A Liver-Centric Multiscale Modeling Framework for Xenobiotics.

We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK) modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics

Standalone simulation of sub-cellular model.

<p>Results of the standalone run of the sub-cellular model using parameter set <b>REFSIM</b> and an initial concentration of APAP of 0.1mM (15<i>μ</i>g/ml).</p

Time course of a standalone simulation of the sinusoid model in CC3D using the parameters set REFSIM.

<p>A simulated 3 second square pulse of APAP was pushed into the left end of the vessel lumen for three seconds starting one second into the simulation. The concentration of APAP in the blood and hepatocytes is given by the heat map scale at left and time progresses from top to bottom. Blood components are created at the periportal (left) end and a constant force is exerted on the blood components to induce blood flow through the simulated sinusoid. The temporal scales was adjusted so that the blood speed in the simulation was equivalent to 200 <i>μ</i>m/s, giving a transit time of a blood component through the sinusoid of one second.</p

Plasma concentrations versus time for APAP and metabolites for HMPCsim6.

<p>Plasma concentrations versus time for APAP and metabolites simulated with the complete multiscale model using the best fit parameter set <b>HMPCsim6</b>. Symbols are as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162428#pone.0162428.g007" target="_blank">Fig 7</a>.</p

Plasma concentrations calculated using parameter set LNsim8.

<p>This parameter set represents a hypothetical chemical species with ADME behavior significantly different than APAP. Symbols are as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162428#pone.0162428.g007" target="_blank">Fig 7</a> and the APAP <i>in</i> <i>vivo</i> data is included for comparison.</p