University of Dundee

MRC DTP 4 Year PhD Programme: Molecular simulation study of the Nrf2-Keap1 pathway, the master regulator of cellular redox homeostasis

This project is offered as part of the University of Dundee 4-year MRC DTP Programme “Quantitative and Interdisciplinary approaches to biomedical science”. This PhD programme brings together leading experts from the School of Life Sciences (SLS), the School of Medicine (SoM) and the School of Science and Engineering (SSE) to train the next generation of scientists at the forefront of international science.  The outstanding biomedical research at the University of Dundee was recognised by its very high rankings in REF 2014, with Dundee rated as the top University for Biological Sciences in the UK.  A wide range of projects are available within this programme crossing exceptional strengths in four key areas: Infection and Disease; Responses to Cellular Stresses; Development, Stem Cells and Neurobiology; and Big Data and Translation.  All students on this programme will receive training in computational biology, mathematical biology and statistics to equip with the quantitative skills in tackling complex biological questions.  In the 1st year, students will carry out 3 rotation projects prior to selection of the final PhD project.

In this project, molecular simulation methods will be employed to fully characterize the Nrf2-Keap1 interaction, thus paving the way for novel drug discovery strategies that target this master regulator of cellular redox homeostasis. Nrf2 is a key transcription factor that orchestratesthecellular response to oxidative stress [1]. Keap1 serves as a redox sensor and the main negative regulatorof Nrf2. Together they play a crucialrole in controlling the cellular redox state. The Nrf2-Keap1 interaction thus has become an attractive target for combating oxidative stress and the prevention and treatment ofmultiple conditions including cancer, neurodegenerative and inflammatory diseases. Disruption of this interaction leadsto Nrf2 activation, which has well-established protective effects in numerous animal models of human disease [1]. The development of small-molecule Nrf2 activators targeting the Nrf2-Keap1 protein-protein interactions is actively being pursued, as most known Nrf2 activators are electrophiles, affecting multiple cellular targets. However, our understanding of the precise molecular details of the Nrf2-Keap1 interaction is limited.Over the past decade, molecular dynamics (MD) simulation has grown into a robust tool for describing interactions and dynamics of biomolecular systemsat atomic resolution. MD simulations often reveal missing features that purely experimental techniques cannot provide, e.g. in solving the atomic-level mechanisms of protein allostery [2] or long-range proton transfer [3].

In this project MD simulations and related computational methods will be used to gain detailed understanding –including structure, dynamics, and energetics –of the protein–protein interaction between Nrf2 and Keap1.Additionally, we will examine the effect of small-molecule disruptors of the Nrf2-Keap1 protein-protein interaction. We have a collection of such compounds and will be getting additional ones through an agreement with GSK (in place in the Dinkova-Kostova lab).

Post-translational modifications of Nrf2 will be explored as an alternative,Keap1-independent,strategy for regulating Nrf2.The student will master the state-of-the-art biomolecular modelling and simulation techniques (MD simulations, homology modelling, docking, free-energy calculations, etc) and carry out large-scale computational studies on HPC resources. The work will be done in close collaboration with the lab of Professor Dinkova-Kostova from the School of Medicine, aworld expert on the Nrf2-Keap1 pathway.

Recent work from the lab can be found in the following references:

1) Cuadrado A, Rojo AI, .., Dinkova-Kostova AT. Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases. Nature Reviews Drug Discovery. 18,295–317 (2019).

2) Bueren-Calabuig JA, Bage MG, Cowling VH, Pisliakov AV. Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations. Nucleic Acids Research. 47 8675–8692 (2019). Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH. Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic Acids Research.44, 10423-36 (2016).

3) Carvalheda CA, Pisliakov AV. Insights into proton translocation in the cbb3 oxidase from large scale MD simulations. Biochem. Biophys. Acta -Bioenerg. 1858, 396-406 (2017).