药效假说在配体从头设计中的适用性探讨

在基于靶蛋白结构的多肽分子设计中,药效假说是从头设计方法的基本前提。虽然该假说是否成立已有不少议论,但尚未见到系统分析的报道。通过对８个蛋白质复物界面做了氨基酸模拟图谱,并从模拟图谱的结构偏差与能量分量的关系,对药效假说的适用条件进行了讨论。同时也给出一个ＨＩＶ－１蛋白酶及抑制剂复合物的功能图谱。从所得结果来看,药效假说在以氨基酸为药效基团时,尽管不少情况下仍然有效,但不是谱遍成立的。     

蛋白质-核酸复合物界面氨基酸与核苷酸偏好性分析

蛋白质-核酸相互作用机制到目前还不是很清楚,尤其是蛋白质与RNA的相互作用。目前,可得到的蛋白质-核酸复合物结构数据不断增多,作者收集了Protein Data Bank数据库中所有的蛋白质-核酸复合物结构数据,对复合物中结合残基和结合核苷酸的偏好性进行了统计分析。发现：1）不同功能的蛋白质-核酸复合物间的结合残基数量存在显著差异;2）在蛋白 质-DNA和蛋白质-RNA复合物界面,碱性氨基酸都是最受欢迎的;3）氨基酸的极性大小及方向在决定它是否与RNA分子进行结合时起到重要的作用,同时发现氨基酸侧链形成的空间位阻会影响氨基酸残基与RNA分子的相互作用;4）随着定义结合残基距离阈值的增大,其氨基酸使用的特异性降低,而受欢迎与不受欢迎的氨基酸种类均没有变化。     

肿瘤坏死因子与其受体相互作用的计算机模拟研究

利用同源模建方法,以肿瘤坏死因子(TNF)R55受体胞外区的晶体结构为参考模板,预测了TNFR75受体胞外区Cys18-Phe147片段的三维结构。根据R55受体胞外区与LT相结合的复合物的晶体结构,预测了TNF与R55及R75胞外区的复合物的三维结构,模拟了TNF与受体之间的相互作用。由于TNF与受体的作用形式是三聚体对三聚体,因此在模拟TNF与受体相互作用时选择了包括一个非对称的TNF三聚体和一个受体(R55或R75)单体的模拟系统。结合已有的突变体实验结果,利用计算机分析手段,发现了一些TNF突变体之所以具有受体选择性的三维结构基础和发挥了关键作用的氨基酸残基以及这些残基之间的主要作用形式。研究深化了对已有的突变体实验结果的认识,建立了不同的实验结果之间的内在关联,为以后有目的的新型突变体设计和实验研究打下了基础。     

氧化磷酸化机制的研究近况

能量转换机理一直是生物能学研究中的一个中心问题.英国Mitchell提出的化学渗透假说从60年代以来获得大量实验的支持,始终是比较流行的一种假说.但近年来,不少科学家又不断发现不少与这一假说相矛盾的现象,并陆续提出新的假想和假说.本文对这一方面的主要情况作一简单介绍.     

肿瘤坏死因子与其受体相互作用的计算机模拟研究

利用同源模建方法,以ＴＮＦＲ５５受体胞外区的晶体结构为参考模板,预测了ＴＮＦＲ７５受体胞外区Ｃｙｓ１８～Ｐｈｅ１４７片段的三维结构．根据Ｒ５５受体胞外区与ＬＴ相结合的复合物的晶体结构,预测了ＴＮＦ与Ｒ５５及Ｒ７５胞外区的复合物的三维结构,模拟了ＴＮＦ与受体之间的相互作用．由于ＴＮＦ与受体的作用形式是三聚体对三聚体,因此在模拟ＴＮＦ与受体相互作用时选择了包括一个非对称的ＴＮＦ三聚体和一个受体（Ｒ５５或Ｒ７５）单体的模拟系统．结合已有的突变体实验结果,利用计算机模拟分析手段,发现了一些ＴＮＦ突变体之所以具有受体选择性的三维结构基础和发挥了关键作用的氨基酸残基以及这些残基之间的主要作用形式．研究深化了对已有的突变体实验结果的认识,建立了不同的实验结果之间的内在关联,为以后有目的的新型突变体设计和实验研究打下了基础．     

北山楂果实中的氨基酸分析

近年来,山楂的单味制剂和复方制剂作为降压药已在临床上得到了广泛的应用。药理研究认为,山楂的黄酮、水解物和三萜酸具有降压作用。但关于山楂氨基酸的成分分析及药理研究,目前尚未见报。为了进一步研究山楂的药效成分和利用山楂资源,我们从北山楂果实中分离鉴定了r-氨基酸,同时对氨基酸成分进行了系统分析。     

植物凝集素的超级家族

凝集素是一类专一、可逆地和糖类结合的蛋白质,迄今已经分离纯化并测定了氨基酸序列的凝集素已有不少,一些凝集素以及它们与配体糖相互结合的复合物的高级结构也已经给出,许多工作已深入到基因水平．就目前已有的知识,说明植物凝集素是一个庞大的蛋白质家族．     

湖南道地白芷氨基酸含量与组成分析

白芷是我国常用中药材的一种,关于白芷镇痛的有效成分,主要认为是异欧前胡素、欧前胡素等香豆素类具有解痉、镇痛等作用的挥发油类化学成分,但白芷镇痛的成分及其机理尚不十分清楚,是否有其他物质也具有一定的药理作用也不得而知,比如说某些药效性氨基酸。该研究采用自动氨基酸分析仪测定了湖南道地茶陵白芷的蛋白质类氨基酸和游离氨基酸的含量,并分析其氨基酸组成。结果表明:总氨基酸检出除Asn以外的其他16种蛋白质氨基酸,含量最高的Arg占总氨基酸的31.21%,接近1/3;必需氨基酸总量达27.01%,其中含量最高的是Leu,占总必需氨基酸的24.14%;药效氨基酸比例较高,在酸水解产物总氨基酸和游离氨基酸中分别达到73.89%和85.78%,其中Arg的含量最高,达1.383g·100g-1,占比为42.24%,游离氨基酸中γ-氨基丁酸、鸟氨酸含量也较高。此外,还含有少量的高半胱氨酸和鹅肌肽等游离非蛋白质氨基酸和短肽;必需氨基酸的组成接近WHO/FAO的建议摄入值,但Met+Cys的RC值最小,为第一限制性氨基酸。这些药效性氨基酸和游离氨基酸可能是茶陵白芷具有良好药效的一个因素,而且茶陵白芷的氨基酸组成和配比较合理、符合人体需要,在强化含硫氨基酸的基础上具有开发成为新型药食同源保健性食品的潜力。研究结果可为进一步研究白芷的药理作用提供依据。     

Hsc70-Auxilin复合物的拉伸分子动力学模拟

Hsc70与auxilin蛋白组成的系统是Hsp70/Hsp40分子伴侣系统家族的一员,在热休克反应中发挥重要作用。本文为得出auxilin蛋白J结构域的关键氨基酸,首先采用由二硫键交联的Hsc70 R171C与auxilin D876C的复合物结晶结构作为初始模型,进行分子动力学模拟,通过比较平衡后的结合部位发现,将形成二硫键的氨基酸突变为原来的氨基酸结构在结合位点上与生化结果较为相近,之后利用此结构通过拉伸动力学模拟分析了auxilin蛋白J结构域与Hsc70的ATPase功能域的解离过程,并探讨了Hsc70与auxilin蛋白之间的相互作用力。结果表明位于HPD loop上的His874,Asp876,Thr879,螺旋Ⅲ上的Glu884,Asn895,Asp896,Ser899,Glu902,Asn903为关键氨基酸,这些数据符合之前核磁共振实验证实的T抗原J结构域的HPD基序和螺旋Ⅲ与Hsc70的ATPase功能域之间的相互作用。     

云南地方特产酒的氨基酸营养

本文测定分析了十一种云南特产酒中十七种氨基酸的含量。十一种酒中主要含鲜甜、药效氨基酸,其中核桃酒、松茸酒、乌鸡宝酒在氨基酸总量、必需、半必需氨基酸含量、赖氨酸含量、鲜甜、药效氨基酸总量都占前三位。     

Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening

The enzyme tRNA-guanine transglycosylase (TGT) is involved in the pathogenicity of Shigellae. As the crystal structure of this protein is known, it is a putative target for the structure-based design of inhibitors. Here we report a crystallographic study of several new ligands exhibiting a 2,6-diamino-3H-quinazolin-4-one scaffold, which has been shown recently to be a promising template for TGT-inhibitors. Crystal structure analysis of these complexes has revealed an unexpected movement of the side-chain of Asp102. A detailed analysis of the water network disrupted by this rotation has lead to the derivation of a new composite pharmacophore. A virtual screening has been performed based on this pharmacophore hypothesis and several new inhibitors of micromolar binding affinity with new skeletons have been discovered.     

Pharmacophore models generation by catalyst and phase consensus-based virtual screening protocol against PI3Kα inhibitors

Phosphoinositide 3-kinases (PI3Ks) family has emerged as promising targets for novel therapeutic agents against neoplastic diseases. Pharmacophore and 3D-quantitative structure–activity relationship modelling were applied to study the structure–activity relationship of PI3K inhibitors. The best HypoGen pharmacophore hypothesis Hypo1 with a correlation coefficient of 0.961 consists of one hydrogen-bond acceptor, one hydrogen-bond donor and two hydrophobic features, whereas the best phase hypothesis AADRRR.378 with favourable statistics (q² = 0.7368, r² = 0.9863) has two hydrogen-bond acceptors, one hydrogen-bond donor and three ring aromatic features. Multiple methods, such as Fischer validation, molecular docking and mapping of test set molecules, were carried out to validate these pharmacophore models. Furthermore, a comparative molecular similarity indices analysis candidate hypothesis model was generated as a supplement of pharmacophore hypothesis. Detailed protein–ligand binding information obtained by Glide was utilised in compound optimisation and virtual screening. A molecular database of 133 known inhibitors and 6179 decoys was built for a screening test to quantitatively analyse various hypotheses and scoring parameters. Finally, we designed a workflow integrating HypoGen pharmacophore searching, phase pharmacophore searching and molecular docking for screening the database. With an improved criterion of enrichment factor (EF = 17.43) and ROC curve (AUC = 0.946), this workflow would provide us an original method for novel PI3K inhibitors.     

Atom-based 3D-QSAR,induced fit docking,and molecular dynamics simulations study of thieno[2,3-b]pyridines negative allosteric modulators of mGluR5

Atom-based three dimensional-quantitative structure–activity relationship (3D-QSAR) model was developed on the basis of 5-point pharmacophore hypothesis (AARRR) with two hydrogen bond acceptors (A) and three aromatic rings for the derivatives of thieno[2,3-b]pyridine, which modulates the activity to inhibit the mGluR5 receptor. Generation of a highly predictive 3D-QSAR model was performed using the alignment of predicted pharmacophore hypothesis for the training set (R²?=?0.84, SD?=?0.26, F?=?45.8, N?=?29) and test set (Q²?=?0.74, RMSE?=?0.235, Pearson-R?=?0.94, N?=?9). The best pharmacophore hypothesis AARRR was selected, and developed three dimensional-quantitative structure activity relationship (3D-QSAR) model also supported the outcome of this study by means of favorable and unfavorable electron withdrawing group and hydrophobic regions of most active compound 42d and least active compound 18b. Following, induced fit docking and binding free energy calculations reveals the reliable binding orientation of the compounds. Finally, molecular dynamics simulations for 100?ns were performed to depict the protein–ligand stability. We anticipate that the resulted outcome could be supportive to discover potent negative allosteric modulators for metabotropic glutamate receptor 5 (mGluR5).     

Pharmacophore identification of KSP inhibitors

A three-dimensional pharmacophore model was developed based on 25 currently available KSP (kinesin spindle protein) inhibitors in Catalyst software package. The best pharmacophore hypothesis (Hypo1), consisting of four chemical features (one hydrogen-bond acceptor, one hydrogen-bond donor, one aromatic ring, and one hydrophobic group), has a correlation coefficient of 0.965. The results of our study provide a valuable tool in designing new leads with desired biological activity by virtual screening.     

Redefining the structure-activity relationships of 2,6-methano-3-benzazocines. Part 6: Opioid receptor binding properties of cyclic variants of 8-carboxamidocyclazocine

A series of 7,8- and 8,9-fused pyrimidinone, aminopyrimidine and pyridone derivatives of 8-carboxamidocyclazocine (8-CAC) have been prepared and evaluated in opioid receptor binding assays. Targets were designed to corroborate a pharmacophore hypothesis regarding the bioactive conformation of the carboxamide of 8-CAC. In addition to the results from this study strongly supporting this pharmacophore hypothesis, a number of novel compounds with high affinity to opioid receptors have been identified.     

Pharmacophore feature prediction and molecular docking approach to identify novel anti‐HCV protease inhibitors

Discovering a potential drug for HCV treatment is a challenging task in the field of drug research. This study initiates with computational screening and modeling of promising ligand molecules. The foremost modeling method involves the identification of novel compound and its molecular interaction based on pharmacophore features. A total of 197 HCV compounds for NS3/4A protein target were screened for our study. The pharmacophore models were generated using PHASE module implemented in Schrodinger suite. The pharmacophore features include one hydrogen bond acceptor, one hydrogen bond donor, and three hydrophobic sites. As a result, based on mentioned hypothesis the model ADHHH.159 corresponds to the CID 59533233. Furthermore, docking was performed using maestro for all the 197 compounds. Among these, the CID 59533313 and 59533233 possess the best binding energy of ?11.75 and ?10.40 kcal/mol, respectively. The interactions studies indicated that the CID complexed with the NS3/4A protein possess better binding affinity with the other compounds. Further the compounds were subjected to calculate the ADME properties. Therefore, it can be concluded that these two compounds could be a potential alternative drug for the development of HCV.     

Pharmacophore modeling,molecular docking and molecular dynamics studies on natural products database to discover novel skeleton as non-purine xanthine oxidase inhibitors

Gout is a common inflammatory arthritis caused by the deposition of urate crystals within joints. It is increasingly in prevalence during the past few decades as shown by the epidemiological survey results. Xanthine oxidase (XO) is a key enzyme to transfer hypoxanthine and xanthine to uric acid, whose overproduction leads to gout. Therefore, inhibiting the activity of xanthine oxidase is an important way to reduce the production of urate. In the study, in order to identify the potential natural products targeting XO, pharmacophore modeling was employed to filter databases. Here, two methods, pharmacophore based on ligand and pharmacophore based on receptor-ligand, were constructed by Discovery Studio. Then GOLD was used to refine the potential compounds with higher fitness scores. Finally, molecular docking and dynamics simulations were employed to analyze the interactions between compounds and protein. The best hypothesis was set as a 3D query to screen database, returning 785 and 297 compounds respectively. A merged set of the above 1082 molecules was subjected to molecular docking, which returned 144 hits with high-fitness scores. These molecules were clustered in four main kinds depending on different backbones. What is more, molecular docking showed that the representative compounds established key interactions with the amino acid residues in the protein, and the RMSD and RMSF of molecular dynamics results showed that these compounds can stabilize the protein. The information represented in the study confirmed previous reports. And it may assist to discover and design new backbones as potential XO inhibitors based on natural products.     

Design and structure-activity relationships of potent and selective inhibitors of undecaprenyl pyrophosphate synthase (UPPS): tetramic, tetronic acids and dihydropyridin-2-ones

Based on a pharmacophore hypothesis substituted tetramic and tetronic acid 3-carboxamides as well as dihydropyridin-2-one-3-carboxamides were investigated as inhibitors of undecaprenyl pyrophosphate synthase (UPPS) for use as novel antimicrobial agents. Synthesis and structure-activity relationship patterns for this class of compounds are discussed. Selectivity data and antibacterial activities for selected compounds are provided.