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Ryan MD, Parkes AL, Corbett D, Dickie AP, Southey M, Andersen OA, Stein DB, Barbeau OR, Sanzone A, Thommes P, Barker J, Cain R, Compper C, Dejob M, Dorali A, Etheridge D, Evans S, Faulkner A, Gadouleau E, Gorman T, Haase D, Holbrow-Wilshaw M, Krulle T, Li X, Lumley C, Mertins B, Napier S, Odedra R, Papadopoulos K, Roumpelakis V, Spear K, Trimby E, Williams J, Zahn M, Keefe AD, Zhang Y, Soutter HT, Centrella PA, Clark MA, Cuozzo JW, Dumelin CE, Deng B, Hunt A, Sigel EA, Troast DM, DeJonge BLM. Discovery of Novel UDP- N-Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa. J Med Chem 2021; 64:14377-14425. [PMID: 34569791 DOI: 10.1021/acs.jmedchem.1c00888] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This study describes a novel series of UDP-N-acetylglucosamine acyltransferase (LpxA) inhibitors that was identified through affinity-mediated selection from a DNA-encoded compound library. The original hit was a selective inhibitor of Pseudomonas aeruginosa LpxA with no activity against Escherichia coli LpxA. The biochemical potency of the series was optimized through an X-ray crystallography-supported medicinal chemistry program, resulting in compounds with nanomolar activity against P. aeruginosa LpxA (best half-maximal inhibitory concentration (IC50) <5 nM) and cellular activity against P. aeruginosa (best minimal inhibitory concentration (MIC) of 4 μg/mL). Lack of activity against E. coli was maintained (IC50 > 20 μM and MIC > 128 μg/mL). The mode of action of analogues was confirmed through genetic analyses. As expected, compounds were active against multidrug-resistant isolates. Further optimization of pharmacokinetics is needed before efficacy studies in mouse infection models can be attempted. To our knowledge, this is the first reported LpxA inhibitor series with selective activity against P. aeruginosa.
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Affiliation(s)
- M Dominic Ryan
- X-Biotix Therapeutics, 465 Waverly Oaks Road, Waltham, Massachusetts 02452, United States
| | - Alastair L Parkes
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - David Corbett
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Anthony P Dickie
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Michelle Southey
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Ole A Andersen
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Daniel B Stein
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Olivier R Barbeau
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Angelo Sanzone
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Pia Thommes
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - John Barker
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Ricky Cain
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Christel Compper
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Magali Dejob
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Alain Dorali
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Donnya Etheridge
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Sian Evans
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Adele Faulkner
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Elise Gadouleau
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Timothy Gorman
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Denes Haase
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | | | - Thomas Krulle
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Xianfu Li
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Christopher Lumley
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Barbara Mertins
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Spencer Napier
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Rajesh Odedra
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Kostas Papadopoulos
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | | | - Kate Spear
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Emily Trimby
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Jennifer Williams
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Michael Zahn
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Anthony D Keefe
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Ying Zhang
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Holly T Soutter
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Paolo A Centrella
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Matthew A Clark
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John W Cuozzo
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | | | - Boer Deng
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Avery Hunt
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Eric A Sigel
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Dawn M Troast
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Boudewijn L M DeJonge
- X-Biotix Therapeutics, 465 Waverly Oaks Road, Waltham, Massachusetts 02452, United States
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2
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Leandro J, Stokka AJ, Teigen K, Andersen OA, Flatmark T. Substituting Tyr 138 in the active site loop of human phenylalanine hydroxylase affects catalysis and substrate activation. FEBS Open Bio 2017; 7:1026-1036. [PMID: 28680815 PMCID: PMC5494296 DOI: 10.1002/2211-5463.12243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 11/22/2022] Open
Abstract
Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l‐phenylalanine (l‐Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l‐Phe is the key player in this transition. X‐ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr138‐loop to the active site in the presence of l‐Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr138 point mutants. A high linear correlation (r2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate‐activated full‐length tetramers. In the tetramers, a correlation (r2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l‐Phe concentration. The new data support a similar functional importance of the Tyr138‐loop in the catalytic domain and the full‐length enzyme homotetramer.
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Affiliation(s)
- João Leandro
- Department of Biomedicine University of Bergen Norway.,Metabolism and Genetics Group Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy University of Lisbon Portugal.,Present address: Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue, Box 1498 New York NY 10029 USA
| | - Anne J Stokka
- Department of Biomedicine University of Bergen Norway.,The Biotechnology Centre of Oslo University of Oslo Norway
| | - Knut Teigen
- Department of Biomedicine University of Bergen Norway
| | - Ole A Andersen
- Department of Biomedicine University of Bergen Norway.,Evotec (UK) Ltd .Abingdon UK
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3
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Zhang J, Chan A, Lippa B, Cross JB, Liu C, Yin N, Romero JAC, Lawrence J, Heney R, Herradura P, Goss J, Clark C, Abel C, Zhang Y, Poutsiaka KM, Epie F, Conrad M, Mahamoon A, Nguyen K, Chavan A, Clark E, Li TC, Cheng RK, Wood M, Andersen OA, Brooks M, Kwong J, Barker J, Parr IB, Gu Y, Ryan MD, Coleman S, Metcalf CA. Structure-based discovery of LpxC inhibitors. Bioorg Med Chem Lett 2017; 27:1670-1680. [DOI: 10.1016/j.bmcl.2017.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
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4
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Mesleh MF, Cross JB, Zhang J, Kahmann J, Andersen OA, Barker J, Cheng RK, Felicetti B, Wood M, Hadfield AT, Scheich C, Moy TI, Yang Q, Shotwell J, Nguyen K, Lippa B, Dolle R, Ryan MD. Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB. Bioorg Med Chem Lett 2016; 26:1314-8. [DOI: 10.1016/j.bmcl.2016.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 11/16/2022]
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Prime ME, Andersen OA, Barker JJ, Brooks MA, Cheng RKY, Toogood-Johnson I, Courtney SM, Brookfield FA, Yarnold CJ, Marston RW, Johnson PD, Johnsen SF, Palfrey JJ, Vaidya D, Erfan S, Ichihara O, Felicetti B, Palan S, Pedret-Dunn A, Schaertl S, Sternberger I, Ebneth A, Scheel A, Winkler D, Toledo-Sherman L, Beconi M, Macdonald D, Muñoz-Sanjuan I, Dominguez C, Wityak J. Discovery and structure-activity relationship of potent and selective covalent inhibitors of transglutaminase 2 for Huntington's disease. J Med Chem 2012; 55:1021-46. [PMID: 22224594 DOI: 10.1021/jm201310y] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tissue transglutaminase 2 (TG2) is a multifunctional protein primarily known for its calcium-dependent enzymatic protein cross-linking activity via isopeptide bond formation between glutamine and lysine residues. TG2 overexpression and activity have been found to be associated with Huntington's disease (HD); specifically, TG2 is up-regulated in the brains of HD patients and in animal models of the disease. Interestingly, genetic deletion of TG2 in two different HD mouse models, R6/1 and R6/2, results in improved phenotypes including a reduction in neuronal death and prolonged survival. Starting with phenylacrylamide screening hit 7d, we describe the SAR of this series leading to potent and selective TG2 inhibitors. The suitability of the compounds as in vitro tools to elucidate the biology of TG2 was demonstrated through mode of inhibition studies, characterization of druglike properties, and inhibition profiles in a cell lysate assay.
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6
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Sutherland TE, Andersen OA, Betou M, Eggleston IM, Maizels RM, van Aalten D, Allen JE. Analyzing airway inflammation with chemical biology: dissection of acidic mammalian chitinase function with a selective drug-like inhibitor. ACTA ACUST UNITED AC 2011; 18:569-79. [PMID: 21609838 PMCID: PMC3115046 DOI: 10.1016/j.chembiol.2011.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 02/21/2011] [Accepted: 02/28/2011] [Indexed: 12/20/2022]
Abstract
Acidic mammalian chitinase (AMCase) is produced in the lung during allergic inflammation and asthma, and inhibition of enzymatic activity has been considered as a therapeutic strategy. However, most chitinase inhibitors are nonselective, additionally inhibiting chitotriosidase activity. Here, we describe bisdionin F, a competitive AMCase inhibitor with 20-fold selectivity for AMCase over chitotriosidase, designed by utilizing the AMCase crystal structure and dicaffeine scaffold. In a murine model of allergic inflammation, bisdionin F-treatment attenuated chitinase activity and alleviated the primary features of allergic inflammation including eosinophilia. However, selective AMCase inhibition by bisdionin F also caused dramatic and unexpected neutrophilia in the lungs. This class of inhibitor will be a powerful tool to dissect the functions of mammalian chitinases in disease and represents a synthetically accessible scaffold to optimize inhibitory properties in terms of airway inflammation.
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Affiliation(s)
- Tara E Sutherland
- Centre for Immunity, Infection and Evolution, and the Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Scotland, UK
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7
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Schüttelkopf AW, Andersen OA, Rao FV, Allwood M, Rush CL, Eggleston IM, van Aalten DMF. Bisdionin C-a rationally designed, submicromolar inhibitor of family 18 chitinases. ACS Med Chem Lett 2011; 2:428-32. [PMID: 24900325 DOI: 10.1021/ml200008b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 03/11/2011] [Indexed: 11/29/2022] Open
Abstract
Chitinases of the GH18 family play important roles in a variety of pathogenic organisms and have also been shown to be involved in human asthma progression, making these enzymes potential drug targets. While a number of potent GH18 chitinase inhibitors have been described, in general, these compounds suffer from limited synthetic accessibility or unfavorable medicinal-chemical properties, making them poor starting points for the development of chitinase-targeted drugs. Exploiting available structural data, we have rationally designed bisdionin C, a submicromolar inhibitor of GH18 enzymes, that possesses desirable druglike properties and tractable chemical synthesis. A crystallographic structure of a chitinase-bisdionin C complex shows the two aromatic systems of the ligand interacting with two conserved tryptophan residues exposed in the active site cleft of the enzyme, while at the same time forming extensive hydrogen-bonding interactions with the catalytic machinery. The observed mode of binding, together with inhibition data, suggests that bisdionin C presents an attractive starting point for the development of specific inhibitors of bacterial-type, but not plant-type, GH 18 chitinases.
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Affiliation(s)
- Alexander W. Schüttelkopf
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Ole A. Andersen
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Francesco V. Rao
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Matthew Allwood
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Christina L. Rush
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Ian M. Eggleston
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Daan M. F. van Aalten
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
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8
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Dixon MJ, Nathubhai A, Andersen OA, van Aalten DMF, Eggleston IM. Solid-phase synthesis of cyclic peptide chitinase inhibitors: SAR of the argifin scaffold. Org Biomol Chem 2009; 7:259-68. [PMID: 19109670 PMCID: PMC2657367 DOI: 10.1039/b815077j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 10/06/2008] [Indexed: 12/01/2022]
Abstract
A new, highly efficient, all-solid-phase synthesis of argifin, a natural product cyclic pentapeptide chitinase inhibitor, is reported. The synthesis features attachment of an orthogonally protected Asp residue to the solid support and assembly of the linear peptide chain by Fmoc SPPS prior to cyclisation and side-chain manipulation on-resin. Introduction of the key N-methyl carbamoyl-substituted Arg side chain is achieved via derivatisation of a selectively protected Orn residue, prior to cleavage from the resin and side-chain deprotection. A severe aspartimide side-reaction observed upon final deprotection is circumvented by the use of a novel aqueous acidolysis procedure. The flexibility of the synthesis is demonstrated by the preparation of a series of argifin analogues designed from the X-ray structure of the natural product in complex with a representative family 18 chitinase.
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Affiliation(s)
- Mark J. Dixon
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, , Claverton Down, Bath, BA2 7AY, UK. ; Fax: ++ 44 01225 386114
| | - Amit Nathubhai
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, , Claverton Down, Bath, BA2 7AY, UK. ; Fax: ++ 44 01225 386114
| | - Ole A. Andersen
- Division of Molecular and Environmental Microbiology, University of Dundee, Dundee, DD1 5EH, UK
| | - Daan M. F. van Aalten
- Division of Molecular and Environmental Microbiology, University of Dundee, Dundee, DD1 5EH, UK
| | - Ian M. Eggleston
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, , Claverton Down, Bath, BA2 7AY, UK. ; Fax: ++ 44 01225 386114
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9
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Dixon MJ, Andersen OA, van Aalten DMF, Eggleston IM. SPPS of the Natural Product Chitinase Inhibitor Argifin: Library Generation and Biological Evaluation. Advances in Experimental Medicine and Biology 2009; 611:143-4. [DOI: 10.1007/978-0-387-73657-0_64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Andersen OA, Nathubhai A, Dixon MJ, Eggleston IM, van Aalten DMF. Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin. ACTA ACUST UNITED AC 2008; 15:295-301. [PMID: 18355729 PMCID: PMC3764403 DOI: 10.1016/j.chembiol.2008.02.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 01/30/2008] [Accepted: 02/05/2008] [Indexed: 11/30/2022]
Abstract
Chitinase inhibitors have chemotherapeutic potential as fungicides, pesticides, and antiasthmatics. Argifin, a natural product cyclopentapeptide, competitively inhibits family 18 chitinases in the nanomolar to micromolar range and shows extensive substrate mimicry. In an attempt to map the active fragments of this large natural product, the cyclopentapeptide was progressively dissected down to four linear peptides and dimethylguanylurea, synthesized using a combination of solution and solid phase peptide synthesis. The peptide fragments inhibit chitinase B1 from Aspergillus fumigatus (AfChiB1), the human chitotriosidase, and chitinase activity in lung homogenates from a murine model of chronic asthma, with potencies ranging from high nanomolar to high micromolar inhibition. X-ray crystallographic analysis of the chitinase-inhibitor complexes revealed that the conformations of the linear peptides were remarkably similar to that of the natural product. Strikingly, the dimethylguanylurea fragment, representing only a quarter of the natural product mass, was found to harbor all significant interactions with the protein and binds with unusually high efficiency. The data provide useful information that could lead to the generation of drug-like, natural product-based chitinase inhibitors.
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Affiliation(s)
- Ole A Andersen
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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11
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Leiros I, Nabong MP, Grøsvik K, Ringvoll J, Haugland GT, Uldal L, Reite K, Olsbu IK, Knævelsrud I, Moe E, Andersen OA, Birkeland NK, Ruoff P, Klungland A, Bjelland S. Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA. EMBO J 2007; 26:2206-17. [PMID: 17396151 PMCID: PMC1852788 DOI: 10.1038/sj.emboj.7601662] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 03/01/2007] [Indexed: 11/08/2022] Open
Abstract
N(1)-methyladenine (m(1)A) and N(3)-methylcytosine (m(3)C) are major toxic and mutagenic lesions induced by alkylation in single-stranded DNA. In bacteria and mammals, m(1)A and m(3)C were recently shown to be repaired by AlkB-mediated oxidative demethylation, a direct DNA damage reversal mechanism. No AlkB gene homologues have been identified in Archaea. We report that m(1)A and m(3)C are repaired by the AfAlkA base excision repair glycosylase of Archaeoglobus fulgidus, suggesting a different repair mechanism for these lesions in the third domain of life. In addition, AfAlkA was found to effect a robust excision of 1,N(6)-ethenoadenine. We present a high-resolution crystal structure of AfAlkA, which, together with the characterization of several site-directed mutants, forms a molecular rationalization for the newly discovered base excision activity.
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Affiliation(s)
- Ingar Leiros
- The Norwegian Structural Biology Centre, University of Tromsø, Tromsø, Norway
| | - Marivi P Nabong
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, Rikshospitalelt-Radiumhospitalet HF, Oslo, Norway
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | - Kristin Grøsvik
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | - Jeanette Ringvoll
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, Rikshospitalelt-Radiumhospitalet HF, Oslo, Norway
| | | | - Lene Uldal
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, Rikshospitalelt-Radiumhospitalet HF, Oslo, Norway
| | - Karen Reite
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, Rikshospitalelt-Radiumhospitalet HF, Oslo, Norway
| | - Inger K Olsbu
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | - Ingeborg Knævelsrud
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Elin Moe
- The Norwegian Structural Biology Centre, University of Tromsø, Tromsø, Norway
| | - Ole A Andersen
- The Norwegian Structural Biology Centre, University of Tromsø, Tromsø, Norway
| | | | - Peter Ruoff
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | - Arne Klungland
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, Rikshospitalelt-Radiumhospitalet HF, Oslo, Norway
| | - Svein Bjelland
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Kristine Bonnevies rd 30, N-4036 Stavanger, Norway. Tel.: +47 51831884; Fax: +47 51831750; E-mail:
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Dixon MJ, Andersen OA, van Aalten DMF, Eggleston IM. First Synthesis of Argadin: A Nanomolar Inhibitor of Family-18 Chitinases. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Dixon MJ, Andersen OA, van Aalten DMF, Eggleston IM. First Synthesis of Argadin: A Nanomolar Inhibitor of Family-18 Chitinases. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600599] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Schüttelkopf AW, Andersen OA, Rao FV, Allwood M, Lloyd C, Eggleston IM, van Aalten DMF. Screening-based discovery and structural dissection of a novel family 18 chitinase inhibitor. J Biol Chem 2006; 281:27278-85. [PMID: 16844689 DOI: 10.1074/jbc.m604048200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Family 18 chitinases play key roles in the life cycles of a variety of organisms ranging from bacteria to man. Very recently it has been shown that one of the mammalian chitinases is highly overexpressed in the asthmatic lung and contributes to the pathogenic process through recruitment of inflammatory cells. Although several potent natural product chitinase inhibitors have been identified, their chemotherapeutic potential or their use as cell biological tools is limited due to their size, complex chemistry, and limited availability. We describe a virtual screening-based approach to identification of a novel, purine-based, chitinase inhibitor. This inhibitor acts in the low micromolar (Ki=2.8+/-0.2 microM) range in a competitive mode. Dissection of the binding mode by x-ray crystallography reveals that the compound, which consists of two linked caffeine moieties, binds in the active site through extensive and not previously observed stacking interactions with conserved, solvent exposed tryptophans. Such exposed aromatics are also present in the structures of many other carbohydrate processing enzymes. The compound exhibits favorable chemical properties and is likely to be useful as a general scaffold for development of pan-family 18 chitinase inhibitors.
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Affiliation(s)
- Alexander W Schüttelkopf
- Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
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Rao FV, Andersen OA, Vora KA, Demartino JA, van Aalten DMF. Methylxanthine drugs are chitinase inhibitors: investigation of inhibition and binding modes. ACTA ACUST UNITED AC 2006; 12:973-80. [PMID: 16183021 DOI: 10.1016/j.chembiol.2005.07.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Revised: 06/10/2005] [Accepted: 07/12/2005] [Indexed: 12/22/2022]
Abstract
Family 18 chitinases play key roles in a range of pathogenic organisms and are overexpressed in the asthmatic lung. By screening a library of marketed drug molecules, we have identified methylxanthine derivatives as possible inhibitor leads. These derivatives, theophylline, caffeine, and pentoxifylline, are used therapeutically as antiinflammatory agents, with pleiotropic mechanisms of action. Here it is shown that they are also competitive inhibitors against a fungal family 18 chitinase, with pentoxifylline being the most potent (K(i) of 37 microM). Crystallographic analysis of chitinase-inhibitor complexes revealed specific interactions with the active site, mimicking the reaction intermediate analog, allosamidin. Mutagenesis identified the key active site residues, conserved in mammalian chitinases, which contribute to inhibitor affinity. Enzyme assays also revealed that these methylxanthines are active against human chitinases.
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Affiliation(s)
- Francesco V Rao
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Scotland
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Dixon MJ, Andersen OA, van Aalten DMF, Eggleston IM. An efficient synthesis of argifin: A natural product chitinase inhibitor with chemotherapeutic potential. Bioorg Med Chem Lett 2005; 15:4717-21. [PMID: 16153835 DOI: 10.1016/j.bmcl.2005.07.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 07/21/2005] [Accepted: 07/26/2005] [Indexed: 11/25/2022]
Abstract
The first synthesis of the cyclopentapeptide family 18 chitinase inhibitor argifin has been achieved by a combination of solid phase and solution chemistry. Synthetic argifin is a nanomolar inhibitor of chitinase B1 from Aspergillus fumigatus and the high-resolution X-ray structure of the synthesized material in complex with the same enzyme is identical to that previously obtained for the natural product.
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Affiliation(s)
- Mark J Dixon
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Affiliation(s)
- Ole A Andersen
- Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH
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Solstad T, Carvalho RN, Andersen OA, Waidelich D, Flatmark T. Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylase. Eur J Biochem 2003; 270:929-38. [PMID: 12603326 DOI: 10.1046/j.1432-1033.2003.03455.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two dimensional electrophoresis has revealed a microheterogeneity in the recombinant human phenylalanine hydroxylase (hPAH) protomer, that is the result of spontaneous nonenzymatic deamidations of labile asparagine (Asn) residues [Solstad, T. and Flatmark, T. (2000) Eur. J. Biochem.267, 6302-6310]. Using of a computer algorithm, the relative deamidation rates of all Asn residues in hPAH have been predicted, and we here verify that Asn32, followed by a glycine residue, as well as Asn28 and Asn30 in a loop region of the N-terminal autoregulatory sequence (residues 19-33) of wt-hPAH, are among the susceptible residues. First, on MALDI-TOF mass spectrometry of the 24 h expressed enzyme, the E. coli 28-residue peptide, L15-K42 (containing three Asn residues), was recovered with four monoisotopic mass numbers (i.e., m/z of 3106.455, 3107.470, 3108.474 and 3109.476, of decreasing intensity) that differed by 1 Da. Secondly, by reverse-phase chromatography, isoaspartyl (isoAsp) was demonstrated in this 28-residue peptide by its methylation by protein-l-isoaspartic acid O-methyltransferase (PIMT; EC 2.1.1.77). Thirdly, on incubation at pH 7.0 and 37 degrees C of the phosphorylated form (at Ser16) of this 28-residue peptide, a time-dependent mobility shift from tR approximately 34 min to approximately 31 min (i.e., to a more hydrophilic position) was observed on reverse-phase chromatography, and the recovery of the tR approximately 34 min species decreased with a biphasic time-course with t0.5-values of 1.9 and 6.2 days. The fastest rate is compatible with the rate determined for the sequence-controlled deamidation of Asn32 (in a pentapeptide without 3D structural interference), i.e., a deamidation half-time of approximately 1.5 days in 150 mm Tris/HCl, pH 7.0 at 37 degrees C. Asn32 is located in a cluster of three Asn residues (Asn28, Asn30 and Asn32) of a loop structure stabilized by a hydrogen-bond network. Deamidation of Asn32 introduces a negative charge and a partial beta-isomerization (isoAsp), which is predicted to result in a change in the backbone conformation of the loop structure and a repositioning of the autoregulatory sequence and thus affect its regulatory properties. The functional implications of this deamidation was further studied by site-directed mutagenesis, and the mutant form (Asn32-->Asp) revealed a 1.7-fold increase in the catalytic efficiency, an increased affinity and positive cooperativity of L-Phe binding as well as substrate inhibition.
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Affiliation(s)
- Therese Solstad
- Department of Biochemistry and Molecular Biology, Proteomic Unit, University of Bergen, Arstadveien 19, N-5009 Bergen, Norway
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Solstad T, Stokka AJ, Andersen OA, Flatmark T. Studies on the regulatory properties of the pterin cofactor and dopamine bound at the active site of human phenylalanine hydroxylase. Eur J Biochem 2003; 270:981-90. [PMID: 12603331 DOI: 10.1046/j.1432-1033.2003.03471.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The catalytic activity of phenylalanine hydroxylase (PAH, phenylalanine 4-monooxygenase EC 1.14.16.1) is regulated by three main mechanisms, i.e. substrate (l-phenylalanine, L-Phe) activation, pterin cofactor inhibition and phosphorylation of a single serine (Ser16) residue. To address the molecular basis for the inhibition by the natural cofactor (6R)-l-erythro-5,6,7,8-tetrahydrobiopterin, its effects on the recombinant tetrameric human enzyme (wt-hPAH) was studied using three different conformational probes, i.e. the limited proteolysis by trypsin, the reversible global conformational transition (hysteresis) triggered by L-Phe binding, as measured in real time by surface plasmon resonance analysis, and the rate of phosphorylation of Ser16 by cAMP-dependent protein kinase. Comparison of the inhibitory properties of the natural cofactor with the available three-dimensional crystal structure information on the ligand-free, the binary and the ternary complexes, have provided important clues concerning the molecular mechanism for the negative modulatory effects. In the binary complex, the binding of the cofactor at the active site results in the formation of stabilizing hydrogen bonds between the dihydroxypropyl side-chain and the carbonyl oxygen of Ser23 in the autoregulatory sequence. L-Phe binding triggers local as well as global conformational changes of the protomer resulting in a displacement of the cofactor bound at the active site by 2.6 A (mean distance) in the direction of the iron and Glu286 which causes a loss of the stabilizing hydrogen bonds present in the binary complex and thereby a complete reversal of the pterin cofactor as a negative effector. The negative modulatory properties of the inhibitor dopamine, bound by bidentate coordination to the active site iron, is explained by a similar molecular mechanism including its reversal by substrate binding. Although the pterin cofactor and the substrate bind at distinctly different sites, the local conformational changes imposed by their binding at the active site have a mutual effect on their respective binding affinities.
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Affiliation(s)
- Therese Solstad
- Department of Biochemistry and Molecular Biology, University of Bergen, Arstadveien 19, N-5009 Bergen, Norway
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Andersen OA, Flatmark T, Hough E. High resolution crystal structures of the catalytic domain of human phenylalanine hydroxylase in its catalytically active Fe(II) form and binary complex with tetrahydrobiopterin. J Mol Biol 2001; 314:279-91. [PMID: 11718561 DOI: 10.1006/jmbi.2001.5061] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structures of the catalytic domain (DeltaN1-102/DeltaC428-452) of human phenylalanine hydroxylase (hPheOH) in its catalytically competent Fe(II) form and binary complex with the reduced pterin cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) have been determined to 1.7 and 1.5 A, respectively. When compared with the structures reported for various catalytically inactive Fe(III) forms, several important differences have been observed, notably at the active site. Thus, the non-liganded hPheOH-Fe(II) structure revealed well defined electron density for only one of the three water molecules reported to be coordinated to the iron in the high-spin Fe(III) form, as well as poor electron density for parts of the coordinating side-chain of Glu330. The reduced cofactor (BH4), which adopts the expected half-semi chair conformation, is bound in the second coordination sphere of the catalytic iron with a C4a-iron distance of 5.9 A. BH4 binds at the same site as L-erythro-7,8-dihydrobiopterin (BH2) in the binary hPheOH-Fe(III)-BH2 complex forming an aromatic pi-stacking interaction with Phe254 and a network of hydrogen bonds. However, compared to that structure the pterin ring is displaced about 0.5 A and rotated about 10 degrees, and the torsion angle between the hydroxyl groups of the cofactor in the dihydroxypropyl side-chain has changed by approximately 120 degrees enabling O2' to make a strong hydrogen bond (2.4 A) with the side-chain oxygen of Ser251. Carbon atoms in the dihydroxypropyl side-chain make several hydrophobic contacts with the protein. The iron is six-coordinated in the binary complex, but the overall coordination geometry is slightly different from that of the Fe(III) form. Most important was the finding that the binding of BH4 causes the Glu330 ligand to change its coordination to the iron when comparing with non-liganded hPheOH-Fe(III) and the binary hPheOH-Fe(III)-BH2 complex.
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Affiliation(s)
- O A Andersen
- Department of Chemistry, University of Tromsø, Tromsø, N-9037, Norway
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Helland R, Berglund GI, Otlewski J, Apostoluk W, Andersen OA, Willassen NP, Smalås AO. High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes. Acta Crystallogr D Biol Crystallogr 1999; 55:139-48. [PMID: 10089404 DOI: 10.1107/s090744499801052x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/1998] [Accepted: 08/03/1998] [Indexed: 11/11/2022]
Abstract
An anionic trypsin from Atlantic salmon and bovine trypsin have been complexed with the squash-seed inhibitors, CMTI-I (Cucurbita maxima trypsin inhibitor I, P1 Arg) and CPTI-II (Cucurbita pepo trypsin inhibitor II, P1 Lys). The crystal structures of three such complexes have been determined to 1.5-1.8 A resolution and refined to crystallographic R factors ranging from 17.6 to 19.3%. The two anionic salmon-trypsin complexes (ST-CPTI and ST-CMTI) and the bovine-trypsin complex (BT-CPTI) have been compared to other trypsin-inhibitor complexes by means of general structure and primary and secondary binding features. In all three new structures, the primary binding residue of the inhibitor binds to trypsin in the classical manner, but with small differences in the primary and secondary binding patterns. Lysine in CPTI-II binds deeper in the specificity pocket of bovine trypsin than lysine in other known lysine-bovine-trypsin complexes, and anionic salmon trypsin lacks some of the secondary binding interactions found in the complexes formed between squash inhibitors and bovine trypsin. The ST-CMTI complex was formed from the reactive-site-cleaved form of the inhibitor. However, well defined electron density was observed for the P1-P1' peptide bond, together with a hydrogen-bonding pattern virtually identical to those of all serine-protease-protein-inhibitor complexes, indicating a resynthesis of the scissile bond.
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Affiliation(s)
- R Helland
- Department of Chemistry, University of Tromso, N-9037 Tromso, Norway
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