生长素作用方式的分子动力学模拟研究

针对植物生长素、受体TIR1、辅酶InsP₆和IAA7底物多肽链进行5组14个体系的分子动力学模拟研究, 比较分析了4个生长素分子IAA, 1-NAA, 2,4-D和2-NAA与受体TIR1之间的相互作用方式以及辅酶InsP₆和IAA7底物多肽链在早期生长素反应中所起的作用. 计算结果表明, 生长素与TIR1的结合能力与生长素活性顺序一致, 生长素的分子结构对于反应活性具有重要影响|中心水分子与生长素之间的氢键作用使得生长素的位置取向有利于与TIR1形成强相互作用|辅酶InsP₆与TIR1形成多个氢键使活性口袋结构稳定, 保证生长素有效地与活性位点结合|在结合生长素后, IAA7运动加剧, 使得生长素犹如激活IAA7多肽活性的“引发器”, 进而引发进一步的生长素反应.     

基于分子模拟方法预测PIP2在双孔钾通道TREK-1上结合位点的研究

磷脂酰肌醇4,5-二磷酸酯(PIP₂)是一类分布在质膜内层的信号磷脂分子, 对钾、 钠和氯等离子通道和转运蛋白等多种跨膜蛋白具有调节作用. TREK-1是一类重要的背景钾通道, 受温度、 机械拉伸及胞内pH等多种因素调节, PIP₂在特定浓度范围内可激活TREK-1通道, 在内面向外膜片钳记录TREK-1通道电流中使用PIP₂抗结剂(如多聚赖氨酸)可导致TREK-1通道关闭. 利用分子对接和全原子分子动力学模拟探索了PIP₂与双孔钾通道TREK-1的相互作用. 分子对接计算结果表明, PIP₂在TREK-1通道上有两个可能的结合位点. 进一步的分子动力学模拟和均力势(PMF)计算结果表明, 其中位于螺旋M4和螺旋M1的位点可能是PIP₂激活TREK-1的优先结合位点. 模拟展示了PIP₂与TREK-1结合的可能构象. PIP₂的肌醇头部磷酸根与位于M1和M4上的碱性残基K45, K304和R311形成稳定盐桥; M1螺旋上的一系列疏水残基对稳定PIP₂的脂肪长链具有关键作用.     

酵母AHAS酶与磺酰脲类抑制剂作用模型的分子对接研究

基于酵母乙酰羟酸合成酶(AHAS)与磺酰脲类抑制剂复合物的晶体结构, 用分子对接方法对AHAS与5个磺酰脲类抑制剂相互作用的方式进行了系统的分子对接研究. 晶体复合物对接和假复合物对接两种模式对接的结果基本相同, 并与实验结果吻合. 在进一步的对接中逐级考虑了辅酶FAD和TPP的影响, 结果表明, 辅酶FAD和TPP的加入, 对AHAS酶与磺酰脲类抑制剂的结合顺序基本没有影响. 其中FAD的加入使AHAS与抑制剂的结合更加稳定, 这主要是由于抑制剂的R2取代基与FAD中的平面基团Flavin环间存在的范德华相互作用所致; 抑制剂与TPP间存在的静电相互作用可能是加速TPP降解的原因.     

C60与铈卟啉相互作用的密度泛函理论研究

应用Perdew-Burke-Ernzerhof (PBE)密度泛函理论对5种可能存在的富勒烯与铈卟啉复合物进行了几何结构优化, 通过分子间距离及结合能数值, 确认了C₆₀和铈卟啉可以通过非键相互作用形成超分子主-客体复合物, 且最有可能的作用位点为C₆₀的C5:6键(相邻五元环与六元环共用碳-碳键). 应用扩展过渡态方法对结合能进行分解, 分解结果显示, 静电能对总吸引能的贡献约为60%, 说明静电作用是复合物稳定存在的最主要因素. 最后对复合物中的电子流向进行了研究, 结果表明复合物中电子的转移与主-客体间相互作用有一定联系, 且电子是从主体铈卟啉流向客体C₆₀.     

洋刀豆脲酶与抑制剂相互作用的分子对接和分子动力学研究

通过洋刀豆脲酶抑制剂的筛选实验得到具有较好抑制活性的化合物2-乙酰基-γ-丁内酯(COM), 其半数抑制浓度在微摩尔浓度级别(IC₅₀＝375 μmol•L^－l). 在此基础上, 使用分子对接和分子动力学(MD)模拟的方法研究洋刀豆脲酶与抑制剂乙酰氧肟酸(AHA)及活性化合物COM之间的相互作用. 用Gold3.0程序将两个小分子与洋刀豆脲酶的晶体结构进行对接, 对接得到的复合物模型使用Amber程序进行MD模拟研究. 模拟过程中, 脲酶结构中的双核镍离子活性中心选用non-bonded模型. 研究结果显示: AHA与洋刀豆脲酶结合时, Ni(1)和Ni(2)均为五配位|COM与洋刀豆脲酶结合时Ni(1)为五配位, Ni(2)为六配位的结合模型更加合理. 这些研究为了解洋刀豆脲酶与抑制剂之间的相互作用提供了重要的参考信息.     

诺氟沙星-DNA复合物的分子动力学模拟

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]₂形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.     

HIV-1整合酶与抑制剂金精三羧酸复合物的分子动力学模拟

用分子对接程序(Autodock)将含有一个Mg²⁺的HIV-1整合酶核心区(以下简称IN-A)与抑制剂小分子金精三羧酸(简称Aurin)进行对接,预测其未知的复合物结构,然后用分子动力学(MD)方法对IN-A与Aurin的对接结果进行了950 ps的模拟.MD模拟结果发现,IN-A与Aurin形成了两个稳定的氢键,Mg²⁺也与Aurin上的氧原子形成了稳定的配键,IN-A与Aurin之间的静电相互作用能和范德华相互作用能的平均值分别为-205.8和-162.7 kJ/mol.根据MD模拟得到的IN-A与Aurin相互作用后的构象变化信息,我们对对接复合物结构进行了修正,给出了更加合理和稳定的复合物预测结构.本工作得到的HIV-1整合酶与抑制剂Aurin的结合模式信息将有助于设计和改造出效果更好的抗HIV-1整合酶的先导化合物.     

多巴胺第三受体蛋白三维结构及其活性位点氨基酸残基

基于牛视紫红质模板蛋白,同源模建多巴胺第三受体（D₃R）蛋白三维结构,在1-棕榈酰-2-油酰-卵磷脂（POPC）膜-水模型环境,开展300 ns分子动力学模拟提炼优化其结构,取得稳定的D₃R蛋白三维结构（2B08-D₃R）.在该蛋白基础上,采用MP2/6-31G（d,p）方法,计算多巴胺（Dop）与氨基酸残基相互作用的结合能,确定五个残基（Asp117、Ser208、His272、Phe269和Thr276）为活性位点.五个活性位点残基分别位于D₃R蛋白跨膜螺旋区TM3、TM5和TM6,组成活性空腔结构.多巴胺分子以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键结合方式保留在D₃R蛋白中,与D₃R蛋白结合能E_b为-97.8 kJ·mol^-1基于3PBL D₃R突变体晶体结构,构建了另外一个含有多巴胺分子的D₃R蛋白结构（Dop-3PBL-D₃R）,确定在该蛋白结构中,多巴胺的活性位点氨基酸是Asp83、His272、Phe269、Phe268和Trp265.在该蛋白结构中,多巴胺分子同样以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键方式结合,与该蛋白相互作用的结合能是-80.5 kJ·mol^-1.     

细胞色素p450 2s1(CYP2s1)三维结构模建及其与维甲酸分子的对接研究

利用同源模建和分子动力学模拟,模建了细胞色素P450(CYP2s1)的三维结构．在模建结构的基础上,分析了活性位点的组成和结构,并进行了与小分子(维甲酸)的分子对接研究．研究结果表明,在由维甲酸和CYP2s1形成的复合物中,非键相互作用较强,其中,GLu411和Ala414是与维甲酸相互作用能最强的两个残基,对复合物的结合起重要作用．     

电子给受体复合物中电荷转移吸收光谱和溶剂效应

用MP2/6-31G^**方法研究了二氯甲烷溶剂分子与电子给体、受体以及电子给受体复合物间的相互作用,结果表明,二氯甲烷与电子受体和电子给受体复合物间有弱氢键相互作用.利用CIS/6-31++G^**方法研究了溶剂与溶质分子间形成氢键对激发态的影响.自然键电荷分析表明,电子给受体复合物的S₀→S₁跃迁导致一个电子从电子给体转移到受体.结合非平衡溶剂化处理和自洽反应场方法研究了溶剂分子与复合物间形成氢键时的电荷转移吸收光谱.计算表明氢键作用导致复合物的电荷转移吸收光谱蓝移.     

Interaction Between 1,2,3-Trichloropropane and Haloalkane Dehalogenase LinB

The haloalkane dehalogenase LinB from Sphingomonas paucimobills UT26 was found to transform the 1,2,3-trichloropropane(TCP) into inorganic halide ions and 2,3-dichloro-1-propanol although the catalytic activity is very low(Kcat=0.005 s-1).In this study,molecular dynamics simulation and docking studies were performed to investigate the binding of TCP to LinB.The docking results indicate that LinB does not restrict TCP to be bound productively in the active site and the water-mediated inhibition occurs in the...     

人类2-氨基3-羧基粘康酸6-半醛脱羧酶(ACMSD)与底物及抑制剂作用模型的理论研究

利用同源模建和分子动力学模拟方法构建了人类2-氨基3-羧基粘康酸6-半醛脱羧酶(hACMSD)的三维结构, 并利用Profile-3D和Procheck等方法评估了模型的可靠性. 在此基础上, 用分子对接程序(Affinity), 将其底物2-氨基3-羧基粘康酸6-半醛(ACMS)和抑制剂喹啉酸(QA)分别与hACMSD进行对接, 获得了复合物结构的理论模型. 通过配体与受体之间相互作用能和结构分析给出了底物和抑制剂的具体结合方式, 明确了hACMSD与底物和抑制剂结合时起重要作用的氨基酸残基.     

H-bond refinement for electron transfer membrane-bound protein–protein complexes: Cytochrome c oxidase and cytochrome c552

In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent. Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.     

Generation of a homology model of the human histamine H<Subscript>3</Subscript> receptor for ligand docking and pharmacophore-based screening

The human histamine H(3) receptor (hH(3)R) is a G-protein coupled receptor (GPCR), which modulates the release of various neurotransmitters in the central and peripheral nervous system and therefore is a potential target in the therapy of numerous diseases. Although ligands addressing this receptor are already known, the discovery of alternative lead structures represents an important goal in drug design. The goal of this work was to study the hH(3)R and its antagonists by means of molecular modelling tools. For this purpose, a strategy was pursued in which a homology model of the hH(3)R based on the crystal structure of bovine rhodopsin was generated and refined by molecular dynamics simulations in a dipalmitoylphosphatidylcholine (DPPC)/water membrane mimic before the resulting binding pocket was used for high-throughput docking using the program GOLD. Alternatively, a pharmacophore-based procedure was carried out where the alleged bioactive conformations of three different potent hH(3)R antagonists were used as templates for the generation of pharmacophore models. A pharmacophore-based screening was then carried out using the program Catalyst. Based upon a database of 418 validated hH(3)R antagonists both strategies could be validated in respect of their performance. Seven hits obtained during this screening procedure were commercially purchased, and experimentally tested in a [(3)H]N(alpha)-methylhistamine binding assay. The compounds tested showed affinities at hH(3)R with K ( i ) values ranging from 0.079 to 6.3 muM.     

New cyclic RGD peptides: synthesis,characterization, and theoretical activity towards αvβ3 integrin

Two new cyclic RGD peptides were prepared using a click chemistry approach. The linear RGDfV peptide was synthesized by solid-phase peptide synthesis using a 9-fluorenylmetoxicarbonyl (Fmoc) strategy and a 2-chlorotrityl chloride resin. After coupling 5-hexynoic acid the peptide was cleaved from the resin and linked to propargylamine. The bis-alkynyl RGDfV peptide was then reacted with two different bis-azides by treatment with copper iodide and triethylamine. These two cyclic RGD peptides were characterized by NMR and HRMS. In order to evaluate the interaction of these new compounds with integrin α_vβ₃ docking experiments were carried out and the results compared with those obtained with cyclo(RGDf[N–Me]V) (Cilengitide). The two new cyclic RGD peptides showed a higher affinity to the α_vβ₃ integrin when compared with Cilengitide thus representing two new potential integrin α_vβ₃ antagonists.     

毒蕈碱型M1受体的同源模建和分子对接

采用同源模建方法对M1受体的三维结构进行了模拟, 将得到的模型分别与M受体完全激动剂乙酰胆碱和M1受体选择性激动剂占诺美林进行分子对接, 形成非特异性激动和特异性激动的受体-配体复合物. 用分子动力学模拟方法分别将未与小分子对接的M1受体、M1受体-乙酰胆碱复合物、M1受体-占诺美林复合物置于磷脂双膜中模拟10 ns. 将模拟后的蛋白质结构与包含活性分子的测试库对接并将结果打分, 以top5%富集因子(EF)作为评价依据, 用占诺美林优化后的M1受体模型的EF为8.0, 用乙酰胆碱优化后M1受体模型的EF为6.5, 非复合物的EF为1.5. 说明M1受体选择性激动剂复合物进行分子动力学模拟后得到的三维结构模型比较合理, 可以作为化合物虚拟筛选的模型对新化合物进行虚拟筛选, 为找到新的选择性M1受体激动剂奠定了基础.     

Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study

Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis. The 3D structures of PPO1 and PPO2 were built through homology modeling, while the 3D crystal structures of PPO3 and PPO4 were retrieved from PDB. Pharmacophore modeling was performed using LigandScout 3.1 software and top five models were selected to screen the libraries (2601 of Aurora and 727, 842 of ZINC). Top 10 hit compounds (C1-10) were short-listed having strong binding affinities for PPO1-4. Drug and synthetic accessibility (SA) scores along with absorption, distribution, metabolism, excretion and toxicity (ADMET) assessment were employed to scrutinize the best lead hit. C4 (name) hit showed the best predicted SA score (5.75), ADMET properties and drug-likeness behavior among the short-listed compounds. Furthermore, docking simulations were performed to check the binding affinity of C1-C10 compounds against target proteins (PPOs). The binding affinity values of complex between C4 and PPOs were higher than those of other complexes (−11.70, −12.1, −9.90 and −11.20 kcal/mol with PPO1, PPO2, PPO3, or PPO4, respectively). From comparative docking energy and binding analyses, PPO2 may be considered as better target for melanogenesis than others. The potential binding modes of C4, C8 and C10 against PPO2 were explored using molecular dynamics simulations. The root mean square deviation and fluctuation (RMSD/RMSF) graphs results depict the significance of C4 over the other compounds. Overall, bioactivity and ligand efficiency profiles suggested that the proposed hit may be more effective inhibitors for melanogenesis.     

Modeling,docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.

Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid–protein interactions, indicating some future applications of ns-LTP-mediated transport.     

细胞色素P450 2f1(CYP2f1)的三维结构模建和与维甲酸的对接研究

利用同源模建和分子动力学模拟方法，模建了细胞色素P450 2f1(CYP2f1)的三维结构．在此基础上，分析了活性位点的组成和结构，并进行了与小分子(维甲酸)的对接研究．研究结果表明，His328，Ser397和Arg417对复合物的结合起重要作用．