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Abuhammad A, Laurieri N, Rice A, Lowe ED, Singh N, Naser SM, Ratrout SS, Churchill GC. Structural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen. J Biomol Struct Dyn 2023; 41:14036-14048. [PMID: 36762717 DOI: 10.1080/07391102.2023.2176925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Bipolar disorder is a major psychiatric disorder associated with cognitive impairment and a high suicide rate. Frontline therapy for this condition includes lithium (Li+)-containing treatments that can exert severe side effects. One target of Li+ is inositol monophosphatase-1 (IMPase1); inhibition of IMPase1 through small-molecule compounds may provide an alternative treatment for bipolar disorder. One such compound is the anti-inflammatory drug ebselen, which is well tolerated and safe; however, ebselen's exact mechanism of action in IMPase1 inhibition is not fully understood, preventing rational design of IMPase1 inhibitors. To fill this gap, we performed crystallographic and biochemical studies to investigate how ebselen inhibits IMPase1. We obtained a structure of IMPase1 in space group P21 after treatment with ebselen that revealed three key active-site loops (residues 33-44, 70-79, and 161-165) that are either disordered or in multiple conformations, supporting a hypothesis whereby dynamic conformational changes may be important for catalysis and ebselen inhibition. Using the thermal shift assay, we confirmed that ebselen significantly destabilizes the enzyme. Molecular docking suggests that ebselen could bind in the vicinity of His217. Investigation of the role of IMPase1 residues His217 and Cys218 suggests that inhibition of IMPase1 by ebselen may not be mediated via covalent modification of the active-site cysteine (Cys218) and is not affected by the covalent modification of other cysteine residues in the structure. Our results suggest that effects previously ascribed to ebselen-dependent inhibition likely result from disruption of essential active-site architecture, preventing activation of the IMPase1-Mg2+ complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Areej Abuhammad
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Nicola Laurieri
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Alistair Rice
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Nisha Singh
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Saleem M Naser
- Research and Development Department, APIs Division, Hikma Pharmaceutical Co. Ltd, Amman, Jordan
| | - Samer S Ratrout
- Research and Development Department, APIs Division, Hikma Pharmaceutical Co. Ltd, Amman, Jordan
| | - Grant C Churchill
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
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2
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Nogara PA, Omage FB, Bolzan GR, Delgado CP, Aschner M, Orian L, Teixeira Rocha JB. In silico Studies on the Interaction between Mpro and PLpro From SARS-CoV-2 and Ebselen, its Metabolites and Derivatives. Mol Inform 2021; 40:e2100028. [PMID: 34018687 PMCID: PMC8236915 DOI: 10.1002/minf.202100028] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022]
Abstract
The COVID‐19 pandemic caused by the SARS‐CoV‐2 has mobilized scientific attention in search of a treatment. The cysteine‐proteases, main protease (Mpro) and papain‐like protease (PLpro) are important targets for antiviral drugs. In this work, we simulate the interactions between the Mpro and PLpro with Ebselen, its metabolites and derivatives with the aim of finding molecules that can potentially inhibit these enzymes. The docking data demonstrate that there are two main interactions between the thiol (−SH) group of Cys (from the protease active sites) and the electrophilic centers of the organoselenium molecules, i. e. the interaction with the carbonyl group (O=C…SH) and the interaction with the Se moiety (Se…SH). Both interactions may lead to an adduct formation and enzyme inhibition. Density Functional Theory (DFT) calculations with Ebselen indicate that the energetics of the thiol nucleophilic attack is more favorable on Se than on the carbonyl group, which is in accordance with experimental data (Jin et al. Nature, 2020, 582, 289–293). Therefore, organoselenium molecules should be further explored as inhibitors of the SARS‐CoV‐2 proteases. Furthermore, we suggest that some metabolites of Ebselen (e. g. Ebselen diselenide and methylebselenoxide) and derivatives ethaselen and ebsulfur should be tested in vitro as inhibitors of virus replication and its proteases.
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Affiliation(s)
- Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, 97105-900, RS, Brazil
| | - Folorunsho Bright Omage
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, 97105-900, RS, Brazil
| | - Gustavo Roni Bolzan
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, 97105-900, RS, Brazil
| | - Cássia Pereira Delgado
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, 97105-900, RS, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, 97105-900, RS, Brazil
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3
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Rahman Z, Bazaz MR, Devabattula G, Khan MA, Godugu C. Targeting H3K9 methyltransferase G9a and its related molecule GLP as a potential therapeutic strategy for cancer. J Biochem Mol Toxicol 2020; 35:e22674. [PMID: 33283949 DOI: 10.1002/jbt.22674] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022]
Abstract
H3K9 methyltransferase (G9a) and its relevant molecule GLP are the SET domain proteins that specifically add mono, di and trimethyl groups on to the histone H3K9, which lead to the transcriptional inactivation of chromatin and reduce the expression of cancer suppressor genes, which trigger growth and progress of several cancer types. Various studies have demonstrated that overexpression of H3K9 methyltransferase G9a and GLP in different kinds of tumors, like lung, breast, bladder, colon, cervical, gastric, skin cancers, hepatocellular carcinoma and hematological malignancies. Several G9a and GLP inhibitors such as BIX-01294, UNC0642, A-366 and DCG066 were developed to combat various cancers; however, there is a need for more effective and less toxic compounds. The current molecular docking study suggested that the selected new compounds such as ninhydrin, naphthoquinone, cysteamine and disulfide cysteamine could be suitable molecules as a G9a and GLP inhibitors. Furthermore, detailed cell based and preclinical animal studies are required to confirm their properties. In the current review, we discussed the role of G9a and GLP mediated epigenetic regulation in the cancers. A thorough literature review was done related to G9a and GLP. The databases used extensively for retrieval of information were PubMed, Medline, Scopus and Science-direct. Further, molecular docking was performed using Maestro Schrodinger version 9.2 software to investigate the binding profile of compounds with Human G9a HMT (PDB ID: 3FPD, 3RJW) and Human GLP MT (PDB ID: 6MBO, 6MBP).
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Affiliation(s)
- Ziaur Rahman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Mohd Rabi Bazaz
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Geetanjali Devabattula
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Mohd Abrar Khan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Chandraiah Godugu
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
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4
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de Munnik M, Lohans CT, Langley GW, Bon C, Brem J, Schofield CJ. A Fluorescence-Based Assay for Screening β-Lactams Targeting the Mycobacterium tuberculosis Transpeptidase Ldt Mt2. Chembiochem 2020; 21:368-372. [PMID: 31322798 PMCID: PMC7028133 DOI: 10.1002/cbic.201900379] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Indexed: 12/24/2022]
Abstract
Mycobacterium tuberculosis l,d-transpeptidases (Ldts), which are involved in cell-wall biosynthesis, have emerged as promising targets for the treatment of tuberculosis. However, an efficient method for testing inhibition of these enzymes is not currently available. We present a fluorescence-based assay for LdtMt2 , which is suitable for high-throughput screening. Two fluorogenic probes were identified that release a fluorophore upon reaction with LdtMt2 , thus making it possible to assess the availability of the catalytic site in the presence of inhibitors. The assay was applied to a panel of β-lactam antibiotics and related inhibitors; the results validate observations that the (carba)penem subclass of β-lactams are more potent Ldt inhibitors than other β-lactam classes, though unexpected variations in potency were observed. The method will enable systematic structure-activity relationship studies on Ldts, thereby facilitating the identification of new antibiotics active against M. tuberculosis.
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Affiliation(s)
- Mariska de Munnik
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher T. Lohans
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of Biomedical and Molecular SciencesQueen's University18 Stuart StreetKingstonONK7L 3N6Canada
| | - Gareth W. Langley
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Present address: Charles River LaboratoriesChesterford Research ParkSaffron WaldenEssexCB10 1XLUK
| | - Corentin Bon
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Present address: Department of Structural Biology and ChemistryInstitut PasteurUMR 3523 CNRSRue du Dr. Roux75015ParisFrance
| | - Jürgen Brem
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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5
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de Munnik M, Lohans CT, Lang PA, Langley GW, Malla TR, Tumber A, Schofield CJ, Brem J. Targeting the Mycobacterium tuberculosis transpeptidase Ldt Mt2 with cysteine-reactive inhibitors including ebselen. Chem Commun (Camb) 2019; 55:10214-10217. [PMID: 31380528 PMCID: PMC6984337 DOI: 10.1039/c9cc04145a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/25/2019] [Indexed: 02/04/2023]
Abstract
The l,d-transpeptidases (Ldts) are promising antibiotic targets for treating tuberculosis. We report screening of cysteine-reactive inhibitors against LdtMt2 from Mycobacterium tuberculosis. Structural studies on LdtMt2 with potent inhibitor ebselen reveal opening of the benzisoselenazolone ring by a nucleophilic cysteine, forming a complex involving extensive hydrophobic interactions with a substrate-binding loop.
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Affiliation(s)
- Mariska de Munnik
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
| | - Christopher T. Lohans
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
- Department of Biomedical and Molecular Sciences
, Queen's University
,
Kingston
, ON
K7L 3N6
, Canada
| | - Pauline A. Lang
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
| | - Gareth W. Langley
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
| | - Tika R. Malla
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
| | - Anthony Tumber
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
| | - Christopher J. Schofield
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
| | - Jürgen Brem
- Chemistry Research Laboratory
, Department of Chemistry
, University of Oxford
,
Oxford
, OX1 3TA
, UK
.
;
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6
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Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry 2019; 58:1627-1647. [PMID: 30789718 PMCID: PMC6503667 DOI: 10.1021/acs.biochem.9b00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The assignment of biochemical functions to hypothetical proteins is challenged by functional diversification within many protein structural superfamilies. This diversification, which is particularly common for metalloenzymes, renders functional annotations that are founded solely on sequence and domain similarities unreliable and often erroneous. Definitive biochemical characterization to delineate functional subgroups within these superfamilies will aid in improving bioinformatic approaches for functional annotation. We describe here the structural and functional characterization of two non-heme-iron oxygenases, TmpA and TmpB, which are encoded by a genomically clustered pair of genes found in more than 350 species of bacteria. TmpA and TmpB are functional homologues of a pair of enzymes (PhnY and PhnZ) that degrade 2-aminoethylphosphonate but instead act on its naturally occurring, quaternary ammonium analogue, 2-(trimethylammonio)ethylphosphonate (TMAEP). TmpA, an iron(II)- and 2-(oxo)glutarate-dependent oxygenase misannotated as a γ-butyrobetaine (γbb) hydroxylase, shows no activity toward γbb but efficiently hydroxylates TMAEP. The product, ( R)-1-hydroxy-2-(trimethylammonio)ethylphosphonate [( R)-OH-TMAEP], then serves as the substrate for the second enzyme, TmpB. By contrast to its purported phosphohydrolytic activity, TmpB is an HD-domain oxygenase that uses a mixed-valent diiron cofactor to enact oxidative cleavage of the C-P bond of its substrate, yielding glycine betaine and phosphate. The high specificities of TmpA and TmpB for their N-trimethylated substrates suggest that they have evolved specifically to degrade TMAEP, which was not previously known to be subject to microbial catabolism. This study thus adds to the growing list of known pathways through which microbes break down organophosphonates to harvest phosphorus, carbon, and nitrogen in nutrient-limited niches.
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Affiliation(s)
- Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Maria-Eirini Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrew J. Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: REG Life Sciences, LLC, South San Francisco, California 94080
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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7
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Nejdl L, Moravanska A, Smerkova K, Mravec F, Krizkova S, Pomorski A, Krężel A, Macka M, Adam V, Vaculovicova M. Short-sweep capillary electrophoresis with a selective zinc fluorescence imaging reagent FluoZin-3 for determination of free and metalothionein-2a-bound Zn2+ ions. Anal Chim Acta 2018. [DOI: 10.1016/j.aca.2018.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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Lenstra DC, Al Temimi AHK, Mecinović J. Inhibition of histone lysine methyltransferases G9a and GLP by ejection of structural Zn(II). Bioorg Med Chem Lett 2018. [PMID: 29519735 DOI: 10.1016/j.bmcl.2018.02.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Histone lysine methyltransferases G9a and GLP are validated targets for the development of new epigenetic drugs. Most, if not all, inhibitors of G9a and GLP target the histone substrate binding site or/and the S-adenosylmethionine cosubstrate binding site. Here, we report an alternative approach for inhibiting the methyltransferase activity of G9a and GLP. For proper folding and enzymatic activity, G9a and GLP contain structural zinc fingers, one of them being adjacent to the S-adenosylmethionine binding site. Our work demonstrates that targeting these labile zinc fingers with electrophilic small molecules results in ejection of structural zinc ions, and consequently inhibition of the methyltransferase activity. Very effective Zn(II) ejection and inhibition of G9a and GLP was observed with clinically used ebselen, disulfiram and cisplatin.
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Affiliation(s)
- Danny C Lenstra
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Abbas H K Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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Khan A, Leśniak RK, Brem J, Rydzik AM, Choi H, Leung IKH, McDonough MA, Schofield CJ, Claridge TDW. Development and application of ligand-based NMR screening assays for γ-butyrobetaine hydroxylase. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00004e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 1H NMR based dual-reporter binding assay for γ-butyrobetaine hydroxylase (BBOX) reveals unexpected structure–activity relationships for isoquinoline-derived inhibitors.
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Affiliation(s)
- A. Khan
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - R. K. Leśniak
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - J. Brem
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - A. M. Rydzik
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - H. Choi
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - I. K. H. Leung
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - M. A. McDonough
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - C. J. Schofield
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - T. D. W. Claridge
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
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