原卟啉原Ⅸ的构象分析

在合理药物设计方法中,当靶标酶的三维结构未知时,对其底物进行构象分析,特别是确定其活性构象,对阐明靶标酶活性中心的空间形状和作用位点具有十分重要的意义.我们曾利用距离比较法确定了原卟啉原氧化酶的底物-原卟啉原Ⅸ的活性构象,本文从构象分析的角度对4种不同构象的原卟啉原Ⅸ分子与二苯醚类分子的晶体学构象进行了几何参数的比较和分析,结果进一步证实了距离比较法所确定的活性构象更为可靠.     

距离比较法(DISCO)构建原卟啉原氧化酶抑制剂药效团模型

在原卟啉原氧化酶(Protox)三维结构未知情况下,利用距离比较法(DISCO),将8个具有代表性结构特征的Protox抑制剂,与其作用底物(基质)原卟啉原IX(ProtogenIX)的分子构象进行迭合,建立了可能的药效团模型;并据此确定了ProtogenIX与Protox相互作用时,可能采取的活性构象。这些信息将有助于设计、开发新型Protox抑制剂。     

光系统Ⅱ抑制剂: 顺式氰基丙烯酸酯化合物的 三维构效关系的电子结构研究

以距离比较法所获得的顺式氰基丙烯酸酯化合物的活性构象为模板,对39个该类化合物采用比较分子场方法进行了三维构效关系的研究。结果表明,所获得的药效团模型具有很好的预测能力。同时采用量子化学的方法对活性构象模板分子电子结构作了讨论。     

光系统Ⅱ抑制剂-顺式氰基丙烯酸酯化合物的三维构效关系和电子结构研究

以距离比较法所获得的顺式氰基丙烯酸酯化合物的活性构象为模板,对39个该类化合物采用比较分子场方法进行了三维构效关系的研究.结果表明,所获得的药效团模型具有很好的预测能力.同时采用量子化学的方法对活性构象模板分子电子结构作了讨论.     

光系统Ⅱ抑制剂—反式氰基丙烯酸酯比较分子场和电子结构研究

对反式氰基丙烯酸酯系列活性分子采用限制性系统搜索方法确定的药效团模型 ,与 9类不同骨架结构的光系统 抑制剂 DISCO模型中的反式氰基丙烯酸酯分子(M- 2 2 )的活性构象为模板所确定的药效团模型是非常相近的。对两种方法所获得的活性构象分子进行了 Co MFA研究 ,其结果是一致的。采用 PM3方法进行了量子化学计算 ,计算结果表明两种模型的构象分子具有相近的电子结构 ,根据分子静电场、立体场和电子结构探讨了该类抑制剂的构效关系。     

抗脂解活性的人参十四肽的结构预测

本文对抗脂解活性的人参多肽的结构进行了分析. 在一级结构的基础上预测了其二级结构含有较多的α螺旋, 后接一段无规卷曲. 应用分子力学方法, 结合晶体数据库信息, 计算了人参中抗脂解十四肽分子的相对构家能量和原子坐标, 模拟了构象能量优化过程, 得到了可能的最低能量构象. 并利用计算机分子图形技术建立了相应的人参抗脂解十四肽的三维分子模型. 模型的空间结构表明构象分析结果与二级预测的结论很好地相符。     

谷胱甘肽分子伞的构象分析及VolSurf表征

使用分子动力学模拟迟火和半经验AMl方法对谷胱甘肽分子伞进行了构象分析 ，结果表明，真空下屏蔽构象和暴露构象的最低能量值相差很小(26.00kJ/mol)。 考虑溶剂效应后，屏蔽构象的能量值最高，暴露构象的能量值最低。屏蔽构象的能 量最低值高于暴露构象的能量最低值89.24kJ/mol，从理论上解释了谷胱甘肽分子 伞在水溶液中呈现暴露构象的原因。利用VolSurf参数分析了分子伞以屏蔽构象穿 透磷脂双分子层的影响因素，结果表明屏蔽构象较小的两亲矩及较大的分子褶皱程 度是其能够穿透细胞膜的主要影响因素，与构象的绝对疏水区域无关。     

味觉化合物的构象与活性的关系

味觉化合物的构象与活性的关系许禄,姚喻元（中国科学院长春应用化学研究所应用谱学开放实验室,长春,１３００２２）关键词味觉化合物,分子力学,构象分析分子结构和味觉的相关性是一个非常活跃的研究领域,许多人从不同的侧面进行这方面的研究,并总结出一定的规律［...     

短裸甲藻毒素(Brevetoxins)的电子结构与构效关系研究

对短裸甲藻毒素衍生物进行了电子结构研究和构象分析,确定了它们的活性部位,探讨了作用方式,讨论了它们的结构-活性关系及受体的相互作用,解释了衍生物之间活性差异的原因。研究结果表明,分子骨架中段环上的烯键,A环及R烯键对活性有重要影响,分子骨架的折曲程度对活性也有较大影响。     

草酰溴一价正离子(BrCO)+2几何构型及反应活性的DFT研究

用密度泛函方法BHandHIYP以6-311 G(d)和6-311 G(2df）为基组对草酰溴的一价正离子(BrCO)2^ 和中性分子(BrCO)2做了构象分析,结果表明,(BrCO)^ 2和(BrCO)2都具有平面反式和交叉式两种构象。交叉式构象存在超共轭现象。此外,对草酰溴离子、中性分子各解离通道初级反应的Gibbs自由能的计算,发现草酰溴离子C-C键解离通道的反应活性总体上大于中性分子,对该反应通道进一步做了反应机理研究,证实了热力学结论。     

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists

Summary In the absence of a 3D structure of the target biomolecule, to propose the 3D requirements for a small molecule to exhibit a particular bioactivity, one must supply both a bioactive conformation and a superposition rule for every active compound. Our strategy identifies both simultaneously. We first generate and optimize all low-energy conformations by any suitable method. For each conformation we then use ALAD-DIN to calculate the location of points to be considered as part of the superposition. These points include atoms in the molecule and projections from the molecule to hydrogen-bond donors and acceptors or charged groups in the binding site. These positions and the relative energy of each conformation are the input to our new program DISCO. It uses a clique-detection method to find superpositions that contain a least one conformation of each molecule and user-specified numbers of point types and chirality. DISCO is fast; for example, it takes about 1 min CPU to propose pharmacophores from 21 conformations of seven molecules. We typically run DISCO several times to compare alternative pharmacophore maps. For D₂ dopamine agonists DISCO shows that the newer 2-aminothiazoles fit the traditional pharmacophore. Using site points correctly identifies the bioactive enantiomers of indoles to compare with catechols whereas using only ligand points leads to selecting the inactive enantiomer for the pharmacophore map. In addition, DISCO reproduces pharmacophore maps of benzodiazepines in the literature and proposes subtle improvements. Our experience suggests that clique-detection methods will find many applications in computational chemistry and computer-assisted molecular design.     

促生长激素释放素三维定量构效关系及药效团模型

用比较分子场分析方法对促生长激素释放素Ｌ－６９２，４２９的系列物进行了三维定量构效研究，得到具有较强预测能力的模型并确定了母体的活性构象，用距离比较方法将Ｌ－６９２，４２９的活性构象与两个活性多肽进行了迭合，找到了可能的药效团，药效团模型显示Ｌ－６９２，４２９的氨基和四唑是氢键的给体和受体，而Ａ和Ｃ环是主要的疏水核心。     

光系统Ⅱ(PSⅡ)抑制剂的比较分子场研究

以光系统Ⅱ抑制剂DISCO(DIStanceCOmparisons)模型的活性构象分子作为模板,利用比较分子场分析方法对三类结构不同的化合物进行了三维构效关系的研究。研究结果有助于对DISCO重叠模型的评估的新型PSⅡ抑制剂的设计与合成。     

High-performance liquid chromatographic assays for protoporphyrinogen oxidase and ferrochelatase in human leucocytes

Rapid, sensitive and specific high-performance liquid chromatographic assays are described for protoporphyrinogen oxidase and ferrochelatase in human leucocytes. The enzyme reaction products were separated and quantitated by reversed-phase high-performance liquid chromatography with fluorescence detection. The optimal pH for the protoporphyrinogen oxidase assay was 8.6 and the Michaelis constant for protoporphyrinogen IX was 9.78 +/- 0.96 microM (mean +/- S.D.). The mean (+/- S.D.) activity of protoporphyrinogen oxidase in fourteen apparently healthy subjects was 0.146 +/- 0.023 nmol protoporphyrin IX per min per mg protein. In one patient with variegate porphyria, the activity was 0.028 nmol protoporphyrin IX per min per mg protein. The optimal pH for ferrochelatase was 7.4 and with protoporphyrin and Zn2+ as substrates, the Michaelis constants were 1.49 and 8.33 microM, respectively. The mean activity of ferrochelatase in ten control subjects was 0.24 nM Zn-protoporphyrin or 2.05 nM Zn-mesoporphyrin formed per h per mg protein.     

EFFECTS OF N-PHENYLIMIDE S-23142 AND N-METHYL MESOPORPHYRIN IX ON THE SYNTHESIS OF THE PHYTOCHROME CHROMOPHORE IN PEA EMBRYONIC AXES

Abstract Treatment of imbibed embryonic axes taken from seeds of Pisum sativum with N-phenylimide S-23142, a herbicide that has been suggested to inhibit protoporphyrin synthesis, or with N -methyl mesoporphyrin IX, an inhibitor of the iron chelatase for heme, resulted in a significant decrease in the amount of spectrophotometrically detectable phytochromc in the axes in both cases. However, the amount of immunochemically detectable phytochrome was not affected by either treatment. If S-23142 inhibits the synthesis of protoporphyrin IX in pea, it appears that the conversion of protoporphyrinogen IX to protoporphyrin IX is involved in the biosynthesis of the phytochrome chromophore. The conversion of protoporphyrin IX to heme (Fe-protoporpbyrin) also appears to be a step in the biosynthesis of the chromophore, since N -methyl mesoporphyrin IX prevented the synthesis of spectrophotometrically detectable phytochrome but did not affect the magnesium chelatase activity required for the synthesis of chlorophyll in pea embryonic axes. The results suggest that protoporphyrinogen IX, protoporphyrin IX and heme are intermediates in the biogenesis of the phytochromc chromophore. The pathway to phytochromobilin might become fixed after protoporphyrin IX, being directed toward the Fe branch for heme rather than to the Mg branch for chlorophyll.     

距离比较法(DISCO)构建ALS抑制剂药效团模型

在乙酰乳酸合成酶（ALS）三维结构未知的情况下,利用距离比较法（DISCO） ,将10 个结构特征具有代表性的ALS抑制剂的分子构象进行叠合,建立了可能的 药效团模型,并初步验证了模型的可靠性。     

Combined Inhibitor Free‐Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence‐based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X‐ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole‐type inhibitors are energetically poised to report faithfully on mannosidase transition‐state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β‐mannanases from families GH26 and GH113. Isofagomine‐type inhibitors are poor mimics of transition‐state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar‐shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active‐site residues involved in substrate recognition.     

Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN

HemN is a radical S‐adenosyl‐l ‐methionine (SAM) enzyme that catalyzes the oxidative decarboxylation of coproporphyrinogen III to produce protoporphyrinogen IX, an intermediate in heme biosynthesis. HemN binds two SAM molecules in the active site, but how these two SAMs are utilized for the sequential decarboxylation of the two propionate groups of coproporphyrinogen III remains largely elusive. Provided here is evidence showing that in HemN catalysis a SAM serves as a hydrogen relay which mediates a radical‐based hydrogen transfer from the propionate to the 5′‐deoxyadenosyl (dAdo) radical generated from another SAM in the active site. Also observed was an unexpected shunt product resulting from trapping of the SAM‐based methylene radical by the vinyl moiety of the mono‐decarboxylated intermediate, harderoporphyrinogen. These results suggest a major revision of the HemN mechanism and reveal a new paradigm of the radical‐mediated hydrogen transfer in radical SAM enzymology.