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Bag S, Liu J, Patil S, Bonowski J, Koska S, Schölermann B, Zhang R, Wang L, Pahl A, Sievers S, Brieger L, Strohmann C, Ziegler S, Grigalunas M, Waldmann H. A divergent intermediate strategy yields biologically diverse pseudo-natural products. Nat Chem 2024; 16:945-958. [PMID: 38365941 PMCID: PMC11164679 DOI: 10.1038/s41557-024-01458-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The efficient exploration of biologically relevant chemical space is essential for the discovery of bioactive compounds. A molecular design principle that possesses both biological relevance and structural diversity may more efficiently lead to compound collections that are enriched in diverse bioactivities. Here the diverse pseudo-natural product (PNP) strategy, which combines the biological relevance of the PNP concept with synthetic diversification strategies from diversity-oriented synthesis, is reported. A diverse PNP collection was synthesized from a common divergent intermediate through developed indole dearomatization methodologies to afford three-dimensional molecular frameworks that could be further diversified via intramolecular coupling and/or carbon monoxide insertion. In total, 154 PNPs were synthesized representing eight different classes. Cheminformatic analyses showed that the PNPs are structurally diverse between classes. Biological investigations revealed the extent of diverse bioactivity enrichment of the collection in which four inhibitors of Hedgehog signalling, DNA synthesis, de novo pyrimidine biosynthesis and tubulin polymerization were identified from four different PNP classes.
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Affiliation(s)
- Sukdev Bag
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Jie Liu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sohan Patil
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jana Bonowski
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lin Wang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Lukas Brieger
- Faculty of Chemistry and Chemical Biology, Inorganic Chemistry, TU Dortmund University, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology, Inorganic Chemistry, TU Dortmund University, Dortmund, Germany
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
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Wang L, Yilmaz F, Yildirim O, Schölermann B, Bag S, Greiner L, Pahl A, Sievers S, Scheel R, Strohmann C, Squire C, Foley DJ, Ziegler S, Grigalunas M, Waldmann H. Discovery of a Novel Pseudo-Natural Product Aurora Kinase Inhibitor Chemotype through Morphological Profiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309202. [PMID: 38569218 DOI: 10.1002/advs.202309202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Indexed: 04/05/2024]
Abstract
The pseudo-natural product (pseudo-NP) concept aims to combine NP fragments in arrangements that are not accessible through known biosynthetic pathways. The resulting compounds retain the biological relevance of NPs but are not yet linked to bioactivities and may therefore be best evaluated by unbiased screening methods resulting in the identification of unexpected or unprecedented bioactivities. Herein, various NP fragments are combined with a tricyclic core connectivity via interrupted Fischer indole and indole dearomatization reactions to provide a collection of highly three-dimensional pseudo-NPs. Target hypothesis generation by morphological profiling via the cell painting assay guides the identification of an unprecedented chemotype for Aurora kinase inhibition with both its relatively highly 3D structure and its physicochemical properties being very different from known inhibitors. Biochemical and cell biological characterization indicate that the phenotype identified by the cell painting assay corresponds to the inhibition of Aurora kinase B.
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Affiliation(s)
- Lin Wang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Furkan Yilmaz
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227, Dortmund, Germany
| | - Okan Yildirim
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Sukdev Bag
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Luca Greiner
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), 44227, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), 44227, Dortmund, Germany
| | - Rebecca Scheel
- Faculty of Chemistry and Inorganic Chemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Inorganic Chemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Christopher Squire
- School of Biological Sciences, University of Auckland, 1142, Auckland, New Zealand
| | - Daniel J Foley
- School of Physical and Chemical Sciences, University of Canterbury, 8041, Christchurch, New Zealand
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227, Dortmund, Germany
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Fairlamb AH, Wyllie S. The critical role of mode of action studies in kinetoplastid drug discovery. FRONTIERS IN DRUG DISCOVERY 2023; 3:fddsv.2023.1185679. [PMID: 37600222 PMCID: PMC7614965 DOI: 10.3389/fddsv.2023.1185679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Understanding the target and mode of action of compounds identified by phenotypic screening can greatly facilitate the process of drug discovery and development. Here, we outline the tools currently available for target identification against the neglected tropical diseases, human African trypanosomiasis, visceral leishmaniasis and Chagas' disease. We provide examples how these tools can be used to identify and triage undesirable mechanisms, to identify potential toxic liabilities in patients and to manage a balanced portfolio of target-based campaigns. We review the primary targets of drugs that are currently in clinical development that were initially identified via phenotypic screening, and whose modes of action affect protein turnover, RNA trans-splicing or signalling in these protozoan parasites.
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Affiliation(s)
- Alan H. Fairlamb
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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