表皮生长因子受体酪氨酸激酶抑制剂的药效团研究

根据一系列表皮生长因子受体酪氨酸激酶抑制剂的三维定量构效关系研究,得到了该类抑制剂的药效团,研究结果与Novartis的药效团模型相当类似。药效团包括一个氢键受体,一个氢键给体,一个疏水区和一个带有氯或溴原子的苯环。该药效团对于研究表皮生长因子受体酪氨酸激酶抑制剂结构与活性的关系具有重要的意义。通过三维数据库搜索可能会得到新的先导化合物。     

新型酪氨酸激酶水分子抑制剂的三维药效团研究

对受体酪氨酸激酶（ＲＴＫ）的药物抑制对控制恶性肿瘤具有重要意义。最近发现的苄叉丙二腈化合物家族对ＲＴＫ中的ＨＥＲ２受体具有的抑制作用。本文对这一系列化合物进行了柔性的三维药效团分析,得到了一个预测能力委好的药效团模型、线性回归系数Ｒ＝０．９９５８。这个模型对于研究此类化合物的结构与活性关系,以及评估此类未知化合性具有重要作用。     

含磷类血管紧张素转化酶抑制剂的3D—QSAR研究

文章利用限制性构象搜寻（Ｃｏｎｓｔｒａｉｎｔｓ Ｓｅａｒｃｈ）,确定了血管紧张素转化酶（ＡＣＥ）掏剂的药效团模型（活性构象或重叠规则）。用比较分子场分析法（Ｃｏｍｐａｒａｔｉｖｅ ＭｏｌｅｃｕｌａｒＦｉｄｌｄ Ａｎａｌｙｓｉｓ,ＣｏＭＦＡ）建立了含磷类ＡＣＥ掏剂的３Ｄ－ＱＳＡＲ模型。较高的交叉验证回归系数（q＾２＝０． ７２１）及此模型对不同类型抑制剂活性的预测结果,说明了其可靠性和较好的活性预测能     

酪氨酸激酶抑制剂的虚拟受体模型方法研究

利用柔性原子受体模型(FLARM)方法对一系列的异黄酮和喹诺酮衍生物表皮生长因子受体酪氨酸激酶抑制剂进行了三维定量构效关系研究,得到了合理的构效关系模型。FLARM方法的计算结果还给出了虚拟的受体模型,该模型说明了抑制剂与受体之间可能的相互作用。这些相互作用包括两个氢键和一个硫-芳香相互作用,以上结果仅仅是由7个化合物得到的。     

一类来氟米特类似物二氢乳清酸脱氢酶抑制剂作用模式的理论研究

目的:来氟米特是当今临床上类风湿关节炎疾病治疗中最具有显著病情缓解作用的抗风湿药物之一.本文分析二氢乳清酸脱氢酶(DHODH)与其抑制剂的相互作用模式,以指导新型抗风湿药物的开发.方法:从1D3H晶体结构出发,采用基于配体-受体复合物相互作用的药效团研究方法,建立来氟米特活性代谢物A771726的药效团模型;以晶体中来氟米特活性代谢物A771726为模版,构建42个来氟米特类似物DHODH抑制剂的结构,经结构叠合,采用自组织分子力场分析方法(SOMFA),建立来氟米特活性代谢类似物DHODH抑制剂三维定量构效关系模型;并探讨DHODH与其抑制剂的相互作用模式.结果与结论:建立了合理的来氟米特活性代谢物药效团模型和DHODH抑制剂三维定量构效关系,并且2种方法所得的模型吻合.确定的DHODH与抑制剂的作用模式,可以指导抑制剂的设计,用于开发新型抗风湿药物.     

六种酪氨酸激酶抑制剂的电子结构与药效关系的理论研究

苯胺喹唑啉类药物是一类典型的小分子表皮生长因子受体酪氨酸激酶抑制剂(EGFRTKIs)。该类化合物是ATP竞争性抑制剂,能抑制蛋白酪氨酸激酶磷酸化,从而阻断肿瘤细胞瀑布式的信号传递,是用于治疗非小细胞肺癌的常用药物。基于量子化学中的密度泛函理论(DFT),采用自洽反应场(SCRF)方法中的极化连续介质模型(Polarized Continuum Model,PCM)模拟水环境,在B3LYP/6-31+G(d)的水平下优化搜索得到了六种苯胺喹唑啉类EGFRTKIs的最稳定几何构型,并在CAM-B3LYP/6-311++G(d,p)水平下对其电子结构性质进行了系统的研究。基于理论计算可以推测此类药物靶点是EGFR受体上的富电子区域,所以分子的最低非占据轨道(LUMO)对于药物与靶点的结合起着关键作用。此外,概念密度泛函分析表明该类药物的垂直电离能、电负性及软硬度参数可能与其药效相关。上述研究结果为进一步改进此类药物的抗肿瘤性能以及设计、合成新型EGFR-TKIs药物分子提供了理论指导与依据。     

GABAA/BZ受体激动剂4-喹啉酮衍生物的DISCOtech及CoMFA研究

γ-氨基丁酸是重要的抑制性神经传递物质,4-喹啉酮衍生物作用于GABAA受体具有广泛的生物活性.本文采用DIS-COtech法构建大鼠GABAA/BZ受体4-喹啉酮衍生物激动剂的药效团模型,同时根据分子骨架叠合规则构建CoMFA模型,模型的交叉验证系数为0.681,非交叉验证系数为0.967,药效团模型和CoMFA模型具有一致性.根据模型分析配体-受体间的相互作用,设计一系列化合物并预报了其活性,为设计高活性的化合物提供参考.     

Comparison and analysis of the structures and binding modes of antifungal SE and CYP51 inhibitors

With the abuse of clinical broad-spectrum antimicrobial agents, immunosuppressive agents, chemotherapy drugs, the emergence of pathogenic fungi resistance is more and more frequent. However, there is still no effective treatment for the fungal resistance. Squalenee epoxidase (SE) and 14 α-demethylase (CYP51) are important antifungal drug targets. In order to achieve a deeper insight into the structural characteristics and the action modes of SE and CYP51inhibitors, the homology model of SE (Candida albicans) was constructed using monooxygenase of Pseudomonas aeruginosa as template, and the reliability of model was confirmed by Ramachandran plots and Verify 3D. Subsequently, the molecular superimposition and molecular docking were performed, and the pharmacophore model based on the CYP51 receptor structure was constructed. The results indicate that SE and CYP51 inhibitors have common structural feature with two parts of essential fragments, which are mainly composed of aromatic groups. In addition, the fragment structures of inhibitors are combined in the similar hydrophobic pockets through the hydrophobic forces. The present study provides a deeper perspective to understand the characteristics and docking modes of SE and CYP51 inhibitors. It can be used to guide the optimization and design of SE and CYP51 inhibitors. In addition, it also provides the oretical support for the development of dual target antifungal inhibitors (SE and CYP51), which can help us solve the problem of fungi resistance.     

有机缓蚀剂定量构效与活性相关的热力学参数量子化学计算值与缓蚀效率的QSAR研究

用AMI和PM3半经验方法对5种缓蚀剂进行了优化计算并将获得的量化参数与缓蚀性能进行构效关系(QSAR)研究,结果表明,由AMI方法得到的不同温度下的缓蚀剂热力学参数焓和熵的量子化学计算值与该缓蚀剂缓蚀实验的腐蚀电流有良好的相关性。根据所得的相关模型可对缓蚀剂在一定温度范围内的腐蚀电流进行预测,进而预测其缓蚀性能。     

基于结构的组蛋白去乙酰化酶抑制剂虚拟筛选

组蛋白去乙酰化酶是抗肿瘤作用的新靶点,基于该酶复合物的三维结构,首先对具有分子多样性的数据库进行了虚拟筛选;然后根据已知HDAC抑制剂的结构特征和筛选的结果,以及与生物大分子互补性,选择合理的构建单元,组建靶向的虚拟组合库;最后进行数据库虚拟筛选,对分子对接的结果进行评分,选择出理论上与HDAC有较好结合能力的化合物,设计了酰胺类、脲类和酰肼类全新结构类型的HDAC抑制剂,初步生物活性评价结果表明,预期有生物活性的化合物显示出一定的HDAC酶抑制活性。     

微电子细胞传感器在抗肿瘤药物分析中的应用研究

研究采用微机械加工技术制备了生物电阻抗检测用的细胞传感器芯片。传感器各通道为50μm的微电极,以交错的方式间隔50μm排列。配以相应的药物微进样系统与控制系统后,将人肺腺癌细胞系A549细胞接种培养于芯片电极表面,研究了人参皂苷Rh2对细胞的作用。阻抗测试结果显示:人参皂苷Rh2具有良好的抑制肿瘤细胞生长作用,表明细胞微电子芯片为抗肿瘤药物的分析与筛选提供了一个良好微传感器测试平台。     

对Rac1蛋白抑制作用的生物还原剂的虚拟筛选

乏氧是肿瘤组织的重要特点,而在肿瘤组织中高表达的 Rac1蛋白是与氧化还原过程密切相关的蛋白质,且参与肿瘤发展的多个过程。Rac1抑制剂可有效抑制肿瘤细胞的侵润与发展。因此,有效的Rac1抑制剂可成为潜在抗癌药物。目前能用于临床治疗肿瘤的 Rac1抑制剂鲜有报道。生物还原剂是一大类对乏氧细胞有特异毒性的化合物,可以靶向作用于乏氧细胞,抑制乏氧肿瘤细胞的生长。本文根据Rac1的三维结构,利用虚拟筛选软件PyRx,在化合物库中对约1.5万个硝基杂环化合物、芳香氮氧化合物、脂肪氮氧化合物、醌类化合物等生物还原剂进行筛选,根据结合能、结合位点、结合模式等条件筛选出6个候选Rac1抑制剂,为靶向乏氧肿瘤细胞的生物还原剂的开发、构效关系研究提供理论依据。     

Binding modes of CCR5-targetting HIV entry inhibitors: partial and full antagonists

Since the CC-chemokine receptor 5 (CCR5) was identified as a major co-receptor for human immunodeficiency virus type 1 (HIV-1) entry into a host cell, CCR5-targetting HIV entry inhibitors have been developed and some of them are currently in clinical trials. Most of these inhibitors also inhibit the physiological chemokine reaction function of CCR5, which is so far considered to be safe to patients based on the observation that individuals that naturally lack CCR5 do not show apparent health problems. Nevertheless, to minimize the toxicity and side effects, it would be ideal to preserve the chemokine receptor activity. In this work, we simulated the flexible docking of two small molecule inhibitors to CCR5 in a solvated phospholipid bilayer environment. One of the inhibitors, aplaviroc has a unique feature of preserving two of the natural chemokine ligands binding to CCR5 and subsequent activation whereas the other one, SCH-C fully blocks chemokine-CCR5 interactions. Our results revealed significantly different binding modes of these two inhibitors although both established extensive interaction networks with CCR5. Comparison of the different binding modes suggests that avoiding the deep insertion of inhibitors into the transmembrane helix bundle may be able to preserve chemokine-CCR5 interactions. These results could help design HIV co-receptor activity-specific inhibitors.     

几种新型双吡唑衍生物缓蚀性能的理论研究

通过量子化学计算中的密度泛函理论(DFT)/B3LYP方法在6-311+G(d,p)水平上对3种新型双毗唑衍生物5,5'-二甲基-4-乙酯基-1'氢-1,3'-二吡唑(Bipl)、1,1',5,5'一四甲基-1氢,1'氢-3,3'-二吡唑(Bip2)和3-(溴甲基)-5,5'-二甲基-1'氢-1,3'-二吡唑(Bip3)的缓释性能与结构关系进行了研究。用Fukui指数分析了分子中反应活性位点。结果表明全局活性参数最高占据轨道能量(E_(HOMO))、偶极矩(μ)、电负性(X)及电子转移数(△N)与缓释性能有良好的关系。缓蚀性能的理论评价结论与实验结果相吻合。     

Molecular docking and molecular dynamics simulation studies of Trypanosoma cruzi triosephosphate isomerase inhibitors. Insights into the inhibition mechanism and selectivity

Trypanosoma cruzi (T. cruzi) triosephosphate isomerase (TcTIM) is a glycolytic enzyme essential for parasite survival and has been considered an interesting target for the development of new antichagasic compounds. The homodimeric enzyme is catalytically active only as a dimer. Interestingly, significant differences exist between the human and parasite TIMs interfaces with a sequence identity of 52%. Therefore, compounds able to specifically disrupt TcTIM but not Homo sapiens TIM (hTIM) dimer interface could become selective antichagasic drugs. In the present work, the binding modes of 1,2,4-thiadiazol, phenazine and 1,2,6-thiadiazine derivatives to TcTIM were investigated using molecular docking combined with molecular dynamics (MD) simulations. The results show that phenazine and 1,2,6-thiadiazine derivatives, 2 and 3, act as dimer-disrupting inhibitors of TcTIM having also allosteric effects in the conformation of the active site. On the other hand, the 1,2,4-thiadiazol derivative 1 binds into the active site causing a significant decrease in enzyme mobility in both monomers. The loss of conformational flexibility upon compound 1 binding suggests that this inhibitor could be preventing essential motions of the enzyme required for optimal activity. The lack of inhibitory activity of 1 against hTIM was also investigated and seems to be related with the high mobility of hTIM which would hinder the formation of a stable ligand–enzyme complex. This work has contributed to understand the mechanism of action of this kind of inhibitors and could result of great help for future rational novel drug design.     

Theoretical studies on binding modes of copper-based nucleases with DNA

In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by “gap DNA”. The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.