1
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Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592531. [PMID: 38766203 PMCID: PMC11100607 DOI: 10.1101/2024.05.04.592531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other - omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.
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Affiliation(s)
- Srijit Seal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Maria-Anna Trapotsi
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Shantanu Singh
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Nigel Greene
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
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2
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Bera S, Kabadwal LM, Banerjee D. Harnessing alcohols as sustainable reagents for late-stage functionalisation: synthesis of drugs and bio-inspired compounds. Chem Soc Rev 2024; 53:4607-4647. [PMID: 38525675 DOI: 10.1039/d3cs00942d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Alcohol is ubiquitous with unparalleled structural diversity and thus has wide applications as a native functional group in organic synthesis. It is highly prevalent among biomolecules and offers promising opportunities for the development of chemical libraries. Over the last decade, alcohol has been extensively used as an environmentally friendly chemical for numerous organic transformations. In this review, we collectively discuss the utilisation of alcohol from 2015 to 2023 in various organic transformations and their application toward intermediates of drugs, drug derivatives and natural product-like molecules. Notable features discussed are as follows: (i) sustainable approaches for C-X alkylation (X = C, N, or O) including O-phosphorylation of alcohols, (ii) newer strategies using methanol as a methylating reagent, (iii) allylation of alkenes and alkynes including allylic trifluoromethylations, (iv) alkenylation of N-heterocycles, ketones, sulfones, and ylides towards the synthesis of drug-like molecules, (v) cyclisation and annulation to pharmaceutically active molecules, and (vi) coupling of alcohols with aryl halides or triflates, aryl cyanide and olefins to access drug-like molecules. We summarise the synthesis of over 100 drugs via several approaches, where alcohol was used as one of the potential coupling partners. Additionally, a library of molecules consisting over 60 fatty acids or steroid motifs is documented for late-stage functionalisation including the challenges and opportunities for harnessing alcohols as renewable resources.
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Affiliation(s)
- Sourajit Bera
- Department of Chemistry, Laboratory of Catalysis and Organic Synthesis, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| | - Lalit Mohan Kabadwal
- Department of Chemistry, Laboratory of Catalysis and Organic Synthesis, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| | - Debasis Banerjee
- Department of Chemistry, Laboratory of Catalysis and Organic Synthesis, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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3
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Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. ARXIV 2024:arXiv:2405.02767v1. [PMID: 38745696 PMCID: PMC11092692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other -omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.
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Affiliation(s)
- Srijit Seal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Maria-Anna Trapotsi
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Shantanu Singh
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Nigel Greene
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
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4
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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] [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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5
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Qin LQ, Sun JY, Chen NY, Li XW, Gao DF, Wang W, Mo DL, Su JC, Su GF, Pan CX. Design and synthesis of pseudo-rutaecarpines as potent anti-inflammatory agents via regulating MAPK/NF-κB pathways to relieve inflammation-induced acute liver injury in mice. Bioorg Chem 2023; 138:106611. [PMID: 37236073 DOI: 10.1016/j.bioorg.2023.106611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
Pseudo-natural products (PNPs) design strategy provides a great valuable entrance to effectively identify of novel bioactive scaffolds. In this report, novel pseudo-rutaecarpines were designed via the combination of several privileged structure units and 46 target compounds were synthesized. Most of them display moderate to potent inhibitory effect on LPS-induced NO production and low cytotoxicity in RAW264.7 macrophage. The results of the anti-inflammatory efficacy and action mechanism of compounds 7l and 8c indicated that they significantly reduced the release of IL-6, IL-1β and TNF-α. Further studies revealed that they can strongly inhibit the activation of NF-κB and MAPK signal pathways. The LPS-induced acute liver injury mice model studies not only confirmed their anti-inflammatory efficacy in vivo but also could effectively relieve the liver injury in mice. The results suggest that compounds 7l and 8c might serve as lead compounds to develop therapeutic drugs for treatment of inflammation.
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Affiliation(s)
- Li-Qing Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China; Department of Chemistry and Pharmaceutical Science, Guilin Normal College, 9 Feihu Road, Gulin 541199, China
| | - Jia-Yi Sun
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Nan-Ying Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Xin-Wei Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - De-Feng Gao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Wang Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Dong-Liang Mo
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Jun-Cheng Su
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Gui-Fa Su
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Cheng-Xue Pan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
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6
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Whitmarsh-Everiss T, Wang Z, Hauberg Hansen C, Depta L, Sassetti E, Rafn Dan O, Pahl A, Sievers S, Laraia L. Identification of Biologically Diverse Tetrahydronaphthalen-2-ols through the Synthesis and Phenotypic Profiling of Chemically Diverse, Estradiol-Inspired Compounds. Chembiochem 2023; 24:e202200555. [PMID: 36594441 DOI: 10.1002/cbic.202200555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 01/04/2023]
Abstract
Combining natural product fragments to design new scaffolds with unprecedented bioactivity is a powerful strategy for the discovery of tool compounds and potential therapeutics. However, the choice of fragments to couple and the biological screens to employ remain open questions in the field. By choosing a primary fragment containing the A/B ring system of estradiol and fusing it to nine different secondary fragments, we were able to identify compounds that modulated four different phenotypes: inhibition of autophagy and osteoblast differentiation, as well as potassium channel and tubulin modulation. The latter two were uncovered by using unbiased morphological profiling with a cell-painting assay. The number of hits and variety in bioactivity discovered validates the use of recombining natural product fragments coupled to phenotypic screening for the rapid identification of biologically diverse compounds.
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Affiliation(s)
- Thomas Whitmarsh-Everiss
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Zhou Wang
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Cecilie Hauberg Hansen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Laura Depta
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Elisa Sassetti
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Oliver Rafn Dan
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
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7
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Prophylaxis of posterior capsule opacification through autophagy activation with indomethacin-eluting intraocular lens. Bioact Mater 2022; 23:539-550. [PMID: 36514385 PMCID: PMC9729928 DOI: 10.1016/j.bioactmat.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/31/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Posterior capsule opacification (PCO) is the most common long-term postoperative complication of cataract surgery, leading to secondary vision loss. Optimized intraocular lens (IOL) structure and appropriate pharmacological intervention, which provides physical barriers and biological inhibition, respectively, can block the migration, proliferation, and epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs) for PCO prophylaxis. Herein, a novel indomethacin-eluting IOL (INDOM-IOL) with an optimized sharper edge and a sustained drug release behavior was developed for PCO prevention. Indomethacin (INDOM), an ophthalmic non-steroidal anti-inflammatory drug (NSAID) used for postoperative ocular inflammation, was demonstrated to not only be able to suppress cell migration and down-regulate the expression of cyclooxygenase-2 (COX-2) and EMT markers, including alpha-smooth muscle actin (α-SMA) and cyclin D1, but also promote the autophagy activation in LECs. Additionally, autophagy was also verified to be a potential therapeutic target for the down-regulation of EMT in LECs. The novel IOL, serving as a drug delivery platform, could carry an adjustable dose of hydrophobic indomethacin with sustained drug release ability for more than 28 days. In the rabbit PCO model, the indomethacin-eluting IOL showed excellent anti-inflammatory and anti-PCO effects. In summary, indomethacin is an effective pharmacological intervention in PCO prophylaxis, and the novel IOL we developed prevented PCO in vivo under its sustained indomethacin release property, which provided a promising approach for PCO prophylaxis in clinical application.
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8
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Grigalunas M, Patil S, Krzyzanowski A, Pahl A, Flegel J, Schölermann B, Xie J, Sievers S, Ziegler S, Waldmann H. Unprecedented Combination of Polyketide Natural Product Fragments Identifies the New Hedgehog Signaling Pathway Inhibitor Grismonone. Chemistry 2022; 28:e202202164. [PMID: 36083197 PMCID: PMC10091983 DOI: 10.1002/chem.202202164] [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: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Pseudo-natural products (pseudo-NPs) are de novo combinations of natural product (NP) fragments that define novel bioactive chemotypes. For their discovery, new design principles are being sought. Previously, pseudo-NPs were synthesized by the combination of fragments originating from biosynthetically unrelated NPs to guarantee structural novelty and novel bioactivity. We report the combination of fragments from biosynthetically related NPs in novel arrangements to yield a novel chemotype with activity not shared by the guiding fragments. We describe the synthesis of the polyketide pseudo-NP grismonone and identify it as a structurally novel and potent inhibitor of Hedgehog signaling. The insight that the de novo combination of fragments derived from biosynthetically related NPs may also yield new biologically relevant compound classes with unexpected bioactivity may be considered a chemical extension or diversion of existing biosynthetic pathways and greatly expands the opportunities for exploration of biologically relevant chemical space by means of the pseudo-NP principle.
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Affiliation(s)
- Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sohan Patil
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Adrian Krzyzanowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Jana Flegel
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Jianing Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
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9
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - 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, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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10
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Davies C, Dötsch L, Ciulla MG, Hennes E, Yoshida K, Gasper R, Scheel R, Sievers S, Strohmann C, Kumar K, Ziegler S, Waldmann H. Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype. Angew Chem Int Ed Engl 2022; 61:e202209374. [PMID: 35959923 DOI: 10.1002/anie.202209374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Indexed: 01/07/2023]
Abstract
Natural product (NP)-inspired design principles provide invaluable guidance for bioactive compound discovery. Pseudo-natural products (PNPs) are de novo combinations of NP fragments to target biologically relevant chemical space not covered by NPs. We describe the design and synthesis of apoxidoles, a novel pseudo-NP class, whereby indole- and tetrahydropyridine fragments are linked in monopodal connectivity not found in nature. Apoxidoles are efficiently accessible by an enantioselective [4+2] annulation reaction. Biological evaluation revealed that apoxidoles define a new potent type IV inhibitor chemotype of indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme considered a target for the treatment of neurodegeneration, autoimmunity and cancer. Apoxidoles target apo-IDO1, prevent heme binding and induce unique amino acid positioning as revealed by crystal structure analysis. Novel type IV apo-IDO1 inhibitors are in high demand, and apoxidoles may provide new opportunities for chemical biology and medicinal chemistry research.
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Affiliation(s)
- Caitlin Davies
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Lara Dötsch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Maria Gessica Ciulla
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Current address: Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, Italy.,Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, 20162, Milan, Italy
| | - Elisabeth Hennes
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Kei Yoshida
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University of Dortmund, Department of Inorganic Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS), Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Technical University of Dortmund, Department of Inorganic Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Kamal Kumar
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Current address: AiCuris Anti-infective Cures AG, Friedrich-Ebert-Str. 475, 42117, Wuppertal, Germany
| | - Slava Ziegler
- 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 of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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11
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Li Y, Cheng S, Tian Y, Zhang Y, Zhao Y. Recent ring distortion reactions for diversifying complex natural products. Nat Prod Rep 2022; 39:1970-1992. [PMID: 35972343 DOI: 10.1039/d2np00027j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2013-2022.Chemical diversification of natural products is an efficient way to generate natural product-like compounds for modern drug discovery programs. Utilizing ring-distortion reactions for diversifying natural products would directly alter the core ring systems of small molecules and lead to the production of structurally complex and diverse compounds for high-throughput screening. We review the ring distortion reactions recently used in complexity-to-diversity (CtD) and pseudo natural products (pseudo-NPs) strategies for diversifying complex natural products. The core ring structures of natural products are altered via ring expansion, ring cleavage, ring edge-fusion, ring spiro-fusion, ring rearrangement, and ring contraction. These reactions can rapidly provide natural product-like collections with properties suitable for a wide variety of biological and medicinal applications. The challenges and limitations of current ring distortion reactions are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We also provide a toolbox for chemists for the application of ring distortion reactions to access natural product-like molecules.
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Affiliation(s)
- Yu Li
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yun Tian
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yanan Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China.
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12
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Davies C, Dötsch L, Ciulla MG, Hennes E, Yoshida K, Gasper R, Scheel R, Sievers S, Strohmann C, Kumar K, Ziegler S, Waldmann H. Identification of a Novel Pseudo‐Natural Product Type IV IDO1 Inhibitor Chemotype. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Caitlin Davies
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Lara Dötsch
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Maria Gessica Ciulla
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Elisabeth Hennes
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Kei Yoshida
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Raphael Gasper
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Crystallography and Biophysics Facility GERMANY
| | - Rebecca Scheel
- Technische Universität Dortmund: Technische Universitat Dortmund Inorganic Chemistry GERMANY
| | - Sonja Sievers
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Compound Management and Screening Center GERMANY
| | - Carsten Strohmann
- Technische Universität Dortmund: Technische Universitat Dortmund Inorganic Chemistry GERMANY
| | - Kamal Kumar
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology: Max-Planck-Institut fur molekulare Physiologie Chemical Biology Otto-Hahn-Str. 11 44227 Dortmund GERMANY
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13
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Foley DJ, Waldmann H. Ketones as strategic building blocks for the synthesis of natural product-inspired compounds. Chem Soc Rev 2022; 51:4094-4120. [PMID: 35506561 DOI: 10.1039/d2cs00101b] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Natural product-inspired compound collections serve as excellent sources for the identification of new bioactive compounds to treat disease. However, such compounds must necessarily be more structurally-enriched than traditional screening compounds, therefore inventive synthetic strategies and reliable methods are needed to prepare them. Amongst the various possible starting materials that could be considered for the synthesis of natural product-inspired compounds, ketones can be especially valuable due to the vast variety of complexity-building synthetic transformations that they can take part in, their high prevalence as commercial building blocks, and relative ease of synthesis. With a view towards developing a unified synthetic strategy for the preparation of next generation bioactive compound collections, this review considers whether ketones could serve as general precursors in this regard, and summarises the opulence of synthetic transformations available for the annulation of natural product ring-systems to ketone starting materials.
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Affiliation(s)
- Daniel J Foley
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand. .,Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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14
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Abstract
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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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