1
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Koller TO, Berger MJ, Morici M, Paternoga H, Bulatov T, Di Stasi A, Dang T, Mainz A, Raulf K, Crowe-McAuliffe C, Scocchi M, Mardirossian M, Beckert B, Vázquez-Laslop N, Mankin A, Süssmuth RD, Wilson DN. Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595107. [PMID: 38826346 PMCID: PMC11142091 DOI: 10.1101/2024.05.21.595107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae. We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
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Affiliation(s)
- Timm O. Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Max J. Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Timur Bulatov
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Tam Dang
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Karoline Raulf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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2
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Dulin CC, Sharma P, Frigo L, Voehler MW, Iverson TM, Bachmann BO. EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster. J Biol Chem 2023:104893. [PMID: 37286037 PMCID: PMC10338323 DOI: 10.1016/j.jbc.2023.104893] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023] Open
Abstract
The everninomicins are bacterially produced antibiotic octasaccharides characterized by the presence of two interglycosidic spirocyclic ortho-δ-lactone (orthoester) moieties. The terminating G- and H-ring sugars, L-lyxose and C-4 branched sugar β-D-eurekanate, are proposed to be biosynthetically derived from nucleotide diphosphate pentose sugar pyranosides; however, the identity of these precursors and their biosynthetic origin remain to be determined. Herein we identify a new glucuronic acid decarboxylase from Micromonospora belonging to the superfamily of short-chain dehydrogenase/reductase enzymes, EvdS6. Biochemical characterization demonstrated that EvdS6 is an NAD+-dependent bifunctional enzyme that produces a mixture of two products, differing in the sugar C-4 oxidation state. This product distribution is atypical for glucuronic acid decarboxylating enzymes, most of which favor production of the reduced sugar and a minority of which favor release of the oxidized product. Spectroscopic and stereochemical analysis of reaction products revealed that the first product released is the oxidatively produced 4-keto-D-xylose and the second product is the reduced D-xylose. X-ray crystallographic analysis of EvdS6 at 1.51 Å resolution with bound co-factor and TDP demonstrated that the overall geometry of the EvdS6 active site is conserved with other SDR enzymes and enabled studies probing structural determinants for the reductive half of the net neutral catalytic cycle. Critical active site threonine and aspartate residues were unambiguously identified as essential in the reductive step of the reaction and resulted in enzyme variants producing almost exclusively the keto sugar. This work defines potential precursors for the G-ring L-lyxose and resolves likely origins of the H-ring β-D-eurekanate sugar precursor.
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Affiliation(s)
- Callie C Dulin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Laura Frigo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
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3
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Zhu M, Wang L, Zhang H, Zhang L, Tan B, Huang Q, Zhu Y, Zhang C. Biosynthesis and Engineered Overproduction of Everninomicins with Promising Activity against Multidrug-Resistant Bacteria. ACS Synth Biol 2023; 12:1520-1532. [PMID: 37084337 DOI: 10.1021/acssynbio.3c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Ribosome-targeting oligosaccharides, everninomicins (EVNs), are promising drug leads with a unique mode of action distinct from that of currently used antibiotics in human therapy. However, the low yields in natural microbial producers hamper an efficient preparation of EVNs for detailed structure-activity relationship analysis. Herein, we enhance the production of EVNs by duplicating the biosynthetic gene cluster (BGC) in Micromonospora sp. SCSIO 07395 and thus obtain multiple EVNs that are sufficient for bioactivity evaluation. EVNs (1-5) are shown to significantly inhibit the growth of multidrug-resistant Gram-positive staphylococcal, enterococcal, and streptococcal strains and Gram-negative pathogens Acinetobacter baumannii and Vibrio cholerae, with micromolar to nanomolar potency, which are comparable or superior to vancomycin, linezolid, and daptomycin. Furthermore, the BGC duplication strategy is proven effective in stepwisely improving titers of the bioactive EVN M (5) from the trace amount to 98.6 mg L-1. Our findings demonstrate the utility of a bioengineering approach for enhanced production and chemical diversification of the medicinally promising EVNs.
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Affiliation(s)
- Mengyi Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lijuan Wang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, College of Veterinary Medicine, Wuhan 430070, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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4
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Koller TO, Scheid U, Kösel T, Herrmann J, Krug D, Boshoff HIM, Beckert B, Evans JC, Schlemmer J, Sloan B, Weiner DM, Via LE, Moosa A, Ioerger TR, Graf M, Zinshteyn B, Abdelshahid M, Nguyen F, Arenz S, Gille F, Siebke M, Seedorf T, Plettenburg O, Green R, Warnke AL, Ullrich J, Warrass R, Barry CE, Warner DF, Mizrahi V, Kirschning A, Wilson DN, Müller R. The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition. J Am Chem Soc 2023; 145:851-863. [PMID: 36603206 PMCID: PMC9853869 DOI: 10.1021/jacs.2c08816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against Mycobacterium tuberculosis. To ensure compound supply for further development, we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by the development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing, and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. These studies open avenues for structure-based scaffold improvement toward development as an antibacterial agent.
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Affiliation(s)
- Timm O. Koller
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ullrich Scheid
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Teresa Kösel
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Jennifer Herrmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Daniel Krug
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,Department
of Pharmacy, Saarland University, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bertrand Beckert
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Joanna C. Evans
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Jan Schlemmer
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Becky Sloan
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Danielle M. Weiner
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Laura E. Via
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Atica Moosa
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas 77843, United States
| | - Michael Graf
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Boris Zinshteyn
- Department
of Molecular Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Maha Abdelshahid
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Fabian Nguyen
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Stefan Arenz
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Franziska Gille
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Maik Siebke
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Tim Seedorf
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Oliver Plettenburg
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Rachel Green
- Department
of Molecular Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anna-Luisa Warnke
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Joachim Ullrich
- MSD
Animal Health Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany
| | - Ralf Warrass
- MSD
Animal Health Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany
| | - Clifton E. Barry
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Digby F. Warner
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Andreas Kirschning
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,
| | - Daniel N. Wilson
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany,
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,Department
of Pharmacy, Saarland University, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany,
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5
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Carneiro LM, Bartoloni FH, Angolini CFF, Keppler AF. Solvent-free synthesis of nitrone-containing template as a chemosensor for selective detection of Cu(II) in water. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120473. [PMID: 34715559 DOI: 10.1016/j.saa.2021.120473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
A state-of-the-art method was developed for repurposing nitrone-containing compounds in the chemosensory field, the ability of the designed molecules to chelate metal cations was evaluated, and their unprecedented solubility in water was confirmed. A facile, rapid, and solvent-free method of synthesizing small molecular mass chemosensors was developed by using a modulative α-aryl-N-aryl nitrone template. α-(Z)-Imidazol-4-ylmethylen-N-phenyl nitrone (Nit1) and α-(Z)-2-pyridyl-N-phenyl nitrone (Nit2) were prepared in 15 min, isolated in less than 60 min with ca. 90% yield, and screened against nine metal cations. Nit1 is a small-molecular-mass compound (188 g mol-1) that is water-soluble and has specificity for sensing Cu2+ with an association constant of K = 1.53 × 1010 and a limit of detection (LOD) of 0.06 ppm. These properties make Nit1 a competitive chemosensor for the detection of Cu2+ in aqueous solution. The nitrone-containing template used in this study is a step forward for new and small chemosensory entities.
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Affiliation(s)
- Leonardo M Carneiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP ZIP CODE 09210-580, Brazil
| | - Fernando H Bartoloni
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP ZIP CODE 09210-580, Brazil
| | - Célio F F Angolini
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP ZIP CODE 09210-580, Brazil
| | - Artur F Keppler
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, Santo André, SP ZIP CODE 09210-580, Brazil.
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6
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Johnson RA, Chan AN, Ward RD, McGlade CA, Hatfield BM, Peters JM, Li B. Inhibition of Isoleucyl-tRNA Synthetase by the Hybrid Antibiotic Thiomarinol. J Am Chem Soc 2021; 143:12003-12013. [PMID: 34342433 DOI: 10.1021/jacs.1c02622] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hybrid antibiotics are an emerging antimicrobial strategy to overcome antibiotic resistance. The natural product thiomarinol A is a hybrid of two antibiotics: holothin, a dithiolopyrrolone (DTP), and marinolic acid, a close analogue of the drug mupirocin that is used to treat methicillin-resistant Staphylococcus aureus (MRSA). DTPs disrupt metal homeostasis by chelating metal ions in cells, whereas mupirocin targets the essential enzyme isoleucyl-tRNA synthetase (IleRS). Thiomarinol A is over 100-fold more potent than mupirocin against mupirocin-sensitive MRSA; however, its mode of action has been unknown. We show that thiomarinol A targets IleRS. A knockdown of the IleRS-encoding gene, ileS, exhibited sensitivity to a synthetic analogue of thiomarinol A in a chemical genomics screen. Thiomarinol A inhibits MRSA IleRS with a picomolar Ki and binds to IleRS with low femtomolar affinity, 1600 times more tightly than mupirocin. We find that thiomarinol A remains effective against high-level mupirocin-resistant MRSA and provide evidence to support a dual mode of action for thiomarinol A that may include both IleRS inhibition and metal chelation. We demonstrate that MRSA develops resistance to thiomarinol A to a substantially lesser degree than mupirocin and the potent activity of thiomarinol A requires hybridity between DTP and mupirocin. Our findings identify a mode of action of a natural hybrid antibiotic and demonstrate the potential of hybrid antibiotics to combat antibiotic resistance.
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Affiliation(s)
- Rachel A Johnson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andrew N Chan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Caylie A McGlade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Breanne M Hatfield
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin 53726, United States
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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7
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Microbial Oligosaccharides with Biomedical Applications. Mar Drugs 2021; 19:md19060350. [PMID: 34205503 PMCID: PMC8234114 DOI: 10.3390/md19060350] [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: 05/21/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial oligosaccharides have been regarded as one of the most appealing natural products attributable to their potent and selective bioactivities, such as antimicrobial activity, inhibition of α-glucosidases and lipase, interference of cellular recognition and signal transduction, and disruption of cell wall biosynthesis. Accordingly, a handful of bioactive oligosaccharides have been developed for the treatment of bacterial infections and type II diabetes mellitus. Given that naturally occurring oligosaccharides have increasingly gained recognition in recent years, a comprehensive review is needed. The current review highlights the chemical structures, biological activities and divergent biosynthetic origins of three subgroups of oligomers including the acarviosine-containing oligosaccharides, saccharomicins, and orthosomycins.
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8
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Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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