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Machine Learning Uncovers Natural Product Modulators of the 5-Lipoxygenase Pathway and Facilitates the Elucidation of Their Biological Mechanisms.

Accepted version
Peer-reviewed

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Type

Article

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Authors

Mikutis, Sigitas 
Lawrinowitz, Stefanie 
Kretzer, Christian 
Dunsmore, Lavinia 
Sketeris, Laurynas 

Abstract

Machine learning (ML) models have made inroads into chemical sciences, with optimization of chemical reactions and prediction of biologically active molecules being prime examples thereof. These models excel where physical experiments are expensive or time-consuming, for example, due to large scales or the need for materials that are difficult to obtain. Studies of natural products suffer from these issues─this class of small molecules is known for its wealth of structural diversity and wide-ranging biological activities, but their investigation is hindered by poor synthetic accessibility and lack of scalability. To facilitate the evaluation of these molecules, we designed ML models that predict which natural products can interact with a particular target or a relevant pathway. Here, we focused on discovering natural products that are capable of modulating the 5-lipoxygenase (5-LO) pathway that plays key roles in lipid signaling and inflammation. These computational approaches led to the identification of nine natural products that either directly inhibit the activity of the 5-LO enzyme or affect the cellular 5-LO pathway. Further investigation of one of these molecules, deltonin, led us to discover a new cell-type-selective mechanism of action. Our ML approach helped deorphanize natural products as well as shed light on their mechanisms and can be broadly applied to other use cases in chemical biology.

Description

Keywords

3101 Biochemistry and Cell Biology, 34 Chemical Sciences, 31 Biological Sciences

Journal Title

ACS Chem Biol

Conference Name

Journal ISSN

1554-8929
1554-8937

Volume Title

Publisher

American Chemical Society (ACS)