1
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Bonifer C, Hanke W, Mühle J, Löhr F, Becker-Baldus J, Nagel J, Schertler GFX, Müller CE, König GM, Hilger D, Glaubitz C. Structural response of G protein binding to the cyclodepsipeptide inhibitor FR900359 probed by NMR spectroscopy. Chem Sci 2024; 15:12939-12956. [PMID: 39148790 PMCID: PMC11323312 DOI: 10.1039/d4sc01950d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/27/2024] [Indexed: 08/17/2024] Open
Abstract
The cyclodepsipeptide FR900359 (FR) and its analogs are able to selectively inhibit the class of Gq proteins by blocking GDP/GTP exchange. The inhibitor binding site of Gq has been characterized by X-ray crystallography, and various binding and functional studies have determined binding kinetics and mode of inhibition. Here we investigate isotope-labeled FR bound to the membrane-anchored G protein heterotrimer by solid-state nuclear magnetic resonance (ssNMR) and in solution by liquid-state NMR. The resulting data allowed us to identify regions of the inhibitor which show especially pronounced effects upon binding and revealed a generally rigid binding mode in the cis conformation under native-like conditions. The inclusion of the membrane environment allowed us to show a deep penetration of FR into the lipid bilayer illustrating a possible access mode of FR into the cell. Dynamic nuclear polarization (DNP)-enhanced ssNMR was used to observe the structural response of specific segments of the Gα subunit to inhibitor binding. This revealed rigidification of the switch I binding site and an allosteric response in the α5 helix as well as suppression of structural changes induced by nucleotide exchange due to inhibition by FR. Our NMR studies of the FR-G protein complex conducted directly within a native membrane environment provide important insights into the inhibitors access via the lipid membrane, binding mode, and structural allosteric effects.
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Affiliation(s)
- Christian Bonifer
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - Wiebke Hanke
- Institute for Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute Forschungsstr. 111, 5232 Villigen PSI Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - Johanna Becker-Baldus
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - Jessica Nagel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn An der Immenburg 4 53121 Bonn Germany
| | - Gebhard F X Schertler
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute Forschungsstr. 111, 5232 Villigen PSI Switzerland
| | - Christa E Müller
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn An der Immenburg 4 53121 Bonn Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Daniel Hilger
- Department of Pharmaceutical Chemistry, University of Marburg 35037 Marburg Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
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2
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Seidinger A, Roberts R, Bai Y, Müller M, Pfeil E, Matthey M, Rieck S, Alenfelder J, König GM, Pfeifer A, Kostenis E, Klinke A, Fleischmann BK, Wenzel D. Pharmacological Gq inhibition induces strong pulmonary vasorelaxation and reverses pulmonary hypertension. EMBO Mol Med 2024; 16:1930-1956. [PMID: 38977926 PMCID: PMC11319782 DOI: 10.1038/s44321-024-00096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 07/10/2024] Open
Abstract
Pulmonary arterial hypertension (PAH) is a life-threatening disease with limited survival. Herein, we propose the pharmacological inhibition of Gq proteins as a novel concept to counteract pulmonary vasoconstriction and proliferation/migration of pulmonary artery smooth muscle cells (PASMCs) in PAH. We demonstrate that the specific pan-Gq inhibitor FR900359 (FR) induced a strong vasorelaxation in large and small pulmonary arteries in mouse, pig, and human subjects ex vivo. Vasorelaxation by FR proved at least as potent as the currently used triple therapy. We also provide in vivo evidence that local pulmonary application of FR prevented right ventricular systolic pressure increase in healthy mice as well as in mice suffering from hypoxia (Hx)-induced pulmonary hypertension (PH). In addition, we demonstrate that chronic application of FR prevented and also reversed Sugen (Su)Hx-induced PH in mice. We also demonstrate that Gq inhibition reduces proliferation and migration of PASMCs in vitro. Thus, our work illustrates a dominant role of Gq proteins for pulmonary vasoconstriction as well as remodeling and proposes direct Gq inhibition as a powerful pharmacological strategy in PH.
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Affiliation(s)
- Alexander Seidinger
- Institute of Physiology, Department of Systems Physiology, Medical Faculty, Ruhr University of Bochum, Bochum, Germany
| | - Richard Roberts
- Pharmacology Research Group, University Hospital of Nottingham, Nottingham, UK
| | - Yan Bai
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - Marion Müller
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, University Hospital of the Ruhr University of Bochum, Bad Oeynhausen, Germany
- Agnes Wittenborg Institute for Translational Cardiovascular Research, Herz- und Diabeteszentrum NRW, University Hospital of the Ruhr University of Bochum, Bad Oeynhausen, Germany
| | - Eva Pfeil
- Molecular-, Cellular-, and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Michaela Matthey
- Institute of Physiology, Department of Systems Physiology, Medical Faculty, Ruhr University of Bochum, Bochum, Germany
| | - Sarah Rieck
- Institute of Physiology I, Life&Brain Center, Medical Faculty, University of Bonn, Bonn, Germany
| | - Judith Alenfelder
- Molecular-, Cellular-, and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Evi Kostenis
- Molecular-, Cellular-, and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Anna Klinke
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, University Hospital of the Ruhr University of Bochum, Bad Oeynhausen, Germany
- Agnes Wittenborg Institute for Translational Cardiovascular Research, Herz- und Diabeteszentrum NRW, University Hospital of the Ruhr University of Bochum, Bad Oeynhausen, Germany
| | - Bernd K Fleischmann
- Institute of Physiology I, Life&Brain Center, Medical Faculty, University of Bonn, Bonn, Germany
| | - Daniela Wenzel
- Institute of Physiology, Department of Systems Physiology, Medical Faculty, Ruhr University of Bochum, Bochum, Germany.
- Institute of Physiology I, Life&Brain Center, Medical Faculty, University of Bonn, Bonn, Germany.
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3
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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024; 41:1020-1059. [PMID: 38411572 PMCID: PMC11253845 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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4
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Berger T, Alenfelder J, Steinmüller S, Heimann D, Gohain N, Petras D, Wang M, Berger R, Kostenis E, Reher R. A MassQL-Integrated Molecular Networking Approach for the Discovery and Substructure Annotation of Bioactive Cyclic Peptides. JOURNAL OF NATURAL PRODUCTS 2024; 87:692-704. [PMID: 38385767 DOI: 10.1021/acs.jnatprod.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The marine sponge-derived fungus Stachylidium bicolor 293 K04 is a prolific producer of specialized metabolites, including certain cyclic tetrapeptides called endolides, which are characterized by the presence of the unusual amino acid N-methyl-3-(3-furyl)-alanine. This rare feature can be used as bait to detect new endolide-like analogs through customized fragment pattern searches of tandem mass spectrometry data using the Mass Spec Query Language (MassQL). Here, we integrate endolide-specific MassQL queries with molecular networking to obtain substructural information guiding the targeted isolation and structure elucidation of the new proline-containing endolides E (1) and F (2). We showed that endolide F (but not E) is a moderate antagonist of the arginine vasopressin V1A receptor, a member of the G protein-coupled receptor superfamily.
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Affiliation(s)
- Tim Berger
- Institute for Pharmaceutical Biology and Biotechnology, Department of Pharmacy, Philipps-University Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Judith Alenfelder
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
| | - Sophie Steinmüller
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
| | - Dominik Heimann
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Namrata Gohain
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Daniel Petras
- Interfaculty of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Mingxun Wang
- Department of Computer Science, University of California Riverside, Riverside, California 92507, United States
| | - Robert Berger
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Evi Kostenis
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology and Biotechnology, Department of Pharmacy, Philipps-University Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
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5
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Hashimoto T, Suenaga H, Amagai K, Hashimoto J, Kozone I, Takahashi S, Shin-Ya K. In Vitro Module Editing Of NRPS Enables Production Of Highly Potent G q -Signaling Inhibitor FR900359 Derived From Unculturable Plant Symbiont. Angew Chem Int Ed Engl 2024; 63:e202317805. [PMID: 38238265 DOI: 10.1002/anie.202317805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Indexed: 02/03/2024]
Abstract
Heterotrimeric G proteins are key mediators in the signaling of G protein-coupled receptors (GPCR) that are involved in a plethora of important physiological processes and thus major targets of pharmaceutical drugs. The cyclic depsipeptides YM-254890 and FR900359 are strong and selective inhibitors of the Gq subfamily of G proteins. FR900359 was first reported to be produced by unculturable plant symbiont, however, a culturable FR900359 producer was discovered recently by the standard strategy, screening of the producing strain from the environment. As another strategy, we introduce herein the different way to supply natural compounds of unculturable microorganism origin. We therefore embarked on constructing an artificial biosynthetic gene cluster (BGC) for FR900359 with YM-254890 BGC as a template using "in vitro module editing" technology, first developed for the modification of type-I PKS BGCs, to edit YM-254890 BGC. The resulting artificial BGCs coding FR900359 were heterologously expressed in the Pseudomonas putida KT2440 host strain.
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Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Keita Amagai
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
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6
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Wei D, Birla H, Dou Y, Mei Y, Huo X, Whitehead V, Osei-Owusu P, Feske S, Patafio G, Tao Y, Hu H. PGE2 Potentiates Orai1-Mediated Calcium Entry Contributing to Peripheral Sensitization. J Neurosci 2024; 44:e0329232023. [PMID: 37952941 PMCID: PMC10851687 DOI: 10.1523/jneurosci.0329-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Peripheral sensitization is one of the primary mechanisms underlying the pathogenesis of chronic pain. However, candidate molecules involved in peripheral sensitization remain incompletely understood. We have shown that store-operated calcium channels (SOCs) are expressed in the dorsal root ganglion (DRG) neurons. Whether SOCs contribute to peripheral sensitization associated with chronic inflammatory pain is elusive. Here we report that global or conditional deletion of Orai1 attenuates Complete Freund's adjuvant (CFA)-induced pain hypersensitivity in both male and female mice. To further establish the role of Orai1 in inflammatory pain, we performed calcium imaging and patch-clamp recordings in wild-type (WT) and Orai1 knockout (KO) DRG neurons. We found that SOC function was significantly enhanced in WT but not in Orai1 KO DRG neurons from CFA- and carrageenan-injected mice. Interestingly, the Orai1 protein level in L3/4 DRGs was not altered under inflammatory conditions. To understand how Orai1 is modulated under inflammatory pain conditions, prostaglandin E2 (PGE2) was used to sensitize DRG neurons. PGE2-induced increase in neuronal excitability and pain hypersensitivity was significantly reduced in Orai1 KO mice. PGE2-induced potentiation of SOC entry (SOCE) was observed in WT, but not in Orai1 KO DRG neurons. This effect was attenuated by a PGE2 receptor 1 (EP1) antagonist and mimicked by an EP1 agonist. Inhibition of Gq/11, PKC, or ERK abolished PGE2-induced SOCE increase, indicating PGE2-induced SOCE enhancement is mediated by EP1-mediated downstream cascade. These findings demonstrate that Orai1 plays an important role in peripheral sensitization. Our study also provides new insight into molecular mechanisms underlying PGE2-induced modulation of inflammatory pain.Significance Statement Store-operated calcium channel (SOC) Orai1 is expressed and functional in dorsal root ganglion (DRG) neurons. Whether Orai1 contributes to peripheral sensitization is unclear. The present study demonstrates that Orai1-mediated SOC function is enhanced in DRG neurons under inflammatory conditions. Global and conditional deletion of Orai1 attenuates complete Freund's adjuvant (CFA)-induced pain hypersensitivity. We also demonstrate that prostaglandin E2 (PGE2) potentiates SOC function in DRG neurons through EP1-mediated signaling pathway. Importantly, we have found that Orai1 deficiency diminishes PGE2-induced SOC function increase and reduces PGE2-induced increase in neuronal excitability and pain hypersensitivity. These findings suggest that Orai1 plays an important role in peripheral sensitization associated with inflammatory pain. Our study reveals a novel mechanism underlying PGE2/EP1-induced peripheral sensitization. Orai1 may serve as a potential target for pathological pain.
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Affiliation(s)
- Dongyu Wei
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - Hareram Birla
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
| | - Yannong Dou
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - Yixiao Mei
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
| | - Xiaodong Huo
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
| | - Victoria Whitehead
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
| | - Patrick Osei-Owusu
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
| | - Stefan Feske
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016
| | - Giovanna Patafio
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
| | - Yuanxiang Tao
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
| | - Huijuan Hu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
- Department of Anesthesiology, Rutgers New Jersey Medical School Newark, Newark, New Jersey 07103
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7
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Sawektreeratana N, Krachangchaeng C, Pittayanurak P, Betterley NM, Chairoungdua A, Wongpan A, Panvongsa W, Janthakit P, Nalaoh P, Promarak V, Nuntasaen N, Reutrakul V, Kuhakarn C, Hongthong S. Mallotumides A-C: Potent Cytotoxic Cycloheptapeptides from the Roots of Mallotus spodocarpus. Org Lett 2023; 25:8183-8187. [PMID: 37902783 DOI: 10.1021/acs.orglett.3c02641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
The structures of potent cytotoxic cycloheptapeptides, mallotumides A-C (1-3, respectively) isolated from the roots of Mallotus spodocarpus Airy Shaw, were elucidated by extensive spectroscopic analysis. The absolute configuration of 1 was determined by single-crystal X-ray crystallographic data. All three cycloheptapeptides exhibited potent cytotoxicity against various cancer cell lines with IC50 values ranging from 0.60 to 4.02 nM.
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Affiliation(s)
| | | | | | | | | | | | - Wittaya Panvongsa
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok 10400, Thailand
| | - Pattarapapa Janthakit
- Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Phattananawee Nalaoh
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Vinich Promarak
- Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | | | | | | | - Sakchai Hongthong
- Division of Chemistry, Faculty of Science and Technology, Rajabhat Rajanagarindra University, Chachoengsao 24000, Thailand
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8
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McAtamney A, Heaney C, Lizama-Chamu I, Sanchez LM. Reducing Mass Confusion over the Microbiome. Anal Chem 2023; 95:16775-16785. [PMID: 37934885 PMCID: PMC10841885 DOI: 10.1021/acs.analchem.3c02408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.
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Affiliation(s)
- Allyson McAtamney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Casey Heaney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Itzel Lizama-Chamu
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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9
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Hanke W, Alenfelder J, Liu J, Gutbrod P, Kehraus S, Crüsemann M, Dörmann P, Kostenis E, Scholz M, König GM. The Bacterial G q Signal Transduction Inhibitor FR900359 Impairs Soil-Associated Nematodes. J Chem Ecol 2023; 49:549-569. [PMID: 37453001 PMCID: PMC10725363 DOI: 10.1007/s10886-023-01442-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
The cyclic depsipeptide FR900359 (FR) is derived from the soil bacterium Chromobacterium vaccinii and known to bind Gq proteins of mammals and insects, thereby abolishing the signal transduction of their Gq protein-coupled receptors, a process that leads to severe physiological consequences. Due to their highly conserved structure, Gq family of proteins are a superior ecological target for FR producing organisms, resulting in a defense towards a broad range of harmful organisms. Here, we focus on the question whether bacteria like C. vaccinii are important factors in soil in that their secondary metabolites impair, e.g., plant harming organisms like nematodes. We prove that the Gq inhibitor FR is produced under soil-like conditions. Furthermore, FR inhibits heterologously expressed Gαq proteins of the nematodes Caenorhabditis elegans and Heterodera schachtii in the micromolar range. Additionally, in vivo experiments with C. elegans and the plant parasitic cyst nematode H. schachtii demonstrated that FR reduces locomotion of C. elegans and H. schachtii. Finally, egg-laying of C. elegans and hatching of juvenile stage 2 of H. schachtii from its cysts is inhibited by FR, suggesting that FR might reduce nematode dispersion and proliferation. This study supports the idea that C. vaccinii and its excreted metabolome in the soil might contribute to an ecological equilibrium, maintaining and establishing the successful growth of plants.
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Affiliation(s)
- Wiebke Hanke
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115, Bonn, Germany
| | - Judith Alenfelder
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115, Bonn, Germany
| | - Jun Liu
- Neural Information Flow, Max Planck Institute for Neurobiology of Behavior - CAESAR, Ludwig-Erhard-Allee 2, D-53175, Bonn, Germany
| | - Philipp Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, D-53115, Bonn, Germany
- Bonn International Graduate School - Land and Food, University of Bonn, Katzenburgweg 9, D-53115, Bonn, Germany
| | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115, Bonn, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115, Bonn, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115, Bonn, Germany
| | - Monika Scholz
- Neural Information Flow, Max Planck Institute for Neurobiology of Behavior - CAESAR, Ludwig-Erhard-Allee 2, D-53175, Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115, Bonn, Germany.
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10
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Johnson ET, Bowman MJ, Gomes RP, Carneiro LC, Dunlap CA. Identification of 2,4-diacetylphloroglucinol production in the genus Chromobacterium. Sci Rep 2023; 13:14292. [PMID: 37653049 PMCID: PMC10471698 DOI: 10.1038/s41598-023-41277-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023] Open
Abstract
The compound 2,4-diacetylphloroglucinol (DAPG) is a broad-spectrum antibiotic that is primarily produced by Pseudomonas spp. DAPG plays an important role in the biocontrol disease suppressing activity of Pseudomonas spp. In the current study, we report the discovery of the DAPG biosynthetic cluster in strains of Chromobacterium vaccinii isolated from Brazilian aquatic environments and the distribution of the biosynthetic cluster in the Chromobacterium genus. Phylogenetic analysis of the phlD protein suggests the biosynthetic cluster probably entered the genus of Chromobacterium after a horizontal gene transfer event with a member of the Pseudomonas fluorescens group. We were able to detect trace amounts of DAPG in wild type cultures and confirm the function of the cluster with heterologous expression in Escherichia coli. In addition, we identified and verified the presence of other secondary metabolites in these strains. We also confirmed the ability of C. vaccinii strains to produce bioactive pigment violacein and bioactive cyclic depsipeptide FR900359. Both compounds have been reported to have antimicrobial and insecticidal activities. These compounds suggest strains of C. vaccinii should be further explored for their potential as biocontrol agents.
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Affiliation(s)
- Eric T Johnson
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, 1815 North University St, Peoria, IL, 61604, USA
| | - Michael J Bowman
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 North University St, Peoria, IL, 61604, USA
| | - Raylane Pereira Gomes
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lilian Carla Carneiro
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Christopher A Dunlap
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, 1815 North University St, Peoria, IL, 61604, USA.
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11
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Murphy A, Corney M, Monson RE, Matilla MA, Salmond GPC, Leeper FJ. Biosynthesis of Antifungal Solanimycin May Involve an Iterative Nonribosomal Peptide Synthetase Module. ACS Chem Biol 2023; 18:1148-1157. [PMID: 37068480 PMCID: PMC10204066 DOI: 10.1021/acschembio.2c00947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Dickeya solani, a plant-pathogenic bacterium, produces solanimycin, a potent hybrid polyketide/nonribosomal peptide (PKS/NRPS) anti-fungal compound. The biosynthetic gene cluster responsible for synthesis of this compound has been identified. Because of instability, the complete structure of the compound has not yet been elucidated, but LC-MS2 identified that the cluster produces two main compounds, solanimycin A and B, differing by a single hydroxyl group. The fragmentation pattern revealed that the central part of solanimycin A is a hexapeptide, Gly-Dha-Dha-Dha-Dha-Dha (where Dha is dehydroalanine). This is supported by isotopic labeling studies using labeled serine and glycine. The N-terminal group is a polyketide-derived C16 acyl group containing a conjugated hexaene, a hydroxyl, and an amino group. The additional hydroxyl group in solanimycin B is on the α-carbon of the glycine residue. The incorporation of five sequential Dha residues is unprecedented because there is only one NRPS module in the cluster that is predicted to activate and attach serine (which is subsequently dehydrated to Dha), meaning that this NRPS module must act iteratively. While a few other iterative NRPS modules are known, they all involve iteration of two or three modules. We believe that the repetitive use of a single module makes the solanimycin biosynthetic pathway unique among NRPSs so far reported.
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Affiliation(s)
- Annabel
C. Murphy
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Matthew Corney
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Rita E. Monson
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - Miguel A. Matilla
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - George P. C. Salmond
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - Finian J. Leeper
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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12
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Voss JH, Crüsemann M, Bartling CR, Kehraus S, Inoue A, König GM, Strømgaard K, Müller CE. Structure-affinity and structure-residence time relationships of macrocyclic Gα q protein inhibitors. iScience 2023; 26:106492. [PMID: 37091255 PMCID: PMC10119753 DOI: 10.1016/j.isci.2023.106492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/02/2023] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
The macrocyclic depsipeptides YM-254890 (YM) and FR900359 (FR) are potent inhibitors of Gαq/11 proteins. They are important pharmacological tools and have potential as therapeutic drugs. The hydrogenated, tritium-labeled YM and FR derivatives display largely different residence times despite similar structures. In the present study we established a competition-association binding assay to determine the dissociation kinetics of unlabeled Gq protein inhibitors. Structure-affinity and structure-residence time relationships were analyzed. Small structural modifications had a large impact on residence time. YM and FR exhibited 4- to 10-fold higher residence times than their hydrogenated derivatives. While FR showed pseudo-irreversible binding, YM displayed much faster dissociation from its target. The isopropyl anchor present in FR and some derivatives was essential for slow dissociation. These data provide a basis for future drug design toward modulating residence times of macrocyclic Gq protein inhibitors, which has been recognized as a crucial determinant for therapeutic outcome.
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Affiliation(s)
- Jan H. Voss
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Christian R.O. Bartling
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Asuka Inoue
- Tohoku University, Graduate School of Pharmaceutical Sciences, Sendai, Miyagi 980-8578, Japan
| | - Gabriele M. König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Corresponding author
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13
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Danneels B, Blignaut M, Marti G, Sieber S, Vandamme P, Meyer M, Carlier A. Cyclitol metabolism is a central feature of Burkholderia leaf symbionts. Environ Microbiol 2023; 25:454-472. [PMID: 36451580 DOI: 10.1111/1462-2920.16292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.
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Affiliation(s)
- Bram Danneels
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Monique Blignaut
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Guillaume Marti
- Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UT3, INP, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Simon Sieber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Marion Meyer
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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14
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Danneels B, Carlier A. Whole-Genome Sequencing of Bacterial Endophytes From Fresh and Preserved Plant Specimens. Methods Mol Biol 2022; 2605:133-155. [PMID: 36520392 DOI: 10.1007/978-1-0716-2871-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many plants harbor symbiotic bacteria in their leaves, sometimes within structures visible with the naked eye. These bacteria play critical roles for host development and defense, but are often not amenable to culture. Gaining insight into the functions of these obligate endophytic bacteria hinges on culture-independent omics approaches, which have seen tremendous development in recent years. We describe in this chapter a set of protocols for the extraction and bioinformatic analysis of bacterial genomic DNA from leaf samples of various origins, including fresh, silica-preserved, or herbarium specimens.
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Affiliation(s)
- Bram Danneels
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.,CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Aurélien Carlier
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France. .,Laboratory of Microbiology, Ghent University, Ghent, Belgium.
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15
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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16
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Abstract
Hereditary symbioses have the potential to drive transgenerational effects, yet the mechanisms responsible for transmission of heritable plant symbionts are still poorly understood. The leaf symbiosis between Dioscorea sansibarensis and the bacterium Orrella dioscoreae offers an appealing model system to study how heritable bacteria are transmitted to the next generation. Here, we demonstrate that inoculation of apical buds with a bacterial suspension is sufficient to colonize newly formed leaves and propagules, and to ensure transmission to the next plant generation. Flagellar motility is not required for movement inside the plant but is important for the colonization of new hosts. Further, tissue-specific regulation of putative symbiotic functions highlights the presence of two distinct subpopulations of bacteria in the leaf gland and at the shoot meristem. We propose that bacteria in the leaf gland dedicate resources to symbiotic functions, while dividing bacteria in the shoot tip ensure successful colonization of meristematic tissue, glands, and propagules. Compartmentalization of intrahost populations together with tissue-specific regulation may serve as a robust mechanism for the maintenance of mutualism in leaf symbiosis.
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17
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Xiao Y, Zhang G, Yang Y, Feng J, Qiu S, Han Z, Geng J, Chen W. Molecular mechanism of acceptor selection in cyclodextrin glycosyltransferases catalyzed ginsenoside transglycosylation. Bioorg Chem 2022; 128:106094. [PMID: 35985160 DOI: 10.1016/j.bioorg.2022.106094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022]
Abstract
Understanding the mechanisms of enzyme specificity is increasingly important from a fundamental viewpoint and for practical applications. Transglycosylation has attracted many attentions due to its importance in improving the functional properties of acceptor substrates both in vivo and in vitro. Cyclodextrin glucanotransferase (CGTase) is one of the key enzymes in transglycosylation, it has a broad substrate spectrum and utilizes sugar as the donor. However, little is known about the acceptor selectivity of CGTase, which greatly hampers efforts toward the rational design of desirable transglycosylated derivatives. In this study, we found that the CGTase from Bacillus circulans, BcCGTase, was able to form glycosylated products with diverse ginsenosides. In particular, it not only carries out diverse mono-, di-, and even higher-order glycosylations via the transfer of glucose moieties to the COGlc positions, but also can glycosylate the C3-OH position of ginsenosides. In contrast, another CGTase from Bacillus licheniformis (BlCGTase) showed relatively specific acceptor preference with only several ginsenosides. Structural comparison between BcCGTase and BlCGTase revealed that the Arg74/K81 position within the acceptor-binding sites of BcCGTase/BlCGTase was responsible for the differences in catalytic specificity for ginsenoside F1. Further mutagenesis confirmed their roles in the acceptor selection. In conclusion, our study not only demonstrates the acceptor selectivity of CGTases, but also provides insight into the catalytic mechanism of CGTases, which will potentially increase the utility of CGTase for biosynthesis of new, rationally designed transglycosylated derivatives.
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Affiliation(s)
- Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guoning Zhang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yingbo Yang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Jiangsu Kanion Pharmaceutical Co., Ltd., Lianyungang 222000, China
| | - Jingxian Feng
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shi Qiu
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhuzhen Han
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiaran Geng
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai 200003, China.
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18
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Reher R, Aron AT, Fajtová P, Stincone P, Wagner B, Pérez-Lorente AI, Liu C, Shalom IYB, Bittremieux W, Wang M, Jeong K, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Scanlan JHW, Hochban PMM, Diederich WE, Molina-Santiago C, Romero D, Selim KA, Sass P, Brötz-Oesterhelt H, Hughes CC, Dorrestein PC, O'Donoghue AJ, Gerwick WH, Petras D. Native metabolomics identifies the rivulariapeptolide family of protease inhibitors. Nat Commun 2022; 13:4619. [PMID: 35941113 PMCID: PMC9358669 DOI: 10.1038/s41467-022-32016-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/12/2022] [Indexed: 11/15/2022] Open
Abstract
The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical activities is the compound purification needed for bioactivity assignments and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we develop a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectrometry. A native metabolomics screen for protease inhibitors from an environmental cyanobacteria community reveals 30 chymotrypsin-binding cyclodepsipeptides. Guided by the native metabolomics results, we select and purify five of these compounds for full structure elucidation via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy as well as evaluation of their biological activities. These results identify rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as a promising approach for drug discovery, chemical ecology, and chemical biology studies. Bioactivity-guided isolation of specialized metabolites is an iterative process. Here, the authors demonstrate a native metabolomics approach that allows for fast screening of complex metabolite extracts against a protein of interest and simultaneous structure annotation.
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Affiliation(s)
- Raphael Reher
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany.,Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Paolo Stincone
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Berenike Wagner
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Alicia I Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Chenxi Liu
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Ido Y Ben Shalom
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tuebingen, Tuebingen, Germany
| | - Marie L Matos-Hernandez
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico
| | - Kelsey L Alexander
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Eduardo J Caro-Diaz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico
| | - C Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - J H William Scanlan
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Phil M M Hochban
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Khaled A Selim
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Peter Sass
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,German Center for Infection Research, Partner Site Tuebingen, Tuebingen, Germany
| | - Chambers C Hughes
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,German Center for Infection Research, Partner Site Tuebingen, Tuebingen, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA.
| | - Daniel Petras
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA. .,Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany. .,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.
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19
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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20
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Chigumba DN, Mydy LS, de Waal F, Li W, Shafiq K, Wotring JW, Mohamed OG, Mladenovic T, Tripathi A, Sexton JZ, Kautsar S, Medema MH, Kersten RD. Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases. Nat Chem Biol 2022; 18:18-28. [PMID: 34811516 DOI: 10.1038/s41589-021-00892-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/02/2021] [Indexed: 12/28/2022]
Abstract
Many bioactive plant cyclic peptides form side-chain-derived macrocycles. Lyciumins, cyclic plant peptides with tryptophan macrocyclizations, are ribosomal peptides (RiPPs) originating from repetitive core peptide motifs in precursor peptides with plant-specific BURP (BNM2, USP, RD22 and PG1beta) domains, but the biosynthetic mechanism for their formation has remained unknown. Here, we characterize precursor-peptide BURP domains as copper-dependent autocatalytic peptide cyclases and use a combination of tandem mass spectrometry-based metabolomics and plant genomics to systematically discover five BURP-domain-derived plant RiPP classes, with mono- and bicyclic structures formed via tryptophans and tyrosines, from botanical collections. As BURP-domain cyclases are scaffold-generating enzymes in plant specialized metabolism that are physically connected to their substrates in the same polypeptide, we introduce a bioinformatic method to mine plant genomes for precursor-peptide-encoding genes by detection of repetitive substrate domains and known core peptide features. Our study sets the stage for chemical, biosynthetic and biological exploration of plant RiPP natural products from BURP-domain cyclases.
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Affiliation(s)
- Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Floris de Waal
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Wenjie Li
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Khadija Shafiq
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jesse W Wotring
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Osama G Mohamed
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Tim Mladenovic
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ashootosh Tripathi
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.,Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Satria Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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21
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Lapadula D, Benovic JL. Targeting Oncogenic Gα q/11 in Uveal Melanoma. Cancers (Basel) 2021; 13:6195. [PMID: 34944815 PMCID: PMC8699590 DOI: 10.3390/cancers13246195] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Uveal melanoma is the most common intraocular cancer in adults and arises from the transformation of melanocytes in the uveal tract. While treatment of the primary tumor is often effective, 36-50% of patients develop metastatic disease primarily to the liver. While various strategies have been used to treat the metastatic disease, there remain no effective treatments that improve survival. Significant insight has been gained into the pathways that are altered in uveal melanoma, with mutually exclusive activating mutations in the GNAQ and GNA11 genes being found in over 90% of patients. These genes encode the alpha subunits of the hetetrotrimeric G proteins, Gq and G11, and mutations result in activation of several important signaling pathways, including phospholipase C and activation of the transcription factor YAP. In this review, we discuss current efforts to target various signaling pathways in the treatment of uveal melanoma including recent efforts to target Gq and G11 in mouse models. While selective targeting of Gq and G11 provides a potential therapeutic strategy to treat uveal melanoma, it is evident that improved inhibitors and methods of delivery are needed.
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Affiliation(s)
| | - Jeffrey L. Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA;
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22
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Pistorius D, Buntin K, Weber E, Richard E, Bouquet C, Wollbrett S, Regenass H, Peón V, Böhm M, Kessler R, Gempeler T, Haberkorn A, Wimmer L, Lanshoeft C, Davis J, Hainzl D, D'Alessio JA, Manchado E, Petersen F. Promoter-Driven Overexpression in Chromobacterium vaccinii Facilitates Access to FR900359 and Yields Novel Low Abundance Analogs. Chemistry 2021; 28:e202103888. [PMID: 34878202 DOI: 10.1002/chem.202103888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Indexed: 11/11/2022]
Abstract
Access to the cyclic depsipeptide FR900359 (FR), a selective Gq/11 protein inhibitor of high pharmacological interest and a potential lead molecule for targeted therapy of cancers with oncogenic GNAQ or GNA11 mutations (encoding Gq and G11 respectively), has been challenging ever since its initial discovery more than three decades ago. The recent discovery of Chromobacterium vaccinii as a cultivable FR producer enables the development of approaches leading to a high-yielding, scalable and sustainable biotechnological process for production of FR, thereby removing this bottleneck. Here we characterize different promoters in exchange of the native promoter of the FR assembly line, resulting in an overexpression mutant with significantly increased production of FR. Thereby, the isolation and structure elucidation of novel FR analogs of low abundance is enabled. Further, we explore the antiproliferative activities of fifteen chromodepsins against uveal melanoma cell lines harboring Gq/11 mutations and characterize the major metabolite of FR formed in plasma.
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Affiliation(s)
- Dominik Pistorius
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Kathrin Buntin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Eric Weber
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Etienne Richard
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Caroline Bouquet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Séverine Wollbrett
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Hugo Regenass
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Victor Peón
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Marcel Böhm
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Régis Kessler
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Thomas Gempeler
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Anne Haberkorn
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Laurin Wimmer
- Chemical & Analytical Development, Technical Research & Development, Global Drug Development, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Christian Lanshoeft
- Pharmakokinetic Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - John Davis
- Pharmacokinetic Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, 250 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Dominik Hainzl
- Pharmacokinetic Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, 250 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Joseph Anthony D'Alessio
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Novartis Pharma AG, 250 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Eusebio Manchado
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Frank Petersen
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
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23
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Klöppel S, Richarz R, Wirtz DA, Vasenda N, König GM, Crüsemann M. A Specialized Dehydrogenase Provides l-Phenyllactate for FR900359 Biosynthesis. Chembiochem 2021; 23:e202100569. [PMID: 34846772 PMCID: PMC9299796 DOI: 10.1002/cbic.202100569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Indexed: 11/30/2022]
Abstract
d‐Phenyllactate (PLA) is a component of the selective Gq protein inhibitor and nonribosomal cyclic depsipeptide FR900359 (FR). Here we report a detailed biochemical investigation of pla biosynthesis and its incorporation into the natural product FR. The enzyme FrsC, member of the lactate/malate dehydrogenase superfamily, was shown to catalyze the formation of l‐PLA from phenylpyruvate. FrsC was kinetically characterized and its substrate specificity determined. Incorporation of l‐PLA was probed by assaying the adenylation domain FrsE‐A3 and feeding studies with a Chromobacterium vaccinii ΔfrsC mutant, confirming preferred activation of l‐PLA followed by on‐line epimerization to d‐pla. Finally, detailed bioinformatic analyses of FrsC revealed its close relation to malate dehydrogenases from primary metabolism and suggest extensions in the substrate binding loop to be responsible for its adaptation to accepting larger aromatic substrates with high specificity.
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Affiliation(s)
- Sophie Klöppel
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - René Richarz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Daniel A Wirtz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Natalia Vasenda
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
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24
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Robinson SL, Piel J, Sunagawa S. A roadmap for metagenomic enzyme discovery. Nat Prod Rep 2021; 38:1994-2023. [PMID: 34821235 PMCID: PMC8597712 DOI: 10.1039/d1np00006c] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
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Affiliation(s)
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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25
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Schindler F, Fragner L, Herpell JB, Berger A, Brenner M, Tischler S, Bellaire A, Schönenberger J, Li W, Sun X, Schinnerl J, Brecker L, Weckwerth W. Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata. Front Mol Biosci 2021; 8:683671. [PMID: 34395523 PMCID: PMC8362603 DOI: 10.3389/fmolb.2021.683671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.
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Affiliation(s)
- Florian Schindler
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Johannes B Herpell
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Andreas Berger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Martin Brenner
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.,Department of Pharmaceutical Sciences/Pharmacognosy, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Sonja Tischler
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Anke Bellaire
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Weimin Li
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Xiaoliang Sun
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Johann Schinnerl
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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26
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Hanke W, Patt J, Alenfelder J, Voss JH, Zdouc MM, Kehraus S, Kim JB, Grujičić GV, Namasivayam V, Reher R, Müller CE, Kostenis E, Crüsemann M, König GM. Feature-Based Molecular Networking for the Targeted Identification of G q-Inhibiting FR900359 Derivatives. JOURNAL OF NATURAL PRODUCTS 2021; 84:1941-1953. [PMID: 34197116 DOI: 10.1021/acs.jnatprod.1c00194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Both the soil bacterium Chromobacterium vaccinii and the bacterial endosymbiont Candidatus Burkholderia crenata of the plant Ardisia crenata are producers of FR900359 (FR). This cyclic depsipeptide is a potent and selective Gq protein inhibitor used extensively to investigate the intracellular signaling of G protein coupled receptors (GPCRs). In this study, the metabolomes of both FR producers were investigated and compared using feature-based molecular networking (FBMN). As a result, 30 previously unknown FR derivatives were identified, one-third being unique to C. vaccinii. Guided by MS, a novel FR derivative, FR-6 (compound 1), was isolated, and its structure unambiguously established. In a whole-cell biosensing assay based on detection of dynamic mass redistribution (DMR) as readout for Gq inhibition, FR-6 suppressed Gq signaling with micromolar potency (pIC50 = 5.56). This functional activity was confirmed in radioligand binding assays (pKi = 7.50). This work demonstrates the power of molecular networking, guiding the way to a novel Gq-inhibiting FR derivative and underlining the potency of FR as a Gq inhibitor.
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Affiliation(s)
- Wiebke Hanke
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Julian Patt
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Judith Alenfelder
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Jan H Voss
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Mitja M Zdouc
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Jung Bong Kim
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Goran V Grujičić
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Raphael Reher
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Evi Kostenis
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
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27
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Hermes C, König GM, Crüsemann M. The chromodepsins - chemistry, biology and biosynthesis of a selective Gq inhibitor natural product family. Nat Prod Rep 2021; 38:2276-2292. [PMID: 33998635 DOI: 10.1039/d1np00005e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to April 2021The bacterial cyclic depsipeptides FR900359 (FR) and YM-254890 (YM) were shown to selectively inhibit Gαq proteins with high potency and selectivity and have recently emerged as valuable pharmacological tools due to their effective mechanism of action. Here, we summarize important aspects of this small and specialized natural product family, for which we propose the name chromodepsins, starting from their discovery, producing organisms and structural variety. We then review biosynthesis, structure-activity relationships and ecological and evolutionary aspects of the chromodepsins. Lastly, we discuss their mechanism of action, potential medicinal applications and future opportunities and challenges for further use and development of these complex inhibitor molecules from nature.
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Affiliation(s)
- Cornelia Hermes
- Institute of Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany.
| | - Gabriele M König
- Institute of Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany.
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany.
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28
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Wuisan ZG, Kresna IDM, Böhringer N, Lewis K, Schäberle TF. Optimization of heterologous Darobactin A expression and identification of the minimal biosynthetic gene cluster. Metab Eng 2021; 66:123-136. [PMID: 33872780 DOI: 10.1016/j.ymben.2021.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/11/2021] [Indexed: 10/21/2022]
Abstract
Darobactin A (DAR) is a ribosomally synthesized and post-translationally modified peptide (RiPP) antibiotic, which was initially identified from bacteria belonging to the genus Photorhabdus. In addition, the corresponding biosynthetic gene cluster (BGC) was identified and subsequently detected in several bacteria genera. DAR represents a highly promising lead structure for the development of novel antibacterial therapeutic agents. It targets the outer membrane protein BamA and is therefore specific for Gram-negative bacteria. This, together with the convincing in vivo activities in mouse infection models, makes it a particular promising candidate for further research. To improve compound supply for further investigation of DAR and to enable production of novel derivatives, establishment of an efficient and versatile microbial production platform for these class of RiPP antibiotics is highly desirable. Here we describe design and construction of a heterologous production and engineering platform for DAR, which will ensure production yield and facilitates structure modification approaches. The known Gram-negative workhorses Escherichia coli and Vibrio natriegens were tested as heterologous hosts. In addition to that, DAR producer strains were generated and optimization of the expression constructs yielded production titers of DAR showing around 10-fold increase and 5-fold decrease in fermentation time compared to the original product description. We also report the identification of the minimal DAR BGC, since only two genes were necessary for heterologous production of the RiPP.
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Affiliation(s)
- Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
| | - I Dewa M Kresna
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, MA, USA, 02115
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany; Branch for Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, 35394, Giessen, Germany; German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany.
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29
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Ge Y, Shi S, Deng JJ, Chen XP, Song Z, Liu L, Lou L, Zhang X, Xiong XF. Design, Synthesis, and Evaluation of Small Molecule Gαq/11 Protein Inhibitors for the Treatment of Uveal Melanoma. J Med Chem 2021; 64:3131-3152. [PMID: 33715360 DOI: 10.1021/acs.jmedchem.0c01977] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Uveal melanoma is the ocular malignancy and mainly driven by oncogenic mutations of Gαq/11 proteins. Previous targeted therapy for melanoma treatment was limited to specific downstream signaling pathway, and inhibiting the "molecular switches" G proteins for melanoma treatment therapy was rarely described. We herein report the discovery of imidazopiperazine derivatives as Gαq/11 protein inhibitors. The most promising compound GQ127 showed good efficacy and safety in inositol monophosphate (IP1) assay by directly inhibiting Gαq/11 proteins. GQ127 induced uveal melanoma cells apoptosis and displayed potent antitumor activities in uveal melanoma cells viability, migration, and invasion. The effects of GQ127 on Gαq/11 signaling pathway were confirmed by analyzing the downstream effectors yes-associated protein (YAP) and extracellular signal-regulated kinase (ERK). More importantly, GQ127 significantly suppressed UM xenograft growth in mouse model without severe toxicity at the testing dose. These findings provide a lead compound that directly targets the Gαq/11 proteins for uveal melanoma treatment.
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Affiliation(s)
- Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Shuo Shi
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Jun-Jie Deng
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Xue-Ping Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Zhendong Song
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Lu Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Linlin Lou
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Xiaolei Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
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30
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Patt J, Alenfelder J, Pfeil EM, Voss JH, Merten N, Eryilmaz F, Heycke N, Rick U, Inoue A, Kehraus S, Deupi X, Müller CE, König GM, Crüsemann M, Kostenis E. An experimental strategy to probe Gq contribution to signal transduction in living cells. J Biol Chem 2021; 296:100472. [PMID: 33639168 PMCID: PMC8024710 DOI: 10.1016/j.jbc.2021.100472] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Heterotrimeric G protein subunits Gαq and Gα11 are inhibited by two cyclic depsipeptides, FR900359 (FR) and YM-254890 (YM), both of which are being used widely to implicate Gq/11 proteins in the regulation of diverse biological processes. An emerging major research question therefore is whether the cellular effects of both inhibitors are on-target, that is, mediated via specific inhibition of Gq/11 proteins, or off-target, that is, the result of nonspecific interactions with other proteins. Here we introduce a versatile experimental strategy to discriminate between these possibilities. We developed a Gαq variant with preserved catalytic activity, but refractory to FR/YM inhibition. A minimum of two amino acid changes were required and sufficient to achieve complete inhibitor resistance. We characterized the novel mutant in HEK293 cells depleted by CRISPR–Cas9 of endogenous Gαq and Gα11 to ensure precise control over the Gα-dependent cellular signaling route. Using a battery of cellular outcomes with known and concealed Gq contribution, we found that FR/YM specifically inhibited cellular signals after Gαq introduction via transient transfection. Conversely, both inhibitors were inert across all assays in cells expressing the drug-resistant variant. These findings eliminate the possibility that inhibition of non-Gq proteins contributes to the cellular effects of the two depsipeptides. We conclude that combined application of FR or YM along with the drug-resistant Gαq variant is a powerful in vitro strategy to discern on-target Gq against off-target non-Gq action. Consequently, it should be of high value for uncovering Gq input to complex biological processes with high accuracy and the requisite specificity.
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Affiliation(s)
- Julian Patt
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Judith Alenfelder
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Eva Marie Pfeil
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Jan Hendrik Voss
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Nicole Merten
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Funda Eryilmaz
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Nina Heycke
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Uli Rick
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Xavier Deupi
- Laboratory of Biomolecular Research and Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
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Hermes C, Richarz R, Wirtz DA, Patt J, Hanke W, Kehraus S, Voß JH, Küppers J, Ohbayashi T, Namasivayam V, Alenfelder J, Inoue A, Mergaert P, Gütschow M, Müller CE, Kostenis E, König GM, Crüsemann M. Thioesterase-mediated side chain transesterification generates potent Gq signaling inhibitor FR900359. Nat Commun 2021; 12:144. [PMID: 33420046 PMCID: PMC7794379 DOI: 10.1038/s41467-020-20418-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
The potent and selective Gq protein inhibitor depsipeptide FR900359 (FR), originally discovered as the product of an uncultivable plant endosymbiont, is synthesized by a complex biosynthetic system comprising two nonribosomal peptide synthetase (NRPS) assembly lines. Here we characterize a cultivable bacterial FR producer, enabling detailed investigations into biosynthesis and attachment of the functionally important FR side chain. We reconstitute side chain assembly by the monomodular NRPS FrsA and the non-heme monooxygenase FrsH, and characterize intermolecular side chain transesterification to the final macrocyclic intermediate FR-Core, mediated by the FrsA thioesterase domain. We harness FrsA substrate promiscuity to generate FR analogs with altered side chains and demonstrate indispensability of the FR side chain for efficient Gq inhibition by comparative bioactivity, toxicity and docking studies. Finally, evolution of FR and side chain biosynthesis is discussed based on bioinformatics analyses. Side chain transesterification boosts potency and target affinity of selective Gq inhibitor natural products. FR900359 (FR) is a Gq protein inhibitor depsipeptide isolated from an uncultivable plant endosymbiont and synthesized by non-ribosomal peptide synthetases. Here, the authors discover a cultivable bacterial FR producer and show that FrsA thioesterase domain catalyses intermolecular transesterification of the FR side chain to the depsipeptide core during biosynthesis, improving Gq inhibition properties.
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Affiliation(s)
- Cornelia Hermes
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - René Richarz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Daniel A Wirtz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Julian Patt
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Wiebke Hanke
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Jan Hendrik Voß
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jim Küppers
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Tsubasa Ohbayashi
- University of Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Avenue de la Terrasse, Gif-sur-Yvette, 91198, France.,Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Judith Alenfelder
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Peter Mergaert
- University of Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Avenue de la Terrasse, Gif-sur-Yvette, 91198, France
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Evi Kostenis
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany.
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Boesgaard MW, Harpsøe K, Malmberg M, Underwood CR, Inoue A, Mathiesen JM, König GM, Kostenis E, Gloriam DE, Bräuner-Osborne H. Delineation of molecular determinants for FR900359 inhibition of G q/11 unlocks inhibition of Gα s. J Biol Chem 2020; 295:13850-13861. [PMID: 32753482 DOI: 10.1074/jbc.ra120.013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/31/2020] [Indexed: 12/28/2022] Open
Abstract
Heterotrimeric G proteins are essential mediators of intracellular signaling of G protein-coupled receptors. The Gq/11 subfamily consists of Gq, G11, G14, and G16 proteins, of which all but G16 are inhibited by the structurally related natural products YM-254890 and FR900359. These inhibitors act by preventing the GDP/GTP exchange, which is necessary for activation of all G proteins. A homologous putative binding site for YM-254890/FR900359 can also be found in members of the other three G protein families, Gs, Gi/o, and G12/13, but none of the published analogs of YM-254890/FR900359 have shown any inhibitory activity for any of these. To explain why the YM-254890/FR900359 scaffold only inhibits Gq/11/14, the present study delineated the molecular selectivity determinants by exchanging amino acid residues in the YM-254890/FR900359-binding site in Gq and Gs We found that the activity of a Gs mutant with a Gq-like binding site for YM-254890/FR900359 can be inhibited by FR900359, and a minimum of three mutations are necessary to introduce inhibition in Gs In all, this suggests that although the YM-254890/FR900359 scaffold has proven unsuccessful to derive Gs, Gi/o, and G12/13 inhibitors, the mechanism of inhibition between families of G proteins is conserved, opening up the possibility of targeting by other, novel inhibitor scaffolds. In lack of a selective Gαs inhibitor, FR900359-sensitive Gαs mutants may prove useful in studies where delicate control over Gαs signaling would be of the essence.
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Affiliation(s)
- Michael W Boesgaard
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michelle Malmberg
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina R Underwood
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Asuka Inoue
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Jesper M Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Evi Kostenis
- Molecular, Cellular, and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - David E Gloriam
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Bhattarai K, Bastola R, Baral B. Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance. ADVANCES IN GENETICS 2020; 105:229-292. [PMID: 32560788 DOI: 10.1016/bs.adgen.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.
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Affiliation(s)
- Keshab Bhattarai
- University of Tübingen, Tübingen, Germany; Center for Natural and Applied Sciences (CENAS), Kathmandu, Nepal
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal.
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34
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Abstract
Heterotrimeric G proteins are the core upstream elements that transduce and amplify the cellular signals from G protein-coupled receptors (GPCRs) to intracellular effectors. GPCRs are the largest family of membrane proteins encoded in the human genome and are the targets of about one-third of prescription medicines. However, to date, no single therapeutic agent exerts its effects via perturbing heterotrimeric G protein function, despite a plethora of evidence linking G protein malfunction to human disease. Several recent studies have brought to light that the Gq family-specific inhibitor FR900359 (FR) is unexpectedly efficacious in silencing the signaling of Gq oncoproteins, mutant Gq variants that mostly exist in the active state. These data not only raise the hope that researchers working in drug discovery may be able to potentially strike Gq oncoproteins from the list of undruggable targets, but also raise questions as to how FR achieves its therapeutic effect. Here, we place emphasis on these recent studies and explain why they expand our pharmacological armamentarium for targeting Gq protein oncogenes as well as broaden our mechanistic understanding of Gq protein oncogene function. We also highlight how this novel insight impacts the significance and utility of using G(q) proteins as targets in drug discovery efforts.
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Affiliation(s)
- Evi Kostenis
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany.
| | - Eva Marie Pfeil
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
| | - Suvi Annala
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
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Kuschak M, Namasivayam V, Rafehi M, Voss JH, Garg J, Schlegel JG, Abdelrahman A, Kehraus S, Reher R, Küppers J, Sylvester K, Hinz S, Matthey M, Wenzel D, Fleischmann BK, Pfeifer A, Inoue A, Gütschow M, König GM, Müller CE. Cell-permeable high-affinity tracers for G q proteins provide structural insights, reveal distinct binding kinetics and identify small molecule inhibitors. Br J Pharmacol 2020; 177:1898-1916. [PMID: 31881095 PMCID: PMC7070167 DOI: 10.1111/bph.14960] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 11/26/2019] [Accepted: 12/01/2019] [Indexed: 12/13/2022] Open
Abstract
Background and Purpose G proteins are intracellular switches that transduce and amplify extracellular signals from GPCRs. The Gq protein subtypes, which are coupled to PLC activation, can act as oncogenes, and their expression was reported to be up‐regulated in cancer and inflammatory diseases. Gq inhibition may be an efficient therapeutic strategy constituting a new level of intervention. However, diagnostic tools and therapeutic drugs for Gq proteins are lacking. Experimental Approach We have now developed Gq‐specific, cell‐permeable 3H‐labelled high‐affinity probes based on the macrocyclic depsipeptides FR900359 (FR) and YM‐254890 (YM). The tracers served to specifically label and quantify Gq proteins in their native conformation in cells and tissues with high accuracy. Key Results FR and YM displayed low nanomolar affinity for Gαq, Gα11 and Gα14 expressed in CRISPR/Cas9 Gαq‐knockout cells, but not for Gα15. The two structurally very similar tracers showed strikingly different dissociation kinetics, which is predicted to result in divergent biological effects. Computational studies suggested a “dowel” effect of the pseudoirreversibly binding FR. A high‐throughput binding assay led to the discovery of novel Gq inhibitors, which inhibited Gq signalling in recombinant cells and primary murine brown adipocytes, resulting in enhanced differentiation. Conclusions and Implications The Gq protein inhibitors YM and FR are pharmacologically different despite similar structures. The new versatile tools and powerful assays will contribute to the advancement of the rising field of G protein research.
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Affiliation(s)
- Markus Kuschak
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Jan H Voss
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Jaspal Garg
- Institute of Pharmacology and Toxicology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jonathan G Schlegel
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Aliaa Abdelrahman
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Raphael Reher
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Jim Küppers
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Katharina Sylvester
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Sonja Hinz
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Michaela Matthey
- Medical Faculty, Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany.,Department of Systems Physiology, Medical Faculty, Ruhr University Bochum, Bochum, Germany
| | - Daniela Wenzel
- Medical Faculty, Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany.,Department of Systems Physiology, Medical Faculty, Ruhr University Bochum, Bochum, Germany
| | - Bernd K Fleischmann
- Medical Faculty, Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Michael Gütschow
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
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36
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Li J, Ge Y, Huang JX, Strømgaard K, Zhang X, Xiong XF. Heterotrimeric G Proteins as Therapeutic Targets in Drug Discovery. J Med Chem 2019; 63:5013-5030. [PMID: 31841625 DOI: 10.1021/acs.jmedchem.9b01452] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heterotrimeric G proteins are molecular switches in GPCR signaling pathways and regulate a plethora of physiological and pathological processes. GPCRs are efficient drug targets, and more than 30% of the drugs in use target them. However, selectively targeting an individual GPCR may be undesirable in various multifactorial diseases in which multiple receptors are involved. In addition, abnormal activation or expression of G proteins is frequently associated with diseases. Furthermore, G proteins harboring mutations often result in malignant diseases. Thus, targeting G proteins instead of GPCRs might provide alternative approaches for combating these diseases. In this review, we discuss the biochemistry of heterotrimeric G proteins, describe the G protein-associated diseases, and summarize the currently known modulators that can regulate the activities of G proteins. The outlook for targeting G proteins to treat diverse diseases is also included in this manuscript.
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Affiliation(s)
- Jian Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Jun-Xiang Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Xiaolei Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
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Antitumor astins originate from the fungal endophyte Cyanodermella asteris living within the medicinal plant Aster tataricus. Proc Natl Acad Sci U S A 2019; 116:26909-26917. [PMID: 31811021 DOI: 10.1073/pnas.1910527116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Medicinal plants are a prolific source of natural products with remarkable chemical and biological properties, many of which have considerable remedial benefits. Numerous medicinal plants are suffering from wildcrafting, and thus biotechnological production processes of their natural products are urgently needed. The plant Aster tataricus is widely used in traditional Chinese medicine and contains unique active ingredients named astins. These are macrocyclic peptides showing promising antitumor activities and usually containing the highly unusual moiety 3,4-dichloroproline. The biosynthetic origins of astins are unknown despite being studied for decades. Here we show that astins are produced by the recently discovered fungal endophyte Cyanodermella asteris We were able to produce astins in reasonable and reproducible amounts using axenic cultures of the endophyte. We identified the biosynthetic gene cluster responsible for astin biosynthesis in the genome of C. asteris and propose a production pathway that is based on a nonribosomal peptide synthetase. Striking differences in the production profiles of endophyte and host plant imply a symbiotic cross-species biosynthesis pathway for astin C derivatives, in which plant enzymes or plant signals are required to trigger the synthesis of plant-exclusive variants such as astin A. Our findings lay the foundation for the sustainable biotechnological production of astins independent from aster plants.
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38
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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40
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Zhang H, Nielsen AL, Strømgaard K. Recent achievements in developing selective Gqinhibitors. Med Res Rev 2019; 40:135-157. [DOI: 10.1002/med.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Hang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co‐innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical SciencesZhengzhou UniversityZhengzhou Henan China
| | - Alexander L. Nielsen
- Department of Drug Design and Pharmacology, Center for BiopharmaceuticalsUniversity of CopenhagenCopenhagen Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for BiopharmaceuticalsUniversity of CopenhagenCopenhagen Denmark
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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Malfacini D, Patt J, Annala S, Harpsøe K, Eryilmaz F, Reher R, Crüsemann M, Hanke W, Zhang H, Tietze D, Gloriam DE, Bräuner-Osborne H, Strømgaard K, König GM, Inoue A, Gomeza J, Kostenis E. Rational design of a heterotrimeric G protein α subunit with artificial inhibitor sensitivity. J Biol Chem 2019; 294:5747-5758. [PMID: 30745359 PMCID: PMC6463727 DOI: 10.1074/jbc.ra118.007250] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/28/2019] [Indexed: 12/31/2022] Open
Abstract
Transmembrane signals initiated by a range of extracellular stimuli converge on members of the Gq family of heterotrimeric G proteins, which relay these signals in target cells. Gq family G proteins comprise Gq, G11, G14, and G16, which upon activation mediate their cellular effects via inositol lipid–dependent and –independent signaling to control fundamental processes in mammalian physiology. To date, highly specific inhibition of Gq/11/14 signaling can be achieved only with FR900359 (FR) and YM-254890 (YM), two naturally occurring cyclic depsipeptides. To further development of FR or YM mimics for other Gα subunits, we here set out to rationally design Gα16 proteins with artificial FR/YM sensitivity by introducing an engineered depsipeptide-binding site. Thereby we permit control of G16 function through ligands that are inactive on the WT protein. Using CRISPR/Cas9-generated Gαq/Gα11-null cells and loss- and gain-of-function mutagenesis along with label-free whole-cell biosensing, we determined the molecular coordinates for FR/YM inhibition of Gq and transplanted these to FR/YM-insensitive G16. Intriguingly, despite having close structural similarity, FR and YM yielded biologically distinct activities: it was more difficult to perturb Gq inhibition by FR and easier to install FR inhibition onto G16 than perturb or install inhibition with YM. A unique hydrophobic network utilized by FR accounted for these unexpected discrepancies. Our results suggest that non-Gq/11/14 proteins should be amenable to inhibition by FR scaffold–based inhibitors, provided that these inhibitors mimic the interaction of FR with Gα proteins harboring engineered FR-binding sites.
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Affiliation(s)
- Davide Malfacini
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Julian Patt
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Suvi Annala
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Funda Eryilmaz
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Wiebke Hanke
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Hang Zhang
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Daniel Tietze
- Eduard Zintl Institute of Inorganic and Physical Chemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jesus Gomeza
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Evi Kostenis
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019; 36:1412-1436. [DOI: 10.1039/c8np00091c] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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Dose B, Niehs SP, Scherlach K, Flórez LV, Kaltenpoth M, Hertweck C. Unexpected Bacterial Origin of the Antibiotic Icosalide: Two-Tailed Depsipeptide Assembly in Multifarious Burkholderia Symbionts. ACS Chem Biol 2018; 13:2414-2420. [PMID: 30160099 DOI: 10.1021/acschembio.8b00600] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Icosalide is an unusual two-tailed lipocyclopeptide antibiotic that was originally isolated from a fungal culture. Yet, its biosynthesis and ecological function have remained enigmatic. By genome mining and metabolic profiling of a bacterial endosymbiont ( Burkholderia gladioli) of the pest beetle Lagria villosa, we unveiled a bacterial origin of icosalide. Functional analysis of the biosynthetic gene locus revealed an unprecedented nonribosomal peptide synthetase (NRPS) that incorporates two β-hydroxy acids by means of two starter condensation domains in different modules. This unusual assembly line, which may inspire new synthetic biology approaches, is widespread among many symbiotic Burkholderia species from diverse habitats. Biological assays showed that icosalide is active against entomopathogenic bacteria, thus adding to the chemical armory protecting beetle offspring. By creating a null mutant, we found that icosalide is a swarming inhibitor, which may play a role in symbiotic interactions and bears the potential for therapeutic applications.
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Affiliation(s)
- Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sarah P. Niehs
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Laura V. Flórez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
- Friedrich Schiller University Jena, 07743 Jena, Germany
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Pinto-Carbó M, Gademann K, Eberl L, Carlier A. Leaf nodule symbiosis: function and transmission of obligate bacterial endophytes. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:23-31. [PMID: 29452904 DOI: 10.1016/j.pbi.2018.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 06/08/2023]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves, and have been used as taxonomic marker since the early 20th century. These structures are present in very diverse taxa, including dicots (Rubiaceae and Primulaceae) and monocots (Dioscorea). The symbionts colonize the plants throughout their life cycles and contribute bioactive secondary metabolites to the association. In this review, we present recent progress in the understanding of these plant-bacteria symbioses, including the modes of transmission, distribution and roles of the symbionts.
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Affiliation(s)
- Marta Pinto-Carbó
- Department of Microbiology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Leo Eberl
- Department of Microbiology, University of Zurich, CH-8008 Zurich, Switzerland
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Reher R, Kuschak M, Heycke N, Annala S, Kehraus S, Dai HF, Müller CE, Kostenis E, König GM, Crüsemann M. Applying Molecular Networking for the Detection of Natural Sources and Analogues of the Selective Gq Protein Inhibitor FR900359. JOURNAL OF NATURAL PRODUCTS 2018; 81:1628-1635. [PMID: 29943987 DOI: 10.1021/acs.jnatprod.8b00222] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The cyclic depsipeptide FR900359 (FR), isolated from the traditional Chinese medicine plant Ardisia crenata, is a potent Gq protein inhibitor and thus a valuable tool to study Gq-mediated signaling of G protein-coupled receptors. Two new FR analogues (3 and 4) were isolated from A. crenata together with the known analogues 1 and 2. The structures of compounds 3 and 4 were established by NMR spectroscopic data and MS-based molecular networking followed by in-depth LCMS2 analysis. The latter approach led to the annotation of further FR analogues 5-9. Comparative bioactivity tests of compounds 1-4 along with the parent molecule FR showed high-affinity binding to Gq proteins in the low nanomolar range (IC50 = 2.3-16.8 nM) for all analogues as well as equipotent inhibition of Gq signaling, which gives important SAR insights into this valuable natural product. Additionally, FR was detected from leaves of five other Ardisia species, among them the non-nodulated leaves of Ardisia lucida, implying a much broader distribution of FR than originally anticipated.
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Affiliation(s)
| | | | | | | | | | - Hao-Fu Dai
- Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , Hainan , China
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Reher R, Kühl T, Annala S, Benkel T, Kaufmann D, Nubbemeyer B, Odhiambo JP, Heimer P, Bäuml CA, Kehraus S, Crüsemann M, Kostenis E, Tietze D, König GM, Imhof D. Deciphering Specificity Determinants for FR900359-Derived Gqα Inhibitors Based on Computational and Structure-Activity Studies. ChemMedChem 2018; 13:1634-1643. [DOI: 10.1002/cmdc.201800304] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Raphael Reher
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Suvi Annala
- Molecular, Cellular and Pharmacobiology Section; Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Tobias Benkel
- Molecular, Cellular and Pharmacobiology Section; Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Desireé Kaufmann
- Eduard Zintl Institute for Inorganic and Physical Chemistry; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Britta Nubbemeyer
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Justin Patrick Odhiambo
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Pascal Heimer
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Charlotte Anneke Bäuml
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section; Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Daniel Tietze
- Eduard Zintl Institute for Inorganic and Physical Chemistry; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Gabriele M. König
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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Special Award in Synthetic Organic Chemistry, Japan: K. Nakanishi / Nauta Pharmacochemistry Award for Medicinal Chemistry and Chemical Biology: C. E. Müller / UCB-Ehrlich Award for Excellence in Medicinal Chemistry: A. Nelson / John C. Bailar Jr. Medal: J. Angew Chem Int Ed Engl 2018; 57:6975. [DOI: 10.1002/anie.201805228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Japanischer Sonderpreis für organische Synthesechemie: K. Nakanishi / Preise der European Federation for Medicinal Chemistry: C. E. Müller und A. Nelson / John C. Bailar Jr. Medal: J. F. Hartwig. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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