1
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Bonatelli ML, Rohwerder T, Popp D, Liu Y, Akay C, Schultz C, Liao KP, Ding C, Reemtsma T, Adrian L, Kleinsteuber S. Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide. Front Microbiol 2023; 14:1223838. [PMID: 37577448 PMCID: PMC10413263 DOI: 10.3389/fmicb.2023.1223838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/27/2023] [Indexed: 08/15/2023] Open
Abstract
Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and an acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA amidase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and likely evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.
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Affiliation(s)
- Maria L. Bonatelli
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Yu Liu
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Caglar Akay
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Carolyn Schultz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Kuan-Po Liao
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Chang Ding
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Chair for Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
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2
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Wojnowska M, Feng X, Chen Y, Deng H, O'Hagan D. Identification of Genes Essential for Fluorination and Sulfamylation within the Nucleocidin Gene Clusters of Streptomyces calvus and Streptomyces virens. Chembiochem 2023; 24:e202200684. [PMID: 36548247 PMCID: PMC10946740 DOI: 10.1002/cbic.202200684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions, most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, but had no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP, we identified two genes (nucW, nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis.
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Affiliation(s)
- Marta Wojnowska
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Xuan Feng
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Yawen Chen
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Hai Deng
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - David O'Hagan
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
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3
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Gorelik DJ, Turner JA, Taylor MS. Catalyst-Controlled, Site-Selective Sulfamoylation of Carbohydrate Derivatives. Org Lett 2022; 24:5249-5253. [PMID: 35729742 DOI: 10.1021/acs.orglett.2c01590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods for site-selective sulfamoylation of secondary hydroxyl groups in pyranosides are described. Using a boronic acid catalyst, selective installation of a Boc-protected sulfamoyl group at the equatorial position of cis-diols in manno- and galacto-configured substrates has been achieved. Activation of trans-diol groups in gluco- and galacto-configured substrates is also possible by employing an organotin catalyst.
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Affiliation(s)
- Daniel J Gorelik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Julia A Turner
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mark S Taylor
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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4
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Xie SC, Metcalfe RD, Dunn E, Morton CJ, Huang SC, Puhalovich T, Du Y, Wittlin S, Nie S, Luth MR, Ma L, Kim MS, Pasaje CFA, Kumpornsin K, Giannangelo C, Houghton FJ, Churchyard A, Famodimu MT, Barry DC, Gillett DL, Dey S, Kosasih CC, Newman W, Niles JC, Lee MC, Baum J, Ottilie S, Winzeler EA, Creek DJ, Williamson N, Parker MW, Brand SL, Langston SP, Dick LR, Griffin MD, Gould AE, Tilley L. Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy. Science 2022; 376:1074-1079. [PMID: 35653481 PMCID: PMC7613620 DOI: 10.1126/science.abn0611] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Aminoacyl transfer RNA (tRNA) synthetases (aaRSs) are attractive drug targets, and we present class I and II aaRSs as previously unrecognized targets for adenosine 5'-monophosphate-mimicking nucleoside sulfamates. The target enzyme catalyzes the formation of an inhibitory amino acid-sulfamate conjugate through a reaction-hijacking mechanism. We identified adenosine 5'-sulfamate as a broad-specificity compound that hijacks a range of aaRSs and ML901 as a specific reagent a specific reagent that hijacks a single aaRS in the malaria parasite Plasmodium falciparum, namely tyrosine RS (PfYRS). ML901 exerts whole-life-cycle-killing activity with low nanomolar potency and single-dose efficacy in a mouse model of malaria. X-ray crystallographic studies of plasmodium and human YRSs reveal differential flexibility of a loop over the catalytic site that underpins differential susceptibility to reaction hijacking by ML901.
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Affiliation(s)
- Stanley C. Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Riley D. Metcalfe
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Craig J. Morton
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shih-Chung Huang
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland,University of Basel, 4003 Basel, Switzerland
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Liting Ma
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Mi-Sook Kim
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | | | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Fiona J. Houghton
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | - Daniel C. Barry
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David L. Gillett
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Clara C. Kosasih
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - William Newman
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Marcus C.S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael W. Parker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia,St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Stephen L. Brand
- Medicines for Malaria Venture, PO Box 1826, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - Steven P. Langston
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Lawrence R. Dick
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia,Seofon Consulting, 30 Tucker Street, Natick, Massachusetts 01760, USA
| | - Michael D.W. Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alexandra E. Gould
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA,For correspondence. Alexandra E. Gould, Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA, (Chemistry) and Leann Tilley, Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia. (Biology)
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia,For correspondence. Alexandra E. Gould, Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA, (Chemistry) and Leann Tilley, Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia. (Biology)
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5
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Pasternak A, Bechthold A, Zechel DL. Identification of genes essential for sulfamate and fluorine incorporation during nucleocidin biosynthesis. Chembiochem 2022; 23:e202200140. [PMID: 35544615 DOI: 10.1002/cbic.202200140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/05/2022] [Indexed: 11/07/2022]
Abstract
Nucleocidin is an adenosine derivative containing 4'-fluoro and 5'-O-sulfamoyl substituents. In this study, nucleocidin biosynthesis is examined in two newly discovered producers, Streptomyces virens B-24331 and Streptomyces aureorectus B-24301, which produce nucleocidin and related derivatives at titres 30-fold greater than S. calvus . This enabled the identification of two new O -acetylated nucleocidin derivatives, and a potential glycosyl- O-acetyltransferase. Disruption of nucJ , nucG , and nucI , within S. virens B-24331, specifying a radical SAM / Fe-S dependent enzyme, sulfatase, and arylsulfatase, respectively, led to loss of 5'-O-sulfamoyl biosynthesis, but not fluoronucleoside production. Disruption of nucN , nucK , and nucO specifying an amidinotransferase, and two sulfotransferases respectively, led to loss of fluoronucleoside production. Identification of S. virens B-24331 as a genetically tractable and high producing strain sets the stage for understanding nucleocidin biosynthesis and highlights the utility of using 16S-RNA sequences to identify alternative producers of valuable compounds in the absence of genome sequence data.
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Affiliation(s)
- Aleksandra Pasternak
- Queen's University Faculty of Arts and Science, Chemistry, 90 Bader Lane, Chernoff Hall, K7L 3N6, Kingston, CANADA
| | - Andreas Bechthold
- Albert-Ludwigs-Universität Freiburg Fakultät für Chemie Pharmazie und Geowissenschaften: Albert-Ludwigs-Universitat Freiburg Fakultat fur Chemie und Pharmazie, Pharmaceutical Biology and Biotechnology, Stefan-Meier-Str. 19, 79104, Freiburg i. Br., GERMANY
| | - David L Zechel
- Queen's University, Department of Chemsitry, Chernoff Hall, K7L 3N6, Kingston, CANADA
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6
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Chen Y, Zhang Q, Feng X, Wojnowska M, O'Hagan D. Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 are producers of the antibiotic nucleocidin and 4'-fluoroadenosine is identified as a co-product. Org Biomol Chem 2021; 19:10081-10084. [PMID: 34779476 DOI: 10.1039/d1ob01898a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genome homology and the presence of a putative biosynthetic gene cluster identified Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 as candidate producers of the antibiotic nucleocidin 1. Indeed when these bacterial strains were cultured in a medium supplemented with fluoride (4 mM) they each produced nucleocidin 1 and the previously identified 4'-fluoro-3'-O-β-glucosylated adenosine 2 and its sulfamylated derivative 3. In both of these cases 4'-fluoroadenosine 9 is also identified as a natural product although it has never been observed during fermentations of Streptomyces calvus, the original source of nucleocidin 1. The identity of 4'-fluoroadenosine 9 was confirmed by a total synthesis as well as by its in vitro enzymatic conversion to metabolite 2 using the glucosyl transferase enzyme, NucGT.
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Affiliation(s)
- Yawen Chen
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Qingzhi Zhang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Xuan Feng
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - Marta Wojnowska
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
| | - David O'Hagan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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7
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Lopez JAV, Nogawa T, Yoshida K, Futamura Y, Osada H. 2-Methylthio-N7-methyl-cis-zeatin, a new antimalarial natural product isolated from a Streptomyces culture. Biosci Biotechnol Biochem 2021; 86:31-36. [PMID: 34734225 DOI: 10.1093/bbb/zbab192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022]
Abstract
2-Methylthio-N7-methyl-cis-zeatin (1) was isolated from the culture broth of Streptomyces sp. 80H647 along with two known purine derivatives, 5'-methylthioinosine (2) and AT-265 (dealanylascamycin, 3). The structure elucidation of compound 1 was accomplished by HRMS and NMR analyses. It inhibited the growth of Plasmodium falciparum 3D7 with a GI50 of 2.4 μM and had no effect on the growth of Arabidopsis at 2 μM. This is the first report of an N7-methylated zeatin-type natural product from Streptomyces and as an antimalarial compound.
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Affiliation(s)
- Julius Adam V Lopez
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Toshihiko Nogawa
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Kazuko Yoshida
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Yushi Futamura
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama, Japan
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8
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Chhibber-Goel J, Yogavel M, Sharma A. Structural analyses of the malaria parasite aminoacyl-tRNA synthetases provide new avenues for antimalarial drug discovery. Protein Sci 2021; 30:1793-1803. [PMID: 34184352 DOI: 10.1002/pro.4148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/12/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Malaria is a parasitic illness caused by the genus Plasmodium from the apicomplexan phylum. Five plasmodial species of P. falciparum (Pf), P. knowlesi, P. malariae, P. ovale, and P. vivax (Pv) are responsible for causing malaria in humans. According to the World Malaria Report 2020, there were 229 million cases and ~ 0.04 million deaths of which 67% were in children below 5 years of age. While more than 3 billion people are at risk of malaria infection globally, antimalarial drugs are their only option for treatment. Antimalarial drug resistance keeps arising periodically and thus threatens the main line of malaria treatment, emphasizing the need to find new alternatives. The availability of whole genomes of P. falciparum and P. vivax has allowed targeting their unexplored plasmodial enzymes for inhibitor development with a focus on multistage targets that are crucial for parasite viability in both the blood and liver stages. Over the past decades, aminoacyl-tRNA synthetases (aaRSs) have been explored as anti-bacterial and anti-fungal drug targets, and more recently (since 2009) aaRSs are also the focus of antimalarial drug targeting. Here, we dissect the structure-based knowledge of the most advanced three aaRSs-lysyl- (KRS), prolyl- (PRS), and phenylalanyl- (FRS) synthetases in terms of development of antimalarial drugs. These examples showcase the promising potential of this family of enzymes to provide druggable targets that stall protein synthesis upon inhibition and thereby kill malaria parasites selectively.
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Affiliation(s)
- Jyoti Chhibber-Goel
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Manickam Yogavel
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Amit Sharma
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India.,ICMR-National Institute of Malaria Research, New Delhi, India
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9
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N-Acetyl-α-hydroxy-β-oxotryptamine, a racemic natural product isolated from Streptomyces sp. 80H647. J Antibiot (Tokyo) 2021; 74:477-479. [PMID: 33879862 DOI: 10.1038/s41429-021-00420-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 03/11/2021] [Indexed: 11/09/2022]
Abstract
N-acetyl-α-hydroxy-β-oxotryptamine (1) along with N-acetyl-β-oxotryptamine (2) and pimprinine (3) were isolated from the culture broth of Streptomyces sp. 80H647. Compound 1 was found to be a racemate via X-ray diffraction analysis and the enantiomers were successfully purified by chiral-phase HPLC. The absolute configuration was assigned by comparison of the calculated and experimental ECD spectra. The α-hydroxy moiety of 1 was vital for cytotoxicity against different cancer cell lines.
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10
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Sguazzin MA, Johnson JW, Magolan J. Hexafluoroisopropyl Sulfamate: A Useful Reagent for the Synthesis of Sulfamates and Sulfamides. Org Lett 2021; 23:3373-3378. [DOI: 10.1021/acs.orglett.1c00855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew A. Sguazzin
- Department of Biochemistry & Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 3Z5, Canada
| | - Jarrod W. Johnson
- Department of Biochemistry & Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 3Z5, Canada
| | - Jakob Magolan
- Department of Biochemistry & Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 3Z5, Canada
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11
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Awakawa T, Barra L, Abe I. Biosynthesis of sulfonamide and sulfamate antibiotics in actinomycete. J Ind Microbiol Biotechnol 2021; 48:6123731. [PMID: 33928358 PMCID: PMC9113183 DOI: 10.1093/jimb/kuab001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/21/2020] [Indexed: 02/04/2023]
Abstract
Abstract
Sulfonamides and sulfamates are a group of organosulfur compounds that contain the signature sulfamoyl structural motif. These compounds were initially only known as synthetic antibacterial drugs but were later also discovered as natural products. Eight highly potent examples have been isolated from actinomycetes to date, illustrating the large biosynthetic repertoire of this bacterial genus. For the biosynthesis of these compounds, several distinct and unique biosynthetic machineries have been discovered, capable to generate the unique S–N bond. For the creation of novel, second generation natural products by biosynthetic engineering efforts, a detailed understanding of the underlying enzyme machinery toward potent structural motifs is crucial. In this review, we aim to summarize the current state of knowledge on sulfonamide and sulfamate biosynthesis. A detailed discussion for the secondary sulfamate ascamycin, the tertiary sulfonamide sulfadixiamycin A, and the secondary sulfonamide SB-203208 is provided and their bioactivities and mode of actions are discussed.
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Affiliation(s)
| | | | - Ikuro Abe
- Correspondence should be addressed to: Lena Barra at
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12
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Feng X, Bello D, O'Hagan D. Isolation of 5'- O-sulfamyladenosine and related 3'- O-β-glucosylated adenosines from the nucleocidin producer Streptomyces calvus. RSC Adv 2021; 11:5291-5294. [PMID: 35423098 PMCID: PMC8694766 DOI: 10.1039/d1ra00235j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/03/2023] Open
Abstract
The isolation of three adenosine based metabolites 6-8 from Streptomyces calvus is reported. The metabolites are structurally related to the fluorine containing antibiotic nucleocidin 1 and two recently identified glycosylated fluoroadenosines 2 and 3, however in this case the three metabolites do not contain a fluorine, suggesting that the biosynthetic enzymes to the fluorometabolites also process their non-fluorinated counterparts.
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Affiliation(s)
- Xuan Feng
- School of Chemistry, University of St Andrews North Haugh, St Andrews, Fife, KY16 9ST UK
| | - Davide Bello
- School of Chemistry, University of St Andrews North Haugh, St Andrews, Fife, KY16 9ST UK
| | - David O'Hagan
- School of Chemistry, University of St Andrews North Haugh, St Andrews, Fife, KY16 9ST UK
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13
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Shi L, Wu Z, Zhang Y, Zhang Z, Fang W, Wang Y, Wan Z, Wang K, Ke S. Herbicidal Secondary Metabolites from Actinomycetes: Structure Diversity, Modes of Action, and Their Roles in the Development of Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:17-32. [PMID: 31809036 DOI: 10.1021/acs.jafc.9b06126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Weeds had caused significant loss for crop production in the process of agriculture. Herbicides have played an important role in securing crop production. However, the high reliance on herbicides has led to environmental issues as well as the evolution of herbicide resistance. Thus, there is an urgent need for new herbicides with safer toxicological profiles and novel modes of action. Actinomycetes produce very diverse bioactive compounds, of which some show potent biopesticidal activity. The herbicidal secondary metabolites from actinomycetes can be classified into several groups, such as amino acids, peptides, nucleosides, macrolides, lactones, amide, amines, etc., some of which have been successfully developed as commercial herbicides. The structure diversity and evolved biological activity of secondary metabolites from actinomycetes can offer opportunities for the development of both directly used bioherbicides and synthetic herbicides with new target sites, and thus, this review focuses on the structure, herbicidal activity, and modes of action of secondary metabolites from actinomycetes.
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Affiliation(s)
- Liqiao Shi
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Zhaoyuan Wu
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Yani Zhang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Zhigang Zhang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Wei Fang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Yueying Wang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Zhongyi Wan
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Kaimei Wang
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
| | - Shaoyong Ke
- Hubei Biopesticide Engineering Research Centre , Hubei Academy of Agricultural Sciences , Wuhan , Hubei 430064 , People's Republic of China
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14
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Feng X, Bello D, Lowe PT, Clark J, O'Hagan D. Two 3'- O-β-glucosylated nucleoside fluorometabolites related to nucleocidin in Streptomyces calvus. Chem Sci 2019; 10:9501-9505. [PMID: 32110306 PMCID: PMC7017864 DOI: 10.1039/c9sc03374b] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
The antibiotic nucleocidin is a product of the soil bacterium Streptomyces calvus T-3018. It is among the very rare fluorine containing natural products but is distinct from the other fluorometabolites in that it is not biosynthesised from 5'-fluorodeoxyadenosine via the fluorinase. It seems to have a unique enzymatic fluorination process. We disclose here the structures of two 4'-fluoro-3'-O-β-glucosylated metabolites (F-Mets I and II) which appear and then disappear before nucleocidin production in batch cultures of S. calvus. Full genome sequencing of S. calvus T-3018 and an analysis of the putative biosynthetic gene cluster for nucleocidin identified UDP-glucose dependent glucosyl transferase (nucGT) and glucosidase (nucGS) genes within the cluster. We demonstrate that these genes express enzymes that have the capacity to attach and remove glucose from the 3'-O-position of adenosine analogues. In the case of F-Met II, deglucosylation with the NucGS glucosidase generates nucleocidin suggesting a role in its biosynthesis. Gene knockouts of nucGT abolished nucelocidin production.
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Affiliation(s)
- Xuan Feng
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - Davide Bello
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - Phillip T Lowe
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - Joshua Clark
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
| | - David O'Hagan
- School of Chemistry , University of St Andrews , North Haugh, St Andrews , Fife , KY16 9ST , UK .
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15
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Zhang S, Xiong H, Lu F, Ma F, Gu Y, Ma P, Xu H, Yang G. Synthesis of N-Acyl Sulfamates from Fluorosulfonates and Potassium Trimethylsilyloxyl Imidates. J Org Chem 2019; 84:15380-15388. [DOI: 10.1021/acs.joc.9b02394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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16
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Osada H. Discovery and applications of nucleoside antibiotics beyond polyoxin. J Antibiot (Tokyo) 2019; 72:855-864. [PMID: 31554959 DOI: 10.1038/s41429-019-0237-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 01/28/2023]
Abstract
Nucleoside antibiotics possess various biological activities such as antibacterial, antifungal, anticancer, and herbicidal activities. RIKEN scientists contributed to this area of research with two representative antifungal nucleoside antibiotics, blasticidin S and polyoxin. Blasticidin S was the first antibiotic exploited in agriculture worldwide. Meanwhile, the polyoxins discovered by Isono and Suzuki are still used globally as an agricultural antibiotic. In this review article, the research on nucleoside antibiotics mainly done by Isono and his collaborators is summarized from the discovery of polyoxin to subsequent investigations.
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Affiliation(s)
- Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako-shi, Saitama, 351-0198, Japan.
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17
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Nocardamin glucuronide, a new member of the ferrioxamine siderophores isolated from the ascamycin-producing strain Streptomyces sp. 80H647. J Antibiot (Tokyo) 2019; 72:991-995. [DOI: 10.1038/s41429-019-0217-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/04/2019] [Accepted: 07/10/2019] [Indexed: 11/09/2022]
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18
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Gulick AM, Aldrich CC. Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes. Nat Prod Rep 2019; 35:1156-1184. [PMID: 30046790 DOI: 10.1039/c8np00044a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to early 2018 The Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) are families of modular enzymes that produce a tremendous diversity of natural products, with antibacterial, antifungal, immunosuppressive, and anticancer activities. Both enzymes utilize a fascinating modular architecture in which the synthetic intermediates are covalently attached to a peptidyl- or acyl-carrier protein that is delivered to catalytic domains for natural product elongation, modification, and termination. An investigation of the structural mechanism therefore requires trapping the often transient interactions between the carrier and catalytic domains. Many novel chemical probes have been produced to enable the structural and functional investigation of multidomain NRPS and PKS structures. This review will describe the design and implementation of the chemical tools that have proven to be useful in biochemical and biophysical studies of these natural product biosynthetic enzymes.
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Affiliation(s)
- Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 955 Main St, Buffalo, NY 14203, USA.
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19
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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20
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Evans CE, Si Y, Matarlo JS, Yin Y, French JB, Tonge PJ, Tan DS. Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE. Biochemistry 2019; 58:1918-1930. [PMID: 30912442 PMCID: PMC6653581 DOI: 10.1021/acs.biochem.9b00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
N-Acyl sulfamoyladenosines (acyl-AMS) have been used
extensively to inhibit adenylate-forming enzymes that are involved in a wide
range of biological processes. These acyl-AMS inhibitors are nonhydrolyzable
mimics of the cognate acyl adenylate intermediates that are bound tightly by
adenylate-forming enzymes. However, the anionic acyl sulfamate moiety presents a
pharmacological liability that may be detrimental to cell permeability and
pharmacokinetic profiles. We have previously developed the acyl sulfamate
OSB-AMS (1) as a potent inhibitor of the adenylate-forming enzyme
MenE, an o-succinylbenzoate-CoA (OSB-CoA) synthetase that is
required for bacterial menaquinone biosynthesis. Herein, we report the use of
computational docking to develop novel, non-acyl sulfamate inhibitors of MenE. A
m-phenyl ether-linked analogue (5) was found
to be the most potent inhibitor (IC50 = 8 μM;
Kd = 244 nM), and its X-ray co-crystal structure
was determined to characterize its binding mode in comparison to the
computational prediction. This work provides a framework for the development of
potent non-acyl sulfamate inhibitors of other adenylate-forming enzymes in the
future.
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21
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Gilles P, Veryser C, Vangrunderbeeck S, Ceusters S, Van Meervelt L, De Borggraeve WM. Synthesis of N-Acyl Sulfamates from Fluorosulfates and Amides. J Org Chem 2018; 84:1070-1078. [DOI: 10.1021/acs.joc.8b02785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Ubukata M. The logic of biologically active small molecules: amazing ability of microorganisms*. Biosci Biotechnol Biochem 2018; 82:1063-1072. [DOI: 10.1080/09168451.2018.1451740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
In this review article, I will outline my way of thinking about biologically active small molecules. The structure of liposidomycin B from Streptomyces species resulted in my initial sense that a structure tells its function. A biologically active small molecule may save directly or indirectly a number of people. Even if the molecule has not been used as a therapeutic agent, it can be used as a useful chemical probe for dissecting a living cell into different biochemical pieces. Such biologically active small molecules derived from microorganisms have been primarily found in cultivable microorganisms that make up only 1% of total microbes in nature. Discovery of novel growth factors, zincmethylphyrin, zinc coproporphyrin, and coproporphyrin enabled laboratory cultivation of previously uncultured Leucobacter sp. These findings might expand the possibility for further discovery of novel therapeutic agents or chemical probes.
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Affiliation(s)
- Makoto Ubukata
- Graduate School of Agriculture, Hokkaido University , Kita-ku, Japan
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23
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Aminoacyl-tRNA synthetases: Structure, function, and drug discovery. Int J Biol Macromol 2018; 111:400-414. [PMID: 29305884 DOI: 10.1016/j.ijbiomac.2017.12.157] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 12/27/2017] [Accepted: 12/29/2017] [Indexed: 01/02/2023]
Abstract
Aminoacyl-tRNA synthetases (AARSs) are the enzymes that catalyze the aminoacylation reaction by covalently linking an amino acid to its cognate tRNA in the first step of protein translation. Beyond this classical function, these enzymes are also known to have a role in several metabolic and signaling pathways that are important for cell viability. Study of these enzymes is of great interest to the researchers due to its pivotal role in the growth and survival of an organism. Further, unfolding the interesting structural and functional aspects of these enzymes in the last few years has qualified them as a potential drug target against various diseases. Here we review the classification, function, and the conserved as well the appended structural architecture of these enzymes in detail, including its association with multi-synthetase complexes. We also considered their role in human diseases in terms of mutations and autoantibodies against AARSs. Finally, we have discussed the available inhibitors against AARSs. This review offers comprehensive information on AARSs under a single canopy that would be a good inventory for researchers working in this area.
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24
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Ishikawa F, Tanabe G, Kakeya H. Activity-Based Protein Profiling of Non-ribosomal Peptide Synthetases. Curr Top Microbiol Immunol 2018; 420:321-349. [PMID: 30178264 DOI: 10.1007/82_2018_133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-ribosomal peptide (NRP) natural products are one of the most promising resources for drug discovery and development because of their wide-ranging of therapeutic potential, and their behavior as virulence factors and signaling molecules. The NRPs are biosynthesized independently of the ribosome by enzyme assembly lines known as the non-ribosomal peptide synthetase (NRPS) machinery. Genetic, biochemical, and bioinformatics analyses have provided a detailed understanding of the mechanism of NRPS catalysis. However, proteomic techniques for natural product biosynthesis remain a developing field. New strategies are needed to investigate the proteomes of diverse producer organisms and directly analyze the endogenous NRPS machinery. Advanced platforms should verify protein expression, protein folding, and activities and also enable the profiling of the NRPS machinery in biological samples from wild-type, heterologous, and engineered bacterial systems. Here, we focus on activity-based protein profiling strategies that have been recently developed for studies aimed at visualizing and monitoring the NRPS machinery and also for rapid labeling, identification, and biochemical analysis of NRPS enzyme family members as required for proteomic chemistry in natural product sciences.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan.
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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25
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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26
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Ji C, Sharma I, Pratihar D, Hudson LL, Maura D, Guney T, Rahme LG, Pesci EC, Coleman JP, Tan DS. Designed Small-Molecule Inhibitors of the Anthranilyl-CoA Synthetase PqsA Block Quinolone Biosynthesis in Pseudomonas aeruginosa. ACS Chem Biol 2016; 11:3061-3067. [PMID: 27658001 PMCID: PMC5117135 DOI: 10.1021/acschembio.6b00575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
The Gram-negative bacterial pathogen Pseudomonas aeruginosa uses three interconnected intercellular
signaling systems regulated
by the transcription factors LasR, RhlR, and MvfR (PqsR), which mediate
bacterial cell–cell communication via small-molecule natural
products and control the production of a variety of virulence factors.
The MvfR system is activated by and controls the biosynthesis of the
quinolone quorum sensing factors HHQ and PQS. A key step in the biosynthesis
of these quinolones is catalyzed by the anthranilyl-CoA synthetase
PqsA. To develop inhibitors of PqsA as novel potential antivirulence
antibiotics, we report herein the design and synthesis of sulfonyladeonsine-based
mimics of the anthranilyl-AMP reaction intermediate that is bound
tightly by PqsA. Biochemical, microbiological, and pharmacological
studies identified two potent PqsA inhibitors, anthranilyl-AMS (1) and anthranilyl-AMSN (2), that decreased HHQ
and PQS production in P. aeruginosa strain
PA14. However, these compounds did not inhibit
production of the virulence factor pyocyanin. Moreover, they exhibited
limited bacterial penetration in compound accumulation studies. This
work provides the most potent PqsA inhibitors reported to date and
sets the stage for future efforts to develop analogues with improved
cellular activity to investigate further the complex relationships
between quinolone biosynthesis and virulence factor production in P. aeruginosa and the therapeutic potential of targeting
PqsA.
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Affiliation(s)
| | | | | | - L. Lynn Hudson
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - Damien Maura
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
| | | | - Laurence G. Rahme
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Shriners Hospitals for
Children Boston, Boston, Massachusetts 02114, United States
| | - Everett C. Pesci
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - James P. Coleman
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
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27
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Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
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28
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Cochrane RVK, Norquay AK, Vederas JC. Natural products and their derivatives as tRNA synthetase inhibitors and antimicrobial agents. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00274a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tRNA synthetase enzymes are promising targets for development of therapeutic agents against infections by parasitic protozoans (e.g. malaria), fungi and yeast, as well as bacteria resistant to current antibiotics.
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Affiliation(s)
| | - A. K. Norquay
- Department of Chemistry
- University of Alberta
- Edmonton
- T6G 2G2 Canada
| | - J. C. Vederas
- Department of Chemistry
- University of Alberta
- Edmonton
- T6G 2G2 Canada
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29
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Ishikawa F, Suzuki T, Dohmae N, Kakeya H. A Multiple-Labeling Strategy for Nonribosomal Peptide Synthetases Using Active-Site-Directed Proteomic Probes for Adenylation Domains. Chembiochem 2015; 16:2590-4. [PMID: 26467472 DOI: 10.1002/cbic.201500481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple-labeling technique with active-site-directed probes for adenylation domains. When applied to gramicidin S-producing and -nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high-resolution identification of low-abundance active NRPS enzymes in native proteomic environments.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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30
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Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL. Biosynthesis of the Fluorinated Natural Product Nucleocidin inStreptomyces calvusIs Dependent on thebldA-Specified Leu-tRNAUUAMolecule. Chembiochem 2015; 16:2498-506. [DOI: 10.1002/cbic.201500402] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Xi Ming Zhu
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stefanie Hackl
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Maulik N. Thaker
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Lindsay Kalan
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Claudia Weber
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Dagmar S. Urgast
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Eva M. Krupp
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Alyssa Brewer
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stephanie Vanner
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Anjuli Szawiola
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Grace Yim
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Jörg Feldmann
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - David L. Zechel
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
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31
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Ishikawa F, Konno S, Suzuki T, Dohmae N, Kakeya H. Profiling Nonribosomal Peptide Synthetase Activities Using Chemical Proteomic Probes for Adenylation Domains. ACS Chem Biol 2015; 10:1989-97. [PMID: 26038981 DOI: 10.1021/acschembio.5b00097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) and polyketide synthases are large diverse families of biosynthetic enzymes that catalyze the synthesis of natural products that display biologically important activities. Genetic investigations have greatly contributed to our understanding of these biosynthetic enzymes; however, proteomic studies are limited. Here we describe the application of active site-directed proteomic probes for adenylation (A) domains to profile the activity of NRPSs directly in native proteomic environments. Derivatization of a 5'-O-N-(aminoacyl)sulfamoyladenosine appended clickable benzophenone functionality enabled activity-based protein profiling of the A-domains in NRPSs in proteomic extracts. These probes were used to identify natural product producing microorganisms, optimize culture conditions, and profile the activity dynamics of NRPSs. Our proteomic approach offers a simple and versatile method to monitor NRPS expression at the protein level and will facilitate the identification of orphan enzymatic pathways involved in secondary metabolite production.
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Affiliation(s)
- Fumihiro Ishikawa
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Sho Konno
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Takehiro Suzuki
- Biomolecular
Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular
Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideaki Kakeya
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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32
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Zhao Y, Yan B, Yang T, Jiang J, Wei H, Zhu X. Purification and crystallographic analysis of a FAD-dependent halogenase from Streptomyces sp. JCM9888. Acta Crystallogr F Struct Biol Commun 2015; 71:972-6. [PMID: 26249684 PMCID: PMC4528926 DOI: 10.1107/s2053230x15009929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/22/2015] [Indexed: 11/10/2022] Open
Abstract
A new FAD (flavin adenine dinucleotide)-dependent halogenase HalY from Streptomyces sp. JCM9888 was reported to be involved in the regioselective halogenation of adenine. HalY is a variant B FAD-dependent halogenase that is most similar to the halogenase PltA involved in pyoluteorin biosynthesis. This study reports the overexpression and purification of HalY with an N-terminal hexahistidine tag, followed by crystallization experiments and X-ray crystallographic analysis. HalY was purified as a monomer in solution and crystallized to give X-ray diffraction to a resolution of 1.7 Å. The crystal belonged to the monoclinic space group P21, with unit-cell parameters a = 41.4, b = 113.4, c = 47.6 Å, α = γ = 90, β = 107.4°, and contained one monomer of HalY in the asymmetric unit, with a calculated Matthews coefficient of 2.3 Å(3) Da(-1) and a solvent content of 46%. The structure of the halogenase CndH was used as a search model in molecular replacement to obtain the initial model of HalY. Manual model building and structure refinement of HalY are in progress.
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Affiliation(s)
- Yanqun Zhao
- College of Life Science, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, Center for Growth, Metabolism and Aging, Sichuan University, Chengdu 610064, People’s Republic of China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Baohua Yan
- College of Life Science, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, Center for Growth, Metabolism and Aging, Sichuan University, Chengdu 610064, People’s Republic of China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Ting Yang
- College of Life Science, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, Center for Growth, Metabolism and Aging, Sichuan University, Chengdu 610064, People’s Republic of China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Jian Jiang
- College of Life Science, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, Center for Growth, Metabolism and Aging, Sichuan University, Chengdu 610064, People’s Republic of China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Heng Wei
- College of Life Science, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, Center for Growth, Metabolism and Aging, Sichuan University, Chengdu 610064, People’s Republic of China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Xiaofeng Zhu
- College of Life Science, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, Center for Growth, Metabolism and Aging, Sichuan University, Chengdu 610064, People’s Republic of China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
- Collaborative Innovation Centre for Biotherapy, People’s Republic of China
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Mujumdar P, Poulsen SA. Natural Product Primary Sulfonamides and Primary Sulfamates. JOURNAL OF NATURAL PRODUCTS 2015; 78:1470-1477. [PMID: 26035239 DOI: 10.1021/np501015m] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Primary sulfonamide and primary sulfamate functional groups feature prominently in the structures of U.S. FDA-approved drugs. However, the natural product chemical space contains few examples of these well-known zinc-binding chemotypes, with just two primary sulfonamide and five primary sulfamate natural products isolated and characterized to date. One of these natural products was isolated from a marine sponge, with the remainder isolated from Streptomyces species. In this review are outlined for the first time the discovery, isolation, striking breadth of bioactivity, and total synthesis (where available) for this rare group of natural products.
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Affiliation(s)
- Prashant Mujumdar
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
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34
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Characterization of biosynthetic genes of ascamycin/dealanylascamycin featuring a 5'-O-sulfonamide moiety in Streptomyces sp. JCM9888. PLoS One 2014; 9:e114722. [PMID: 25479601 PMCID: PMC4257720 DOI: 10.1371/journal.pone.0114722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023] Open
Abstract
Ascamycin (ACM) and dealanylascamycin (DACM) are nucleoside antibiotics elaborated by Streptomyces sp. JCM9888. The later shows broad spectrum inhibition activity to various gram-positive and gram-negative bacteria, eukaryotic Trypanosoma and is also toxic to mice, while ascamycin is active against very limited microorganisms, such as Xanthomonas. Both compounds share an unusual 5′-O-sulfonamide moiety which is attached to an adenosine nucleoside. In this paper, we first report on the 30 kb gene cluster (23 genes, acmA to acmW) involved in the biosynthesis of these two antibiotics and a biosynthetic assembly line was proposed. Of them, six genes (AcmABGKIW) are hypothetical genes involved in 5′-O-sulfonamide formation. Two flavin adenine dinucleotide (FAD)-dependent chlorinase genes acmX and acmY were characterized which are significantly remote from acmA-W and postulated to be required for adenine C2-halogenation. Notably gene disruption of acmE resulted in a mutant which could only produce dealanylascamycin but was blocked in its ability to biosynthesize ascamycin, revealing its key role of conversion of dealanylascamycin to ascamycin.
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35
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Davis TD, Gerry CJ, Tan DS. General platform for systematic quantitative evaluation of small-molecule permeability in bacteria. ACS Chem Biol 2014; 9:2535-44. [PMID: 25198656 PMCID: PMC4245172 DOI: 10.1021/cb5003015] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery.
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Affiliation(s)
- Tony D. Davis
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
| | - Christopher J. Gerry
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
| | - Derek S. Tan
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
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36
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Spillane W, Malaubier JB. Sulfamic Acid and Its N- and O-Substituted Derivatives. Chem Rev 2013; 114:2507-86. [DOI: 10.1021/cr400230c] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- William Spillane
- School
of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Jean-Baptiste Malaubier
- Manufacturing Science
and
Technology, Roche Ireland Limited, Clarecastle, Co. Clare, Ireland
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37
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Engelhart CA, Aldrich CC. Synthesis of chromone, quinolone, and benzoxazinone sulfonamide nucleosides as conformationally constrained inhibitors of adenylating enzymes required for siderophore biosynthesis. J Org Chem 2013; 78:7470-81. [PMID: 23805993 DOI: 10.1021/jo400976f] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MbtA catalyzes the first committed step of mycobactin biosynthesis in Mycobacterium tuberculosis (Mtb) and is responsible for the incorporation of salicylic acid into the mycobactin siderophores. 5'-O-[N-(Salicyl)sulfamoyl]adenosine (Sal-AMS) is an extremely potent nucleoside inhibitor of MbtA that possesses excellent activity against whole-cell Mtb but suffers from poor bioavailability. In an effort to improve the bioavailability, we have designed four conformationally constrained analogues of Sal-AMS that remove two rotatable bonds and the ionized sulfamate group on the basis of computational and structural studies. Herein we describe the synthesis, biochemical, and microbiological evaluation of chromone-, quinolone-, and benzoxazinone-3-sulfonamide derivatives of Sal-AMS. We developed new chemistry to assemble these three heterocycles from common β-ketosulfonamide intermediates. The synthesis of the chromone- and quinolone-3-sulfonamide intermediates features formylation of a β-ketosulfonamide employing dimethylformamide dimethyl acetal to afford an enaminone that can react intramolecularly with a phenol or intermolecularly with a primary amine via addition-elimination reaction(s). The benzoxazinone-3-sulfonamide was prepared by nitrosation of a β-ketosulfonamide followed by intramolecular nucleophilic aromatic substitution. Mitsunobu coupling of these bicyclic sulfonamides with a protected adenosine derivative followed by global deprotection provides a concise synthesis of the respective inhibitors.
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Affiliation(s)
- Curtis A Engelhart
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, USA
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38
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Duckworth BP, Nelson KM, Aldrich CC. Adenylating enzymes in Mycobacterium tuberculosis as drug targets. Curr Top Med Chem 2012; 12:766-96. [PMID: 22283817 DOI: 10.2174/156802612799984571] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/08/2011] [Indexed: 11/22/2022]
Abstract
Adenylation or adenylate-forming enzymes (AEs) are widely found in nature and are responsible for the activation of carboxylic acids to intermediate acyladenylates, which are mixed anhydrides of AMP. In a second reaction, AEs catalyze the transfer of the acyl group of the acyladenylate onto a nucleophilic amino, alcohol, or thiol group of an acceptor molecule leading to amide, ester, and thioester products, respectively. Mycobacterium tuberculosis encodes for more than 60 adenylating enzymes, many of which represent potential drug targets due to their confirmed essentiality or requirement for virulence. Several strategies have been used to develop potent and selective AE inhibitors including highthroughput screening, fragment-based screening, and the rationale design of bisubstrate inhibitors that mimic the acyladenylate. In this review, a comprehensive analysis of the mycobacterial adenylating enzymes will be presented with a focus on the identification of small molecule inhibitors. Specifically, this review will cover the aminoacyl tRNAsynthetases (aaRSs), MenE required for menaquinone synthesis, the FadD family of enzymes including the fatty acyl- AMP ligases (FAAL) and the fatty acyl-CoA ligases (FACLs) involved in lipid metabolism, and the nonribosomal peptide synthetase adenylation enzyme MbtA that is necessary for mycobactin synthesis. Additionally, the enzymes NadE, GuaA, PanC, and MshC involved in the respective synthesis of NAD, guanine, pantothenate, and mycothiol will be discussed as well as BirA that is responsible for biotinylation of the acyl CoA-carboxylases.
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39
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Dixit SS, Upadhayaya RS, Chattopadhyaya J. New parasite inhibitors encompassing novel conformationally-locked 5′-acyl sulfamoyl adenosines. Org Biomol Chem 2012; 10:6121-9. [DOI: 10.1039/c2ob25879j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Abstract
Once considered to be isolation artifacts or chemical "mistakes" of nature, the number of naturally occurring organohalogen compounds has grown from a dozen in 1954 to >5000 today. Of these, at least 25% are halogenated alkaloids. This is not surprising since nitrogen-containing pyrroles, indoles, carbolines, tryptamines, tyrosines, and tyramines are excellent platforms for biohalogenation, particularly in the marine environment where both chloride and bromide are plentiful for biooxidation and subsequent incorporation into these electron-rich substrates. This review presents the occurrence of all halogenated alkaloids, with the exception of marine bromotyrosines where coverage begins where it left off in volume 61 of The Alkaloids. Whereas the biological activity of these extraordinary compounds is briefly cited for some examples, a future volume of The Alkaloids will present full coverage of this topic and will also include selected syntheses of halogenated alkaloids. Natural organohalogens of all types, especially marine and terrestrial halogenated alkaloids, comprise a rapidly expanding class of natural products, in many cases expressing powerful biological activity. This enormous proliferation has several origins: (1) a revitalization of natural product research in a search for new drugs, (2) improved compound characterization methods (multidimensional NMR, high-resolution mass spectrometry), (3) specific enzyme-based and other biological assays, (4) sophisticated collection methods (SCUBA and remote submersibles for deep ocean marine collections), (5) new separation and purification techniques (HPLC and countercurrent separation), (6) a greater appreciation of traditional folk medicine and ethobotany, and (7) marine bacteria and fungi as novel sources of natural products. Halogenated alkaloids are truly omnipresent in the environment. Indeed, one compound, Q1 (234), is ubiquitous in the marine food web and is found in the Inuit from their diet of whale blubber. Given the fact that of the 500,000 estimated marine organisms--which are the source of most halogenated alkaloids--only a small percentage have been investigated for their chemical content, it is certain that myriad new halogenated alkaloids are awaiting discovery. For example, it is estimated that nearly 4000 species of bryozoans have not been examined for their chemical content. The few species that have been studied contain some extraordinary halogenated alkaloids, such as hinckdentine A (610) and the chartellines (611-613). Of the estimated 1.5 million species of fungi, secondary metabolites have been characterized from only 5000 species. The future seems bright for the collector of halogenated alkaloids!
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA.
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41
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Lu X, Zhou R, Sharma I, Li X, Kumar G, Swaminathan S, Tonge PJ, Tan DS. Stable analogues of OSB-AMP: potent inhibitors of MenE, the o-succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis. Chembiochem 2011; 13:129-36. [PMID: 22109989 DOI: 10.1002/cbic.201100585] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 12/15/2022]
Abstract
MenE, the o-succinylbenzoate (OSB)-CoA synthetase from bacterial menaquinone biosynthesis, is a promising new antibacterial target. Sulfonyladenosine analogues of the cognate reaction intermediate, OSB-AMP, have been developed as inhibitors of the MenE enzymes from Mycobacterium tuberculosis (mtMenE), Staphylococcus aureus (saMenE) and Escherichia coli (ecMenE). Both a free carboxylate and a ketone moiety on the OSB side chain are required for potent inhibitory activity. OSB-AMS (4) is a competitive inhibitor of mtMenE with respect to ATP (K(i) =5.4±0.1 nM) and a noncompetitive inhibitor with respect to OSB (K(i) =11.2±0.9 nM). These data are consistent with a Bi Uni Uni Bi Ping-Pong kinetic mechanism for these enzymes. In addition, OSB-AMS inhibits saMenE with K(i)(app) =22±8 nM and ecMenE with K(i)(OSB) =128±5 nM. Putative active-site residues, Arg222, which may interact with the OSB aromatic carboxylate, and Ser302, which may bind the OSB ketone oxygen, have been identified through computational docking of OSB-AMP with the unliganded crystal structure of saMenE. A pH-dependent interconversion of the free keto acid and lactol forms of the inhibitors is also described, along with implications for inhibitor design.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology and Chemistry Program and Tri-Institutional Research Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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42
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Enhanced Production of the Fluorinated Nucleoside Antibiotic Nucleocidin by a rifR-Resistant Mutant of Streptomyces calvus IFO13200. ACTA ACUST UNITED AC 2009. [DOI: 10.3209/saj.saj230205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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43
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Lu X, Zhang H, Tonge PJ, Tan DS. Mechanism-based inhibitors of MenE, an acyl-CoA synthetase involved in bacterial menaquinone biosynthesis. Bioorg Med Chem Lett 2008; 18:5963-6. [PMID: 18762421 PMCID: PMC2628629 DOI: 10.1016/j.bmcl.2008.07.130] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/22/2022]
Abstract
Menaquinone (vitamin K(2)) is an essential component of the electron transfer chain in many pathogens, including Mycobacterium tuberculosis and Staphylococcus aureus, and menaquinone biosynthesis is a potential target for antibiotic drug discovery. We report herein a series of mechanism-based inhibitors of MenE, an acyl-CoA synthetase that catalyzes adenylation and thioesterification of o-succinylbenzoic acid (OSB) during menaquinone biosynthesis. The most potent compound inhibits MenE with an IC(50) value of 5.7microM.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10065, USA
| | - Huaning Zhang
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Peter J. Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Derek S. Tan
- Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10065, USA
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44
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Characterization of copper(II) interactions with sinefungin, a nucleoside antibiotic: combined potentiometric, spectroscopic and DFT studies. Bioinorg Chem Appl 2008:53521. [PMID: 18273386 PMCID: PMC2216065 DOI: 10.1155/2007/53521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 11/09/2007] [Indexed: 11/25/2022] Open
Abstract
Interactions between sinefungin and copper(II) ions were investigated. Stoichiometry and stability constants of the
metal-free system and two mononuclear complexes present in solution were determined on the basis of potentiometric
data analysis. The results were compared to the Cu(II)-ornithine system due to structural similarities between both
molecules. Combined spectroscopic and theoretical studies allowed for determination of coordination pattern for
the Cu(II)-sinefungin complexes. At acidic pH, copper is bound in “glycine-like” coordination mode, identical with that
of ornithine. This involves α-amino group and the carboxyl oxygen. At higher pH, a “bis-complex” is formed by two
sinefungin molecules. The second ligand binds in equatorial position displacing two water molecules, what results
in the stable {2N,2O} coordination. Both axial positions are supposed to be occupied by N1 nitrogen donors of adenine
moiety, what is confirmed by DFT calculations. They interact indirectly with copper(II) through water molecules as the
result of dominant syn conformation of purine.
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45
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Taguchi H, Ohkubo A, Sekine M, Seio K, Kakeya H, Osada H, Sasaki T. Synthesis and biological properties of new phosmidosine analogs having an N-acylsulfamate linkage. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:647-54. [PMID: 16838852 DOI: 10.1080/15257770600686360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A new phosmidosine analog 10, in which the proline and 8-oxoadenosine moieties were linked by an N-acyl sulfamate linkage, was successfully synthesized by the sulfamoylation of an 8-oxoadenosine derivative 5 followed by coupling with an L-proline derivative 8. An L-alanine-substituted derivative 13 and its derivative 14 without the alanyl residue were also synthesized. The morphological reversion activity of these synthetic compounds in v-src(ts) NRK cells and their antitumor activity in L1210 and KB cells were studied. As the result, neither L-proline- nor L-alanine-substituted phosmidosine analogs 10 and 13 showed any antitumor activity. Contrary to these results, the derivative 14 lacking the amino acid residue showed potent antitumor activities against cancer cells.
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Affiliation(s)
- Haruhiko Taguchi
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama, Japan
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46
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Affiliation(s)
- K H Schram
- College of Pharmacy, University of Arizona, Tucson
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47
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Somu RV, Boshoff H, Qiao C, Bennett EM, Barry CE, Aldrich CC. Rationally Designed Nucleoside Antibiotics That Inhibit Siderophore Biosynthesis of Mycobacterium tuberculosis. J Med Chem 2005; 49:31-4. [PMID: 16392788 DOI: 10.1021/jm051060o] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A rationally designed nucleoside inhibitor of Mycobacterium tuberculosis growth (MIC(99) = 0.19 microM) that disrupts siderophore biosynthesis was identified. The activity is due to inhibition of the adenylate-forming enzyme MbtA which is involved in biosynthesis of the mycobactins.
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Affiliation(s)
- Ravindranadh V Somu
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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48
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Bernier S, Dubois DY, Habegger-Polomat C, Gagnon LP, Lapointe J, Chênevert R. Glutamylsulfamoyladenosine and pyroglutamylsulfamoyladenosine are competitive inhibitors of E. coli glutamyl-tRNA synthetase. J Enzyme Inhib Med Chem 2005; 20:61-7. [PMID: 15895686 DOI: 10.1080/14756360400002007] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
5'-O-[N-(L-glutamyl)-sulfamoyl] adenosine is a potent competitive inhibitor of E. coli glutamyl-tRNA synthetase with respect to glutamic acid (K(i) = 2.8 nM) and is the best inhibitor of this enzyme. It is a weaker inhibitor of mammalian glutamyl-tRNA synthetase (K(i) = 70 nM). The corresponding 5'-O-[N-(L-pyroglutamyl)-sulfamoyl] adenosine is a weak inhibitor (K(i) = 15 microM) of the E. coli enzyme.
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Affiliation(s)
- Stéphane Bernier
- Département de chimie, Faculté des sciences et de génie, Centre de recherche sur la fonction, la structure et l'ingénierie des protéines (CREFSIP), Université Laval, Québec, Canada G1K 7P4
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Structure-activity relationship of phosmidosine: importance of the 7,8-dihydro-8-oxoadenosine residue for antitumor activity. Bioorg Med Chem 2005; 12:5193-201. [PMID: 15351402 DOI: 10.1016/j.bmc.2004.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Revised: 07/08/2004] [Accepted: 07/08/2004] [Indexed: 10/26/2022]
Abstract
To study the structure-activity relationship of phosmidosine, a variety of phosmidosine derivatives 9a-g were synthesized by condensation of N-diisopropyl N'-(N-tritylprolyl)phosphorodiamidite 6 with appropriately protected nucleoside derivatives 7a-g. As the result, replacement of the 7,8-dihydro-8-oxoadenine base by adenine and 6-N-acetyladenine did not affect the antitumor activity. However, phosmidosine derivatives containing uracil, cytosine, and guanine in place of the 7,8-dihydro-8-oxoadenine base did not show significant activity. A plausible explanation for the selective expression of phosmidosine compared with that of phosmidosine analogs having other amino acids in place of proline is also discussed. These results suggest that phosmidosine serves as an inhibitor of prolyl adenosine 5'-phosphate (prolyl-AMP) to inhibit the peptide synthesis in cancer-related cells.
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Winum JY, Scozzafava A, Montero JL, Supuran CT. Therapeutic applications of sulfamates. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.14.9.1273] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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