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Abstracts of publications related to QASR QASR相关出版物摘要
Pub Date : 2006-09-19 DOI: 10.1002/qsar.19900090309
F. Darvas, Z. Darvas
s of publications related to QSAR Editor: Ferenc Darvas, Budapest Technical Editor: Zsuzsanna Darvas, Budapest
编辑:Ferenc Darvas,布达佩斯技术编辑:Zsuzsanna Darvas,布达佩斯
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引用次数: 0
Mechanistic Study on N‐Demethylation Catalyzed with P450 by Quantitative Structure Activity Relationship using Electronic Properties of 4‐Substituted N,N‐Dimethylaniline 基于4 -取代N,N -二甲基苯胺电子性质的定量构效关系研究P450催化N -去甲基化的机理
Pub Date : 2002-12-01 DOI: 10.1002/QSAR.200290004
A. Nanbo, T. Nanbo
The mechanism of N-demethylation by P-450 was investigated using MO calculation of 4-substituted N,N-dimethylaniline. The reactivities of the compounds and their intermediates were examined using the energies of HOMO and SOMO, and frontier electron densities. QSAR analysis using these electronic parameters indicated that one-electron first transfers from nitrogen to P-450 and the resultant cation radical forms α-amino radical, followed by hydroxylation and N-demethylation.
采用MO计算方法研究了4-取代N,N-二甲基苯胺的N-去甲基化机理。用HOMO和SOMO能量和前沿电子密度检测了化合物及其中间体的反应性。利用这些电子参数进行的QSAR分析表明,单电子首先从氮转移到P-450,生成的阳离子自由基形成α-氨基自由基,然后是羟基化和n -去甲基化。
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引用次数: 4
3D QSAR of Serotonin Transporter Ligands: CoMFA and CoMSIA Studies 5 -羟色胺转运体配体的三维QSAR: CoMFA和CoMSIA研究
Pub Date : 2002-12-01 DOI: 10.1002/QSAR.200290000
Julia Wellsow, H. Machulla, K. Kovar
The main purpose of this study was the investigation of quantitative structure-activity relationships of serotonin transporter ligands with regard to the future development of potential new and selective PET radiotracers for the serotonin transporter. A heterogeneous data set of 19 selective and non-selective serotonin reuptake inhibitors was used. Affinity data for both the serotonin transporter and the norepinephrine transporter was available. As a necessary prerequisite for our 3D QSAR studies a reasonable alignment of the compounds was developed using GASP. It was based on an existing pharmacophore model. In addition to the widely used CoMFA method, the somewhat newer CoMSIA method was applied. Statistically reliable CoMFA models for both the serotonin transporter (q 2 =0.538) and the norepinephrine transporter (q 2 =0.445) were developed, further improving the internal predictability by applying region focusing for the serotonin transporter (q 2 =0.674). These models were compared with the CoMSIA models for the serotonin and the norepinephrine transporter that yielded comparable cross-validated correlation coefficients (q 2 =0.531 and q 2 =0.502, respectively). Certain structural features that are distinctive of each transporter and important for high binding affinity were identified. Highly comparable results were obtained for CoMFA and CoMSIA. Both methods were applied to elucidate structural requirements for serotonin transporter selectivity. The resulting CoMSIA map provides important information for lead optimization with respect to selectivity enhancement.
本研究的主要目的是对5 -羟色胺转运体配体的定量构效关系进行研究,以期为5 -羟色胺转运体开发潜在的新型和选择性PET放射性示踪剂。使用了19种选择性和非选择性血清素再摄取抑制剂的异质性数据集。血清素转运体和去甲肾上腺素转运体的亲和数据是可用的。作为我们3D QSAR研究的必要先决条件,使用GASP开发了化合物的合理排列。它是基于一个现有的药效团模型。除了广泛使用的CoMFA法外,还采用了较新的CoMSIA法。对血清素转运体(q 2 =0.538)和去甲肾上腺素转运体(q 2 =0.445)均建立了统计可靠的CoMFA模型,通过对血清素转运体(q 2 =0.674)应用区域聚焦进一步提高了内部可预测性。将这些模型与CoMSIA的血清素和去甲肾上腺素转运体模型进行比较,得出可比较的交叉验证相关系数(q2 =0.531和q2 =0.502)。确定了每种转运蛋白特有的某些结构特征,这些特征对高结合亲和力很重要。CoMFA和CoMSIA结果具有高度可比性。两种方法均用于阐明血清素转运体选择性的结构要求。所得到的CoMSIA图谱为铅的选择性优化提供了重要的信息。
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引用次数: 15
Theoretical Prediction of the Phenoxyl Radical Formation Capacity and Cyclooxygenase Inhibition Relationships by Phenolic Compounds 酚类化合物对苯氧基自由基形成能力及环加氧酶抑制关系的理论预测
Pub Date : 2002-12-01 DOI: 10.1002/QSAR.200290003
J. Ruiz, R. Pouplana
Due to the importance of the O-H bond dissociation in the antioxidant mechanism of anti-inflammatory phenols, we studied the biradical process Ph-OH → PhO . +H . for 25 phenolic compounds using ah initio calculations. Enthalpies of reaction (ΔH r ), changes in the electron density at the O-H bond critical point (ρ O H ) and total atomic charges of ortho and para carbon atoms strongly correlate with the in vitro inhibition of cyclooxygenase activity by phenols. The most active compounds have large values of the electron density at the O-H bond (ρ O H ), thus favouring the O-H bond dissociation. In contrast, inactive compounds have small values of the electron density at the O-H bond (ρ O H ), thus reducing the hydrogen donation ability. These results are also supported by the representation of the molecular electrostatic potentials maps. The prediction of the cyclooxygenase inhibitory activity of the proposed QSAR equations is analysed using the multilineal (MLR) method. Finally, the differences in biological activity are examined by analysing the binding interactions of active compounds in the pocket site of human COX-2 enzyme structure derived from crystallographic X -ray data.
鉴于O-H键解离在抗炎酚类化合物抗氧化机制中的重要作用,我们研究了Ph-OH→PhO的双自由基过程。+ H。25种酚类化合物使用从头计算。反应焓(ΔH r)、O-H键临界点的电子密度变化(ρ O H)和邻位碳原子和对位碳原子的总电荷与酚类物质对环加氧酶活性的体外抑制密切相关。最活跃的化合物在O-H键处具有较大的电子密度(ρ O H),因此有利于O-H键的解离。相反,非活性化合物在O-H键上的电子密度(ρ O H)值较小,从而降低了给氢能力。这些结果也得到了分子静电势图的支持。利用多线性(MLR)方法对所建立的QSAR方程的环加氧酶抑制活性进行了预测。最后,通过晶体X射线数据分析人类COX-2酶结构口袋部位活性化合物的结合相互作用,研究了生物活性的差异。
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引用次数: 9
Scaffold Searching: Automated Identification of Similar Ring Systems for the Design of Combinatorial Libraries 支架搜索:组合文库设计中相似环系统的自动识别
Pub Date : 2002-12-01 DOI: 10.1002/QSAR.200290001
M. Bohl, J. Dunbar, E. Gifford, D. Wild, P. Willett, D. Wilton
Rigid ring systems can be used to position receptor-binding functional groups in 3D space and they thus play an increasingly important role in the design of combinatorial libraries. This paper discusses the use of shape-similarity methods to identify ring systems that are structurally similar to, and aligned with, a user-defined target ring system. These systems can be used as alternative scaffolds for the construction of a combinatorial library.
刚性环系统可用于定位三维空间中的受体结合官能团,因此它们在组合文库的设计中发挥着越来越重要的作用。本文讨论了使用形状相似方法来识别与用户定义的目标环系统在结构上相似并对齐的环系统。这些系统可以用作构建组合库的替代支架。
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引用次数: 19
Identification of diverse database subsets using property-based and fragment-based molecular descriptions 使用基于属性和基于片段的分子描述识别不同的数据库子集
Pub Date : 2002-12-01 DOI: 10.1002/QSAR.200290002
Mark Ashton, J. Barnard, F. Casset, M. Charlton, G. Downs, D. Gorse, J. Holliday, R. Lahana, P. Willett
This paper reports a comparison of calculated molecular properties and of 2D fragment bit-strings when used for the selection of structurally diverse subsets of a file of 44295 compounds. MaxMin dissimilarity-based selection and k-means cluster-based selection are used to select subsets containing between 1% and 20% of the file. Investigation of the numbers of bioactive molecules in the selected subsets suggest: that the MaxMin subsets are noticeably superior to the k-means subsets; that the property-based descriptors are marginally superior to the fragment-based descriptors; and that both approaches are noticeably superior to random selection.
本文报道了计算分子性质和二维片段位串的比较,用于选择结构不同的44295个化合物的文件子集。基于MaxMin不相似度的选择和基于k-means聚类的选择用于选择包含1%到20%文件的子集。对所选子集中生物活性分子数量的调查表明:MaxMin子集明显优于k-means子集;基于属性的描述符略优于基于片段的描述符;两种方法都明显优于随机选择。
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引用次数: 63
Distance Profiles (DiP): A translationally and rotationally invariant 3D structure descriptor capturing steric properties of molecules 距离轮廓(DiP):一种平动和旋转不变的三维结构描述符,捕捉分子的空间性质
Pub Date : 2002-11-01 DOI: 10.1002/1521-3838(200211)21:5<507::AID-QSAR507>3.0.CO;2-L
K. Baumann
A novel translationally and rotationally invariant structure descriptor based on the distribution of 3D-atom pairs is described. The new Distance Profiles (DiP) descriptor was applied to two data sets which were previously studied with various 3D-QSAR techniques. DiP compares favorably to the other descriptors for these two data sets and obtains better models in both cases. Since DiP is used in combination with variable selection to achieve interpretability, special emphasize was put on validating the derived models. Avoiding overfitted models was accomplished by constraining the maximum number of variables allowed to select, and by using leave-50%-out cross-validation instead of leave-one-out cross-validation as objective function in variable selection. Furthermore, the derived models were validated with a permutation test where the entire variable selection procedure is repeated each time the response data are scrambled.
提出了一种基于三维原子对分布的平动和旋转不变结构描述子。新的距离剖面(DiP)描述符应用于之前使用各种3D-QSAR技术研究过的两个数据集。对于这两个数据集,DiP比其他描述符更有利,并且在这两种情况下都能获得更好的模型。由于DiP与变量选择结合使用以实现可解释性,因此特别强调验证派生模型。通过限制允许选择的最大变量数,并使用留50%的交叉验证而不是留一个交叉验证作为变量选择的目标函数,避免了模型的过拟合。此外,衍生模型通过排列测试进行验证,其中每次响应数据被打乱时重复整个变量选择过程。
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引用次数: 16
Rapid Prediction of Human Intestinal Absorption 人体肠道吸收快速预测
Pub Date : 2002-11-01 DOI: 10.1002/1521-3838(200211)21:5<493::AID-QSAR493>3.0.CO;2-5
E. Deretey, M. Feher, Jonathan M. Schmidt
This work describes the modeling of human intestinal absorption using one- and two-descriptor nonlinear models. Molecules with known transport mechanisms other than passive transport were removed from the dataset. The human intestinal absorption data were fitted to symmetric and asymmetric sigmoidal curves and surfaces that were based on the arctangent function. The descriptors employed in the models are the sum of hydrogen bond donors and acceptors and the calculated SlogP octanol-water partition coefficient. Despite the simplicity of the model, the quality of fits and predictions is comparable to more complex approaches. As descriptors and predicted values can be calculated rapidly, the method is ideally suited for qualitative predictions for large virtual libraries and the results from de novo design.
这项工作描述了人类肠道吸收的建模使用一个和两个描述符非线性模型。除被动输运外,具有已知输运机制的分子从数据集中删除。人体肠道吸收数据拟合成基于反正切函数的对称和非对称s型曲线和曲面。模型中使用的描述符是氢键供体和受体的总和和计算的logp辛醇-水分配系数。尽管模型很简单,但拟合和预测的质量可与更复杂的方法相媲美。由于描述符和预测值可以快速计算,该方法非常适合大型虚拟库的定性预测和从头设计的结果。
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引用次数: 28
Estimation of pKa Using Semiempirical Molecular Orbital Methods. Part 1: Application to Phenols and Carboxylic Acids. 用半经验分子轨道法估计pKa。第1部分:酚类和羧酸的应用。
Pub Date : 2002-11-01 DOI: 10.1002/1521-3838(200211)21:5<457::AID-QSAR457>3.0.CO;2-5
B. Tehan, E. J. Lloyd, M. Wong, W. Pitt, J. Montana, D. Manallack, E. Gancia
The electronic properties of small molecules can be calculated quickly and with a reasonable degree of accuracy using semiempirical QM methods. In this study a set of QM properties derived from frontier electron theory have been used to produce a predictive model of the dissociation constants of phenols, benzoic acids and aliphatic carboxylic acids. The pK a values and structures of nearly 500 compounds were extracted from the Physprop database for this purpose. Multiple linear regression was used to search for relationships between pK a and the calculated QM properties. In most cases only a single independent variable, electrophilic superdelocalisability, was needed to produce a good model of pK a . The advantages of our approach are in the speed of calculation and the simplicity of the resultant models. The merits of using semiempirical methods to predict pK a are discussed in relation to previous studies.
利用半经验量子力学方法可以快速、准确地计算小分子的电子性质。在这项研究中,一组由前沿电子理论导出的QM性质被用于产生苯酚,苯甲酸和脂肪族羧酸的解离常数的预测模型。为此,从Physprop数据库中提取了近500种化合物的pK值和结构。使用多元线性回归来搜索pK a与计算的QM性质之间的关系。在大多数情况下,只需要一个独立的变量,即亲电超离域性,就可以得到一个好的pK - a模型。这种方法的优点在于计算速度快,所得到的模型简单。结合以往的研究,讨论了用半经验方法预测pK - a的优点。
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引用次数: 101
Estimation of pKa Using Semiempirical Molecular Orbital Methods. Part 2: Application to Amines, Anilines and Various Nitrogen Containing Heterocyclic Compounds. 用半经验分子轨道法估计pKa。第二部分:胺类、苯胺类及各种含氮杂环化合物的应用。
Pub Date : 2002-11-01 DOI: 10.1002/1521-3838(200211)21:5<473::AID-QSAR473>3.0.CO;2-D
B. Tehan, E. J. Lloyd, M. Wong, W. Pitt, E. Gancia, D. Manallack
The pK a of a compound directly influences its biopharmaceutical profile. This article describes the development of a method for estimating pK a values for a number of nitrogen containing chemical structures using semiempirical QM properties derived from frontier electron theory. Typically, the property giving the best correlation with pK d was the electrophilic superdelocalisability of the nitrogen atom resulting in regression equations with r 2 values up to 0.94. The advantages of this technique are in the simplicity of the models and the speed of calculation, suggesting that this method could be widely applied to the estimation of pK a values. The success of this approach is discussed in relation to other methods.
化合物的pK直接影响其生物制药特性。本文描述了一种利用前沿电子理论推导的半经验量子力学性质来估计一些含氮化学结构的pK a值的方法。通常,与pK d相关性最好的性质是氮原子的亲电超离域性,导致r2值高达0.94的回归方程。该方法的优点是模型简单,计算速度快,可以广泛应用于pK - a值的估计。并结合其他方法讨论了这种方法的成功。
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引用次数: 63
期刊
Quantitative Structure-activity Relationships
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