Authors: Zinken, Sarah
Title: Application of the cell painting assay for pseudo-natural product projects
Language (ISO): en
Abstract: Considering that natural products (NPs) underwent evolutionary selection to bind to their biological targets and therefore represent biologically prevalidated chemical matter, they can serve as a valuable source of inspiration. In the pseudo-NP (PNP) approach, NP fragments are combined by means of chemical methodologies in new arrangements that are not observed in nature. PNPs are designed to share the NP fragments’ high probability to bind to macromolecular targets but also may explore novel areas of biological space as they are structurally distinct from NPs. Phenotypic screening methods, particularly the cell-painting assay (CPA), have been investigated as powerful tools for the biological evaluation of PNPs since they may have unexpected bioactivities. Herein, a PNP class derived from a quinine- and azaindole-fragments was proven to inhibit the autophagy signalling pathway. Comparison of its morphological profile from the CPA to reference compound profiles with annotated bioactivity hinted towards a kinase target. Further investigation proved this hypothesis and identified VPS34 kinase as a potential autophagy-related target. This study highlighted the impact that the CPA can have on the target identification of bioactive PNPs. CPA analysis of diverse PNP compound classes derived from a small fragment subset, allowed the investigation of fragment combinations on morphological profiles. It was shown that fragments can either have a dominating or non-dominating effect on the morphological activity of PNPs that could also be proven in behaviour predictions. This led to the suggestion to use non-dominating fragments to design PNPs with unique and potentially novel bioactivities. Taking inspiration from previous PNP examples, a novel chromane- and 4H-quinoline-derived compound class was designed. The development of a suitable synthetic route resulted in a chromaline compound library that was subsequently tested in the CPA. Comparison with the inspiring PNP classes (chromopynone and pyrroquinoline) revealed, that both fragments were non-dominating and therefore suitable for the design of unique PNPs. Furthermore, the novel chromaline compound class showed high chemical and morphological diversity. Overall, design strategies with the guiding principle of PNPs were employed to generate compound libraries that were evaluated and biologically characterised by the cell painting assay.
Subject Headings: Pseudo-Naturstoffe
Pseudo-natural products
Small molecules
Cell painting assay
Morphological profiling
Phenotypic assays
Autophagy
Subject Headings (RSWK): Naturstoffchemie
Autophagie, Physiologie
URI: http://hdl.handle.net/2003/41055
http://dx.doi.org/10.17877/DE290R-22902
Issue Date: 2022
Appears in Collections:Chemische Biologie

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