Studying Targeted Protein Degradation Using a Quantitative Systems Pharmacology (QSP) Approach for Proteolysis Targeting Chimeras (PROTACs)
Cesar Pichardo-Almarza (1), Nuria Folguera-Blasco (1), Linda Irons (2), Holly Kimko (3)
AstraZeneca, Systems Medicine, Clinical Pharmacology and Quantitative Pharmacology ; (1) Cambridge, UK; (2) Waltham, US ; (3) Gaithersburg, US
Introduction: Targeted protein degradation is showing promising results for the treatment of various diseases, in particular cancer [1], mainly through the development of new therapies based on Proteolysis Targeting Chimeras (PROTACs) [2]. This work presents a computational framework for simulation of mechanistic models describing the dynamics of PROTACs and their impact on ubiquitination and protein degradation. The framework provides an efficient and convenient way to evaluate specific kinetic model parameters (e.g., binding affinities) and dosing scenarios allowing to study different PROTAC molecules.
The QSP modelling framework is modular and flexible. Having its implementation in Matlab® allows the possibility to expand the model in case new mechanisms are needed or additional submodels are required to include pharmacodynamic effects related to protein levels.
Objectives:
- Developing a mechanistic modelling framework (QSP approach) for the study of PROTACs.
- Including relevant mechanisms in the model related to binding kinetics, ubiquitination, ternary complex formation and its effect on protein degradation.
- Using data collected from the literature to validate the QSP modelling approach, e.g. comparing concentration/degradation curves.
- Implementing the QSP model in mathematical software, including modules for an easier manipulation of the model equations and parameters.
- Creating simulation scenarios to help with the understanding of PROTACs mode of action.
- Building a modelling and simulation platform allowing the study of different compounds and the possibility of future expansions to include additional mechanisms.
Methods: The modelling framework is based on ordinary differential equations (ODEs) describing binding kinetics, ternary complex formation, ubiquitination and degradation derived from the understanding of PROTACs used in oncology, such as PROTACs for Bruton’s tyrosine kinase (BTK) degradation relevant in hepatocellular carcinoma [3, 4]. Equations for the binding kinetics are based on the law of mass action with binding rates and affinities obtained from in vitro assays and/or literature [5]. Model equations also include the formation of the PROTAC binary and ternary complexes with E3 ligase and the target protein (also following mass action kinetics). The formation of the ternary complex initiates the cascade of reactions for protein ubiquitination and proteasomal degradation leading to a final reaction of the target protein degradation.
The full QSP model for PROTACs was implemented in a modular way in Matlab®, clearly describing different modules related to: (1) PROTAC administration and target engagement; (2) Binary/Ternary complex formation, ubiquitination and proteasomal degradation; (3) Target Protein degradation. Parameter values can be adjusted for different PROTACs and individual modules can be modified to increase (or decrease) the granularity of the model. The simulation environment allows the user to see results for the dynamics of the different components of the model (e.g. ternary complexes, targeted protein, etc), evaluating the effect of different PROTAC concentrations on protein degradation with the option of creating concentration/protein degradation curves for further analyses.
Results: The QSP modelling platform allows to explore PROTACs’ dynamics under different case scenarios when changing relevant parameter values, e.g. kinetic rates related to target/ligase turnover, compound depletion, ubiquitination. The modelling framework can also be extended to account for competition with metabolites and endogenous ligands, capturing the main dynamical features observed in other PROTAC modelling publications [6, 7] (such as the hook effect), which validates of the correct implementation of the QSP model.
Simulation results evaluating the mode of action of PROTACs and their effect on targeted protein degradation are encouraging, as they highlight the potential use of computational tools to aid drug development.
Conclusions: This work is a clear example on how mechanistic modelling can be used to study PROTACs. The QSP modelling framework allows the model to be adapted to different compounds with various MoAs by including compound specific data for model refinement. The combination of theoretical understanding and experimental data (e.g., binding kinetics) makes systems modelling a great tool to better understand the peculiarities of new therapeutic modalities.
References:
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[2] K. Li and C. M. Crews, ‘PROTACs: past, present and future’, Chem Soc Rev, vol. 51, no. 12, pp. 5214–5236, Jun. 2022
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