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Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example

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  • Elena Kutumova

    (Department of Computational Biology, Sirius University of Science and Technology, 354340 Sochi, Russia
    Bioinformatics Laboratory, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
    Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia)

  • Ilya Akberdin

    (Department of Computational Biology, Sirius University of Science and Technology, 354340 Sochi, Russia
    Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia
    Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia)

  • Ilya Kiselev

    (Department of Computational Biology, Sirius University of Science and Technology, 354340 Sochi, Russia
    Bioinformatics Laboratory, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
    Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia)

  • Ruslan Sharipov

    (Department of Computational Biology, Sirius University of Science and Technology, 354340 Sochi, Russia
    Bioinformatics Laboratory, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
    Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia
    Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia)

  • Fedor Kolpakov

    (Department of Computational Biology, Sirius University of Science and Technology, 354340 Sochi, Russia
    Bioinformatics Laboratory, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
    Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia)

Abstract

Here we describe a toolkit for presenting physiologically based pharmacokinetic (PBPK) models in a modular graphical view in the BioUML platform. Firstly, we demonstrate the BioUML capabilities for PBPK modeling tested on an existing model of nanoparticles delivery to solid tumors in mice. Secondly, we provide guidance on the conversion of the PBPK model code from a text modeling language like Berkeley Madonna to a visual modular diagram in the BioUML. We give step-by-step explanations of the model transformation and demonstrate that simulation results from the original model are exactly the same as numerical results obtained for the transformed model. The main advantage of the proposed approach is its clarity and ease of perception. Additionally, the modular representation serves as a simplified and convenient base for in silico investigation of the model and reduces the risk of technical errors during its reuse and extension by concomitant biochemical processes. In summary, this article demonstrates that BioUML can be used as an alternative and robust tool for PBPK modeling.

Suggested Citation

  • Elena Kutumova & Ilya Akberdin & Ilya Kiselev & Ruslan Sharipov & Fedor Kolpakov, 2022. "Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example," Mathematics, MDPI, vol. 10(7), pages 1-20, April.
    • Handle: RePEc:gam:jmathe:v:10:y:2022:i:7:p:1176-:d:786904
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    References listed on IDEAS

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    1. Leland H. Hartwell & John J. Hopfield & Stanislas Leibler & Andrew W. Murray, 1999. "From molecular to modular cell biology," Nature, Nature, vol. 402(6761), pages 47-52, December.
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