dapagliflozin model

This repository provides the dapagliflozin physiologically based pharmacokinetics/ pharmacodynamics (PBPK/PD) model.

The model is distributed as SBML format available from dapagliflozin_body_flat.xml with corresponding SBML4humans model report and model equations.

The COMBINE archive is available from dapagliflozin_model.omex. The FAIR assessment is available from dapagliflozin_model_fair.xlsx.

Comp submodels

• liver submodel dapagliflozin_liver.xml with SBML4humans report and equations.
• kidney submodel dapagliflozin_kidney.xml with SBML4humans report and equations.
• intestine submodel dapagliflozin_intestine.xml with SBML4humans report and equations.
• whole-body submodel dapagliflozin_body.xml with SBML4humans report and equations.

How to cite

To cite the model repository

Nemitz, N., Elias, M. & König, M. (2025). Physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) model of dapagliflozin.
Zenodo. https://doi.org/10.5281/zenodo.13987865

To cite the main publication

Nike Nemitz, Michelle Elias, Matthias König A Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin in Type 2 Diabetes Mellitus: The Effect of Dosing, Hepatorenal Impairment, and Food Pharmaceutics 2026, 18(3), 287; doi:10.3390/pharmaceutics18030287

To cite the reproducibility publication

Michelle Elias, Mariia Myshkina, Nike Nemitz, Matthias König Reproducibility of a Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin Physiome. February 19, 2026; doi:10.36903/physiome.31368556

License

• Source Code: MIT
• Documentation: CC BY-SA 4.0
• Models: CC BY-SA 4.0

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Run simulations

python

Clone the repository

git clone https://github.com/matthiaskoenig/dapagliflozin-model.git
cd dapagliflozin-model

uv

Setup environment with uv (https://docs.astral.sh/uv/getting-started/installation/)

uv venv
uv sync

Run the complete analysis:

uv run run_dapagliflozin -a all -r results

pip

If you use pip install the package via

pip install -e .

Run the complete analysis in the environment via:

run run_dapagliflozin -a all -r results

docker

Simulations can also be run within a docker container:

docker run -v "${PWD}/results:/results" -it matthiaskoenig/dapagliflozin:latest /bin/bash

Run the complete analysis:

uv run run_dapagliflozin -a all -r /results

The results are written into the mounted /results folder on the host.

In case of permission issues with the mounted folder, adjust ownership and access rights with:

sudo chown $(id -u):$(id -g) -R "${PWD}/results"
sudo chmod 775 "${PWD}/results"

Funding

Matthias König was supported by the Federal Ministry of Research, Technology and Space (BMFTR, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA). This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B).

© 2024-2026 Nike Nemitz, Michelle Elias & Matthias König, Systems Medicine of the Liver