The side effects of potential drug candidates can be difficult to predict in the early stages of drug discovery, as even standard screening processes cannot capture the full context of a substance’s effect on cells. Catching potential adverse side effects as early as possible can prevent the loss of time and money spent developing a substance that is later found to have these adverse effects. A new approach to drug discovery demonstrated by researchers from the Max Planck Institute of Molecular Physiology uses a morphological fingerprinting technique to perform high-throughput screening for unanticipated side effects in thousands of substances.
The technique used by the researchers in this study is called cell painting, and involves the multiplex staining of several functional areas of a cell at once. When the cells are exposed to a chemical substance and imaged by a microscope, hundreds of cellular parameters are recorded to create a morphological “fingerprint” of the substance’s effect on the cell. The fingerprints created by a particular substance can be computationally compared to the fingerprints of known reference substances in order to draw conclusions about its effects, including any unanticipated side effects. One example of a common off-target effect is tubulin-binding, which can disrupt cell division and lead to cell death. While tubulin-binding is used as a mechanism for many cancer drugs, it would be considered an adverse side effect for many other types of therapies.
The researchers used the cell painting assays to screen a library of about 15,000 compounds, revealing that more than 1% of the substances had a tubulin-modifying effect, including a large number of known reference substances not previously known to have an influence on tubulin. The team showed that small-molecule tubulin binders have similar cell painting fingerprints to one another, making this technique a valuable tool for predicting microtubule-binding activity during early compound discovery screens. This research was published in Cell Chemical Biology.
“Reference substances play an essential role in the interpretation of a screen, so they should be carefully evaluated and tested. The compounds identified by the Cell painting show a wide variety of chemical scaffolds and even small chemical modifications can have a dramatic impact on the tubulin-binding properties of a compound. This risk is ubiquitous, especially during the compound optimization phase, where existing atoms are exchanged or removed and new atoms are added in order to improve the pharmacological properties,” said corresponding author Slava Ziegler. “Additional morphological profiling during the search for hits and their optimisation could not only help unmask side effects such as tubulin modulation early on, but also identify desired and new bioactivities. Moreover, this approach could save time and money as it helps to early assess whether a promising substance has what it takes to become a useful compound or not.”
Photo: A diagram showing morphological profiling by means of a cell painting assay, enabling identification of tubulin-targeting compounds. Credit: Max Planck Institute of Molecular Physiology