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Simbiology v 5

Manufactured by MathWorks
Sourced in United States

Simbiology® v.5.8.2 is a software product developed by MathWorks that provides a platform for modeling and simulating biological systems. The core function of Simbiology® is to enable users to create, analyze, and simulate models of biological processes, such as biochemical reactions, gene regulatory networks, and cell signaling pathways.

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4 protocols using simbiology v 5

1

PBPK Modeling of ATV, RTV, and RIF

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The model was designed using Simbiology® v.5.8.2, a product of MATLAB® v.R2019a (MathWorks, Natick, MA, USA; 2019). Some of the key assumptions considered in the simulations were first-order kinetics, blood flow-limited distribution, no drug reabsorption from the colon, and instant distribution of the drug in tissues and organs (well-stirred model), except in the liver where the distribution of ATV was refined by a mechanistic transport-based model that included active efflux (P-gp) and uptake mediated transport of the drug. For ATV and RTV, a full PBPK model was applied, while RIF was applied in a three-compartment PBPK model (absorption, distribution, and elimination).
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2

Whole-Body PBPK Modeling of Drug Pharmacokinetics

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A whole body PBPK model constructed using Simbiology v. 5.8.2, a product of MATLAB® R2019a v. 9.6.0 (MathWorks, Natick, MA, United States 2013), was used to generate a cohort of 100 individuals aged 18–60 years (50% female and 50% male). The following assumptions were made during simulations: 1) instant and uniform drug distribution (well-stirred model) across each compartment (tissue/organ); 2) no reabsorption of the drug from the colon; and 3) drug distribution was limited by blood flow. No ethical approval was required as results for this investigation were generated virtually.
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3

PBPK Modeling of Intradermal ISL

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A PBPK model was developed for ISL in Simbiology v5.8, a product of Matlab 2018a (MathWorks, Natick, MA, USA). Drug distribution in the intradermal MAP compartments was described using permeability-limited, first-order kinetics. The drug distribution in the remaining whole-body PBPK model was described using blood-flow-limited, first-order kinetics with well-stirred compartments that assumed instant distribution of the drug. Furthermore, it was assumed that there was no absorption of orally dosed drug from the large intestine. Physicochemical, pharmacokinetic, in vitro, and in vivo data for ISL and ISL-TP were sourced from the literature or, if unavailable, were estimated via curve fitting to the observed clinical data. Where applicable, concentration–time profile data were extracted from graphs using the Plot Digitizer Tool v4.5 (WebPlotDigitizer, Pacifica, California, USA). The PBPK model was verified against observed clinical data for both ISL and ISL-TP. Specifically, clinical data for ISL 0.5–30 mg single oral dose and ISL 60 mg and 120 mg once-monthly oral dose regimens were used. For model verification and application, virtual cohorts consisting of 50 male and 50 female patients aged 18–60 years were simulated.
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4

Cabotegravir Pharmacokinetics PBPK Modeling

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A PBPK model was developed for the prediction of cabotegravir pharmacokinetics in Simbiology v5.8, a product of Matlab 2018a (MathWorks, Natick, MA, USA). Excluding the intradermal MAP compartments, drug distribution in the PBPK model was described using blood-flow-limited, first-order kinetics with well-stirred compartments that assumed instant distribution of the drug. Drug distribution in the intradermal MAP compartments was described using permeability-limited, first-order kinetics. Physicochemical, pharmacokinetic, in vitro, and in vivo data for cabotegravir were sourced from the literature or, if unavailable, were estimated using an empirical pharmacokinetic model in the R programming environment v4.0.3 (The R Foundation, Vienna, Austria) and via curve-fitting to observed data in the PBPK model. Where applicable, concentration time profile data were extracted from graphs using the Plot Digitizer Tool v4.5 (WebPlotDigitizer, Pacifica, CA, USA). For PBPK model predictions in rats, virtual cohorts of 100 rats were simulated. For PBPK model predictions in humans, virtual cohorts consisting of 50 male and 50 female patients aged 18–60 years were simulated.
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