Dynamical Modelling and Analysis of mTOR associated Biological Networks in Survival Mechanisms

Abstract

Cellular homeostasis is a continuous phenomenon that if compromised can lead to several disorders including cancer. There is a need to understand the dynamics of cellular proliferation to get deeper insights into the prevalence of cancer. Mechanistic Target of Rapamycin (mTOR) is implicated as the central regulator of the metabolic pathway involved in growth whereas its two distinct complexes mTORC1 and mTORC2 perform particular functions in cellular propagation. To date, mTORC1 is a well defined therapeutic target to inhibit uncontrolled cell division, while the role of mTORC2 is not well characterized. Therefore, the current study is designed to understand the signaling dynamics of mTOR and its partner proteins such as PI3K, PTEN, mTORC2, PKB (Akt), mTORC1, and FOXO. For this purpose, a qualitative model of mTOR-associated Biological Regulatory Network (BRN) is constructed to predict its regulatory behaviors which may not be predictable otherwise. The depleted expression of PTEN and FOXO along with the overexpression of PI3K, mTORC2, mTORC1 and Akt is predicted as a stable steady state which is in accordance with their observed expression levels in the progression of various cancers. The qualitative model also predicts the homeostasis of all the entities in the form of qualitative cycles. The significant qualitative (discrete) cycle is identified by analyzing betweenness centralities of the qualitative (discrete) states. This cycle is further refined as a linear hybrid automaton model with the production (activation) and degradation (inhibition) time delays in order to analyze the real-time constraints for its existence. The analysis of the hybrid model provides a formal proof that during homeostasis the inhibition time delay of Akt is less than the inhibition time delay ofmTORC2. In conclusion, our observations characterize that in homeostasis Akt is degraded with a faster rate than mTORC2 which suggests that the inhibition of Akt along with the activation of mTORC2 may be a better therapeutic strategy for the treatment of cancer. In living organisms, cellular functions are executed and controlled by gene xii Abstract regulatory networks. Malfunctioning of controlled regulation can lead to pathogenesis. Crosstalk in biological regulation has a significant impact on maintaining homeostasis within organisms. In this study, a timed Hybrid Petri Nets approach is used to model the biological regulatory network of the crosstalk of AMPK, PI3K and MAPK signaling networks to infer mode-switching and overall change in the network dynamics of cellular growth, energy expenditure and fuel metabolism. Simulations are performed to demonstrate the feedback interactions between these pathways and switches that drive changes in the cellular dynamics. Our results shows that during early sleep hours PI3K and MAPK pathways are active which is followed by the activation of AMPK in late sleep hours. As the mammalian target of rapamycin (mTOR) regulated pathway has been found most commonly activated and deregulated in cancer, so there is a need to understand the underlying mechanism of its key interacting proteins. Structural insights of proteins so far undiscovered will unravel these phenomenons. 3D structure of mTORC2 is built using several ab−initio protein structure prediction tools and homology modelling algorithm of Modeller. The quality and validation of the obtained models were accessed using Errat, PROSA and Qmean softwares while the Ramachandran plot was used to access the overall stereochemical properties of the proteins. The individual protein subunits were finally docked using HADDOCK webserver. This approach will aid in understanding the function of individual proteins and a step forward towards drug designing against cancer.