On some novel extended topochemical atom (ETA) parameters for effective encoding of chemical information and modelling of fundamental physicochemical properties

Extended topochemical atom (ETA) indices developed by our group have been extensively applied in our previous reports for toxicity and ecotoxicity modelling in the field of quantitative structure–activity relationships (QSARs). In the present study these indices have been further explored by defining additional novel parameters to model n-octanol–water partition coefficient (two data sets; n?=?168 and 139), water solubility (n?=?193), molar refractivity (n?=?166), and aromatic substituent constants π, MR, σ _m, and σ _p (n?=?99). All the models developed in the present study have undergone rigorous internal and external validation tests and the models have high statistical significance and prediction potential. In terms of Q ² and r ² values the models developed for the datasets of whole molecules are better than those previously reported, with topochemically arrived unique (TAU) indices on the same datasets of chemicals. An attempt has also been made to develop models using non-ETA topological and information indices. Interestingly, ETA and non-ETA models have been found to have similar predictive capacity.     

基于DFT和分子连接性指数方法研究醇类化合物的水溶解度和分配系数

将DFT方法计算得到的量化参数和分子连接性指数联合应用到60个醇类化合物的溶解度和辛醇/水分配系数的QSPR研究中,分别通过逐步回归得到具有显著统计意义的4个参数和5个参数的QSPR方程.以此4个参数和5个参数分别作为输入参数,采用BPNN,RBFNN方法建立了QSPR预测模型,使用Latin-partition交叉验证方法评价模型的预测能力.BPNN,RBFNN模型对溶解度预测的相关系数分别为0.993和0.994,而对辛醇/水分配系数预测的相关系数分别0.990和0.997,结果令人满意.     

SDS-Based Biomembrane Mimetic Chromatography for Prediction of Human Drug Transport as an in Vitro Technique

The main oral drug absorption barriers are fluid cell membranes, and generally drugs are absorbed by a passive diffusion mechanism. On the other hand, the blood–brain barrier (BBB) is considered to be the main barrier to drug transport into the central nervous system (CNS). The BBB restricts the passive diffusion of many drugs from blood to brain. Biopartitioning micellar chromatography (BMC), a mode of micellar liquid chromatography that uses micellar mobile phases in adequate experimental conditions, can be useful as an in vitro system in mimicking the drug partitioning process into biological systems. In this study, relationships between the BMC retention data of a heterogeneous set of 12 drugs and their pharmacokinetics parameters (human oral drug absorption and BBB penetration ability) are studied and the predictive ability of the models is evaluated. Modeling of log k _BMC of these compounds was established by multiple linear regression in two different concentrations (0.07 and 0.09 M) of sodium dodecyl sulfate (SDS). The results showed a fair correlation between human oral drug absorption and BMC retention data in 0.09 M SDS (R ² = 0.864) and a good correlation between the blood–brain distribution coefficient and BMC retention data in 0.07 M of SDS (R ² = 0.887). Application of the developed models to a prediction set demonstrated that the model is also reliable with good predictive accuracy. The external and internal validation results showed that the predicted values are in good agreement with the experimental value.     

Prediction of drug solubility from molecular structure using a drug-like training set

Using a training set of 191 drug-like compounds extracted from the AQUASOL database a quantitative structure-property relationship (QSPR) study was conducted employing a set of simple structural and physicochemical properties to predict aqueous solubility. The resultant regression model comprised five parameters (ClogP, molecular weight, indicator variable for aliphatic amine groups, number of rotatable bonds and number of aromatic rings) and demonstrated acceptable statistics (r2 = 0.87, s = 0.51, F = 243.6, n = 191). The model was applied to two test sets consisting of a drug-like set of compounds (r2 = 0.80, s = 0.68, n = 174) and a set of agrochemicals (r2 = 0.88, s = 0.65, n = 200). Using the established general solubility equation (GSE) on the training and drug-like test set gave poorer results than the current study. The agrochemical test set was predicted with equal accuracy using the GSE and the QSPR equation. The results of this study suggest that increasing molecular size, rigidity and lipophilicity decrease solubility whereas increasing conformational flexibility and the presence of a non-conjugated amine group increase the solubility of drug-like compounds. Indeed, the proposed structural parameters make physical sense and provide simple guidelines for modifying solubility during lead optimisation.     

Estimation of aqueous solubility of chemical compounds using E-state indices.

The molecular weight and electrotopological E-state indices were used to estimate by Artificial Neural Networks aqueous solubility for a diverse set of 1291 organic compounds. The neural network with 33-4-1 neurons provided highly predictive results with r(2) = 0.91 and RMS = 0.62. The used parameters included several combinations of E-state indices with similar properties. The calculated results were similar to those published for these data by Huuskonen (2000). However, in the current study only E-state indices were used without need of additional indices (the molecular connectivity, shape, flexibility and indicator indices) also considered in the previous study. In addition, the present neural network contained three times less hidden neurons. Smaller neural networks and use of one homogeneous set of parameters provides a more robust model for prediction of aqueous solubility of chemical compounds. Limitations of the developed method for prediction of large compounds are discussed. The developed approach is available online at http://www.lnh.unil.ch/~itetko/logp.     

Visualization of large-scale aqueous solubility data using a novel hierarchical data visualization technique

It is a difficult task to recognize the trends in molecular physical properties relevant to a specific chemical class and find a way to optimize potential compounds. We present here a novel hierarchical data visualization technique, named "HeiankyoView", to visualize large-scale multidimensional chemical information. HeiankyoView represents hierarchically organized data objects by mapping leaf nodes as colored square icons and nonleaf nodes as rectangular borders. In this way, data objects can be expressed as equishaped icons without overlapping one another in the two-dimensional display space. HeiankyoView has been applied to visualize aqueous solubility data for 908 compounds collected from the published literature. When the results of a recursive partitioning analysis and hierarchical clustering analysis were visualized, the trends hidden in the solubility data could be effectively displayed as intuitively understandable visual images. Most interestingly, the data visualization technique, without any statistical computations, was able to assist us in extracting from such large-scale data meaningful information establishing that ClogP and the molecular weight are critical factors in determining aqueous solubility. Thus, HeiankyoView is a powerful tool to help us understand structure-activity relationships intuitively from a large-scale data set.