1
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Ferrinho S, Connaris H, Mouncey NJ, Goss RJM. Compendium of Metabolomic and Genomic Datasets for Cyanobacteria: Mined the Gap. Water Res 2024; 256:121492. [PMID: 38593604 DOI: 10.1016/j.watres.2024.121492] [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] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Cyanobacterial blooms, producing toxic secondary metabolites, are becoming increasingly common phenomena in the face of rising global temperatures. They are the world's most abundant photosynthetic organisms, largely owing their success to a range of highly diverse and complex natural products possessing a broad spectrum of different bioactivities. Over 2600 compounds have been isolated from cyanobacteria thus far, and their characterisation has revealed unusual and useful chemistries and motifs including alkynes, halogens, and non-canonical amino acids. Genome sequencing of cyanobacteria lags behind natural product isolation, with only 19% of cyanobacterial natural products associated with a sequenced organism. Recent advances in meta(genomics) provide promise to narrow this gap and has also facilitated the uprise of combined genomic and metabolomic approaches, heralding a new era of discovery of novel compounds. Analyses of the datasets described within this manuscript reveal the asynchrony of current genomic and metabolomic data, highlight the chemical diversity of cyanobacterial natural products. Linked to this manuscript, we make these manually curated datasets freely accessible for the public to facilitate further research in this important area.
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Affiliation(s)
- Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.
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2
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Abraham E, Lawther HA, Wang Y, Zarins-Tutt JS, Rivera GS, Wu C, Connolly JA, Florence G, Agbo M, Gao H, Goss RJM. The Identification and Heterologous Expression of the Biosynthetic Gene Cluster Encoding the Antibiotic and Anticancer Agent Marinomycin. Biomolecules 2024; 14:117. [PMID: 38254717 PMCID: PMC10813093 DOI: 10.3390/biom14010117] [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: 12/19/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
With the rise in antimicrobial resistance, there is an urgent need for new classes of antibiotic with which to treat infectious disease. Marinomycin, a polyene antibiotic from a marine microbe, has been shown capable of killing methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREF), as well as having promising activity against melanoma. An attractive solution to the photoprotection of this antibiotic has been demonstrated. Here, we report the identification and analysis of the marinomycin biosynthetic gene cluster (BGC), and the biosynthetic assembly of the macrolide. The marinomycin BGC presents a challenge in heterologous expression due to its large size and high GC content, rendering the cluster prone to rearrangement. We demonstrate the transformation of Streptomyces lividans using a construct containing the cluster, and the heterologous expression of the encoded biosynthetic machinery and production of marinomycin B.
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Affiliation(s)
- Emily Abraham
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Hannah A. Lawther
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Yunpeng Wang
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Joseph S. Zarins-Tutt
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | | | - Chengcang Wu
- Intact Genomics, St. Louis, MO 63132, USA (C.W.)
| | - Jack A. Connolly
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Gordon Florence
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Matthias Agbo
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Hong Gao
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Rebecca J. M. Goss
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
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3
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Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov 2023; 22:895-916. [PMID: 37697042 DOI: 10.1038/s41573-023-00774-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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] [Accepted: 07/20/2023] [Indexed: 09/13/2023]
Abstract
Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.
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Affiliation(s)
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - David Meijer
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Marina Gorostiola González
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- ONCODE institute, Leiden, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Florian Huber
- Center for Digitalization and Digitality, Hochschule Düsseldorf, Düsseldorf, Germany
| | - Stefan Leopold-Messer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | - Tristan de Rond
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
- Pharmaceuticals R&D, Bayer AG, Berlin, Germany
| | - Marcy J Balunas
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles", Université Paris-Saclay, CNRS, BioCIS, Orsay, France
| | - Doris A van Bergeijk
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Chase M Clark
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chao Du
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Francesca Grisoni
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | | | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Drug Bioinformatics, Medical Faculty, Saarland University, Homburg, Germany
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Hyunwoo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University Seoul, Goyang-si, Republic of Korea
| | - Tiago F Leao
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Joleen Masschelein
- Center for Microbiology, VIB-KU Leuven, Heverlee, Belgium
- Department of Biology, KU Leuven, Heverlee, Belgium
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Philippe Schwaller
- Laboratory of Artificial Chemical Intelligence, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Michael A Skinnider
- Adapsyn Bioscience, Hamilton, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Barbara Zdrazil
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK
| | - Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), Institute for Bioinformatics and Medical Informatics (IBMI), University of Tuebingen, Tuebingen, Germany
| | | | - Pierre Guyomard
- Bonsai team, CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Université de Lille, Villeneuve d'Ascq Cedex, France
| | - Andrea Volkamer
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for infection research (DZIF), Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Saarbrücken, Germany.
- German Center for infection research (DZIF), Braunschweig, Germany.
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany.
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Serina L Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Dübendorf, Switzerland.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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4
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Wang Y, Ferrinho S, Connaris H, Goss RJM. The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria. Biomolecules 2023; 13:1218. [PMID: 37627283 PMCID: PMC10452541 DOI: 10.3390/biom13081218] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.
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Affiliation(s)
- Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
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5
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Molyneux S, Goss RJM. Fully Aqueous and Air-Compatible Cross-Coupling of Primary Alkyl Halides with Aryl Boronic Species: A Possible and Facile Method. ACS Catal 2023; 13:6365-6374. [PMID: 37180963 PMCID: PMC10167655 DOI: 10.1021/acscatal.3c00252] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Aqueous transformations confer many advantages, including decreased environmental impact and increased opportunity for biomolecule modulation. Although several studies have been conducted to enable the cross-coupling of aryl halides in aqueous conditions, until now a process for the cross-coupling of primary alkyl halides in aqueous conditions was missing from the catalytic toolbox and considered impossible. Alkyl halide coupling in water suffers from severe problems. The reasons for this include the strong propensity for β-hydride elimination, the need for highly air- and water-sensitive catalysts and reagents, and the intolerance of many hydrophilic groups to cross-coupling conditions. Here, we report a broadly applicable and readily accessible process for the cross-coupling of water-soluble alkyl halides in water and air by using simple and commercially available bench-stable reagents. The trisulfonated aryl phosphine TXPTS in combination with a water-soluble palladium salt Na2PdCl4 allowed for the Suzuki-Miyaura coupling of water-soluble alkyl halides with aryl boronic acids, boronic esters, and borofluorate salts in mild, fully aqueous conditions. Multiple challenging functionalities, including unprotected amino acids, an unnatural halogenated amino acid within a peptide, and herbicides can be diversified in water. Structurally complex natural products were used as testbeds to showcase the late-stage tagging methodology of marine natural products to enable liquid chromatography-mass spectrometry (LC-MS) detection. This enabling methodology therefore provides a general method for the environmentally friendly and biocompatible derivatization of sp3 alkyl halide bonds.
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Affiliation(s)
- Samuel Molyneux
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K.
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K.
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6
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Lai HE, Obled AMC, Chee SM, Morgan RM, Lynch R, Sharma SV, Moore SJ, Polizzi KM, Goss RJM, Freemont PS. GenoChemetic Strategy for Derivatization of the Violacein Natural Product Scaffold. ACS Chem Biol 2021; 16:2116-2123. [PMID: 34648268 PMCID: PMC8609527 DOI: 10.1021/acschembio.1c00483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Natural products and their analogues are often challenging to synthesize due to their complex scaffolds and embedded functional groups. Solely relying on engineering the biosynthesis of natural products may lead to limited compound diversity. Integrating synthetic biology with synthetic chemistry allows rapid access to much more diverse portfolios of xenobiotic compounds, which may accelerate the discovery of new therapeutics. As a proof-of-concept, by supplementing an Escherichia coli strain expressing the violacein biosynthesis pathway with 5-bromo-tryptophan in vitro or tryptophan 7-halogenase RebH in vivo, six halogenated analogues of violacein or deoxyviolacein were generated, demonstrating the promiscuity of the violacein biosynthesis pathway. Furthermore, 20 new derivatives were generated from 5-brominated violacein analogues via the Suzuki-Miyaura cross-coupling reaction directly using the crude extract without prior purification. Herein we demonstrate a flexible and rapid approach to access a diverse chemical space that can be applied to a wide range of natural product scaffolds.
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Affiliation(s)
- Hung-En Lai
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Alan M. C. Obled
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Soo Mei Chee
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, London W12 0BZ, U.K
| | - Rhodri M. Morgan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Rosemary Lynch
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Sunil V. Sharma
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Simon J. Moore
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Karen M. Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Rebecca J. M. Goss
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, London W12 0BZ, U.K
- UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, U.K
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7
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Sharma SV, Pubill-Ulldemolins C, Marelli E, Goss RJM. An expedient, mild and aqueous method for Suzuki-Miyaura diversification of (hetero)aryl halides or (poly)chlorinated pharmaceuticals. Org Chem Front 2021; 8:5722-5727. [PMID: 34745636 PMCID: PMC8506956 DOI: 10.1039/d1qo00919b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022]
Abstract
The development of mild, aqueous conditions for the cross-coupling of highly functionalized (hetero)aryl chlorides or bromides is attractive, enabling their functionalization and diversification. Herein, we report a general method for Suzuki–Miyaura cross-coupling at 37 °C in aqueous media in the presence of air. We demonstrate application of this general methodology for derivatisation of (poly)chlorinated, medicinally active compounds and halogenated amino acids. The approach holds the potential to be a useful tool for late-stage functionalization or analogue generation. Simple, aqueous and direct cross-coupling of diverse and complex (hetero)aromatic halides and active pharmaceutical agents.![]()
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Affiliation(s)
- Sunil V Sharma
- School of Chemistry and BSRC, University of St Andrews St Andrews KY16 9ST UK
| | | | - Enrico Marelli
- School of Chemistry and BSRC, University of St Andrews St Andrews KY16 9ST UK
| | - Rebecca J M Goss
- School of Chemistry and BSRC, University of St Andrews St Andrews KY16 9ST UK
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8
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Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
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Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
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9
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Adamson CS, Chibale K, Goss RJM, Jaspars M, Newman DJ, Dorrington RA. Correction: Antiviral drug discovery: preparing for the next pandemic. Chem Soc Rev 2021; 50:9346. [PMID: 34346445 DOI: 10.1039/d1cs90064a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Antiviral drug discovery: preparing for the next pandemic' by Catherine S. Adamson et al., Chem. Soc. Rev., 2021, 50, 3647-3655, DOI: .
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Affiliation(s)
- Catherine S Adamson
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, Scotland, UK
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10
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Cartmell C, Abou Fayad A, Lynch R, Sharma SV, Hauck N, Gust B, Goss RJM. SynBio-SynChem Approaches to Diversifying the Pacidamycins through the Exploitation of an Observed Pictet-Spengler Reaction. Chembiochem 2021; 22:712-716. [PMID: 33058439 PMCID: PMC7898326 DOI: 10.1002/cbic.202000594] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/12/2020] [Indexed: 11/09/2022]
Abstract
A nonenzymatic Pictet-Spengler reaction has been postulated to give rise to a subset of naturally occurring uridyl peptide antibiotics (UPAs). Here, using a combination of strain engineering and synthetic chemistry, we demonstrate that Pictet-Spengler chemistry may be employed to generate even greater diversity in the UPAs. We use an engineered strain to afford access to meta-tyrosine containing pacidamycin 4. Pictet-Spengler diversification of this compound using a small series of aryl-aldehydes was achieved with some derivatives affording remarkable diastereomeric control.
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Affiliation(s)
- Christopher Cartmell
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
- Department of ChemistryUniversity of Prince Edward Island CharlottetownPrince Edward IslandC1A 4P3Canada
| | - Antoine Abou Fayad
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
- Department of Experimental Pathology, Immunology and Microbiology Faculty of Medicine. Center of Infectious Disease Research (CIDR) WHO Collaborating Center for Reference and Research on Bacterial PathogensAmerican University of BeirutRiad El-Solh/Beirut1107 2020Lebanon
| | - Rosemary Lynch
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
| | - Nils Hauck
- Pharmazeutische Biologie, Pharmazeutisches InstitutEberhard-Karls-UniversitätAuf der Morgenstelle 872076TübingenGermany
| | - Bertolt Gust
- Pharmazeutische Biologie, Pharmazeutisches InstitutEberhard-Karls-UniversitätAuf der Morgenstelle 872076TübingenGermany
| | - Rebecca J. M. Goss
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
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11
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Abstract
Clinically approved antiviral drugs are currently available for only 10 of the more than 220 viruses known to infect humans. The SARS-CoV-2 outbreak has exposed the critical need for compounds that can be rapidly mobilised for the treatment of re-emerging or emerging viral diseases, while vaccine development is underway. We review the current status of antiviral therapies focusing on RNA viruses, highlighting strategies for antiviral drug discovery and discuss the challenges, solutions and options to accelerate drug discovery efforts.
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Affiliation(s)
- Catherine S Adamson
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland, UK
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12
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Davis K, Gkotsi DS, Smith DRM, Goss RJM, Caputi L, O’Connor SE. Nicotiana benthamiana as a Transient Expression Host to Produce Auxin Analogs. Front Plant Sci 2020; 11:581675. [PMID: 33329644 PMCID: PMC7714751 DOI: 10.3389/fpls.2020.581675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/26/2020] [Indexed: 05/29/2023]
Abstract
Plant secondary metabolites have applications for the food, biofuel, and pharmaceutical industries. Recent advances in pathway elucidation and host expression systems now allow metabolic engineering of plant metabolic pathways to produce "new-to-nature" derivatives with novel biological activities, thereby amplifying the range of industrial uses for plant metabolites. Here we use a transient expression system in the model plant Nicotiana benthamiana to reconstitute the two-step plant-derived biosynthetic pathway for auxin (indole acetic acid) to achieve accumulation up to 500 ng/g fresh mass (FM). By expressing these plant-derived enzymes in combination with either bacterial halogenases and alternative substrates, we can produce both natural and new-to-nature halogenated auxin derivatives up to 990 ng/g FM. Proteins from the auxin synthesis pathway, tryptophan aminotransferases (TARs) and flavin-dependent monooxygenases (YUCs), could be transiently expressed in combination with four separate bacterial halogenases to generate halogenated auxin derivatives. Brominated auxin derivatives could also be observed after infiltration of the transfected N. benthamiana with potassium bromide and the halogenases. Finally, the production of additional auxin derivatives could also be achieved by co-infiltration of TAR and YUC genes with various tryptophan analogs. Given the emerging importance of transient expression in N. benthamiana for industrial scale protein and product expression, this work provides insight into the capacity of N. benthamiana to interface bacterial genes and synthetic substrates to produce novel halogenated metabolites.
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Affiliation(s)
- Katharine Davis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Danai S. Gkotsi
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Duncan R. M. Smith
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
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13
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Hao X, Yu J, Wang Y, Connolly JA, Liu Y, Zhang Y, Yu L, Cen S, Goss RJM, Gan M. Zelkovamycins B–E, Cyclic Octapeptides Containing Rare Amino Acid Residues from an Endophytic Kitasatospora sp. Org Lett 2020; 22:9346-9350. [DOI: 10.1021/acs.orglett.0c03565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Jiaqing Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
- School of Pharmacy, Jining Medical College, Jining, Shandong 276800, P. R. China
| | - Yujia Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Jack A. Connolly
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Yufeng Liu
- School of Pharmacy, Jining Medical College, Jining, Shandong 276800, P. R. China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
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14
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Michailidou F, Chung C, Brown MJB, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Corrigendum: Pac13 is a Small Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2020; 59:12573. [DOI: 10.1002/anie.202000990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Michailidou F, Chung C, Brown MJB, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Berichtigung: Pac13 is a Small Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Gkotsi DS, Ludewig H, Sharma SV, Connolly JA, Dhaliwal J, Wang Y, Unsworth WP, Taylor RJK, McLachlan MMW, Shanahan S, Naismith JH, Goss RJM. A marine viral halogenase that iodinates diverse substrates. Nat Chem 2019; 11:1091-1097. [PMID: 31611633 PMCID: PMC6875430 DOI: 10.1038/s41557-019-0349-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/09/2019] [Indexed: 11/23/2022]
Abstract
Oceanic cyanobacteria are the most abundant oxygen-generating phototrophs on our planet, and therefore, important to life. These organisms are infected by viruses called cyanophages, recently shown to encode metabolic genes that modulate host photosynthesis, phosphorus cycling and nucleotide metabolism. Herein, we report the characterisation of a wild type flavin-dependent viral halogenase (VirX1) from a cyanophage. Notably, halogenases have been previously associated with secondary metabolism, tailoring natural products. Exploration of this viral halogenase reveals it capable of regioselective halogenation of a diverse range of substrates, with a preference for forming aryl iodide species; this has potential implications for the metabolism of the infected host. Until recently, a flavin-dependent halogenase (FDH) capable of iodination in vitro had not been reported. VirX1 is interesting from a biocatalytic perspective showing strikingly broad substrate flexibility, and a clear preference for iodination, as illustrated by kinetic analysis. These factors together render it an attractive tool for synthesis.
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Affiliation(s)
- Danai S Gkotsi
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Hannes Ludewig
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Sunil V Sharma
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Jack A Connolly
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Jagwinder Dhaliwal
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | - Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK
| | | | | | - Matthew M W McLachlan
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, UK.,QEDDI, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen Shanahan
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, UK
| | - James H Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, UK.,Research Complex at Harwell, Rutherford Laboratory, Didcot, UK.,The Rosalind Franklin Institute, Didcot, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK. .,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK.
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17
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Bailey CS, Zarins-Tutt JS, Agbo M, Gao H, Diego-Taboada A, Gan M, Hamed RB, Abraham ER, Mackenzie G, Evans PA, Goss RJM. A natural solution to photoprotection and isolation of the potent polyene antibiotic, marinomycin A. Chem Sci 2019; 10:7549-7553. [PMID: 31588306 PMCID: PMC6761879 DOI: 10.1039/c9sc01375j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/20/2019] [Indexed: 01/07/2023] Open
Abstract
The photoprotection and isolation of marinomycin A using sporopollenin exine capsules (SpECs) derived from the spores of the plant Lycopodium clavatum is described. The marinomycins have a particularly short half-life in natural light, which severely impacts their potential biological utility given that they display potent antibiotic and anticancer activity. The SpEC encapsulation of the marinomycin A dramatically increases the half-life of the polyene macrodiolide to the direct exposure to UV radiation by several orders of magnitude, thereby making this a potentially useful strategy for other light sensitive bioactive agents. In addition, we report that the SpECs can also be used to selectively extract culture broths that contain the marinomycins, which provides a significantly higher recovery than with conventional XAD resins and provides concomitant photoprotection.
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Affiliation(s)
- Christopher S Bailey
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Joseph S Zarins-Tutt
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Matthias Agbo
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Hong Gao
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Alberto Diego-Taboada
- Department of Chemistry & Biochemistry , University of Hull , HU6 7RX , UK .
- Sporomex Ltd. , Medina House, 2 Station Avenue, East Yorkshire , Bridlington , YO16 4LZ , UK
| | - Maoluo Gan
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Refaat B Hamed
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Emily R Abraham
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - Grahame Mackenzie
- Department of Chemistry & Biochemistry , University of Hull , HU6 7RX , UK .
- Sporomex Ltd. , Medina House, 2 Station Avenue, East Yorkshire , Bridlington , YO16 4LZ , UK
| | - P Andrew Evans
- Department of Chemistry , Queen's University , 90 Bader Lane , Kingston , ON K7L 3N6 , Canada .
| | - Rebecca J M Goss
- Department of Chemistry , BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
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18
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Pubill‐Ulldemolins C, Sharma SV, Cartmell C, Zhao J, Cárdenas P, Goss RJM. Heck Diversification of Indole-Based Substrates under Aqueous Conditions: From Indoles to Unprotected Halo-tryptophans and Halo-tryptophans in Natural Product Derivatives. Chemistry 2019; 25:10866-10875. [PMID: 31125453 PMCID: PMC6772188 DOI: 10.1002/chem.201901327] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/21/2019] [Indexed: 12/17/2022]
Abstract
The blending of synthetic chemistry with biosynthetic processes provides a powerful approach to synthesis. Biosynthetic halogenation and synthetic cross-coupling have great potential to be used together, for small molecule generation, access to natural product analogues and as a tool for chemical biology. However, to enable enhanced generality of this approach, further synthetic tools are needed. Though considerable research has been invested in the diversification of phenylalanine and tyrosine, functionalisation of tryptophans thorough cross-coupling has been largely neglected. Tryptophan is a key residue in many biologically active natural products and peptides; in proteins it is key to fluorescence and dominates protein folding. To this end, we have explored the Heck cross-coupling of halo-indoles and halo-tryptophans in water, showing broad reaction scope. We have demonstrated the ability to use this methodology in the functionalisation of a brominated antibiotic (bromo-pacidamycin), as well as a marine sponge metabolite, barettin.
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Affiliation(s)
- Cristina Pubill‐Ulldemolins
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
- Present address: Department of ChemistrySchool of Life SciencesUniversity of SussexBrightonBN19QJUK
| | - Sunil V. Sharma
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | | | - Jinlian Zhao
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal ChemistryUppsala UniversityUppsala75123Sweden
| | - Rebecca J. M. Goss
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
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19
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Grüschow S, Sadler JC, Sharratt PJ, Goss RJM. Phenylalanine meta-Hydroxylase: A Single Residue Mediates Mechanistic Control of Aromatic Amino Acid Hydroxylation. Chembiochem 2019; 21:417-422. [PMID: 31318464 PMCID: PMC7027792 DOI: 10.1002/cbic.201900320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/15/2019] [Indexed: 01/31/2023]
Abstract
The rare nonproteinogenic amino acid, meta‐l‐tyrosine is biosynthetically intriguing. Whilst the biogenesis of tyrosine from phenylalanine is well characterised, the mechanistic basis for meta‐hydroxylation is unknown. Herein, we report the analysis of 3‐hydroxylase (Phe3H) from Streptomyces coeruleorubidus. Insights from kinetic analyses of the wild‐type enzyme and key mutants as well as of the biocatalytic conversion of synthetic isotopically labelled substrates and fluorinated substrate analogues advance understanding of the process by which meta‐hydroxylation is mediated, revealing T202 to play an important role. In the case of the WT enzyme, a deuterium label at the 3‐position is lost, whereas in in the T202A mutant 75 % retention is observed, with loss of stereospecificity. These data suggest that one of two possible mechanisms is at play; direct, enzyme‐catalysed deprotonation following electrophilic aromatic substitution or stereospecific loss of one proton after a 1,2‐hydride shift. Furthermore, our kinetic parameters for Phe3H show efficient regiospecific generation of meta‐l‐tyrosine from phenylalanine and demonstrate the enzyme's ability to regiospecifically hydroxylate unnatural fluorinated substrates.
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Affiliation(s)
- Sabine Grüschow
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
| | - Joanna C Sadler
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
| | - Peter J Sharratt
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
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20
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Renault YJG, Lynch R, Marelli E, Sharma SV, Pubill-Ulldemolins C, Sharp JA, Cartmell C, Cárdenas P, Goss RJM. Buchwald Hartwig diversification of unprotected halotryptophans, halotryptophan containing tripeptides and the natural product barettin in aqueous conditions. Chem Commun (Camb) 2019; 55:13653-13656. [DOI: 10.1039/c9cc02554e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Providing a tool to enhance natural product diversification, we report the first Buchwald Hartwig late stage modification in water of short peptides and the natural product barettin.
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Affiliation(s)
| | - Rosemary Lynch
- Department of Chemistry & BSRC University of St Andrews St Andrews
- UK
| | - Enrico Marelli
- Department of Chemistry & BSRC University of St Andrews St Andrews
- UK
| | - Sunil V. Sharma
- Department of Chemistry & BSRC University of St Andrews St Andrews
- UK
| | - Cristina Pubill-Ulldemolins
- Department of Chemistry & BSRC University of St Andrews St Andrews
- UK
- Department of Chemistry
- School of Life Sciences
- University of Sussex
| | - Joshua A. Sharp
- Department of Chemistry & BSRC University of St Andrews St Andrews
- UK
| | | | - Paco Cárdenas
- Department of Medicinal Chemistry
- Uppsala University
- Uppsala 75123
- Sweden
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21
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Pinedo C, Wright SAI, Collado IG, Goss RJM, Castoria R, Hrelia P, Maffei F, Durán-Patrón R. Isotopic Labeling Studies Reveal the Patulin Detoxification Pathway by the Biocontrol Yeast Rhodotorula kratochvilovae LS11. J Nat Prod 2018; 81:2692-2699. [PMID: 30460844 DOI: 10.1021/acs.jnatprod.8b00539] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Patulin (1) is a mycotoxin contaminant in fruit and vegetable products worldwide. Biocontrol agents, such as the yeast Rhodotorula kratochvilovae strain LS11, can reduce patulin (1) contamination in food. R. kratochvilovae LS11 converts patulin (1) into desoxypatulinic acid (DPA) (5), which is less cytotoxic than the mycotoxin (1) to in vitro human lymphocytes. In the present study, we report our investigations into the pathway of degradation of patulin (1) to DPA (5) by R. kratochvilovae. Isotopic labeling experiments revealed that 5 derives from patulin (1) through the hydrolysis of the γ-lactone ring and subsequent enzymatic modifications. The ability of patulin (1) and DPA (5) to cause genetic damage was also investigated by the cytokinesis-block micronucleus cytome assay on in vitro human lymphocytes. Patulin (1) was demonstrated to cause much higher chromosomal damage than DPA (5).
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Affiliation(s)
- Cristina Pinedo
- Departamento de Química Orgánica, Facultad de Ciencias , Universidad de Cádiz , Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, 11510 , Puerto Real , Cádiz , Spain
| | - Sandra A I Wright
- Section of Biology, Faculties of Health and Occupational Studies & Engineering and Sustainable Development , University of Gävle , 801 76 Gävle , Sweden
| | - Isidro G Collado
- Departamento de Química Orgánica, Facultad de Ciencias , Universidad de Cádiz , Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, 11510 , Puerto Real , Cádiz , Spain
| | - Rebecca J M Goss
- School of Chemistry, Biomedical Sciences Research Complex , University of St Andrews , Fife , Scotland KY169ST , United Kingdom
| | - Raffaello Castoria
- Dipartimento Agricoltura, Ambiente, Alimenti , Università degli Studi del Molise , Via F. De Sanctis snc , 86100 Campobasso , Italy
| | - Patrizia Hrelia
- Dipartimento di Farmacia e Biotecnologie , Alma Mater Studiorum-Università di Bologna , Via Irnerio, 48 , 40126 Bologna , Italy
| | - Francesca Maffei
- Dipartimento di Scienze per la Qualità della Vita , Alma Mater Studiorum-Università di Bologna , Campus Rimini, Corso D'Augusto 237 , 47921 Rimini , Italy
| | - Rosa Durán-Patrón
- Departamento de Química Orgánica, Facultad de Ciencias , Universidad de Cádiz , Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, 11510 , Puerto Real , Cádiz , Spain
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22
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Michailidou F, Chung CW, Brown MJB, Bent AF, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2017; 56:12492-12497. [PMID: 28786545 PMCID: PMC5656905 DOI: 10.1002/anie.201705639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/28/2017] [Indexed: 01/27/2023]
Abstract
The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.
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Affiliation(s)
- Freideriki Michailidou
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.,GSK, Stevenage, SG1 2NY, UK
| | | | | | - Andrew F Bent
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - James H Naismith
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | | | | | - Sunil V Sharma
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
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23
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Michailidou F, Chung C, Brown MJB, Bent AF, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Freideriki Michailidou
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
- GSK Stevenage SG1 2NY UK
| | | | | | - Andrew F. Bent
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - James H. Naismith
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | | | | | - Sunil V. Sharma
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Rebecca J. M. Goss
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
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24
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Sharma SV, Tong X, Pubill-Ulldemolins C, Cartmell C, Bogosyan EJA, Rackham EJ, Marelli E, Hamed RB, Goss RJM. Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo. Nat Commun 2017; 8:229. [PMID: 28794415 PMCID: PMC5550429 DOI: 10.1038/s41467-017-00194-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/07/2017] [Indexed: 01/21/2023] Open
Abstract
Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C–Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living cultures. Coupling synthetic biology and chemical reactions in cells is a challenging task. The authors engineer bacteria capable of generating bromo-metabolites, develop a mild Suzuki-Miyaura cross-coupling reaction compatible with cell growth and carry out the cross-coupling chemistry in live cell cultures.
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Affiliation(s)
- Sunil V Sharma
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Xiaoxue Tong
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Cristina Pubill-Ulldemolins
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Christopher Cartmell
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Emma J A Bogosyan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Analytical Development, GSK, Cobden Street, Montrose, Angus, DD10 8EA, UK
| | - Emma J Rackham
- School of Chemistry, University of East, Norwich, NR4 7TJ, UK.,School of Medicine, University of East Anglia, Bob Champion Research and Education Building, James Watson Road, Norwich, NR4 7UQ, UK
| | - Enrico Marelli
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Refaat B Hamed
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. .,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
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25
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Reed J, Stephenson MJ, Miettinen K, Brouwer B, Leveau A, Brett P, Goss RJM, Goossens A, O'Connell MA, Osbourn A. A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules. Metab Eng 2017; 42:185-193. [PMID: 28687337 PMCID: PMC5555447 DOI: 10.1016/j.ymben.2017.06.012] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/19/2017] [Accepted: 06/30/2017] [Indexed: 01/09/2023]
Abstract
Plants are an excellent source of drug leads. However availability is limited by access to source species, low abundance and recalcitrance to chemical synthesis. Although plant genomics is yielding a wealth of genes for natural product biosynthesis, the translation of this genetic information into small molecules for evaluation as drug leads represents a major bottleneck. For example, the yeast platform for artemisinic acid production is estimated to have taken >150 person years to develop. Here we demonstrate the power of plant transient transfection technology for rapid, scalable biosynthesis and isolation of triterpenes, one of the largest and most structurally diverse families of plant natural products. Using pathway engineering and improved agro-infiltration methodology we are able to generate gram-scale quantities of purified triterpene in just a few weeks. In contrast to heterologous expression in microbes, this system does not depend on re-engineering of the host. We next exploit agro-infection for quick and easy combinatorial biosynthesis without the need for generation of multi-gene constructs, so affording an easy entrée to suites of molecules, some new-to-nature, that are recalcitrant to chemical synthesis. We use this platform to purify a suite of bespoke triterpene analogs and demonstrate differences in anti-proliferative and anti-inflammatory activity in bioassays, providing proof of concept of this system for accessing and evaluating medicinally important bioactives. Together with new genome mining algorithms for plant pathway discovery and advances in plant synthetic biology, this advance provides new routes to synthesize and access previously inaccessible natural products and analogs and has the potential to reinvigorate drug discovery pipelines.
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Affiliation(s)
- James Reed
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Michael J Stephenson
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Karel Miettinen
- Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Bastiaan Brouwer
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Aymeric Leveau
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Rebecca J M Goss
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; School of Chemistry, University of St Andrews, KY16 9ST, UK
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Maria A O'Connell
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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26
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Smith DRM, Uria AR, Helfrich EJN, Milbredt D, van Pée KH, Piel J, Goss RJM. An Unusual Flavin-Dependent Halogenase from the Metagenome of the Marine Sponge Theonella swinhoei WA. ACS Chem Biol 2017; 12:1281-1287. [PMID: 28198609 DOI: 10.1021/acschembio.6b01115] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Uncultured bacteria from sponges have been demonstrated to be responsible for the generation of many potent, bioactive natural products including halogenated metabolites.1 The identification of gene clusters from the metagenomes of such bacterial communities enables the discovery of enzymes that mediate new and useful chemistries and allows insight to be gained into the biogenesis of potentially pharmacologically important natural products. Here we report a new pathway to the keramamides (krm); the first functional evidence for the existence of a distinct producer in the Theonella swinhoei WA chemotype is revealed, and a key enzyme on the pathway, a unique flavin-dependent halogenase with a broad substrate specificity, with potential as a useful new biocatalytic tool, is described.
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Affiliation(s)
- Duncan R. M. Smith
- School
of Chemistry, University of St Andrews, St Andrews KY16 9ST, United Kingdom
| | - Agustinus R. Uria
- Institute
of Microbiology, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Eric J. N. Helfrich
- Institute
of Microbiology, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | | | | | - Jörn Piel
- Institute
of Microbiology, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Rebecca J. M. Goss
- School
of Chemistry, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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27
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Marelli E, Renault Y, Sharma SV, Nolan SP, Goss RJM. Mild, Aqueous α-Arylation of Ketones: Towards New Diversification Tools for Halogenated Metabolites and Drug Molecules. Chemistry 2017; 23:3832-3836. [PMID: 28195381 DOI: 10.1002/chem.201700680] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 02/13/2017] [Indexed: 11/11/2022]
Abstract
The palladium-catalysed aqueous α-arylation of ketones was developed and tested for a large variety of reaction partners. These mild conditions enabled the coupling of aryl/alkyl-ketones with N-protected halotryptophans, heterocyclic haloarenes, and challenging base-sensitive compounds. The synthetic potential of this new methodology for the diversification of complex bioactive molecules was exemplified by derivatising prochlorperazine. The methodology is mild, aqueous and flexible, representing a means of functionalizing a wide range of halo-aromatics and therefore has the potential to be extended to complex molecule diversification.
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Affiliation(s)
- Enrico Marelli
- EaStCHEM, School of Chemistry and BSRC, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Yohann Renault
- EaStCHEM, School of Chemistry and BSRC, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Sunil V Sharma
- EaStCHEM, School of Chemistry and BSRC, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Steven P Nolan
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Inorganic and Physical Chemistry, Universiteit Gent, Krijgslaan 281-S3, 9000, Ghent, Belgium
| | - Rebecca J M Goss
- EaStCHEM, School of Chemistry and BSRC, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
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28
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Corr MJ, Sharma SV, Pubill-Ulldemolins C, Bown RT, Poirot P, Smith DRM, Cartmell C, Abou Fayad A, Goss RJM. Sonogashira diversification of unprotected halotryptophans, halotryptophan containing tripeptides; and generation of a new to nature bromo-natural product and its diversification in water. Chem Sci 2017; 8:2039-2046. [PMID: 28451322 PMCID: PMC5398305 DOI: 10.1039/c6sc04423a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/09/2016] [Indexed: 12/20/2022] Open
Abstract
The blending together of synthetic chemistry with natural product biosynthesis represents a potentially powerful approach to synthesis; to enable this, further synthetic tools and methodologies are needed. To this end, we have explored the first Sonogashira cross-coupling to halotryptophans in water. Broad reaction scope is demonstrated and we have explored the limits of the scope of the reaction. We have demonstrated this methodology to work excellently in the modification of model tripeptides. Furthermore, through precursor directed biosynthesis, we have generated for the first time a new to nature brominated natural product bromo-cystargamide, and demonstrated the applicability of our reaction conditions to modify this novel metabolite.
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Affiliation(s)
- M J Corr
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - S V Sharma
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - C Pubill-Ulldemolins
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - R T Bown
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - P Poirot
- Ecole Nationale Supérieure de Chimie de Lille , France
| | - D R M Smith
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - C Cartmell
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
| | - A Abou Fayad
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Microbial Natural Products (MINS) , Saarland University , E8.166123 Saarbrücken , Germany
| | - R J M Goss
- Department of Chemistry & BSRC , University of St Andrews , St Andrews , KY16 9ST , UK .
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29
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Zarins-Tutt JS, Abraham ER, Bailey CS, Goss RJM. Bluegenics: Bioactive Natural Products of Medicinal Relevance and Approaches to Their Diversification. Prog Mol Subcell Biol 2017; 55:159-186. [PMID: 28238038 DOI: 10.1007/978-3-319-51284-6_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] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nature provides a valuable resource of medicinally relevant compounds, with many antimicrobial and antitumor agents entering clinical trials being derived from natural products. The generation of analogues of these bioactive natural products is important in order to gain a greater understanding of structure activity relationships; probing the mechanism of action, as well as to optimise the natural product's bioactivity and bioavailability. This chapter critically examines different approaches to generating natural products and their analogues, exploring the way in which synthetic and biosynthetic approaches may be blended together to enable expeditious access to new designer natural products.
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Affiliation(s)
| | - Emily R Abraham
- School of Chemistry, University of St Andrews, St Andrews, Scotland, UK
| | | | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, St Andrews, Scotland, UK.
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30
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Tong X, Barberi TT, Botting CH, Sharma SV, Simmons MJH, Overton TW, Goss RJM. Rapid enzyme regeneration results in the striking catalytic longevity of an engineered, single species, biocatalytic biofilm. Microb Cell Fact 2016; 15:180. [PMID: 27769259 PMCID: PMC5073922 DOI: 10.1186/s12934-016-0579-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Engineering of single-species biofilms for enzymatic generation of fine chemicals is attractive. We have recently demonstrated the utility of an engineered Escherichia coli biofilm as a platform for synthesis of 5-halotryptophan. E. coli PHL644, expressing a recombinant tryptophan synthase, was employed to generate a biofilm. Its rapid deposition, and instigation of biofilm formation, was enforced by employing a spin-down method. The biofilm presents a large three-dimensional surface area, excellent for biocatalysis. The catalytic longevity of the engineered biofilm is striking, and we had postulated that this was likely to largely result from protection conferred to recombinant enzymes by biofilm's extracellular matrix. SILAC (stable isotopic labelled amino acids in cell cultures), and in particular dynamic SILAC, in which pulses of different isotopically labelled amino acids are administered to cells over a time course, has been used to follow the fate of proteins. To explore within our spin coated biofilm, whether the recombinant enzyme's longevity might be in part due to its regeneration, we introduced pulses of isotopically labelled lysine and phenylalanine into medium overlaying the biofilm and followed their incorporation over the course of biofilm development. RESULTS Through SILAC analysis, we reveal that constant and complete regeneration of recombinant enzymes occurs within spin coated biofilms. The striking catalytic longevity within the biofilm results from more than just simple protection of active enzyme by the biofilm and its associated extracellular matrix. The replenishment of recombinant enzyme is likely to contribute significantly to the catalytic longevity observed for the engineered biofilm system. CONCLUSIONS Here we provide the first evidence of a recombinant enzyme's regeneration in an engineered biofilm. The recombinant enzyme was constantly replenished over time as evidenced by dynamic SILAC, which suggests that the engineered E. coli biofilms are highly metabolically active, having a not inconsiderable energetic demand. The constant renewal of recombinant enzyme highlights the attractive possibility of utilising this biofilm system as a dynamic platform into which enzymes of interest can be introduced in a "plug-and-play" fashion and potentially be controlled through promoter switching for production of a series of desired fine chemicals.
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Affiliation(s)
- Xiaoxue Tong
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Tania Triscari Barberi
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Sunil V Sharma
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Mark J H Simmons
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B152TT, UK
| | - Tim W Overton
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B152TT, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK.
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31
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Ittiamornkul K, Zhu Q, Gkotsi DS, Smith DRM, Hillwig ML, Nightingale N, Goss RJM, Liu X. Promiscuous indolyl vinyl isonitrile synthases in the biogenesis and diversification of hapalindole-type alkaloids. Chem Sci 2015; 6:6836-6840. [PMID: 29861925 PMCID: PMC5947517 DOI: 10.1039/c5sc02919h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/03/2015] [Indexed: 12/02/2022] Open
Abstract
Promiscuous cis-indolyl vinyl isonitrile biosynthetic pathway allowed the preparatively useful generation of nine halosubstituted antibiotic analogues with increased lipophilicity.
The hapalindole-type alkaloids naturally show striking late stage diversification of what was believed to be a conserved intermediate, cis-indolyl vinyl isonitrile (1a). Here we demonstrate enzymatically, as well as through applying a synthetic biology approach, that the pathway generating 1a (itself, a potent natural broad-spectrum antibiotic) is also dramatically flexible. We harness this to enable early stage diversification of the natural product and generation of a wide range of halo-analogues of 1a. This approach allows the preparatively useful generation of a series of antibiotics with increased lipophilicity over that of the parent antibiotic.
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Affiliation(s)
- Kuljira Ittiamornkul
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA , USA 15260 . ; Tel: +1-412-624-6932
| | - Qin Zhu
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA , USA 15260 . ; Tel: +1-412-624-6932
| | - Danai S Gkotsi
- School of Chemistry and BSRC , University of St. Andrews , St. Andrews , KY16 9ST , U.K
| | - Duncan R M Smith
- School of Chemistry and BSRC , University of St. Andrews , St. Andrews , KY16 9ST , U.K
| | - Matthew L Hillwig
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA , USA 15260 . ; Tel: +1-412-624-6932
| | - Nicole Nightingale
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA , USA 15260 . ; Tel: +1-412-624-6932
| | - Rebecca J M Goss
- School of Chemistry and BSRC , University of St. Andrews , St. Andrews , KY16 9ST , U.K
| | - Xinyu Liu
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA , USA 15260 . ; Tel: +1-412-624-6932
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32
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Fayad AA, Pubill-Ulldemolins C, Sharma SV, Day D, Goss RJM. A One-Pot Synthesis of Symmetrical and Unsymmetrical Dipeptide Ureas. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Willemse T, Van Imp K, Goss RJM, Van Vlijmen HWT, Schepens W, Maes BUW, Ballet S. Inside Back Cover: Suzuki-Miyaura Diversification of Amino Acids and Dipeptides in Aqueous Media (ChemCatChem 14/2015). ChemCatChem 2015. [DOI: 10.1002/cctc.201500742] [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: 11/06/2022]
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34
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Willemse T, Van Imp K, Goss RJM, Van Vlijmen HWT, Schepens W, Maes BUW, Ballet S. Suzuki-Miyaura Diversification of Amino Acids and Dipeptides in Aqueous Media. ChemCatChem 2015. [DOI: 10.1002/cctc.201500190] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Rodolis MT, Mihalyi A, Ducho C, Eitel K, Gust B, Goss RJM, Bugg TDH. Mechanism of action of the uridyl peptide antibiotics: an unexpected link to a protein-protein interaction site in translocase MraY. Chem Commun (Camb) 2015; 50:13023-5. [PMID: 25222373 DOI: 10.1039/c4cc06516f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The pacidamycin and muraymycin uridyl peptide antibiotics show some structural resemblance to an Arg-Trp-x-x-Trp sequence motif for protein-protein interaction between bacteriophage ϕX174 protein E and E. coli translocase MraY. Members of the UPA class, and a synthetic uridine-peptide analogue, were found to show reduced levels of inhibition to F288L or E287A mutant MraY enzymes, implying that the UPAs interact at this extracellular site as part of the enzyme inhibition mechanism.
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Affiliation(s)
- Maria T Rodolis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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36
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Smith DRM, Willemse T, Gkotsi DS, Schepens W, Maes BUW, Ballet S, Goss RJM. The first one-pot synthesis of L-7-iodotryptophan from 7-iodoindole and serine, and an improved synthesis of other L-7-halotryptophans. Org Lett 2014; 16:2622-5. [PMID: 24805161 DOI: 10.1021/ol5007746] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A simple and scalable one-pot biotransformation enables direct access to L-halotryptophans, including L-7-iodotryptophan, from the corresponding haloindoles. The biotransformation utilizes an easy to prepare bacterial cell lysate that may be stored as the lyophilizate for several months and utilized as a catalyst as and when required.
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Affiliation(s)
- Duncan R M Smith
- School of Chemistry and BSRC, University of St. Andrews , St. Andrews, KY16 9ST, U.K
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37
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Gao H, Grüschow S, Barke J, Seipke RF, Hill LM, Orivel J, Yu DW, Hutchings M, Goss RJM. Filipins: the first antifungal “weed killers” identified from bacteria isolated from the trap-ant. RSC Adv 2014. [DOI: 10.1039/c4ra09875g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Allomerus ants cultivate fungus to fabricate their insect traps. Speculation is that the ants employ actinomycetes to help achieve fungal monoculture. From an associated actinomycete we identify the first antifungal compounds and encoding genes.
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Affiliation(s)
- Hong Gao
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Sabine Grüschow
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
| | - Jörg Barke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Ryan F. Seipke
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | | | - Jérôme Orivel
- CNRS
- UMR Ecologie des Forêts de Guyane
- Campus Agronomique
- 97379 Kourou Cedex, France
| | - Douglas W. Yu
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
| | - Matthew Hutchings
- School of Biological Sciences
- University of East Anglia
- Norwich, UK NR4 7TJ
| | - Rebecca J. M. Goss
- School of Chemistry
- University of St. Andrews
- St. Andrews, UK KY16 9ST
- School of Chemistry
- University of East Anglia
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38
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Owatworakit A, Townsend B, Louveau T, Jenner H, Rejzek M, Hughes RK, Saalbach G, Qi X, Bakht S, Roy AD, Mugford ST, Goss RJM, Field RA, Osbourn A. Glycosyltransferases from oat (Avena) implicated in the acylation of avenacins. J Biol Chem 2013; 288:3696-704. [PMID: 23258535 PMCID: PMC3567625 DOI: 10.1074/jbc.m112.426155] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 10/10/2012] [Revised: 12/18/2012] [Indexed: 11/06/2022] Open
Abstract
Plants produce a huge array of specialized metabolites that have important functions in defense against biotic and abiotic stresses. Many of these compounds are glycosylated by family 1 glycosyltransferases (GTs). Oats (Avena spp.) make root-derived antimicrobial triterpenes (avenacins) that provide protection against soil-borne diseases. The ability to synthesize avenacins has evolved since the divergence of oats from other cereals and grasses. The major avenacin, A-1, is acylated with N-methylanthranilic acid. Previously, we have cloned and characterized three genes for avenacin synthesis (for the triterpene synthase SAD1, a triterpene-modifying cytochrome P450 SAD2, and the serine carboxypeptidase-like acyl transferase SAD7), which form part of a biosynthetic gene cluster. Here, we identify a fourth member of this gene cluster encoding a GT belonging to clade L of family 1 (UGT74H5), and show that this enzyme is an N-methylanthranilic acid O-glucosyltransferase implicated in the synthesis of avenacin A-1. Two other closely related family 1 GTs (UGT74H6 and UGT74H7) are also expressed in oat roots. One of these (UGT74H6) is able to glucosylate both N-methylanthranilic acid and benzoic acid, whereas the function of the other (UGT74H7) remains unknown. Our investigations indicate that UGT74H5 is likely to be key for the generation of the activated acyl donor used by SAD7 in the synthesis of the major avenacin, A-1, whereas UGT74H6 may contribute to the synthesis of other forms of avenacin that are acylated with benzoic acid.
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Affiliation(s)
| | - Belinda Townsend
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom, and
| | | | - Helen Jenner
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom, and
| | - Martin Rejzek
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Richard K. Hughes
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Gerhard Saalbach
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Xiaoquan Qi
- From the Department of Metabolic Biology and
| | | | - Abhijeet Deb Roy
- the School of Chemical Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | | | - Rebecca J. M. Goss
- the School of Chemical Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Robert A. Field
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Tromans DR, Stevenson CEM, Goss RJM, Lawson DM. Crystallization and preliminary X-ray analysis of Pac17 from the pacidamycin-biosynthetic cluster of Streptomyces coeruleorubidus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:971-4. [PMID: 22869135 PMCID: PMC3412786 DOI: 10.1107/s1744309112029144] [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: 05/22/2012] [Accepted: 06/26/2012] [Indexed: 11/10/2022]
Abstract
Pac17 is an uncharacterized protein from the pacidamycin gene cluster of the soil bacterium Streptomyces coeruleorubidus. It is implicated in the biosynthesis of the core diaminobutyric acid residue of the antibiotic, although its precise role is uncertain at present. Given that pacidamycins inhibit translocase I of Pseudomonas aeruginosa, a clinically unexploited antibiotic target, they offer new hope in the search for antibacterial agents directed against this important pathogen. Crystals of Pac17 were grown by vapour diffusion and X-ray data were collected at a synchrotron to a resolution of 1.9 Å from a single crystal. The crystal belonged to space group C2, with unit-cell parameters a = 214.12, b = 70.88, c = 142.22 Å, β = 92.96°. Preliminary analysis of these data suggests that the asymmetric unit consists of one Pac17 homotetramer, with an estimated solvent content of 49.0%.
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Affiliation(s)
- Daniel R Tromans
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
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40
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Abstract
Natural product analogue generation is important, providing tools for chemical biology, enabling structure activity relationship determination and insight into the way in which natural products interact with their target biomolecules. The generation of analogues is also often necessary in order to improve bioavailability and to fine tune compounds' activity. This review provides an overview of the catalogue of approaches available for accessing series of analogues. Over the last few years there have been major advances in genome sequencing and the development of tools for biosynthetic pathway engineering; it is therefore becoming increasingly easy to combine molecular biology and synthetic organic chemistry in order to enable expeditious access to series of natural products. This review outlines the various ways of combining biology and chemistry that have been applied to analogue generation, drawing upon a series of examples to illustrate each approach.
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Affiliation(s)
- Rebecca J M Goss
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, UKNR4 7TJ
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41
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Winn M, Foulkes JM, Perni S, Simmons MJH, Overton TW, Goss RJM. Biofilms and their engineered counterparts: A new generation of immobilised biocatalysts. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20085f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Abstract
We describe methods used to isolate and identify antifungal compounds from actinomycete strains associated with the leaf-cutter ant Acromyrmex octospinosus. These ants use antibiotics produced by symbiotic actinomycete bacteria to protect themselves and their fungal cultivar against bacterial and fungal infections. The fungal cultivar serves as the sole food source for the ant colony, which can number up to tens of thousands of individuals. We describe how we isolate bacteria from leaf-cutter ants collected in Trinidad and analyze the antifungal compounds made by two of these strains (Pseudonocardia and Streptomyces spp.), using a combination of genome analysis, mutagenesis, and chemical isolation. These methods should be generalizable to a wide variety of insect-symbiont situations. Although more time consuming than traditional activity-guided fractionation methods, this approach provides a powerful technique for unlocking the complete biosynthetic potential of individual strains and for avoiding the problems of rediscovery of known compounds. We describe the discovery of a novel nystatin compound, named nystatin P1, and identification of the biosynthetic pathway for antimycins, compounds that were first described more than 60 years ago. We also report that disruption of two known antifungal pathways in a single Streptomyces strain has revealed a third, and likely novel, antifungal plus four more pathways with unknown products. This validates our approach, which clearly has the potential to identify numerous new compounds, even from well-characterized actinomycete strains.
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Affiliation(s)
- Ryan F Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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43
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Ragab AE, Grüschow S, Tromans DR, Goss RJM. Biogenesis of the Unique 4′,5′-Dehydronucleoside of the Uridyl Peptide Antibiotic Pacidamycin. J Am Chem Soc 2011; 133:15288-91. [DOI: 10.1021/ja206163j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Amany E. Ragab
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Sabine Grüschow
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Daniel R. Tromans
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Rebecca J. M. Goss
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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Seipke RF, Barke J, Brearley C, Hill L, Yu DW, Goss RJM, Hutchings MI. A single Streptomyces symbiont makes multiple antifungals to support the fungus farming ant Acromyrmex octospinosus. PLoS One 2011; 6:e22028. [PMID: 21857911 PMCID: PMC3153929 DOI: 10.1371/journal.pone.0022028] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [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: 04/21/2011] [Accepted: 06/13/2011] [Indexed: 11/18/2022] Open
Abstract
Attine ants are dependent on a cultivated fungus for food and use antibiotics produced by symbiotic Actinobacteria as weedkillers in their fungus gardens. Actinobacterial species belonging to the genera Pseudonocardia, Streptomyces and Amycolatopsis have been isolated from attine ant nests and shown to confer protection against a range of microfungal weeds. In previous work on the higher attine Acromyrmex octospinosus we isolated a Streptomyces strain that produces candicidin, consistent with another report that attine ants use Streptomyces-produced candicidin in their fungiculture. Here we report the genome analysis of this Streptomyces strain and identify multiple antibiotic biosynthetic pathways. We demonstrate, using gene disruptions and mass spectrometry, that this single strain has the capacity to make candicidin and multiple antimycin compounds. Although antimycins have been known for >60 years we report the sequence of the biosynthetic gene cluster for the first time. Crucially, disrupting the candicidin and antimycin gene clusters in the same strain had no effect on bioactivity against a co-evolved nest pathogen called Escovopsis that has been identified in ∼30% of attine ant nests. Since the Streptomyces strain has strong bioactivity against Escovopsis we conclude that it must make additional antifungal(s) to inhibit Escovopsis. However, candicidin and antimycins likely offer protection against other microfungal weeds that infect the attine fungal gardens. Thus, we propose that the selection of this biosynthetically prolific strain from the natural environment provides A. octospinosus with broad spectrum activity against Escovopsis and other microfungal weeds.
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Affiliation(s)
- Ryan F. Seipke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (RFS); (MIH)
| | - Jörg Barke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Charles Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Lionel Hill
- Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Douglas W. Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- State Key Laboratory of Genetic Resources, and Evolution, Ecology, Conservation, and Environment Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Rebecca J. M. Goss
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew I. Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (RFS); (MIH)
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Rackham EJ, Grüschow S, Goss RJM. Revealing the first uridyl peptide antibiotic biosynthetic gene cluster and probing pacidamycin biosynthesis. Bioeng Bugs 2011; 2:218-21. [PMID: 21829097 DOI: 10.4161/bbug.2.4.15877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
There is an urgent need for new antibiotics with resistance continuing to emerge toward existing classes. The pacidamycin antibiotics possess a novel scaffold and exhibit unexploited bioactivity rendering them attractive research targets. We recently reported the first identification of a biosynthetic cluster encoding uridyl peptide antibiotic assembly and the engineering of pacidamycin biosynthesis into a heterologous host. We report here our methods toward identifying the biosynthetic cluster. Our initial experiments employed conventional methods of probing a cosmid library using PCR and Southern blotting, however it became necessary to adopt a state-of-the-art genome scanning and in silico hybridization approach to pin point the cluster. Here we describe our "real" and "virtual" probing methods and contrast the benefits and pitfalls of each approach.
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Affiliation(s)
- Emma J Rackham
- School of Chemistry, University of East Anglia, Norwich, UK
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46
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Affiliation(s)
- Andreas N Tsoligkas
- School of Chemical Engineering, Birmingham University, Edgbaston, Birmingham, UK
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47
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Abstract
Saponins are polar molecules that consist of a triterpene or steroid aglycone with one or more sugar chains. They are one of the most numerous and diverse groups of plant natural products. These molecules have important ecological and agronomic functions, contributing to pest and pathogen resistance and to food quality in crop plants. They also have a wide range of commercial applications in the food, cosmetics and pharmaceutical sectors. Although primarily found in plants, saponins are produced by certain other organisms, including starfish and sea cucumbers. The under explored biodiversity of this class of natural products is likely to prove to be a vital resource for discovery of high-value compounds. This review will focus on the biological activity of some of the best-studied examples of saponins, on the relationship between structure and function, and on prospects for synthesis of ‘‘designer’’ saponins.
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Affiliation(s)
- Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, UK.
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48
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Oelke AJ, Antonietti F, Bertone L, Cranwell PB, France DJ, Goss RJM, Hofmann T, Knauer S, Moss SJ, Skelton PC, Turner RM, Wuitschik G, Ley SV. Total Synthesis of Chloptosin: A Dimeric Cyclohexapeptide. Chemistry 2011; 17:4183-94. [DOI: 10.1002/chem.201003216] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Indexed: 11/06/2022]
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49
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Grüschow S, Rackham EJ, Goss RJM. Diversity in natural product families is governed by more than enzyme promiscuity alone: establishing control of the pacidamycin portfolio. Chem Sci 2011. [DOI: 10.1039/c1sc00378j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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50
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Tate EW, Goss RJM. Highlights from the 46th EUCHEM Conference on stereochemistry, Bürgenstock, Switzerland, May 2011. Chem Commun (Camb) 2011; 47:10869-73. [DOI: 10.1039/c1cc90123k] [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: 11/21/2022]
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