Establishing selective autophagy as novel target for therapeutic interventions in neurodegenerative diseases

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Background Autophagy is a homeostatic process that ensures the quality of cellular proteome and genome, by degrading damaged components such as protein aggregates and dysfunctional cellular organelles. Key to the initial autophagy cascade is the versatile regulator protein p62. It functions as an adapter for misfolded protein cargoes, and delivers them to autophagosomes for lysosomal proteolysis. Emerging data (including from supervisor 2) suggest that cargo-loaded p62 undergoes self-oligomerisation and formation of disulphide-linked conjugates, as part of its activation mechanism. Korolchuk and others have also discovered small molecule tool compounds that mimic the physiological mechanism of p62 activation, and promote autophagy in a selective manner.Hypothesis and aimsWe hypothesise that tool compounds allow for a mechanistic understanding towards the activation of p62 at the molecular and cellular level. Defining such mechanism of action will increase our confidence in p62 as a potential therapeutic target for the clearance of disease-causing neuronal aggregates (e.g. tau and a-synuclein).This multi-disciplinary project, supervised by expertise in the biology of autophagy (Korolchuk) and structural biology and drug discovery (Yue), with additional collaborations established for the fields of medicinal chemistry and stem cell biology, aims to: - determine how p62 recognises its ligands (tool compounds, protein cargoes) at the molecular level;- explore the inter-dependence of p62 oligomers and disulphide-linked conjugates in the activation process;- establish the capacity in which tool compounds can induce autophagic degradation of disease-relevant protein aggregates in a p62-dependent manner.MethodologyThe student will use a panel of protein structural (crystallography) and biophysical (ITC, SPR) approaches to determine the binding modes and determinants of p62 ligands, complemented by mutagenesis studies. The molecular basis of p62 oligomers and disulphide-linked conjugates will be characterised by high-end fluorescence microscopy and cryo-electron microscopy techniques. The effect of tool compounds on the autophagic degradation of tau and a-synuclein will be investigated in p62 knockout cell lines with stable re-expression of wild type and mutant p62 constructs. Where applicable, neuronal models of neurodegenerative diseases can be employed to study aggregate formation and cell viability in physiological context.Potential impact Autophagy up-regulation is widely recognized as a therapeutic strategy for the treatment of age-related neurodegenerative diseases such as Parkinson's Disease and Alzheimer's Disease, and Dementia with Lewy Bodies, in which autophagy impairment is implicated as a disease driver. However, existing autophagy activators have poor specificity and selectivity, and cause pleiotropic effects which limit their clinical potential. The project will serve to provide confidence in the concept of targeting p62, exploiting its activation mechanism for the generation of new therapeutics much needed towards currently untreatable age-related diseases. Outputs for this PhD work will form a solid foundation for downstream drug development programme towards this goal.