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

Area of Science:

• Cellular biology
• Chemical biology
• Pharmacology

Background:

• Morphological profiling offers an unbiased approach to identify small molecule bioactivity.
• Identifying the mode of action for compounds with non-protein targets is challenging with traditional methods.
• Cell painting assay (CPA) captures rich cellular morphology data.

Purpose of the Study:

• To identify compounds biosimilar to the iron chelator deferoxamine using CPA.
• To demonstrate that morphological profiling can identify compounds with shared physiological responses, irrespective of their specific targets.
• To explore the utility of morphological fingerprints in understanding mechanisms of action.

Main Methods:

• Utilized cell painting assay (CPA) for unbiased morphological profiling.
• Employed hierarchical clustering to analyze morphological fingerprints.
• Compared morphological profiles of structurally diverse compounds with known targets.

Main Results:

• Identified a cluster of structurally different compounds exhibiting biosimilarity to deferoxamine.
• This cluster shared a common mode of action: cell-cycle modulation in S or G2 phase, not a shared target.
• Hierarchical clustering revealed subclusters correlating with specific mechanisms of action.

Conclusions:

• Morphological profiling via CPA is effective for identifying compounds with shared physiological responses and modes of action.
• This approach is valuable for discovering bioactivity, especially for compounds with non-traditional targets.
• Morphological fingerprints can predict target-related bioactivity and aid in mechanism of action elucidation.