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SimRFlow: An R-based workflow for automated high-throughput PBPK simulation with the Simcyp® simulator.

Hiba Khalidi1, Anthonia Onasanwo1, Barira Islam1

  • 1Certara, Simcyp® Division, Sheffield, United Kingdom.

Frontiers in Pharmacology
|September 12, 2022
PubMed
Summary
This summary is machine-generated.

SimRFlow is a high-throughput physiologically based pharmacokinetic (PBPK) modeling tool that automates data curation and runs simulations using the Simcyp® simulator. This efficient workflow enables rapid PBPK analysis for numerous compounds without manual data preparation.

Keywords:
PBPK modellingRautomated data collectionhigh-throughputmodular workflowpharmacokineticssimcyp simulatorsimulation

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Area of Science:

  • Pharmacokinetics and Drug Metabolism
  • Computational Chemistry
  • Systems Biology

Background:

  • Physiologically based pharmacokinetic (PBPK) modeling is crucial for predicting drug behavior in vivo.
  • High-throughput screening of drug candidates requires efficient and automated modeling tools.
  • Manual data curation for PBPK simulations is a significant bottleneck in drug discovery.

Purpose of the Study:

  • To develop an automated, high-throughput PBPK modeling workflow.
  • To integrate data curation, simulation, and visualization into a single tool.
  • To facilitate rapid PBPK analysis for large compound libraries.

Main Methods:

  • Developed SimRFlow, an R Shiny application utilizing Certara's Simcyp® simulator.
  • Automated data collection from ChEMBL, Norman Suspect List, and httk-R databases.
  • Implemented three modules: Data Collection, Simulation (Monte Carlo), and Data Visualization.
  • Supported oral, intravenous, and dermal administration routes with customizable simulation parameters.

Main Results:

  • SimRFlow automates the curation of physicochemical and experimental data.
  • The tool performs high-throughput Monte Carlo simulations for virtual subjects.
  • Generates summary statistics, tissue concentration-time profiles, and detailed results databases.
  • Provides an R Shiny interface with extensive visualization options for compound-specific profiles and parameter comparisons.

Conclusions:

  • SimRFlow significantly reduces the time and effort required for PBPK simulations.
  • Enables efficient screening of numerous compounds without manual data input.
  • Facilitates understanding of compound-specific pharmacokinetic profiles and predictions.