PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell

  1. Daniel Bergman
  2. Lauren Marazzi
  3. Mukti Chowkwale
  4. Deepa Maheshvare M
  5. Supriya Bidanta
  6. Tarunendu Mapder
  7. Jialun Li

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Abstract

Pharmacokinetics and pharmacodynamics are key considerations in any study of molecular therapies. It is thus imperative to factor their effects in to any in silico model of biological tissue involving such therapies. Furthermore, creation of a standardized and flexible framework will benefit the community by increasing access to such modules and enhancing their communicability. PhysiCell is an open source physics-based cell simulator, i.e. a platform for modeling biological tissue, that is quickly being adopted and utilized by the mathematical biology community. We present here PhysiPKPD, an open source PhysiCell-based package that allows users to include PKPD in PhysiCell models.

Availability & Implementation

The source code for PhysiPKPD is located here: https://github.com/drbergman/PhysiPKPD .

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    Abstract

    This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.72 and has published the reviews under the same license. These are as follows.

    **Reviewer 1. Jeffrey West **

    This is a very nice & useful extension to PhysiCell, in order to model PK/PD dynamics in agent-based simulations. Overall, the description of the software is good and easy to follow, but I offer a few suggestions for clarity:

    1. In "Statement of Need" -- the phrase "how much gets to the cells and what they then do to the cells" is vague and casual -- maybe use standard terms like drug exposure & response to describe PK/PD relationships
    2. Final sentence in "Statement of Need" that says "Substrates can target any cell type with PD dynamics" -- can you elaborate? Does this indicate that every cell type can have unique PD dynamics?
    3. In "Implementation" authors refer to Figure 2A and 2B but figure 2 only has one panel -- perhaps this should be figure 1A/B?
    4. In "Pharmacodynamics" -- "the list of PK substrates and the list of PDsubstrates need not have any relationship" -- this is slightly confusing. I assume that every substrate can have associated PK dynamics without having an PD dynamic, but is the opposite true? If so, how what is the drug dispersal / decay rate?
    5. Finally, the discussion section is focused mainly on future steps. I think it would be helpful for the discussion to focus more on current advantages and functionality. This is the publication record for this software, and as is often the case, future steps may be subject to change.

    **Reviewer 2. Boris Aguilar **

    Is the code executable?

    This code can not be in an. executable form as is an extension to PhysiCell

    Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?

    I am not familiar with running PhysiCell

    Have any claims of performance been sufficiently tested and compared to other commonly-used packages?

    Author claim this is the first time PKPD module has been added to PhysiCell.

    • I think there is mistake in calling Figure 1 in Installation sections, should be Figure 1.
    • Reference to PhysiBoSS missing
    • Figure 1 - I think there is mistake in calling Figure 1 in Installation section, should be Figure 1.
  2. Version published to 10.1101/2022.09.12.507681v1 on bioRxiv