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Khushi S, Salim AA, Capon RJ. Case Studies in Molecular Network-Guided Marine Biodiscovery. Mar Drugs 2023; 21:413. [PMID: 37504944 PMCID: PMC10381900 DOI: 10.3390/md21070413] [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: 06/22/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
In reviewing a selection of recent case studies from our laboratory, we revealed some lessons learned and benefits accrued from the application of mass spectrometry (MS/MS) molecular networking in the field of marine sponge natural products. Molecular networking proved pivotal to our discovery of many new natural products and even new classes of natural product, some of which were opaque to alternate dereplication and prioritization strategies. Case studies included the discovery of: (i) trachycladindoles, an exceptionally rare class of bioactive indole alkaloid previously only known from a single southern Australia sample of Trachycladus laevispirulifer; (ii) dysidealactams, an unprecedented class of sesquiterpene glycinyl-lactam and glycinyl-imide from a Dysidea sp., a sponge genera often discounted as having been exhaustively studied; (iii) cacolides, an unprecedented family of sesterterpene α-methyl-γ-hydroxybutenolides from a Cacospongia sp., all too easily mischaracterized and deprioritized during dereplication as a well-known class of sponge sesterterpene tetronic acids; and (iv) thorectandrins, a new class of indole alkaloid which revealed unexpected insights into the chemical and biological properties of the aplysinopsins, one of the earliest and more extensively reported class of sponge natural products.
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Affiliation(s)
- Shamsunnahar Khushi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Angela A Salim
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
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Giri R, Hoedt EC, Khushi S, Salim AA, Bergot AS, Schreiber V, Thomas R, McGuckin MA, Florin TH, Morrison M, Capon RJ, Ó Cuív P, Begun J. Secreted NF-κB suppressive microbial metabolites modulate gut inflammation. Cell Rep 2022; 39:110646. [PMID: 35417687 DOI: 10.1016/j.celrep.2022.110646] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 05/09/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence suggests that microbiome-host crosstalk regulates intestinal immune activity and predisposition to inflammatory bowel disease (IBD). NF-κB is a master regulator of immune function and a validated target for the treatment of IBD. Here, we identify five Clostridium strains that suppress immune-mediated NF-κB activation in epithelial cell lines, PBMCs, and gut epithelial organoids from healthy human subjects and patients with IBD. Cell-free culture supernatant from Clostridium bolteae AHG0001 strain, but not the reference C. bolteae BAA-613 strain, suppresses inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice. The in vivo responses to Clostridium bolteae AHG0001 and BAA-613 mirror the in vitro activity. Thus, using our in vitro screening of bacteria capable of suppressing NF-κB in the context of IBD and using an ex vivo organoid-based approach, we identify a strain capable of alleviating colitis in a relevant pre-clinical animal model of IBD.
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Affiliation(s)
- Rabina Giri
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Shamsunnahar Khushi
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela A Salim
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne-Sophie Bergot
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Veronika Schreiber
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Michael A McGuckin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Timothy H Florin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark Morrison
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Robert J Capon
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Páraic Ó Cuív
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Jakob Begun
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia.
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Khushi S, Salim AA, Elbanna AH, Nahar L, Bernhardt PV, Capon RJ. Dysidealactams and Dysidealactones: Sesquiterpene Glycinyl-Lactams, Imides, and Lactones from a Dysidea sp. Marine Sponge Collected in Southern Australia. J Nat Prod 2020; 83:1577-1584. [PMID: 32243140 DOI: 10.1021/acs.jnatprod.0c00041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A GNPS molecular networking approach mapped a library of 960 southern Australian marine sponges and prioritized Dysidea sp. (CMB-01171) for chemical investigation. Although the published natural products literature on Australian Dysidea sponges extends back over half a century and suffers from the perception of being near exhausted, fractionation of Dysidea sp. (CMB-01171) led to the discovery of a family of 10 new biosynthetically and chemically related sesquiterpenes. Detailed spectroscopic analysis guided structure elucidation identified dysidealactams A-F (1-6), dysidealactones A and B (7 and 8), and two solvolysis artifacts, 9 and 10. The dysidealactams A-D (1-4) incorporate a rare glycinyl-lactam functionality, while dysidealactam E (5) is particularly noteworthy in incorporating an unprecedented glycinyl-imide moiety. In addition to expanding knowledge of Dysidea natural products, this study demonstrates the value of applying GNPS molecular networking to map chemical diversity and prioritize the selection of marine sponge extracts for more detailed chemical analysis.
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Affiliation(s)
- Shamsunnahar Khushi
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Angela A Salim
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Ahmed H Elbanna
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Laizuman Nahar
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Robert J Capon
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
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Khushi S, Nahar L, Salim AA, Capon RJ. Trachycladindoles H–M: Molecular Networking Guided Exploration of a Library of Southern Australian Marine Sponges. Aust J Chem 2020. [DOI: 10.1071/ch19567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A global natural product social (GNPS) molecular network guided search of a library of 960 southern Australian marine sponge extracts successfully detected a deep-water Great Australian Bight sponge, Geodia sp. (CMB-01063), as a new source of a rare class of indolo-imidazole alkaloids previously believed to be unique to a single specimen of Trachycladus laevispirulifer (CMB-03397). Chemical analysis of CMB-01063 detected the known trachycladindoles A–G (1–7), and led to the isolation, characterisation, and structure elucidation of the new trachycladindoles H–M (8–13). Structures for 8–13 were assigned on the basis of detailed spectroscopic analysis, with comparison to authentic standards of 1–7.
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