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Biochemical Thermodynamic Modelling of Cellular Bioenergetics: A Quantitative Systems Pharmacology Approach

Kelly, RA (2018) Biochemical Thermodynamic Modelling of Cellular Bioenergetics: A Quantitative Systems Pharmacology Approach. Doctoral thesis, Liverpool John Moores University.

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In this thesis, thermodynamic-based mathematical modelling is combined with experimental in vitro extracellular flux analysis in order to assess drug redox cycling and cellular bioenergetics. It is widely accepted that pharmacological activity of certain classes of drugs (e.g. anticancer, antimalarial) is related to their ability to accept one or two electrons. However, pharmacological activity via redox cycling is an understated mechanism of toxicity associated with many classes of drugs. In particular, oxidative stress as a result of redox cycling plays a pivotal role in the cause of cardiac toxicity. For example, doxorubicin is an anti-neoplastic drug used to treat cancer. It has strong links to redox cycling-induced cardiac toxicity associated directly with elevated levels of reactive oxygen species (ROS) and oxidative stress within the mitochondria. The underlying mechanisms of redox cycling is very difficult to elucidate, due to the fleeting existence of the radical species. However, assessment of such cellular bioenergetics can be ameliorated with the aid of computational assistance. In chapter 2 the development of a novel thermodynamic-based in silico model of doxorubicin redox cycling is described, which is parameterized using data from in vitro extracellular flux analysis. The model is used to simulate mitochondrial-specific ROS, with its outputs confirmed against in vitro data. Chapter 3 describes construction of a pH-dependent thermodynamic model of hepatic glycolytic flux, used to determine the role of the monocarboxylate transporter 1 flux during extracellular acidification. Finally, chapter 4 describes a thermodynamic-based in silico model of mitochondrial bioenergetics, capable of simulating oxygen consumption rates of a cohort of in vitro human primary hepatocyte data. The model is finally used to simulate perturbations in key bioenergetic variables and reaction fluxes, illustrating the resulting changes on mitochondrial pH, membrane potential and subsequent oxygen consumption rates.

Item Type: Thesis (Doctoral)
Uncontrolled Keywords: Bioenergetics; Redox; Quantitative systems pharmacology
Subjects: Q Science > QA Mathematics
Q Science > QD Chemistry
Q Science > QH Natural history > QH301 Biology
R Medicine > RM Therapeutics. Pharmacology
Divisions: Applied Mathematics (merged with Comp Sci 10 Aug 20)
Date Deposited: 12 Jan 2018 09:31
Last Modified: 08 Nov 2022 14:06
DOI or ID number: 10.24377/LJMU.t.00007754
Supervisors: Webb, S, Chadwick, A, Leedale, J and Harrell, A
URI: https://researchonline.ljmu.ac.uk/id/eprint/7754
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