1
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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. Adv Sci (Weinh) 2024:e2309202. [PMID: 38569218 DOI: 10.1002/advs.202309202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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2
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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 2024:10.1038/s41557-024-01458-4. [PMID: 38365941 DOI: 10.1038/s41557-024-01458-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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3
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Sim R, Yang C, Yang YY. Chemical Proteomics and Morphological Profiling Revealing MYDGF as a Target for Synthetic Anticancer Macromolecules. Biomacromolecules 2024; 25:1047-1057. [PMID: 38225889 DOI: 10.1021/acs.biomac.3c01101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Biodegradable guanidinium-functionalized polycarbonates kill cancer cells via membrane translocation without causing resistance after repeated use, but the exact molecular targets of the polycarbonates are unknown. Here, we investigate the protein targets of the polycarbonates through affinity-based protein profiling and report myeloid-derived growth factor (MYDGF) as the main protein target. Direct binding of the polycarbonates to MYDGF protein is validated through biolayer interferometry. MYDGF is overexpressed in a range of cancer cells, and knockdown of MYDGF is shown to reduce cell proliferation in cancer cells. Through morphological profiling, we also identify similarities in phenotypic effects of the functionalized polycarbonates with topoisomerase I inhibitors, MDM2 inhibitors, and phosphatidylinositol 3kinase inhibitors against cancer cells, suggesting a common mechanism through the PIK3/AKT pathway leading to apoptosis. These findings present the first macromolecular compound targeting MYDGF and may serve as an example for MYDGF modulation as a potential new target for macromolecular chemotherapeutic development.
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Affiliation(s)
- Rachel Sim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Chuan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Way, Centros #06-01, Singapore 138668, Singapore
| | - Yi Yan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Way, Centros #06-01, Singapore 138668, Singapore
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4
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Aoyama H, Davies C, Liu J, Pahl A, Kirchhoff JL, Scheel R, Sievers S, Strohmann C, Grigalunas M, Waldmann H. Collective Synthesis of Sarpagine and Macroline Alkaloid-Inspired Compounds. Chemistry 2024; 30:e202303027. [PMID: 37755456 DOI: 10.1002/chem.202303027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 09/28/2023]
Abstract
Design strategies that can access natural-product-like chemical space in an efficient manner may facilitate the discovery of biologically relevant compounds. We have employed a divergent intermediate strategy to construct an indole alkaloid-inspired compound collection derived from two different molecular design principles, i.e. biology-oriented synthesis and pseudo-natural products. The divergent intermediate was subjected to acid-catalyzed or newly discovered Sn-mediated conditions to selectively promote intramolecular C- or N-acylation, respectively. After further derivatization, a collection totalling 84 compounds representing four classes was obtained. Morphological profiling via the cell painting assay coupled with a subprofile analysis showed that compounds derived from different design principles have different bioactivity profiles. The subprofile analysis suggested that a pseudo-natural product class is enriched in modulators of tubulin, and subsequent assays led to the identification of compounds that suppress in vitro tubulin polymerization and mitotic progression.
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Affiliation(s)
- Hikaru Aoyama
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Caitlin Davies
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Jie Liu
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Compound Management and Screening Center, 44227, Dortmund, Germany
| | - Jan-Lukas Kirchhoff
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Compound Management and Screening Center, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry, Chemical Biology, 44227, Dortmund, Germany
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5
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Xie J, Pahl A, Krzyzanowski A, Krupp A, Liu J, Koska S, Schölermann B, Zhang R, Bonowski J, Sievers S, Strohmann C, Ziegler S, Grigalunas M, Waldmann H. Synthetic Matching of Complex Monoterpene Indole Alkaloid Chemical Space. Angew Chem Int Ed Engl 2023; 62:e202310222. [PMID: 37818743 DOI: 10.1002/anie.202310222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are endowed with high structural and spatial complexity and characterized by diverse biological activities. Given this complexity-activity combination in MIAs, rapid and efficient access to chemical matter related to and with complexity similar to these alkaloids would be highly desirable, since such compound classes might display novel bioactivity. We describe the design and synthesis of a pseudo-natural product (pseudo-NP) collection obtained by the unprecedented combination of MIA fragments through complexity-generating transformations, resulting in arrangements not currently accessible by biosynthetic pathways. Cheminformatic analyses revealed that both the pseudo-NPs and the MIAs reside in a unique and common area of chemical space with high spatial complexity-density that is only sparsely populated by other natural products and drugs. Investigation of bioactivity guided by morphological profiling identified pseudo-NPs that inhibit DNA synthesis and modulate tubulin. These results demonstrate that the pseudo-NP collection occupies similar biologically relevant chemical space that Nature has endowed MIAs with.
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Affiliation(s)
- Jianing Xie
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Anna Krupp
- Faculty of Chemistry, Inorganic Chemistry, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Jie Liu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Jana Bonowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry, Inorganic Chemistry, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Slava Ziegler
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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6
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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7
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Harrison PJ, Gupta A, Rietdijk J, Wieslander H, Carreras-Puigvert J, Georgiev P, Wählby C, Spjuth O, Sintorn IM. Evaluating the utility of brightfield image data for mechanism of action prediction. PLoS Comput Biol 2023; 19:e1011323. [PMID: 37490493 PMCID: PMC10403126 DOI: 10.1371/journal.pcbi.1011323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 08/04/2023] [Accepted: 07/02/2023] [Indexed: 07/27/2023] Open
Abstract
Fluorescence staining techniques, such as Cell Painting, together with fluorescence microscopy have proven invaluable for visualizing and quantifying the effects that drugs and other perturbations have on cultured cells. However, fluorescence microscopy is expensive, time-consuming, labor-intensive, and the stains applied can be cytotoxic, interfering with the activity under study. The simplest form of microscopy, brightfield microscopy, lacks these downsides, but the images produced have low contrast and the cellular compartments are difficult to discern. Nevertheless, by harnessing deep learning, these brightfield images may still be sufficient for various predictive purposes. In this study, we compared the predictive performance of models trained on fluorescence images to those trained on brightfield images for predicting the mechanism of action (MoA) of different drugs. We also extracted CellProfiler features from the fluorescence images and used them to benchmark the performance. Overall, we found comparable and largely correlated predictive performance for the two imaging modalities. This is promising for future studies of MoAs in time-lapse experiments for which using fluorescence images is problematic. Explorations based on explainable AI techniques also provided valuable insights regarding compounds that were better predicted by one modality over the other.
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Affiliation(s)
- Philip John Harrison
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Ankit Gupta
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Jonne Rietdijk
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Håkan Wieslander
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Polina Georgiev
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Carolina Wählby
- Science for Life Laboratory, Uppsala, Sweden
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Ida-Maria Sintorn
- Department of Information Technology, Uppsala University, Uppsala, Sweden
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8
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Thomson TM. On the importance for drug discovery of a transnational Latin American database of natural compound structures. Front Pharmacol 2023; 14:1207559. [PMID: 37426821 PMCID: PMC10324963 DOI: 10.3389/fphar.2023.1207559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Affiliation(s)
- Timothy M. Thomson
- Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Universidad Peruana Cayetano Heredia, Lima, Peru
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9
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Pahl A, Schölermann B, Lampe P, Rusch M, Dow M, Hedberg C, Nelson A, Sievers S, Waldmann H, Ziegler S. Morphological subprofile analysis for bioactivity annotation of small molecules. Cell Chem Biol 2023:S2451-9456(23)00159-9. [PMID: 37385259 DOI: 10.1016/j.chembiol.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023]
Abstract
Fast prediction of the mode of action (MoA) for bioactive compounds would immensely foster bioactivity annotation in compound collections and may early on reveal off-targets in chemical biology research and drug discovery. Morphological profiling, e.g., using the Cell Painting assay, offers a fast, unbiased assessment of compound activity on various targets in one experiment. However, due to incomplete bioactivity annotation and unknown activities of reference compounds, prediction of bioactivity is not straightforward. Here we introduce the concept of subprofile analysis to map the MoA for both, reference and unexplored compounds. We defined MoA clusters and extracted cluster subprofiles that contain only a subset of morphological features. Subprofile analysis allows for the assignment of compounds to, currently, twelve targets or MoA. This approach enables rapid bioactivity annotation of compounds and will be extended to further clusters in the future.
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Affiliation(s)
- Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Beate Schölermann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Philipp Lampe
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Marion Rusch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Mark Dow
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christian Hedberg
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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10
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Liu J, Mallick S, Xie Y, Grassin C, Lucas B, Schölermann B, Pahl A, Scheel R, Strohmann C, Protzel C, Berg T, Merten C, Ziegler S, Waldmann H. Morphological Profiling Identifies the Motor Protein Eg5 as Cellular Target of Spirooxindoles. Angew Chem Int Ed Engl 2023; 62:e202301955. [PMID: 36929571 DOI: 10.1002/anie.202301955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/18/2023]
Abstract
Oxindoles and iso-oxindoles are natural product-derived scaffolds that provide inspiration for the design and synthesis of novel biologically relevant compound classes. Notably, the spirocyclic connection of oxindoles with iso-oxindoles has not been explored by nature but promises to provide structurally related compounds endowed with novel bioactivity. Therefore, methods for their efficient synthesis and the conclusive discovery of their cellular targets are highly desirable. We describe a selective RhIII -catalyzed scaffold-divergent synthesis of spirooxindole-isooxindoles and spirooxindole-oxindoles from differently protected diazooxindoles and N-pivaloyloxy aryl amides which includes a functional group-controlled Lossen rearrangement as key step. Unbiased morphological profiling of a corresponding compound collection in the Cell Painting assay efficiently identified the mitotic kinesin Eg5 as the cellular target of the spirooxindoles, defining a unique Eg5 inhibitor chemotype.
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Affiliation(s)
- Jie Liu
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Shubhadip Mallick
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Yusheng Xie
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Corentin Grassin
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, University-Street 150, 44801, Bochum, Germany
| | - Belén Lucas
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Beate Schölermann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
- Compound Management and Screening Center, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Street 6, 44221, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Street 6, 44221, Dortmund, Germany
| | - Christoph Protzel
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Thorsten Berg
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Christian Merten
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, University-Street 150, 44801, Bochum, Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Street 6, 44221, Dortmund, Germany
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11
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Okolo EA, Pahl A, Sievers S, Pask CM, Nelson A, Marsden SP. Scaffold Remodelling of Diazaspirotricycles Enables Synthesis of Diverse sp 3 -Rich Compounds With Distinct Phenotypic Effects. Chemistry 2023; 29:e202203992. [PMID: 36722618 PMCID: PMC10946999 DOI: 10.1002/chem.202203992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
A 'top down' scaffold remodelling approach to library synthesis was applied to spirotricyclic ureas prepared by a complexity-generating oxidative dearomatisation. Eighteen structurally-distinct, sp3 -rich scaffolds were accessed from the parent tricycle through ring addition, cleavage and expansion strategies. Biological screening of a small compound library based on these scaffolds using the cell-painting assay demonstrated distinctive phenotypic responses engendered by different library members, illustrating the functional as well as structural diversity of the compounds.
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Affiliation(s)
| | - Axel Pahl
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Sonja Sievers
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | | | - Adam Nelson
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
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12
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Zhang Z, Lee KCM, Siu DMD, Lo MCK, Lai QTK, Lam EY, Tsia KK. Morphological profiling by high-throughput single-cell biophysical fractometry. Commun Biol 2023; 6:449. [PMID: 37095203 PMCID: PMC10126163 DOI: 10.1038/s42003-023-04839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Complex and irregular cell architecture is known to statistically exhibit fractal geometry, i.e., a pattern resembles a smaller part of itself. Although fractal variations in cells are proven to be closely associated with the disease-related phenotypes that are otherwise obscured in the standard cell-based assays, fractal analysis with single-cell precision remains largely unexplored. To close this gap, here we develop an image-based approach that quantifies a multitude of single-cell biophysical fractal-related properties at subcellular resolution. Taking together with its high-throughput single-cell imaging performance (~10,000 cells/sec), this technique, termed single-cell biophysical fractometry, offers sufficient statistical power for delineating the cellular heterogeneity, in the context of lung-cancer cell subtype classification, drug response assays and cell-cycle progression tracking. Further correlative fractal analysis shows that single-cell biophysical fractometry can enrich the standard morphological profiling depth and spearhead systematic fractal analysis of how cell morphology encodes cellular health and pathological conditions.
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Affiliation(s)
- Ziqi Zhang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dickson M D Siu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Michelle C K Lo
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Queenie T K Lai
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Edmund Y Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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13
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Heinrich L, Kumbier K, Li L, Altschuler SJ, Wu LF. Selection of Optimal Cell Lines for High-Content Phenotypic Screening. ACS Chem Biol 2023; 18:679-685. [PMID: 36920184 PMCID: PMC10127200 DOI: 10.1021/acschembio.2c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
High-content microscopy offers a scalable approach to screen against multiple targets in a single pass. Prior work has focused on methods to select "optimal" cellular readouts in microscopy screens. However, methods to select optimal cell line models have garnered much less attention. Here, we provide a roadmap for how to select the cell line or lines that are best suited to identify bioactive compounds and their mechanism of action (MOA). We test our approach on compounds targeting cancer-relevant pathways, ranking cell lines in two tasks: detecting compound activity ("phenoactivity") and grouping compounds with similar MOA by similar phenotype ("phenosimilarity"). Evaluating six cell lines across 3214 well-annotated compounds, we show that optimal cell line selection depends on both the task of interest (e.g., detecting phenoactivity vs inferring phenosimilarity) and distribution of MOAs within the compound library. Given a task of interest and a set of compounds, we provide a systematic framework for choosing optimal cell line(s). Our framework can be used to reduce the number of cell lines required to identify hits within a compound library and help accelerate the pace of early drug discovery.
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Affiliation(s)
- Louise Heinrich
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California 94158, United States
| | - Karl Kumbier
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California 94158, United States
| | - Li Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California 94158, United States
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California 94158, United States
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California 94158, United States
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14
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Abstract
Propelled by the striking advances in optical microscopy and deep learning (DL), the role of imaging in lab-on-a-chip has dramatically been transformed from a silo inspection tool to a quantitative "smart" engine. A suite of advanced optical microscopes now enables imaging over a range of spatial scales (from molecules to organisms) and temporal window (from microseconds to hours). On the other hand, the staggering diversity of DL algorithms has revolutionized image processing and analysis at the scale and complexity that were once inconceivable. Recognizing these exciting but overwhelming developments, we provide a timely review of their latest trends in the context of lab-on-a-chip imaging, or coined optofluidic imaging. More importantly, here we discuss the strengths and caveats of how to adopt, reinvent, and integrate these imaging techniques and DL algorithms in order to tailor different lab-on-a-chip applications. In particular, we highlight three areas where the latest advances in lab-on-a-chip imaging and DL can form unique synergisms: image formation, image analytics and intelligent image-guided autonomous lab-on-a-chip. Despite the on-going challenges, we anticipate that they will represent the next frontiers in lab-on-a-chip imaging that will spearhead new capabilities in advancing analytical chemistry research, accelerating biological discovery, and empowering new intelligent clinical applications.
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Affiliation(s)
- Dickson M D Siu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong.
| | - Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong.
| | - Bob M F Chung
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Justin S J Wong
- Conzeb Limited, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
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15
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Abstract
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
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Affiliation(s)
- Miquel Duran-Frigola
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,Ersilia
Open Source Initiative, 28 Belgrave Road, CB1 3DE, Cambridge, United Kingdom,
| | - Marko Cigler
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,
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16
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Heinrich L, Kumbier K, Li L, Altschuler SP, Wu LF. Selection of optimal cell lines for high-content phenotypic screening. bioRxiv 2023:2023.01.11.523662. [PMID: 36711978 PMCID: PMC9882115 DOI: 10.1101/2023.01.11.523662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
High-content microscopy offers a scalable approach to screen against multiple targets in a single pass. Prior work has focused on methods to select "optimal" cellular readouts in microscopy screens. However, methods to select optimal cell line models have garnered much less attention. Here, we provide a roadmap for how to select the cell line or lines that are best suited to identify bioactive compounds and their mechanism of action (MOA). We test our approach on compounds targeting cancer-relevant pathways, ranking cell lines in two tasks: detecting compound activity ("phenoactivity") and grouping compounds with similar MOA by similar phenotype ("phenosimilarity"). Evaluating six cell lines across 3214 well-annotated compounds, we show that optimal cell line selection depends on both the task of interest (e.g. detecting phenoactivity vs. inferring phenosimilarity) and distribution of MOAs within the compound library. Given a task of interest and set of compounds, we provide a systematic framework for choosing optimal cell line(s). Our framework can be used to reduce the number of cell lines required to identify hits within a compound library and help accelerate the pace of early drug discovery.
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Affiliation(s)
- Louise Heinrich
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California, 94158, United States
| | - Karl Kumbier
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California, 94158, United States
| | - Li Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California, 94158, United States
| | - Steven P Altschuler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California, 94158, United States
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Fancisco, California, 94158, United States
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17
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Tjaden A, Knapp S, Müller S. Annotation of the Effect of Chemogenomic Compounds on Cell Health Using High-Content Microscopy in Live-Cell Mode. Methods Mol Biol 2023; 2706:59-73. [PMID: 37558941 DOI: 10.1007/978-1-0716-3397-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The characterization of chemogenomic libraries with respect to their general effect on cellular health represents essential data for the annotation of phenotypic responses. Here, we describe a multidimensional high-content live cell assay that allows to examine cell viability in different cell lines, based on their nuclear morphology as well as modulation of small molecules of tubulin structure, mitochondrial health, and membrane integrity. The protocol monitors cells during a time course of 48 h using osteosarcoma cells, human embryonic kidney cells, and untransformed human fibroblasts as an example. The described protocol can be easily established and it can be adapted to other cell lines or other parameters important for cellular health.
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Affiliation(s)
- Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany.
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18
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Schölermann B, Bonowski J, Grigalunas M, Burhop A, Xie Y, Hoock JGF, Liu J, Dow M, Nelson A, Nowak C, Pahl A, Sievers S, Ziegler S. Identification of Dihydroorotate Dehydrogenase Inhibitors Using the Cell Painting Assay. Chembiochem 2022; 23:e202200475. [PMID: 36134475 PMCID: PMC9828254 DOI: 10.1002/cbic.202200475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/21/2022] [Indexed: 02/03/2023]
Abstract
Profiling approaches have been increasingly employed for the characterization of disease-relevant phenotypes or compound perturbation as they provide a broad, unbiased view on impaired cellular states. We report that morphological profiling using the cell painting assay (CPA) can detect modulators of de novo pyrimidine biosynthesis and of dihydroorotate dehydrogenase (DHODH) in particular. The CPA can differentiate between impairment of pyrimidine and folate metabolism, which both affect cellular nucleotide pools. The identified morphological signature is shared by inhibitors of DHODH and the functionally tightly coupled complex III of the mitochondrial respiratory chain as well as by UMP synthase, which is downstream of DHODH. The CPA appears to be particularly suited for the detection of DHODH inhibitors at the site of their action in cells. As DHODH is a validated therapeutic target, the CPA will enable unbiased identification of DHODH inhibitors and inhibitors of de novo pyrimidine biosynthesis for biological research and drug discovery.
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Affiliation(s)
- Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Jana Bonowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Annina Burhop
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Yusheng Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Joseph G. F. Hoock
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Jie Liu
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Mark Dow
- School of Chemistry andAstbury Centre for Structural Molecular BiologyUniversity of LeedsLS2 9JTLeedsUK
| | - Adam Nelson
- School of Chemistry andAstbury Centre for Structural Molecular BiologyUniversity of LeedsLS2 9JTLeedsUK
| | - Christine Nowak
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany,Compound Management and Screening Center44227DortmundGermany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany,Compound Management and Screening Center44227DortmundGermany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
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19
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Wesseler F, Lohmann S, Riege D, Halver J, Roth A, Pichlo C, Weber S, Takamiya M, Müller E, Ketzel J, Flegel J, Gihring A, Rastegar S, Bertrand J, Baumann U, Knippschild U, Peifer C, Sievers S, Waldmann H, Schade D. Phenotypic Discovery of Triazolo[1,5- c]quinazolines as a First-In-Class Bone Morphogenetic Protein Amplifier Chemotype. J Med Chem 2022; 65:15263-15281. [DOI: 10.1021/acs.jmedchem.2c01199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Wesseler
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Compound Management and Screening Center COMAS, Max Planck Institute of Molecular Physiology (MPI), 44227 Dortmund, Germany
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Stefan Lohmann
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Daniel Riege
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Jonas Halver
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Aileen Roth
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Christian Pichlo
- Department of Chemistry, University of Cologne, Greinstraße 6, 50939 Cologne, Germany
| | - Sabrina Weber
- Institute of Biological and Chemical Systems - Biological Information Processing at Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems - Biological Information Processing at Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Eva Müller
- Department of Orthopedic Surgery, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Jana Ketzel
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Jana Flegel
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Adrian Gihring
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing at Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Jessica Bertrand
- Department of Orthopedic Surgery, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ulrich Baumann
- Department of Chemistry, University of Cologne, Greinstraße 6, 50939 Cologne, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Sonja Sievers
- Compound Management and Screening Center COMAS, Max Planck Institute of Molecular Physiology (MPI), 44227 Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227Dortmund, Germany
| | - Herbert Waldmann
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227Dortmund, Germany
| | - Dennis Schade
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
- Partner Site Kiel, DZHK, German Center for Cardiovascular Research, 24105 Kiel, Germany
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20
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Abstract
Small molecule chemical probes are valuable tools for interrogating protein biological functions and relevance as a therapeutic target. Rigorous validation of chemical probe parameters such as cellular potency and selectivity is critical to unequivocally linking biological and phenotypic data resulting from treatment with a chemical probe to the function of a specific target protein. A variety of modern technologies are available to evaluate cellular potency and selectivity, target engagement, and functional response biomarkers of chemical probe compounds. Here, we review these technologies and the rationales behind using them for the characterization and validation of chemical probes. In addition, large-scale phenotypic characterization of chemical probes through chemical genetic screening is increasingly leading to a wealth of information on the cellular pharmacology and disease involvement of potential therapeutic targets. Extensive compound validation approaches and integration of phenotypic information will lay foundations for further use of chemical probes in biological discovery. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada;
| | - David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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21
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Vulliard L, Hancock J, Kamnev A, Fell CW, Ferreira da Silva J, Loizou JI, Nagy V, Dupré L, Menche J. BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. Bioinformatics 2022; 38:1692-1699. [PMID: 34935929 PMCID: PMC8896612 DOI: 10.1093/bioinformatics/btab853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION High-content imaging screens provide a cost-effective and scalable way to assess cell states across diverse experimental conditions. The analysis of the acquired microscopy images involves assembling and curating raw cellular measurements into morphological profiles suitable for testing biological hypotheses. Despite being a critical step, general-purpose and adaptable tools for morphological profiling are lacking and no solution is available for the high-performance Julia programming language. RESULTS Here, we introduce BioProfiling.jl, an efficient end-to-end solution for compiling and filtering informative morphological profiles in Julia. The package contains all the necessary data structures to curate morphological measurements and helper functions to transform, normalize and visualize profiles. Robust statistical distances and permutation tests enable quantification of the significance of the observed changes despite the high fraction of outliers inherent to high-content screens. This package also simplifies visual artifact diagnostics, thus streamlining a bottleneck of morphological analyses. We showcase the features of the package by analyzing a chemical imaging screen, in which the morphological profiles prove to be informative about the compounds' mechanisms of action and can be conveniently integrated with the network localization of molecular targets. AVAILABILITY AND IMPLEMENTATION The Julia package is available on GitHub: https://github.com/menchelab/BioProfiling.jl. We also provide Jupyter notebooks reproducing our analyses: https://github.com/menchelab/BioProfilingNotebooks. The data underlying this article are available from FigShare, at https://doi.org/10.6084/m9.figshare.14784678.v2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Loan Vulliard
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna 1030, Austria
| | - Joel Hancock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna 1030, Austria
| | - Anton Kamnev
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
| | - Christopher W Fell
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Neurology, Medical University of Vienna, Vienna 1090, Austria
| | - Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Vanja Nagy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Neurology, Medical University of Vienna, Vienna 1090, Austria
| | - Loïc Dupré
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR1291, CNRS UMR5051, Toulouse III Paul Sabatier University, Toulouse 31024, France
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22
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Abstract
![]()
Natural products
are the result of Nature’s exploration
of biologically relevant chemical space through evolution and an invaluable
source of bioactive small molecules for chemical biology and medicinal
chemistry. Novel concepts for the discovery of new bioactive compound
classes based on natural product structure may enable exploration
of wider biologically relevant chemical space. The pseudo-natural
product concept merges the relevance of natural product structure
with efficient exploration of chemical space by means of fragment-based
compound development to inspire the discovery of new bioactive chemical
matter through de novo combination of natural product
fragments in unprecedented arrangements. The novel scaffolds retain
the biological relevance of natural products but are not obtainable
through known biosynthetic pathways which can lead to new chemotypes
that may have unexpected or unprecedented bioactivities. Herein, we
cover the workflow of pseudo-natural product design and development,
highlight recent examples, and discuss a cheminformatic analysis in
which a significant portion of biologically active synthetic compounds
were found to be pseudo-natural products. We compare the concept to
natural evolution and discuss pseudo-natural products as the human-made
equivalent, i.e. the chemical evolution of natural product structure.
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Affiliation(s)
- Michael Grigalunas
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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23
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Muroi M, Osada H. Two-dimensional electrophoresis–cellular thermal shift assay (2DE-CETSA) for target identification of bioactive compounds. Methods Enzymol 2022; 675:425-437. [DOI: 10.1016/bs.mie.2022.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products-Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021; 60:15705-15723. [PMID: 33644925 PMCID: PMC8360037 DOI: 10.1002/anie.202016575] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/27/2021] [Indexed: 01/05/2023]
Abstract
Pseudo-natural products (PNPs) combine natural product (NP) fragments in novel arrangements not accessible by current biosynthesis pathways. As such they can be regarded as non-biogenic fusions of NP-derived fragments. They inherit key biological characteristics of the guiding natural product, such as chemical and physiological properties, yet define small molecule chemotypes with unprecedented or unexpected bioactivity. We iterate the design principles underpinning PNP scaffolds and highlight their syntheses and biological investigations. We provide a cheminformatic analysis of PNP collections assessing their molecular properties and shape diversity. We propose and discuss how the iterative analysis of NP structure, design, synthesis, and biological evaluation of PNPs can be regarded as a human-driven branch of the evolution of natural products, that is, a chemical evolution of natural product structure.
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Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyPrivate Bag 4800Christchurch8140New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: Department of ChemistryTechnical University of Denmark, kemitorvet 2072800 Kgs.LyngbyDenmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
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