SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling

Authors

  • Mohammad Shahid,

    1. Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Dahlmannstr. 2, 53113 Bonn, Germany.
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  • Muhammad Shahzad Cheema,

    1. Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Dahlmannstr. 2, 53113 Bonn, Germany.
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  • Alexander Klenner,

    1. Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany.
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  • Erfan Younesi,

    1. Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany.
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  • Martin Hofmann-Apitius

    Corresponding author
    1. Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany.
    • Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany.
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Abstract

Systems pharmacological modeling of drug mode of action for the next generation of multitarget drugs may open new routes for drug design and discovery. Computational methods are widely used in this context amongst which support vector machines (SVM) have proven successful in addressing the challenge of classifying drugs with similar features. We have applied a variety of such SVM-based approaches, namely SVM-based recursive feature elimination (SVM-RFE). We use the approach to predict the pharmacological properties of drugs widely used against complex neurodegenerative disorders (NDD) and to build an in-silico computational model for the binary classification of NDD drugs from other drugs. Application of an SVM-RFE model to a set of drugs successfully classified NDD drugs from non-NDD drugs and resulted in overall accuracy of ∼80 % with 10 fold cross validation using 40 top ranked molecular descriptors selected out of total 314 descriptors. Moreover, SVM-RFE method outperformed linear discriminant analysis (LDA) based feature selection and classification. The model reduced the multidimensional descriptors space of drugs dramatically and predicted NDD drugs with high accuracy, while avoiding over fitting. Based on these results, NDD-specific focused libraries of drug-like compounds can be designed and existing NDD-specific drugs can be characterized by a well-characterized set of molecular descriptors.

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