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Variable Elimination Approaches for Data-Noise Reduction in 3D QSAR Calculations

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 9273))

Abstract

In the last several decades, the drug research has moved to involve various IT technologies in order to rationalize the design of novel bioactive chemical compounds. An important role among these computer-aided drug design (CADD) methods is played by a technique known as quantitative structure-activity relationship (QSAR). The approach is utilized to find a statistically significant model correlating the biological activity with more or less extent data derived from the chemical structures. The present article deals with approaches for discriminating unimportant information in the data input within the three dimensional variant of QSAR – 3D QSAR. Special attention is turned to uninformative and iterative variable elimination (UVE/IVE) methods applicable in connection with partial least square regression (PLS). Herein, we briefly introduce 3D QSAR approach by analyzing 30 antituberculotics. The analysis is examined by four UVE/IVE-PLS based data-noise reduction methods.

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References

  1. Brown, A.C., Fraser, T.R.: XX.—On the Connection between Chemical Constitution and Physiological Action. Part II.—On the Physiological Action of the Ammonium Bases derived from Atropia and Conia. Trans. Roy. Soc. Edinburgh 25, 693–739 (1869)

    Article  Google Scholar 

  2. Hansch, C., Fujita, T.: ρ-σ-π Analysis. A method for the correlation of biological activity and chemical structure. J. Am. Chem. Soc. 86, 1616–1626 (1964)

    Article  Google Scholar 

  3. Free, S.M., Wilson, J.W.: A mathematical contribution to structure-activity studies. J. Med. Chem. 7, 395–399 (1964)

    Article  Google Scholar 

  4. Cramer Iii, R.D.: Partial least squares (PLS): its strengths and limitations. Perspect. Drug. Discov. 1, 269–278 (1993)

    Article  Google Scholar 

  5. Dolezal, R., Korabecny, J., Malinak, D., Honegr, J., Musilek, K., Kuca, K.: Ligand-based 3D QSAR analysis of reactivation potency of mono- and bis-pyridinium aldoximes toward VX-inhibited rat acetylcholinesterase. J. Mol. Graph. Model. 56c, 113–129 (2014)

    Google Scholar 

  6. Tropsha, A., Gramatica, P., Gombar, V.K.: The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. QSAR Comb. Sci. 22, 69–77 (2003)

    Article  Google Scholar 

  7. Chuang, Y.C., Chang, C.H., Lin, J.T., Yang, C.N.: Molecular modelling studies of sirtuin 2 inhibitors using three-dimensional structure-activity relationship analysis and molecular dynamics simulations. Mol. Biosyst. 11, 723–733 (2015)

    Article  Google Scholar 

  8. Kastenholz, M.A., Pastor, M., Cruciani, G., Haaksma, E.E., Fox, T.: GRID/CPCA: a new computational tool to design selective ligands. J. Med. Chem. 43, 3033–3044 (2000)

    Article  Google Scholar 

  9. Bro, R., Elden, L.: PLS works. J. Chemometr. 23, 69–71 (2009)

    Article  Google Scholar 

  10. Centner, V., Massart, D.L., de Noord, O.E., de Jong, S., Vandeginste, B.M., Sterna, C.: Elimination of uninformative variables for multivariate calibration. Anal. Chem. 68, 3851–3858 (1996)

    Article  Google Scholar 

  11. Polanski, J., Gieleciak, R.: The comparative molecular surface analysis (CoMSA) with modified uniformative variable elimination-PLS (UVE-PLS) method: application to the steroids binding the aromatase enzyme. J. Chem. Inf. Comp. Sci. 43, 656–666 (2003)

    Article  Google Scholar 

  12. Gieleciak, R., Polanski, J.: Modeling robust QSAR. 2. iterative variable elimination schemes for CoMSA: application for modeling benzoic acid pKa values. J. Chem. Inf. Model. 47, 547–556 (2007)

    Article  Google Scholar 

  13. Mehmood, T., Liland, K.H., Snipen, L., Sæbø, S.: A review of variable selection methods in partial least squares regression. Chemometr. Intel. Lab. 118, 62–69 (2012)

    Article  Google Scholar 

  14. Pastor, M., Cruciani, G., Clementi, S.: Smart region definition: a new way to improve the predictive ability and interpretability of three-dimensional quantitative structure-activity relationships. J. Med. Chem. 40, 1455–1464 (1997)

    Article  Google Scholar 

  15. Dolezal, R., Waisser, K., Petrlikova, E., Kunes, J., Kubicova, L., Machacek, M., Kaustova, J., Dahse, H.M.: N-Benzylsalicylthioamides: Highly Active Potential Antituberculotics. Arch. Pharm. 342, 113–119 (2009)

    Article  Google Scholar 

  16. Waisser, K., Matyk, J., Kunes, J., Dolezal, R., Kaustova, J., Dahse, H.M.: Highly Active Potential Antituberculotics: 3-(4-Alkylphenyl)-4-thioxo-2H-1,3-benzoxazine-2(3H)-ones and 3-(4-Alkylphenyl)-2H-1,3-benzoxazine-2,4(3H)-dihiones Substituted in Ring-B by Halogen. Archiv Der Pharmazie 341, 800–803 (2008)

    Article  Google Scholar 

  17. Tosco, P., Balle, T., Shiri, F.: Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J. Comput. Aid. Mol. Des. 25, 777–783 (2011)

    Article  Google Scholar 

  18. Tosco, P., Balle, T.: Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields. J. Mol. Model. 17, 201–208 (2011)

    Article  Google Scholar 

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Correspondence to Rafael Dolezal .

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Dolezal, R. et al. (2015). Variable Elimination Approaches for Data-Noise Reduction in 3D QSAR Calculations. In: Pereira, F., Machado, P., Costa, E., Cardoso, A. (eds) Progress in Artificial Intelligence. EPIA 2015. Lecture Notes in Computer Science(), vol 9273. Springer, Cham. https://doi.org/10.1007/978-3-319-23485-4_33

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  • DOI: https://doi.org/10.1007/978-3-319-23485-4_33

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-23484-7

  • Online ISBN: 978-3-319-23485-4

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