Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in variable selection. A novel hybrid approach comprising GA and PLS for variable selection developed in our group (GAPLS) is described. The more advanced method for comparative molecular field analysis (CoMFA) modeling called GA-based region selection (GARGS) is described as well. Applications of GAPLS and GARGS to QSAR and 3D-QSAR problems are shown with some representative examples. GA can be hybridized with nonlinear modeling methods such as artificial neural networks (ANN) for providing useful tools in chemometric and QSAR.     

GA strategy for variable selection in QSAR studies: application of GA-based region selection to a 3D-QSAR study of acetylcholinesterase inhibitors

Comparative molecular field analysis (CoMFA) with partial least squares (PLS) is one of the most frequently used tools in three-dimensional quantitative structure-activity relationships (3D-QSAR) studies. Although many successful CoMFA applications have proved the value of this approach, there are some problems in its proper application. Especially, the inability of PLS to handle the low signal-to-noise ratio (sample-to-variable ratio) has attracted much attention from QSAR researchers as an exciting research target, and several variable selection methods have been proposed. More recently, we have developed a novel variable selection method for CoMFA modeling (GARGS: genetic algorithm-based region selection), and its utility has been demonstrated in the previous paper (Kimura, T., et al. J. Chem. Inf. Comput. Sci. 1998, 38, 276-282). The purpose of this study is to evaluate whether GARGS can pinpoint known molecular interactions in 3D space. We have used a published set of acetylcholinesterase (AChE) inhibitors as a test example. By applying GARGS to a data set of AChE inhibitors, several improved models with high internal prediction and low number of field variables were obtained. External validation was performed to select a final model among them. The coefficient contour maps of the final GARGS model were compared with the properties of the active site in AChE and the consistency between them was evaluated.     

Determination of total sulfur in diesel fuel employing NIR spectroscopy and multivariate calibration

A method for sulfur determination in diesel fuel employing near infrared spectroscopy, variable selection and multivariate calibration is described. The performances of principal component regression (PCR) and partial least square (PLS) chemometric methods were compared with those shown by multiple linear regression (MLR), performed after variable selection based on the genetic algorithm (GA) or the successive projection algorithm (SPA). Ninety seven diesel samples were divided into three sets (41 for calibration, 30 for internal validation and 26 for external validation), each of them covering the full range of sulfur concentrations (from 0.07 to 0.33% w/w). Transflectance measurements were performed from 850 to 1800 nm. Although principal component analysis identified the presence of three groups, PLS, PCR and MLR provided models whose predicting capabilities were independent of the diesel type. Calibration with PLS and PCR employing all the 454 wavelengths provided root mean square errors of prediction (RMSEP) of 0.036% and 0.043% for the validation set, respectively. The use of GA and SPA for variable selection provided calibration models based on 19 and 9 wavelengths, with a RMSEP of 0.031% (PLS-GA), 0.022% (MLR-SPA) and 0.034% (MLR-GA). As the ASTM 4294 method allows a reproducibility of 0.05%, it can be concluded that a method based on NIR spectroscopy and multivariate calibration can be employed for the determination of sulfur in diesel fuels. Furthermore, the selection of variables can provide more robust calibration models and SPA provided more parsimonious models than GA.     

Determining the quality of insulating oils using near infrared spectroscopy and wavelength selection

This study presents an analytical method for determining interfacial tension and relative density in insulating oils using near infrared spectrometry (NIR). Five different strategies of regression were evaluated: partial least squares (PLS) with significant regression coefficients selected by jack-knife algorithm; interval PLS (iPLS); multiple linear regression (MLR) with variable selection by genetic algorithm (MLR/GA), successive projections algorithm (MLR/SPA) and stepwise strategy (SR/MLR). The overall results point to MLR/SPA as the best modeling strategy. The strategy is simpler and uses fewer spectral variables.     

A new and efficient variable selection algorithm based on ant colony optimization. Applications to near infrared spectroscopy/partial least-squares analysis

A new variable selection algorithm is described, based on ant colony optimization (ACO). The algorithm aim is to choose, from a large number of available spectral wavelengths, those relevant to the estimation of analyte concentrations or sample properties when spectroscopic analysis is combined with multivariate calibration techniques such as partial least-squares (PLS) regression. The new algorithm employs the concept of cooperative pheromone accumulation, which is typical of ACO selection methods, and optimizes PLS models using a pre-defined number of variables, employing a Monte Carlo approach to discard irrelevant sensors. The performance has been tested on a simulated system, where it shows a significant superiority over other commonly employed selection methods, such as genetic algorithms. Several near infrared spectroscopic experimental data sets have been subjected to the present ACO algorithm, with PLS leading to improved analytical figures of merit upon wavelength selection. The method could be helpful in other chemometric activities such as classification or quantitative structure-activity relationship (QSAR) problems.     

化学计量学在过程分析中的应用及进展

评述了化学计量学方法在生产过程分析中各个方面 ,如过程优化、过程模拟、仪器及仪器校正、过程监测等方面的应用 ,并展望了化学计量学在过程分析中的应用前景     

A Quantitative Structure–Activity Relationship Study of Calpeptin (Calpain Inhibitor) as an Anticancer Agent

Calpeptin analogs show anticancer properties with inhibition of calpain. In this work, we applied a quantitative structure–activity relationship (QSAR) model on 34 calpeptin derivatives to select the most appropriate compound. QSAR was employed to generate the models and predict the more significant compounds through a series of calpeptin derivatives. The HyperChem, Gaussian 09, and Dragon software programs were used for geometry optimization of the molecules. The 2D and 3D molecular structures were drawn by ChemDraw (Ultra 16.0) and Chem3D (Pro16.0) software. The Unscrambler program was used for the analysis of data. Multiple linear regression (MLR‐MLR), partial least‐squares (MLR‐PLS1), principal component regression (MLR‐PCR), a genetic algorithm‐artificial neural networks (GA‐ANN), and a novel similarity analysis‐artificial neural network (SA‐ANN) method were used to create QSAR models. Among the three MLR models, MLR‐MLR provided better statistical parameters. The R² and RMSE of the prediction were estimated as 0.8248 and 0.26, respectively. Nevertheless, the constructed model using GA‐ANN revealed the best statistical parameters among the studied methods (R² test = 0.9643, RMSE test = 0.0155, R² train = 0.9644, RMSE train = 0.0139). The GA‐ANN model is found to be the most favorable method among the statistical methods and can be employed for designing new calpeptin analogs as potent calpain inhibitors in cancer treatment.     

Modeling based on subspace orthogonal projections for QSAR and QSPR research

A novel projection modeling method for quantitative structure activity relationship (QSAR) and quantitative structure property relationship (QSPR) is developed in this paper. Orthogonalization of block variables is introduced to deal with the problem of variable selection. Projections based on least squares are used to construct the modeling space in order to search for the best regression directions for chemical modeling. A suitable prediction space for such a model is further defined to confine the usage range of the model. Three real data sets were analyzed to check the performance of the proposed modeling method. The results obtained from Monte‐Carlo cross‐validation (MCCV) showed that the proposed modeling method might provide better results for QSAR and QSPR modeling than PCR and PLS with respect to both fitting and prediction abilities. Copyright © 2007 John Wiley & Sons, Ltd.     

Modeling robust QSAR. 2. iterative variable elimination schemes for CoMSA: application for modeling benzoic acid pKa values

A variety of issues decide the efficiency of 3D QSAR methods, and their practical importance for drug design is still controversial. This refers both to the predictive ability and the possibility for the indication of these areas within 3D molecular representations that are responsible for biological or chemical effects. Technically, the latter comes down to the selection or elimination of the reliable variables during 3D QSAR modeling using the Partial Least-Squares (PLS) method. In this paper we used a series of benzoic acids to test the dependence between the predictive ability and variable selection performance of PLS with Iterative Variable Elimination (IVE-PLS) in the Comparative Molecular Surface Analysis (CoMSA) modeling of Hammett constant which correlates with the pKa values. Modeling this chemical effect allowed us to select the IVE-PLS variant that plots the contour maps indicating a carboxylic function, i.e., the region including the dissociation reaction center that determines the respective pKa values. In fact, it appeared that a novel robust IVE version is capable of the indication of the proper contour plots independent of the method used for the calculation of partial atomic charges (AM1 or Gasteiger-Marsili).     

Chemometric QSAR studies of antifungal azoxy compounds

Summary Quantitative structure-activity relationships (QSARs) for 16 azoxy compounds with antifungal activity have been studied by the combined approach of a partial least-squares method and factorial design. The PLS model equation suggested the structural requirements of two substituents, R₁ and R₂, for the antifungal activity. The sterically bulky and hydrophobic R₁ substituents and electron-withdrawing R₂ substituents are favorable for the activity. We propose candidate compounds which are more potent than the compounds based on QSAR data. In this study, we show that the chemometric approach is a powerful tool for QSAR studies and drug design.Abbreviations PLS partial least squares - FD factorial design - MLR multiple linear regression - PPs principal properties     

甲基烷烃结构与色谱保留指数相关性的拓扑指数法研究

计算了207个甲基烷烃的127个拓扑指数变量,把变量选择方法GAPLS方法引入到定量结构与气相色谱保留关系研究中,对127个拓扑指数变量进行选择,得到了含7个变量的化合物的定量结构与色谱保留指数关系(QSRR)模型,其复相关系数的平方为0.99998,标准偏差为2.88。交互验证的复相关系数为0.99997,交互验证的预测标准偏差为2.95,表明该模型具有良好的稳定性和可靠性。对获得的7个变量进行了合理的结构解释,表明甲基烷烃色谱保留指数完全能用拓扑指数来精确表征。