1
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Prats Luján A, Faizan Bhat M, Acosta Marko EE, Fodran P, Poelarends GJ. Exploiting Nitroreductases for the Tailored Photoenzymatic Synthesis of Structurally Diverse Heterocyclic Compounds. Chemistry 2024; 30:e202402380. [PMID: 39011613 DOI: 10.1002/chem.202402380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/17/2024]
Abstract
N-heterocyclic compounds have a broad range of applications and their selective synthesis is very appealing for the pharmaceutical and agrochemical industries. Herein we report the usage of the flavin-dependent nitroreductase BaNTR1 for the photoenzymatic synthesis of various anthranils and quinolines from retro-synthetically designed o-nitrophenyl-substituted carbonyl substrates, achieving high conversions (up to >99 %) and good product yields (up to 96 %). Whereas the effective production of anthranils required the inclusion of H2O2 in the reaction mixtures to accumulate the needed hydroxylamine intermediates, the formation of quinolines required the use of anaerobic or reducing conditions to efficiently generate the essential amine intermediates. Critical to our success was the high chemoselectivity of BaNTR1, performing selective reduction of the nitro group without reduction of the carbonyl moiety or the activated carbon-carbon double bond. The results highlight the usefulness of an innocuous chlorophyll- and nitroreductase-based photoenzymatic system for the tailored synthesis of diverse N-heterocycles from simple nitro compounds.
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Affiliation(s)
- Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Mohammad Faizan Bhat
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Edgar Eduardo Acosta Marko
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter Fodran
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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2
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Russo S, Luján AP, Fraaije MW, Poelarends GJ. Synthesis of Pharmaceutically Relevant Arylamines Enabled by a Nitroreductase from Bacillus tequilensis. Chembiochem 2024; 25:e202300846. [PMID: 38502784 DOI: 10.1002/cbic.202300846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Arylamines are essential building blocks for the manufacture of valuable pharmaceuticals, pigments and dyes. However, their current industrial production involves the use of chemocatalytic procedures with a significant environmental impact. As a result, flavin-dependent nitroreductases (NRs) have received increasing attention as sustainable catalysts for more ecofriendly synthesis of arylamines. In this study, we assessed a novel NR from Bacillus tequilensis, named BtNR, for the synthesis of pharmaceutically relevant arylamines, including valuable synthons used in the manufacture of blockbuster drugs such as vismodegib, sonidegib, linezolid and sildenafil. After optimizing the enzymatic reaction conditions, high conversion of nitroaromatics to arylamines (up to 97 %) and good product yields (up to 56 %) were achieved. Our results indicate that BtNR has a broad substrate scope, including bulky nitro benzenes, nitro pyrazoles and nitro pyridines. Hence, BtNR is an interesting biocatalyst for the synthesis of pharmaceutically relevant amine-functionalized aromatics, providing an attractive alternative to traditional chemical synthesis methodologies.
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Affiliation(s)
- Sara Russo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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3
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Luján AP, Bhat MF, Tsaturyan S, van Merkerk R, Fu H, Poelarends GJ. Tailored photoenzymatic systems for selective reduction of aliphatic and aromatic nitro compounds fueled by light. Nat Commun 2023; 14:5442. [PMID: 37673927 PMCID: PMC10482925 DOI: 10.1038/s41467-023-41194-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
The selective enzymatic reduction of nitroaliphatic and nitroaromatic compounds to aliphatic amines and amino-, azoxy- and azo-aromatics, respectively, remains a persisting challenge for biocatalysis. Here we demonstrate the light-powered, selective photoenzymatic synthesis of aliphatic amines and amino-, azoxy- and azo-aromatics from the corresponding nitro compounds. The nitroreductase from Bacillus amyloliquefaciens, in synergy with a photocatalytic system based on chlorophyll, promotes selective conversions of electronically-diverse nitroarenes into a series of aromatic amino, azoxy and azo products with excellent yield (up to 97%). The exploitation of an alternative nitroreductase from Enterobacter cloacae enables the tailoring of a photoenzymatic system for the challenging synthesis of aliphatic amines from nitroalkenes and nitroalkanes (up to 90% yield). This photoenzymatic reduction overcomes the competing bio-Nef reaction, typically hindering the complete enzymatic reduction of nitroaliphatics. The results highlight the usefulness of nitroreductases to create selective photoenzymatic systems for the synthesis of precious chemicals, and the effectiveness of chlorophyll as an innocuous photocatalyst, enabling the use of sunlight to drive the photobiocatalytic reactions.
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Affiliation(s)
- Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Mohammad Faizan Bhat
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sona Tsaturyan
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Haigen Fu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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4
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Day MA, Jarrom D, Rajah N, Searle PF, Hyde EI, White SA. Oxygen-insensitive nitroreductase E. coli NfsA, but not NfsB, is inhibited by fumarate. Proteins 2023; 91:585-592. [PMID: 36443029 PMCID: PMC10953011 DOI: 10.1002/prot.26451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
Escherichia coli NfsA and NfsB are founding members of two flavoprotein families that catalyze the oxygen-insensitive reduction of nitroaromatics and quinones by NAD(P)H. This reduction is required for the activity of nitrofuran antibiotics and the enzymes have also been proposed for use with nitroaromatic prodrugs in cancer gene therapy and biocatalysis, but the roles of the proteins in vivo in bacteria are not known. NfsA is NADPH-specific whereas NfsB can also use NADH. The crystal structures of E. coli NfsA and NfsB and several analogs have been determined previously. In our crystal trials, we unexpectedly observed NfsA bound to fumarate. We here present the X-ray structure of the E. coli NfsA-fumarate complex and show that fumarate acts as a weak inhibitor of NfsA but not of NfsB. The structural basis of this differential inhibition is conserved in the two protein families and occurs at fumarate concentrations found in vivo, so impacting the efficacy of these proteins.
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Affiliation(s)
- Martin A. Day
- School of BiosciencesUniversity of BirminghamBirminghamUK
- Institute for Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - David Jarrom
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Navina Rajah
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Peter F. Searle
- Institute for Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - Eva I. Hyde
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Scott A. White
- School of BiosciencesUniversity of BirminghamBirminghamUK
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5
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Sviatenko LK, Gorb L, Leszczynski J. NTO Degradation by Nitroreductase: A DFT Study. J Phys Chem B 2022; 126:5991-6006. [PMID: 35926135 DOI: 10.1021/acs.jpcb.2c04153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of the possible mechanism for all steps of reduction of NTO by oxygen-insensitive nitroreductase, as one of the pathways for NTO environmental degradation, was performed by computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Obtained results reveal an overall sequence for NTO transformation into ATO (5-amino-1,2,4-triazol-3-one) with the flavin mononucleotide (FMN) cofactor of nitroreductase. Reduction of the nitro group to the nitroso group and the nitroso group to the hydroxylamino group follow a similar mechanism that consists of the sequential electron and proton transfer from the flavin cofactor. The hydride transfer mechanism may contribute to reduction of the nitroso group by the anionic form of the reduced flavin cofactor. Reduction of 5-(hydroxylamino)-1,2,4-triazol-3-one by the neutral form of the reduced flavin is impossible, whereas reduction of the hydroxylamino group to the amino group occurs with the anionic form of the reduced cofactor by a mechanism involving an initial proton transfer from the hydroxonium ion followed by two electrons and one proton transfers from the flavin cofactor. Small activation energies and high exothermicity support the significant contribution of oxygen-insensitive nitroreductase and other enzymes, containing FMN as a cofactor, to NTO degradation in the environment.
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Affiliation(s)
- Liudmyla K Sviatenko
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics & Atmospheric Sciences, Jackson State University, Jackson, Mississippi 39217, United States
| | - Leonid Gorb
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotny Str., Kyiv 03143, Ukraine
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics & Atmospheric Sciences, Jackson State University, Jackson, Mississippi 39217, United States
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6
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Musila JM, Rokita SE. Sequence Conservation Does Not Always Signify a Functional Imperative as Observed in the Nitroreductase Superfamily. Biochemistry 2022; 61:703-711. [PMID: 35319879 PMCID: PMC9018611 DOI: 10.1021/acs.biochem.2c00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Consensus sequences have the potential to help classify the structure and function of proteins and highlight key regions that may contribute to their biological properties. Often, the level of significance will track with the extent of sequence conservation, but this should not be considered universal. Arg and Lys dominate a position adjacent to the N1 and C2 carbonyl of flavin mononucleotide (FMN) bound in the proteins of the nitroreductase superfamily. Although this placement satisfies expectations for stabilizing the reduced form of FMN, the substitution of these residues in three subfamilies promoting distinct reactions demonstrates their importance to catalysis as only modest. Replacing Arg34 with Lys, Gln, or Glu enhances FMN binding to a flavin destructase (BluB) by twofold and diminishes FMN turnover by no more than 25%. Similarly, replacing Lys14 with Arg, Gln, or Glu in a nitroreductase (NfsB) does not perturb the binding of the substrate nitrofurazone. The catalytic efficiency does decrease by 21-fold for the K14Q variant, but no change in the midpoint potential of FMN was observed with any of the variants. Equivalent substitution at Arg38 in iodotyrosine deiodinase (IYD) affects catalysis even more modestly (<10-fold). While the Arg/Lys to Glu substitution inactivates NfsB and IYD, this change also stabilizes one-electron transfer in IYD contrary to predictions based on other classes of flavoproteins. Accordingly, functional correlations developed in certain structural superfamilies may not necessarily translate well to other superfamilies.
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Affiliation(s)
- Jonathan M Musila
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Steven E Rokita
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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7
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Hughes DL. Highlights of the Recent Patent Literature─Focus on Biocatalysis Innovation. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David L. Hughes
- Private location: 6755 Mira Mesa Boulevard, Suite 123-217, San Diego, California 92121, United States
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8
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Sun Z, Xu B, Spisak S, Kavran JM, Rokita SE. The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana. J Biol Chem 2021; 297:101385. [PMID: 34748729 PMCID: PMC8668982 DOI: 10.1016/j.jbc.2021.101385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
The nitroreductase superfamily of enzymes encompasses many flavin mononucleotide (FMN)-dependent catalysts promoting a wide range of reactions. All share a common core consisting of an FMN-binding domain, and individual subgroups additionally contain one to three sequence extensions radiating from defined positions within this core to support their unique catalytic properties. To identify the minimum structure required for activity in the iodotyrosine deiodinase subgroup of this superfamily, attention was directed to a representative from the thermophilic organism Thermotoga neapolitana (TnIYD). This representative was selected based on its status as an outlier of the subgroup arising from its deficiency in certain standard motifs evident in all homologues from mesophiles. We found that TnIYD lacked a typical N-terminal sequence and one of its two characteristic sequence extensions, neither of which was found to be necessary for activity. We also show that TnIYD efficiently promotes dehalogenation of iodo-, bromo-, and chlorotyrosine, analogous to related deiodinases (IYDs) from humans and other mesophiles. In addition, 2-iodophenol is a weak substrate for TnIYD as it was for all other IYDs characterized to date. Consistent with enzymes from thermophilic organisms, we observed that TnIYD adopts a compact fold and low surface area compared with IYDs from mesophilic organisms. The insights gained from our investigations on TnIYD demonstrate the advantages of focusing on sequences that diverge from conventional standards to uncover the minimum essentials for activity. We conclude that TnIYD now represents a superior starting structure for future efforts to engineer a stable dehalogenase targeting halophenols of environmental concern.
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Affiliation(s)
- Zuodong Sun
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bing Xu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shaun Spisak
- Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jennifer M Kavran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Steven E Rokita
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.
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9
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Čėnas N, Nemeikaitė-Čėnienė A, Kosychova L. Single- and Two-Electron Reduction of Nitroaromatic Compounds by Flavoenzymes: Mechanisms and Implications for Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168534. [PMID: 34445240 PMCID: PMC8395237 DOI: 10.3390/ijms22168534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Nitroaromatic compounds (ArNO2) maintain their importance in relation to industrial processes, environmental pollution, and pharmaceutical application. The manifestation of toxicity/therapeutic action of nitroaromatics may involve their single- or two-electron reduction performed by various flavoenzymes and/or their physiological redox partners, metalloproteins. The pivotal and still incompletely resolved questions in this area are the identification and characterization of the specific enzymes that are involved in the bioreduction of ArNO2 and the establishment of their contribution to cytotoxic/therapeutic action of nitroaromatics. This review addresses the following topics: (i) the intrinsic redox properties of ArNO2, in particular, the energetics of their single- and two-electron reduction in aqueous medium; (ii) the mechanisms and structure-activity relationships of reduction in ArNO2 by flavoenzymes of different groups, dehydrogenases-electrontransferases (NADPH:cytochrome P-450 reductase, ferredoxin:NADP(H) oxidoreductase and their analogs), mammalian NAD(P)H:quinone oxidoreductase, bacterial nitroreductases, and disulfide reductases of different origin (glutathione, trypanothione, and thioredoxin reductases, lipoamide dehydrogenase), and (iii) the relationships between the enzymatic reactivity of compounds and their activity in mammalian cells, bacteria, and parasites.
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Affiliation(s)
- Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-5-223-4392
| | - Aušra Nemeikaitė-Čėnienė
- State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08406 Vilnius, Lithuania;
| | - Lidija Kosychova
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
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10
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Dillon KM, Matson JB. A Review of Chemical Tools for Studying Small Molecule Persulfides: Detection and Delivery. ACS Chem Biol 2021; 16:1128-1141. [PMID: 34114796 DOI: 10.1021/acschembio.1c00255] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hydrogen sulfide (H2S) has gained significant attention as a potent bioregulator in the redox metabolome, but it is just one of many reactive sulfur species (RSS). Recently, small molecule persulfides (structure RSSH) have emerged as RSS of particular interest due to their enhanced antioxidant abilities compared to H2S and their ability to directly convert protein thiols into protein persulfides, suggesting that persulfides may have distinct physiological functions from H2S. However, persulfides exhibit instability and cross-reactivity that hampers the elucidation of their precise biological roles. As such, chemists have designed chemical tools and techniques to facilitate the study of persulfides under various conditions. These molecules and methods include persulfide trapping reagents and sensors, as well as compounds that degrade in response to various triggers to release persulfides, termed persulfide donors. There now exist a variety of persulfide donor classes, some of which possess tissue-targeting capabilities designed to mimic localized endogenous production of RSS. This Review briefly covers the physicochemical properties of persulfides, the endogenous production of small molecule persulfides, and their reactions with protein thiols and other reactive species. These introductory sections are followed by a discussion of chemical tools used in persulfide chemical biology, with critical analysis of recent advancements in the field and commentary on potential directions for future research.
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Affiliation(s)
- Kearsley M. Dillon
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - John B. Matson
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
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11
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Hyde EI, Chau AKW, Smith LJ. Backbone assignment of E. coli NfsB and the effects of addition of the cofactor analogue nicotinic acid. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:143-151. [PMID: 33423170 PMCID: PMC7974150 DOI: 10.1007/s12104-020-09997-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
E. coli nitroreductase NfsB (also called NfnB) has been studied extensively, largely due to its potential for cancer gene therapy. A homodimeric flavoprotein of 216 residues, it catalyses the reduction of nitroaromatics to cytotoxic hydroxylamines by NADH and NADPH and also the reduction of quinones to hydroxyquinones. Its role in vivo is not known but it is postulated to be involved in reducing oxidative stress. The crystal structures of the wild type protein and several homologues have been determined in the absence and presence of ligands, including nicotinate as a mimic of the headpiece of the nicotinamide cofactors. There is little effect on the overall structure of the protein on binding ligands, but, from the B factors, there appears to be a decrease in mobility of 2 helices near the active site. As a first step towards examining the dynamics of the protein in solution with and without ligand, we have assigned the backbone 13C, 15N, and 1HN resonances of NfsB and examined the effect of the binding of nicotinate on the amide 15N, and 1HN shifts.
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Affiliation(s)
- Eva I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Alex Ka-Wing Chau
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Legislative Council Complex, Central, Hong Kong
| | - Lorna J Smith
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK.
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12
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Dillon KM, Morrison HA, Powell CR, Carrazzone RJ, Ringel-Scaia VM, Winckler EW, Council-Troche RM, Allen IC, Matson JB. Targeted Delivery of Persulfides to the Gut: Effects on the Microbiome. Angew Chem Int Ed Engl 2021; 60:6061-6067. [PMID: 33511734 PMCID: PMC7967250 DOI: 10.1002/anie.202014052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Indexed: 12/16/2022]
Abstract
Persulfides (R-SSH) have been hypothesized as potent redox modulators and signaling compounds. Reported herein is the synthesis, characterization, and in vivo evaluation of a persulfide donor that releases N-acetyl cysteine persulfide (NAC-SSH) in response to the prokaryote-specific enzyme nitroreductase. The donor, termed NDP-NAC, decomposed in response to E. coli nitroreductase, resulting in release of NAC-SSH. NDP-NAC elicited gastroprotective effects in mice that were not observed in animals treated with control compounds incapable of persulfide release or in animals treated with Na2 S. NDP-NAC induced these effects by the upregulation of beneficial small- and medium-chain fatty acids and through increasing growth of Turicibacter sanguinis, a beneficial gut bacterium. It also decreased the populations of Synergistales bacteria, opportunistic pathogens implicated in gastrointestinal infections. This study reveals the possibility of maintaining gut health or treating microbiome-related diseases by the targeted delivery of reactive sulfur species.
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Affiliation(s)
- Kearsley M. Dillon
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Holly A. Morrison
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chadwick R. Powell
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ryan J. Carrazzone
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Veronica M. Ringel-Scaia
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ethan W. Winckler
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - R. McAlister Council-Troche
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Irving C. Allen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - John B. Matson
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
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13
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Dillon KM, Morrison HA, Powell CR, Carrazzone RJ, Ringel‐Scaia VM, Winckler EW, Council‐Troche RM, Allen IC, Matson JB. Targeted Delivery of Persulfides to the Gut: Effects on the Microbiome. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Kearsley M. Dillon
- Department of Chemistry Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute Virginia Tech Blacksburg VA 24061 USA
| | - Holly A. Morrison
- Department of Biomedical Sciences and Pathobiology Virginia-Maryland College of Veterinary Medicine Virginia Tech Blacksburg VA 24061 USA
| | - Chadwick R. Powell
- Department of Chemistry Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute Virginia Tech Blacksburg VA 24061 USA
| | - Ryan J. Carrazzone
- Department of Chemistry Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute Virginia Tech Blacksburg VA 24061 USA
| | - Veronica M. Ringel‐Scaia
- Department of Biomedical Sciences and Pathobiology Virginia-Maryland College of Veterinary Medicine Virginia Tech Blacksburg VA 24061 USA
| | - Ethan W. Winckler
- Department of Chemistry Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute Virginia Tech Blacksburg VA 24061 USA
| | - R. McAlister Council‐Troche
- Department of Biomedical Sciences and Pathobiology Virginia-Maryland College of Veterinary Medicine Virginia Tech Blacksburg VA 24061 USA
| | - Irving C. Allen
- Department of Biomedical Sciences and Pathobiology Virginia-Maryland College of Veterinary Medicine Virginia Tech Blacksburg VA 24061 USA
| | - John B. Matson
- Department of Chemistry Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute Virginia Tech Blacksburg VA 24061 USA
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Bornadel A, Bisagni S, Pushpanath A, Slabu I, LePaih J, Cherney AH, Mennen SM, Hedley SJ, Tedrow J, Dominguez B. Process Development and Protein Engineering Enhanced Nitroreductase-Catalyzed Reduction of 2-Methyl-5-nitro-pyridine. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amin Bornadel
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Serena Bisagni
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Ahir Pushpanath
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Iustina Slabu
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Jacques LePaih
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Alan H. Cherney
- Amgen, Inc., MS 29-1-A, One Amgen Center Drive, Thousand Oaks 91320-1799, California, United States
| | - Steven M. Mennen
- Amgen, Inc., MS 29-1-A, One Amgen Center Drive, Thousand Oaks 91320-1799, California, United States
| | - Simon J. Hedley
- Amgen, Inc., MS 29-1-A, One Amgen Center Drive, Thousand Oaks 91320-1799, California, United States
| | - Jason Tedrow
- Department of Drug Substance Technologies, Amgen Inc., Cambridge, Massachusetts 02142, United States
| | - Beatriz Dominguez
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
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Motta GE, Molognoni L, Daguer H, Angonese M, da Silva Correa Lemos AL, Dafre AL, De Dea Lindner J. The potential of bacterial cultures to degrade the mutagen 2-methyl-1,4-dinitro-pyrrole in a processed meat model. Food Res Int 2020; 136:109441. [PMID: 32846544 DOI: 10.1016/j.foodres.2020.109441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/22/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023]
Abstract
Processed meats are classified by the International Agency for Research on Cancer as category 1 because their consumption increase the incidence of colorectal and stomach cancers. Meat processing widely employs nitrite and sorbate as preservatives. When these preservatives are concomitantly used in non-compliant processes, they may react and produce the mutagen 2-methyl-1,4-dinitro-pyrrole (DNMP). This study aimed to evaluate the ability of different bacteria isolated from food matrices to biodegrade DNMP in in vitro reactions and in a processed meat model. A possible mechanism of biodegradation was also tested. In vitro experiments were performed in two steps. In the first one, only one strain out of 13 different species did not interact with DNMP. In the following step, an empirical conversion factor was calculated to assess the conversion of DNMP to 4-amino-2-methyl-1-nitro-pyrrole by the strains. The most efficient strains were Staphylococcus xylosus LYOCARNI SXH-01, Lactobacillus fermentum LB-UFSC 0017, and Lactobacillus casei LB-UFSC 0019, which yielded conversion factors of 0.62, 0.60, and 0.43, respectively. Thus, such strains were individually added to the processed meat model and completely degraded the DNMP. Moreover, S. xylosus degraded DNMP in less than 30 min. The enzymatic mechanism was evaluated using its cell-free extract. It showed that, in the aerobic system, reduction rates were 30.321 and 22.411 nmol/mg of protein/min using NADH and NADPH, respectively. A DNMP reductase was assigned to the extract and a potential presence of an oxygen insensitive nitroreductase type I B was considered. Thus, biotechnological processes may be an efficient strategy to eliminate the DNMP from meat products and to increase food safety.
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Affiliation(s)
- Gabriel Emiliano Motta
- Universidade Federal de Santa Catarina (UFSC), Departamento de Ciência e Tecnologia de Alimentos, Florianópolis, SC 88034-001, Brazil
| | - Luciano Molognoni
- Universidade Federal de Santa Catarina (UFSC), Departamento de Ciência e Tecnologia de Alimentos, Florianópolis, SC 88034-001, Brazil; Ministério da Agricultura, Pecuária e Abastecimento, Laboratório Federal de Defesa Agropecuária (SLAV/SC/LANAGRO/RS), São José, SC 88102-600, Brazil; Instituto Catarinense de Sanidade Agropecuária (ICASA), Florianópolis, SC 88034-001, Brazil
| | - Heitor Daguer
- Ministério da Agricultura, Pecuária e Abastecimento, Laboratório Federal de Defesa Agropecuária (SLAV/SC/LANAGRO/RS), São José, SC 88102-600, Brazil
| | - Mariana Angonese
- Universidade Federal de Santa Catarina (UFSC), Departamento de Ciência e Tecnologia de Alimentos, Florianópolis, SC 88034-001, Brazil
| | - Ana Lucia da Silva Correa Lemos
- Secretaria da Agricultura e do Abastecimento do Estado de São Paulo, Instituto de Tecnologia de Alimentos (ITAL), Centro de Tecnologia de Carnes, Campinas, SP 13073-001, Brazil
| | - Alcir Luiz Dafre
- UFSC, Departamento de Bioquímica, Florianópolis, SC 88034-001, Brazil
| | - Juliano De Dea Lindner
- Universidade Federal de Santa Catarina (UFSC), Departamento de Ciência e Tecnologia de Alimentos, Florianópolis, SC 88034-001, Brazil.
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16
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Degradation of High Energy Materials Using Biological Reduction: A Rational Way to Reach Bioremediation. Int J Mol Sci 2019; 20:ijms20225556. [PMID: 31703334 PMCID: PMC6888211 DOI: 10.3390/ijms20225556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Explosives molecules have been widely used since World War II, leading to considerable contamination of soil and groundwater. Recently, bioremediation has emerged as an environmentally friendly approach to solve such contamination issues. However, the 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) explosive, which has very low solubility in water, does not provide satisfying results with this approach. In this study, we used a rational design strategy for improving the specificity of the nitroreductase from E. Cloacae (PDB ID 5J8G) toward HMX. We used the Coupled Moves algorithm from Rosetta to redesign the active site around HMX. Molecular Dynamics (MD) simulations and affinity calculations allowed us to study the newly designed protein. Five mutations were performed. The designed nitroreductase has a better fit with HMX. We observed more H-bonds, which productively stabilized the HMX molecule for the mutant than for the wild type enzyme. Thus, HMX’s nitro groups are close enough to the reductive cofactor to enable a hydride transfer. Also, the HMX affinity for the designed enzyme is better than for the wild type. These results are encouraging. However, the total reduction reaction implies numerous HMX derivatives, and each of them has to be tested to check how far the reaction can’ go.
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17
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Cofactor F420-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis. Catalysts 2019. [DOI: 10.3390/catal9100868] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F420 also has electrochemical properties that make it suitable as an alternative to nicotinamide cofactors for use in asymmetric reduction reactions. However, cofactor F420-dependent enzymes remain under-explored as a resource for biocatalysis. This review considers the cofactor F420-dependent enzyme families with the greatest potential for the discovery of new biocatalysts: the flavin/deazaflavin-dependent oxidoreductases (FDORs) and the luciferase-like hydride transferases (LLHTs). The characterized F420-dependent reductions that have the potential for adaptation for biocatalysis are discussed, and the enzymes best suited for use in the reduction of oxidized cofactor F420 to allow cofactor recycling in situ are considered. Further discussed are the recent advances in the production of cofactor F420 and its functional analog FO-5′-phosphate, which remains an impediment to the adoption of this family of enzymes for industrial biocatalytic processes. Finally, the prospects for the use of this cofactor and dependent enzymes as a resource for industrial biocatalysis are discussed.
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18
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Synthesis and Biological Evaluation of Lipophilic Nucleoside Analogues as Inhibitors of Aminoacyl-tRNA Synthetases. Antibiotics (Basel) 2019; 8:antibiotics8040180. [PMID: 31600972 PMCID: PMC6963541 DOI: 10.3390/antibiotics8040180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022] Open
Abstract
Emerging antibiotic resistance in pathogenic bacteria and reduction of compounds in the existing antibiotics discovery pipeline is the most critical concern for healthcare professionals. A potential solution aims to explore new or existing targets/compounds. Inhibition of bacterial aminoacyl-tRNA synthetase (aaRSs) could be one such target for the development of antibiotics. The aaRSs are a group of enzymes that catalyze the transfer of an amino acid to their cognate tRNA and therefore play a pivotal role in translation. Thus, selective inhibition of these enzymes could be detrimental to microbes. The 5′-O-(N-(L-aminoacyl)) sulfamoyladenosines (aaSAs) are potent inhibitors of the respective aaRSs, however due to their polarity and charged nature they cannot cross the bacterial membranes. In this work, we increased the lipophilicity of these existing aaSAs in an effort to promote their penetration through the bacterial membrane. Two strategies were followed, either attaching a (permanent) alkyl moiety at the adenine ring via alkylation of the N6-position or introducing a lipophilic biodegradable prodrug moiety at the alpha-terminal amine, totaling eight new aaSA analogues. All synthesized compounds were evaluated in vitro using either a purified Escherichiacoli aaRS enzyme or in presence of total cellular extract obtained from E. coli. The prodrugs showed comparable inhibitory activity to the parent aaSA analogues, indicating metabolic activation in cellular extracts, but had little effect on bacteria. During evaluation of the N6-alkylated compounds against different microbes, the N6-octyl containing congener 6b showed minimum inhibitory concentration (MIC) of 12.5 µM against Sarcina lutea while the dodecyl analogue 6c displayed MIC of 6.25 µM against Candidaalbicans.
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19
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Williams EM, Rich MH, Mowday AM, Ashoorzadeh A, Copp JN, Guise CP, Anderson RF, Flanagan JU, Smaill JB, Patterson AV, Ackerley DF. Engineering Escherichia coli NfsB To Activate a Hypoxia-Resistant Analogue of the PET Probe EF5 To Enable Non-Invasive Imaging during Enzyme Prodrug Therapy. Biochemistry 2019; 58:3700-3710. [PMID: 31403283 DOI: 10.1021/acs.biochem.9b00376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gene-directed enzyme prodrug therapy (GDEPT) uses tumor-tropic vectors to deliver prodrug-converting enzymes such as nitroreductases specifically to the tumor environment. The nitroreductase NfsB from Escherichia coli (NfsB_Ec) has been a particular focal point for GDEPT and over the past 25 years has been the subject of several engineering studies seeking to improve catalysis of prodrug substrates. To facilitate clinical development, there is also a need to enable effective non-invasive imaging capabilities. SN33623, a 5-nitroimidazole analogue of 2-nitroimidazole hypoxia probe EF5, has potential for PET imaging exogenously delivered nitroreductases without generating confounding background due to tumor hypoxia. However, we show here that SN33623 is a poor substrate for NfsB_Ec. To address this, we used assay-guided sequence and structure analysis to identify two conserved residues that block SN33623 activation in NfsB_Ec and close homologues. Introduction of the rational substitutions F70A and F108Y into NfsB_Ec conferred high levels of SN33623 activity and enabled specific labeling of E. coli expressing the engineered enzyme. Serendipitously, the F70A and F108Y substitutions also substantially improved activity with the anticancer prodrug CB1954 and the 5-nitroimidazole antibiotic prodrug metronidazole, which is a potential biosafety agent for targeted ablation of nitroreductase-expressing vectors.
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Affiliation(s)
- Elsie M Williams
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand
| | - Michelle H Rich
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand
| | - Alexandra M Mowday
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand
| | - Amir Ashoorzadeh
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand
| | - Janine N Copp
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand
| | - Christopher P Guise
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Robert F Anderson
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Jack U Flanagan
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - David F Ackerley
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
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20
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Si Y, Basak S, Li Y, Merino J, Iuliano JN, Walker SG, Tonge PJ. Antibacterial Activity and Mode of Action of a Sulfonamide-Based Class of Oxaborole Leucyl-tRNA-Synthetase Inhibitors. ACS Infect Dis 2019; 5:1231-1238. [PMID: 31007018 DOI: 10.1021/acsinfecdis.9b00071] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzoxaboroles are a class of boron-containing compounds with a broad range of biological activities. A subset of benzoxaboroles have antimicrobial activity due primarily to their ability to inhibit leucyl-tRNA synthetase (LeuRS) via the oxaborole tRNA-trapping mechanism, which involves the formation of a stable tRNALeu-benzoxaborole adduct in which the boron atom interacts with the 2'- and 3'-oxygen atoms of the terminal 3' tRNA adenosine. We sought to identify other antibacterial targets for this promising class of compounds by means of mode-of-action studies, and we selected a nitrophenyl sulfonamide based oxaborole (PT638) as a probe molecule because it had potent antibacterial activity (MIC of 0.4 μg/mL against methicillin-resistant Staphylococcus aureus) but did not inhibit LeuRS (IC50 > 100 μM). Analogues of PT638 were synthesized to explore the importance of the sulfonamide linker and the impact of altering the functionalization of the phenyl ring. These structure-activity-relationship studies revealed that the nitro substituent was essential for activity. To identify the target for PT638, we raised resistant strains of S. aureus, and whole-genome sequencing revealed mutations in leuRS, suggesting that the target for this compound was indeed LeuRS, despite the lack of enzyme inhibition. Subsequent analysis of PT638 metabolism demonstrated that bacterial nitroreductases readily converted this compound into the amino analogue, which inhibited LeuRS with an IC50 of 3.0 ± 1.2 μM, demonstrating that PT638 is thus a prodrug.
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Abstract
The 19th International Symposium on Flavins and Flavoproteins was held from 2⁻6 July 2017 in Groningen, The Netherlands.[...].
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