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QSAR Anti-HIV Feature Selection and Prediction for Drug Discovery Using Genetic Algorithm and Machine Learning Algorithms

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Computational Intelligence in Recent Communication Networks

Abstract

This work presents an approach that uses both genetic algorithm (GA) and many machine learning algorithms (MLA) for feature selection molecular descriptors in a quantitative structure-activity relationships (QSAR) classification and prediction problem. The MLA is used to evaluate an individual population in the GA process. So the fitness function is introduced and defined by the best accuracy classification of the GA and MLA combination. The proposed approach has been implemented and tested using a data set with experimental value antihuman immunodeficiency virus (anti-HIV) molecules. The classification parameters sensibility is equal to 0.99, specificity is equal to 0.91, and accuracy is equal to 0.98. These results reveal the capacity for achieving data subset of molecular descriptors, with high predictive capacity as well as the effectiveness and robustness of the proposed approach.

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References

  1. UNAIDS, Ending the AIDS epidemic 2020: Global HIV Statistics, (2020)

    Google Scholar 

  2. C.P. Swathik, K.D. Jaspreet, M. Vidhi, R. Navaneethan, J. Mannu, S. Durai, Quantitative structure-activity relationship (QSAR): modeling approaches to biological applications. Encycl. Bioinforma. Comput. Biol. 2, 661–676 (2019)

    Google Scholar 

  3. I. Hdoufane, J. Stoycheva, A. Tadjer, D. Villemin, M. Najdoska-Bogdanov, J. Bogdanov, D. Cherqaoui, QSAR and molecular docking studies of indole-based analogs as HIV-1 attachment inhibitors. J. Mol. Struct. 1193, 429–443 (2019)

    Article  Google Scholar 

  4. R. Todeschini, V. Consonni, Molecular Descriptors for Chemoinformatics (Wiley-VCH, 2009)

    Book  Google Scholar 

  5. M. Eklund, U. Norinder, S. Boyer, L. Carlsson, Choosing feature selection and learning algorithms in QSAR. J. Chem. Inf. Model. 54(3), 837–843 (2014)

    Article  Google Scholar 

  6. F. Grisoni, V. Consonni, R. Todeschini, Impact of molecular descriptors on computational models, in Computational Chemogenomics. Methods in Molecular Biology, ed. by J. Brown, vol. 1825, (Humana Press, New York, 2018)

    Google Scholar 

  7. X.Y. Liu, Y. Liang, S. Wang, Z.Y. Yang, H.S. Ye, Hybrid genetic algorithm with wrapper-embedded approaches for feature selection. IEEE Access. 6, 22863–22874 (2018)

    Article  Google Scholar 

  8. B. Wutzl, K. Leibnitz, F. Rattay, M. Kronbichler, M. Murata, S.M. Golaszewski, Genetic algorithms for feature selection when classifying severe chronic disorders of consciousness. PLoS One 14(7), 1–16 (2019)

    Article  Google Scholar 

  9. K. Nagasubramanian, S. Jones, S. Sarkar, A.K. Singh, A. Singh, B. Ganapathysubramanian, Hyperspectral band selection using genetic algorithm and support vector machines for early identification of charcoal rot disease in soybean stems. Plant Methods 14(86), 1–13 (2018)

    Google Scholar 

  10. H. Labjar, M. Kissi, R. Mouhibi, O. Khadir, H. Chaair, M. Zahouily, QSAR study of 1-(3, 3-diphenylpropyl)-piperidinyl amides and ureas using genetic algorithms and artificial neural networks. Int. J. Bioinforma. Res. Appl. 12(2), 116–128 (2016)

    Article  Google Scholar 

  11. N. Salari, S. Shohaimi, F. Najafi, M. Nallappan, I. Karishnarajah, A novel hybrid classification model of genetic algorithms, modified k-nearest neighbor and developed backpropagation neural network. PLoS One 9(11), 1–50 (2014)

    Article  Google Scholar 

  12. A.K. Srivastava, D. Singh, A.S. Pandey, T. Maini, A novel feature selection and short-term Price forecasting based on a decision tree (J48) model. Energies 12, 1–17 (2019)

    Article  Google Scholar 

  13. C.P. Swathik, K.D. Jaspreet, M. Vidhi, R. Navaneethan, J. Mannu, S. Durai, Quantitative structure-activity relationship (QSAR): modeling approaches to biological applications. Encycl. Bioinform. Comput. Biol. 2, 661–676 (2019)

    Google Scholar 

  14. B. Liu, H. He, H. Luo, T. Zhang, J. Jiang, Artificial intelligence and big data facilitated targeted drug discovery. Stroke Vasc. Neurol. 4, 206–213 (2019)

    Article  Google Scholar 

  15. A. Racz, D. Bajusz, K. Héberger, Intercorrelation limits in molecular descriptor preselection for QSAR/QSPR. Mol. Inf. 38, 1–6 (2019)

    Article  Google Scholar 

  16. J. H. Holland. Adaptation in Natural and Artificial Systems. (Ann Arbor, MI, University of Michigan Press. 1992)

    Google Scholar 

  17. E. Pourbasheer, R. Aalizadeh, M.R. Ganjali, P. Norouzi, J. Shadmanesh, QSAR study of ACK1 inhibitors by genetic algorithm–multiple linear regression (GA–MLR). J. Saudi Chem. Soc. 18, 681–688 (2014)

    Article  Google Scholar 

  18. I.I. Baskin, D. Winkler, I.V. Tetko, A renaissance of neural networks in drug discovery. Expert Opin. Drug Discovery 11, 785–795 (2016)

    Article  Google Scholar 

  19. P. Pradeep, R.J. Povinelli, S. White, S.J. Merrill, An ensemble model of QSAR tools for regulatory risk assessment. J. Chem. 8(48), 1–9 (2016)

    Google Scholar 

  20. T.K. Shameera Ahamed, V.K. Rajan, K. Sabira, K. Muraleedharan, QSAR classification-based virtual screening followed by molecular docking studies for identification of potential inhibitors of 5-lipoxygenase. Comput. Biol. Chem. 77, 154–166 (2018)

    Article  Google Scholar 

  21. K. Lee, M. Lee, D. Kim, Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server. BMC Bioinf. 18, 75–86 (2017)

    Article  Google Scholar 

  22. L. Wen, Q. Li, W. Li, Q. Cai, Y.M. Cai, A QSAR study based on SVM for the compound of hydroxyl benzoic esters. Bioinorg. Chem. Appl., 1–10 (2017)

    Google Scholar 

  23. H. Tanaka, H. Takashima, M. Ubasawa, K. Sekiya, I. Nitta, M. Baba, S. Shigata, R.T. Walker, E. De Clercq, T. Miyasaka, Structure-activity relationships of 1-[(2-hydroxyethoxy) methyl]-6-(phenylthio) thymine (HEPT) analogues: effect of substitutions at the C-6 phenyl ring and the C-5 position on anti-HIV-1 activity. J. Med. Chem. 35, 337–345 (1992)

    Article  Google Scholar 

  24. R. Garg, S.P. Gupta, H. Gao, M.S. Babu, A.K. Debnath, Comparative quantitative structure-activity relationships studies on anti-HIV drugs. Chem. Rev. 99, 3525–3601 (1999)

    Article  Google Scholar 

  25. H. Bazoui, M. Zahouily, S. Boulajaaj, S. Sebti, D. Zakarya, QSAR for anti-HIV activity of HEPT derivatives. SAR QSAR Environ. Res. 13(6), 567–577 (2002)

    Article  Google Scholar 

  26. MMP, molecular modelling pro-Demo (TM) Revision 301 demo. ChemSW Software (TM)

    Google Scholar 

  27. S. Anacleto de Souza, L.G. Leonardo Ferreira, S. Aldo de Oliveira, D. Adriano Andricopulo, Quantitative structure–activity relationships for structurally diverse Chemotypes having anti-Trypanosoma cruzi activity. Int. J. Mol. Sci. 20, 1–21 (2019)

    Google Scholar 

  28. L. Wen, Q. Li, W. Li, Q. Cai, Y.M. Cai, A QSAR study based on SVM for the compound of hydroxyl benzoic esters. Bioinorg. Chem. Appl., 1–10 (2017)

    Google Scholar 

  29. S.M. Marunnan, B.P. Pulikkal, A. Jabamalairaj, S. Bandaru, M. Yadav, A. Nayarisseri, V.A. Doss, Development of MLR and SVM aided QSAR models to identify common SAR of GABA uptake herbal inhibitors used in the treatment of schizophrenia. Curr. Neuropharmacol. 15(8), 1085–1092 (2017)

    Article  Google Scholar 

  30. S.K. Chakravarti, S.R.M. Alla, Descriptor free QSAR modeling using deep learning with long short-term memory neural networks. Front. Artif. Intell. 2(17), 1–18 (2019)

    Google Scholar 

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Correspondence to Mohamed Kissi .

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Labjar, H., Labjar, N., Kissi, M. (2022). QSAR Anti-HIV Feature Selection and Prediction for Drug Discovery Using Genetic Algorithm and Machine Learning Algorithms. In: Ouaissa, M., Boulouard, Z., Ouaissa, M., Guermah, B. (eds) Computational Intelligence in Recent Communication Networks . EAI/Springer Innovations in Communication and Computing. Springer, Cham. https://doi.org/10.1007/978-3-030-77185-0_12

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