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Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto. Molecules 2023; 28:molecules28041646. [PMID: 36838633 PMCID: PMC9958762 DOI: 10.3390/molecules28041646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.
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2
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CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria. Cell Chem Biol 2021; 29:696-710.e4. [PMID: 34508657 DOI: 10.1016/j.chembiol.2021.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/19/2021] [Accepted: 08/20/2021] [Indexed: 12/31/2022]
Abstract
With the advent of genome sequencing and mining technologies, secondary metabolite biosynthetic gene clusters (BGCs) within bacterial genomes are becoming easier to predict. For subsequent BGC characterization, clustered regularly interspaced short palindromic repeats (CRISPR) has contributed to knocking out target genes and/or modulating their expression; however, CRISPR is limited to strains for which robust genetic tools are available. Here we present a strategy that combines CRISPR with chassis-independent recombinase-assisted genome engineering (CRAGE), which enables CRISPR systems in diverse bacteria. To demonstrate CRAGE-CRISPR, we select 10 polyketide/non-ribosomal peptide BGCs in Photorhabdus luminescens as models and create their deletion and activation mutants. Subsequent loss- and gain-of-function studies confirm 22 secondary metabolites associated with the BGCs, including a metabolite from a previously uncharacterized BGC. These results demonstrate that the CRAGE-CRISPR system is a simple yet powerful approach to rapidly perturb expression of defined BGCs and to profile genotype-phenotype relationships in bacteria.
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3
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Zhao L, Le Chapelain C, Brachmann AO, Kaiser M, Groll M, Bode HB. Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-like Proteasome Inhibitors from Photorhabdus laumondii. Chembiochem 2021; 22:1582-1588. [PMID: 33452852 PMCID: PMC8248439 DOI: 10.1002/cbic.202100014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 12/22/2022]
Abstract
The glidobactin-like natural products (GLNPs) glidobactin A and cepafungin I have been reported to be potent proteasome inhibitors and are regarded as promising candidates for anticancer drug development. Their biosynthetic gene cluster (BGC) plu1881-1877 is present in entomopathogenic Photorhabdus laumondii but silent under standard laboratory conditions. Here we show the largest subset of GLNPs, which are produced and identified after activation of the silent BGC in the native host and following heterologous expression of the BGC in Escherichia coli. Their chemical diversity results from a relaxed substrate specificity and flexible product release in the assembly line of GLNPs. Crystal structure analysis of the yeast proteasome in complex with new GLNPs suggests that the degree of unsaturation and the length of the aliphatic tail are critical for their bioactivity. The results in this study provide the basis to engineer the BGC for the generation of new GLNPs and to optimize these natural products resulting in potential drugs for cancer therapy.
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Affiliation(s)
- Lei Zhao
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438Frankfurt am MainGermany
- Institute of BotanyJiangsu Province and Chinese Academy of Sciences210014NanjingP. R. China
| | - Camille Le Chapelain
- Center for Integrated Protein Science Munich (CIPSM)Department of ChemistryTechnical University of Munich85748GarchingGermany
| | - Alexander O. Brachmann
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438Frankfurt am MainGermany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute4002BaselSwitzerland
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM)Department of ChemistryTechnical University of Munich85748GarchingGermany
| | - Helge B. Bode
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438Frankfurt am MainGermany
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe University Frankfurt60438Frankfurt am MainGermany
- Senckenberg Gesellschaft für Naturforschung60325Frankfurt am MainGermany
- Department of Natural Products in Organismic InteractionsMax-Planck-Institute for Terrestrial Microbiology35043MarburgGermany
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4
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Hubbell GE, Tepe JJ. Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors. RSC Chem Biol 2020; 1:305-332. [PMID: 33791679 PMCID: PMC8009326 DOI: 10.1039/d0cb00111b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
The 20S proteasome is a valuable target for the treatment of a number of diseases including cancer, neurodegenerative disease, and parasitic infection. In an effort to discover novel inhibitors of the 20S proteasome, many reseaarchers have looked to natural products as potential leads for drug discovery. The following review discusses the efforts made in the field to isolate and identify natural products as inhibitors of the proteasome. In addition, we describe some of the modifications made to natural products in order to discover more potent and selective inhibitors for potential disease treatment.
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Affiliation(s)
- Grace E. Hubbell
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
| | - Jetze J. Tepe
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
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5
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Zwick CR, Renata H. Harnessing the biocatalytic potential of iron- and α-ketoglutarate-dependent dioxygenases in natural product total synthesis. Nat Prod Rep 2020; 37:1065-1079. [PMID: 32055818 PMCID: PMC7426249 DOI: 10.1039/c9np00075e] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to the end of 2019Iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGs) represent a versatile and intriguing enzyme family by virtue of their ability to directly functionalize unactivated C-H bonds at the cost of αKG and O2. Fe/αKGs play an important role in the biosynthesis of natural products, valuable biologically active secondary metabolites frequently pursued as drug leads. The field of natural product total synthesis seeks to contruct these molecules as effeciently as possible, although natural products continue to challenge chemists due to their intricate structural complexity. Chemoenzymatic approaches seek to remedy the shortcomings of traditional synthetic methodology by combining Nature's biosynthetic machinery with traditional chemical methods to efficiently construct natural products. Although other oxygenase families have been widely employed for this purpose, Fe/αKGs remain underutilized. The following review will cover recent chemoenzymatic total syntheses involving Fe/αKG enzymes. Additionally, related information involving natural product biosynthesis, methods development, and non-chemoenzymatic total syntheses will be discussed to inform retrosynthetic logic and synthetic design.
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Affiliation(s)
- Christian R Zwick
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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6
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Pierce MR, Robinson RM, Ibarra-Rivera TR, Pirrung MC, Dolloff NG, Bachmann AS. Syrbactin proteasome inhibitor TIR-199 overcomes bortezomib chemoresistance and inhibits multiple myeloma tumor growth in vivo. Leuk Res 2019; 88:106271. [PMID: 31778912 DOI: 10.1016/j.leukres.2019.106271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 12/20/2022]
Abstract
Multiple myeloma (MM) and mantle cell lymphoma (MCL) are blood cancers that respond to proteasome inhibitors. Three FDA-approved drugs that block the proteasome are currently on the market, bortezomib, carfilzomib, and ixazomib. While these proteasome inhibitors have demonstrated clinical efficacy against refractory and relapsed MM and MCL, they are also associated with considerable adverse effects including peripheral neuropathy and cardiotoxicity, and tumor cells often acquire drug resistance. TIR-199 belongs to the syrbactin class, which constitutes a novel family of irreversible proteasome inhibitors. In this study, we compare TIR-199 head-to-head with three FDA-approved proteasome inhibitors. We demonstrate that TIR-199 selectively inhibits to varying degrees the sub-catalytic proteasomal activities (C-L/β1, T-L/β2, and CT-L/β5) in three actively dividing MM cell lines, with Ki50 (CT-L/β5) values of 14.61 ± 2.68 nM (ARD), 54.59 ± 10.4 nM (U266), and 26.8 ± 5.2 nM (MM.1R). In most instances, this range was comparable with the activity of ixazomib. However, TIR-199 was more effective than bortezomib, carfilzomib, and ixazomib in killing bortezomib-resistant MM and MCL cell lines, as judged by a low resistance index (RI) between 1.7 and 2.2, which implies that TIR-199 indiscriminately inhibits both bortezomib-sensitive and bortezomib-resistant MM and MCL cells at similar concentrations. Importantly, TIR-199 reduced the tumor burden in a MM mouse model (p < 0.01) confirming its potency in vivo. Given the fact that there is still no cure for MM, the further development of TIR-199 or similar molecules that belong to the syrbactin class of proteasome inhibitors is warranted.
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Affiliation(s)
- Marquicia R Pierce
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI 49503, USA
| | - Reeder M Robinson
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
| | | | - Michael C Pirrung
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA; Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - Nathan G Dolloff
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
| | - André S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI 49503, 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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8
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Amatuni A, Renata H. Identification of a lysine 4-hydroxylase from the glidobactin biosynthesis and evaluation of its biocatalytic potential. Org Biomol Chem 2019; 17:1736-1739. [PMID: 30320324 DOI: 10.1039/c8ob02054j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the functional characterization of GlbB, a lysine 4-hydroxylase from the glidobactin biosynthetic gene cluster. Despite its narrow substrate specificity, GlbB is able to catalyze the hydroxylation of l-lysine with excellent total turnover number and complete regio- and diastereoselectivity. The synthetic utility of GlbB is illustrated by its use in the efficient preparation of a key dipeptide fragment of glidobactin.
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Affiliation(s)
- Alexander Amatuni
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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9
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Wesche F, He Y, Bode HB. Solid-phase enrichment and analysis of electrophilic natural products. Beilstein J Org Chem 2017; 13:405-409. [PMID: 28382178 PMCID: PMC5355884 DOI: 10.3762/bjoc.13.43] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/25/2022] Open
Abstract
In search for new natural products, which may lead to the development of new drugs for all kind of applications, novel methods are needed. Here we describe the identification of electrophilic natural products in crude extracts via their reactivity against azide as a nucleophile followed by their subsequent enrichment using a cleavable azide-reactive resin (CARR). Using this approach, natural products carrying epoxides and α,β-unsaturated enones as well as several unknown compounds were identified in crude extracts from entomopathogenic Photorhabdus bacteria.
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Affiliation(s)
- Frank Wesche
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Yue He
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany
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10
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Cochrane SA, Surgenor RR, Khey KMW, Vederas JC. Total Synthesis and Stereochemical Assignment of the Antimicrobial Lipopeptide Cerexin A1. Org Lett 2015; 17:5428-31. [PMID: 26465807 DOI: 10.1021/acs.orglett.5b02779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isolation and total synthesis of the antimicrobial lipopeptide cerexin A1 is reported. This synthesis includes the preparation of orthogonally protected γ-hydroxylysine, utilizing a nitrile Reformatsky-type reaction as a key step to yield both diastereomers more efficiently than previously reported methods. The configuration of the β-hydroxyl in the lipid tail was determined by the use of a modified Ohrui-Akasaka approach. Furthermore, new cerexin analogues from Bacillus mycoides ATCC 21929 were isolated and characterized, revealing an ε-amino succinylation of a hydroxylysine residue that is unusual in a nonribosomal peptide synthetase product.
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Affiliation(s)
- Stephen A Cochrane
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Richard R Surgenor
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Kevin M W Khey
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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11
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Bian X, Huang F, Wang H, Klefisch T, Müller R, Zhang Y. Heterologous production of glidobactins/luminmycins in Escherichia coli Nissle containing the glidobactin biosynthetic gene cluster from Burkholderia DSM7029. Chembiochem 2014; 15:2221-4. [PMID: 25147087 DOI: 10.1002/cbic.201402199] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 11/09/2022]
Abstract
Natural product peptide-based proteasome inhibitors show great potential as anticancer drugs. Here we have cloned the biosynthetic gene cluster of a potent proteasome inhibitor-glidobactin from Burkholderia DSM7029-and successfully detected glidobactins/luminmycins in E. coli Nissle. We have also improved the yield of glidobactin A tenfold by promoter change in a heterologous host. In addition, two new biosynthetic intermediates were identified by comparative MS/MS fragmentation analysis. Identification of acyclic luminmycin E implies substrate specificity of the TE domain for cyclization. The establishment of a heterologous expression system for syrbactins provided the basis for the generation of new syrbactins as proteasome inhibitors by molecular engineering, but the TE domain's specificity cannot be ignored.
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Affiliation(s)
- Xiaoying Bian
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, (Germany); Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, ShandaNanlu 27, 250100 Jinan, (China)
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12
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Dudler R. The role of bacterial phytotoxins in inhibiting the eukaryotic proteasome. Trends Microbiol 2013; 22:28-35. [PMID: 24284310 DOI: 10.1016/j.tim.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/25/2013] [Accepted: 10/30/2013] [Indexed: 11/19/2022]
Abstract
The ubiquitin-26S proteasome degradation system (UPS) plays a pivotal role in almost all aspects of plant life, including defending against pathogens. Although the proteasome is important for plant immunity, it has been found to be also exploited by pathogens using effectors to increase their virulence. Recent work on the XopJ effector and syringolin A/syrbactins has highlighted host proteasome inhibition as a virulence strategy of pathogens. This review will focus on these recent developments.
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Affiliation(s)
- Robert Dudler
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.
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13
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Rentsch A, Landsberg D, Brodmann T, Bülow L, Girbig AK, Kalesse M. Synthese und Pharmakologie von Proteasom-Inhibitoren. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207900] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Rentsch A, Landsberg D, Brodmann T, Bülow L, Girbig AK, Kalesse M. Synthesis and pharmacology of proteasome inhibitors. Angew Chem Int Ed Engl 2013; 52:5450-88. [PMID: 23526565 DOI: 10.1002/anie.201207900] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Indexed: 12/17/2022]
Abstract
Shortly after the discovery of the proteasome it was proposed that inhibitors could stabilize proteins which ultimately would trigger apoptosis in tumor cells. The essential questions were whether small molecules would be able to inhibit the proteasome without generating prohibitive side effects and how one would derive these compounds. Fortunately, "Mother Nature" has generated a wide variety of natural products that provide distinct selectivities and specificities. The chemical synthesis of these natural products finally provided access to analogues and optimized drugs of which two different classes have been approved for the treatment of malignancies. Despite these achievements, additional lead structures derived from nature are under investigation and will be discussed with regard to their biological potential and chemical challenges.
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Affiliation(s)
- Andreas Rentsch
- Institut für Organische Chemie and Centre of Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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15
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Dudler R. Manipulation of host proteasomes as a virulence mechanism of plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:521-42. [PMID: 23725468 DOI: 10.1146/annurev-phyto-082712-102312] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ubiquitin-26S proteasome degradation system (UPS) in plants is involved in the signal transduction of many cellular processes, including host immune responses triggered by pathogen attack. Attacking pathogens produce effectors that are translocated into host cells, where they interfere with the host's defense signaling in very specific ways. Perhaps not surprising in view of the broad involvement of the host proteasome in plant immunity, certain bacterial effectors exploit or require the host UPS for their action, as currently best studied in Pseudomonas syringae. Intriguingly, some P. syringae strains also secrete the virulence factor syringolin A, which irreversibly inhibits the proteasome by a novel mechanism. Here, the role of the UPS in plant defense and its exploitation by effectors are summarized, and the biology, taxonomic distribution, and emerging implications for virulence strategies of syringolin A and similar compounds are discussed.
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Affiliation(s)
- Robert Dudler
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland.
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16
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Dudnik A, Bigler L, Dudler R. Heterologous expression of a Photorhabdus luminescens syrbactin-like gene cluster results in production of the potent proteasome inhibitor glidobactin A. Microbiol Res 2012; 168:73-6. [PMID: 23079192 DOI: 10.1016/j.micres.2012.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/20/2012] [Accepted: 09/18/2012] [Indexed: 02/03/2023]
Abstract
Syrbactins are cyclic peptide derivatives which are known to inhibit the eukaryotic proteasome by irreversible covalent binding to its catalytic sites. The only two members of this family characterized to date, syringolin A and glidobactin A, are secreted by certain strains of Pseudomonas syringae pv. syringae and strain K481-B101 from the order Burkholderiales, respectively. Syrbactins are the products of mixed non-ribosomal peptide/polyketide synthases encoded by gene clusters with a characteristic architecture. Similar, but not identical gene clusters are present in several other bacterial genomes, including that of Photorhabdus luminescens subsp. laumondii TT01, which is therefore hypothesized to be able to produce a syrbactin-type proteasome inhibitor. Here we report the cloning of the putative syrbactins synthetase encoding gene cluster of Ph. luminescens into a cosmid vector and its heterologous expression in Pseudomonas putida. Analysis of culture supernatants of transformed Ps. putida by HPLC and mass spectrometry revealed the presence of glidobactin A, indicating that the syrbactins-like gene cluster of Ph. luminescens encodes a glidobactin A synthetase and that this organism has the capacity to synthesize glidobactin A.
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Affiliation(s)
- Alexey Dudnik
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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17
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Opoku-Ansah J, Ibarra-Rivera TR, Pirrung MC, Bachmann AS. Syringolin B-inspired proteasome inhibitor analogue TIR-203 exhibits enhanced biological activity in multiple myeloma and neuroblastoma. PHARMACEUTICAL BIOLOGY 2012; 50:25-29. [PMID: 22196580 DOI: 10.3109/13880209.2011.626784] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CONTEXT The bacterium Pseudomonas syringae pv. syringae (Pss) is a pathogen of many plant species and causes, for example, brown spot disease in bean plants (Phaseolus vulgaris). Pss excretes the syringolins, natural product molecules that act as a virulence factors and inhibit the proteasome of the host plants. OBJECTIVE Proteasome inhibitors belong to an important class of anticancer agents and bortezomib (Velcade(®)) has been Food and Drug Administration-approved for the treatment of multiple myeloma (MM) and mantle cell lymphoma. Syringolins represent a new class of proteasome inhibitors and the present work was undertaken to design a potent syringolin-inspired analogue (TIR-203) for anticancer drug development. MATERIALS AND METHODS TIR-203 was tested against human MM and neuroblastoma (NB) cells. Cancer cells were treated with TIR-203 at various concentrations (0-10 µM) and the cell viability was measured using the MTS assay. To determine the effects on proteasomal activities, the cell culture-based proteasome inhibition assay was used. Syringolin A (SylA) and bortezomib were included as controls. RESULTS TIR-203 inhibited the cell proliferation of MM and NB cells in a dose-dependent manner at significantly lower concentrations than SylA. In MM cells, TIR-203 effectively inhibited the chymotrypsin-like (CT-L), caspase-like (C-L), and trypsin-like (T-L) activities of the proteasome. In NB cells, TIR-203 inhibited the CT-L and C-L activities, but not the T-L activity. DISCUSSION AND CONCLUSIONS The newly designed proteasome inhibitor TIR-203 is more potent than the natural product SylA and strongly inhibits the cell viability and proteasomal activity of MM and NB cells.
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Affiliation(s)
- John Opoku-Ansah
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, USA
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18
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Ibarra-Rivera TR, Opoku-Ansah J, Ambadi S, Bachmann AS, Pirrung MC. Syntheses and cytotoxicity of syringolin B-based proteasome inhibitors. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.09.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Krahn D, Ottmann C, Kaiser M. The chemistry and biology of syringolins, glidobactins and cepafungins (syrbactins). Nat Prod Rep 2011; 28:1854-67. [PMID: 21904761 DOI: 10.1039/c1np00048a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Syrbactin is a subordinate term for the syringolin, glidobactin and cepafungin natural product families. Their grouping is based on their related molecular frameworks, similar biosynthesis pathways and, most importantly, identical modes-of-action, being irreversible proteasome inhibition. With this report, we aim to review their chemical biology, describing their common, but also differential characteristics.
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Affiliation(s)
- Daniel Krahn
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Germany
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Linington RG, Clark BR, Trimble EE, Almanza A, Ureña LD, Kyle DE, Gerwick WH. Antimalarial peptides from marine cyanobacteria: isolation and structural elucidation of gallinamide A. JOURNAL OF NATURAL PRODUCTS 2009; 72:14-7. [PMID: 19161344 PMCID: PMC2760338 DOI: 10.1021/np8003529] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As part of a continuing program to identify novel treatments for neglected parasitic diseases, the Panama International Cooperative Biodiversity Group (ICBG) program has been investigating the antimalarial potential of secondary metabolites from Panamanian marine cyanobacteria. From over 60 strains of cyanobacteria evaluated in our biological screens, the organic extract of a Schizothrix species from a tropical reef near Piedras Gallinas (Caribbean coast of Panama) showed potent initial antimalarial activity against the W2 chloroquine-resistant strain of Plasmodium falciparum. Bioassay-guided fractionation followed by 2D NMR analysis afforded the planar structure of a new and highly functionalized linear peptide, gallinamide A. Subsequent degradation and derivatization methods were used to determine the absolute configuration at most stereogenic centers in this unusual new metabolite.
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Affiliation(s)
- Roger G Linington
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA.
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Krasnoff SB, Keresztes I, Gillilan RE, Szebenyi DME, Donzelli BGG, Churchill ACL, Gibson DM. Serinocyclins A and B, cyclic heptapeptides from Metarhizium anisopliae. JOURNAL OF NATURAL PRODUCTS 2007; 70:1919-1924. [PMID: 18044842 DOI: 10.1021/np070407i] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Two new cyclic heptapeptides, serinocyclins A (1) and B (2), were isolated from conidia of the entomopathogenic fungus Metarhizium anisopliae. Structures were elucidated by a combination of mass spectrometric, NMR, and X-ray diffraction techniques. Serinocyclin A (1) contains three serine units, a hydroxyproline (Hyp), a beta-alanine (beta-Ala), and two uncommon nonproteinogenic amino acids, 1-aminocyclopropane-1-carboxylic acid (Acc) and gamma-hydroxylysine (HyLys). The peptide sequence established for 1 by NMR is cyclo-(Acc-Hyp-Ser1-HyLys-beta-Ala-Ser2-Ser3). Serinocyclin B (2) has Lys in place of the HyLys unit found in 1. Chiral amino acid analysis indicated the presence in both compounds of one (2 S,4 R)-Hyp, two L-Ser, and one D-Ser residue. A Lys found in the hydrolyzate of 2 was established as D-configured. A crystal structure of 1 established the position of the D-Ser (Ser2) and the absolute configuration of the HyLys unit (2 R,4 S). The absence of methyl groups is unusual among fungal peptides and, along with the charged lysyl side chain and multiple hydroxyl groups, contributes to the polar nature of the compounds. Serinocyclin A produced a sublethal locomotory defect in mosquito larvae at an EC 50 of 59 ppm.
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Minowa Y, Araki M, Kanehisa M. Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol 2007; 368:1500-17. [PMID: 17400247 DOI: 10.1016/j.jmb.2007.02.099] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 02/19/2007] [Accepted: 02/22/2007] [Indexed: 11/23/2022]
Abstract
We developed a highly accurate method to predict polyketide (PK) and nonribosomal peptide (NRP) structures encoded in microbial genomes. PKs/NRPs are polymers of carbonyl/peptidyl chains synthesized by polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS). We analyzed domain sequences corresponding to specific substrates and physical interactions between PKSs/NRPSs in order to predict which substrates (carbonyl/peptidyl units) are selected and assembled into highly ordered chemical structures. The predicted PKs/NRPs were represented as the sequences of carbonyl/peptidyl units to extract the structural motifs efficiently. We applied our method to 4529 PKSs/NRPSs and found 619 PKs/NRPs. We also collected 1449 PKs/NRPs whose chemical structures have been determined experimentally. The structural sequences were compared using the Smith-Waterman algorithm, and clustered into 271 clusters. From the compound clusters, we extracted 33 structural motifs that are significantly related with their bioactivities. We used the structural motifs to infer functions of 13 novel PKs/NRPs clusters produced by Pseudomonas spp. and Burkholderia spp. and found a putative virulence factor. The integrative analysis of genomic and chemical information given here will provide a strategy to predict the chemical structures, the biosynthetic pathways, and the biological activities of PKs/NRPs, which is useful for the rational design of novel PKs/NRPs.
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Affiliation(s)
- Yohsuke Minowa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan.
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Franco A, Pisarewicz K, Moller C, Mora D, Fields GB, Marì F. Hyperhydroxylation: A New Strategy for Neuronal Targeting by Venomous Marine Molluscs. MOLLUSCS 2006; 43:83-103. [PMID: 17153339 DOI: 10.1007/978-3-540-30880-5_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Venomous marine molluscs belonging to the genus Conus (cone snails) utilize a unique neurochemical strategy to capture their prey. Their venom is composed of a complex mixture of highly modified peptides (conopeptides) that interact with a wide range of neuronal targets. In this chapter, we describe a set of modifications based upon the hydroxylation of polypeptidic chains that are defining within the neurochemical strategy used by cone snails to capture their prey. In particular, we present a differential hydroxylation strategy that affects the neuronal targeting of a new set of a-conotoxins, mini-M conotoxins, conophans, and y-hydroxyconophans. Differential hydroxylation, preferential hydroxylation and hyperhydroxylation have been observed in these conopeptide families as a means of augmenting the venom arsenal used by cone snails for neuronal targeting and prey capture.
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Affiliation(s)
- A Franco
- Department of Chemistry & Biochemistry, Centre of Excellence in Biomedical and Marine Biotechnology, Florida Atlantic University, 777 Glades Rd., Boca Raton, 33431 Florida, USA
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Amrein H, Makart S, Granado J, Shakya R, Schneider-Pokorny J, Dudler R. Functional analysis of genes involved in the synthesis of syringolin A by Pseudomonas syringae pv. syringae B301 D-R. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2004; 17:90-97. [PMID: 14714872 DOI: 10.1094/mpmi.2004.17.1.90] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Strains of the phytopathogenic bacterium Pseudomonas syringae pv. syringae secrete a family of structurally closely related peptide derivatives dubbed syringolins, of which syringolin A is the major variant. The function of syringolins in the interaction of P. syringae pv. syringae with their host plants presently is unknown. It is hypothesized that they may constitute virulence factors. However, syringolins are determinants recognized and reacted to by nonhost plant species, and syringolin A has been shown to induce hypersensitive death of cells colonized by powdery mildew in wheat and, thus, to reprogram a compatible interaction into an incompatible one. Syringolin A is an unusual derivative of a tripeptide that contains a 12-membered ring consisting of the amino acids 5-methyl-4-amino-2-hexenoic acid and 3,4-dehydrolysine, two nonproteinogenic amino acids. Here we report the cloning, sequencing, and analysis of genes involved in the biosynthesis of syringolin A. The genes encode proteins consisting of modules typical for nonribosomal peptide synthetases and type I polyketide synthetases, as well as proteins likely involved in the transcriptional regulation of syringolin A biosynthesis and in syringolin A export. The structure and arrangement of the modules lead to the formulation of a model explaining the synthesis of the tripeptide, including the formation of the two nonproteinogenic amino acids in the ring structure of syringolin A.
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Affiliation(s)
- Hans Amrein
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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Hensens OD. Modern spectroscopic approaches to structure elucidation. BIOTECHNOLOGY (READING, MASS.) 1994; 26:389-444. [PMID: 7749313 DOI: 10.1016/b978-0-7506-9003-4.50020-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- O D Hensens
- Merck Research Laboratories, Rahway, New Jersey, USA
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Meng Q, Hesse M. Synthetic approaches toward glidobamine, the core structure of the glidobactin antibiotics. Tetrahedron 1991. [DOI: 10.1016/s0040-4020(01)86557-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
The study of antibiotics and other fermentation products has shown that a seemingly unlimited number of compounds with diverse structures are produced by microorganisms. The continued high rate of discovery of new chemical entities, in the light of the abundance of microbial products already described, is due to creative screening procedures that incorporate such features as the emphasis on unusual microorgnaisms, their special propagation and fermentation requirements, supersensitive and highly selective assays, genetic engineering both for the biosynthesis of new compounds and in the development of screening systems, early in vivo evaluation, improved isolation techniques, modern procedures for structure determination, computer-assisted identification, and an efficient multidisciplinary approach. This review focuses on the genesis and development of the gamut of methodologies that have led to the successful detection of the wide variety of novel secondary metabolites that include antibacterial, antigungal, antiviral and antitumour antibiotics, enzyme inhibitors, pharmacologically and immunologically active agents, products useful in agriculture and animal husbandry, microbial regulators, and other compounds for which no bioactive role has yet been found.
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Affiliation(s)
- C M Franco
- Microbiology Department, Hoechst Centre for Basic Research, Hoechst India Limited, Lal Bahadur Shastri Marg, Mulund, Bombay
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