title: BioDMET: a physiologically based pharmacokinetic simulation tool for assessing proposed solutions to complex biological problems.
abstract: We developed a detailed, whole-body physiologically based pharmacokinetic (PBPK) modeling tool for calculating the distribution of pharmaceutical agents in the various tissues and organs of a human or animal as a function of time. Ordinary differential equations (ODEs) represent the circulation of body fluids through organs and tissues at the macroscopic level, and the biological transport mechanisms and biotransformations within cells and their organelles at the molecular scale. Each major organ in the body is modeled as composed of one or more tissues. Tissues are made up of cells and fluid spaces. The model accounts for the circulation of arterial and venous blood as well as lymph. Since its development was fueled by the need to accurately predict the pharmacokinetic properties of imaging agents, BioDMET is more complex than most PBPK models. The anatomical details of the model are important for the imaging simulation endpoints. Model complexity has also been crucial for quickly adapting the tool to different problems without the need to generate a new model for every problem. When simpler models are preferred, the non-critical compartments can be dynamically collapsed to reduce unnecessary complexity. BioDMET has been used for imaging feasibility calculations in oncology, neurology, cardiology, and diabetes. For this purpose, the time concentration data generated by the model is inputted into a physics-based image simulator to establish imageability criteria. These are then used to define agent and physiology property ranges required for successful imaging. BioDMET has lately been adapted to aid the development of antimicrobial therapeutics. Given a range of built-in features and its inherent flexibility to customization, the model can be used to study a variety of pharmacokinetic and pharmacodynamic problems such as the effects of inter-individual differences and disease-states on drug pharmacokinetics and pharmacodynamics, dosing optimization, and inter-species scaling. While developing a tool to aid imaging agent and drug development, we aimed at accelerating the acceptance and broad use of PBPK modeling by providing a free mechanistic PBPK software that is user friendly, easy to adapt to a wide range of problems even by non-programmers, provided with ready-to-use parameterized models and benchmarking data collected from the peer-reviewed literature.
authors.affiliation: Computational Biology and Biostatistics Laboratory, General Electric Global Research Center, One Research Circle, Niskayuna, NY 12309, USA.
authors.forename: John F
authors.initials: JF
authors.lastname: Graf
authors.forename: Bernhard J
authors.initials: BJ
authors.lastname: Scholz
authors.forename: Maria I
authors.initials: MI
authors.lastname: Zavodszky
mesh_terms: D000465:Algorithms; D000825:Animal Structures / Q000378:metabolism; D000818:Animals; D001692:Biological Transport / Q000502:physiology; D001711:Biotransformation / Q000502:physiology; D001826:Body Fluids / Q000378:metabolism; D002439:Cefotaxime / Q000031:analogs & derivatives / Q000493:pharmacokinetics; D002511:Cephalosporins / Q000493:pharmacokinetics; D003198:Computer Simulation; D003287:Contrast Media / Q000493:pharmacokinetics; D016208:Databases, Factual; D005057:Eukaryotic Cells / Q000378:metabolism; D006168:Guinea Pigs; D000882:Haplorhini; D006801:Humans; D020407:Internet; D007472:Iohexol / Q000493:pharmacokinetics; D051379:Mice; D008954:Models, Biological; D004364:Pharmaceutical Preparations / Q000097:blood / Q000737:chemistry / Q000378:metabolism; D010599:Pharmacokinetics; D051381:Rats; D015203:Reproducibility of Results; D012984:Software; D014018:Tissue Distribution / Q000502:physiology; D014584:User-Computer Interface; D000097572:Cefpirome
chemical_list: D002439:Cefotaxime; D002511:Cephalosporins; D003287:Contrast Media; D007472:Iohexol; D004364:Pharmaceutical Preparations; D000097572:Cefpirome; C033356:cefodizime