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Durcik M, Cotman AE, Toplak Ž, Možina Š, Skok Ž, Szili PE, Czikkely M, Maharramov E, Vu TH, Piras MV, Zidar N, Ilaš J, Zega A, Trontelj J, Pardo LA, Hughes D, Huseby D, Berruga-Fernández T, Cao S, Simoff I, Svensson R, Korol SV, Jin Z, Vicente F, Ramos MC, Mundy JEA, Maxwell A, Stevenson CEM, Lawson DM, Glinghammar B, Sjöström E, Bohlin M, Oreskär J, Alvér S, Janssen GV, Sterk GJ, Kikelj D, Pal C, Tomašič T, Peterlin Mašič L. New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus. J Med Chem 2023; 66:3968-3994. [PMID: 36877255 PMCID: PMC10041525 DOI: 10.1021/acs.jmedchem.2c01905] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
A new series of dual low nanomolar benzothiazole inhibitors of bacterial DNA gyrase and topoisomerase IV were developed. The resulting compounds show excellent broad-spectrum antibacterial activities against Gram-positive Enterococcus faecalis, Enterococcus faecium and multidrug resistant (MDR) Staphylococcus aureus strains [best compound minimal inhibitory concentrations (MICs): range, <0.03125-0.25 μg/mL] and against the Gram-negatives Acinetobacter baumannii and Klebsiella pneumoniae (best compound MICs: range, 1-4 μg/mL). Lead compound 7a was identified with favorable solubility and plasma protein binding, good metabolic stability, selectivity for bacterial topoisomerases, and no toxicity issues. The crystal structure of 7a in complex with Pseudomonas aeruginosa GyrB24 revealed its binding mode at the ATP-binding site. Expanded profiling of 7a and 7h showed potent antibacterial activity against over 100 MDR and non-MDR strains of A. baumannii and several other Gram-positive and Gram-negative strains. Ultimately, in vivo efficacy of 7a in a mouse model of vancomycin-intermediate S. aureus thigh infection was also demonstrated.
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Affiliation(s)
- Martina Durcik
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Andrej Emanuel Cotman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Žan Toplak
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Štefan Možina
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Petra Eva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Márton Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Elvin Maharramov
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Thu Hien Vu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Maria Vittoria Piras
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Jurij Trontelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Luis A Pardo
- Max Planck Institute for Multidisciplinary Sciences, Oncophysiology, Hermann-Rein-Str. 3, Göttingen 37075, Germany
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Douglas Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Tália Berruga-Fernández
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Ivailo Simoff
- Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) Department of Pharmacy, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Richard Svensson
- Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) Department of Pharmacy, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Sergiy V Korol
- Department of Medical Cell Biology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Zhe Jin
- Department of Medical Cell Biology, Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Francisca Vicente
- Fundación Medina, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, Granada 18016, Spain
| | - Maria C Ramos
- Fundación Medina, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, Granada 18016, Spain
| | - Julia E A Mundy
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Björn Glinghammar
- Department of Chemical and Pharmaceutical Toxicology, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Eva Sjöström
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Martin Bohlin
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Joanna Oreskär
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Sofie Alvér
- Department of Chemical Processes and Pharmaceutical Development, RISE Research Institutes of Sweden, Södertälje 15136, Sweden
| | - Guido V Janssen
- Medicinal Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
| | - Geert Jan Sterk
- Medicinal Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Csaba Pal
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
| | - Lucija Peterlin Mašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia
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Cotman A, Durcik M, Benedetto Tiz D, Fulgheri F, Secci D, Sterle M, Možina Š, Skok Ž, Zidar N, Zega A, Ilaš J, Peterlin Mašič L, Tomašič T, Hughes D, Huseby DL, Cao S, Garoff L, Berruga Fernández T, Giachou P, Crone L, Simoff I, Svensson R, Birnir B, Korol SV, Jin Z, Vicente F, Ramos MC, de la Cruz M, Glinghammar B, Lenhammar L, Henderson SR, Mundy JEA, Maxwell A, Stevenson CEM, Lawson DM, Janssen GV, Sterk GJ, Kikelj D. Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa. J Med Chem 2023; 66:1380-1425. [PMID: 36634346 PMCID: PMC9884090 DOI: 10.1021/acs.jmedchem.2c01597] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.
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Affiliation(s)
- Andrej
Emanuel Cotman
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Davide Benedetto Tiz
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Federica Fulgheri
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Daniela Secci
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Maša Sterle
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Štefan Možina
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Žiga Skok
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Diarmaid Hughes
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Douglas L. Huseby
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Sha Cao
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Linnéa Garoff
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Talía Berruga Fernández
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Paraskevi Giachou
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Lisa Crone
- Department
of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Ivailo Simoff
- Drug
Optimization and Pharmaceutical Profiling Platform (UDOPP), Department
of Pharmacy, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Richard Svensson
- Drug
Optimization and Pharmaceutical Profiling Platform (UDOPP), Department
of Pharmacy, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Bryndis Birnir
- Department
of Medical Cell Biology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Sergiy V. Korol
- Department
of Medical Cell Biology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Zhe Jin
- Department
of Medical Cell Biology, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
| | - Francisca Vicente
- Fundación
MEDINA, Avenida del Conocimiento
34, Parque Tecnológico Ciencias de la Salud, 18016 Granada, Spain
| | - Maria C. Ramos
- Fundación
MEDINA, Avenida del Conocimiento
34, Parque Tecnológico Ciencias de la Salud, 18016 Granada, Spain
| | - Mercedes de la Cruz
- Fundación
MEDINA, Avenida del Conocimiento
34, Parque Tecnológico Ciencias de la Salud, 18016 Granada, Spain
| | - Björn Glinghammar
- Department
Chemical Process and Pharmaceutical Development, Unit Chemical and
Pharmaceutical Safety, RISE Research Institutes
of Sweden, 15136 Södertälje, Sweden
| | - Lena Lenhammar
- Department
of Medical Sciences, Uppsala University
Hospital, 75185 Uppsala, Sweden
| | - Sara R. Henderson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Julia E. A. Mundy
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Clare E. M. Stevenson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M. Lawson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Guido V. Janssen
- Medicinal
Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Geert Jan Sterk
- Medicinal
Chemistry Division, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia,. Phone: (+386)1476-9500. Fax: (+386)1425-8031
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3
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Skok Ž, Barančoková M, Benek O, Cruz CD, Tammela P, Tomašič T, Zidar N, Mašič LP, Zega A, Stevenson CEM, Mundy JEA, Lawson DM, Maxwell A, Kikelj D, Ilaš J. Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors. ACS Med Chem Lett 2020; 11:2433-2440. [PMID: 33329764 PMCID: PMC7734788 DOI: 10.1021/acsmedchemlett.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
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We
designed and synthesized a series of inhibitors of the bacterial
enzymes DNA gyrase and DNA topoisomerase IV, based on our recently
published benzothiazole-based inhibitor bearing an oxalyl moiety.
To improve the antibacterial activity and retain potent enzymatic
activity, we systematically explored the chemical space. Several strategies
of modification were followed: varying substituents on the pyrrole
carboxamide moiety, alteration of the central scaffold, including
variation of substitution position and, most importantly, modification
of the oxalyl moiety. Compounds with acidic, basic, and neutral properties
were synthesized. To understand the mechanism of action and binding
mode, we have obtained a crystal structure of compound 16a, bearing a primary amino group, in complex with the N-terminal domain
of E. coli gyrase B (24 kDa) (PDB: 6YD9). Compound 15a, with a low molecular weight of 383
Da, potent inhibitory activity on E. coli gyrase
(IC50 = 9.5 nM), potent antibacterial activity on E. faecalis (MIC = 3.13 μM), and efflux impaired E. coli strain (MIC = 0.78 μM), is an important contribution
for the development of novel gyrase and topoisomerase IV inhibitors
in Gram-negative bacteria.
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Affiliation(s)
- Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Ondřej Benek
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 500 03 Hradec Králové, Czech Republic
| | - Cristina Durante Cruz
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Clare E. M. Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Julia E. A. Mundy
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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Farrow SC, Kamileen MO, Caputi L, Bussey K, Mundy JEA, McAtee RC, Stephenson CRJ, O'Connor SE. Biosynthesis of an Anti-Addiction Agent from the Iboga Plant. J Am Chem Soc 2019; 141:12979-12983. [PMID: 31364847 PMCID: PMC6706869 DOI: 10.1021/jacs.9b05999] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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(−)-Ibogaine
and (−)-voacangine are plant derived
psychoactives that show promise as treatments for opioid addiction.
However, these compounds are produced by hard to source plants, making
these chemicals difficult for broad-scale use. Here we report the
complete biosynthesis of (−)-voacangine, and de-esterified
voacangine, which is converted to (−)-ibogaine by heating,
enabling biocatalytic production of these compounds. Notably, (−)-ibogaine
and (−)-voacangine are of the opposite enantiomeric configuration
compared to the other major alkaloids found in this natural product
class. Therefore, this discovery provides insight into enantioselective
enzymatic formal Diels–Alder reactions.
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Affiliation(s)
- Scott C Farrow
- Department of Natural Product Biosynthesis , Max Planck Institute of Chemical Ecology , Hans-Knöll-Straße 8 , 07745 Jena , Germany
| | - Mohamed O Kamileen
- Department of Natural Product Biosynthesis , Max Planck Institute of Chemical Ecology , Hans-Knöll-Straße 8 , 07745 Jena , Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis , Max Planck Institute of Chemical Ecology , Hans-Knöll-Straße 8 , 07745 Jena , Germany
| | - Kate Bussey
- Department of Biological Chemistry , John Innes Centre , Norwich Research Park, Norwich NR4 7UH , United Kingdom
| | - Julia E A Mundy
- Department of Biological Chemistry , John Innes Centre , Norwich Research Park, Norwich NR4 7UH , United Kingdom
| | - Rory C McAtee
- Willard Henry Dow Laboratory, Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Corey R J Stephenson
- Willard Henry Dow Laboratory, Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis , Max Planck Institute of Chemical Ecology , Hans-Knöll-Straße 8 , 07745 Jena , Germany
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