Painted Cells and Scrambled Jigsaws

A team at the Max Planck Institute of Molecular Physiology, Dortmund, Germany, have found that many well-characterized active ingredients could affect cholesterol homeostasis – a feature that may prevent SARS-CoV-2 from infecting host cells and may explain the activity of those compounds.

Led by Herbert Waldmann, head of the department of Chemical Biology, and Slava Ziegler, a project leader at the institute, the researchers screened over 15,000 molecules and used an assay technique – cell painting – to profile and compare the molecules’ activity in cells to that of previously identified active substances. 

“In cell painting, upon treatment with small molecules, cells are simultaneously stained with six different dyes to detect their various compartments,” Ziegler says. “The use of multiple dyes enables greater coverage of cellular phenotypes and activities within a single experiment and without necessitating genetic modification.”

Following this assay, the team found that some molecules influenced the cholesterol balance within cells – changing patterns of cholesterol biosynthesis. “We realized that a huge number of characterized compounds with diverse targets had extremely similar morphological profiles,” says Ziegler. “We simply could not leave those compounds alone and therefore set out to figure out what they had in common.” The scientists now believe that this mechanism may explain why these types of compounds have been detected as hits in anti-SARS-CoV-2 screens of repurposing drug libraries.

Data increasingly suggest that SARS-CoV-2 relies on membrane cholesterol for entry into host cells, Ziegler explains. “The activity elicited by the active compounds we identified affects cells’ ability to export cholesterol from lysosomes. The lower cholesterol levels, therefore, trigger the expression of cholesterol biosynthesis genes. These cellular changes influence a variety of processes that rely on proper lysosomal function or membrane cholesterol, such as autophagy and viral infection. Therefore, caution should be taken when drawing conclusions regarding these compounds, since their cellular activity may be related to their physicochemical properties rather than to a given target.”

At present, the team in Dortmund is analyzing further bioactivity clusters containing compounds with highly diverse bioactivity annotations. Their work in this area is far from over, but Ziegler remains excited. “This means that we have more riddles to solve and more puzzle pieces to put together – and I am looking forward to this detective work!”