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Biochemical network of drug-induced enzyme production: Parameter estimation based on the periodic dosing response measurement

Volodymyr Lynnyk, Štěpán Papáček, Branislav Rehák (2021)

Kybernetika

The well-known bottleneck of systems pharmacology, i. e., systems biology applied to pharmacology, refers to the model parameters determination from experimentally measured datasets. This paper represents the development of our earlier studies devoted to inverse (ill-posed) problems of model parameters identification. The key feature of this research is the introduction of control (or periodic forcing by an input signal being a drug intake) of the nonlinear model of drug-induced enzyme production...

Mapping directed networks.

Crofts, Jonathan J., Estrada, Ernesto, Higham, Desmond J., Taylor, Alan (2010)

ETNA. Electronic Transactions on Numerical Analysis [electronic only]

On parameter estimation in an in vitro compartmental model for drug-induced enzyme production in pharmacotherapy

Jurjen Duintjer Tebbens, Ctirad Matonoha, Andreas Matthios, Štěpán Papáček (2019)

Applications of Mathematics

A pharmacodynamic model introduced earlier in the literature for in silico prediction of rifampicin-induced CYP3A4 enzyme production is described and some aspects of the involved curve-fitting based parameter estimation are discussed. Validation with our own laboratory data shows that the quality of the fit is particularly sensitive with respect to an unknown parameter representing the concentration of the nuclear receptor PXR (pregnane X receptor). A detailed analysis of the influence of that parameter...

Regulatory network of drug-induced enzyme production: parameter estimation based on the periodic dosing response measurement

Papáček, Štěpán, Lynnyk, Volodymyr, Rehák, Branislav (2021)

Programs and Algorithms of Numerical Mathematics

The common goal of systems pharmacology, i.e. systems biology applied to the field of pharmacology, is to rely less on trial and error in designing an input-output systems, e.g. therapeutic schedules. In this paper we present, on the paradigmatic example of a regulatory network of drug-induced enzyme production, the further development of the study published by Duintjer Tebbens et al. (2019) in the Applications of Mathematics. Here, the key feature is that the nonlinear model in form of an ODE system...

Testing the method of multiple scales and the averaging principle for model parameter estimation of quasiperiodic two time-scale models

Papáček, Štěpán, Matonoha, Ctirad (2023)

Programs and Algorithms of Numerical Mathematics

Some dynamical systems are characterized by more than one time-scale, e.g. two well separated time-scales are typical for quasiperiodic systems. The aim of this paper is to show how singular perturbation methods based on the slow-fast decomposition can serve for an enhanced parameter estimation when the slowly changing features are rigorously treated. Although the ultimate goal is to reduce the standard error for the estimated parameters, here we test two methods for numerical approximations of...

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