Morphological Profiling Identifies a Common Mode of Action for Small Molecules with Different Targets

Abstract

Unbiased morphological profiling of bioactivity, for example, in the cell painting assay (CPA), enables the identification of a small molecule's mode of action based on its similarity to the bioactivity of reference compounds, irrespective of the biological target or chemical similarity. This is particularly important for small molecules with nonprotein targets as these are rather difficult to identify with widely employed target-identification methods. We employed morphological profiling using the CPA to identify compounds that are biosimilar to the iron chelator deferoxamine. Structurally different compounds with different annotated cellular targets provoked a shared physiological response, thereby defining a cluster based on their morphological fingerprints. This cluster is based on a shared mode of action and not on a shared target, that is, cell-cycle modulation in the S or G2 phase. Hierarchical clustering of morphological fingerprints revealed subclusters that are based on the mechanism of action and could be used to predict target-related bioactivity.

A phenomics approach for antiviral drug discovery

“…Thus, despite not being able to recapitulate the antiviral activities of all the tested compounds, we have obtained valuable information that can be used to further understand their biological effect. For instance, in line with several previous studies showing that compounds with similar MoA result in similar phenotypic profiles [ 4 , 40 , 41 ], for novel compounds such as the ones we tested, the comparison of their morphological profiles against the ones of a reference set could aid in the identification of their MoA. In fact, the unsupervised clustering of the morphological profiles (Fig.…”

From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems

“…Autoquin sequesters Fe 2+ in the lysosomes, ultimately resulting in cell death, a mechanism which would be difficult to resolve with the methodologies covered in this review. This and other examples illustrate the value of cell painting assays to unravel unconventional MOAs [141][142][143]. Profiling of RNA-small molecule interactions has become more accessible through pioneering work of the Disney group [144].…”

Pseudo Natural Products—Chemical Evolution of Natural Product Structure

“…Fore xample,i ti sa ne xcellent tool for identifying compounds that interfere with lysosomal activity, [57] and metal ion chelators. [58] In the context of pseudo-NPs,t he CPAwas able to identify the target of pyrano-furo-pyridones as mitochondrial complex Id ue to the high biosimilarity of these compounds with the reported complex Ii nhibitor aumitin. [59] Thet arget of the azaindole-fused quinine,A zaquindole-1, was identified as the lipid kinase VPS34 due to the high biosimilarity of this compound to the selective VPS34 inhibitor SAR405.…”

“…Crucially, and unlike chemoproteomic target identification strategies, the CPA can identify targets and modes‐of‐action that occur as a result of the modulation of a non‐protein target. For example, it is an excellent tool for identifying compounds that interfere with lysosomal activity, [57] and metal ion chelators [58] . In the context of pseudo‐NPs, the CPA was able to identify the target of pyrano‐furo‐pyridones as mitochondrial complex I due to the high biosimilarity of these compounds with the reported complex I inhibitor aumitin [59] .…”