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Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002

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Date
15/01/2017
Author
Goltsov, Alexey
Tashkandi, Ghassan
Langdon, Simon P.
Harrison, David J.
Bown, James L.
Keywords
Kinetic modelling
PI3K
mTOR1
PTEN
Rapamycin
BEZ235
RC0254 Neoplasms. Tumors. Oncology (including Cancer)
RM Therapeutics. Pharmacology
NDAS
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Abstract
The phosphatidylinositide 3-kinases (PI3K) and mammalian target of rapamycin-1 (mTOR1) are two key targets for anti-cancer therapy. Predicting the response of the PI3K/AKT/mTOR1 signalling pathway to targeted therapy is made difficult because of network complexities. Systems biology models can help explore those complexities but the value of such models is dependent on accurate parameterisation. Motivated by a need to increase accuracy in kinetic parameter estimation, and therefore the predictive power of the model, we present a framework to integrate kinetic data from enzyme assays into a unified enzyme kinetic model. We present exemplar kinetic models of PI3K and mTOR1, calibrated on in vitro enzyme data and founded on Michaelis-Menten (MM) approximation. We describe the effects of an allosteric mTOR1 inhibitor (Rapamycin) and ATP-competitive inhibitors (BEZ2235 and LY294002) that show dual inhibition of mTOR1 and PI3K. We also model the kinetics of phosphatase and tensin homolog (PTEN), which modulates sensitivity of the PI3K/AKT/mTOR1 pathway to these drugs. Model validation with independent data sets allows investigation of enzyme function and drug dose dependencies in a wide range of experimental conditions. Modelling of the mTOR1 kinetics showed that Rapamycin has an IC50 independent of ATP concentration and that it is a selective inhibitor of mTOR1 substrates S6K1 and 4EBP1: it retains 40% of mTOR1 activity relative to 4EBP1 phosphorylation and inhibits completely S6K1 activity. For the dual ATP-competitive inhibitors of mTOR1 and PI3K, LY294002 and BEZ235, we derived the dependence of the IC50 on ATP concentration that allows prediction of the IC50 at different ATP concentrations in enzyme and cellular assays. Comparison of the drug effectiveness in enzyme and cellular assays showed that some features of these drugs arise from signalling modulation beyond the on-target action and MM approximation and require a systems-level consideration of the whole PI3K/PTEN/AKT/mTOR1 network in order to understand mechanisms of drug sensitivity and resistance in different cancer cell lines. We suggest that using these models in systems biology investigation of the PI3K/AKT/mTOR1 signalling in cancer cells can bridge the gap between direct drug target action and the therapeutic response to these drugs and their combinations.
Citation
Goltsov , A , Tashkandi , G , Langdon , S P , Harrison , D J & Bown , J L 2017 , ' Kinetic modelling of in vitro data of PI3K, mTOR1, PTEN enzymes and on-target inhibitors Rapamycin, BEZ235, and LY294002 ' , European Journal of Pharmaceutical Sciences , vol. 97 , pp. 170-181 . https://doi.org/10.1016/j.ejps.2016.11.008
Publication
European Journal of Pharmaceutical Sciences
Status
Peer reviewed
DOI
https://doi.org/10.1016/j.ejps.2016.11.008
ISSN
0928-0987
Type
Journal article
Rights
© 2016, Elsevier. This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at www.sciencedirect.com / https://doi.org/10.1016/j.ejps.2016.11.008
Description
This work was supported by grants from the Northwood Trust (AG, JB), personal support to AG from Scottish Informatics and Computer Science Alliance (SICSA), and EU support for the Concerted Action CASyM (DJH).
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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/12033

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