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Salveson PJ, Moyer AP, Said MY, Gӧkçe G, Li X, Kang A, Nguyen H, Bera AK, Levine PM, Bhardwaj G, Baker D. Expansive discovery of chemically diverse structured macrocyclic oligoamides. Science 2024; 384:420-428. [PMID: 38662830 DOI: 10.1126/science.adk1687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug design.
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Affiliation(s)
- Patrick J Salveson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Meerit Y Said
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gizem Gӧkçe
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Hannah Nguyen
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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2
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Moussa AY, Lambert C, Stradal TE, Ashrafi S, Maier W, Stadler M, Helaly SE. New Peptaibiotics and a Cyclodepsipeptide from Ijuhya vitellina: Isolation, Identification, Cytotoxic and Nematicidal Activities. Antibiotics (Basel) 2020; 9:antibiotics9030132. [PMID: 32235703 PMCID: PMC7148537 DOI: 10.3390/antibiotics9030132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 11/17/2022] Open
Abstract
Fungal associations with nematodes have attracted scientific attention because of the need to develop new biocontrol agents. In this context, Ijuhya vitellina, an antagonistic fungus previously isolated from the plant parasitic cyst nematode Heterodera filipjevi, was selected to carry out an in-depth metabolomic study for its active metabolites. Herein, three new nonapeptide peptaibols with leucinostatin based sequences were isolated and identified by 1, 2D NMR, and HR-ESI-MS-MS. The absolute configuration was assigned based on Marfay’s analysis and Mosher ester formation. The new leucinostatins manifested moderate nematicidal effect against the plant pathogenic nematode Pratylenchus penetrans with LD90 values ranging from 5 to 7 µg/mL. Furthermore, a cyclodepsipeptide, named arthrichitin D, with five amino acid residues attached to a 3-hydroxy-2,4-dimethylhexadeca-4,6-dienoic fatty acid chain was discovered and showed weak nematicidal effect against Caenorhabditis elegans. Chaetoglobosin B and its 19-O-acetyl derivative were also obtained as minor metabolites, and the activity of chaetoglobosin B on the actin cytoskeleton of mammalian cells was assessed.
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Affiliation(s)
- Ashaimaa Y. Moussa
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany;
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Abbassia, 11566 Cairo, Egypt
| | - Christopher Lambert
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany; (C.L.); (T.E.B.S.)
| | - Theresia E.B. Stradal
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany; (C.L.); (T.E.B.S.)
| | - Samad Ashrafi
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI)–Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany; (S.A.); (W.M.)
| | - Wolfgang Maier
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI)–Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany; (S.A.); (W.M.)
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany;
- Correspondence: (M.S.); (S.E.H.)
| | - Soleiman E. Helaly
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany;
- Department of Chemistry, Faculty of Science, Aswan University, 81528 Aswan, Egypt
- Correspondence: (M.S.); (S.E.H.)
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3
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Sarojini V, Cameron AJ, Varnava KG, Denny WA, Sanjayan G. Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function. Chem Rev 2019; 119:10318-10359. [PMID: 31418274 DOI: 10.1021/acs.chemrev.8b00737] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.
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Affiliation(s)
- Vijayalekshmi Sarojini
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology , Wellington 6140 , New Zealand
| | - Alan J Cameron
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | - Kyriakos G Varnava
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | | | - Gangadhar Sanjayan
- Division of Organic Chemistry , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411 008 , India
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4
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Sharma R, Singh VP, Singh D, Yusuf F, Kumar A, Vishwakarma RA, Chaubey A. Optimization of nonribosomal peptides production by a psychrotrophic fungus: Trichoderma velutinum ACR-P1. Appl Microbiol Biotechnol 2016; 100:9091-9102. [DOI: 10.1007/s00253-016-7622-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/02/2016] [Indexed: 02/03/2023]
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5
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Mohamed-Benkada M, François Pouchus Y, Vérité P, Pagniez F, Caroff N, Ruiz N. Identification and Biological Activities of Long-Chain Peptaibols Produced by a Marine-Derived Strain ofTrichoderma longibrachiatum. Chem Biodivers 2016; 13:521-30. [DOI: 10.1002/cbdv.201500159] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 12/11/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Mustapha Mohamed-Benkada
- Département de Biotechnologie; Faculté des Sciences de la Nature et de la Vie; Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB); El Mnaouar, B.P. 1505 Bir El Djir 31000 Oran Algeria
| | | | - Philippe Vérité
- Laboratoire de Chimie Analytique; Faculté de Médecine et Pharmacie; Université de Rouen; FR-76000 Rouen
| | - Fabrice Pagniez
- Laboratoire de Parasitologie et Mycologie Médicale, IICiMed; Faculté de Pharmacie; Université de Nantes; FR-44000 Nantes
| | - Nathalie Caroff
- Laboratoire Thérapeutiques Cliniques et Expérimentales des Infections; Faculté de Médecine; Université de Nantes; FR-44000 Nantes
| | - Nicolas Ruiz
- Faculté de Pharmacie, MMS; Université de Nantes; FR-44000 Nantes
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6
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Neumann NKN, Stoppacher N, Zeilinger S, Degenkolb T, Brückner H, Schuhmacher R. The peptaibiotics database--a comprehensive online resource. Chem Biodivers 2016; 12:743-51. [PMID: 26010663 DOI: 10.1002/cbdv.201400393] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Indexed: 01/29/2023]
Abstract
In this work, we present the 'Peptaibiotics Database' (PDB), a comprehensive online resource, which intends to cover all Aib-containing non-ribosomal fungal peptides currently described in scientific literature. This database shall extend and update the recently published 'Comprehensive Peptaibiotics Database' and currently consists of 1,297 peptaibiotic sequences. In a literature survey, a total of 235 peptaibiotic sequences published between January 2013 and June 2014 have been compiled, and added to the list of 1,062 peptides in the recently published 'Comprehensive Peptaibiotics Database'. The presented database is intended as a public resource freely accessible to the scientific community at peptaibiotics-database.boku.ac.at. The search options of the previously published repository and the presentation of sequence motif searches have been extended significantly. All of the available search options can be combined to create complex database queries. As a public repository, the presented database enables the easy upload of new peptaibiotic sequences or the correction of existing informations. In addition, an administrative interface for maintenance of the content of the database has been implemented, and the design of the database can be easily extended to store additional information to accommodate future needs of the 'peptaibiomics community'.
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Affiliation(s)
- Nora K N Neumann
- Center for Analytical Chemistry, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Straße 20, A-3430 Tulln, (phone: +43-2272-66280)
| | - Norbert Stoppacher
- Center for Analytical Chemistry, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Straße 20, A-3430 Tulln, (phone: +43-2272-66280).,Bureau International des Poids et Mesures, Pavillon de Breteuil, F-92312 Sèvres Cedex
| | - Susanne Zeilinger
- Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060 Vienna
| | - Thomas Degenkolb
- Research Center for Biosystems, Land Use and Nutrition, Department of Applied Entomology, University of Giessen, Heinrich-Buff-Ring 26.32, D-35392 Gießen
| | - Hans Brückner
- Research Center for Biosystems, Land Use and Nutrition, Department of Food Sciences, University of Giessen, Heinrich-Buff-Ring 26.32, D-35392 Gießen
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology IFA-Tulln, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Straße 20, A-3430 Tulln, (phone: +43-2272-66280).
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7
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Development and validation of LC–MS methods for peptaibol quantification in fungal extracts according to their lengths. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1009-1010:25-33. [DOI: 10.1016/j.jchromb.2015.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/20/2015] [Accepted: 11/21/2015] [Indexed: 01/31/2023]
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8
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Degenkolb T, Vilcinskas A. Metabolites from nematophagous fungi and nematicidal natural products from fungi as an alternative for biological control. Part I: metabolites from nematophagous ascomycetes. Appl Microbiol Biotechnol 2015; 100:3799-812. [PMID: 26715220 PMCID: PMC4824826 DOI: 10.1007/s00253-015-7233-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/29/2015] [Accepted: 12/02/2015] [Indexed: 11/29/2022]
Abstract
Plant-parasitic nematodes are estimated to cause global annual losses of more than US$ 100 billion. The number of registered nematicides has declined substantially over the last 25 years due to concerns about their non-specific mechanisms of action and hence their potential toxicity and likelihood to cause environmental damage. Environmentally beneficial and inexpensive alternatives to chemicals, which do not affect vertebrates, crops, and other non-target organisms, are therefore urgently required. Nematophagous fungi are natural antagonists of nematode parasites, and these offer an ecophysiological source of novel biocontrol strategies. In this first section of a two-part review article, we discuss 83 nematicidal and non-nematicidal primary and secondary metabolites found in nematophagous ascomycetes. Some of these substances exhibit nematicidal activities, namely oligosporon, 4',5'-dihydrooligosporon, talathermophilins A and B, phomalactone, aurovertins D and F, paeciloxazine, a pyridine carboxylic acid derivative, and leucinostatins. Blumenol A acts as a nematode attractant. Other substances, such as arthrosporols and paganins, play a decisive role in the life cycle of the producers, regulating the formation of reproductive or trapping organs. We conclude by considering the potential applications of these beneficial organisms in plant protection strategies.
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Affiliation(s)
- Thomas Degenkolb
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany. .,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchester Strasse 2, 35394, Giessen, Germany.
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9
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Arnhold FS, Linden A, Heimgartner H. Synthesis of Cyclopentapeptides with Three to Five Aib Units. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201400359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Arnhold FS, Linden A, Heimgartner H. Synthesis of Aib- and Phe(2Me)-Containing Cyclopentapeptides. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201400323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Biosynthesis and Molecular Genetics of Peptaibiotics—Fungal Peptides Containing Alpha, Alpha-Dialkyl Amino Acids. Fungal Biol 2015. [DOI: 10.1007/978-1-4939-2531-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 2014; 31:1348-75. [PMID: 25156669 DOI: 10.1039/c4np00046c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are a primary modality for fungal peptidic natural product assembly and are responsible for some of the best known, most useful, and most destructive fungal metabolites. Through genome sequencing and computer-assisted recognition of modular motifs of catalytic domains, one can now confidently identify most NRPS biosynthetic genes of a fungal strain. The biosynthetic gene clusters responsible for two of the most important classes of NRP fungal derived drugs, cyclosporine and the echinocandins, have been recently characterized by genomic sequencing and annotation. Complete biosynthetic gene clusters for the pneumocandins and echinocandins have been mapped at the genetic level and functionally characterized to some extent. Genomic sequencing of representative strains of most of the variants in the echinocandin family, including the wild-type of the three fungal strains employed for industrial-scale production of caspofungin, micafungin and anidulofungin, has enabled characterization of the basic architecture of the echinocandin NRPS pathways. A comparative analysis of how pathway genes cause variations in lipoinitiation, biosynthesis of the non-proteinogenic amino acids, amino acid substitutions, and hydroxylations and sulfonations of the core peptide and contribute to the molecular diversity of the family is presented. We also review new information on the natural functions of NRPs, the differences between fungal and bacterial NRPSs, and functional characterization of selected NRPS gene clusters. Continuing discovery of the new fungal nonribosomal peptides has contributed new structural diversity and potential insights into their biological functions among other natural peptides and peptaibiotics. We therefore provide an update on new peptides, depsipeptides and peptaibols discovered in the Fungi since 2009.
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Affiliation(s)
- Gerald Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Centre at Houston, Houston, Texas 77054, USA.
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Carroux A, Van Bohemen AI, Roullier C, Robiou du Pont T, Vansteelandt M, Bondon A, Zalouk-Vergnoux A, Pouchus YF, Ruiz N. Unprecedented 17-residue peptaibiotics produced by marine-derived Trichoderma atroviride. Chem Biodivers 2013; 10:772-86. [PMID: 23681725 DOI: 10.1002/cbdv.201200398] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Indexed: 11/07/2022]
Abstract
In the course of investigations on marine-derived toxigenic fungi, five strains of Trichoderma atroviride were studied for their production of peptaibiotics. While these five strains were found to produce classical 19-residue peptaibols, three of them exhibited unusual peptidic sodium-adduct [M + 2 Na](2+) ion peaks at m/z between 824 and 854. The sequencing of these peptides led to two series of unprecedented 17-residue peptaibiotics based on the model Ac-XXX-Ala-Ala-XXX-XXX-Gln-Aib-Aib-Aib-Ala/Ser-Lxx-Aib-Pro-XXX-Aib-Lxx-[C(129) ]. The C-terminus of these new peptides was common to all of them, and its elemental formula C5 H9 N2 O2 was established by HR-MS. It could correspond to the cyclized form of N(δ) -hydroxyornithine which has already been observed at the C-terminus of various peptidic siderophores. The comparison of the sequences of 17- and 19-residue peptides showed similarities for positions 1-16. This observation seems to indicate a common biosynthesis pathway. Both new 17-residue peptaibiotics and 19-residue peptaibols exhibited weak in vitro cytotoxicities against KB cells.
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Affiliation(s)
- Angélique Carroux
- University of Nantes, LUNAM, Faculty of Pharmacy, MMS, F-44000 Nantes
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Caumes C, Fernandes C, Roy O, Hjelmgaard T, Wenger E, Didierjean C, Taillefumier C, Faure S. Cyclic α,β-tetrapeptoids: sequence-dependent cyclization and conformational preference. Org Lett 2013; 15:3626-9. [PMID: 23806006 DOI: 10.1021/ol401478j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The presence of at least one N-Cα branched side chain is crucial for successful cyclization of α,β-tetrapeptoids. The ctct amide sequence revealed in the crystal structure of the 14-membered cyclotetrapeptoid 8 is also the most populated conformation in solution and is reminiscent of the predominant amide arrangement of the 12-membered cyclic tetrapeptides (CTPs).
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Affiliation(s)
- Cécile Caumes
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP10448, F-63000 Clermont-Ferrand, France
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15
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Stoppacher N, Neumann NKN, Burgstaller L, Zeilinger S, Degenkolb T, Brückner H, Schuhmacher R. The Comprehensive Peptaibiotics Database. Chem Biodivers 2013; 10:734-43. [DOI: 10.1002/cbdv.201200427] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 11/10/2022]
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16
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Chakraborty S, Tyagi P, Tai DF, Lee GH, Peng SM. A lead (II) 3D coordination polymer based on a marine cyclic peptide motif. Molecules 2013; 18:4972-85. [PMID: 23624650 PMCID: PMC6270303 DOI: 10.3390/molecules18054972] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/16/2013] [Accepted: 04/24/2013] [Indexed: 11/23/2022] Open
Abstract
The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-L-Ser-L-Pro-L-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network in the crystalline state. The polymerization of a heavy metal ion with a rigid asymmetric cyclic tetrapeptide represents the first example of a new class of macrocyclic complexes.
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Affiliation(s)
| | - Pooja Tyagi
- Department of Chemistry, National Dong-Hwa University, Hualien 974, Taiwan
| | - Dar-Fu Tai
- Department of Chemistry, National Dong-Hwa University, Hualien 974, Taiwan
| | - Gene-Hsiang Lee
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Shie-Ming Peng
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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17
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Jokela J, Oftedal L, Herfindal L, Permi P, Wahlsten M, Døskeland SO, Sivonen K. Anabaenolysins, novel cytolytic lipopeptides from benthic Anabaena cyanobacteria. PLoS One 2012; 7:e41222. [PMID: 22829929 PMCID: PMC3400675 DOI: 10.1371/journal.pone.0041222] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/19/2012] [Indexed: 11/26/2022] Open
Abstract
Two novel cyclic lipopeptides, anabaenolysin A and anabaenolysin B, were isolated from two benthic cyanobacterial strains of the genus Anabaena. This novel class of cyanobacterial lipopeptides has a general structure of a small peptide ring consisting of four amino acids from which two are proteinogenic and two unusual; glycine1, glycine2, 2-(3-amino-5-oxytetrahydrofuran-2-yl)-2-hydroxyacetic acid3 and a long unsaturated C18 β-amino acid4 with a conjugated triene structure. They are distinguished by the presence of a conjugated dienic structure in the C18 β-amino acid present in anabaenolysin A but not in anabaenolysin B. Conjugated triene structure generates a typical UV spectrum for anabaenolysins for easy recognition. Anabaenolysin A constituted up to 400 ppm of the cyanobacterial dry weight. We found evidence of thirteen variants of anabaenolysins in one cyanobacterial strain. This suggests that the anabaenolysins are an important class of secondary metabolites in benthic Anabaena cyanobacteria. Both anabaenolysin A and B had cytolytic activity on a number of mammalian cell lines.
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Affiliation(s)
- Jouni Jokela
- Division of Microbiology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Linn Oftedal
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Lars Herfindal
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Translational Signaling Group, Haukeland University Hospital, Bergen, Norway
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matti Wahlsten
- Division of Microbiology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Kaarina Sivonen
- Division of Microbiology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
- * E-mail:
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Eid M, Rippa S, Castano S, Desbat B, Chopineau J, Rossi C, Béven L. Exploring the membrane mechanism of the bioactive peptaibol ampullosporin a using lipid monolayers and supported biomimetic membranes. JOURNAL OF BIOPHYSICS (HINDAWI PUBLISHING CORPORATION : ONLINE) 2011; 2010:179641. [PMID: 21403824 PMCID: PMC3042626 DOI: 10.1155/2010/179641] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/09/2010] [Accepted: 12/20/2010] [Indexed: 05/12/2023]
Abstract
Ampullosporin A is an antimicrobial, neuroleptic peptaibol, the behavior of which was investigated in different membrane mimetic environments made of egg yolk L-α-phosphatidylcholine. In monolayers, the peptaibol adopted a mixed α/3(10)-helical structure with an in-plane orientation. The binding step was followed by the peptide insertion into the lipid monolayer core. The relevance of the inner lipid leaflet nature was studied by comparing ampullosporin binding on a hybrid bilayer, in which this leaflet was a rigid alkane layer, and on supported fluid lipid bilayers. The membrane binding was examined by surface plasmon resonance spectroscopy and the effect on lipid dynamics was explored using fluorescence recovery after photobleaching. In the absence of voltage and at low concentration, ampullosporin A substantially adsorbed onto lipid surfaces and its interaction with biomimetic models was strongly modified depending on the inner leaflet structure. At high concentration, ampullosporin A addition led to the lipid bilayers disruption.
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Affiliation(s)
- Marguerita Eid
- UMR 6022 CNRS Génie Enzymatique et Cellulaire, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne Cedex, France
| | - Sonia Rippa
- UMR 6022 CNRS Génie Enzymatique et Cellulaire, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne Cedex, France
| | - Sabine Castano
- CBMN, Chimie et Biologie des Membranes et des Nanoobjets CNRS, UMR 5248, Université de Bordeaux I, ENITAB, 33607 Pessac, France
| | - Bernard Desbat
- CBMN, Chimie et Biologie des Membranes et des Nanoobjets CNRS, UMR 5248, Université de Bordeaux I, ENITAB, 33607 Pessac, France
| | - Joël Chopineau
- CNRS, UMR 5253 Institut Charles Gerhardt, Université Montpellier 2, Ecole Nationale Supérieure de Chimie de Montpellier, Université Montpellier 1, 34093 Montpellier Cedex, France
- Université de Nîmes, 30000 Nîmes, France
| | - Claire Rossi
- UMR 6022 CNRS Génie Enzymatique et Cellulaire, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne Cedex, France
| | - Laure Béven
- UMR 6022 CNRS Génie Enzymatique et Cellulaire, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne Cedex, France
- INRA, UMR 1090 Génomique Diversité et Pouvoir Pathogène, 33883 Villenave d'Ornon, France
- Université de Bordeaux 2, UMR 1090 Génomique Diversité Pouvoir Pathogène, 33883 Villenave d'Ornon Cedex, France
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Mukherjee PK, Wiest A, Ruiz N, Keightley A, Moran-Diez ME, McCluskey K, Pouchus YF, Kenerley CM. Two classes of new peptaibols are synthesized by a single non-ribosomal peptide synthetase of Trichoderma virens. J Biol Chem 2010; 286:4544-54. [PMID: 21123172 DOI: 10.1074/jbc.m110.159723] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptaibols are a group of small peptides having a high α-aminoisobutyric acid (Aib) content and produced by filamentous fungi, especially by the members of the genus Trichoderma (anamorph Hypocrea). These antibiotics are economically important for their anti-microbial and anti-cancer properties as well as ability to induce systemic resistance in plants against microbial invasion. In this study we present sequences of two classes (11-residue and 14-residue) of peptaibols produced by the biocontrol fungus Trichoderma virens. Of the 35 11-residue peptaibols sequenced, 18 are hitherto not described, and all the 53 14-residue sequences described by us here are new. We have also identified a peptaibol synthetase (non-ribosomal peptide synthetase, NRPS) with 14 complete modules in the genome of this fungus and disruption of this single gene (designated as tex2) resulted in the loss of both the classes of peptaibols. We, thus present here an unprecedented case where a single NRPS encodes for two classes of peptaibols. The new peptaibols identified here could have applications as therapeutic agents for the management of human and plant health.
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Affiliation(s)
- Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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Samuels GJ, Ismaiel A, Bon MC, De Respinis S, Petrini O. Trichoderma asperellum sensu lato consists of two cryptic species. Mycologia 2010; 102:944-66. [PMID: 20648760 DOI: 10.3852/09-243] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Analysis of a worldwide collection of strains of Trichoderma asperellum sensu lato using multilocus genealogies of four genomic regions (tef1, rpb2, act, ITS1, 2 and 5.8s rRNA), sequence polymorphism-derived (SPD) markers, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) of the proteome and classical mycological techniques revealed two morphologically cryptic sister species within T. asperellum, T. asperellum, T. asperelloides sp. nov. and a third closely related but morphologically distinct species. T. yunnanense. Trichoderma asperellum and T. asperelloides have wide sympatric distribution on multiple continents; T. yunnanense is represented by a single strain from China. Several strains reported in the literature or represented in GenBank as T. asperellum are re-identified as T. asperelloides. Four molecular SPD typing patterns (I-IV) were found over a large geographic range. Patterns I-III were produced only by T. asperellum and pattern IV by T. asperelloides and T. yunnanense. Pattern I was found in North America, South America, Africa and Europe and Asia (Saudi Arabia). Pattern III was found in Africa, North America, South America and Asia, not in Europe. Pattern II was found only in Cameroon (central Africa) and Peru. Pattern IV was found in all continents. All SPD II pattern strains formed a strongly supported subclade within the T. asperellum clade in the phylogenetic tree based on rpb2 and MLS (combined multilocus sequence). The diversity of DNA sequences, SPD markers and polypeptides in T. asperellum suggests that further speciation is under way within T. asperellum. MALDI-TOF MS distinguished T. yunnanense from related taxa by UPGMA clustering, but separation between T. asperellum and T. asperelloides was less clear.
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Affiliation(s)
- Gary J Samuels
- United States Department of Agriculture, Agriculture Research Service, Systematic Mycology & Microbiology Laboratory, Room 304, B-0lla, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA.
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De Respinis S, Vogel G, Benagli C, Tonolla M, Petrini O, Samuels GJ. MALDI-TOF MS of Trichoderma: a model system for the identification of microfungi. Mycol Prog 2009. [DOI: 10.1007/s11557-009-0621-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Newkirk TL, Bowers AA, Williams RM. Discovery, biological activity, synthesis and potential therapeutic utility of naturally occurring histone deacetylase inhibitors. Nat Prod Rep 2009; 26:1293-320. [PMID: 19779641 DOI: 10.1039/b817886k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Tenaya L Newkirk
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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Ren J, Xue C, Tian L, Xu M, Chen J, Deng Z, Proksch P, Lin W. Asperelines A-F, peptaibols from the marine-derived fungus Trichoderma asperellum. JOURNAL OF NATURAL PRODUCTS 2009; 72:1036-1044. [PMID: 19514743 DOI: 10.1021/np900190w] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fermentation of the marine-derived fungus Trichoderma asperellum, collected from the sediment of the Antarctic Penguin Island, resulted in the isolation of six new peptaibols named asperelines A-F (1-6), which are characterized by an acetylated N-terminus and a C-terminus containing an uncommon prolinol residue. Structures were determined by extensive 1D and 2D NMR ((1)H-(1)H COSY, HMQC, HMBC, NOESY) spectroscopic data analysis combined with ESIMS/MS fragmentation. The absolute configurations of the amino acid residues possessing a chiral alpha-carbon and of the prolinol residue were determined to be L and S, respectively, using a new method of (1)H NMR spectroscopic comparison of complexes formed between the chiral reagent Ru(D(4)-Por*)CO and amino acids derived from the peptaibols with those formed with reference standards.
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Affiliation(s)
- Jinwei Ren
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People's Republic of China
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Brückner H, Becker D, Gams W, Degenkolb T. Aib and iva in the biosphere: neither rare nor necessarily extraterrestrial. Chem Biodivers 2009; 6:38-56. [PMID: 19180454 DOI: 10.1002/cbdv.200800331] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fourty-nine species and strains of filamentous fungi of the genera Acremonium, Bionectria, Clonostachys, Emericellopsis, Hypocrea/Trichoderma, Lecythophora, Monocillium, Nectriopsis, Niesslia, Tolypocladium, and Wardomyces, deposited with the culture collection of the Centraalbureau voor Schimmelcultures (CBS) in Utrecht, The Netherlands, were grown on nutrient agar plates. Organic extracts of mycelia were analyzed after acidic total hydrolysis and derivatization by GC/SIM-MS on Chirasil-L-Val for the presence of Aib (=alpha-aminoisobutyric acid, 2-methylalanine) and DL-Iva (=isovaline, 2-ethylalanine). In 37 of the hydrolysates, Aib was detected, and in several of them D-Iva or mixtures of D- and L-Iva. Non-proteinogenic Aib, in particular, is a highly specific marker for a distinctive group of fungal polypeptides named peptaibols or, comprehensively, peptaibiotics, i.e., peptides containing Aib and displaying (anti)biotic activities. The biotic synthesis of these amino acids by filamentous fungi contradicts the still widespread belief that alpha,alpha-dialkyl-alpha-amino acids do not or rarely occur in the biosphere and, if detected, are of extraterrestrial origin. The abundant production of peptaibiotics by cosmopolitan species of microfungi has also to be considered in the discussion on the occurrence of Aib and Iva in ancient and recent sediments. The detection of trace amounts of Aib in ice samples of Antarctica that are devoid of meteorites might also be related to the presence of Aib-producing microorganisms, being either indigenous psychrophiles, or being transported and localized by mechanisms related to bioaerosols and cryoconites. The presence of microfungi being capable of producing alpha,alpha-dialkyl alpha-amino acids in terrestrial samples, and possible contamination of extraterrestrial materials are pointed out to be of relevance for the reliable interpretation of cosmogeochemical data.
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Affiliation(s)
- Hans Brückner
- Interdisciplinary Research Centre for Biosystems, Land Use and Nutrition (IFZ), Department of Food Sciences, Institute of Nutritional Science, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen.
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Theis C, Degenkolb T, Brückner H. Studies on the Selective Trifluoroacetolytic Scission of Native Peptaibols and Model Peptides Using HPLC and ESI-CID-MS. Chem Biodivers 2008; 5:2337-55. [DOI: 10.1002/cbdv.200890200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Degenkolb T, Brückner H. Peptaibiomics: Towards a Myriad of Bioactive Peptides Containing Cα-Dialkylamino Acids? Chem Biodivers 2008; 5:1817-43. [DOI: 10.1002/cbdv.200890171] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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The Trichoderma brevicompactum clade: a separate lineage with new species, new peptaibiotics, and mycotoxins. Mycol Prog 2008. [DOI: 10.1007/s11557-008-0563-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Degenkolb T, von Döhren H, Fog Nielsen K, Samuels G, Brückner H. Recent Advances and Future Prospects in Peptaibiotics, Hydrophobin, and Mycotoxin Research, and Their Importance for Chemotaxonomy ofTrichoderma andHypocrea. Chem Biodivers 2008; 5:671-80. [DOI: 10.1002/cbdv.200890064] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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