Project description
Fluorescent probes shine light on the ‘dark matter’ in cells
High-throughput drug screening is critical to drug development. It relies on automated testing of thousands of chemical or biological compounds for their interactions with biological targets. However, the dilute buffer environment is quite different from the crowded in vivo intracellular compartment in which many, many molecules are moving around and interacting in a very small space. A candidate that performs well in a drug screen may not do so in a living cell where its motion and activity will be impeded by many obstacles generating all sorts of forces at relatively short range. The EU-funded PArtCell project is creating artificial cells that mimic weak non-specific interactions. This unique preparation will rely on a matrix developed on the basis of data obtained using engineered fluorescent probes to measure the interactions in healthy and stressed living cells. PArtCell will not only shine light on this ‘dark matter of biology’ but also enable screening of therapeutic targets under conditions mimicking nature.
Objective
In the crowded cell, nonspecific interactions between biomolecules alter biochemical equilibria. This matrix of weak nonspecific interactions is composed of hydrophobic, electrostatic, H-bonding, van der Waals, and steric interactions, and is “the dark matter of biology”.
Inaccurate prediction of the behaviour of biomolecules inside cells hampers drug discovery: A high throughput drug screen against a purified target protein in dilute buffer ignores the presence of these weak interactions and results are less relevant. High throughput screens directly in cells are however more difficult to control, interpret and measure.
PArtCell provides a key advance by combining the high level of control and ease of high-throughput screening on purified proteins, with the relevance of screening in the native environment.
The aim is to construct artificial cells that provide a physiologically relevant drug-screening platform.
We will achieve this aim by constructing artificial cells with a matrix of weak nonspecific interactions akin living cells as verified with newly engineered fluorescent probes. The probes measure hydrophobicity, electrostatics and steric effects, as well as the physicochemical state of pathogenic condensates, in healthy and stressed living cells. With this information, we will benchmark artificial cells. Drug screens are applied against pathogenic oligomers that we now can observe in these well-characterized artificial cells.
This research will update textbook knowledge and provide the molecular origin of the matrix of weak nonspecific interactions in living cells. It provides a platform that allows screening against targets under native-like conditions not achievable with other methods. This research thus provides a new opportunity to screen drugs against diseases for which we have no cure yet.
Fields of science
Programme(s)
Funding Scheme
ERC-COG - Consolidator GrantHost institution
3584 CS Utrecht
Netherlands