形成的6个氢键可以有效地将紫杉醚固定在活性口袋中.     

新烟碱类化合物药效构象的分子对接研究

从烟碱型乙酰胆碱受体(nACHR)-烟碱(nicotine)复合体晶体模型出发, 采用SYBYL 6.92软件包中FlexX分子对接模块对新烟碱类化合物的3种已上市化合物吡虫啉、噻虫啉、烯啶虫胺和3种吡虫啉的结构衍生物同受体蛋白作用的精确模型进行了研究. 通过全局搜索方法构建配体的构象库进行对接, 依据构象间RMS值对结果进行分类结合CScore打分函数数据对对接结果进行筛选, 最终给出合理的新烟碱类化合物-烟碱型乙酰胆碱受体的药效作用构象模型: 配体吡啶环上氮原子通过水分子同受体Leu102, Met114形成氢键并且咪唑环或噻唑环上亲水侧链同受体CYS187或SER186形成氢键, 疏水侧链同疏水部位A (TYR164, TRP53, TYR89以及TYR185残基), 或疏水部位B (TYR132, CYS187和CYS188)相互作用. 此模型同早先有关文献报道的试验结果部分吻合, 充分表明了其合理性. 同时依据本构象模型, 在新烟碱类化合物结构方面提出了一些改良建议并为研究其高选择性指出方向.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

二芳基三嗪类HIV-1逆转录酶抑制剂的分子对接及3D-QSAR研究

对40个二芳基三嗪类HIV-1逆转录酶抑制剂进行了分子对接研究,结果表明,2个疏水性芳香取代基团与结合口袋底部形成的疏水和范德华相互作用、三嗪环母核及其R4取代基与结合位点产生的氢键和静电作用以及R4取代基与袋口形成的空间位阻效应是影响该系列化合物活性的重要因素.根据对接优势构象进行分子叠合和比较分子相似性指数分析(C...     

GPCR A2A AR腺苷受体蛋白的激动剂结合及其诱导的蛋白活性开关构象变化

运用分子动力学模拟,研究了腺苷酸（激动剂）与A2AAR腺苷受体蛋白的相互作用和配体结合诱导的蛋白动力学变化．识别了与腺苷酸结合力强于0．5kcal／mol的关键基团：A63^2．61,I66^2．64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52和N253^6.55,观察到腺苷酸没有与L167^5.28相互作用,这一结果支持了L167^5.28是抑制剂特异性结合位点,不与激动剂结合．未结合配体（激动剂或抑制剂）的单体A2AAR和腺苷酸结合后的A2AAR在构象上有三个不同功能性开关．腺苷酸结合可以诱导A2AAR腺苷受体蛋白的构象调整,使得三个功能性开关器件的构象与单体A2AAR不同．     

PTP1B和1,2-萘醌类抑制剂的分子动力学模拟

采用分子动力学和分子力学相结合的方法 ,研究了一类 1,2 萘醌类抑制剂与酪氨酸蛋白磷酸酯酶PTP1B之间的相互作用模式 .计算得到的抑制剂和靶酶之间的相互作用模式显示范德华相互作用、疏水相互作用以及氢键作用是主要的作用模式 .计算结果还表明抑制剂和PTP1B的相互作用能ΔE越低 ,抑制剂活性越高 .通过计算各种能量对ΔE的贡献 ,以及对复合物结构参数的分析 ,发现抑制剂和受体之间疏水相互作用是造成抑制剂活性差别的主要原因 .这为设计其他非酸类抑制剂提供了信息     

PTPlB和1，2-萘醌类抑制剂的分子动力学模拟

采用分子动力学和分子力学相结合的方法，研究了一类1，2-萘醌类抑制剂与酪氨酸蛋白磷酸酯酶PTP1B之间的相互作用模式．计算得到的抑制剂和靶酶之间的相互作用模式显示范德华相互作用、疏水相互作用以及氢键作用是主要的作用模式．计算结果还表明抑制剂和PTP1B的相互作用能△E越低，抑制剂活性越高．通过计算各种能量对△E的贡献，以及对复合物结构参数的分析，发现抑制剂和受体之间疏水相互作用是造成抑制剂活性差别的主要原因．这为设计其他非酸类抑制剂提供了信息．     

1.73分辨率天花粉蛋白晶体中的水结构

本文报道的天花粉蛋白晶体中水的结构模型,包括了133个水分子,其中118个同蛋白的原子成氢键。天花粉蛋白内部有4个分立的水分子,其中2个水分子W251和W252分剔与A5螺旋变形部位的残基156Gln和157Ser的侧链成氢键,对维持活性部位的构象有贡献。晶体中水结构的比较结果表明,核糖体接近蛋白时,会诱导蛋白活性部位残基的构象发生变化,使各催化基团按催化效果最佳的构象排布,并激活一个水分子(W257)直接参与核糖体失活作用。     

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.     

基于QSAR/QSSR的苯并三唑化合物选择性抑制PTP-1B的研究

蛋白酪氨酸磷酸酶1B (PTP-1B)特异性抑制剂是近年来治疗II型糖尿病药物研发的热点. PTP-1B与T细胞蛋白酪氨酸磷酸酶(TCPTP)同源性很高, 为了避免在使用PTP-1B抑制剂过程中对TCPTP产生交叉抑制, 则需要设计开发对PTP-1B具有高活性和高特异选择性的小分子化合物. 苯并三唑类化合物对PTP-1B的抑制活性很高, 并且其中一些化合物对PTP-1B表现出了较好的特异选择性, 具有良好的药用开发前景. 通过CoMFA和CoMSIA两种方法分别对该类化合物进行了三维定量结构-活性关系(3D-QSAR)和三维定量结构-选择性关系(3D-QSSR)研究, 并建立了相关的预测模型. 计算结果表明PTP-1B中的Arg24与化合物的氢键相互作用是提高选择性的重要因素, 并且在R2位引入氢键供体且体积较大的强供电子基团, 将有利于化合物抑制活性的提高, 而在R2位取代基的末端引入氢键受体且体积较大的强吸电子基团, 将有利于化合物选择性的提高.     

Role of the key mutation in the selective binding of avian and human influenza hemagglutinin to sialosides revealed by quantum-mechanical calculations

The selective binding between avian and human influenza A viral hemagglutinins (HA) subtype H3 and Neu5Acα2-3 and α2-6Gal (avian α2-3, human α2-6) is qualitatively rationalized by the fragment molecular orbital (FMO) method. We suggest a general model of analyzing protein-ligand interactions based on the electrostatic, polarization, dispersion, and desolvation components obtained from quantum-mechanical calculations at the MP2/6-31G(d) level with the polarizable continuum model of solvation. The favorable avian H3 (A/duck/Ukraine/1963)-avian α2-3 binding arises from the hydrophilic interaction between Gal-4 OH and side-chain NH(2)CO on Gln226, which is supported by the intermolecular hydrogen-bond network to the 1-COO group on Neu5Ac moiety. A substitution of Gln226Leu in the avian H3 HA1 domain increases the binding affinity to human α2-6 due to the Leu226···human α2-6 dispersion with a small entropic penalty during the complex formation. The remarkable human H3 (A/Aichi/2/1968)-human α2-6 binding is not governed by the Ser228-OH···OH-9 Neu5Ac hydrogen bond. These fragment-based chemical aspects can help design monovalent inhibitors of the influenza viral HA-sialoside binding and the simulation studies on the viral HAs-human α2-6 binding.     

The assembly-inducing laulimalide/peloruside a binding site on tubulin: molecular modeling and biochemical studies with [³H]peloruside A

We used synthetic peloruside A for the commercial preparation of [3H]peloruside A. The radiolabeled compound bound to preformed tubulin polymer in amounts stoichiometric with the polymer's tubulin content, with an apparent K(d) value of 0.35 μM. A less active peloruside A analogue, (11-R)-peloruside A and laulimalide acted as competitive inhibitors of the binding of the [3H]peloruside A, with apparent K(i) values of 9.3 and 0.25 μM, respectively. Paclitaxel, epothilone B, and discodermolide had essentially no ability to inhibit [3H]peloruside A binding, confirming that these compounds bind to a different site on tubulin polymer. We modeled both laulimalide and peloruside A into the binding site on β-tubulin that was identified by Huzil et al. (J. Mol. Biol. 2008, 378, 1016-1030), but our model provides a more reasonable structural basis for the protein-ligand interaction. There is a more complete desolvation of the peloruside A ligand and a greater array of favorable hydrophobic and electrostatic interactions exhibited by peloruside A at its β-tubulin binding site. In addition, the protein architecture in our peloruside A binding model was suitable for binding laulimalide. With the generation of both laulimalide and peloruside A binding models, it was possible to delineate the structural basis for the greater activity of laulimalide relative to peloruside A and to rationalize the known structure-activity relationship data for both compounds.     

Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening

Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hotspots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.     

Systematic profiling of taxol and its analogues (taxalogues) binding to β-tubulin and molecular analysis of their effects on microtubule stabilization

Microtubules are highly dynamic polymers of α/β-tubulin that represent major components of the cytoskeleton and have been established as an attractive druggable target of tumors. Taxol, also known as Paclitaxel, is a microtubule-stabilizing agent that binds stoichiometrically to a specific site in β-tubulin, where is out of but nearby the interacting interface of α/β-tubulin complex, to improve the complex stability through an allosterically regulatory mechanism. In this study, the systematic binding profile of taxol and its 22 structurally diverse, medicinally relevant analogues (termed as taxalogues) to the specific site of β-tubulin as well as their effects on the α/β-tubulin complex stability were created and investigated by using structural modeling, dynamics simulation, and energetics analysis. Two helices H1 and H2 of β-tubulin were identified as key hotspots at the α/β-tubulin interface to mediate the binding event of β-tubulin to α-tubulin. Taxalogue binding can trigger a conformational displacement in the H1 and H2 to elicit the stabilization (or destabilization) of α/β-tubulin. However, strong taxalogue binding potency to β-tubulin does not mean effective α/β-tubulin stabilization; there is only an indirect, moderate correlation between them. Cell viability assay revealed that the taxalogue-induced α/β-tubulin stabilization, but not the taxalogue binding, directly influences the antitumor activity of taxalogues. The activity increases in the order: SB-T-1214 < docetaxel < taxol < larotaxel < cisplatin < cabazitaxel.     

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out ～3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms β-hairpins, H3 and H2B adopt α-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy.     

微量热法研究α-环糊精与新型表面活性剂的包结作用

在298.15 K下用微量热法研究了α-环糊精与3-烷氧基-2-羟丙基三甲基溴化铵在水溶液中的包结作用.实验结果表明,随着疏水链CnH2n＋1O中碳原子数目n的增加(n=7、8、12、14), 主-客体包合物的化学计量比由1 :1为主变为2 :1为主. 各包合物都相当稳定,对应于n=7、8、12、14所得实验稳定常数分别为,β1=1.95×103 dm3•mol－1、β1=2.62×103 dm3•mol－1、β2=3.06×106 dm6•mol－2、β2=13.75×106 dm6•mol－2.包合物的形成均是焓驱动过程.包合物的平衡常数随烷氧基(CnH2n＋1O)中碳原子数目n的增加而增大,而包合物生成过程的标准反应焓(ΔHΘ)和标准反应熵(ΔSΘ)都随n的增加而减小.从主、客体的微观结构及包合物形成前后表面活性剂离子憎水基团周围溶剂分子排列结构的变化出发对实验结果进行了讨论.     

混合价配位聚合物 - [Cu(en)2H2O]2&#8226;8H2O的水热合成与晶体结构

在水热条件下合成了一个新的混合价配位聚合物 [Cu(en)2H2O]2&#8226;8H2O, 并对其进行了元素分析, IR, UV, TG-DSC等表征. X射线单晶衍射结果表明, 化合物属于单斜晶系, P21/c空间群, 晶胞参数a＝1.88678(12) nm, b＝2.30383(14) nm, c＝2.61234(16) nm, α＝90°, β＝95.844(1)°, γ＝90°, V＝11.2964(12) nm3, Z＝4, Dc＝3.954 g/cm3, R1＝0.0975, wR2＝0.2041. 结构测定结果表明, 聚合物中杂多阴离子骨架通过氧桥相连并形成一维无限链. 热性质研究表明, 形成标题化合物后杂多阴离子骨架分解温度大约在600.4 ℃, 热稳定性较母体杂多酸明显增强.     

Synthesis and Binding of Mannose-Specific Synthetic Carbohydrate Receptors

Synthetic carbohydrate receptors (SCRs) that selectively recognize cell-surface glycans could be used for detection, drug delivery, or as therapeutics. Here we report the synthesis of seven new C_2h symmetric tetrapodal SCRs. The structures of these SCRs possess a conserved biaryl core, and they vary in the four heterocyclic binding groups that are linked to the biaryl core via secondary amines. Supramolecular association between these SCRs and five biologically relevant C¹-O-octyloxy glycans, α/β-glucoside ( α/β-Glc ), α/β-mannoside ( α/β-Man ), and β-galactoside ( β-Gal ), was studied by mass spectrometry, ¹H NMR titrations, and molecular modeling. These studies revealed that selectivity can be achieved in these tetrapodal SCRs by varying the heterocyclic binding group. We found that SCR017 (3-pyrrole), SCR021 (3-pyridine), and SCR022 (2-phenol) bind only to β-Glc. SCR019 (3-indole) binds only to β-Man. SCR020 (2-pyridine) binds β-Man and α-Man with a preference to the latter. SCR018 (2-indole) binds α-Man and β-Gal with a preference to the former. The glycan guests bound within their SCR hosts in one of three supramolecular geometries: center-parallel, center-perpendicular, and off-center. Many host–guest combinations formed higher stoichiometry complexes, 2:1 glycan⋅SCR or 1:2 glycan⋅SCR , where the former are driven by positive allosteric cooperativity induced by glycan–glycan contacts.     

黑果枸杞叶多糖LRLP3的结构、抗氧化活性及免疫活性

黑果枸杞叶经水提醇沉, 离子交换柱层析和凝胶柱层析分离纯化, 得到平均分子量为79400的均一多糖组分LRLP3. 对该多糖的理化性质、 结构、 抗氧化活性及免疫活性的研究结果表明, LRLP3为多分支结构, 主链为(1→3)βGalp, 大部分半乳糖6位存在分支; 支链由(1→6)βGalp, (1→4)βGalp, (1→3)βAraf, (1→3)αArap, (1→5)βAraf和(1→2,4)αRhap组成, 非还原末端由αAraf, βGalp和βGlcp组成. LRLP3具有较强的还原能力, 可显著清除1,1-二苯基-2-三硝基苯肼(DPPH)自由基、 羟自由基和超氧阴离子自由基, 有效抑制Cu²⁺/H₂O₂诱导的蛋白氧化损伤和H₂O₂诱导的细胞氧化损伤. LRLP3在体外对未经诱导和经刀豆蛋白(ConA)或脂多糖(LPS)诱导的小鼠脾细胞增殖均有促进作用.