High-throughput screening for compounds that modify autophagy

The objective of this project is the identification and characterization of novel small molecule compounds that modulate the autophagic flux within cells. Autophagy effector proteins are functionally altered in several diseases such as cancer, cardiomyopathies or degenerative diseases of the central nervous system. Small molecule modulators of autophagy could thus serve as tools for studying autophagy-related pathways or even modulate disease-associated phenotypes as a future therapeutic intervention strategy.

The primary objective for the ESR is the development of a screening process that accurately monitors the ability of compounds to modulate autophagy based on in house expertise (GFP-RFP-LC3 dual-reporter). The goal is to develop industrial quality primary biochemical or cell-based assays with the capacity to process thousands of compounds per week. Hit compound selection will be supported by high-content secondary assays and measurements in cell-based systems, including human iPSC-based models. The PhD student will test reconstitution systems and establish the assay robustness in terms of classical high-throughput screening quality criteria including: Z’ factor (quantifies variation in high and low controls relative to the assay window); pharmacological response to standard compounds (to be defined and/or provided by consortium partners); and the temporal and spatial stability of the signal. The optimal screening collection will be carefully pre-selected from the available library of >800,000 compounds with support by pharmacophore and compound docking approaches available in-house. High content-based primary or secondary assays will be developed on the Opera confocal microplate imaging system to confirm compound activity in cellular systems.

In parallel, the ESR will also validate > 30 modulators previously identified by Fraunhofer IME ScreeningPort using a screening approach exploiting GFP-RFP-LC3 dual-reporter. These compounds provide a good starting point for hit validation and profiling in sophisticated secondary assays for autophagy available through consortium partners.

The most promising validated candidate molecules resulting from both approaches will be further optimised by the PhD student for the pre-clinical development of new drug candidates and tested for the effects on autophagy in relevant in vivo models developed within DRIVE.