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.     

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.     

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。     

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.     

辛味中药与嗅觉受体相互作用的分子模拟

采用分子模拟的方法, 在Schrdinger软件平台上, 用同源模建的方法构建了嗅觉受体OR1D2, OR7D4和OR51E1的三维结构模型. 运用分子动力学模块Desmond将与激动剂以及抑制剂分别对接的嗅觉受体复合物置于磷脂双膜中进行模拟. 最后将辛味中药的小分子分别对接到嗅觉受体中, 并与苦味中药的对接结果相对照, 依据实验结果, 讨论辛味中药发挥作用的分子机制. 该研究着重于同源模建、分子动力学和分子对接技术的综合应用, 探讨辛味中药化学成分与嗅觉受体的相互作用及其分子机理, 为从分子层面揭示辛味中药的药效物质基础提供帮助, 也为中药药性的研究提供了新的思路和方法.     

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...     

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.     

基于虚拟筛选从中药中发现抗铜绿假单胞菌的活性成分

针对铜绿假单胞菌的耐药性问题,采用虚拟筛选技术快速筛选出具有抗铜绿假单胞菌活性的中药成分.采用AutoDock Vina程序对铜绿假单胞菌LasR信号受体蛋白的2UV0、3IX3和6MVM三个共晶结构进行方法学研究,然后利用Lipinsky规则对陶术中药数据库进行初步筛选,通过分子对接进行再次筛选,并对满足Lip-in...     

神经介素B受体与拮抗剂、激动剂的分子模拟研究

大鼠神经介素B受体(rat neuromedin B receptor, rNMBR)属于G蛋白偶联受体(G-protein coupled receptor, GPCR) A家族的成员. GPCR的结构特征和在信号传导中的重要作用决定了其可以作为很好的药物靶标. 关于rNMBR与内源性激动剂神经介素B (neuromedin B, NMB)以及与非肽类拮抗剂pd168368作用机制的研究对于合理设计受体药物分子有重要的指导意义. 在这一研究中, 我们使用同源模建, 构建受体的三维结构, 进行分子对接和分子动力学的计算. 基于受体三维结构, 通过10 ns的空载受体、激动剂-受体、拮抗剂-受体的分子动力学模拟, 探讨受体与激动剂与拮抗剂的作用机制. 研究表明rNMB-R中跨膜(transmembrane, TM)螺旋3, 5, 6, 7参与配体的结合. NMB与受体的结合, 使受体转变为活性构象, 而受体同拮抗剂pd168368恰好相反.     

分子生物色谱用于中药活性成分筛选及质量控制方法的研究

报道了近期工作进展,首先阐述了分子生物色谱的基本原理及特点,然后介绍了分子生物色谱对多种中药、不同产地的同种中药活性成分谱图模式的比较,结合已有的工作对活性成分筛选方法、相互作用研究、质量控制方法发展做了细致的说明,并讨论了其发展方向及前景。     

Discovery of New Inhibitors of eEF2K from Traditional Chinese Medicine Based on In Silico Screening and In Vitro Experimental Validation

Eukaryotic elongation factor 2 kinase (eEF2K) is a highly conserved α kinase and is increasingly considered as an attractive therapeutic target for cancer as well as other diseases. However, so far, no selective and potent inhibitors of eEF2K have been identified. In this study, pharmacophore screening, homology modeling, and molecular docking methods were adopted to screen novel inhibitor hits of eEF2K from the traditional Chinese medicine database (TCMD), and then cytotoxicity assay and western blotting were performed to verify the validity of the screen. Resultantly, after two steps of screening, a total of 1077 chemicals were obtained as inhibitor hits for eEF2K from all 23,034 compounds in TCMD. Then, to verify the validity, the top 10 purchasable chemicals were further analyzed. Afterward, Oleuropein and Rhoifolin, two reported antitumor chemicals, were found to have low cytotoxicity but potent inhibitory effects on eEF2K activity. Finally, molecular dynamics simulation, pharmacokinetic and toxicological analyses were conducted to evaluate the property and potential of Oleuropein and Rhoifolin to be drugs. Together, by integrating in silico screening and in vitro biochemical studies, Oleuropein and Rhoifolin were revealed as novel eEF2K inhibitors, which will shed new lights for eEF2K-targeting drug development and anticancer therapy.     

我国中药出口贸易发展现状分析及对策研究

对中药出口贸易的发展现状进行了分析,从机遇与挑战方面阐述了其发展趋势,对中药实现现代化,推动国际化,知识产权保护以及如何消除贸易壁垒等方面提出了对策及建议。由于国家政府各项政策的倾斜,将进一步加快我国中药产业的发展,从现代化走向国际化。     

治疗脑血管疾病中成药中镁含量的测定及临床意义

利用原子吸收分光光度法测定了10种脑血管药物中镁的含量。结果表明,复方银杏胶丸中镁含量较低,脉通中镁含量较高。该结果为探讨镁元素与脑血管疾病的关系以及临床上合理用药提供了有用的数据。     

治疗脑血管疾病中成药中铅含量的测定及临床意义

采用原子吸收分光光度法测定了十种治疗脑血管疾病的中成药中铅含量。结果表明,十种中成药中铅含量有一定的差异。该结果为讨论铅元素与脑血管疾病中扣成药药效关系提供了有用的数据。     

中药质量评价关键问题与分析方法探讨

该文针对我国目前中药质量评价体系现状,总结了中药质量评价的关键科学问题,并围绕"发现"与"控制"有效成分的中药质量评价方法进行探讨.笔者结合多年中药质量分析研究工作经验,分析了中药"谱-效"关系研究、全时段等基线多波长融合指纹图谱、生物活性测定法3种质量评价与检测方法的研究内容、手段、适用范围等,为丰富、完善中药质量控...     

Building the Pharmacophore Model of HIV-1 Integrase Strand Transfer Inhibitors and Studying Their Inhibition Mechanism

The replication of HIV-1 requires the integration of its cyclic DNA into host DNA by HIV-1 integrase (IN), which includes two important reactions, 3'-processing and strand transfer, both catalyzed by HIV-1 IN. Disrupting either of the reactions will fulfill the purpose of inhibiting the replication of HIV-1. In this paper, pharmacophore modeling and molecular docking are employed to investigate the inhibition mechanism of the HIV-1 IN strand transfer inhibitors (INSTIs). Based on the results, we suggest that the inhibition mechanism of INSTIs involves the inhibitor chelating the cofactors Mg2+ and its forming hydrogen bonds with some crucial residues adjacent to the DDE active center.     

From Myricetin to the Discovery of Novel Natural Human ENPP1 Inhibitors: A Virtual Screening,Molecular Docking,Molecular Dynamics Simulation,and MM/GBSA Study

It was recently revealed that naturally occurring myricetin can inhibit ectonucleotidase ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which, in turn, can treat ischemic cardiac injury. However, due to myricetin’s poor druggability, its further developments are relatively limited, which necessitates the discovery of novel ENPP1-inhibiting myricetin analogs as alternatives. In this study, the binding model of myricetin with ENPP1 was elucidated by molecular docking and molecular dynamics studies. Subsequently, virtual screening on the self-developed flavonoid natural product database (FNPD), led to the identification of two flavonoid glycosides (Cas No: 1397173-50-0 and 1169835-58-8), as potential ENPP1 inhibitors. Docking scores and MM/GBSA binding energies predicted that they might have higher inhibitory effects than myricetin. This study provides a strong foundation for the future development of ischemic cardiac injury drugs.     

Virtual Screening and In Vitro Evaluation of PD-1 Dimer Stabilizers for Uncoupling PD-1/PD-L1 Interaction from Natural Products

Genetic mutations accumulated overtime could generate many growth and survival advantages for cancer cells, but these mutations also mark cancer cells as targets to be eliminated by the immune system. To evade immune surveillance, cancer cells adopted different intrinsic molecules to suppress immune response. PD-L1 is frequently overexpressed in many cancer cells, and its engagement with PD-1 on T cells diminishes the extent of cytotoxicity from the immune system. To resume immunity for fighting cancer, several therapeutic antibodies disrupting the PD-1/PD-L1 interaction have been introduced in clinical practice. However, their immunogenicity, low tissue penetrance, and high production costs rendered these antibodies beneficial to only a limited number of patients. PD-L1 dimer formation shields the interaction interface for PD-1 binding; hence, screening for small molecule compounds stabilizing the PD-L1 dimer may make immune therapy more effective and widely affordable. In the current study, 111 candidates were selected from over 180,000 natural compound structures through virtual screening, contact fingerprint analysis, and pharmacological property prediction. Twenty-two representative candidates were further evaluated in vitro. Two compounds were found capable of inhibiting the PD-1/PD-L1 interaction and promoting PD-L1 dimer formation. Further structure optimization and clinical development of these lead inhibitors will eventually lead to more effective and affordable immunotherapeutic drugs for cancer patients.     

Novel and Potential Small Molecule Scaffolds as DYRK1A Inhibitors by Integrated Molecular Docking-Based Virtual Screening and Dynamics Simulation Study

The dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a novel, promising and emerging biological target for therapeutic intervention in neurodegenerative diseases, especially in Alzheimer’s disease (AD). The molMall database, comprising rare, diverse and unique compounds, was explored for molecular docking-based virtual screening against the DYRK1A protein, in order to find out potential inhibitors. Ligands exhibiting hydrogen bond interactions with key amino acid residues such as Ile165, Lys188 (catalytic), Glu239 (gk+1), Leu241 (gk+3), Ser242, Asn244, and Asp307, of the target protein, were considered potential ligands. Hydrogen bond interactions with Leu241 (gk+3) were considered key determinants for the selection. High scoring structures were also docked by Glide XP docking in the active sites of twelve DYRK1A related protein kinases, viz. DYRK1B, DYRK2, CDK5/p25, CK1, CLK1, CLK3, GSK3β, MAPK2, MAPK10, PIM1, PKA, and PKCα, in order to find selective DYRK1A inhibitors. MM/GBSA binding free energies of selected ligand–protein complexes were also calculated in order to remove false positive hits. Physicochemical and pharmacokinetic properties of the selected six hit ligands were also computed and related with the proposed limits for orally active CNS drugs. The computational toxicity webserver ProTox-II was used to predict the toxicity profile of selected six hits (molmall IDs 9539, 11352, 15938, 19037, 21830 and 21878). The selected six docked ligand–protein systems were exposed to 100 ns molecular dynamics (MD) simulations to validate their mechanism of interactions and stability in the ATP pocket of human DYRK1A kinase. All six ligands were found to be stable in the ATP binding pocket of DYRK1A kinase.