α1A-肾上腺素受体的同源模建及其对接研究

以β2肾上腺素受体(β2-AR)为模板,采用同源模建和分子动力学模拟构建了人类α1A-肾上腺素受体(α1A-AR)的三维结构模型,并利用PROCHECK,PROSA和WHAT-IF评估了模型的合理性.所得的结构采用分子对接程序Flexidock与激动剂去甲肾上腺素和拮抗剂西罗多辛分别进行对接,结果表明,2种配基具有相似...     

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-乙酰且H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.     

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.     

大麻素受体CB1三维结构的同源模建及其对接研究

大麻素CB1受体属于G蛋白偶联受体. 以牛视紫红质的晶体结构为模板, 利用同源模建法对CB1受体的三维结构进行了模拟, 并采用分子动力学方法对模型进行了修正和优化. 在此基础上, 分析了活性位点的组成和结构, 研究了拮抗剂利莫那班与CB1受体的对接, 明确了CB1受体与利莫那班结合时起重要作用的氨基酸残基. 发现利莫那班与CB1受体残基Lys192形成氢键相互作用是CB1受体拮抗剂的重要分子作用基础.     

人类胞外信号调节激酶1的同源模建及其抑制剂的对接与结构改造

通过同源模建和分子动力学模拟构建了人类胞外信号调节激酶1(hERK1)的三维结构,并利用profile-3D和procheck方法评估了模型的合理性.对所得的结构使用分子对接程序Affinity和CDOCKER进行了两种抑制剂的对接.结果显示这两种抑制剂与酶的结合方式相似,它们均与残基K36,Q87之间存在氢键作用,二者取代基的不同导致了抑制能力的差别.基于对接结果分析,对已知抑制剂进行结构改造,得到了一个理论上结合能力更强的抑制剂.它在保持与K36和Q87之间氢键的同时,又与残基D93,K96,S135形成了四条氢键,显著提高了与酶的相互作用.对接相互作用能显著下降,MM-PBSA结合自由能降为负值,这些均体现了抑制能力的提高.本工作对于针对该酶的抑制剂设计和相关疾病的新药开发具有理论指导价值.     

人类腺苷受体A3亚型拮抗剂的构效关系分析

构建人类腺苷受体A3亚型药效团模型和三维蛋白结构模型用于作用模式研究.以18个来源于文献具有腺苷受体A3亚型拮抗活性的化合物作为训练集,使用HypoGen方法构建药效团模型.通过同源模建和分子动力学模拟构建了人类腺苷受体A3亚型的三维蛋白模型,并利用PROCHECK方法评估该模型的合理性,对所得的结构使用分子对接程序进行作用模式分析,药效团模型和同源模建结果相互匹配较好.使用新药效团模型对MDL药物数据库(MDDR)中包含的约120000个化合物进行虚拟筛选,得到了8个候选化合物,用于进一步的生物学评价和活性测定.本工作对于人类腺苷受体A3亚型拮抗剂的设计和抗哮喘药物的研发具有一定的理论指导和应用价值.     

鲍曼不动杆菌LpxC的同源模建及分子对接

鲍曼不动杆菌已成为最普遍的医院致病菌,且耐药情况严峻.LpxC作为新抗菌药物靶点被大量研究,但鲍曼不动杆菌LpxC晶体尚未解析得到,基于其结构的药物设计等工作无法开展.以铜绿假单胞菌LpxC晶体结构为模板,通过同源模建方法获得鲍曼不动杆菌LpxC结构模型.较好的Ramachandran plot分布和Profile-3D结果验证了模型的合理性.用分子动力学模拟优化鲍曼不动杆菌LpxC模型,修补部分不合理构象.后续分子对接结果显示S构型的苄氧乙酰基羟肟酸类抑制剂比R构型分子能更有效地结合在F191,H237和K238组成的较浅口袋中,这可能是S构型抑制剂活性更高的主要因素,模拟结果与实验数据吻合较好.     

人类丝氨酸消旋酶的同源模建及其与多肽类抑制剂的分子对接

利用同源模建和分子动力学模拟方法构建了人类丝氨酸消旋酶(hSR)的三维结构, 并利用profile-3D和procheck方法评估了模型的可靠性. 在此基础上用分子对接程序(affinity)将多肽类抑制剂A和B分别与hSR进行对接, 获得了其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此类抑制剂与hSR的具体结合方式, 明确了hSR与此类抑制剂结合时起重要作用的氨基酸残基, 为基于人类丝氨酸消旋酶三维结构的药物设计提供重要的参考信息.     

G-蛋白偶联受体GPR120分子模建研究

新的长链脂肪酸受体G-蛋白偶联受体120 (G-protein-coupled receptor120, GPR120)是2型糖尿病的潜在治疗靶标. 由于其晶体结构迄今尚未获得, 成为基于结构的新药设计的瓶颈. 首先, 以人体β2肾上腺能素受体(human β2 adrenergic receptor, β2AR)晶体结构为模板, 通过同源模建方法构建GPR120三维结构, 对整个体系进行包膜的分子动力学模拟. 然后采用分子对接技术模建了GPR120的小分子激动剂GW9508与GPR120的相互作用模型, 发现了受体分子识别的关键性残基, 为开展定点突变实验提供了指导意义. 所建模型为研究受体与配体作用提供了合理的初始结构, 此方法也适用于其他G蛋白偶联受体的分子模建.     

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．     

CCK1受体的同源模拟和分子对接研究

采用同源建模法对CCK1受体的三维结构进行了模拟,并采用分子动力学方法对模型进行修正和优化,再采用与训练集激动剂和拮抗剂分子对接的方法分别得到激动状态和拮抗状态CCK1受体的三维结构模型。得到的模型使用DOCK对接软件对训练集中的分子进行对接,所得结果与其实际活性拟合度较好,说明我们建立的激动和拮抗状态下的CCK1受体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。     

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.     

Homology Modeling of Cry1Ac Toxin-binding Alkaline Phosphatase Receptor from Helicoverpa armigera and Its Functional Interpretation

Alkaline phosphatases (ALPs) attached to the midgut membrane with glycosyl phosphotidyl inositol (GPI) have been proposed as the putative Cry1Ac toxin receptor in Helicoverpa armigera. Activated toxins bind to ALP receptors on the brush border membrane vesicle (BBMV) of the midgut epithelium, which activates intracellular oncotic pathways and leads to cell death. However, with the long‐term use of Cry toxin, insects can develop a strong resistance to insecticidal delta‐endotoxins. Although the molecular mechanism of insect resistance has not been fully understood, insects develop resistance to biopesticides due to changes of toxins binding to midgut receptors. So, it is a good idea to investigate the molecular mechanism of insect resistance by analyzing ALP receptor from Helicoverpa armigera (Ha‐ALP). Based on crystal structure of shrimp alkaline phosphatase, the three‐dimensional structure of the Cry1Ac toxin‐binding Ha‐ALP receptor was obtained by homology modeling and the model was further evaluated using PROSA energy and ERRAT. The important role of binding of toxin to GalNAc on Ha‐ALP was discussed in the aspect of Cry1Ac toxicity. Specific recognition sites of the binding of oligosaccharides to Ha‐ALP were predicted. Post‐translational modification of ALP provides insights into the functional properties of ALP and leads to profound understanding of receptor and toxin interactions.     

μ阿片受体的三维结构预测及活性位点分析

通过对比多个与μ阿片受体同属G蛋白偶联受体的视紫质蛋白序列,选择以同源性最高的牛视紫质蛋白(PDB编号:1F88)为模板,采用同源模建的方法,基于Composer程序,构建了μ阿片受体的三维结构模型,并预测了其二级结构.模型的可靠性经Ramachandran图和ProTable验证,用Site ID确定了μ阿片受体的活性位点,得到了与文献报道相吻合的结果,并预测了新的可能的关键性氨基酸,为合理设计μ阿片受体的激动剂和拮抗剂提供重要依据,进一步指导药物分子设计.     

Using Homology Modeling, Molecular Dynamics and Molecular Docking Techniques to Identify Inhibitor Binding Regions of Somatostatin Receptor 1

The G protein coupled receptor(GPCR), one of the members in the superfamily, which consists of thousands of integral membrane proteins, exerts a wide variety of physiological functions and responses to a large portion of the drug targets. The 3D structure of somatostatin receptor 1(SSTR1) was modeled and refined by means of homology modeling and molecular dynamics simulation. This model was assessed by Verify-3D and Vadar, which confirmed the reliability of the refined model. The interaction between the inhibitor cysteamine, somatostatin(SST) and SSTR1 was investigated by a molecular docking program, Affinity. The binding module not only showed the crucial residues involved in the interaction, but also provided important information about the interaction between SSTR1 on the one hand and ligands on the other, which might be the significant evidence for the structure-based design.     

Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology

Overexpression of the adenosine A₁ receptor (A₁AR) has been detected in various cancer cell lines. However, the role of A₁AR in tumor development is still unclear. Thirteen A₁AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. We have investigated the pharmacology of the mutations located at the 7-transmembrane domain using a yeast system. Concentration–growth curves were obtained with the full agonist CPA and compared to the wild type hA₁AR. H78L^3.23 and S246T^6.47 showed increased constitutive activity, while only the constitutive activity of S246T^6.47 could be reduced to wild type levels by the inverse agonist DPCPX. Decreased constitutive activity was observed on five mutant receptors, among which A52V^2.47 and W188C^5.46 showed a diminished potency for CPA. Lastly, a complete loss of activation was observed in five mutant receptors. A selection of mutations was also investigated in a mammalian system, showing comparable effects on receptor activation as in the yeast system, except for residues pointing toward the membrane. Taken together, this study will enrich the view of the receptor structure and function of A₁AR, enlightening the consequences of these mutations in cancer. Ultimately, this may provide an opportunity for precision medicine for cancer patients with pathological phenotypes involving these mutations.     

Irreversible Antagonists for the Adenosine A2B Receptor

Blockade of the adenosine A_2B receptor (A_2BAR) represents a potential novel strategy for the immunotherapy of cancer. In the present study, we designed, synthesized, and characterized irreversible A_2BAR antagonists based on an 8-p-sulfophenylxanthine scaffold. Irreversible binding was confirmed in radioligand binding and bioluminescence resonance energy transfer(BRET)-based Gα₁₅ protein activation assays by performing ligand wash-out and kinetic experiments. p-(1-Propylxanthin-8-yl)benzene sulfonyl fluoride (6a, PSB-21500) was the most potent and selective irreversible A_2BAR antagonist of the present series with an apparent K_i value of 10.6 nM at the human A_2BAR and >38-fold selectivity versus the other AR subtypes. The corresponding 3-cyclopropyl-substituted xanthine derivative 6c (PSB-21502) was similarly potent, but was non-selective versus A₁- and A_2AARs. Attachment of a reactive sulfonyl fluoride group to an elongated xanthine 8-substituent (12, K_i 7.37 nM) resulted in a potent, selective, reversibly binding antagonist. Based on previous docking studies, the lysine residue K269^7.32 was proposed to react with the covalent antagonists. However, the mutant K269L behaved similarly to the wildtype A_2BAR, indicating that 6a and related irreversible A_2BAR antagonists do not interact with K269^7.32. The new irreversible A_2BAR antagonists will be useful tools and have the potential to be further developed as therapeutic drugs.