Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

ABSTRACT

Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.     

Transition metal substituted tungstophosphoric compound catalyzed oxidation of hexanol to hexanal with hydrogen peroxide

Summary The oxidation of hexanol in the presence of the Keggin-type heteropoly compounds (HPCs) H₃PMo_nW_12-nO₄₀ (denoted as PMo_nW_12-n, n=0,1) and Na₅PW₁₁ZO₃₉ (denoted as PW₁₁Z, Z = Mn, Fe, Co, Ni, Cu and Zn) was carried out to produce hexanal and hexanoic acid. The reaction was conducted in tert-butanol (t-BuOH), using cetylpyridinium bromide (CPB) salts of HPA and 15% aqueous H₂O₂ as oxidant under mild condition. The PMoW₁₁ catalyst showed higher hexanol conversion of 25%, the lowest selectivity to hexanal of 64.4% and an efficient utilization of H₂O₂ of 34%. Over the transition metal substituted PW₁₁Z catalysts decomposition of H₂O₂ was rapid. For these PW₁₁Z catalysts, the efficient utilization of H₂O₂ decreased to 9% or even lower. By means of IR, UV-visible and GC-MS techniques the catalysts were characterized.     

2,2'-二乙炔基-1,1'-联萘为模板构筑的新的环芳化合物的合成及其光学性质

基于2,2'-二取代的联萘衍生物在手性构型上高度稳定的特点,分别以光学活性的(R)-和(S)-2,2'-二乙炔基-1,1'-联萘为模板,设计了2个有趣的拓扑环芳分子四联萘笼状对映异构体(R,R,R,R)-2和(S,S,S,S)-2.其合成路线涉及保护基的控制导入、苯连接桥的链接、保护基的脱去以及偶合成环反应4个步骤.用MS,IR,UV-Vis,1HNMR,13CNMR和元素分析等技术对其进行了表征,并比较了其光学性质.研究结果表明,采用这种模板合成方法能够有效地获得具有单一手性的目标化合物.镜像特征的圆二色(CD)谱和比旋光度[α]D的测定结果清楚地反映了它们的对映异构关系.     

DNA光复活作用机理研究中的模型化合物

用模型化合物模拟光解酶诱导的DNA光复活作用，能深入认识其作用机理。介 绍了用于DNA光复活机理研究的各种模型化合物的合成，并综述了由模型化合物研 究得到的光复活机理，以及底物嘧啶二聚体的修复效率受外界因素的影响。     

Synthesis of perfluoroalkyl-containing multifunctional groups compounds for textile finishing

A new kind of perfluoroalkyl-containing multifunctional groups compound was designed. Treatment of 1H,1H,2H,2H-perfluorooctyltrichlorosilane (4) with allylmagnesium bromide provided key intermediate 1H,1H,2H,2H-perfluorooctyltriallylsilane (2). Hydroboration followed by oxidation, epoxidation and dihydroxylation of 2 gave perfluoroalkyl-containing multifunctional groups compound 1a, 1b and 1c, respectively.     

Zn-Al-Ce三元类水滑石的制备及性质研究

采用共沉淀法，水热合成层状化合物一硝酸根柱撑锌铝铈三元类水滑石，分别测定了各种单一金属盐溶液及M^2 ／M^3 摩尔比为2，Ce^3 ／Al^3 摩尔比为0．25的混合金属盐的NaOH滴定曲线，并利用XRD对不同条件下合成产物进行物相分析。实验结果表明：在M^2 ／M^2 =2，Ce^3 ／Al^3 =0．07～0．50，pH=5．8～6．5条件下进行多种离子共沉淀，并经120℃、6h水热处理后，均能合成结构单一的ZnAlCe—HTLLcs，利用TG—DTlA、FT—IR、ICP对合成物进行了表征，筛选出适宜的合成条件，并对HTLcs层状结构的热行为进行初步研究，结果表明ZnAlCe—HTLcs热稳定性较差，层间结合水、层板羟基及层间客体物种(NO3^-)失去温度在240℃左右，易于转化为复合氧化物，将此复合氧化物应用于NO的催化?肖除反应，680℃下NO的转化率高达近100％。     

黄素酶的模拟

本综述介绍模拟黄素酶的进展, 涉及两条途径: 半合成黄素酶和黄素酶模型化合物。     

吡啶酮系偶氮类化合物可见吸收光谱的预测

利用密度泛函的B3LYP方法, 在6-311G*基组水平对吡啶酮系偶氮类化合物进行构型优化, 并进行了自然键轨道(NBO)分析, 然后用TDDFT方法和ZINDO/S方法分别计算了它们的可见吸收光谱, 结果均与实验值十分吻合. 通过对比发现, 对于最高吸收波长的计算, ZINDO/S能以较快的速度得到较好的结果. 在用ZINDO/S计算的过程中, 回归分析发现π-π重叠加权因子(OWF_π-π)与染料分子吡啶环上两个羰基氧原子平均电荷Z_O有较好的线性关系: OWF_π-π＝0.11425－1.04178ZO, 这一关系不仅可从量子化学的角度进行解释, 而且可用于同类染料可见吸收光谱的预测. 分子轨道的研究表明, 这些化合物的最高可见吸收波长主要对应着共轭体系中给电子体到受电子体的电子跃迁.     

Structure and magnetic properties of Ca14MnP11

The compound Ca₁₄MnP₁₁ crystallizes in the Ca₁₄AlSb₁₁ structure type with the tetragonal space group I4₁/acd (Z=8) and lattice parameters of , c=20.7565(9) at 90 K. The structure consists of MnP₄⁹⁻ tetrahedron, P₃⁷⁻ trimer, 4 P³⁻ isolated anions and 14 Ca²⁺ cations. Similar to other compounds of this structure type containing phosphorous, the P₃⁷⁻ trimer has a central P atom that is best modeled in the structure as being equally split between two sites. In addition, there is no additional distortion of the manganese-containing tetrahedron compared with the main group analog, Ca₁₄GaP₁₁, suggesting that the Mn oxidation state is Mn²⁺. Temperature-dependent magnetic susceptibility shows that the compound is paramagnetic over the entire temperature range measured (2-300 K). The data can be fit with a modified Curie-Weiss law and provide an effective magnetic moment of 5.80 (2) B.M. with a Weiss constant of −2.13(2) K and . This moment is significantly higher than those measured for any of the Mn-containing analogs and is consistent with Mn²⁺. This result will be discussed in light of the electron counting scheme for Mn compounds of the Ca₁₄AlSb₁₁ structure-type.     

The Biological Effects of Forsythia Leaves Containing the Cyclic AMP Phosphodiesterase 4 Inhibitor Phillyrin

Forsythia fruit (Forsythia suspensa Vahl (Oleaceae)) is a common component of Kampo medicines for treating the common cold, influenza, and allergies. The main polyphenolic compounds in the leaves of F. suspensa are pinoresinol β-d-glucoside, phillyrin and forsythiaside, and their levels are higher in the leaves of the plant than in the fruit. It is known that polyphenolic compounds stimulate lipid catabolism in the liver and suppress dyslipidemia, thereby attenuating diet-induced obesity and polyphenolic anti-oxidants might attenuate obesity in animals consuming high-fat diets. Recently, phillyrin was reported as a novel cyclic AMP phosphodiesterase 4 (PDE4) inhibitor derived from forsythia fruit. It was expected that the leaves of F. suspensa might display anti-obesity effects and serve as a health food material. In this review, we summarized our studies on the biological effects of forsythia leaves containing phillyrin and other polyphenolic compounds, particularly against obesity, atopic dermatitis, and influenza A virus infection, and its potential as a phytoestrogen.