Support Vector Machine-Based Quantitative Structure-Activity Relationship Study of Cholesteryl Ester Transfer Protein Inhibitors

2D QSAR studies on a series of (4S,5R)-5-[3,5-bis(trifluoromethyl)phenyl]-4-methyl-1,3-oxazolidin-2-one as CETP inhibitors

Cardiovascular disease (CVD) is one of the major causes of human death. Preliminary evidence indicates that the inhibition treatment of Cholesteryl Ester Transfer Protein (CETP) causes the most pronounced increase in HDL cholesterol reported so far. Merck has disclosed certain (4S,5R)-5-[3,5-bis(trifluoromethyl)phenyl]-4-methyl-1,3-oxazolidin-2-one derivatives, which show potent CETP inhibitory activity. Therefore, it would be desirable to develop computational models to facilitate the screening of these inhibitors. In the present work, quantitative structure-activity relationship (QSAR) models have been developed to predict the therapeutic potency of 108 derivatives of (4S,5R)-5-[3,5-bis(trifluoromethyl)phenyl]-4-methyl-1,3-oxazolidin-2-one: Multiple Linear Regression (MLR), Support Vector Regression (SVR) and Feedforward Neural Network using Particle Swarm Optimization (FNN-PSO). Six descriptors were selected using genetic algorithms, whereas, internal and external validation of the models was performed according to all available validation strategies. It was shown that CETP inhibitory activity is mainly governed by electronegativity, the structure of the molecule, and the electronic properties. The best results were obtained with the SVR model. The results obtained may assist in the design of new CETP inhibitors.

Prediction of Anti-Malarial Activity Based on Deep Belief Network

Malaria is a kind of disease that greatly threatens human health. Nearly half of the world’s population is at risk of malaria. Anti-malarial drugs which are sought, developed and synthesized keep malaria under control, having received increasing attention in drug discovery field. Machine learning techniques have been used widely in drug research and development. On the basis of semi-supervised machine learning for molecular descriptions, this research develops a multilayer deep belief network (DBN) that can be used to identify whether compounds have the anti-malarial activity. Firstly, the influence of feature dimensions on predicting accuracy is discussed. Furthermore, the proposed model is applied to contrast shallow machine learning and supervised machine learning with the similar deep architecture. The research results show that the proposed model can predict anti-malarial activity accurately. The stable performance on the evaluation metrics confirms the practicability of our model. The proposed DBN model performs better than other shallow supervised models and deep supervised models. Moreover, it could be applied to reduce the cost and the time of drug discovery.

Application of genetic algorithm-support vector machine (GA-SVM) for prediction of BK-channels activity

The support vector machine (SVM), which is a novel algorithm from the machine learning community, was used to develop quantitative structure-activity relationship (QSAR) for BK-channel activators. The data set was divided into 57 molecules of training and 14 molecules of test sets. A large number of descriptors were calculated and genetic algorithm (GA) was used to select variables that resulted in the best-fitted for models. A comparison between the obtained results using SVM with those of multi-parameter linear regression (MLR) revealed that SVM model was much better than MLR model. The improvements are due to the fact that the activity of the compounds demonstrates non-linear correlations with the selected descriptors. Also distances between Oxygen and Chlorine atoms, the mass, the van der Waals volume, the electronegativity, and the polarizability of the molecules are the main independent factors contributing to the BK-channels activity of the studied compounds.